[svn-upgrade] Integrating new upstream version, ncbi-tools6 (6.1.20080302)

409 files changed, 94826 insertions, 34620 deletions

diff --git a/VERSION b/VERSION
index 469fe3b9..b28843f9 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-Sun Aug 26 12:03:24 EDT 2007
+Sun Mar 2 10:14:50 EST 2008
diff --git a/access/makeacc.unx b/access/makeacc.unx
index 631b6b9d..d657b222 100644
--- a/access/makeacc.unx
+++ b/access/makeacc.unx
@@ -27,3 +27,5 @@ asntool -m mla2.asn -o asnmla2.h
 mv asnmla2.h ../asnstat/
 asntool -m mla2.asn -M ../asn/pub.asn,../asn/biblio.asn,../asn/medline.asn,../asn/medlars.asn,../asn/pubmed.asn -G -B objmla2 -I mlkludge.h -K asnmla2.h -Z
 
+asntool -m seqtable.asn -M ../asn/seqloc.asn -G -B objtable -K asntable.h -Z
+
diff --git a/access/mla2api.c b/access/mla2api.c
index f4e17539..52389bd6 100644
--- a/access/mla2api.c
+++ b/access/mla2api.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/30/07
 *
-* $Revision: 1.8 $
+* $Revision: 1.14 $
 *
 * File Description: 
 *
@@ -528,18 +528,18 @@ static void SplitMLAuthName (
   *p = '\0';
 
   if (sbuf [0]) {
-    if (StringCmp (sbuf, "1d") == 0)
-      p = StringMove (suffix, "I.");
-    else if (StringCmp (sbuf, "2d") == 0)
-      p = StringMove (suffix, "II.");
-    else if (StringCmp (sbuf, "3d") == 0)
-      p = StringMove (suffix, "III.");
+    if (StringCmp (sbuf, "1d") == 0 || StringCmp (sbuf, "1st") == 0)
+      p = StringMove (suffix, "I");
+    else if (StringCmp (sbuf, "2d") == 0 || StringCmp (sbuf, "2nd") == 0)
+      p = StringMove (suffix, "II");
+    else if (StringCmp (sbuf, "3d") == 0 || StringCmp (sbuf, "3rd") == 0)
+      p = StringMove (suffix, "III");
     else if (StringCmp (sbuf, "4th") == 0)
-      p = StringMove (suffix, "IV.");
+      p = StringMove (suffix, "IV");
     else if (StringCmp (sbuf, "5th") == 0)
-      p = StringMove (suffix, "V.");
+      p = StringMove (suffix, "V");
     else if (StringCmp (sbuf, "6th") == 0)
-      p = StringMove (suffix, "VI.");
+      p = StringMove (suffix, "VI");
     else if (StringCmp (sbuf, "Sr") == 0)
       p = StringMove (suffix, "Sr.");
     else if (StringCmp (sbuf, "Jr") == 0)
@@ -666,6 +666,123 @@ NLM_EXTERN void ChangeMlaBackMLAuthorsToSTD (
   ChangeCitArtMLAuthorsToSTD (cap);
 }
 
+typedef struct ejour {
+  CharPtr  journal_name;
+  Int2     starting_year;
+} EjourData, PNTR EjourDataPtr;
+
+static EjourData mla2_ejour_list [] = {
+ {"Acta Crystallograph. Sect. F Struct. Biol. Cryst. Commun.",     0 },
+ {"Acta Vet. Scand.",                                           2006 },
+ {"Afr. J. Biotechnol.",                                           0 },
+ {"Ambul. Surg.",                                               2005 },
+ {"Ann. Clin. Microbiol. Antimicrob.",                             0 },
+ {"Biol. Direct",                                                  0 },
+ {"Biotecnol. Apl.",                                            2002 },
+ {"BMC Biochem.",                                                  0 },
+ {"BMC Bioinformatics",                                            0 },
+ {"BMC Biotechnol.",                                               0 },
+ {"BMC Cancer",                                                    0 },
+ {"BMC Cell Biol.",                                                0 },
+ {"BMC Dermatol.",                                                 0 },
+ {"BMC Dev. Biol.",                                                0 },
+ {"BMC Ecol.",                                                     0 },
+ {"BMC Evol. Biol.",                                               0 },
+ {"BMC Genet.",                                                    0 },
+ {"BMC Genomics",                                                  0 },
+ {"BMC Immunol.",                                                  0 },
+ {"BMC Infect. Dis.",                                              0 },
+ {"BMC Med. Genet.",                                               0 },
+ {"BMC Microbiol.",                                                0 },
+ {"BMC Mol. Biol.",                                                0 },
+ {"BMC Pharmacol.",                                                0 },
+ {"BMC Physiol.",                                                  0 },
+ {"BMC Plant Biol.",                                               0 },
+ {"BMC Struct. Biol.",                                             0 },
+ {"BMC Vet. Res.",                                                 0 },
+ {"Breast Cancer Res.",                                         2005 },
+ {"Cancer Cell Int.",                                              0 },
+ {"Cancer Immun.",                                                 0 },
+ {"Cell Commun. Signal",                                           0 },
+ {"Cell Struct. Funct.",                                        2005 },
+ {"Cell. Mol. Biol. (Noisy-le-grand)",                          2004 },
+ {"Colomb. Med.",                                               1998 },
+ {"Crit. Rev. Oral Biol. Med.",                                 2002 },
+ {"Dermatol. Online J.",                                           0 },
+ {"Electron. J. Biotechnol.",                                      0 },
+ {"Eur. J. Genet. Mol. Toxicol.",                                  0 },
+ {"Evol. Bioinform. Online",                                       0 },
+ {"Front. Zool.",                                                  0 },
+ {"Fungal Planet",                                                 0 },
+ {"Genome Biol.",                                               2005 },
+ {"Geochem. Trans.",                                               0 },
+ {"Hereditas",                                                  2004 },
+ {"Hum. Genomics",                                              2004 },
+ {"Infect. Agents Cancer",                                         0 },
+ {"J. Exp. Clin. Assist. Reprod.",                                 0 },
+ {"J. Plankton Res.",                                              0 },
+ {"JOP",                                                           0 },
+ {"Kinetoplastid Biol Dis",                                        0 },
+ {"Malar. J.",                                                     0 },
+ {"Microb. Cell Fact.",                                            0 },
+ {"Mol. Syst. Biol.",                                              0 },
+ {"Mol. Vis.",                                                     0 },
+ {"Neoplasia",                                                  2005 },
+ {"Nucl. Recept.",                                                 0 },
+ {"Pharmacologyonline",                                            0 },
+ {"Plant Methods",                                                 0 },
+ {"PLoS Biol.",                                                 2006 },
+ {"PLoS ONE",                                                      0 },
+ {"Redox Rep.",                                                 2004 },
+ {"Reprod. Biol. Endocrinol.",                                     0 },
+ {"Retrovirology",                                                 0 },
+ {"Saline Syst.",                                                  0 },
+ {"Sci. STKE",                                                     0 },
+ {"ScientificWorldJournal",                                        0 },
+ {"Tech. Tips Online",                                             0 },
+ {"Virol. J.",                                                     0 },
+ {NULL,                                                            0 }
+};
+
+NLM_EXTERN Boolean Mla2IsEPubOnlyJournal (
+  CharPtr jta,
+  Int2Ptr starting_yearP
+)
+
+{
+  EjourDataPtr  ejp;
+  Int2          L, R, mid;
+
+  if (starting_yearP != NULL) {
+    *starting_yearP = 0;
+  }
+
+  if (StringHasNoText (jta)) return FALSE;
+
+  L = 0;
+  R = sizeof (mla2_ejour_list) / sizeof (mla2_ejour_list [0]) - 1; /* -1 because now NULL terminated */
+
+  while (L < R) {
+    mid = (L + R) / 2;
+    ejp = &(mla2_ejour_list [mid]);
+    if (ejp != NULL && StringICmp (ejp->journal_name, jta) < 0) {
+      L = mid + 1;
+    } else {
+      R = mid;
+    }
+  }
+
+  ejp = &(mla2_ejour_list [R]);
+  if (ejp != NULL && StringICmp (ejp->journal_name, jta) == 0) {
+    if (starting_yearP != NULL) {
+      *starting_yearP = ejp->starting_year;
+    }
+    return TRUE;
+  }
+
+  return FALSE;
+}
+
 NLM_EXTERN Int2 Mla2CorrectCitArt (
   CitArtPtr newcap,
   CitArtPtr oldcap
diff --git a/access/mla2api.h b/access/mla2api.h
index b89fcf93..c36699d6 100644
--- a/access/mla2api.h
+++ b/access/mla2api.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/30/07
 *
-* $Revision: 1.5 $
+* $Revision: 1.7 $
 *
 * File Description: 
 *
@@ -163,6 +163,11 @@ NLM_EXTERN void ChangeMlaBackMLAuthorsToSTD (
   MlaBackPtr mbp 
 );
 
+NLM_EXTERN Boolean Mla2IsEPubOnlyJournal (
+  CharPtr jta,
+  Int2Ptr starting_yearP
+);
+
 /*
    Mla2CorrectCitArt takes the original and fetched CitArt and
    fixes author types, compares author lists for differences,
diff --git a/access/pmfapi.c b/access/pmfapi.c
index 9f536138..197594ed 100644
--- a/access/pmfapi.c
+++ b/access/pmfapi.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   5/5/00
 *
-* $Revision: 1.91 $
+* $Revision: 1.96 $
 *
 * File Description: 
 *
@@ -158,18 +158,18 @@ static void SplitMLAuthorName (
   *p = '\0';
 
   if (sbuf [0]) {
-    if (StringCmp (sbuf, "1d") == 0)
-      p = StringMove (suffix, "I.");
-    else if (StringCmp (sbuf, "2d") == 0)
-      p = StringMove (suffix, "II.");
-    else if (StringCmp (sbuf, "3d") == 0)
-      p = StringMove (suffix, "III.");
+    if (StringCmp (sbuf, "1d") == 0 || StringCmp (sbuf, "1st") == 0)
+      p = StringMove (suffix, "I");
+    else if (StringCmp (sbuf, "2d") == 0 || StringCmp (sbuf, "2nd") == 0)
+      p = StringMove (suffix, "II");
+    else if (StringCmp (sbuf, "3d") == 0 || StringCmp (sbuf, "3rd") == 0)
+      p = StringMove (suffix, "III");
     else if (StringCmp (sbuf, "4th") == 0)
-      p = StringMove (suffix, "IV.");
+      p = StringMove (suffix, "IV");
     else if (StringCmp (sbuf, "5th") == 0)
-      p = StringMove (suffix, "V.");
+      p = StringMove (suffix, "V");
     else if (StringCmp (sbuf, "6th") == 0)
-      p = StringMove (suffix, "VI.");
+      p = StringMove (suffix, "VI");
     else if (StringCmp (sbuf, "Sr") == 0)
       p = StringMove (suffix, "Sr.");
     else if (StringCmp (sbuf, "Jr") == 0)
@@ -381,6 +381,75 @@ NLM_EXTERN CONN PubSeqFetchOpenConnection (
   return conn;
 }
 
+NLM_EXTERN CONN PubSeqFetchTraceOpenConnection (
+  Int4 tid,
+  Int2 retcode,
+  Int4 flags
+)
+
+{
+  Char     buf [32];
+  CONN     conn;
+  Char     query [64];
+#ifdef OS_UNIX
+  CharPtr  str;
+#endif
+
+  if (tid < 1) return NULL;
+  if (retcode < 0 || retcode > 4) {
+    retcode = 0;
+  }
+  if (flags < 0) {
+    flags = 1;
+  }
+
+#ifdef PUB_SEQ_FETCH_DEBUG
+  sprintf (query, "val=0:TRACE:%ld&save=idf&view=1&maxplex=%d&extrafeat=%ld", (long) tid, (int) retcode, (long) flags);
+  return QUERY_OpenUrlQuery ("www.ncbi.nlm.nih.gov", 80, "/entrez/viewer.fcgi",
+                             query, "Entrez2Tool", 30, eMIME_T_NcbiData,
+                             eMIME_AsnText, eENCOD_None, 0);
+#endif
+
+  sprintf (query, "val=0:TRACE:%ld&maxplex=%d&extrafeat=%ld", (long) tid, (int) retcode, (long) flags);
+  conn = QUERY_OpenServiceQuery ("SeqFetch", query, 30);
+
+#ifdef OS_UNIX
+  if (! log_query_url_set) {
+    str = (CharPtr) getenv ("PUBSEQ_FETCH_LOG_URL");
+    if (StringDoesHaveText (str)) {
+      if (StringICmp (str, "TRUE") == 0) {
+        log_query_url = TRUE;
+      }
+    }
+    log_query_url_set = TRUE;
+  }
+#endif
+
+  if (conn == NULL) {
+    MakeDateTimeStamp (buf);
+    if (StringHasNoText (buf)) {
+      StringCpy (buf, "?");
+    }
+    ErrPostEx (SEV_ERROR, 0, 0, "PubSeqFetchTraceOpenConnection failed for ti %ld, date/time %s", (long) tid, buf);
+    return conn;
+  }
+
+#ifdef OS_UNIX
+  if (log_query_url) {
+    str = CONN_Description (conn);
+    if (str == NULL) {
+      ErrPostEx (SEV_ERROR, 0, 0, "CONN_Description failed for ti %ld", (long) tid);
+    } else {
+      ErrPostEx (SEV_ERROR, 0, 0, "CONN_Description for ti %ld is %s", (long) tid, str);
+    }
+    MemFree (str);
+  }
+#endif
+
+  return conn;
+}
+
+
 static CharPtr girevtxt = "cmd=seqid&txt=on&seqid=fasta&val=";
 
 NLM_EXTERN CONN GiRevHistOpenConnection (
@@ -1023,10 +1092,39 @@ static void ConfirmGiInSep (
   }
 }
 
-NLM_EXTERN SeqEntryPtr PubSeqSynchronousQuery (
+
+static void ConfirmTiInSep (
+  BioseqPtr bsp,
+  Pointer userdata
+)
+
+{
+  Int4          ti;
+  PsConfirmPtr  psp;
+  SeqIdPtr      sip;
+  DbtagPtr      dbtag;
+
+  if (bsp == NULL || userdata == NULL) return;
+  psp = (PsConfirmPtr) userdata;
+  for (sip = bsp->id; sip != NULL; sip = sip->next) {
+    if (sip->choice != SEQID_GENERAL) continue;
+    dbtag = (DbtagPtr) sip->data.ptrvalue;
+    if (dbtag == NULL || StringCmp (dbtag->db, "ti") != 0 || dbtag->tag == NULL) continue;
+    if (dbtag->tag->str == NULL && dbtag->tag->id > 0) {
+      ti = dbtag->tag->id;
+      if (psp->gi == 0 || ti == psp->uid) {
+        psp->gi = ti;
+      }
+    }
+  }
+}
+
+
+NLM_EXTERN SeqEntryPtr PubSeqSynchronousQueryEx (
   Int4 uid,
   Int2 retcode,
-  Int4 flags
+  Int4 flags,
+  Boolean is_trace
 )
 
 {
@@ -1055,7 +1153,11 @@ NLM_EXTERN SeqEntryPtr PubSeqSynchronousQuery (
   }
 #endif
 
-  conn = PubSeqFetchOpenConnection (uid, retcode, flags);
+  if (is_trace) {
+    conn = PubSeqFetchTraceOpenConnection (uid, retcode, flags);
+  } else {
+    conn = PubSeqFetchOpenConnection (uid, retcode, flags);
+  }
 
   if (conn == NULL) return NULL;
 
@@ -1084,11 +1186,18 @@ NLM_EXTERN SeqEntryPtr PubSeqSynchronousQuery (
   if (sep != NULL) {
     ps.uid = uid;
     ps.gi = 0;
-    VisitBioseqsInSep (sep, (Pointer) &ps, ConfirmGiInSep);
+    if (is_trace) {
+      VisitBioseqsInSep (sep, (Pointer) &ps, ConfirmTiInSep);
+    } else {
+      VisitBioseqsInSep (sep, (Pointer) &ps, ConfirmGiInSep);
+    }
     if (ps.gi != uid) {
       ErrPostEx (SEV_ERROR, 0, 0,
-                 "PubSeqSynchronousQuery requested gi %ld but received gi %ld",
-                 (long) uid, (long) ps.gi);
+                 "PubSeqSynchronousQuery requested %s %ld but received %s %ld",
+                 is_trace ? "ti" : "gi",
+                 (long) uid,
+                 is_trace ? "ti" : "gi",
+                 (long) ps.gi);
     }
   } else {
     MakeDateTimeStamp (buf);
@@ -1096,7 +1205,8 @@ NLM_EXTERN SeqEntryPtr PubSeqSynchronousQuery (
       StringCpy (buf, "?");
     }
     ErrPostEx (SEV_ERROR, 0, 0,
-               "PubSeqSynchronousQuery failed for gi %ld, date/time %s, URL is %s",
+               "PubSeqSynchronousQuery failed for %s %ld, date/time %s, URL is %s",
+               is_trace ? "ti" : "gi",
                (long) uid, buf, str);
   }
 
@@ -1105,6 +1215,28 @@ NLM_EXTERN SeqEntryPtr PubSeqSynchronousQuery (
   return sep;
 }
 
+
+NLM_EXTERN SeqEntryPtr PubSeqSynchronousQuery (
+  Int4 uid,
+  Int2 retcode,
+  Int4 flags
+)
+
+{
+  return PubSeqSynchronousQueryEx (uid, retcode, flags, FALSE);
+}
+
+
+NLM_EXTERN SeqEntryPtr PubSeqSynchronousQueryTI (
+  Int4 uid,
+  Int2 retcode,
+  Int4 flags
+)
+
+{
+  return PubSeqSynchronousQueryEx (uid, retcode, flags, TRUE);
+}
+
 NLM_EXTERN CharPtr GiRevHistSynchronousQuery (
   Int4 uid,
   Int4 num,
@@ -1565,9 +1697,10 @@ NLM_EXTERN Int4 AccnListCheckQueue (
   return QUERY_CheckQueue (queue);
 }
 
-/* object manager registerable fetch function */
+/* object manager registerable fetch functions */
 
 static CharPtr pubseqfetchproc = "PubSeqBioseqFetch";
+static CharPtr tracefetchproc = "TraceBioseqFetch";
 static CharPtr pubseqseqidtogi = "PubSeqSeqIdForGi";
 static CharPtr pubseqgitoseqid = "PubSeqGiForSeqId";
 
@@ -1693,6 +1826,61 @@ static Int2 LIBCALLBACK PubSeqBioseqFetchFunc (Pointer data)
   return OM_MSG_RET_DONE;
 }
 
+static Int2 LIBCALLBACK TraceBioseqFetchFunc (Pointer data)
+
+{
+  BioseqPtr         bsp;
+  DbtagPtr          dbt;
+  Int4              flags = -1;
+  ObjectIdPtr       oip;
+  OMUserDataPtr     omdp = NULL;
+  OMProcControlPtr  ompcp;
+  ObjMgrProcPtr     ompp;
+  Int2              retcode = 0;
+  SeqEntryPtr       sep = NULL;
+  SeqIdPtr          sip;
+  Int4              uid = 0;
+
+  ompcp = (OMProcControlPtr) data;
+  if (ompcp == NULL) return OM_MSG_RET_ERROR;
+  ompp = ompcp->proc;
+  if (ompp == NULL) return OM_MSG_RET_ERROR;
+  sip = (SeqIdPtr) ompcp->input_data;
+  if (sip == NULL) return OM_MSG_RET_ERROR;
+
+  omdp = ObjMgrGetUserData (ompcp->input_entityID, ompp->procid, OMPROC_FETCH, 0);
+  if (omdp != NULL) {
+    uid = omdp->userdata.intvalue;
+    if (uid == 0) return OM_MSG_RET_ERROR;
+  } else if (sip->choice == SEQID_GENERAL) {
+    dbt = (DbtagPtr) sip->data.ptrvalue;
+    if (dbt == NULL) return OM_MSG_RET_OK;
+    if (StringICmp (dbt->db, "ti") != 0) return OM_MSG_RET_OK;
+    oip = dbt->tag;
+    if (oip == NULL || oip->id == 0) return OM_MSG_RET_OK;
+    uid = oip->id;
+  }
+
+  if (uid == 0) return OM_MSG_RET_OK;
+
+  sep = PubSeqSynchronousQueryTI (uid, retcode, flags);
+
+  if (sep == NULL) {
+    return OM_MSG_RET_OK;
+  }
+  bsp = BioseqFindInSeqEntry (sip, sep);
+
+  ompcp->output_data = (Pointer) bsp;
+  ompcp->output_entityID = ObjMgrGetEntityIDForChoice (sep);
+
+  omdp = ObjMgrAddUserData (ompcp->output_entityID, ompp->procid, OMPROC_FETCH, 0);
+  if (omdp != NULL) {
+    omdp->userdata.intvalue = uid;
+  }
+
+  return OM_MSG_RET_DONE;
+}
+
 static Int2 LIBCALLBACK PubSeqSeqIdForGiFunc (Pointer data)
 
 {
@@ -1776,6 +1964,10 @@ static Int2 LIBCALLBACK PubSeqGiForSeqIdFunc (Pointer data)
 NLM_EXTERN Boolean PubSeqFetchEnable (void)
 
 {
+  ObjMgrProcLoad (OMPROC_FETCH, tracefetchproc, tracefetchproc,
+                  OBJ_SEQID, 0, OBJ_BIOSEQ, 0, NULL,
+                  TraceBioseqFetchFunc, PROC_PRIORITY_DEFAULT);
+
   ObjMgrProcLoad (OMPROC_FETCH, pubseqfetchproc, pubseqfetchproc,
                   OBJ_SEQID, 0, OBJ_BIOSEQ, 0, NULL,
                   PubSeqBioseqFetchFunc, PROC_PRIORITY_DEFAULT);
@@ -1805,6 +1997,10 @@ NLM_EXTERN Boolean PubSeqFetchEnableEx (
 
 {
   if (fetch) {
+    ObjMgrProcLoad (OMPROC_FETCH, tracefetchproc, tracefetchproc,
+                    OBJ_SEQID, 0, OBJ_BIOSEQ, 0, NULL,
+                    TraceBioseqFetchFunc, PROC_PRIORITY_DEFAULT);
+
     ObjMgrProcLoad (OMPROC_FETCH, pubseqfetchproc, pubseqfetchproc,
                     OBJ_SEQID, 0, OBJ_BIOSEQ, 0, NULL,
                     PubSeqBioseqFetchFunc, PROC_PRIORITY_DEFAULT);
@@ -1840,6 +2036,10 @@ NLM_EXTERN void PubSeqFetchDisable (void)
   ObjMgrProcPtr  ompp;
 
   omp = ObjMgrGet ();
+  ompp = ObjMgrProcFind (omp, 0, tracefetchproc, OMPROC_FETCH);
+  if (ompp != NULL) {
+    ObjMgrFreeUserData (0, ompp->procid, OMPROC_FETCH, 0);
+  }
   ompp = ObjMgrProcFind (omp, 0, pubseqfetchproc, OMPROC_FETCH);
   if (ompp != NULL) {
     ObjMgrFreeUserData (0, ompp->procid, OMPROC_FETCH, 0);
@@ -2439,6 +2639,7 @@ static CharPtr inferencePrefix [] = {
   "nucleotide motif",
   "protein motif",
   "ab initio prediction",
+  "alignment",
   NULL
 };
 
diff --git a/access/pmfapi.h b/access/pmfapi.h
index 40ddab53..3a0f4b4b 100644
--- a/access/pmfapi.h
+++ b/access/pmfapi.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   5/5/00
 *
-* $Revision: 1.28 $
+* $Revision: 1.29 $
 *
 * File Description: 
 *
@@ -74,6 +74,12 @@ NLM_EXTERN CONN PubSeqFetchOpenConnection (
   Int4 flags
 );
 
+NLM_EXTERN CONN PubSeqFetchTraceOpenConnection (
+  Int4 tid,
+  Int2 retcode,
+  Int4 flags
+);
+
 NLM_EXTERN CONN GiRevHistOpenConnection (
   Int4 uid,
   Int4 num,
@@ -135,6 +141,19 @@ NLM_EXTERN PubmedEntryPtr PubMedSynchronousQuery (
   Int4 uid
 );
 
+NLM_EXTERN SeqEntryPtr PubSeqSynchronousQueryEx (
+  Int4 uid,
+  Int2 retcode,
+  Int4 flags,
+  Boolean is_trace
+);
+
+NLM_EXTERN SeqEntryPtr PubSeqSynchronousQueryTI (
+  Int4 uid,
+  Int2 retcode,
+  Int4 flags
+);
+
 NLM_EXTERN SeqEntryPtr PubSeqSynchronousQuery (
   Int4 uid,
   Int2 retcode,
diff --git a/access/tax3api.c b/access/tax3api.c
index 67720f14..5a537224 100644
--- a/access/tax3api.c
+++ b/access/tax3api.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/8/04
 *
-* $Revision: 1.28 $
+* $Revision: 1.35 $
 *
 * File Description: 
 *
@@ -52,12 +52,29 @@
 
 /* low-level connection functions */
 
+static Boolean text_tax_asn = FALSE;
+static Boolean text_tax_set = FALSE;
+
 NLM_EXTERN CONN Tax3OpenConnection (
   void
 )
 
 {
-  return QUERY_OpenServiceQuery ("TaxService3", NULL, 30);
+#ifdef OS_UNIX
+  CharPtr  str;
+
+  if (! text_tax_set) {
+    str = (CharPtr) getenv ("TEXT_TAX_ASN");
+    if (StringDoesHaveText (str)) {
+      if (StringICmp (str, "TRUE") == 0) {
+        text_tax_asn = TRUE;
+      }
+    }
+    text_tax_set = TRUE;
+  }
+#endif
+
+  return QUERY_OpenServiceQuery (text_tax_asn ? "TaxService3Text" : "TaxService3", NULL, 30);
 }
 
 #ifdef OS_MAC
@@ -98,7 +115,7 @@ NLM_EXTERN Taxon3ReplyPtr Tax3WaitForReply (
 #endif
   }
   if (status == eIO_Success) {
-    aicp = QUERY_AsnIoConnOpen ("rb", conn);
+    aicp = QUERY_AsnIoConnOpen (text_tax_asn ? "r" : "rb", conn);
     t3ry = Taxon3ReplyAsnRead (aicp->aip, NULL);
     QUERY_AsnIoConnClose (aicp);
   }
@@ -124,7 +141,7 @@ NLM_EXTERN Taxon3ReplyPtr Tax3SynchronousQuery (
 
   if (conn == NULL) return NULL;
 
-  aicp = QUERY_AsnIoConnOpen ("wb", conn);
+  aicp = QUERY_AsnIoConnOpen (text_tax_asn ? "w" : "wb", conn);
 
   Taxon3RequestAsnWrite (t3rq, aicp->aip, NULL);
 
@@ -155,7 +172,7 @@ NLM_EXTERN Boolean Tax3AsynchronousQuery (
 
   if (conn == NULL) return FALSE;
 
-  aicp = QUERY_AsnIoConnOpen ("wb", conn);
+  aicp = QUERY_AsnIoConnOpen (text_tax_asn ? "w" : "wb", conn);
 
   Taxon3RequestAsnWrite (t3rq, aicp->aip, NULL);
 
@@ -187,7 +204,7 @@ NLM_EXTERN Taxon3ReplyPtr Tax3ReadReply (
   Taxon3ReplyPtr  t3ry = NULL;
 
   if (conn != NULL && status == eIO_Success) {
-    aicp = QUERY_AsnIoConnOpen ("rb", conn);
+    aicp = QUERY_AsnIoConnOpen (text_tax_asn ? "r" : "rb", conn);
     t3ry = Taxon3ReplyAsnRead (aicp->aip, NULL);
     QUERY_AsnIoConnClose (aicp);
   }
@@ -250,6 +267,23 @@ NLM_EXTERN Taxon3RequestPtr CreateMultiTaxon3Request (ValNodePtr org_list)
   return t3rp;
 }
 
+
+static Boolean HasMisspellingFlag (T3DataPtr t)
+{
+  T3StatusFlagsPtr status;
+
+  if (t == NULL) return FALSE;
+  status = t->status;
+  while (status != NULL) {
+    if (StringCmp (status->property, "misspelled_name") == 0) {
+      return TRUE;
+    }
+    status = status->next;
+  }
+  return FALSE;
+}
+
+
 NLM_EXTERN ValNodePtr Taxon3GetOrgRefList (ValNodePtr org_list)
 {
   Taxon3RequestPtr t3rq;
@@ -295,7 +329,11 @@ NLM_EXTERN ValNodePtr Taxon3GetOrgRefList (ValNodePtr org_list)
             tdp = (T3DataPtr) trp->data.ptrvalue;
             if (tdp != NULL) {
               t3orp = (OrgRefPtr)(tdp->org);
-              ValNodeAddPointer (&response_list, 3, (Pointer) t3orp);
+              if (HasMisspellingFlag (tdp)) {
+                ValNodeAddPointer (&response_list, 4, (Pointer) t3orp);
+              } else {
+                ValNodeAddPointer (&response_list, 3, (Pointer) t3orp);
+              }
               tdp->org = NULL;
             }
             break;
@@ -748,7 +786,6 @@ static Boolean DoTaxonIdsMatch (OrgRefPtr org1, OrgRefPtr org2)
 
 NLM_EXTERN void Taxon3CheckOrgInSeqEntry (SeqEntryPtr sep, ValNodePtr PNTR not_found, ValNodePtr PNTR bad_match)
 {
-  ValNodePtr   biop_list = NULL;
   ValNodePtr   request_list = NULL;
   ValNodePtr   response_list = NULL;
   ValNodePtr   biop_vnp, response_vnp;
@@ -883,6 +920,33 @@ static ValNodePtr FreeOrgRefValNodeList (ValNodePtr vnp)
 }
 
 
+static Boolean EndsWithSp (CharPtr str)
+{
+  Int4 len;
+
+  if (StringHasNoText (str)) return FALSE;
+  len = StringLen (str);
+  if (len < 4) return FALSE;
+  if (StringCmp (str + len - 4, " sp.") == 0) return TRUE;
+  return FALSE;
+}
+
+
+static CharPtr RemoveSp (CharPtr orig)
+{
+  CharPtr cpy = NULL;
+  Int4    len;
+
+  len = StringLen (orig);
+  if (len >= 4 && StringCmp (orig + len - 4, " sp.") == 0) {
+    cpy = (CharPtr) MemNew (sizeof (Char) * len - 3);
+    StringNCpy (cpy, orig, len - 4);
+    cpy[len - 4] = 0;
+  }
+  return cpy;
+}
+
+  
 static void AddRequestOrgForString (CharPtr str, CharPtr host, ValNodePtr PNTR request_list, ValNodePtr PNTR req_host_list)
 {
   OrgRefPtr    request_org;
@@ -894,28 +958,38 @@ static void AddRequestOrgForString (CharPtr str, CharPtr host, ValNodePtr PNTR r
     return;
   }
 
-  request_org = OrgRefNew();
-  request_org->taxname = StringSave (str);
-  ValNodeAddPointer (request_list, 3, request_org);
-  ValNodeAddPointer (req_host_list, 0, host);
-
-  /* if more than one word, try chopping off last to see if abbreviated name looks up */
-  word1_len = StringCSpn (str, " ");
-  if (word1_len == 0) return;
-  space_len = StringSpn (str + word1_len, " ");
-  if (space_len == 0) return;
-  word2_len = StringCSpn (str + word1_len + space_len, " ");
-  if (word2_len == 0) return;
-  if (isspace (*(str + word1_len + space_len + word2_len)))
-  {
-    cpy = StringSave (str);    
-    cp = StringRChr (cpy, ' ');
-    if (cp != NULL)
+  /* if ends with " sp.", remove " sp." */
+  cpy = RemoveSp (host);
+  if (cpy != NULL) {
+    request_org = OrgRefNew();
+    request_org->taxname = cpy;
+    ValNodeAddPointer (request_list, 3, request_org);
+    ValNodeAddPointer (req_host_list, 0, host);
+  } else {
+    request_org = OrgRefNew();
+    request_org->taxname = StringSave (str);
+    ValNodeAddPointer (request_list, 3, request_org);
+    ValNodeAddPointer (req_host_list, 0, host);
+
+     
+    /* if more than one word, try chopping off last to see if abbreviated name looks up */
+    word1_len = StringCSpn (str, " ");
+    if (word1_len == 0) return;
+    space_len = StringSpn (str + word1_len, " ");
+    if (space_len == 0) return;
+    word2_len = StringCSpn (str + word1_len + space_len, " ");
+    if (word2_len == 0) return;
+    if (isspace (*(str + word1_len + space_len + word2_len)))
     {
-      *cp = 0;
-      AddRequestOrgForString (cpy, host, request_list, req_host_list);
+      cpy = StringSave (str);    
+      cp = StringRChr (cpy, ' ');
+      if (cp != NULL)
+      {
+        *cp = 0;
+        AddRequestOrgForString (cpy, host, request_list, req_host_list);
+      }
+      cpy = MemFree (cpy);
     }
-    cpy = MemFree (cpy);
   }
 }
 
@@ -1083,26 +1157,13 @@ static void AddBioSourcesToSpecificHostChecklist (ValNodePtr biop_list, ValNodeP
 }
 
 
-static Boolean EndsWithSp (CharPtr str)
-{
-  Int4 len;
-
-  if (StringHasNoText (str)) return FALSE;
-  len = StringLen (str);
-  if (len < 4) return FALSE;
-  if (StringCmp (str + len - 4, " sp.") == 0) return TRUE;
-  return FALSE;
-}
-
-
-NLM_EXTERN Boolean IsOrgModSpecificHostToBeChecked (OrgModPtr mod, Boolean for_validator)
+NLM_EXTERN Boolean IsOrgModSpecificHostToBeChecked (OrgModPtr mod, Boolean for_validator, Boolean check_single_word)
 {
   CharPtr   cp;
   Boolean   any_upper = FALSE, any_space = FALSE;
 
   if (mod != NULL && mod->subtype == ORGMOD_nat_host
-      && !StringHasNoText (mod->subname)
-      && (!for_validator || !EndsWithSp(mod->subname)))
+      && !StringHasNoText (mod->subname))
   {
     cp = mod->subname;
     while (*cp != 0 && (!any_upper || !any_space))
@@ -1121,7 +1182,7 @@ NLM_EXTERN Boolean IsOrgModSpecificHostToBeChecked (OrgModPtr mod, Boolean for_v
       }
       cp++;
     }
-    if (any_upper && any_space)
+    if (any_upper && (any_space || check_single_word))
     {
       return TRUE;
     }
@@ -1130,7 +1191,7 @@ NLM_EXTERN Boolean IsOrgModSpecificHostToBeChecked (OrgModPtr mod, Boolean for_v
 }
 
 
-static Boolean HasSpecificHostToBeChecked (BioSourcePtr biop, Boolean for_validator)
+static Boolean HasSpecificHostToBeChecked (BioSourcePtr biop, Boolean for_validator, Boolean check_single_word)
 {
   OrgModPtr mod;
 
@@ -1138,7 +1199,7 @@ static Boolean HasSpecificHostToBeChecked (BioSourcePtr biop, Boolean for_valida
   mod = biop->org->orgname->mod;
   while (mod != NULL)
   {
-    if (IsOrgModSpecificHostToBeChecked (mod, for_validator))
+    if (IsOrgModSpecificHostToBeChecked (mod, for_validator, check_single_word))
     {
       return TRUE;
     }
@@ -1223,6 +1284,7 @@ static Boolean MatchesCommonName (CharPtr txt, CharPtr common_name)
 typedef struct spechostgather {
   ValNodePtr list;
   Boolean    for_validator;
+  Boolean    check_single_word;
 } SpecHostGatherData, PNTR SpecHostGatherPtr;
 
 static void AddSpecificHostBioSourceFeatToList (SeqFeatPtr sfp, Pointer userdata)
@@ -1232,7 +1294,7 @@ static void AddSpecificHostBioSourceFeatToList (SeqFeatPtr sfp, Pointer userdata
   if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || userdata == NULL) return;
 
   p = (SpecHostGatherPtr) userdata;
-  if (HasSpecificHostToBeChecked (sfp->data.value.ptrvalue, p->for_validator))
+  if (HasSpecificHostToBeChecked (sfp->data.value.ptrvalue, p->for_validator, p->check_single_word))
   {
     ValNodeAddPointer (&(p->list), OBJ_SEQFEAT, sfp);
   }
@@ -1246,18 +1308,19 @@ static void AddSpecificHostBioSourceDescToList (SeqDescrPtr sdp, Pointer userdat
   if (sdp == NULL || sdp->choice != Seq_descr_source || userdata == NULL) return;
 
   p = (SpecHostGatherPtr) userdata;
-  if (HasSpecificHostToBeChecked (sdp->data.ptrvalue, p->for_validator))
+  if (HasSpecificHostToBeChecked (sdp->data.ptrvalue, p->for_validator, p->check_single_word))
   {
     ValNodeAddPointer (&(p->list), OBJ_SEQDESC, sdp);
   }
 }
 
 
-static ValNodePtr GetSpecificHostBioSourceList (SeqEntryPtr sep, Boolean for_validator)
+static ValNodePtr GetSpecificHostBioSourceList (SeqEntryPtr sep, Boolean for_validator, Boolean check_single_word)
 {
   SpecHostGatherData   d;
   
   d.for_validator = for_validator;
+  d.check_single_word = check_single_word;
   d.list = NULL;
   VisitFeaturesInSep (sep, &d, AddSpecificHostBioSourceFeatToList);
   VisitDescriptorsInSep (sep, &d, AddSpecificHostBioSourceDescToList);
@@ -1351,8 +1414,79 @@ FormatSpecificHostRequests
 }
 
 
+static Boolean IsShorterVersionOfEarlierMatch (ValNodePtr request_vnp, ValNodePtr request_list, ValNodePtr response_list)
+{
+  OrgRefPtr this_org, earlier_org, earlier_response;
+  Int4      len;
+  Boolean   found = FALSE;
+
+  if (request_vnp == NULL || request_list == NULL) return FALSE;
+  this_org = (OrgRefPtr) request_vnp->data.ptrvalue;
+  if (this_org == NULL || StringHasNoText (this_org->taxname)) return FALSE;
+  len = StringLen (this_org->taxname);
+  while (request_list != NULL && request_list != request_vnp && !found && response_list != NULL)
+  {
+    earlier_org = (OrgRefPtr) request_list->data.ptrvalue;
+    earlier_response = (OrgRefPtr) response_list->data.ptrvalue;
+    if (earlier_org != NULL && earlier_response != NULL
+        && StringNCmp (earlier_org->taxname, this_org->taxname, len) == 0
+        && (MatchesCommonName (earlier_org->taxname, earlier_response->common)
+            || MatchesSynonym (earlier_org->taxname, earlier_response)
+            || MatchesGenBankSynonym (earlier_org->taxname, earlier_response)))
+    { 
+      found = TRUE;
+    }
+
+    request_list = request_list->next;
+    response_list = response_list->next;
+  }
+  return found;
+}
+
+
+static Boolean MatchWithSp (CharPtr request, CharPtr response)
+{
+  CharPtr cpy = NULL;
+  Boolean rval = FALSE;
+
+  if (StringCmp (request, response) == 0) {
+    rval = TRUE;
+  } else {
+    cpy = RemoveSp (request);
+    if (cpy != NULL && StringCmp (cpy, response) == 0) {
+      rval = TRUE;
+    }
+    cpy = MemFree (cpy);
+  }
+  return rval;
+}
+
+
+static Boolean FindMatchInResponseOrgList (CharPtr request_str, ValNodePtr response_list)
+{
+  ValNodePtr vnp;
+  OrgRefPtr  org;
+  Boolean    rval = FALSE;
+
+  if (StringHasNoText (request_str) || response_list == NULL) {
+    return FALSE;
+  }
+
+  for (vnp = response_list; vnp != NULL && !rval; vnp = vnp->next) {
+    org = (OrgRefPtr) vnp->data.ptrvalue;
+    if (org != NULL) {
+      if (MatchesCommonName (request_str, org->common)
+          || MatchesSynonym (request_str, org)) {
+        rval = TRUE;
+      }
+    }
+  }
+  return rval;
+}
+
+
 /* Want to check that specific host names are valid */
-NLM_EXTERN ValNodePtr Taxon3CheckSpecificHostInSeqEntry (SeqEntryPtr sep, Boolean for_validator)
+NLM_EXTERN ValNodePtr Taxon3CheckSpecificHostInSeqEntry (SeqEntryPtr sep, Boolean for_validator, Boolean check_single_word)
 {
   ValNodePtr   biop_list = NULL;
   ValNodePtr   req_host_list = NULL, spec_host_list = NULL;
@@ -1362,11 +1496,11 @@ NLM_EXTERN ValNodePtr Taxon3CheckSpecificHostInSeqEntry (SeqEntryPtr sep, Boolea
   ValNodePtr   check_list, check_vnp;
   OrgRefPtr    request_org, response_org;
   SpecificHostCheckPtr p;
-  Boolean              has_taxname, has_bad;
+  Boolean              has_taxname, has_bad, all_synonyms;
   ValNodePtr           bad_biop_list = NULL;
-  Int4                 level;
+  ErrSev               level;
     
-  biop_list = GetSpecificHostBioSourceList (sep, for_validator);
+  biop_list = GetSpecificHostBioSourceList (sep, for_validator, check_single_word);
 
   /* get a list of unique specific_host values */
   spec_host_list = GetListOfUniqueSpecificHostValues (biop_list);
@@ -1401,23 +1535,37 @@ NLM_EXTERN ValNodePtr Taxon3CheckSpecificHostInSeqEntry (SeqEntryPtr sep, Boolea
         has_bad = FALSE;
         request_vnp = p->request_list;
         response_vnp = p->response_list;
+        all_synonyms = TRUE;
         while (!has_taxname && request_vnp != NULL && response_vnp != NULL)
         {
           request_org = (OrgRefPtr) request_vnp->data.ptrvalue;
           response_org = (OrgRefPtr) response_vnp->data.ptrvalue;
-          if (response_org == NULL)
+          if (response_vnp->choice == 4) 
           {
             has_bad = TRUE;
+          }  
+          else if (response_org == NULL)
+          {
+            if (!IsShorterVersionOfEarlierMatch(request_vnp, p->request_list, p->response_list)
+                && !FindMatchInResponseOrgList (request_org->taxname, p->response_list))
+            {
+              has_bad = TRUE;
+            }
           }
-          else if (StringCmp (request_org->taxname, response_org->taxname) == 0)
+          else if (MatchWithSp (request_org->taxname, response_org->taxname))
           {
             has_taxname = TRUE;
+          }          
+          else if (MatchesCommonName (request_org->taxname, response_org->common)
+                   || MatchesSynonym (request_org->taxname, response_org)
+                   || MatchesGenBankSynonym (request_org->taxname, response_org))
+          {
+            /* it's a synonym */
           }
-          else if (!MatchesCommonName (request_org->taxname, response_org->common)
-                   && ! MatchesSynonym (request_org->taxname, response_org)
-                   && ! MatchesGenBankSynonym (request_org->taxname, response_org))
+          else
           {
             has_bad = TRUE;
+            all_synonyms = FALSE;
           }
           request_vnp = request_vnp->next;
           response_vnp = response_vnp->next;
@@ -1557,6 +1705,7 @@ static CharPtr StringIsFirstPartOfItemInList (CharPtr str, ValNodePtr list)
   return NULL;
 }
 
+
 static ValNodePtr GetFixesForOneSpecificHostValue (SpecificHostCheckPtr p)
 {
   CharPtr new_taxname = NULL, old_taxname = NULL;
@@ -1578,10 +1727,12 @@ static ValNodePtr GetFixesForOneSpecificHostValue (SpecificHostCheckPtr p)
     response_org = (OrgRefPtr) response_vnp->data.ptrvalue;
     if (response_org == NULL)
     {
-      /* no data */
-      ValNodeAddPointer (&failed_requests, 0, StringSave (request_org->taxname));
+      if (!FindMatchInResponseOrgList (request_org->taxname, p->response_list)) {
+        /* no data */
+        ValNodeAddPointer (&failed_requests, 0, StringSave (request_org->taxname));
+      }
     }
-    else if (StringCmp (request_org->taxname, response_org->taxname) == 0)
+    else if (MatchWithSp (request_org->taxname, response_org->taxname))
     {
       /* found taxname */
       /* is it just a shorter version of an earlier failed request? */
@@ -1617,7 +1768,7 @@ static ValNodePtr GetFixesForOneSpecificHostValue (SpecificHostCheckPtr p)
 }
 
 
-NLM_EXTERN ValNodePtr Taxon3GetSpecificHostFixesInSeqEntry (SeqEntryPtr sep)
+NLM_EXTERN ValNodePtr Taxon3GetSpecificHostFixesInSeqEntry (SeqEntryPtr sep, Boolean check_single_word)
 {
   ValNodePtr   biop_list = NULL;
   ValNodePtr   req_host_list = NULL, spec_host_list = NULL;
@@ -1625,11 +1776,10 @@ NLM_EXTERN ValNodePtr Taxon3GetSpecificHostFixesInSeqEntry (SeqEntryPtr sep)
   ValNodePtr   response_list = NULL;
   ValNodePtr   check_list, check_vnp;
   SpecificHostCheckPtr p;
-  Int4                 level;
-  Boolean              rval = FALSE;
+  ErrSev               level;
   ValNodePtr           fix_list = NULL;
   
-  biop_list = GetSpecificHostBioSourceList (sep, FALSE);
+  biop_list = GetSpecificHostBioSourceList (sep, FALSE, check_single_word);
 
   /* get a list of unique specific_host values */
   spec_host_list = GetListOfUniqueSpecificHostValues (biop_list);
@@ -1673,12 +1823,12 @@ NLM_EXTERN ValNodePtr Taxon3GetSpecificHostFixesInSeqEntry (SeqEntryPtr sep)
 }
 
 
-NLM_EXTERN Boolean Taxon3FixSpecificHostInSeqEntry (SeqEntryPtr sep)
+NLM_EXTERN Boolean Taxon3FixSpecificHostInSeqEntry (SeqEntryPtr sep, Boolean check_single_word)
 {
   ValNodePtr fix_list, vnp;
   Boolean    rval = FALSE;
 
-  fix_list = Taxon3GetSpecificHostFixesInSeqEntry (sep);
+  fix_list = Taxon3GetSpecificHostFixesInSeqEntry (sep, check_single_word);
   for (vnp = fix_list; vnp != NULL; vnp = vnp->next)
   {
     rval |= ApplyOneSpecificHostFix (vnp->data.ptrvalue);
@@ -1825,8 +1975,7 @@ NLM_EXTERN ValNodePtr GetOrganismTaxLookupFailuresInSeqEntry (SeqEntryPtr sep)
   ValNodePtr   request_list = NULL;
   ValNodePtr   response_list = NULL;
   ValNodePtr   req_vnp, resp_vnp;
-  Int4                 level;
-  Boolean              rval = FALSE;
+  ErrSev               level;
   ValNodePtr           failed_list = NULL, vnp;
   OrgRefPtr            request_org;
   
diff --git a/access/tax3api.h b/access/tax3api.h
index ff7cc916..629eeb1f 100644
--- a/access/tax3api.h
+++ b/access/tax3api.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/8/04
 *
-* $Revision: 1.15 $
+* $Revision: 1.16 $
 *
 * File Description: 
 *
@@ -137,9 +137,9 @@ NLM_EXTERN void Taxon3ReplaceOrgInSeqEntry (SeqEntryPtr sep, Boolean keep_syn);
 NLM_EXTERN void Taxon3CheckOrgInSeqEntry (SeqEntryPtr sep, ValNodePtr PNTR not_found, ValNodePtr PNTR bad_match);
 NLM_EXTERN void CheckTaxNamesAgainstTaxDatabase (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list);
 
-NLM_EXTERN Boolean IsOrgModSpecificHostToBeChecked (OrgModPtr mod, Boolean for_validator);
-NLM_EXTERN ValNodePtr Taxon3CheckSpecificHostInSeqEntry (SeqEntryPtr sep, Boolean for_validator);
-NLM_EXTERN Boolean Taxon3FixSpecificHostInSeqEntry (SeqEntryPtr sep);
+NLM_EXTERN Boolean IsOrgModSpecificHostToBeChecked (OrgModPtr mod, Boolean for_validator, Boolean check_single_word);
+NLM_EXTERN ValNodePtr Taxon3CheckSpecificHostInSeqEntry (SeqEntryPtr sep, Boolean for_validator, Boolean check_single_word);
+NLM_EXTERN Boolean Taxon3FixSpecificHostInSeqEntry (SeqEntryPtr sep, Boolean check_single_word);
 
 typedef struct specifichostfix {
   ValNodePtr feat_or_desc;
@@ -151,7 +151,7 @@ typedef struct specifichostfix {
 extern ValNodePtr SpecificHostFixListFree (ValNodePtr vnp);
 extern Boolean ApplyOneSpecificHostFix (SpecificHostFixPtr s);
 /* returns ValNodePtr list of SpecificHostFixPtr */
-NLM_EXTERN ValNodePtr Taxon3GetSpecificHostFixesInSeqEntry (SeqEntryPtr sep);
+NLM_EXTERN ValNodePtr Taxon3GetSpecificHostFixesInSeqEntry (SeqEntryPtr sep, Boolean check_single_word);
 
 NLM_EXTERN ValNodePtr GetOrganismTaxLookupFailuresInSeqEntry (SeqEntryPtr sep);
 
diff --git a/algo/blast/api/blast_api.c b/algo/blast/api/blast_api.c
index a088090e..e605f036 100644
--- a/algo/blast/api/blast_api.c
+++ b/algo/blast/api/blast_api.c
@@ -1,4 +1,4 @@
-/* $Id: blast_api.c,v 1.50 2007/07/27 18:02:26 papadopo Exp $
+/* $Id: blast_api.c,v 1.53 2008/02/13 22:35:49 camacho Exp $
 ***************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -284,6 +284,7 @@ s_BlastHSPStreamSetUp(BLAST_SequenceBlk* query, BlastQueryInfo* query_info,
                                 options->score_options, &blasthit_params);
         *hsp_stream =
             Blast_HSPListCollectorInitMT(options->program, blasthit_params,
+                                         options->ext_options, TRUE,
                                          kNumResults, lock);
     } else {
         /* Initialize the queue HSP stream for tabular formatting. */
@@ -718,7 +719,7 @@ Blast_RunSearch(SeqLoc* query_seqloc,
           }
     }
 
-    status = LookupTableWrapInit(query, lookup_options, 
+    status = LookupTableWrapInit(query, lookup_options, query_options,
                         lookup_segments, sbp, &lookup_wrap, rps_info, &core_msg);
     if (core_msg)
     {
diff --git a/algo/blast/api/blast_input.c b/algo/blast/api/blast_input.c
index 364d1dfc..abb2312e 100644
--- a/algo/blast/api/blast_input.c
+++ b/algo/blast/api/blast_input.c
@@ -1,5 +1,5 @@
 #ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: blast_input.c,v 1.30 2007/05/07 13:27:15 kans Exp $";
+static char const rcsid[] = "$Id: blast_input.c,v 1.31 2008/01/10 15:43:35 madden Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 /* ===========================================================================
 *
@@ -117,11 +117,18 @@ BLAST_GetQuerySeqLoc(FILE *infp, Boolean query_is_na, Uint1 strand,
       }
 
       if (query_bsp == NULL) {
-         ErrPostEx(SEV_FATAL, 0, 0, "Unable to obtain bioseq\n");
+         ErrPostEx(SEV_FATAL, 0, 0, "Unable to obtain bioseq for sequence number %ld", (long) query_count-1);
          *ctr += query_index;
          return -1;
       }
 
+      if (query_bsp->length <= 0) {
+         ErrPostEx(SEV_FATAL, 0, 0, "Sequence number %ld had length %ld", (long) query_count-1, (long) query_bsp->length);
+         *ctr += query_index;
+         return -1;
+      }
+
+
       
       /* Original from and to are 1-offsets, except when they are 0's,
          in which case they are start and end of sequence respectively */
diff --git a/algo/blast/api/blast_options_api.c b/algo/blast/api/blast_options_api.c
index 12c0f855..9e248e8f 100644
--- a/algo/blast/api/blast_options_api.c
+++ b/algo/blast/api/blast_options_api.c
@@ -1,4 +1,4 @@
-/* $Id: blast_options_api.c,v 1.24 2007/03/20 15:17:16 kans Exp $
+/* $Id: blast_options_api.c,v 1.25 2007/12/14 17:11:29 madden Exp $
 ***************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -323,6 +323,14 @@ Int2 SBlastOptionsSetDbGeneticCode(SBlastOptions* options, Int4 gc)
 
     options->db_options->genetic_code = gc;
 
+    if (GenCodeSingletonFind(gc) == NULL)
+    {
+       Uint1* gcode = NULL;
+       BLAST_GeneticCodeFind(options->db_options->genetic_code, &gcode);
+       GenCodeSingletonAdd(options->db_options->genetic_code, gcode);
+       free(gcode);
+    }
+
     return status;
     
 }
diff --git a/algo/blast/api/dust_filter.c b/algo/blast/api/dust_filter.c
index 29097583..f233b3fd 100644
--- a/algo/blast/api/dust_filter.c
+++ b/algo/blast/api/dust_filter.c
@@ -1,5 +1,5 @@
 #ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: dust_filter.c,v 1.10 2007/01/24 14:31:16 madden Exp $";
+static char const rcsid[] = "$Id: dust_filter.c,v 1.12 2007/12/19 22:05:56 camacho Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 /*
@@ -175,9 +175,7 @@ s_GetFilteringLocations(BLAST_SequenceBlk* query_blk, BlastQueryInfo* query_info
                   /* Reverse this relative to the part of the query being searched, leave it up to 
                     BlastMaskLocToSeqLoc to put it into the context of the entire query sequence (and
                     not just that part being searched). */
-                  filter_slp_rev = BlastSeqLocReverse(filter_slp, query_length);
-                  filter_slp = BlastSeqLocFree(filter_slp);
-                  filter_slp = filter_slp_rev;
+                  BlastSeqLocReverse(filter_slp, query_length);
             }
             else
             {
diff --git a/algo/blast/api/repeats_filter.c b/algo/blast/api/repeats_filter.c
index 61259273..b31f73be 100644
--- a/algo/blast/api/repeats_filter.c
+++ b/algo/blast/api/repeats_filter.c
@@ -1,5 +1,5 @@
 #ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: repeats_filter.c,v 1.18 2007/03/12 16:13:36 madden Exp $";
+static char const rcsid[] = "$Id: repeats_filter.c,v 1.19 2007/12/19 21:56:48 camacho Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 /*
@@ -150,10 +150,9 @@ s_FillMaskLocFromBlastHSPResults(SeqLoc* query_seqloc, BlastHSPResults* results,
             }
         }
         /* Make the intervals unique */
-        ordered_loc_list = BlastSeqLocCombine(loc_list, REPEAT_MASK_LINK_VALUE);
-
-        /* Free the list of locations that's no longer needed. */
-        loc_list = BlastSeqLocFree(loc_list);
+        BlastSeqLocCombine(&loc_list, REPEAT_MASK_LINK_VALUE);
+        ordered_loc_list = loc_list;
+        loc_list = NULL;
 
         mask->seqloc_array[query_index*kNumContexts] = ordered_loc_list;
     }
diff --git a/algo/blast/api/seqsrc_readdb.c b/algo/blast/api/seqsrc_readdb.c
index 5b1d35bd..fcf48a68 100644
--- a/algo/blast/api/seqsrc_readdb.c
+++ b/algo/blast/api/seqsrc_readdb.c
@@ -1,4 +1,4 @@
-/*  $Id: seqsrc_readdb.c,v 1.57 2007/05/15 15:29:56 camacho Exp $
+/*  $Id: seqsrc_readdb.c,v 1.59 2008/01/02 14:00:35 madden Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -29,7 +29,7 @@
  */
 
 #ifndef SKIP_DOXYGEN_PROCESSING
-static char const rcsid[] = "$Id: seqsrc_readdb.c,v 1.57 2007/05/15 15:29:56 camacho Exp $";
+static char const rcsid[] = "$Id: seqsrc_readdb.c,v 1.59 2008/01/02 14:00:35 madden Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/api/seqsrc_readdb.h>
@@ -142,7 +142,7 @@ s_ReaddbGetName(void* readdb_handle, void* ignoreme)
 {
     ReadDBFILEPtr rdfp = (ReadDBFILEPtr) readdb_handle;
 
-    return readdb_get_filename(rdfp);
+    return readdb_get_full_filename(rdfp);
 }
 
 /** Retrieves the date of the BLAST database.
@@ -342,7 +342,7 @@ s_ReadDbGetNextOidListChunk(ReadDBFILEPtr rdfp, BlastSeqSrcIterator* itr,
             bit_start = 0;
          }
 
-         if (oidindex == itr->chunk_sz || !rdfp->next) {
+         if (oidindex == itr->chunk_sz || (oidindex && !rdfp->next)) {
             itr->itr_type = eOidList;
             itr->current_pos = 0;
             *last_oid_assigned = rdfp->start + gi;
diff --git a/algo/blast/composition_adjustment/redo_alignment.c b/algo/blast/composition_adjustment/redo_alignment.c
index 8182c8c3..995b4f24 100644
--- a/algo/blast/composition_adjustment/redo_alignment.c
+++ b/algo/blast/composition_adjustment/redo_alignment.c
@@ -31,7 +31,7 @@
  */
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] =
-    "$Id: redo_alignment.c,v 1.11 2006/06/29 16:50:07 gertz Exp $";
+    "$Id: redo_alignment.c,v 1.13 2007/10/25 15:55:36 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <stdlib.h>
@@ -943,6 +943,29 @@ Blast_RedoAlignParamsNew(Blast_MatrixInfo ** pmatrix_info,
     return params;
 }
 
+#define MINIMUM_LENGTH_NEAR_IDENTICAL 50
+
+
+static Boolean s_preliminaryTestNearIdentical(BlastCompo_QueryInfo query_info[], 
+				   s_WindowInfo *window)
+{
+  BlastCompo_Alignment *align; /*first alignment in this window*/
+  int queryIndex, queryLength;
+
+  if ((window->hspcnt > 1) ||
+      (window->hspcnt < 1))
+    return(FALSE);
+  align = window->align;
+  queryIndex = align->queryIndex;
+  queryLength = query_info[queryIndex].seq.length;
+  if ((align->queryEnd - align->queryStart) !=
+      (align->matchEnd - align->matchStart))
+    return(FALSE);
+  if ((align->matchEnd - align->matchStart +1) <
+      (MIN(queryLength,  MINIMUM_LENGTH_NEAR_IDENTICAL)))
+    return(FALSE);
+  return(TRUE);
+}
 
 /* Documented in redo_alignment.h. */
 int
@@ -995,11 +1018,19 @@ Blast_RedoOneMatch(BlastCompo_Alignment ** alignments,
         BlastCompo_SequenceData * query;       /* query data for this window */
         /* the composition of this query */
         Blast_AminoAcidComposition * query_composition;  
+	Boolean nearIdenticalStatus; /*are query and subject nearly
+				       identical in the aligned part?*/
 
         window = windows[window_index];
+
+        nearIdenticalStatus = s_preliminaryTestNearIdentical(query_info,  
+						  window);
         status =
             callbacks->get_range(matchingSeq, &window->subject_range,
-                                 &subject);
+                                 &subject, 
+				 &query_info[window->align->queryIndex].seq,
+				 query_info[window->align->queryIndex].origin,
+				 window->align, nearIdenticalStatus);
         if (status != 0) {
             goto window_index_loop_cleanup;
         }
@@ -1141,22 +1172,31 @@ Blast_RedoOneMatchSmithWaterman(BlastCompo_Alignment ** alignments,
         BlastCompo_SequenceData subject = {0,}; 
         /* subject data for this window */
         BlastCompo_SequenceData * query;       /* query data for this window */
+        int query_offset; /*offset if there are multiple queries*/
         /* the composition of this query */
         Blast_AminoAcidComposition * query_composition;  
         double searchsp;                  /* effective search space */
-
+	Boolean nearIdenticalStatus; /*are query and subject nearly
+				       identical in the aligned part?*/
         /* adjust_search_failed is true only if Blast_AdjustScores
          * is called and returns a nonzero value */
         int adjust_search_failed = FALSE;
+
         
         window = windows[window_index];
         query_index = window->query_range.context;
         query = &query_info[query_index].seq;
+        query_offset = query_info[query_index].origin;
         query_composition = &query_info[query_index].composition;
         searchsp = query_info[query_index].eff_search_space;
 
-        status = callbacks->get_range(matchingSeq, &window->subject_range,
-                                      &subject);
+        nearIdenticalStatus = s_preliminaryTestNearIdentical(query_info,  
+						  window);
+
+        status =
+            callbacks->get_range(matchingSeq, &window->subject_range,
+                                 &subject, 
+				 query,  query_offset, window->align, nearIdenticalStatus);
         if (status != 0) 
             goto window_index_loop_cleanup;
             
diff --git a/algo/blast/composition_adjustment/redo_alignment.h b/algo/blast/composition_adjustment/redo_alignment.h
index 08e58f08..27467e63 100644
--- a/algo/blast/composition_adjustment/redo_alignment.h
+++ b/algo/blast/composition_adjustment/redo_alignment.h
@@ -1,4 +1,4 @@
-/* $Id: redo_alignment.h,v 1.11 2007/05/23 15:55:29 kazimird Exp $
+/* $Id: redo_alignment.h,v 1.12 2007/10/11 14:25:37 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -191,12 +191,22 @@ calc_lambda_type(double * probs, int min_score, int max_score,
  *
  * @param sequence        a sequence
  * @param range           the range to get
- * @param data            the data obtained
+ * @param data            the matching sequence data obtained
+ * @param queryData       the sequence data for the query
+ * @param queryOffset     offset for align if there are multiple queries
+ * @param align           information about the alignment between query and subject
+ * @param shouldTestIdentical did alignment pass a preliminary test in
+ *                       redo_alignment.c that indicates the sequence
+ *                        pieces may be near identical
  */
 typedef int
 get_range_type(const BlastCompo_MatchingSequence * sequence,
                const BlastCompo_SequenceRange * range,
-               BlastCompo_SequenceData * data);
+               BlastCompo_SequenceData * data,
+	       const BlastCompo_SequenceData * queryData,
+	       const int queryOffset,
+	       const BlastCompo_Alignment *align,
+	       const Boolean shouldTestIdentical);
 
 /**
  * Function type: Calculate the traceback for one alignment by
diff --git a/algo/blast/core/blast_aalookup.c b/algo/blast/core/blast_aalookup.c
index 056115a1..2a2bd22f 100644
--- a/algo/blast/core/blast_aalookup.c
+++ b/algo/blast/core/blast_aalookup.c
@@ -1,4 +1,4 @@
-/* $Id: blast_aalookup.c,v 1.7 2007/04/11 15:55:30 kazimird Exp $
+/* $Id: blast_aalookup.c,v 1.10 2007/11/27 16:25:55 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] =
-    "$Id: blast_aalookup.c,v 1.7 2007/04/11 15:55:30 kazimird Exp $";
+    "$Id: blast_aalookup.c,v 1.10 2007/11/27 16:25:55 kazimird Exp $";
 #endif                          /* SKIP_DOXYGEN_PROCESSING */
 
 /** Structure containing information needed for adding neighboring words. 
@@ -848,14 +848,41 @@ static void s_CompressedLookupAddEncoded(
                                      Uint1* w,
                                      Int4 query_offset)
 {
-    Int4 alphabet_size = lookup->compressed_alphabet_size;
-    Int4 word_length = lookup->word_length;
-    Int4 index = 0;
-    Int4 i;
-
-    for (i = word_length - 1; i >= 0; i--)
-        index = index * alphabet_size + w[i];
+    Int4 index;
+
+    static const Int4 W7p1[] = { 0, 10, 20, 30, 40, 50, 60, 70, 80, 90};
+    static const Int4 W7p2[] = { 0, 100, 200, 300, 400, 500, 600, 700, 800,
+                                 900};
+    static const Int4 W7p3[] = { 0, 1000, 2000, 3000, 4000, 5000, 6000,
+                                 7000, 8000, 9000};
+    static const Int4 W7p4[] = { 0, 10000, 20000, 30000, 40000, 50000, 60000,
+                                 70000, 80000, 90000};
+    static const Int4 W7p5[] = { 0, 100000, 200000, 300000, 400000, 500000,
+                                 600000, 700000, 800000, 900000};
+    static const Int4 W7p6[] = { 0, 1000000, 2000000, 3000000, 4000000,
+                                 5000000, 6000000, 7000000, 8000000, 9000000};
     
+    static const Int4 W6p1[] = { 0, 15, 30, 45, 60, 75, 90, 105, 120, 135,
+                                 150, 165, 180, 195, 210};
+    static const Int4 W6p2[] = { 0, 225, 450, 675, 900, 1125, 1350, 1575,
+                                 1800, 2025, 2250, 2475, 2700, 2925, 3150};
+    static const Int4 W6p3[] = { 0, 3375, 6750, 10125, 13500, 16875, 20250,
+                                 23625, 27000, 30375, 33750, 37125, 40500,
+                                 43875, 47250};
+    static const Int4 W6p4[] = { 0, 50625, 101250, 151875, 202500, 253125,
+                                 303750, 354375, 405000, 455625, 506250,
+                                 556875, 607500, 658125, 708750};
+    static const Int4 W6p5[] = { 0, 759375, 1518750, 2278125, 3037500,
+                                 3796875, 4556250, 5315625, 6075000, 6834375,
+                                 7593750, 8353125, 9112500, 9871875, 10631250};
+
+    if(lookup->word_length == 7)
+        index =  w[0] + W7p1[w[1]] + W7p2[w[2]] + W7p3[w[3]] +
+                        W7p4[w[4]] + W7p5[w[5]] + W7p6[w[6]];
+    else
+        index = w[0] + W6p1[w[1]] + W6p2[w[2]] + W6p3[w[3]] +
+                       W6p4[w[4]] + W6p5[w[5]];
+
     s_CompressedLookupAddWordHit(lookup, index, query_offset);
 }
 
@@ -889,11 +916,62 @@ typedef struct CompressedNeighborInfo {
     Int4 compressed_alphabet_size;  /**< for use with compressed alphabet */
     Int4 wordsize;       /**< number of residues in a word */
     Int4 **matrix;       /**< the substitution matrix */
-    Int4 *row_max;       /**< maximum possible score for each row of the matrix */
+    Int4 row_max[BLASTAA_SIZE]; /**< maximum possible score for each
+                                     row of the matrix */
     Int4 query_offset;   /**< a single query offset to index */
     Int4 threshold;      /**< the score threshold for neighboring words */
+    Int4 matrixSorted[BLASTAA_SIZE][BLASTAA_SIZE]; /**< version of substitution
+                                                       matrix whose rows are
+                                                       sorted by score */
+    Uint1 matrixSortedChar[BLASTAA_SIZE][BLASTAA_SIZE];/**< matrix with
+                                              the letters permuted identically
+                                              to that of matrixSorted */
 } CompressedNeighborInfo;
 
+/** Structure used as a helper for sorting matrix according to substitution
+ * score
+ */
+typedef struct LetterAndScoreDifferencePair{
+    Int4  diff;  /**< score difference from row maximum */
+    Uint1 letter; /**< given protein letter */
+} LetterAndScoreDifferencePair;
+
+/** callback for the "sort" */
+int ScoreDifferenceSort(const void * a, const void *b ){
+    return (((LetterAndScoreDifferencePair*)a)->diff - 
+            ((LetterAndScoreDifferencePair*)b)->diff);
+}
+
+/** Prepare "score sorted" version of the substitution matrix"
+ * @param info Pointer to the NeighborInfo structure.
+ */
+static void s_loadSortedMatrix(CompressedNeighborInfo* info) {
+
+    LetterAndScoreDifferencePair sortTable[BLASTAA_SIZE];
+    Int4 i;
+    Int4 longChar, shortChar;
+
+    for (longChar = 0; longChar < BLASTAA_SIZE; longChar++) {
+        for (shortChar = 0; shortChar < 
+                        info->compressed_alphabet_size; shortChar++) {
+      
+            sortTable[shortChar].diff = info->row_max[longChar] -
+                                        info->matrix[longChar][shortChar];
+            sortTable[shortChar].letter = shortChar;
+        }
+
+        qsort(sortTable, info->compressed_alphabet_size,
+              sizeof(LetterAndScoreDifferencePair), ScoreDifferenceSort);
+
+        for (i = 0; i < info->compressed_alphabet_size; i++) {
+            Uint1 letter = sortTable[i].letter;
+
+            info->matrixSorted[longChar][i] = info->matrix[longChar][letter];
+            info->matrixSortedChar[longChar][i] = letter;
+        }
+    }
+}
+
 /** Very similar to s_AddWordHitsCore
  * @param info Pointer to the NeighborInfo structure.
  * @param score The partial sum of the score.
@@ -907,8 +985,10 @@ static void s_CompressedAddWordHitsCore(CompressedNeighborInfo * info,
     Int4 wordsize = info->wordsize;
     Uint1 *query_word = info->query_word;
     Uint1 *subject_word = info->subject_word;
-    Int4 *row;
     Int4 i;
+    Int4 *rowSorted;
+    Uint1 *charSorted;
+    Int4 currQueryChar = query_word[current_pos]; 
     
     /* remove the maximum score of letters that align with the query letter
        at position 'current_pos'. Later code will align the entire alphabet
@@ -916,63 +996,57 @@ static void s_CompressedAddWordHitsCore(CompressedNeighborInfo * info,
        the row of the score matrix corresponding to the query letter at
        current_pos */
 
-    score -= info->row_max[query_word[current_pos]];
-    row = info->matrix[query_word[current_pos]];
-    
+    score -= info->row_max[currQueryChar];
+    rowSorted = info->matrixSorted[currQueryChar];
+    charSorted = info->matrixSortedChar[currQueryChar];
+
     if (current_pos == wordsize - 1) {
         
         /* The recursion has bottomed out, and we can produce complete
-           subject words. Pass the entire alphabet through the last position
-           in the subject word, then save the query offset in all lookup
-           table positions corresponding to subject words that yield a high
-           enough score */
+           subject words. Pass (a portion of) the alphabet through the 
+           last position in the subject word, then saving the query offset 
+           in the lookup table position corresponding to subject word i */
 
         BlastCompressedAaLookupTable *lookup = info->lookup;
         Int4 query_offset = info->query_offset;
         
-        for (i = 0; i < compressed_alphabet_size; i++) {
-            if (score + row[i] >= threshold) {
-                subject_word[current_pos] = i;
-                s_CompressedLookupAddEncoded(lookup, subject_word, 
-                                             query_offset);
+        for (i = 0; i < compressed_alphabet_size && 
+               (score + rowSorted[i] >= threshold); i++) {
+            subject_word[current_pos] = charSorted[i];
+            s_CompressedLookupAddEncoded(lookup, subject_word, 
+                                         query_offset);
 #ifdef LOOKUP_VERBOSE
-                lookup->neighbor_matches++;
+            lookup->neighbor_matches++;
 #endif
-            }
         }
         return;
     }
 
-    /* Otherwise, pass the entire alphabet through position current_pos of
-       the subject word, and recurse on all words that could possibly exceed
-       the threshold later */
+    /* Otherwise, pass (a portion of) the alphabet through position 
+       current_pos of the subject word, and recurse on all words that 
+       could possibly exceed the threshold later */
 
-    for (i = 0; i < compressed_alphabet_size; i++) {
-        if (score + row[i] >= threshold) {
-            subject_word[current_pos] = i;
-            s_CompressedAddWordHitsCore(info, score + row[i], 
-                                        current_pos + 1);
-        }
+    for (i = 0; i < compressed_alphabet_size && 
+           (score + rowSorted[i] >= threshold); i++) {
+        subject_word[current_pos] = charSorted[i];
+        s_CompressedAddWordHitsCore(info, score + rowSorted[i], 
+                                    current_pos + 1);
     }
 }
 
 /** Add neighboring words to the lookup table (compressed alphabet).
- * @param lookup Pointer to the lookup table.
- * @param compressed_matrix Pointer to the substitution matrix.
+ * @param info Pointer to the NeighborInfo structure.
  * @param query Pointer to the query sequence.
  * @param query_offset offset where the word occurs in the query
- * @param row_max maximum possible score for each row of the matrix
  */
-static void s_CompressedAddWordHits(BlastCompressedAaLookupTable * lookup,
-                                Int4 ** compressed_matrix,
-                                Uint1 * query, Int4 query_offset,
-                                Int4 * row_max)
+static void s_CompressedAddWordHits(CompressedNeighborInfo * info,
+                                    Uint1 * query, Int4 query_offset)
 {
     Uint1 *w = query + query_offset;
     Uint1 s[32];   /* larger than any possible wordsize */
     Int4 score;
     Int4 i;
-    CompressedNeighborInfo info;
+    BlastCompressedAaLookupTable * lookup = info->lookup;
 
 #ifdef LOOKUP_VERBOSE
     lookup->exact_matches++;
@@ -987,7 +1061,7 @@ static void s_CompressedAddWordHits(BlastCompressedAaLookupTable * lookup,
         if (c >= lookup->compressed_alphabet_size) /* "non-20 aa": skip it*/
             return;
 
-        score += compressed_matrix[w[i]][c];
+        score += info->matrix[w[i]][c];
     }
 
     /* If the self-score is above the threshold, then the neighboring
@@ -1012,25 +1086,19 @@ static void s_CompressedAddWordHits(BlastCompressedAaLookupTable * lookup,
 
     /* Set up the structure of information to be used during the recursion */
 
-    info.lookup = lookup;
-    info.query_word = w;
-    info.subject_word = s;
-    info.compressed_alphabet_size = lookup->compressed_alphabet_size;
-    info.wordsize = lookup->word_length;
-    info.matrix = compressed_matrix;
-    info.row_max = row_max;
-    info.query_offset = query_offset;
-    info.threshold = lookup->threshold;
+    info->query_word = w;
+    info->subject_word = s;
+    info->query_offset = query_offset;
 
     /* compute the largest possible score that any neighboring word can have; 
        this maximum will gradually be replaced by exact scores as subject
        words are built up */
 
-    score = row_max[w[0]];
+    score = info->row_max[w[0]];
     for (i = 1; i < lookup->word_length; i++)
-        score += row_max[w[i]];
+        score += info->row_max[w[i]];
 
-    s_CompressedAddWordHitsCore(&info, score, 0);
+    s_CompressedAddWordHitsCore(info, score, 0);
 }
 
 /**
@@ -1050,7 +1118,7 @@ static void s_CompressedAddNeighboringWords(
                                   BlastSeqLoc * location)
 {
     Int4 i, j;
-    Int4 row_max[BLASTAA_SIZE];
+    CompressedNeighborInfo info;
     BlastSeqLoc *loc;
     Int4 offset;
 
@@ -1060,11 +1128,21 @@ static void s_CompressedAddNeighboringWords(
        row of the score matrix */
 
     for (i = 0; i < lookup->alphabet_size; i++) {
-        row_max[i] = compressed_matrix[i][0];
+        info.row_max[i] = compressed_matrix[i][0];
         for (j = 1; j < lookup->compressed_alphabet_size; j++)
-            row_max[i] = MAX(row_max[i], compressed_matrix[i][j]);
+            info.row_max[i] = MAX(info.row_max[i], compressed_matrix[i][j]);
     }
 
+    /* Set up the structure of information to be used during the recursion */
+    info.lookup = lookup;
+    info.compressed_alphabet_size = lookup->compressed_alphabet_size;
+    info.wordsize = lookup->word_length;
+    info.matrix = compressed_matrix;
+    info.threshold = lookup->threshold;
+
+    s_loadSortedMatrix(&info); 
+
+
     /* Walk through the query and index all the words */
 
     for (loc = location; loc; loc = loc->next){
@@ -1072,8 +1150,7 @@ static void s_CompressedAddNeighboringWords(
         Int4 to = loc->ssr->right - lookup->word_length + 1;
 
         for (offset = from; offset <= to; offset++){
-            s_CompressedAddWordHits(lookup, compressed_matrix, 
-                                    query->sequence, offset, row_max);
+            s_CompressedAddWordHits(&info, query->sequence, offset);
         }
     }
 }
diff --git a/algo/blast/core/blast_aascan.c b/algo/blast/core/blast_aascan.c
index 1f0132f2..4a1aef26 100644
--- a/algo/blast/core/blast_aascan.c
+++ b/algo/blast/core/blast_aascan.c
@@ -1,4 +1,4 @@
-/* $Id: blast_aascan.c,v 1.7 2007/04/11 15:55:30 kazimird Exp $
+/* $Id: blast_aascan.c,v 1.9 2007/11/08 22:55:41 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] =
-    "$Id: blast_aascan.c,v 1.7 2007/04/11 15:55:30 kazimird Exp $";
+    "$Id: blast_aascan.c,v 1.9 2007/11/08 22:55:41 kazimird Exp $";
 #endif                          /* SKIP_DOXYGEN_PROCESSING */
 
 /**
@@ -152,7 +152,8 @@ static Int4 s_BlastCompressedAaScanSubject(
                               BlastOffsetPair * NCBI_RESTRICT offset_pairs,
                               Int4 array_size)
 {
-    Int4 index;
+    Int4 index=0;
+    Int4 preshift; /* used for 2-stage index calculation */
     Uint1 *s;
     Uint1 *s_first;
     Uint1 *s_last;
@@ -182,42 +183,60 @@ static Int4 s_BlastCompressedAaScanSubject(
     pv_array_bts = lookup->pv_array_bts;
 
     /* prime the index */
-    index = s_ComputeCompressedIndex(word_length - 1, s_first,
-                                     compressed_alphabet_size,
-                                     &skip, lookup);
+    for(s = s_first; s <= s_last; s++){
+        index = s_ComputeCompressedIndex(word_length - 1, s,
+                                         compressed_alphabet_size,
+                                         &skip, lookup);
+        if(!skip)
+          break;
+    }
 
-    next_char = ((subject->length > word_length)? s_first[word_length-1] : 0);
+    next_char = ((s <= s_last)? s[word_length-1] : 0);
+    preshift = (Int4)((((Int8)index) * recip) >> 32); 
 
-    for (s = s_first; s <= s_last; s++) {
+    /* main scanning loop */
+    for (; s <= s_last; s++) {
        /* compute the index value */
 
        compressed_char = scaled_compress_table[next_char];
        next_char = s[word_length];
-
-       if (compressed_char < 0) {
-          /* skip all words containing this (ignored) letter */
-          skip = word_length; 
-          continue;
-       } 
-       else {
-          /* we have to remove the oldest letter from the
-             index and add in the next letter. The latter is easy,
-             but since the compressed alphabet size is not a
-             power of two the former requires a remainder and
-             multiply, assuming the old letter is in the high part
-             of the index. For this reason, we reverse the order
-             of the letters and keep the oldest in the low part
-             of index, so that a single divide (implemented via
-             reciprocal multiplication) does the removal */
-
-          index = (Int4)((((Int8)index) * recip) >> 32) + compressed_char;
-
-          if (skip) {
-             if (--skip) /* still skipping? */
-                continue;
-          }
-       }
       
+       if(compressed_char < 0){ /* flush (rare) "bad" character(s) */
+         preshift = 0;
+         s++;
+         for(skip = word_length-1; skip && (s <= s_last) ; s++){
+           compressed_char = scaled_compress_table[next_char];
+           next_char = s[word_length];
+           
+           if(compressed_char < 0){ /* not again! */
+             skip = word_length-1;
+             preshift = 0;
+             continue;
+           }
+           
+           index = preshift + compressed_char;
+           preshift = (Int4)((((Int8)( index )) * recip) >> 32);
+           skip--;
+         }
+         
+         s--; /*undo the following increment*/
+         continue;
+       }
+
+       /* we have to remove the oldest letter from the
+          index and add in the next letter. The latter is easy,
+          but since the compressed alphabet size is not a
+          power of two the former requires a remainder and
+          multiply, assuming the old letter is in the high part
+          of the index. For this reason, we reverse the order
+          of the letters and keep the oldest in the low part
+          of index, so that a single divide (implemented via
+          reciprocal multiplication) does the removal.
+          Index calculation done in two steps to let the CPU do 
+          out-of-order execution. */
+       
+       index = preshift + compressed_char;
+       preshift = (Int4)((((Int8)( index )) * recip) >> 32);
 
        /* if there are hits */
        if (PV_TEST(pv, index, pv_array_bts)) {
diff --git a/algo/blast/core/blast_def.h b/algo/blast/core/blast_def.h
index b7d6bc6e..14475d56 100644
--- a/algo/blast/core/blast_def.h
+++ b/algo/blast/core/blast_def.h
@@ -1,4 +1,4 @@
-/* $Id: blast_def.h,v 1.79 2007/03/20 14:55:37 kazimird Exp $
+/* $Id: blast_def.h,v 1.83 2008/01/31 23:55:41 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -42,18 +42,18 @@ extern "C" {
 
 /****************************** Constants *********************************/
 
-extern const int kDustLevel;  /**< Level parameter used by dust. */
-extern const int kDustWindow; /**< Window parameter used by dust. */
-extern const int kDustLinker; /**< Parameter used by dust to link together close low-complexity segments. */
+NCBI_XBLAST_EXPORT extern const int kDustLevel;  /**< Level parameter used by dust. */
+NCBI_XBLAST_EXPORT extern const int kDustWindow; /**< Window parameter used by dust. */
+NCBI_XBLAST_EXPORT extern const int kDustLinker; /**< Parameter used by dust to link together close low-complexity segments. */
 
-extern const int kSegWindow;  /**< Window that SEG examines at once. */
-extern const double kSegLocut;   /**< Locut parameter for SEG. */
-extern const double kSegHicut;   /**< Hicut parameter for SEG. */
+NCBI_XBLAST_EXPORT extern const int kSegWindow;  /**< Window that SEG examines at once. */
+NCBI_XBLAST_EXPORT extern const double kSegLocut;   /**< Locut parameter for SEG. */
+NCBI_XBLAST_EXPORT extern const double kSegHicut;   /**< Hicut parameter for SEG. */
 
 /** Maximum number of HPSs to be saved in an ungapped search.
  * Value defined in blast_options.c
  */
-extern const int kUngappedHSPNumMax; 
+NCBI_XBLAST_EXPORT extern const int kUngappedHSPNumMax; 
 
 /******************** Preprocessor definitions ******************************/
 
diff --git a/algo/blast/core/blast_dynarray.c b/algo/blast/core/blast_dynarray.c
index 3f667dcd..67d267bf 100644
--- a/algo/blast/core/blast_dynarray.c
+++ b/algo/blast/core/blast_dynarray.c
@@ -1,4 +1,4 @@
-/* $Id: blast_dynarray.c,v 1.6 2007/03/20 14:55:37 kazimird Exp $
+/* $Id: blast_dynarray.c,v 1.7 2007/11/08 22:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -34,13 +34,16 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_dynarray.c,v 1.6 2007/03/20 14:55:37 kazimird Exp $";
+    "$Id: blast_dynarray.c,v 1.7 2007/11/08 22:55:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include "blast_dynarray.h"
 #include <algo/blast/core/blast_util.h>
 #include <algo/blast/core/blast_message.h>  /* for error codes */
 
+/** factor by which these arrays are resized */
+const size_t kResizeFactor = 2;
+
 SDynamicUint4Array* DynamicUint4ArrayFree(SDynamicUint4Array* arr)
 {
     if ( !arr ) {
@@ -85,12 +88,14 @@ s_DynamicUint4Array_ReallocIfNecessary(SDynamicUint4Array* arr)
 
     if (arr->num_used+1 > arr->num_allocated) {
         /* we need more room for elements */
-        arr->num_allocated *= 2;
-        arr->data = (Uint4*) realloc(arr->data, 
-                                     arr->num_allocated * sizeof(Uint4));
-        if ( !arr->data ) {
+        Uint4* reallocation = 
+            (Uint4*) realloc(arr->data, 
+                     kResizeFactor * arr->num_allocated * sizeof(*arr->data));
+        if ( !reallocation ) {
             return BLASTERR_MEMORY;
         }
+        arr->data = reallocation;
+        arr->num_allocated *= kResizeFactor;
     }
     return 0;
 }
@@ -104,7 +109,8 @@ DynamicUint4Array_Append(SDynamicUint4Array* arr, Uint4 element)
     if ( (retval = s_DynamicUint4Array_ReallocIfNecessary(arr)) != 0) {
         return retval;
     }
-    arr->data[arr->num_used++] = element;
+    arr->data[arr->num_used] = element;
+    arr->num_used++;
     return retval;
 }
 
@@ -130,12 +136,14 @@ DynamicUint4Array_Copy(SDynamicUint4Array* dest,
     Uint4 i = 0;        /* index into arrays */
 
     if (dest->num_allocated < src->num_allocated) {
-        dest->num_allocated = src->num_allocated;
-        dest->data = (Uint4*) realloc(dest->data, 
-                                      dest->num_allocated * sizeof(Uint4));
-        if ( !dest->data ) {
-            return -1;
+        /* we need more room for elements */
+        Uint4* reallocation = (Uint4*) realloc(dest->data,
+                                     src->num_allocated * sizeof(*dest->data));
+        if ( !reallocation ) {
+            return BLASTERR_MEMORY;
         }
+        dest->data = reallocation;
+        dest->num_allocated = src->num_allocated;
     }
 
     for (i = 0; i < src->num_used; i++) {
@@ -203,12 +211,13 @@ s_DynamicInt4Array_ReallocIfNecessary(SDynamicInt4Array* arr)
 
     if (arr->num_used+1 > arr->num_allocated) {
         /* we need more room for elements */
-        arr->num_allocated *= 2;
-        arr->data = (Int4*) realloc(arr->data, 
-                                     arr->num_allocated * sizeof(Int4));
-        if ( !arr->data ) {
+        Int4* reallocation = (Int4*) realloc(arr->data,
+                     kResizeFactor * arr->num_allocated * sizeof(*arr->data));
+        if ( !reallocation ) {
             return BLASTERR_MEMORY;
         }
+        arr->data = reallocation;
+        arr->num_allocated *= kResizeFactor;
     }
     return 0;
 }
@@ -222,7 +231,8 @@ DynamicInt4Array_Append(SDynamicInt4Array* arr, Int4 element)
     if ( (retval = s_DynamicInt4Array_ReallocIfNecessary(arr)) != 0) {
         return retval;
     }
-    arr->data[arr->num_used++] = element;
+    arr->data[arr->num_used] = element;
+    arr->num_used++;
     return retval;
 }
 
@@ -272,12 +282,13 @@ s_DynamicSGenCodeNodeArray_ReallocIfNecessary(SDynamicSGenCodeNodeArray* arr)
 
     if (arr->num_used+1 > arr->num_allocated) {
         /* we need more room for elements */
-        arr->num_allocated *= 2;
-        arr->data = (SGenCodeNode*) realloc(arr->data, 
-                                     arr->num_allocated * sizeof(SGenCodeNode));
-        if ( !arr->data ) {
+        SGenCodeNode* reallocation = (SGenCodeNode*) realloc(arr->data,
+                     kResizeFactor * arr->num_allocated * sizeof(*arr->data));
+        if ( !reallocation ) {
             return BLASTERR_MEMORY;
         }
+        arr->data = reallocation;
+        arr->num_allocated *= kResizeFactor;
     }
     return 0;
 }
diff --git a/algo/blast/core/blast_encoding.c b/algo/blast/core/blast_encoding.c
index 23e5db9e..90d88df5 100644
--- a/algo/blast/core/blast_encoding.c
+++ b/algo/blast/core/blast_encoding.c
@@ -1,4 +1,4 @@
-/* $Id: blast_encoding.c,v 1.6 2006/08/29 21:56:34 camacho Exp $
+/* $Id: blast_encoding.c,v 1.7 2008/01/24 21:25:45 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] =
-    "$Id: blast_encoding.c,v 1.6 2006/08/29 21:56:34 camacho Exp $";
+    "$Id: blast_encoding.c,v 1.7 2008/01/24 21:25:45 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/blast_encoding.h>
@@ -77,6 +77,16 @@ const Uint1 BLASTNA_TO_NCBI4NA[BLASTNA_SIZE] = {
      0      /* Gap, 15 */
 };
 
+const char BLASTNA_TO_IUPACNA[BLASTNA_SIZE] = {
+    'A', 'C', 'G', 'T', 'R', 'Y', 'M', 'K', 
+    'W', 'S', 'B', 'D', 'H', 'V', 'N', '-'
+};
+
+const char NCBI4NA_TO_IUPACNA[BLASTNA_SIZE] = {
+    '-', 'A', 'C', 'M', 'G', 'R', 'S', 'V',
+    'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'
+};
+
 const Uint1 IUPACNA_TO_BLASTNA[128]={
 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
 15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
@@ -114,30 +124,3 @@ const char NCBISTDAA_TO_AMINOACID[BLASTAA_SIZE] = {
 
 const Uint1 kProtSentinel = NULLB;
 const Uint1 kNuclSentinel = 0xF;
-
-/*
- * ===========================================================================
- * $Log: blast_encoding.c,v $
- * Revision 1.6  2006/08/29 21:56:34  camacho
- * +NCBISTDAA_TO_AMINOACID
- *
- * Revision 1.5  2006/03/31 17:32:40  camacho
- * Added constants for sentinel values
- *
- * Revision 1.4  2006/02/16 18:47:18  camacho
- * + encoding translations for O and J
- *
- * Revision 1.3  2004/11/02 17:56:48  camacho
- * Add DOXYGEN_SKIP_PROCESSING to guard rcsid string
- *
- * Revision 1.2  2004/05/19 14:52:02  camacho
- * 1. Added doxygen tags to enable doxygen processing of algo/blast/core
- * 2. Standardized copyright, CVS $Id string, $Log and rcsid formatting and i
- *    location
- * 3. Added use of @todo doxygen keyword
- *
- * Revision 1.1  2004/04/07 03:10:56  camacho
- * Initial revision
- *
- * ===========================================================================
- */
diff --git a/algo/blast/core/blast_encoding.h b/algo/blast/core/blast_encoding.h
index f34c3d41..071e3376 100644
--- a/algo/blast/core/blast_encoding.h
+++ b/algo/blast/core/blast_encoding.h
@@ -1,4 +1,4 @@
-/*  $Id: blast_encoding.h,v 1.12 2006/11/21 16:37:56 papadopo Exp $
+/*  $Id: blast_encoding.h,v 1.18 2008/01/24 21:25:45 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -36,6 +36,7 @@
 #define ALGO_BLAST_CORE___BLAST_ENCODING__H
 
 #include <algo/blast/core/ncbi_std.h>
+#include <algo/blast/core/blast_export.h>
 
 /** @addtogroup AlgoBlast
  *
@@ -64,22 +65,28 @@ typedef enum {
 
 /** Translates between ncbi4na and blastna. The first four elements
  *	of this array match ncbi2na. */
-extern const Uint1 NCBI4NA_TO_BLASTNA[];
+NCBI_XBLAST_EXPORT extern const Uint1 NCBI4NA_TO_BLASTNA[];
 
 /** Translates between blastna and ncbi4na. */
-extern const Uint1 BLASTNA_TO_NCBI4NA[];
+NCBI_XBLAST_EXPORT extern const Uint1 BLASTNA_TO_NCBI4NA[];
 
 /** Translates between iupacna and blastna. */
-extern const Uint1 IUPACNA_TO_BLASTNA[];
+NCBI_XBLAST_EXPORT extern const Uint1 IUPACNA_TO_BLASTNA[];
 
 /** Translates between iupacna and ncbi4na. */
-extern const Uint1 IUPACNA_TO_NCBI4NA[];
+NCBI_XBLAST_EXPORT extern const Uint1 IUPACNA_TO_NCBI4NA[];
 
 /** Translates between ncbieaa and ncbistdaa. */
-extern const Uint1 AMINOACID_TO_NCBISTDAA[];
+NCBI_XBLAST_EXPORT extern const Uint1 AMINOACID_TO_NCBISTDAA[];
 
 /** Translates between ncbieaa and ncbistdaa. */
-extern const char NCBISTDAA_TO_AMINOACID[];
+NCBI_XBLAST_EXPORT extern const char NCBISTDAA_TO_AMINOACID[];
+
+/** Translates between blastna and iupacna. */
+NCBI_XBLAST_EXPORT extern const char BLASTNA_TO_IUPACNA[];
+
+/** Translates between ncbi4na and iupacna. */
+NCBI_XBLAST_EXPORT extern const char NCBI4NA_TO_IUPACNA[];
 
 #define BLAST2NA_SIZE 4     /**< Size of compressed nucleic acid alphabet */
 #define BLASTNA_SIZE 16     /**< Size of nucleic acid alphabet */
@@ -92,9 +99,9 @@ extern const char NCBISTDAA_TO_AMINOACID[];
 #define NCBI4NA_SEQ_CODE 4  /**< == Seq_code_ncbi4na */	
 
 /** Sentinel byte for protein sequences */
-extern const Uint1 kProtSentinel;
+NCBI_XBLAST_EXPORT extern const Uint1 kProtSentinel;
 /** Sentinel nibble for nucleotide sequences */
-extern const Uint1 kNuclSentinel;
+NCBI_XBLAST_EXPORT extern const Uint1 kNuclSentinel;
 
 #ifdef __cplusplus
 }
@@ -102,47 +109,4 @@ extern const Uint1 kNuclSentinel;
 
 /* @} */
 
-
-/*
- * ===========================================================================
- * $Log: blast_encoding.h,v $
- * Revision 1.12  2006/11/21 16:37:56  papadopo
- * minor
- *
- * Revision 1.11  2006/08/29 21:56:30  camacho
- * +NCBISTDAA_TO_AMINOACID
- *
- * Revision 1.10  2006/07/05 15:42:22  papadopo
- * change the amino acid alphabet size from 26 to 28
- *
- * Revision 1.9  2006/04/28 20:43:41  camacho
- * Remove C++-style comments
- *
- * Revision 1.8  2006/03/31 17:31:49  camacho
- * Added constants for sentinel values
- *
- * Revision 1.7  2005/12/19 16:19:18  papadopo
- * add define for size of ncbi2na alphabet
- *
- * Revision 1.6  2005/05/10 16:07:35  camacho
- * Changed *_ENCODING #defines to EBlastEncoding enumeration
- *
- * Revision 1.5  2004/11/24 16:00:39  dondosha
- * Added and/or fixed doxygen comments
- *
- * Revision 1.4  2004/06/21 12:53:54  camacho
- * Remove PSI_ALPHABET_SIZE as it is identical to BLASTAA_SIZE
- *
- * Revision 1.3  2004/04/09 14:48:05  camacho
- * Added doxygen comments
- *
- * Revision 1.2  2004/04/07 19:05:44  camacho
- * Minor fix in #ifdef guards
- *
- * Revision 1.1  2004/04/07 03:10:20  camacho
- * Initial revision
- *
- * ===========================================================================
- */
-
 #endif  /* ALGO_BLAST_CORE___BLAST_ENCODING__H */
diff --git a/algo/blast/core/blast_engine.c b/algo/blast/core/blast_engine.c
index df8d362c..eadf2997 100644
--- a/algo/blast/core/blast_engine.c
+++ b/algo/blast/core/blast_engine.c
@@ -1,4 +1,4 @@
-/* $Id: blast_engine.c,v 1.249 2007/08/23 20:25:30 kazimird Exp $
+/* $Id: blast_engine.c,v 1.251 2008/01/31 23:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -55,7 +55,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_engine.c,v 1.249 2007/08/23 20:25:30 kazimird Exp $";
+    "$Id: blast_engine.c,v 1.251 2008/01/31 23:55:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/blast_engine.h>
@@ -81,8 +81,8 @@ static char const rcsid[] =
 
 NCBI_XBLAST_EXPORT const int   kBlastMajorVersion = 2;
 NCBI_XBLAST_EXPORT const int   kBlastMinorVersion = 2;
-NCBI_XBLAST_EXPORT const int   kBlastPatchVersion = 17;
-NCBI_XBLAST_EXPORT const char* kBlastReleaseDate = "Aug-26-2007";
+NCBI_XBLAST_EXPORT const int   kBlastPatchVersion = 18;
+NCBI_XBLAST_EXPORT const char* kBlastReleaseDate = "Feb-03-2008";
 
 /** Structure to be passed to s_BlastSearchEngineCore, containing pointers 
     to various preallocated structures and arrays. */
@@ -860,7 +860,6 @@ BLAST_PreliminarySearchEngine(EBlastProgramType program_number,
    Boolean gapped_calculation = score_options->gapped_calculation;
    BlastScoreBlk* sbp = gap_align->sbp;
    BlastSeqSrcIterator* itr;
-   Int4 default_db_genetic_code = db_options->genetic_code;
    const Boolean kNucleotide = (program_number == eBlastTypeBlastn ||
                                 program_number == eBlastTypePhiBlastn);
 
@@ -939,7 +938,7 @@ BLAST_PreliminarySearchEngine(EBlastProgramType program_number,
       if (Blast_SubjectIsTranslated(program_number) && 
           seq_arg.seq->gen_code_string == NULL) {
           seq_arg.seq->gen_code_string = 
-              GenCodeSingletonFind(default_db_genetic_code);
+              GenCodeSingletonFind(db_options->genetic_code);
           ASSERT(seq_arg.seq->gen_code_string);
       }
       status = 
diff --git a/algo/blast/core/blast_filter.c b/algo/blast/core/blast_filter.c
index eb9f0762..7bc1c141 100644
--- a/algo/blast/core/blast_filter.c
+++ b/algo/blast/core/blast_filter.c
@@ -1,4 +1,4 @@
-/* $Id: blast_filter.c,v 1.89 2007/07/05 14:25:35 kazimird Exp $
+/* $Id: blast_filter.c,v 1.92 2008/01/31 23:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -30,7 +30,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_filter.c,v 1.89 2007/07/05 14:25:35 kazimird Exp $";
+    "$Id: blast_filter.c,v 1.92 2008/01/31 23:55:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/blast_util.h>
@@ -313,7 +313,7 @@ BlastFilteringOptionsFromString(EBlastProgramType program_number, const char* in
 			ptr = s_LoadOptionsToBuffer(ptr+1, buffer);
 			if (buffer[0] != NULLB)
                         {
-                                int window, level, linker;
+                                int window = 0, level = 0, linker = 0;
 				status = s_ParseDustOptions(buffer, &level, &window, &linker);
                                 if (status)
                                 {
@@ -440,35 +440,71 @@ static BlastSeqLoc* s_BlastSeqLocNodeDup(BlastSeqLoc* source)
     return BlastSeqLocNew(NULL, source->ssr->left, source->ssr->right);
 }
 
-/** Prepend node to the head of the list and return the new head of the list */
-static BlastSeqLoc* s_BlastSeqLocPrepend(BlastSeqLoc* head, BlastSeqLoc* node)
+/** Calculates number of links in a chain of BlastSeqLoc's.
+ * @param var Chain of BlastSeqLoc structures [in]
+ * @return Number of links in the chain.
+ */
+static Int4 s_BlastSeqLocLen(const BlastSeqLoc* var)
 {
-    if ( !node ) {
-        return NULL;
+    BlastSeqLoc* itr = NULL;
+    Int4 retval = 0;
+   
+    for (itr = (BlastSeqLoc*)var; itr; itr = itr->next, retval++) {
+        ;
     }
-    node->next = head;
-    return node;
+    return retval;
+}
+
+/** Converts a BlastSeqLoc list to an array of pointers, each pointing to an
+ * element of the list passed in to this function and the last element points
+ * to NULL 
+ * @param list List to convert to an array of pointers [in]
+ * @count number of elements populated in the array [out]
+ */
+static BlastSeqLoc**
+s_BlastSeqLocListToArrayOfPointers(const BlastSeqLoc* list, Int4* count)
+{
+    BlastSeqLoc* tmp,** retval;
+    Int4 i;
+    *count = 0;
+
+    if (list == NULL) 
+       return NULL;
+
+    *count = s_BlastSeqLocLen(list);
+    retval = (BlastSeqLoc**) calloc(((size_t)(*count)+1), sizeof(BlastSeqLoc*));
+    for (tmp = (BlastSeqLoc*)list, i = 0; tmp != NULL && i < *count; i++) {
+        retval[i] = tmp;
+        tmp = tmp->next;
+    }
+    return retval;
 }
 
 /** Reverse elements in the list 
- * @param head pointer to pointer to the head of the list. After this call,
- * this is set to NULL [in|out]
- * @return the new head of the list or NULL if argument is NULL
+ * @param head pointer to pointer to the head of the list. [in|out]
+ * (this is not declared static so that it can be tested in the unit tests
  */
-static BlastSeqLoc* s_BlastSeqLocListReverse(BlastSeqLoc** head)
+NCBI_XBLAST_EXPORT
+void BlastSeqLocListReverse(BlastSeqLoc** head)
 {
-    BlastSeqLoc* retval = NULL;     /* return value */
-    BlastSeqLoc* itr = NULL;        /* iterator */
+    BlastSeqLoc** ptrs = NULL;  /* array of pointers to BlastSeqLoc elements */
+    Int4 num_elems = 0, i = 0;
 
     if ( !head ) {
-        return NULL;
+        return;
     }
 
-    for (itr = *head; itr; itr = itr->next) {
-        retval = s_BlastSeqLocPrepend(retval, s_BlastSeqLocNodeDup(itr));
+    ptrs = s_BlastSeqLocListToArrayOfPointers(*head, &num_elems);
+    if (num_elems == 0) {
+        return;
     }
-    *head = BlastSeqLocFree(*head);
-    return retval;
+    ASSERT(ptrs);
+    *head = ptrs[num_elems-1];
+    for (i = num_elems-1; i > 0; i--) {
+        ptrs[i]->next = ptrs[i-1];
+    }
+    ptrs[0]->next = NULL;
+    sfree(ptrs);
 }
 
 BlastSeqLoc* BlastSeqLocNodeFree(BlastSeqLoc* loc)
@@ -715,98 +751,49 @@ static int s_SeqRangeSortByStartPosition(const void *vp1, const void *vp2)
       return 0;
 }
 
-/** Calculates number of links in a chain of BlastSeqLoc's.
- * @param var Chain of BlastSeqLoc structures [in]
- * @return Number of links in the chain.
- */
-static Int4 s_BlastSeqLocLen(BlastSeqLoc* var)
-{
-     Int4 count=0;
-   
-     while (var)
-     {
-         count++;
-         var = var->next;
-     }
-
-     return count;
-}
-
-/** Sort a list of BlastSeqLoc structures
- * @param list List of BlastSeqLoc's [in]
- * @param compar Comparison function to use [in]
- * @return Sorted list.  
- */
-static BlastSeqLoc* 
-s_BlastSeqLocSort (BlastSeqLoc* list,
-                 int (*compar )(const void *, const void *))
+void
+BlastSeqLocCombine(BlastSeqLoc** mask_loc, Int4 link_value)
 {
-        BlastSeqLoc* tmp,** head;
-        Int4 count, i;
+    BlastSeqLoc** ptrs = NULL;
+    Int4 i = 0, num_elems = 0;
 
-        if (list == NULL) 
-           return NULL;
+    /* Break up the list into an array of pointers and sort it */
+    ptrs = s_BlastSeqLocListToArrayOfPointers(*mask_loc, &num_elems);
+    if (num_elems == 0) {
+        return;
+    }
+    ASSERT(ptrs);
+    qsort(ptrs, (size_t)num_elems, sizeof(*ptrs), 
+          s_SeqRangeSortByStartPosition);
 
-        count = s_BlastSeqLocLen (list);
-        head = (BlastSeqLoc* *) calloc (((size_t) count + 1), sizeof (BlastSeqLoc*));
-        for (tmp = list, i = 0; tmp != NULL && i < count; i++) {
-                head [i] = tmp;
-                tmp = tmp->next;
+    /* Merge the overlapping elements */
+    {
+        BlastSeqLoc* curr_tail = *mask_loc = ptrs[0];
+        for (i = 0; i < num_elems - 1; i++) {
+            const SSeqRange* next_ssr = ptrs[i+1]->ssr;
+            const Int4 stop = curr_tail->ssr->right;
+
+            if ((stop + link_value) > next_ssr->left) {
+                curr_tail->ssr->right = MAX(stop, next_ssr->right);
+                ptrs[i+1] = BlastSeqLocNodeFree(ptrs[i+1]);
+            } else {
+                curr_tail = ptrs[i+1];
+            }
         }
+    }
 
-        qsort (head, (size_t) count, sizeof (BlastSeqLoc*), compar);
-        for (i = 0; i < count; i++) {
-                tmp = head [i];
-                tmp->next = head [i + 1];
+    /* Rebuild the linked list */
+    {
+        BlastSeqLoc* tail = *mask_loc;
+        for (i = 1; i < num_elems; i++) {
+            if (ptrs[i]) {
+                tail->next = ptrs[i];
+                tail = ptrs[i];
+            }
         }
-        list = head [0];
-        sfree (head);
-
-        return list;
-}
-
-BlastSeqLoc*
-BlastSeqLocCombine(BlastSeqLoc* mask_loc, Int4 link_value)
-{
-   BlastSeqLoc* retval = NULL;
-   BlastSeqLoc* retval_tail = NULL;
-   Int4 start, stop;	/* Used to merge overlapping SeqLoc's. */
-   BlastSeqLoc* loc_head=NULL,* loc_var=NULL;
-   
-   if ( !mask_loc ) {
-      return NULL;
-   }
-
-   /* Copy the BlastSeqLoc-s and sort them by starting position. */
-   loc_head = loc_var = s_BlastSeqLocSort(BlastSeqLocListDup(mask_loc),
-                                          s_SeqRangeSortByStartPosition);
-   if ( !loc_head ) {
-       return NULL;
-   }
-   start = loc_head->ssr->left;
-   stop = loc_head->ssr->right;
-
-   for (; loc_var; loc_var = loc_var->next) {
-       SSeqRange* ssr = loc_var->next ? loc_var->next->ssr : NULL;
-
-       if (ssr && ((stop + link_value) > ssr->left)) {
-          stop = MAX(stop, ssr->right);
-       } else {
-          /* Cache the tail of the list to avoid the overhead of traversing the
-           * list when appending to it */
-          retval_tail = BlastSeqLocNew((retval_tail ? &retval_tail : &retval), 
-                                       start, stop);
-          if (loc_var->next) {
-              start = ssr->left;
-              stop = ssr->right;
-          }
-       }
-   }
-
-   /* Free memory allocated for the temporary list of BlastSeqLoc-s */
-   BlastSeqLocFree(loc_head);
-
-   return retval;
+        tail->next = NULL;
+    }
+    sfree(ptrs);
 }
 
 Int2 
@@ -853,8 +840,7 @@ BLAST_ComplementMaskLocations(EBlastProgramType program_number,
       }
       
       if (BlastIsReverseStrand(kIsNucl, context)) {
-         mask_loc->seqloc_array[context] = 
-             s_BlastSeqLocListReverse(&mask_loc->seqloc_array[context]);
+         BlastSeqLocListReverse(&mask_loc->seqloc_array[context]);
       }
       loc = mask_loc->seqloc_array[context];
 
@@ -958,23 +944,13 @@ BlastSetUp_Filter(EBlastProgramType program_number,
 	return status;
 }
 
-BlastSeqLoc*
-BlastSeqLocReverse(const BlastSeqLoc* filter_in, Int4 query_length)
+void
+BlastSeqLocReverse(BlastSeqLoc* masks, Int4 query_length)
 {
-   BlastSeqLoc* filter_out = NULL;   /* Return variable. */
-
-   while (filter_in)
-   {
-        Int4 start, stop;
-        SSeqRange* loc = filter_in->ssr;
-        
-        start = query_length - 1 - loc->right;
-        stop = query_length - 1 - loc->left;
-        BlastSeqLocNew(&filter_out, start, stop);
-        filter_in = filter_in->next;
-   }
-
-   return filter_out;
+    for(; masks; masks = masks->next) {
+        masks->ssr->left    = query_length - 1 - masks->ssr->right;
+        masks->ssr->right   = query_length - 1 - masks->ssr->left;
+    }
 }
 
 /** Calculates the mask locations one context at a time.
@@ -999,7 +975,6 @@ s_GetFilteringLocationsForOneContext(BLAST_SequenceBlk* query_blk,
     Int2 status = 0;
     Int4 query_length = 0;      /* Length of query described by SeqLocPtr. */
     Int4 context_offset;
-    BlastSeqLoc *filter_slp = NULL;     /* SeqLocPtr computed for filtering. */
     Uint1 *buffer;              /* holds sequence for plus strand or protein. */
 
     const Boolean kIsNucl = (program_number == eBlastTypeBlastn);
@@ -1018,16 +993,14 @@ s_GetFilteringLocationsForOneContext(BLAST_SequenceBlk* query_blk,
                                query_length, 
                                0, 
                                filter_options, 
-                               &filter_slp, 
+                               filter_out, 
                                blast_message);
     if (status)
          return status;
 
-    if (BlastIsReverseStrand(kIsNucl, context) == TRUE)
-    {  /* Reverse this as it's on minus strand. */
-          BlastSeqLoc* tmp = BlastSeqLocReverse(filter_slp, query_length);
-          filter_slp = BlastSeqLocFree(filter_slp);
-          filter_slp = tmp;
+    if (BlastIsReverseStrand(kIsNucl, context) == TRUE) {  
+        /* Reverse this as it's on minus strand. */
+        BlastSeqLocReverse(*filter_out, query_length);
     }
 
     /* Extract the mask locations corresponding to this query 
@@ -1045,17 +1018,16 @@ s_GetFilteringLocationsForOneContext(BLAST_SequenceBlk* query_blk,
             ASSERT(context < query_blk->lcase_mask->total_size);
             lcase_mask_slp = query_blk->lcase_mask->seqloc_array[context];
             /* Set location list to NULL, to allow safe memory deallocation, 
-              ownership transferred to filter_slp below. */
+              ownership transferred to filter_out below. */
             query_blk->lcase_mask->seqloc_array[context] = NULL;
         }
 
         /* Attach the lower case mask locations to the filter locations and 
            combine them */
-        BlastSeqLocAppend(&filter_slp, lcase_mask_slp);
+        BlastSeqLocAppend(filter_out, lcase_mask_slp);
     }
 
-    *filter_out = BlastSeqLocCombine(filter_slp, 0);
-    filter_slp = BlastSeqLocFree(filter_slp);
+    BlastSeqLocCombine(filter_out, 0);
 
 	return 0;
 }
diff --git a/algo/blast/core/blast_filter.h b/algo/blast/core/blast_filter.h
index 7ba86ed3..4692336d 100644
--- a/algo/blast/core/blast_filter.h
+++ b/algo/blast/core/blast_filter.h
@@ -1,4 +1,4 @@
-/* $Id: blast_filter.h,v 1.39 2007/07/25 12:55:50 kazimird Exp $
+/* $Id: blast_filter.h,v 1.41 2007/12/20 22:55:46 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -47,8 +47,10 @@ extern "C" {
 #endif
 
 /** BLASTNA element used to mask bases in BLAST */
+NCBI_XBLAST_EXPORT
 extern const Uint1 kNuclMask;
 /** NCBISTDAA element used to mask residues in BLAST */
+NCBI_XBLAST_EXPORT
 extern const Uint1 kProtMask;
 
 /** Repeats filtering default options. */
@@ -86,6 +88,7 @@ BlastSeqLoc* BlastSeqLocNew(BlastSeqLoc** head, Int4 from, Int4 to);
  * @returns pointer to the second argument to this function (i.e.: tail of the
  * list)
  */
+NCBI_XBLAST_EXPORT
 BlastSeqLoc* BlastSeqLocAppend(BlastSeqLoc** head, BlastSeqLoc* node);
 
 /** Deallocate a single BlastSeqLoc structure and its contents, without
@@ -93,6 +96,7 @@ BlastSeqLoc* BlastSeqLocAppend(BlastSeqLoc** head, BlastSeqLoc* node);
  * @param node structure to deallocate [in]
  * @return NULL
  */
+NCBI_XBLAST_EXPORT
 BlastSeqLoc* BlastSeqLocNodeFree(BlastSeqLoc* node);
 
 /** Deallocate all BlastSeqLoc objects in a chain.
@@ -108,29 +112,25 @@ BlastSeqLoc* BlastSeqLocFree(BlastSeqLoc* loc);
  * @return NULL on NULL input or memory allocation failure, else a copy of the
  * list and its contents
  */
+NCBI_XBLAST_EXPORT
 BlastSeqLoc* BlastSeqLocListDup(BlastSeqLoc* head);
 
-/** Converts reverse strand coordinates to forward strand.
- * @param filter_in BlastSeqLoc to be reversed [in]
+/** Converts reverse strand coordinates to forward strand in place.
+ * @param masks BlastSeqLoc to be reversed [in|out]
  * @param query_length length of query [in]
- * @return reversed BlastSeqLoc
  */
 NCBI_XBLAST_EXPORT
-BlastSeqLoc* BlastSeqLocReverse(const BlastSeqLoc* filter_in, 
-                                Int4 query_length);
+void BlastSeqLocReverse(BlastSeqLoc* masks, Int4 query_length);
 
-/** Go through all mask locations in one sequence, 
- * combine any that overlap. Deallocate the memory for the locations that 
- * were on the list, produce a new (merged) list of locations. 
- * @param mask_loc The list of masks to be merged [in] 
+/** Go through all mask locations in one sequence and combine any that overlap,
+ * deallocating the unneeded locations.
+ * @param mask_loc The list of masks to be merged (in place) [in|out] 
  * @param link_value Largest gap size between locations for which they
  *                   should be linked together [in] 
- * @return The new (merged) list of masks or NULL if mask_loc is NULL or memory
- * allocation failure.
 */
 NCBI_XBLAST_EXPORT
-BlastSeqLoc*
-BlastSeqLocCombine(BlastSeqLoc* mask_loc, Int4 link_value);
+void
+BlastSeqLocCombine(BlastSeqLoc** mask_loc, Int4 link_value);
 
 /** Allocate memory for a BlastMaskLoc.
  * @param total number of contexts for which SSeqLocs should be allocated 
@@ -172,6 +172,7 @@ BlastMaskLoc* BlastMaskLocFree(BlastMaskLoc* mask_loc);
  * @note This function does NOT take into consideration the strands requested
  * to be searched, which is INCONSISTENT with what the C++ API does.
  */
+NCBI_XBLAST_EXPORT
 Int2 BlastMaskLocDNAToProtein(BlastMaskLoc* mask_loc, 
                               const BlastQueryInfo* query_info);
 
@@ -180,6 +181,7 @@ Int2 BlastMaskLocDNAToProtein(BlastMaskLoc* mask_loc,
  * @param mask_loc Mask locations structure [in|out]
  * @param query_info Query information structure, containing contexts data [in]
  */
+NCBI_XBLAST_EXPORT
 Int2 BlastMaskLocProteinToDNA(BlastMaskLoc* mask_loc, 
                               const BlastQueryInfo* query_info);
 
@@ -198,6 +200,7 @@ Int2 BlastMaskLocProteinToDNA(BlastMaskLoc* mask_loc,
  * @param complement_mask Linked list of SSeqRange*s in the concatenated 
  *                        sequence to be indexed in the lookup table . [out]
  */
+NCBI_XBLAST_EXPORT
 Int2 
 BLAST_ComplementMaskLocations(EBlastProgramType program_number, 
    const BlastQueryInfo* query_info, const BlastMaskLoc* mask_loc, 
diff --git a/algo/blast/core/blast_hits.c b/algo/blast/core/blast_hits.c
index 5acc284f..02d04ed2 100644
--- a/algo/blast/core/blast_hits.c
+++ b/algo/blast/core/blast_hits.c
@@ -1,4 +1,4 @@
-/* $Id: blast_hits.c,v 1.211 2007/07/27 18:25:29 kazimird Exp $
+/* $Id: blast_hits.c,v 1.217 2008/02/14 15:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -32,7 +32,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_hits.c,v 1.211 2007/07/27 18:25:29 kazimird Exp $";
+    "$Id: blast_hits.c,v 1.217 2008/02/14 15:55:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/ncbi_math.h>
@@ -570,10 +570,18 @@ Blast_HSPReevaluateWithAmbiguitiesUngapped(BlastHSP* hsp, Uint1* query_start,
                                       best_q_end, best_s_start, best_s_end);
 } 
 
-Int2
-Blast_HSPGetNumIdentities(Uint1* query, Uint1* subject, 
-                          BlastHSP* hsp, Int4* num_ident_ptr, 
-                          Int4* align_length_ptr)
+/** Calculate number of identities in a regular HSP.
+ * @param query The query sequence [in]
+ * @param subject The uncompressed subject sequence [in]
+ * @param hsp All information about the HSP [in]
+ * @param num_ident_ptr Number of identities [out]
+ * @param align_length_ptr The alignment length, including gaps [out]
+ * @return 0 on success, -1 on invalid parameters or error
+ */
+static Int2
+s_Blast_HSPGetNumIdentities(const Uint1* query, const Uint1* subject, 
+                            const BlastHSP* hsp, Int4* num_ident_ptr, 
+                            Int4* align_length_ptr)
 {
    Int4 i, num_ident, align_length, q_off, s_off;
    Uint1* q,* s;
@@ -583,11 +591,11 @@ Blast_HSPGetNumIdentities(Uint1* query, Uint1* subject,
    q_off = hsp->query.offset;
    s_off = hsp->subject.offset;
 
-   if (!subject || !query)
+   if ( !subject || !query || !hsp )
       return -1;
 
-   q = &query[q_off];
-   s = &subject[s_off];
+   q = (Uint1*) &query[q_off];
+   s = (Uint1*) &subject[s_off];
 
    num_ident = 0;
    align_length = 0;
@@ -630,14 +638,25 @@ Blast_HSPGetNumIdentities(Uint1* query, Uint1* subject,
       }
    }
 
-   *align_length_ptr = align_length;
+   if (align_length_ptr) {
+       *align_length_ptr = align_length;
+   }
    *num_ident_ptr = num_ident;
    return 0;
 }
 
-Int2
-Blast_HSPGetOOFNumIdentities(Uint1* query, Uint1* subject, 
-   BlastHSP* hsp, EBlastProgramType program, 
+/** Calculate number of identities in an HSP for an out-of-frame alignment.
+ * @param query The query sequence [in]
+ * @param subject The uncompressed subject sequence [in]
+ * @param hsp All information about the HSP [in]
+ * @param program BLAST program (blastx or tblastn) [in]
+ * @param num_ident_ptr Number of identities [out]
+ * @param align_length_ptr The alignment length, including gaps [out]
+ * @return 0 on success, -1 on invalid parameters or error
+ */
+static Int2
+s_Blast_HSPGetOOFNumIdentities(const Uint1* query, const Uint1* subject, 
+   const BlastHSP* hsp, EBlastProgramType program, 
    Int4* num_ident_ptr, Int4* align_length_ptr)
 {
    Int4 num_ident, align_length;
@@ -651,11 +670,11 @@ Blast_HSPGetOOFNumIdentities(Uint1* query, Uint1* subject,
 
    if (program == eBlastTypeTblastn ||
        program == eBlastTypeRpsTblastn) {
-       q = &query[hsp->query.offset];
-       s = &subject[hsp->subject.offset];
+       q = (Uint1*) &query[hsp->query.offset];
+       s = (Uint1*) &subject[hsp->subject.offset];
    } else {
-       s = &query[hsp->query.offset];
-       q = &subject[hsp->subject.offset];
+       s = (Uint1*) &query[hsp->query.offset];
+       q = (Uint1*) &subject[hsp->subject.offset];
    }
    num_ident = 0;
    align_length = 0;
@@ -701,25 +720,39 @@ Blast_HSPGetOOFNumIdentities(Uint1* query, Uint1* subject,
       }
    }
 
-   *align_length_ptr = align_length;
+   if (align_length_ptr) {
+       *align_length_ptr = align_length;
+   }
    *num_ident_ptr = num_ident;
 
    return 0;
 }
 
-/** Calculates number of identities and alignment lengths of an HSP and 
- * determines whether this HSP should be kept or deleted. The num_ident
- * field of the BlastHSP structure is filled here.
- * @param program_number Type of BLAST program [in]
- * @param hsp An HSP structure [in] [out]
- * @param query Query sequence [in]
- * @param subject Subject sequence [in]
- * @param score_options Scoring options, needed to distinguish the 
- *                      out-of-frame case. [in]
- * @param hit_options Hit saving options containing percent identity and
- *                    HSP length thresholds.
- * @return FALSE if HSP passes the test, TRUE if it should be deleted.
- */ 
+Int2
+Blast_HSPGetNumIdentities(const Uint1* query, 
+                          const Uint1* subject, 
+                          BlastHSP* hsp, 
+                          const BlastScoringOptions* score_options,
+                          Int4* align_length_ptr)
+{
+    Int2 retval = 0;
+
+    /* Calculate alignment length and number of identical letters. 
+       Do not get the number of identities if the query is not available */
+    if (score_options->is_ooframe) {
+        retval = s_Blast_HSPGetOOFNumIdentities(query, subject, hsp, 
+                                               score_options->program_number, 
+                                               &hsp->num_ident, 
+                                               align_length_ptr);
+    } else {
+        retval = s_Blast_HSPGetNumIdentities(query, subject, hsp, 
+                                            &hsp->num_ident, 
+                                            align_length_ptr);
+    }
+
+    return retval;
+}
+
 Boolean
 Blast_HSPTestIdentityAndLength(EBlastProgramType program_number, 
                                BlastHSP* hsp, Uint1* query, Uint1* subject, 
@@ -728,19 +761,14 @@ Blast_HSPTestIdentityAndLength(EBlastProgramType program_number,
 {
    Int4 align_length = 0;
    Boolean delete_hsp = FALSE;
+   Int2 status = 0;
 
    ASSERT(hsp && query && subject && score_options && hit_options);
 
-   /* Calculate alignment length and number of identical letters. 
-      Do not get the number of identities if the query is not available */
-   if (score_options->is_ooframe) {
-       Blast_HSPGetOOFNumIdentities(query, subject, hsp, program_number, 
-                                    &hsp->num_ident, &align_length);
-   } else {
-       Blast_HSPGetNumIdentities(query, subject, hsp, 
-                                 &hsp->num_ident, &align_length);
-   }
-      
+   status = Blast_HSPGetNumIdentities(query, subject, hsp, score_options,
+                                      &align_length);
+   ASSERT(status == 0);
+
    /* Check whether this HSP passes the percent identity and minimal hit 
       length criteria, and delete it if it does not. */
    if ((hsp->num_ident * 100.0 < 
@@ -1928,6 +1956,7 @@ Blast_HSPListReevaluateWithAmbiguitiesUngapped(EBlastProgramType program,
       /* Wrap subject sequence block into a BlastSeqSrcGetSeqArg structure, which is 
          needed by the BlastSeqSrc API. */
       BlastSeqSrcGetSeqArg seq_arg;
+      memset((void*) &seq_arg, 0, sizeof(seq_arg));
       seq_arg.oid = subject_blk->oid;
       seq_arg.encoding =
          (kTranslateSubject ? eBlastEncodingNcbi4na : eBlastEncodingNucleotide);
@@ -2377,6 +2406,15 @@ s_EvalueCompareHSPLists(const void* v1, const void* v2)
    return 0;
 }
 
+/** Callback for sorting hsp lists by their best e-value/score, in 
+ * reverse order - from higher e-value to lower (lower score to higher).
+*/
+static int
+s_EvalueCompareHSPListsRev(const void* v1, const void* v2)
+{
+   return s_EvalueCompareHSPLists(v2, v1);
+}
+
 /********************************************************************************
           Functions manipulating BlastHitList's
 ********************************************************************************/
@@ -2638,6 +2676,22 @@ Int2 Blast_HSPResultsSortByEvalue(BlastHSPResults* results)
    return 0;
 }
 
+Int2 Blast_HSPResultsReverseSort(BlastHSPResults* results)
+{
+   Int4 index;
+   BlastHitList* hit_list;
+
+   for (index = 0; index < results->num_queries; ++index) {
+      hit_list = results->hitlist_array[index];
+      if (hit_list && hit_list->hsplist_count > 1) {
+         qsort(hit_list->hsplist_array, hit_list->hsplist_count, 
+               sizeof(BlastHSPList*), s_EvalueCompareHSPListsRev);
+      }
+      s_BlastHitListPurge(hit_list);
+   }
+   return 0;
+}
+
 Int2 Blast_HSPResultsReverseOrder(BlastHSPResults* results)
 {
    Int4 index;
diff --git a/algo/blast/core/blast_hits.h b/algo/blast/core/blast_hits.h
index 42fff55e..7e8445e1 100644
--- a/algo/blast/core/blast_hits.h
+++ b/algo/blast/core/blast_hits.h
@@ -1,4 +1,4 @@
-/* $Id: blast_hits.h,v 1.106 2007/07/27 18:25:30 kazimird Exp $
+/* $Id: blast_hits.h,v 1.108 2008/02/14 15:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -263,35 +263,27 @@ Blast_HSPReevaluateWithAmbiguitiesUngapped(BlastHSP* hsp,
    const BlastInitialWordParameters* word_params, 
    BlastScoreBlk* sbp, Boolean translated);
 
-/** Calculate number of identities in an HSP.
+/** Calculate number of identities in an HSP and set the BlastHSP::num_ident
+ * field (unconditionally)
  * @param query The query sequence [in]
  * @param subject The uncompressed subject sequence [in]
- * @param hsp All information about the HSP [in]
- * @param num_ident_ptr Number of identities [out]
- * @param align_length_ptr The alignment length, including gaps [out]
+ * @param hsp All information about the HSP, the output of this function will
+ * be stored in its num_ident field [in|out]
+ * @param score_options Scoring options [in]
+ * @param align_length_ptr The alignment length, including gaps (optional) [out]
+ * @return 0 on success, -1 on invalid parameters or error
  */
 NCBI_XBLAST_EXPORT
 Int2
-Blast_HSPGetNumIdentities(Uint1* query, Uint1* subject, BlastHSP* hsp, 
-                          Int4* num_ident_ptr, Int4* align_length_ptr);
-
-/** Calculate number of identities in an HSP for an out-of-frame alignment.
- * @param query The query sequence [in]
- * @param subject The uncompressed subject sequence [in]
- * @param hsp All information about the HSP [in]
- * @param program BLAST program (blastx or tblastn) [in]
- * @param num_ident_ptr Number of identities [out]
- * @param align_length_ptr The alignment length, including gaps [out]
- */
-NCBI_XBLAST_EXPORT
-Int2
-Blast_HSPGetOOFNumIdentities(Uint1* query, Uint1* subject, BlastHSP* hsp, 
-                             EBlastProgramType program, Int4* num_ident_ptr, 
-                             Int4* align_length_ptr);
-
-/** Calculates number of identities and alignment lengths of an HSP and 
- * determines whether this HSP should be kept or deleted. The num_ident
- * field of the BlastHSP structure is filled here.
+Blast_HSPGetNumIdentities(const Uint1* query, 
+                          const Uint1* subject, 
+                          BlastHSP* hsp, 
+                          const BlastScoringOptions* score_options,
+                          Int4* align_length_ptr);
+
+/** Calculates number of identities and alignment lengths of an HSP via
+ * Blast_HSPGetNumIdentities and determines whether this HSP should be kept or
+ * deleted. 
  * @param program_number Type of BLAST program [in]
  * @param hsp An HSP structure [in] [out]
  * @param query Query sequence [in]
@@ -640,7 +632,7 @@ Int2 Blast_HitListUpdate(BlastHitList* hit_list, BlastHSPList* hsp_list);
  * represent alignments to the same query sequence
  * @param old_hit_list_ptr Pointer to original HitList, will be NULLed 
  *                          out on return [in|out]
- * @param combined_hsp_list_ptr Pointer to the combined list of HSPs [in|out]
+ * @param combined_hit_list_ptr Pointer to the combined HitList [in|out]
  * @param contexts_per_query The number of different contexts that can
  *             occur in hits from old_hit_list and combined_hit_list [in]
  * @param split_offsets the query offset that marks the boundary between
@@ -681,6 +673,10 @@ BlastHSPResults* Blast_HSPResultsFree(BlastHSPResults* results);
 /** Sort each hit list in the BLAST results by best e-value */
 NCBI_XBLAST_EXPORT
 Int2 Blast_HSPResultsSortByEvalue(BlastHSPResults* results);
+/** Sort each hit list in the BLAST results by best e-value, in reverse
+    order. */
+NCBI_XBLAST_EXPORT
+Int2 Blast_HSPResultsReverseSort(BlastHSPResults* results);
 
 /** Reverse order of HSP lists in each hit list in the BLAST results. 
  * This allows to return HSP lists from the end of the arrays when reading
diff --git a/algo/blast/core/blast_hspstream.c b/algo/blast/core/blast_hspstream.c
index 38efe78a..ee4cfa81 100644
--- a/algo/blast/core/blast_hspstream.c
+++ b/algo/blast/core/blast_hspstream.c
@@ -1,4 +1,4 @@
-/*  $Id: blast_hspstream.c,v 1.8 2007/07/27 18:25:30 kazimird Exp $
+/*  $Id: blast_hspstream.c,v 1.9 2007/12/07 18:25:41 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -33,7 +33,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_hspstream.c,v 1.8 2007/07/27 18:25:30 kazimird Exp $";
+    "$Id: blast_hspstream.c,v 1.9 2007/12/07 18:25:41 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/blast_hspstream.h>
@@ -150,7 +150,8 @@ void Blast_HSPStreamResultBatchReset(BlastHSPStreamResultBatch *batch)
 {
     Int4 i;
     for (i = 0; i < batch->num_hsplists; i++) {
-        sfree(batch->hsplist_array[i]);
+        batch->hsplist_array[i] = 
+           Blast_HSPListFree(batch->hsplist_array[i]);
     }
     batch->num_hsplists = 0;
 }
diff --git a/algo/blast/core/blast_kappa.c b/algo/blast/core/blast_kappa.c
index 88012767..ccea695c 100644
--- a/algo/blast/core/blast_kappa.c
+++ b/algo/blast/core/blast_kappa.c
@@ -1,4 +1,4 @@
-/* $Id: blast_kappa.c,v 1.86 2007/05/22 20:55:36 kazimird Exp $
+/* $Id: blast_kappa.c,v 1.94 2008/02/14 15:55:42 kazimird Exp $
  * ==========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] =
-"$Id: blast_kappa.c,v 1.86 2007/05/22 20:55:36 kazimird Exp $";
+"$Id: blast_kappa.c,v 1.94 2008/02/14 15:55:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <float.h>
@@ -44,6 +44,7 @@ static char const rcsid[] =
 #include <algo/blast/core/blast_util.h>
 #include <algo/blast/core/blast_gapalign.h>
 #include <algo/blast/core/blast_filter.h>
+#include <algo/blast/core/blast_traceback.h>
 #include <algo/blast/core/link_hsps.h>
 #include <algo/blast/core/gencode_singleton.h>
 #include "blast_psi_priv.h"
@@ -295,7 +296,7 @@ s_HSPListFromDistinctAlignments(BlastCompo_Alignment ** alignments,
                                 BlastQueryInfo* queryInfo)
 {
     int status = 0;                    /* return code for any routine called */
-    const int unknown_value = 0;   /* dummy constant to use when a
+    static const int unknown_value = 0;   /* dummy constant to use when a
                                       parameter value is not known */
     BlastCompo_Alignment * align;  /* an alignment in the list */
     BlastHSPList * hsp_list;       /* the new HSP list */
@@ -381,7 +382,7 @@ s_HSPListFromDistinctAlignments(BlastCompo_Alignment ** alignments,
 static int
 s_HitlistEvaluateAndPurge(int * pbestScore, double *pbestEvalue,
                           BlastHSPList * hsp_list,
-			  const BlastSeqSrc* seqSrc,
+                          const BlastSeqSrc* seqSrc,
                           int subject_length,
                           EBlastProgramType program_number,
                           BlastQueryInfo* queryInfo,
@@ -395,7 +396,7 @@ s_HitlistEvaluateAndPurge(int * pbestScore, double *pbestEvalue,
     int status = 0;
     *pbestEvalue = DBL_MAX;
     *pbestScore  = 0;
-    if (hitParams->options->do_sum_stats) {
+    if (hitParams->do_sum_stats) {
         status = BLAST_LinkHsps(program_number, hsp_list, queryInfo,
                                 subject_length, sbp,
                                 hitParams->link_hsp_params, TRUE);
@@ -427,6 +428,70 @@ s_HitlistEvaluateAndPurge(int * pbestScore, double *pbestEvalue,
     return status == 0 ? 0 : -1;
 }
 
+#if 0
+/** Compute the number of identities for the HSPs in the hsp_list
+ * @note this only works for blastp right now and it's not currently being used
+ * because we cannot reliably calculate the number of identities for queries
+ * that have hard masking applied to them (which is the default).
+ * 
+ * @param query_blk the query sequence data [in]
+ * @param query_info structure describing the query_blk structure [in]
+ * @param seq_src source of subject sequence data [in]
+ * @param hsp_list list of HSPs to be processed [in|out]
+ * @param scoring_options scoring options [in]
+ */
+static void
+s_ComputeNumIdentities(const BLAST_SequenceBlk* query_blk,
+                       const BlastQueryInfo* query_info,
+                       const BlastSeqSrc* seq_src,
+                       BlastHSPList* hsp_list,
+                       const BlastScoringOptions* scoring_options)
+{
+    Uint1* query = NULL;
+    Uint1* subject = NULL;
+    const EBlastProgramType program_number = scoring_options->program_number;
+    const Boolean kIsOutOfFrame = scoring_options->is_ooframe;
+    const EBlastEncoding encoding = Blast_TracebackGetEncoding(program_number);
+    BlastSeqSrcGetSeqArg seq_arg;
+    Int2 status = 0;
+    int i;
+
+    if ( !hsp_list || program_number != eBlastTypeBlastp ) {
+        return;
+    }
+
+    /* Initialize the subject */
+    {
+        memset((void*) &seq_arg, 0, sizeof(seq_arg));
+        seq_arg.oid = hsp_list->oid;
+        seq_arg.encoding = encoding;
+        status = BlastSeqSrcGetSequence(seq_src, (void*) &seq_arg);
+        ASSERT(status == 0);
+        subject = seq_arg.seq->sequence;
+    }
+
+    for (i = 0; i < hsp_list->hspcnt; i++) {
+        BlastHSP* hsp = hsp_list->hsp_array[i];
+
+        /* Initialize the query */
+        if (program_number == eBlastTypeBlastx && kIsOutOfFrame) {
+            Int4 context = hsp->context - hsp->context % CODON_LENGTH;
+            Int4 context_offset = query_info->contexts[context].query_offset;
+            query = query_blk->oof_sequence + CODON_LENGTH + context_offset;
+        } else {
+            query = query_blk->sequence + 
+                query_info->contexts[hsp->context].query_offset;
+        }
+
+        status = Blast_HSPGetNumIdentities(query, subject, hsp, 
+                                           scoring_options, 0);
+        ASSERT(status == 0);
+    }
+    BlastSeqSrcReleaseSequence(seq_src, (void*) &seq_arg);
+    BlastSequenceBlkFree(seq_arg.seq);
+}
+#endif
+
 
 /**
  * A callback routine: compute lambda for the given score
@@ -801,6 +866,48 @@ s_MatchingSequenceRelease(BlastCompo_MatchingSequence * self)
     }
 }
 
+#define MINUMUM_FRACTION_NEAR_IDENTICAL 0.98
+
+/**
+ * Test whether the aligned parts of two sequences that
+ * have a high-scoring gapless alignment are nearly identical
+ *
+ * @param seqData           subject sequence
+ * @param queryData         query sequence
+ * @param align             information about the alignment
+ * @param rangeOffset       offset for subject sequence (used for tblastn)
+ *
+ * @return                  TRUE if the aligned portions are nearly identical
+ */
+static Boolean 
+s_TestNearIdentical(const BlastCompo_SequenceData *seqData, 
+		 const BlastCompo_SequenceData *queryData, 
+		    const int queryOffset,   
+		 const BlastCompo_Alignment *align,
+		 const int rangeOffset)
+{
+  int numIdentical = 0;
+  double fractionIdentical;
+  int qPos, sPos; /*positions in query and subject;*/
+  int qEnd; /*end of query*/
+
+  qPos = align->queryStart - queryOffset;
+  qEnd = align->queryEnd - queryOffset;
+  sPos = align->matchStart - rangeOffset;
+  while (qPos < qEnd)  {
+      if (queryData->data[qPos] == seqData->data[sPos])
+	numIdentical++;
+      sPos++;
+      qPos++;
+  }
+  fractionIdentical = ((double) numIdentical/
+  (double) (align->queryEnd - align->queryStart));
+  if (fractionIdentical >= MINUMUM_FRACTION_NEAR_IDENTICAL)
+    return(TRUE);
+  else
+    return(FALSE);
+}
+
 
 /**
  * Initialize a new matching sequence, obtaining information about the
@@ -918,13 +1025,23 @@ s_DoSegSequenceData(BlastCompo_SequenceData * seqData,
  * @param self          the sequence from which to obtain the data [in]
  * @param range         the range and translation frame to get [in]
  * @param seqData       the resulting data [out]
+ * @param queryData     the query sequence [in]
+ * @param queryOffset   offset for align if there are multiple queries
+ * @param align          information about the alignment between query and subject
+ * @param shouldTestIdentical did alignment pass a preliminary test in
+ *                       redo_alignment.c that indicates the sequence
+ *                        pieces may be near identical
  *
  * @return 0 on success; -1 on failure
  */
 static int
 s_SequenceGetTranslatedRange(const BlastCompo_MatchingSequence * self,
                              const BlastCompo_SequenceRange * range,
-                             BlastCompo_SequenceData * seqData )
+                             BlastCompo_SequenceData * seqData,
+			     const BlastCompo_SequenceData * queryData,
+			     const int queryOffset,
+			     const BlastCompo_Alignment *align,
+			     const Boolean shouldTestIdentical)
 {
     int status = 0;
     BlastKappa_SequenceInfo * local_data; /* BLAST-specific
@@ -970,6 +1087,9 @@ s_SequenceGetTranslatedRange(const BlastCompo_MatchingSequence * self,
         seqData->length = translated_length;
 
         if ( !(KAPPA_TBLASTN_NO_SEG_SEQUENCE) ) {
+	  if ((!shouldTestIdentical) || 
+            (shouldTestIdentical && 
+	     (!s_TestNearIdentical(seqData, queryData, queryOffset, align, range->begin)))) {
             status = s_DoSegSequenceData(seqData, eBlastTypeTblastn);
             if (status != 0) {
                 free(seqData->buffer);
@@ -977,6 +1097,7 @@ s_SequenceGetTranslatedRange(const BlastCompo_MatchingSequence * self,
                 seqData->data = NULL;
                 seqData->length = 0;
             }
+	  }
         }
     }
     return status;
@@ -989,13 +1110,25 @@ s_SequenceGetTranslatedRange(const BlastCompo_MatchingSequence * self,
  * @param self          a protein sequence [in]
  * @param range         the range to get [in]
  * @param seqData       the resulting data [out]
+ * @param queryData     the query sequence [in]
+ * @param queryOffset   offset for align if there are multiple queries
+ * @param align          information about the alignment 
+ *                         between query and subject [in]
+ * @param shouldTestIdentical did alignment pass a preliminary test in
+ *                       redo_alignment.c that indicates the sequence
+ *                        pieces may be near identical [in]
  *
  * @return 0 on success; -1 on failure
  */
 static int
 s_SequenceGetProteinRange(const BlastCompo_MatchingSequence * self,
                           const BlastCompo_SequenceRange * range,
-                          BlastCompo_SequenceData * seqData )
+                          BlastCompo_SequenceData * seqData,
+			  const BlastCompo_SequenceData * queryData,
+			  const int queryOffset,
+			  const BlastCompo_Alignment *align,
+			  const Boolean shouldTestIdentical)
+
 {
     int status = 0;       /* return status */
     Int4       idx;       /* loop index */
@@ -1030,7 +1163,12 @@ s_SequenceGetProteinRange(const BlastCompo_MatchingSequence * self,
         }
     }
     if ( !(KAPPA_BLASTP_NO_SEG_SEQUENCE) ) {
+      if ((!shouldTestIdentical) || 
+	  (shouldTestIdentical && 
+	   (!s_TestNearIdentical(seqData, queryData, queryOffset, align, 0)))) {
+	status = -1;
         status = s_DoSegSequenceData(seqData, eBlastTypeBlastp);
+      }
     }
     /* Fit the data to the range. */
     seqData ->data    = &seqData->data[range->begin - 1];
@@ -1052,20 +1190,32 @@ s_SequenceGetProteinRange(const BlastCompo_MatchingSequence * self,
  * @param self          sequence information [in]
  * @param range        range specifying the range of data [in]
  * @param seqData       the sequence data obtained [out]
+ * @param seqData       the resulting data [out]
+ * @param queryData     the query sequence [in]
+ * @param queryOffset   offset for align if there are multiple queries
+ * @param align          information about the alignment between query and subject
+ * @param shouldTestIdentical did alignment pass a preliminary test in
+ *                       redo_alignment.c that indicates the sequence
+ *                        pieces may be near identical
  *
  * @return 0 on success; -1 on failure
  */
 static int
 s_SequenceGetRange(const BlastCompo_MatchingSequence * self,
                    const BlastCompo_SequenceRange * range,
-                   BlastCompo_SequenceData * seqData )
+                   BlastCompo_SequenceData * seqData,
+		   const BlastCompo_SequenceData * queryData,
+		   const int queryOffset,
+		   const BlastCompo_Alignment *align,
+		   const Boolean shouldTestIdentical)
 {
     BlastKappa_SequenceInfo * seq_info = self->local_data;
     if (seq_info->prog_number ==  eBlastTypeTblastn) {
         /* The sequence must be translated. */
-        return s_SequenceGetTranslatedRange(self, range, seqData);
+      return s_SequenceGetTranslatedRange(self, range, seqData,
+					  queryData, queryOffset, align, shouldTestIdentical);
     } else {
-        return s_SequenceGetProteinRange(self, range, seqData);
+      return s_SequenceGetProteinRange(self, range, seqData, queryData, queryOffset, align, shouldTestIdentical);
     }
 }
 
@@ -1741,7 +1891,7 @@ s_GetAlignParams(BlastKappa_GappingParamsContext * context,
     /* is this a positiion-based search */
     Boolean positionBased = (Boolean) (context->sbp->psi_matrix != NULL);
     /* will BLAST_LinkHsps be called to assign e-values */
-    Boolean do_link_hsps = (hitParams->options->do_sum_stats);
+    Boolean do_link_hsps = (hitParams->do_sum_stats);
     ECompoAdjustModes compo_adjust_mode =
         (ECompoAdjustModes) extendParams->options->compositionBasedStats;
     
@@ -1922,8 +2072,10 @@ Blast_RedoAlignmentCore(EBlastProgramType program_number,
         return -1;   /* Unsupported matrix */
     }
     /*****************/
-    inclusion_ethresh =
-        (psiOptions != NULL) ? psiOptions->inclusion_ethresh : 0;
+    inclusion_ethresh = (psiOptions /* this can be NULL for CBl2Seq */
+                         ? psiOptions->inclusion_ethresh 
+                         : PSI_INCLUSION_ETHRESH);
+    ASSERT(inclusion_ethresh != 0.0);
 
     /* Initialize savedParams */
     savedParams =
@@ -2094,7 +2246,7 @@ Blast_RedoAlignmentCore(EBlastProgramType program_number,
                 status_code =
                     s_HitlistEvaluateAndPurge(&bestScore, &bestEvalue,
                                               hsp_list,
-					      seqSrc,
+                                              seqSrc,
                                               matchingSeq.length,
                                               program_number,
                                               queryInfo, query_index,
@@ -2112,6 +2264,10 @@ Blast_RedoAlignmentCore(EBlastProgramType program_number,
                     s_HSPListNormalizeScores(hsp_list,
                                              kbp->Lambda, kbp->logK,
                                              localScalingFactor);
+                    /* currently commented out, see function definition for
+                      explanation
+                     s_ComputeNumIdentities(queryBlk, queryInfo, seqSrc,
+                                           hsp_list, scoringParams->options);*/
                     status_code =
                         BlastCompo_HeapInsert(&redoneMatches[query_index],
                                               hsp_list, bestEvalue,
diff --git a/algo/blast/core/blast_nalookup.c b/algo/blast/core/blast_nalookup.c
index ed9674a7..d4dd7c5a 100644
--- a/algo/blast/core/blast_nalookup.c
+++ b/algo/blast/core/blast_nalookup.c
@@ -1,4 +1,4 @@
-/* $Id: blast_nalookup.c,v 1.6 2007/02/14 20:25:43 kazimird Exp $
+/* $Id: blast_nalookup.c,v 1.8 2008/01/31 23:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -32,10 +32,11 @@
 #include <algo/blast/core/lookup_util.h>
 #include <algo/blast/core/blast_encoding.h>
 #include <algo/blast/core/blast_util.h>
+#include <algo/blast/core/blast_filter.h>
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] =
-    "$Id: blast_nalookup.c,v 1.6 2007/02/14 20:25:43 kazimird Exp $";
+    "$Id: blast_nalookup.c,v 1.8 2008/01/31 23:55:42 kazimird Exp $";
 #endif                          /* SKIP_DOXYGEN_PROCESSING */
 
 /** bitfield used to detect ambiguities in uncompressed
@@ -316,10 +317,46 @@ static Int4 s_BlastSmallNaLookupFinalize(Int4 **thin_backbone,
     return 0;
 }
 
+static BlastSeqLoc* s_SeqLocListInvert(BlastSeqLoc* locations, Int4 length)
+{
+     BlastSeqLoc* retval = NULL;
+     BlastSeqLoc* tail = NULL;  /* Tail of the list. */
+     Int4 start, stop;
+
+     ASSERT(locations);
+
+     start = 0;
+     stop = MAX( 0, locations->ssr->left);
+
+     if (stop - start > 2)
+        tail = BlastSeqLocNew(&retval, start, stop);
+
+     while (locations)
+     {
+         start = locations->ssr->right;
+         locations = locations->next;
+
+         if (locations)
+             stop = locations->ssr->left;
+         else
+             stop = length;
+
+         if (stop - start > 2)
+         {
+            if (retval == NULL)
+               tail = BlastSeqLocNew(&retval, start, stop);
+            else
+               tail = BlastSeqLocNew(&tail, start, stop);
+         }
+     }
+     return retval;
+}
+
 Int4 BlastSmallNaLookupTableNew(BLAST_SequenceBlk* query, 
                            BlastSeqLoc* locations,
                            BlastSmallNaLookupTable * *lut,
                            const LookupTableOptions * opt, 
+                           const QuerySetUpOptions* query_options,
                            Int4 lut_width)
 {
     Int4 status = 0;
@@ -344,6 +381,13 @@ Int4 BlastSmallNaLookupTableNew(BLAST_SequenceBlk* query,
                                       BITS_PER_NUC,
                                       lookup->lut_word_length,
                                       query, locations);
+    if (locations && lookup->word_length > lookup->lut_word_length && 
+       ((query_options->filtering_options && SBlastFilterOptionsMaskAtHash(query_options->filtering_options)) ||
+        (query_options->filter_string && strstr(query_options->filter_string, "m"))))
+    {
+       lookup->masked_locations = s_SeqLocListInvert(locations, query->length);
+    }
+
     status = s_BlastSmallNaLookupFinalize(thin_backbone, lookup, query);
     if (status != 0) {
         lookup = BlastSmallNaLookupTableDestruct(lookup);
@@ -359,6 +403,8 @@ BlastSmallNaLookupTable *BlastSmallNaLookupTableDestruct(
 {
     sfree(lookup->final_backbone);
     sfree(lookup->overflow);
+    if (lookup->masked_locations)
+       lookup->masked_locations = BlastSeqLocFree(lookup->masked_locations);
     sfree(lookup);
     return NULL;
 }
diff --git a/algo/blast/core/blast_nalookup.h b/algo/blast/core/blast_nalookup.h
index 413f926f..8b9b5ac7 100644
--- a/algo/blast/core/blast_nalookup.h
+++ b/algo/blast/core/blast_nalookup.h
@@ -1,4 +1,4 @@
-/* $Id: blast_nalookup.h,v 1.8 2007/03/13 17:55:34 kazimird Exp $
+/* $Id: blast_nalookup.h,v 1.10 2008/01/31 23:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -74,6 +74,7 @@ typedef struct BlastSmallNaLookupTable {
     Int4  overflow_size;   /**< Number of elements in the overflow array */
     void *scansub_callback;  /**< function for scanning subject sequences */
     void *extend_callback;  /**< function for extending hits */
+    BlastSeqLoc* masked_locations; /**< masked locations, only non-NULL for soft-masking. */
 } BlastSmallNaLookupTable;
 
 /** Create a new small nucleotide lookup table.
@@ -83,6 +84,7 @@ typedef struct BlastSmallNaLookupTable {
  *        e.g. [0,length-1] for full sequence. NULL means no sequence. [in]
  * @param lut Pointer to the lookup table to be created [out]
  * @param opt Options for lookup table creation [in]
+ * @param query_options query options used to get filtering options [in]
  * @param lut_width The number of nucleotides in one lookup table word [in]
  * @return 0 if successful, nonzero on failure
  */
@@ -90,6 +92,7 @@ Int4 BlastSmallNaLookupTableNew(BLAST_SequenceBlk* query,
                                 BlastSeqLoc* locations,
                                 BlastSmallNaLookupTable * *lut,
                                 const LookupTableOptions * opt,
+                                const QuerySetUpOptions* query_options,
                                 Int4 lut_width);
 
 /** Free a small nucleotide lookup table.
diff --git a/algo/blast/core/blast_options.c b/algo/blast/core/blast_options.c
index 1c9484f6..81e875b7 100644
--- a/algo/blast/core/blast_options.c
+++ b/algo/blast/core/blast_options.c
@@ -1,4 +1,4 @@
-/* $Id: blast_options.c,v 1.205 2007/05/22 20:55:36 kazimird Exp $
+/* $Id: blast_options.c,v 1.207 2007/10/25 15:55:36 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_options.c,v 1.205 2007/05/22 20:55:36 kazimird Exp $";
+    "$Id: blast_options.c,v 1.207 2007/10/25 15:55:36 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/blast_options.h>
@@ -458,7 +458,7 @@ BlastInitialWordOptionsNew(EBlastProgramType program,
       (*options)->gap_trigger = BLAST_GAP_TRIGGER_NUCL;
       (*options)->x_dropoff = BLAST_UNGAPPED_X_DROPOFF_NUCL;
    }
-   (*options)->ungapped_extension = TRUE;
+
    (*options)->program_number = program;
 
    return 0;
@@ -473,8 +473,8 @@ BlastInitialWordOptionsValidate(EBlastProgramType program_number,
 
    ASSERT(options);
 
-   /* For some blastn variants (i.e., megablast), and for PHI BLAST there is no
-    * ungapped extension. */
+   /* PHI-BLAST has no ungapped extension phase.  Megablast may not have it,
+    but generally does now. */
    if (program_number != eBlastTypeBlastn  &&
        (!Blast_ProgramIsPhiBlast(program_number)) &&
        options->x_dropoff <= 0.0)
@@ -515,7 +515,7 @@ BlastExtensionOptionsFree(BlastExtensionOptions* options)
 }
 
 Int2
-BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions* *options)
+BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions* *options, Boolean gapped)
 
 {
 	*options = (BlastExtensionOptions*) 
@@ -541,7 +541,7 @@ BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions* *opti
 
     /** @todo how to determine this for PSI-BLAST bootstrap run (i.e. when
      * program is blastp? */
-    if (Blast_QueryIsPssm(program) && ! Blast_SubjectIsTranslated(program)) {
+    if (gapped && (Blast_QueryIsPssm(program) && ! Blast_SubjectIsTranslated(program))) {
         (*options)->compositionBasedStats = eCompositionBasedStats;
     }
 
@@ -985,7 +985,8 @@ BLAST_FillLookupTableOptions(LookupTableOptions* options,
    if (word_size)
       options->word_size = word_size;
    if ((program_number == eBlastTypeTblastn ||
-        program_number == eBlastTypeBlastp) && 
+        program_number == eBlastTypeBlastp ||
+        program_number == eBlastTypeBlastx) && 
        word_size > 5)
        options->lut_type = eCompressedAaLookupTable;
 
@@ -1141,13 +1142,14 @@ LookupTableOptionsValidate(EBlastProgramType program_number,
     } else if (program_number != eBlastTypeBlastn && options->word_size > 5)
     {
         if (program_number == eBlastTypeBlastp ||
-            program_number == eBlastTypeTblastn)
+            program_number == eBlastTypeTblastn ||
+            program_number == eBlastTypeBlastx)
         {
             if (options->word_size > 7) {
                 Blast_MessageWrite(blast_msg, eBlastSevError, 
                                    kBlastMessageNoContext,
                                    "Word-size must be less than "
-                                   "8 for a tblastn search");
+                                   "8 for a tblastn, blastp or blastx search");
                 return BLASTERR_OPTION_VALUE_INVALID;
             }
         }
@@ -1169,13 +1171,16 @@ LookupTableOptionsValidate(EBlastProgramType program_number,
     }
 
     if (program_number == eBlastTypeBlastp ||
-        program_number == eBlastTypeTblastn)
+        program_number == eBlastTypeTblastn ||
+        program_number == eBlastTypeBlastx)
     {
         if (options->word_size > 5 &&
             options->lut_type != eCompressedAaLookupTable) {
-           Blast_MessageWrite(blast_msg, eBlastSevError, kBlastMessageNoContext,
-                         "Blastp or Tblastn with word size > 5 requires a "
-                         "compressed alphabet lookup table");
+           Blast_MessageWrite(blast_msg, eBlastSevError,
+                              kBlastMessageNoContext,
+                              "Blastp, Blastx or Tblastn with word size"
+                              " > 5 requires a "
+                              "compressed alphabet lookup table");
            return BLASTERR_OPTION_VALUE_INVALID;
         }
         else if (options->lut_type == eCompressedAaLookupTable &&
@@ -1412,10 +1417,11 @@ Int2 BLAST_InitDefaultOptions(EBlastProgramType program_number,
    if ((status=BlastInitialWordOptionsNew(program_number, word_options)))
       return status;
 
-   if ((status = BlastExtensionOptionsNew(program_number, ext_options)))
+   if ((status=BlastScoringOptionsNew(program_number, score_options)))
       return status;
 
-   if ((status=BlastScoringOptionsNew(program_number, score_options)))
+   if ((status = BlastExtensionOptionsNew(program_number, ext_options,
+                                       (*score_options)->gapped_calculation)))
       return status;
 
    if ((status=BlastHitSavingOptionsNew(program_number, hit_options,
@@ -1464,6 +1470,22 @@ static Int2 s_BlastExtensionScoringOptionsValidate(EBlastProgramType program_num
 	}
     }
 
+    if (ext_options->compositionBasedStats != eNoCompositionBasedStats)
+    {
+            if (!Blast_QueryIsPssm(program_number) && program_number != eBlastTypeTblastn && 
+                 program_number != eBlastTypeBlastp) {
+			Blast_MessageWrite(blast_msg, eBlastSevWarning, kBlastMessageNoContext,
+                            "Compositional adjustments are only supported with blastp or tblastn");
+			return BLASTERR_OPTION_VALUE_INVALID;
+            }
+            if (!score_options->gapped_calculation) {
+			Blast_MessageWrite(blast_msg, eBlastSevWarning, kBlastMessageNoContext,
+                            "Compositional adjustments are only supported for gapped searches");
+			return BLASTERR_OPTION_VALUE_INVALID;
+            }
+            
+    }
+
     return 0;
 }
                    
diff --git a/algo/blast/core/blast_options.h b/algo/blast/core/blast_options.h
index 69891352..b7167d0d 100644
--- a/algo/blast/core/blast_options.h
+++ b/algo/blast/core/blast_options.h
@@ -1,4 +1,4 @@
-/* $Id: blast_options.h,v 1.146 2007/05/22 20:55:36 kazimird Exp $
+/* $Id: blast_options.h,v 1.149 2008/01/24 21:25:45 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -132,7 +132,7 @@ extern "C" {
 /** default dropoff for the final gapped extension with traceback */
 #define BLAST_GAP_X_DROPOFF_FINAL_PROT 25 /**< default dropoff (all protein-
                                                based gapped extensions) */
-#define BLAST_GAP_X_DROPOFF_FINAL_NUCL 50 /**< default dropoff for nucleotide
+#define BLAST_GAP_X_DROPOFF_FINAL_NUCL 100 /**< default dropoff for nucleotide
                                                gapped extensions) */
 #define BLAST_GAP_X_DROPOFF_FINAL_TBLASTX 0 /**< default dropoff for tblastx */
 
@@ -184,8 +184,6 @@ typedef struct LookupTableOptions {
    Int4 mb_template_length; /**< Length of the discontiguous words */
    Int4 mb_template_type; /**< Type of a discontiguous word template */
    char* phi_pattern;  /**< PHI-BLAST pattern */
-   Int4 max_num_patterns; /**< Maximal number of patterns allowed for 
-                             PHI-BLAST */
    EBlastProgramType program_number; /**< indicates blastn, blastp, etc. */
 } LookupTableOptions;
 
@@ -243,8 +241,6 @@ typedef struct BlastInitialWordOptions {
    double gap_trigger; /**< Score in bits for starting gapped extension */
    Int4 window_size; /**< Maximal allowed distance between 2 hits in case 2 
                         hits are required to trigger the extension */
-   Boolean ungapped_extension; /**< Should the ungapped extension be 
-                                  performed? */
    double x_dropoff; /**< X-dropoff value (in bits) for the ungapped 
                          extension */
    EBlastProgramType program_number; /**< indicates blastn, blastp, etc. */
@@ -308,8 +304,6 @@ typedef struct BlastHitSavingOptions {
    Int4 hsp_num_max; /**< Maximal number of HSPs to save for one database 
                         sequence */
    Int4 total_hsp_limit; /**< Maximal total number of HSPs to keep */
-   Int4 hsp_range_max; /**< Maximal number of HSPs to save in a region: 
-                          used for culling only */
    Int4 culling_limit; /**< If the query range of an HSP is contained in
                             at least this many higher-scoring HSPs, throw
                             away the HSP as redundant (turned off if zero) */
@@ -441,24 +435,28 @@ typedef struct BlastDatabaseOptions {
  * @param dust_options object to free
  * @return NULL pointer
  */
+NCBI_XBLAST_EXPORT
 SDustOptions* SDustOptionsFree(SDustOptions* dust_options);
 
 /** Allocates memory for SDustOptions, fills in defaults.
  * @param dust_options options that are being returned [in|out]
  * @return zero on sucess
  */
+NCBI_XBLAST_EXPORT
 Int2 SDustOptionsNew(SDustOptions* *dust_options);
 
 /** Frees SSegOptions.
  * @param seg_options object to free [in]
  * @return NULL pointer
  */
+NCBI_XBLAST_EXPORT
 SSegOptions* SSegOptionsFree(SSegOptions* seg_options);
 
 /** Allocates memory for SSegOptions, fills in defaults. [in|out]
  * @param seg_options options that are being returned [in|out]
  * @return zero on sucess
  */
+NCBI_XBLAST_EXPORT
 Int2 SSegOptionsNew(SSegOptions* *seg_options);
 
 /** Resets name of db for repeat filtering.
@@ -466,24 +464,28 @@ Int2 SSegOptionsNew(SSegOptions* *seg_options);
  * @param dbname name of the database(s) [in]
  * @return zero on sucess
  */
+NCBI_XBLAST_EXPORT
 Int2 SRepeatFilterOptionsResetDB(SRepeatFilterOptions* *repeat_options, const char* dbname);
 
 /** Frees SRepeatFilterOptions.
  * @param repeat_options object to free [in]
  * @return NULL pointer
  */
+NCBI_XBLAST_EXPORT
 SRepeatFilterOptions* SRepeatFilterOptionsFree(SRepeatFilterOptions* repeat_options);
 
 /** Allocates memory for SRepeatFilterOptions, fills in defaults.
  * @param repeat_options options that are being returned [in|out]
  * @return zero on sucess
  */
+NCBI_XBLAST_EXPORT
 Int2 SRepeatFilterOptionsNew(SRepeatFilterOptions* *repeat_options);
 
 /** Frees SBlastFilterOptions and all subservient structures.
  * @param filter_options object to free
  * @return NULL pointer
  */
+NCBI_XBLAST_EXPORT
 SBlastFilterOptions* SBlastFilterOptionsFree(SBlastFilterOptions* filter_options);
 
 /**  Merges two sets of options together, taking the non-default one as preferred.  if
@@ -493,6 +495,7 @@ SBlastFilterOptions* SBlastFilterOptionsFree(SBlastFilterOptions* filter_options
  * @param opt2 second set of options [in]
  * @return zero on success. 
  */
+NCBI_XBLAST_EXPORT
 Int2 SBlastFilterOptionsMerge(SBlastFilterOptions** combined, const SBlastFilterOptions* opt1,
        const SBlastFilterOptions* opt2);
 
@@ -510,12 +513,14 @@ typedef enum EFilterOptions {
  * @param type specify either dust or seg (now) with EFilterOptions [in]
  * @return zero on sucess
  */
+NCBI_XBLAST_EXPORT
 Int2 SBlastFilterOptionsNew(SBlastFilterOptions* *filter_options, EFilterOptions type);
 
 /** Queries whether masking should be done only for the lookup table or for the entire search.
  * @param filter_options the object to be queried [in]
  * @return TRUE or FALSE, FALSE if filter_options is NULL.
  */
+NCBI_XBLAST_EXPORT
 Boolean SBlastFilterOptionsMaskAtHash(const SBlastFilterOptions* filter_options);
 
 /** Validates filter options to ensure that program and options are consistent
@@ -525,6 +530,7 @@ Boolean SBlastFilterOptionsMaskAtHash(const SBlastFilterOptions* filter_options)
  * @param blast_message error or warning (optional) [out] 
  * @return zero on success
  */
+NCBI_XBLAST_EXPORT
 Int2 SBlastFilterOptionsValidate(EBlastProgramType program_number, const SBlastFilterOptions* filter_options, 
        Blast_Message* *blast_message);
 
@@ -604,10 +610,11 @@ BlastExtensionOptionsFree(BlastExtensionOptions* options);
 /** Allocate memory for BlastExtensionOptions and fill with default values.
  * @param program Program number (blastn, blastp, etc.) [in]
  * @param options The options that are being returned [out]
+ * @param gapped The search is gapped [in]
 */
 NCBI_XBLAST_EXPORT
 Int2
-BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions* *options);
+BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions* *options, Boolean gapped);
 
 /** Fill non-default values in the BlastExtensionOptions structure.
  * @param options The options structure [in] [out]
@@ -688,6 +695,7 @@ Int2 BlastScoringOptionsDup(BlastScoringOptions* *new_opt, const BlastScoringOpt
  * @param matrix_name New matrix name. If NULL, old matrix name is left 
  *                    as is. [in]
  */
+NCBI_XBLAST_EXPORT
 Int2 BlastScoringOptionsSetMatrix(BlastScoringOptions* opts,
                                   const char* matrix_name);
 
@@ -902,6 +910,7 @@ Int2 BLAST_ValidateOptions(EBlastProgramType program_number,
  * @param threshold returns suggested value [in|out]
  * @return zero on success
  */
+NCBI_XBLAST_EXPORT
 Int2 BLAST_GetSuggestedThreshold(EBlastProgramType program_number, 
                                  const char* matrixName, 
                                  double* threshold);
@@ -914,6 +923,7 @@ Int2 BLAST_GetSuggestedThreshold(EBlastProgramType program_number,
  * @param window_size returns suggested value [in|out]
  * @return zero on success
  */
+NCBI_XBLAST_EXPORT
 Int2 BLAST_GetSuggestedWindowSize(EBlastProgramType program_number, 
                                  const char* matrixName, 
                                  Int4* window_size);
diff --git a/algo/blast/core/blast_parameters.c b/algo/blast/core/blast_parameters.c
index a910dfc4..d1f832b5 100644
--- a/algo/blast/core/blast_parameters.c
+++ b/algo/blast/core/blast_parameters.c
@@ -1,4 +1,4 @@
-/* $Id: blast_parameters.c,v 1.36 2007/05/22 20:55:36 kazimird Exp $
+/* $Id: blast_parameters.c,v 1.38 2007/10/25 15:55:36 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -30,7 +30,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_parameters.c,v 1.36 2007/05/22 20:55:36 kazimird Exp $";
+    "$Id: blast_parameters.c,v 1.38 2007/10/25 15:55:36 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/blast_parameters.h>
@@ -186,6 +186,11 @@ BlastInitialWordParametersNew(EBlastProgramType program_number,
    p = *parameters = (BlastInitialWordParameters*)calloc(1, 
                                      sizeof(BlastInitialWordParameters));
 
+   if (Blast_ProgramIsPhiBlast(program_number))
+      p->ungapped_extension = FALSE;
+   else
+      p->ungapped_extension = TRUE;
+
    p->cutoffs = (BlastUngappedCutoffs *)calloc(
            (size_t)(query_info->last_context+1), sizeof(BlastUngappedCutoffs));
 
@@ -665,13 +670,14 @@ BlastHitSavingParametersNew(EBlastProgramType program_number,
    if (params == NULL)
       return 1;
 
+   params->do_sum_stats = options->do_sum_stats;
    params->options = (BlastHitSavingOptions *) options;
    /* Each context gets its own gapped cutoff data */
    params->cutoffs = (BlastGappedCutoffs *)calloc(
                                         (size_t)(query_info->last_context+1),
                                         sizeof(BlastGappedCutoffs));
 
-   if (options->do_sum_stats) {
+   if (params->do_sum_stats) {
       BlastLinkHSPParametersNew(program_number, gapped_calculation,
                                 &params->link_hsp_params);
 
@@ -695,6 +701,7 @@ BlastHitSavingParametersNew(EBlastProgramType program_number,
                   /* A nonpositive value of max_protein_gap disables linking */
                   params->link_hsp_params =
                       BlastLinkHSPParametersFree(params->link_hsp_params);
+                  params->do_sum_stats = FALSE;
               } else { /* the value of max_protein_gap is positive */
                   params->link_hsp_params->longest_intron = max_protein_gap;
               }
@@ -940,6 +947,9 @@ CalculateLinkHSPCutoffs(EBlastProgramType program, BlastQueryInfo* query_info,
  * ===========================================================================
  *
  * $Log: blast_parameters.c,v $
+ * Revision 1.38  2007/10/25 15:55:36  kazimird
+ * Synchronized with the C++ Toolkit.
+ *
  * Revision 1.36  2007/05/22 20:55:36  kazimird
  * Synchronized with the C++ Toolkit.
  *
diff --git a/algo/blast/core/blast_parameters.h b/algo/blast/core/blast_parameters.h
index 1c02aa97..82fd9a22 100644
--- a/algo/blast/core/blast_parameters.h
+++ b/algo/blast/core/blast_parameters.h
@@ -1,4 +1,4 @@
-/* $Id: blast_parameters.h,v 1.18 2007/05/22 20:55:36 kazimird Exp $
+/* $Id: blast_parameters.h,v 1.20 2007/10/25 15:55:36 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -115,6 +115,8 @@ typedef struct BlastInitialWordParameters {
                                         seeds? */
    Int4 nucl_score_table[256]; /**< the combined score of all match/mismatch
                                     combinations for aligning four bases */
+   Boolean ungapped_extension; /**< Should an ungapped extension be
+                                  performed? */
 } BlastInitialWordParameters;
     
 /** Computed values used as parameters for gapped alignments.
@@ -167,6 +169,9 @@ typedef struct BlastHitSavingParameters {
                                                is not done if NULL. */
    Boolean restricted_align; /**< TRUE if approximate score-only gapped
                                   alignment is used */
+   Boolean do_sum_stats;  /**< TRUE if sum stats will be used.  Can override the
+                                  do_sum_stats Boolean in the options if criteria for 
+                                  doing sum stats are not met.  */
 } BlastHitSavingParameters;
 
 /** Because approximate gapped alignment adds extra overhead,
diff --git a/algo/blast/core/blast_psi.c b/algo/blast/core/blast_psi.c
index 3299206c..58f6d8cf 100644
--- a/algo/blast/core/blast_psi.c
+++ b/algo/blast/core/blast_psi.c
@@ -1,6 +1,6 @@
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] =
-    "$Id: blast_psi.c,v 1.33 2006/11/21 17:07:09 papadopo Exp $";
+    "$Id: blast_psi.c,v 1.34 2007/12/07 18:25:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 /* ===========================================================================
  *
@@ -181,7 +181,9 @@ PSICreatePssmWithDiagnostics(const PSIMsa* msap,                    /* [in] */
     }
 
     status = _PSIComputeFreqRatios(msa, seq_weights, sbp, aligned_block, 
-                                   options->pseudo_count, internal_pssm);
+                                   options->pseudo_count, 
+                                   options->nsg_compatibility_mode,
+                                   internal_pssm);
     if (status != PSI_SUCCESS) {
         s_PSICreatePssmCleanUp(pssm, packed_msa, msa, aligned_block, 
                                seq_weights, internal_pssm);
diff --git a/algo/blast/core/blast_psi_priv.c b/algo/blast/core/blast_psi_priv.c
index 49f4b9e0..aa14067c 100644
--- a/algo/blast/core/blast_psi_priv.c
+++ b/algo/blast/core/blast_psi_priv.c
@@ -1,6 +1,6 @@
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] =
-    "$Id: blast_psi_priv.c,v 1.67 2006/12/05 22:03:00 camacho Exp $";
+    "$Id: blast_psi_priv.c,v 1.68 2007/12/07 18:25:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 /* ===========================================================================
  *
@@ -1801,6 +1801,7 @@ _PSIComputeFreqRatios(const _PSIMsa* msa,
                       const BlastScoreBlk* sbp,
                       const _PSIAlignedBlock* aligned_blocks,
                       Int4 pseudo_count,
+                      Boolean nsg_compatibility_mode,
                       _PSIInternalPssmData* internal_pssm)
 {
     /* Subscripts are indicated as follows: N_i, where i is a subscript of N */
@@ -1858,7 +1859,11 @@ _PSIComputeFreqRatios(const _PSIMsa* msa,
 
                 denominator = alpha + kBeta;
 
-                ASSERT(denominator != 0.0);
+                if (nsg_compatibility_mode && denominator == 0.0) {
+                    return PSIERR_UNKNOWN;
+                } else {
+                    ASSERT(denominator != 0.0);
+                }
                 qOverPEstimate = numerator/denominator;
 
                 /* Note artificial multiplication by standard probability
@@ -2449,241 +2454,3 @@ _PSISaveDiagnostics(const _PSIMsa* msa,
 
     return PSI_SUCCESS;
 }
-
-/*
- * ===========================================================================
- * $Log: blast_psi_priv.c,v $
- * Revision 1.67  2006/12/05 22:03:00  camacho
- * Minor fix for structure group customization
- *
- * Revision 1.66  2006/11/21 17:07:31  papadopo
- * rearrange headers
- *
- * Revision 1.65  2006/11/20 15:48:00  camacho
- * Relocation of dynamic array functions/definitions
- *
- * Revision 1.64  2006/11/15 16:19:53  camacho
- * Pacify compiler
- *
- * Revision 1.63  2006/11/14 17:24:12  camacho
- * eliminate compiler warning
- *
- * Revision 1.62  2006/11/14 15:37:19  camacho
- * PSSM engine performance optimizations
- *
- * Revision 1.61  2006/08/30 13:30:20  camacho
- * Remove inline
- *
- * Revision 1.60  2006/08/29 22:17:56  camacho
- * Use NCBISTDAA_TO_AMINOACID
- *
- * Revision 1.59  2006/04/19 19:16:49  camacho
- * Refactoring of structure group customization and addition of validation
- *
- * Revision 1.58  2006/02/16 18:47:18  camacho
- * + encoding translations for O and J
- *
- * Revision 1.57  2005/11/18 20:09:45  camacho
- * Fixes for backwards compatibility with C toolkit PSSM engine for certain corner
- * cases.
- *
- * Revision 1.56  2005/10/17 18:34:54  camacho
- * Remove abort() call when sequence weights are not checked
- *
- * Revision 1.55  2005/10/05 14:09:30  camacho
- * Port change in revision 6.76 of posit.c
- *
- * Revision 1.54  2005/10/03 20:42:41  camacho
- * Minor
- *
- * Revision 1.53  2005/04/21 20:26:57  camacho
- * Relax validation in s_PSIValidateAlignedColumns so that query sequence can be
- * the only aligned sequence for a given column of the multiple sequence
- * alignment.
- *
- * Revision 1.52  2005/03/22 15:35:10  camacho
- * Fix to enable backwards compatibility with old PSSM engine when the query is
- * the only sequence aligned for a given column of the multiple sequence
- * alignment.
- *
- * Revision 1.51  2005/03/07 18:46:05  camacho
- * Removed dead code
- *
- * Revision 1.50  2005/02/23 17:32:57  camacho
- * Minor
- *
- * Revision 1.49  2005/02/23 17:24:41  camacho
- * 1. Moved prototype of _PSIUpdateLambdaK to blast_psi_priv.h
- * 2. Removed unneeded fields from Kappa_compactSearchItems
- * 3. Doxygen fixes
- *
- * Revision 1.48  2005/02/22 22:49:55  camacho
- * + impala_scaling_factor, first cut
- *
- * Revision 1.47  2005/02/14 14:07:49  camacho
- * Changes to use SBlastScoreMatrix
- *
- * Revision 1.46  2005/01/31 16:50:21  camacho
- * 1. Moved constants to private header.
- * 2. Changed signature of functions to copy matrices.
- *
- * Revision 1.45  2004/12/15 16:19:27  camacho
- * Remove compiler warning
- *
- * Revision 1.44  2004/12/15 03:17:11  ucko
- * Revert previous change, as VERIFY is not necessarily #defined.
- *
- * Revision 1.43  2004/12/15 02:50:50  camacho
- * Replace ASSERT with VERIFY
- *
- * Revision 1.42  2004/12/13 22:26:59  camacho
- * Consolidated structure group customizations in option: nsg_compatibility_mode
- *
- * Revision 1.41  2004/12/09 15:22:56  dondosha
- * Renamed some functions dealing with BlastScoreBlk and Blast_KarlinBlk structures
- *
- * Revision 1.40  2004/12/08 15:06:01  camacho
- * Call _PSIUpdatePositionCounts is needed after purging query sequence for
- * structure group customization, thus this function has been changed to reset the
- * appropriate _PSIMsa fields so that residue counts/aligned sequences are
- * reported accurately.
- *
- * Revision 1.39  2004/12/07 22:07:34  camacho
- * Add sanity checks for purge identity threshold
- *
- * Revision 1.38  2004/11/29 13:53:23  camacho
- * Renamed Blast_ScoreFreq structure free function
- *
- * Revision 1.37  2004/11/23 21:48:21  camacho
- * Removed local initialization of ideal Karlin-Altschul parameters
- *
- * Revision 1.36  2004/11/22 14:38:48  camacho
- * + option to set % identity threshold to PSSM engine
- *
- * Revision 1.35  2004/11/18 16:25:32  camacho
- * Rename _PSIGetStandardProbabilities to BLAST_GetStandardAaProbabilities
- *
- * Revision 1.34  2004/11/15 16:54:36  camacho
- * break long lines
- *
- * Revision 1.33  2004/11/15 16:32:37  dondosha
- * Changed constant names and static functions names in accordance with C++ toolkit guidelines
- *
- * Revision 1.32  2004/11/15 14:21:43  camacho
- * Correction to _PSIValidateAlignedColumns when the query sequence should be accounted
- *
- * Revision 1.31  2004/11/02 20:37:30  camacho
- * Doxygen fixes
- *
- * Revision 1.30  2004/10/19 14:28:38  camacho
- * Fix memory access error
- *
- * Revision 1.29  2004/10/18 14:33:14  camacho
- * 1. Added validation routines
- * 2. Fixed bug in calculating sequence weights
- * 3. Expanded error codes
- *
- * Revision 1.28  2004/10/13 16:03:00  camacho
- * Add assertions as sanity checks
- *
- * Revision 1.27  2004/10/01 13:59:22  camacho
- * Use calloc where needed
- *
- * Revision 1.26  2004/09/23 19:51:44  camacho
- * Added sanity checks
- *
- * Revision 1.25  2004/09/17 02:06:34  camacho
- * Renaming of diagnostics structure fields
- *
- * Revision 1.24  2004/09/14 21:17:02  camacho
- * Add structure group customization to ignore query
- *
- * Revision 1.23  2004/08/31 16:13:28  camacho
- * Documentation changes
- *
- * Revision 1.22  2004/08/13 22:32:16  camacho
- * Refactoring of _PSIPurgeSimilarAlignments to use finite state machine
- *
- * Revision 1.21  2004/08/04 20:18:26  camacho
- * 1. Renaming of structures and functions that pertain to the internals of PSSM
- *    engine.
- * 2. Updated documentation (in progress)
- *
- * Revision 1.20  2004/08/02 13:25:49  camacho
- * 1. Various renaming of structures, in progress
- * 2. Addition of PSIDiagnostics structures, in progress
- *
- * Revision 1.19  2004/07/29 19:16:02  camacho
- * Moved PSIExtractQuerySequenceInfo
- *
- * Revision 1.18  2004/07/22 19:06:18  camacho
- * 1. Fix in _PSICheckSequenceWeights.
- * 2. Added functions to calculate information content.
- * 3. Cleaned up PSIComputeFreqRatios.
- * 4. Removed unneeded code to set populate extra column in PSSMs.
- * 5. Added collection of information content and gapless column weights to
- * diagnostics structure
- *
- * Revision 1.17  2004/07/06 15:23:54  camacho
- * Fix memory acccess error
- *
- * Revision 1.16  2004/07/02 19:40:48  camacho
- * Fixes for handling out-of-memory conditions
- *
- * Revision 1.15  2004/07/02 18:00:25  camacho
- * 1. Document rationale for order in which sequences are compared in
- *    _PSIPurgeNearIdenticalAlignments.
- * 2. Fix in _PSIPurgeSimilarAlignments to take into account the X residues
- * 3. Refactorings in sequence weight calculation functions:
- *    - Simplification of _PSICheckSequenceWeights
- *    - Addition of _PSISpreadGapWeights
- *    - Reorganization of _PSICalculateNormalizedSequenceWeights
- *
- * Revision 1.14  2004/06/25 20:31:11  camacho
- * Remove C++ comments
- *
- * Revision 1.13  2004/06/25 20:16:50  camacho
- * 1. Minor fixes to sequence weights calculation
- * 2. Add comments
- *
- * Revision 1.12  2004/06/21 12:52:44  camacho
- * Replace PSI_ALPHABET_SIZE for BLASTAA_SIZE
- *
- * Revision 1.11  2004/06/17 20:47:21  camacho
- * Minor fix to extent sizes
- *
- * Revision 1.10  2004/06/16 15:22:47  camacho
- * Fixes to add new unit tests
- *
- * Revision 1.9  2004/06/09 14:21:03  camacho
- * Removed msvc compiler warnings
- *
- * Revision 1.8  2004/06/08 17:30:06  dondosha
- * Compiler warnings fixes
- *
- * Revision 1.7  2004/06/07 14:18:24  dondosha
- * Added some variables initialization, to remove compiler warnings
- *
- * Revision 1.6  2004/05/28 17:35:03  camacho
- * Fix msvc6 warnings
- *
- * Revision 1.5  2004/05/28 16:00:09  camacho
- * + first port of PSSM generation engine
- *
- * Revision 1.4  2004/05/19 14:52:02  camacho
- * 1. Added doxygen tags to enable doxygen processing of algo/blast/core
- * 2. Standardized copyright, CVS $Id string, $Log and rcsid formatting and i
- *    location
- * 3. Added use of @todo doxygen keyword
- *
- * Revision 1.3  2004/05/06 14:01:40  camacho
- * + _PSICopyDoubleMatrix
- *
- * Revision 1.2  2004/04/07 22:08:37  kans
- * needed to include blast_def.h for sfree prototype
- *
- * Revision 1.1  2004/04/07 19:11:17  camacho
- * Initial revision
- *
- * ===========================================================================
- */
diff --git a/algo/blast/core/blast_psi_priv.h b/algo/blast/core/blast_psi_priv.h
index a2078347..a8e04ffc 100644
--- a/algo/blast/core/blast_psi_priv.h
+++ b/algo/blast/core/blast_psi_priv.h
@@ -1,4 +1,4 @@
-/*  $Id: blast_psi_priv.h,v 1.33 2006/11/22 15:35:17 papadopo Exp $
+/*  $Id: blast_psi_priv.h,v 1.34 2007/12/07 18:25:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -347,6 +347,8 @@ _PSISequenceWeightsFree(_PSISequenceWeights* seq_weights);
 #define PSIERR_STARTINGGAP      (-10)
 /** Found flanking gap at end of alignment */
 #define PSIERR_ENDINGGAP        (-11)
+/** Unknown error */
+#define PSIERR_UNKNOWN          (-255)
 
 /****************************************************************************/
 /* Function prototypes for the various stages of the PSSM generation engine */
@@ -412,6 +414,8 @@ _PSIComputeSequenceWeights(const _PSIMsa* msa,
  * @param aligned_blocks data structure describing the aligned blocks'
  * properties for each position of the multiple sequence alignment [in]
  * @param pseudo_count pseudo count constant [in]
+ * @param nsg_compatibility_mode set to true to emulate the structure group's
+ * use of PSSM engine in the cddumper application. By default should be FALSE
  * @param internal_pssm PSSM being computed [out]
  * @return PSIERR_BADPARAM if arguments are NULL, PSI_SUCCESS otherwise
  */
@@ -421,6 +425,7 @@ _PSIComputeFreqRatios(const _PSIMsa* msa,
                       const BlastScoreBlk* sbp,
                       const _PSIAlignedBlock* aligned_blocks,
                       Int4 pseudo_count,
+                      Boolean nsg_compatibility_mode,
                       _PSIInternalPssmData* internal_pssm);
 
 /** Converts the PSSM's frequency ratios obtained in the previous stage to a 
@@ -625,126 +630,4 @@ _PSIValidateMSA_StructureGroup(const _PSIMsa* msa);
 }
 #endif
 
-
-/*
- * ===========================================================================
- *
- * $Log: blast_psi_priv.h,v $
- * Revision 1.33  2006/11/22 15:35:17  papadopo
- * doxygen fixes
- *
- * Revision 1.32  2006/11/21 17:07:38  papadopo
- * rearrange headers
- *
- * Revision 1.31  2006/11/14 15:37:19  camacho
- * PSSM engine performance optimizations
- *
- * Revision 1.30  2006/04/19 19:16:49  camacho
- * Refactoring of structure group customization and addition of validation
- *
- * Revision 1.29  2005/05/24 12:49:24  camacho
- * doxygen fix
- *
- * Revision 1.28  2005/05/10 16:07:51  camacho
- * Changed *_ENCODING #defines to EBlastEncoding enumeration
- *
- * Revision 1.27  2005/03/23 14:04:24  camacho
- * doxygen fix
- *
- * Revision 1.26  2005/03/22 15:35:10  camacho
- * Fix to enable backwards compatibility with old PSSM engine when the query is
- * the only sequence aligned for a given column of the multiple sequence
- * alignment.
- *
- * Revision 1.25  2005/02/28 13:40:11  camacho
- * Minor doxygen fix
- *
- * Revision 1.24  2005/02/23 17:24:41  camacho
- * 1. Moved prototype of _PSIUpdateLambdaK to blast_psi_priv.h
- * 2. Removed unneeded fields from Kappa_compactSearchItems
- * 3. Doxygen fixes
- *
- * Revision 1.23  2005/02/22 22:49:34  camacho
- * + impala_scaling_factor, first cut
- *
- * Revision 1.22  2005/01/31 16:50:21  camacho
- * 1. Moved constants to private header.
- * 2. Changed signature of functions to copy matrices.
- *
- * Revision 1.21  2004/12/13 22:26:59  camacho
- * Consolidated structure group customizations in option: nsg_compatibility_mode
- *
- * Revision 1.20  2004/12/08 15:06:02  camacho
- * Call _PSIUpdatePositionCounts is needed after purging query sequence for
- * structure group customization, thus this function has been changed to reset the
- * appropriate _PSIMsa fields so that residue counts/aligned sequences are
- * reported accurately.
- *
- * Revision 1.19  2004/12/07 22:07:34  camacho
- * Add sanity checks for purge identity threshold
- *
- * Revision 1.18  2004/11/26 14:22:54  camacho
- * doxygen fixes
- *
- * Revision 1.17  2004/11/22 14:38:48  camacho
- * + option to set % identity threshold to PSSM engine
- *
- * Revision 1.16  2004/11/18 16:25:32  camacho
- * Rename _PSIGetStandardProbabilities to BLAST_GetStandardAaProbabilities
- *
- * Revision 1.15  2004/11/02 20:37:30  camacho
- * Doxygen fixes
- *
- * Revision 1.14  2004/10/18 14:33:14  camacho
- * 1. Added validation routines
- * 2. Fixed bug in calculating sequence weights
- * 3. Expanded error codes
- *
- * Revision 1.13  2004/08/31 16:13:28  camacho
- * Documentation changes
- *
- * Revision 1.12  2004/08/04 20:18:26  camacho
- * 1. Renaming of structures and functions that pertain to the internals of PSSM
- *    engine.
- * 2. Updated documentation (in progress)
- *
- * Revision 1.11  2004/08/02 13:25:49  camacho
- * 1. Various renaming of structures, in progress
- * 2. Addition of PSIDiagnostics structures, in progress
- *
- * Revision 1.10  2004/07/29 19:16:02  camacho
- * Moved PSIExtractQuerySequenceInfo
- *
- * Revision 1.9  2004/07/22 19:05:58  camacho
- * 1. Removed information content from _PSISequenceWeights structure.
- * 2. Added functions to calculate information content.
- *
- * Revision 1.8  2004/07/02 17:57:57  camacho
- * Made _PSIUpdatePositionCounts non-static
- *
- * Revision 1.7  2004/06/21 12:52:44  camacho
- * Replace PSI_ALPHABET_SIZE for BLASTAA_SIZE
- *
- * Revision 1.6  2004/06/17 20:46:59  camacho
- * doxygen fixes
- *
- * Revision 1.5  2004/06/09 14:20:30  camacho
- * Updated comments
- *
- * Revision 1.4  2004/05/28 16:00:10  camacho
- * + first port of PSSM generation engine
- *
- * Revision 1.3  2004/05/06 14:01:40  camacho
- * + _PSICopyDoubleMatrix
- *
- * Revision 1.2  2004/04/07 21:43:47  camacho
- * Removed unneeded #include directive
- *
- * Revision 1.1  2004/04/07 19:11:17  camacho
- * Initial revision
- *
- *
- * ===========================================================================
- */
-
 #endif /* !ALGO_BLAST_CORE__BLAST_PSI_PRIV__H */
diff --git a/algo/blast/core/blast_query_info.h b/algo/blast/core/blast_query_info.h
index 8da94ef9..c799e3ce 100644
--- a/algo/blast/core/blast_query_info.h
+++ b/algo/blast/core/blast_query_info.h
@@ -1,4 +1,4 @@
-/* $Id: blast_query_info.h,v 1.4 2006/11/21 16:44:39 papadopo Exp $
+/* $Id: blast_query_info.h,v 1.5 2007/12/20 22:55:46 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -101,6 +101,7 @@ Int4 Blast_GetQueryIndexFromContext(Int4 context, EBlastProgramType program);
  * (query_index < BlastQueryInfo::num_queries) [in]
  * @return the search space of the query sequence requested or 0 if this is not
  * set */
+NCBI_XBLAST_EXPORT
 Int8
 BlastQueryInfoGetEffSearchSpace(const BlastQueryInfo* qinfo,
                                 EBlastProgramType program,
@@ -113,6 +114,7 @@ BlastQueryInfoGetEffSearchSpace(const BlastQueryInfo* qinfo,
  * (query_index < BlastQueryInfo::num_queries) [in]
  * @param eff_searchsp the effective search space to use [in]
  */
+NCBI_XBLAST_EXPORT
 void
 BlastQueryInfoSetEffSearchSpace(BlastQueryInfo* qinfo,
                                 EBlastProgramType program,
@@ -127,6 +129,7 @@ BlastQueryInfoSetEffSearchSpace(BlastQueryInfo* qinfo,
  * (query_index < BlastQueryInfo::num_queries) [in]
  * @return the length of the query sequence requested
  */
+NCBI_XBLAST_EXPORT
 Int4 BlastQueryInfoGetQueryLength(const BlastQueryInfo* qinfo,
                                   EBlastProgramType program,
                                   Int4 query_index);
@@ -166,6 +169,7 @@ Int4 BSearchContextInfo(Int4 n, const BlastQueryInfo * A);
  * @param qinfo  Query info structure. [in/out]
  * @return Number of bytes for all queries and inter-query marks.
  */
+NCBI_XBLAST_EXPORT
 Uint4
 QueryInfo_GetSeqBufLen(const BlastQueryInfo* qinfo);
 
diff --git a/algo/blast/core/blast_seg.h b/algo/blast/core/blast_seg.h
index 7c02d818..70f2a1b5 100644
--- a/algo/blast/core/blast_seg.h
+++ b/algo/blast/core/blast_seg.h
@@ -1,4 +1,4 @@
-/* $Id: blast_seg.h,v 1.17 2006/11/21 16:45:08 papadopo Exp $
+/* $Id: blast_seg.h,v 1.18 2007/11/28 15:55:56 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -38,11 +38,11 @@
 #include <algo/blast/core/ncbi_std.h>
 #include <algo/blast/core/blast_def.h>
 
+
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-
 /** Structure to hold parameters for seg search.
  */
 typedef struct SegParameters
@@ -60,11 +60,13 @@ typedef struct SegParameters
 /** Allocated SeqParameter struct for proteins and fills with default values.
  * @return pointer to SegParameters
  */
+NCBI_XBLAST_EXPORT
 SegParameters* SegParametersNewAa (void);
 
 /** Free SegParameters structure
  * @param sparamsp object to be freed [in]
  */
+NCBI_XBLAST_EXPORT
 void SegParametersFree(SegParameters* sparamsp);
 
 /** Runs seg on a protein sequence in ncbistdaa.
@@ -76,6 +78,7 @@ void SegParametersFree(SegParameters* sparamsp);
  * @param seg_locs resulting locations for filtering [out]
  * @return zero on success
  */
+NCBI_XBLAST_EXPORT
 Int2 SeqBufferSeg (Uint1* sequence, Int4 length, Int4 offset,
                    SegParameters* sparamsp, BlastSeqLoc** seg_locs);
 
diff --git a/algo/blast/core/blast_seqsrc.c b/algo/blast/core/blast_seqsrc.c
index 77d62e70..d90c2d56 100644
--- a/algo/blast/core/blast_seqsrc.c
+++ b/algo/blast/core/blast_seqsrc.c
@@ -1,4 +1,4 @@
-/*  $Id: blast_seqsrc.c,v 1.34 2007/05/15 15:55:30 kazimird Exp $
+/*  $Id: blast_seqsrc.c,v 1.35 2008/02/14 15:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -36,7 +36,7 @@
 #ifndef SKIP_DOXYGEN_PROCESSING
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_seqsrc.c,v 1.34 2007/05/15 15:55:30 kazimird Exp $";
+    "$Id: blast_seqsrc.c,v 1.35 2008/02/14 15:55:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 #endif
 
@@ -259,8 +259,6 @@ BlastSeqSrcReleaseSequence(const BlastSeqSrc* seq_src,
 #ifdef KAPPA_PRINT_DIAGNOSTICS
 
 static const size_t kInitialGiListSize = 10;
-const Int2 kBadParameter = -1;
-const Int2 kOutOfMemory = -2;
 
 Blast_GiList*
 Blast_GiListNew(void)
@@ -280,7 +278,7 @@ Blast_GiListNewEx(size_t list_size)
     if ( !retval->data ) {
         return Blast_GiListFree(retval);
     }
-    retval->num_allocated = kInitialGiListSize;
+    retval->num_allocated = list_size;
 
     return retval;
 }
diff --git a/algo/blast/core/blast_seqsrc.h b/algo/blast/core/blast_seqsrc.h
index ca4a6d48..bf626984 100644
--- a/algo/blast/core/blast_seqsrc.h
+++ b/algo/blast/core/blast_seqsrc.h
@@ -1,4 +1,4 @@
-/*  $Id: blast_seqsrc.h,v 1.47 2007/05/08 13:25:30 kazimird Exp $
+/*  $Id: blast_seqsrc.h,v 1.48 2007/08/28 17:25:29 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -195,12 +195,22 @@ typedef struct BlastSeqSrcGetSeqArg {
      * eBlastEncodingNucleotide, etc [in] */
     EBlastEncoding encoding;
 
-    /** Specify true here to disable this OID's ranges before fetching.
+    /** Specify true here to disable this OID's ranges before
+     * fetching.  OID ranges are a (somewhat complicated) performance
+     * feature that allows less nucleotide unpacking to be done in
+     * some cases.  If in doubt, specify FALSE here.
      * TRUE to disable ranges, FALSE to use them if they exist [in] */
     Boolean enable_ranges;
 
-    /** Sequence to return, if NULL, it should allocated by GetSeqBlkFnPtr, else
-     * its contents are freed and the structure is reused [out]*/
+    /** Check whether an OID is excluded due to overlapping filtering.
+     * The disease is rare, and the test for it is somewhat expensive,
+     * so it is deferred to the traceback stage.
+     * TRUE to disable ranges, FALSE to use them if they exist [in] */
+    Boolean check_oid_exclusion;
+
+    /** Sequence to return, if NULL, it should allocated by GetSeqBlkFnPtr
+     * (using BlastSeqBlkNew or BlastSetUp_SeqBlkNew), else its contents are 
+     * freed (using BlastSequenceBlkClean) and the structure is reused [out]*/
     BLAST_SequenceBlk* seq;
 } BlastSeqSrcGetSeqArg;
 
@@ -220,7 +230,7 @@ Int2
 BlastSeqSrcGetSequence(const BlastSeqSrc* seq_src, 
                        void* sequence);
 
-/** Retrieve sequence length.
+/** Retrieve sequence length (number of residues/bases)
  * @param seq_src the BLAST sequence source [in]
  * @param oid ordinal id of the sequence desired (should be Uint4) [in]
  */
diff --git a/algo/blast/core/blast_setup.h b/algo/blast/core/blast_setup.h
index 70e6275c..0772062a 100644
--- a/algo/blast/core/blast_setup.h
+++ b/algo/blast/core/blast_setup.h
@@ -1,4 +1,4 @@
-/*  $Id: blast_setup.h,v 1.64 2007/04/26 20:55:30 kazimird Exp $
+/*  $Id: blast_setup.h,v 1.65 2007/12/20 22:55:46 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -211,6 +211,7 @@ Int2 BlastSetup_ScoreBlkInit(BLAST_SequenceBlk* query_blk,
  * @param from Starting offset of a sequence interval [in]
  * @param to Ending offset of a sequence interval [in]
  */
+NCBI_XBLAST_EXPORT
 void
 BlastSeqLoc_RestrictToInterval(BlastSeqLoc* *mask, Int4 from, Int4 to);
 
@@ -226,6 +227,7 @@ BlastSeqLoc_RestrictToInterval(BlastSeqLoc* *mask, Int4 from, Int4 to);
  * @param blast_message will be filled in if pattern not found on query [in][out]
  * @return Status, 0 on success, -1 on error.
  */
+NCBI_XBLAST_EXPORT
 Int2 
 Blast_SetPHIPatternInfo(EBlastProgramType            program,
                         const SPHIPatternSearchBlk * pattern_blk,
@@ -239,6 +241,7 @@ Blast_SetPHIPatternInfo(EBlastProgramType            program,
  * @note In the case of a Blast2Sequences search, this function assumes a
  * single sequence and returns the length of the first sequence only
  */
+NCBI_XBLAST_EXPORT
 void
 BLAST_GetSubjectTotals(const BlastSeqSrc* seqsrc,
                        Int8* total_length,
diff --git a/algo/blast/core/blast_stat.c b/algo/blast/core/blast_stat.c
index 25a3a764..99c37e44 100644
--- a/algo/blast/core/blast_stat.c
+++ b/algo/blast/core/blast_stat.c
@@ -1,4 +1,4 @@
-/* $Id: blast_stat.c,v 1.157 2007/05/22 20:55:36 kazimird Exp $
+/* $Id: blast_stat.c,v 1.158 2007/09/24 14:55:29 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -50,7 +50,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_stat.c,v 1.157 2007/05/22 20:55:36 kazimird Exp $";
+    "$Id: blast_stat.c,v 1.158 2007/09/24 14:55:29 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/blast_stat.h>
@@ -2491,7 +2491,16 @@ Blast_ScoreBlkKbpUngappedCalc(EBlastProgramType program,
    stdrfp = Blast_ResFreqFree(stdrfp);
 
    if (valid_context == FALSE)
-     status = 1;  /* Not a single context was valid. */
+   {   /* No valid contexts were found. */
+       /* Message for non-translated search issued above. */
+       if (Blast_QueryIsTranslated(program) ) {
+            Blast_MessageWrite(blast_message, eBlastSevWarning, kBlastMessageNoContext,
+                "Could not calculate ungapped Karlin-Altschul parameters due "
+                "to an invalid query sequence or its translation. Please verify the "
+                "query sequence(s) and/or filtering options");
+       }
+       status = 1;  /* Not a single context was valid. */
+   }
 
    /* Set ungapped Blast_KarlinBlk* alias */
    sbp->kbp = Blast_QueryIsPssm(program) ? sbp->kbp_psi : sbp->kbp_std;
diff --git a/algo/blast/core/blast_traceback.c b/algo/blast/core/blast_traceback.c
index 1605621f..33526f9d 100644
--- a/algo/blast/core/blast_traceback.c
+++ b/algo/blast/core/blast_traceback.c
@@ -1,4 +1,4 @@
-/* $Id: blast_traceback.c,v 1.204 2007/07/27 18:25:30 kazimird Exp $
+/* $Id: blast_traceback.c,v 1.206 2007/12/07 18:25:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -50,7 +50,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: blast_traceback.c,v 1.204 2007/07/27 18:25:30 kazimird Exp $";
+    "$Id: blast_traceback.c,v 1.206 2007/12/07 18:25:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/blast_traceback.h>
@@ -455,7 +455,7 @@ Blast_TracebackFromHSPList(EBlastProgramType program_number,
               query_info->contexts[hsp->context].query_offset;
           query_length = query_info->contexts[hsp->context].query_length;
       }
-      
+
       /* preliminary RPS blast alignments have not had
          the composition-based correction applied yet, so
          we cannot reliably check whether an HSP is contained
@@ -1200,6 +1200,8 @@ BLAST_ComputeTraceback(EBlastProgramType program_number,
             seq_arg.oid = batch->hsplist_array[0]->oid;
             seq_arg.encoding = encoding;
             seq_arg.enable_ranges = kSubjectRanges;
+            seq_arg.check_oid_exclusion = TRUE;
+            
             BlastSequenceBlkClean(seq_arg.seq);
             if (BlastSeqSrcGetSequence(seq_src, (void*) &seq_arg) < 0) {
                Blast_HSPStreamResultBatchReset(batch);
@@ -1314,7 +1316,7 @@ BLAST_ComputeTraceback(EBlastProgramType program_number,
 
       }         /* loop over all batches */
 
-      Blast_HSPStreamResultBatchFree(batch);
+      batch = Blast_HSPStreamResultBatchFree(batch);
       BlastSequenceBlkFree(seq_arg.seq);
    }
 
diff --git a/algo/blast/core/hspstream_collector.c b/algo/blast/core/hspstream_collector.c
index e10be08c..d6a2ce04 100644
--- a/algo/blast/core/hspstream_collector.c
+++ b/algo/blast/core/hspstream_collector.c
@@ -1,4 +1,4 @@
-/*  $Id: hspstream_collector.c,v 1.19 2007/07/27 18:25:30 kazimird Exp $
+/*  $Id: hspstream_collector.c,v 1.22 2008/02/14 15:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -34,7 +34,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: hspstream_collector.c,v 1.19 2007/07/27 18:25:30 kazimird Exp $";
+    "$Id: hspstream_collector.c,v 1.22 2008/02/14 15:55:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 
@@ -50,11 +50,18 @@ static char const rcsid[] =
 static BlastHSPStream* 
 s_BlastHSPListCollectorFree(BlastHSPStream* hsp_stream) 
 {
+   int index=0;
    BlastHSPListCollectorData* stream_data = 
       (BlastHSPListCollectorData*) GetData(hsp_stream);
    stream_data->x_lock = MT_LOCK_Delete(stream_data->x_lock);
    SBlastHitsParametersFree(stream_data->blasthit_params);
    Blast_HSPResultsFree(stream_data->results);
+   for (index=0; index < stream_data->num_hsplists; index++)
+   {
+        stream_data->sorted_hsplists[index] =
+            Blast_HSPListFree(stream_data->sorted_hsplists[index]);
+   }
+   sfree(stream_data->sort_by_score);
    sfree(stream_data->sorted_hsplists);
    sfree(stream_data);
    sfree(hsp_stream);
@@ -90,6 +97,19 @@ s_BlastHSPListCollectorClose(BlastHSPStream* hsp_stream)
    if (stream_data->results == NULL || stream_data->results_sorted)
       return;
 
+   if (stream_data->sort_by_score) {
+       if (stream_data->sort_by_score->sort_on_read) {
+           Blast_HSPResultsReverseSort(stream_data->results);
+       } else {
+           /* Reverse the order of HSP lists, because they will be returned
+              starting from end, for the sake of convenience */
+           Blast_HSPResultsReverseOrder(stream_data->results);
+       }
+       stream_data->results_sorted = TRUE;
+       stream_data->x_lock = MT_LOCK_Delete(stream_data->x_lock);
+       return;
+   }
+
    results = stream_data->results;
    num_hsplists = stream_data->num_hsplists;
 
@@ -168,13 +188,47 @@ s_BlastHSPListCollectorRead(BlastHSPStream* hsp_stream,
    if (!stream_data->results_sorted)
       s_BlastHSPListCollectorClose(hsp_stream);
 
-   /* return the next HSPlist out of the collection stored */
+   if (stream_data->sort_by_score) {
+       Int4 last_hsplist_index = -1, index = 0;
+       BlastHitList* hit_list = NULL;
+       BlastHSPResults* results = stream_data->results;
+
+       /* Find index of the first query that has results. */
+       for (index = stream_data->sort_by_score->first_query_index; 
+            index < results->num_queries; ++index) {
+          if (results->hitlist_array[index] && 
+              results->hitlist_array[index]->hsplist_count > 0)
+             break;
+       }
+       if (index >= results->num_queries)
+          return kBlastHSPStream_Eof;
+
+       stream_data->sort_by_score->first_query_index = index;
+
+       hit_list = results->hitlist_array[index];
+       last_hsplist_index = hit_list->hsplist_count - 1;
+
+       *hsp_list_out = hit_list->hsplist_array[last_hsplist_index];
+       /* Assign the query index here so the caller knows which query this HSP 
+          list comes from */
+       (*hsp_list_out)->query_index = index;
+       /* Dequeue this HSP list by decrementing the HSPList count */
+       --hit_list->hsplist_count;
+       if (hit_list->hsplist_count == 0) {
+          /* Advance the first query index, without checking that the next
+           * query has results - that will be done on the next call. */
+          ++stream_data->sort_by_score->first_query_index;
+       }
+   } else {
+       /* return the next HSPlist out of the collection stored */
 
-   if (!stream_data->num_hsplists)
-      return kBlastHSPStream_Eof;
+       if (!stream_data->num_hsplists)
+          return kBlastHSPStream_Eof;
 
-   *hsp_list_out = stream_data->sorted_hsplists[--stream_data->num_hsplists];
+       *hsp_list_out = 
+           stream_data->sorted_hsplists[--stream_data->num_hsplists];
 
+   }
    return kBlastHSPStream_Success;
 }
 
@@ -355,6 +409,16 @@ fprintf(stderr, "No hits to query %d\n", global_query);
                           SplitQueryBlk_GetChunkOverlapSize(squery_blk));
    }
 
+   /* Sort to the canonical order, which the merge may not have done. */
+   for (i = 0; i < results2->num_queries; i++) {
+       BlastHitList *hitlist = results2->hitlist_array[i];
+       if (hitlist == NULL)
+           continue;
+
+       for (j = 0; j < hitlist->hsplist_count; j++)
+           Blast_HSPListSortByScore(hitlist->hsplist_array[j]);
+   }
+
    stream2->results_sorted = FALSE;
 
 #if _DEBUG_VERBOSE
@@ -471,6 +535,8 @@ s_BlastHSPListCollectorNew(BlastHSPStream* hsp_stream, void* args)
 BlastHSPStream* 
 Blast_HSPListCollectorInitMT(EBlastProgramType program, 
                              SBlastHitsParameters* blasthit_params,
+                             const BlastExtensionOptions* extn_opts,
+                             Boolean sort_on_read,
                              Int4 num_queries, MT_LOCK lock)
 {
     BlastHSPListCollectorData* stream_data = 
@@ -488,6 +554,18 @@ Blast_HSPListCollectorInitMT(EBlastProgramType program,
     stream_data->results = Blast_HSPResultsNew(num_queries);
 
     stream_data->results_sorted = FALSE;
+
+    /* This is needed to meet a pre-condition of the composition-based
+     * statistics code */
+    if ((Blast_QueryIsProtein(program) || Blast_QueryIsPssm(program)) &&
+        extn_opts->compositionBasedStats != 0) {
+        stream_data->sort_by_score = 
+            (SSortByScoreStruct*)calloc(0, sizeof(SSortByScoreStruct));
+        stream_data->sort_by_score->sort_on_read = sort_on_read;
+        stream_data->sort_by_score->first_query_index = 0;
+    } else {
+        stream_data->sort_by_score = NULL;
+    }
     stream_data->x_lock = lock;
 
     info.constructor = &s_BlastHSPListCollectorNew;
@@ -499,9 +577,11 @@ Blast_HSPListCollectorInitMT(EBlastProgramType program,
 BlastHSPStream* 
 Blast_HSPListCollectorInit(EBlastProgramType program, 
                            SBlastHitsParameters* blasthit_params,
+                           const BlastExtensionOptions* extn_opts,
+                           Boolean sort_on_read,
                            Int4 num_queries)
 {
-   return Blast_HSPListCollectorInitMT(program, blasthit_params, 
-                                       num_queries, NULL);
+   return Blast_HSPListCollectorInitMT(program, blasthit_params, extn_opts,
+                                       sort_on_read, num_queries, NULL);
 }
 
diff --git a/algo/blast/core/hspstream_collector.h b/algo/blast/core/hspstream_collector.h
index df076c96..e7cc5bc8 100644
--- a/algo/blast/core/hspstream_collector.h
+++ b/algo/blast/core/hspstream_collector.h
@@ -1,4 +1,4 @@
-/*  $Id: hspstream_collector.h,v 1.9 2007/07/27 18:25:30 kazimird Exp $
+/*  $Id: hspstream_collector.h,v 1.10 2008/02/14 15:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -46,6 +46,15 @@
 extern "C" {
 #endif
 
+/** Auxiliary structure to allow sorting the results by score for the
+ * composition-based statistics code */
+typedef struct SSortByScoreStruct {
+    Boolean sort_on_read;    /**< Should the results be sorted on the first read
+                               call? */
+    Int4 first_query_index;  /**< Index of the first query to try getting
+                               results from */
+} SSortByScoreStruct;
+
 /** Default implementation of BlastHSPStream */
 typedef struct BlastHSPListCollectorData {
    EBlastProgramType program;           /**< BLAST program type */
@@ -59,6 +68,10 @@ typedef struct BlastHSPListCollectorData {
    BlastHSPResults* results;/**< Structure for saving HSP lists */
    Boolean results_sorted;  /**< Have the results already been sorted? 
                                Set to true after the first read call. */
+   /**< Non-NULL if the results should be sorted by score as opposed to subject
+    * OID. This is necessary to meet a pre-condition of the composition-based
+    * statistics processing */
+   SSortByScoreStruct* sort_by_score;
    MT_LOCK x_lock;   /**< Mutex for writing and reading results. */
                                   
 } BlastHSPListCollectorData;
@@ -67,6 +80,10 @@ typedef struct BlastHSPListCollectorData {
  * locking facility must be instantiated before this function is called. 
  * @param program Type of BlAST program [in]
  * @param blasthit_params Specifies how many hits to save etc. [in]
+ * @param extn_opts Extension options to determine composition-based statistics
+ * mode [in]
+ * @param sort_on_read Should results be sorted on the first read call? Only
+ * applicable if composition-based statistics is on [in]
  * @param num_queries Number of query sequences in this BLAST search [in]
  * @param lock        Pointer to locking structure for writing by multiple
  *                    threads. Locking will not be performed if NULL. [in]
@@ -74,17 +91,25 @@ typedef struct BlastHSPListCollectorData {
 BlastHSPStream* 
 Blast_HSPListCollectorInitMT(EBlastProgramType program, 
                              SBlastHitsParameters* blasthit_params, 
+                             const BlastExtensionOptions* extn_opts,
+                             Boolean sort_on_read,
                              Int4 num_queries, MT_LOCK lock);
 
 /** Initialize the collector HSP stream for a single-threaded search, i.e. 
  * no locking is done when reading/writing from/to the stream.
  * @param program Type of BlAST program [in]
  * @param blasthit_params Specifies how many hits to save etc. [in]
+ * @param extn_opts Extension options to determine composition-based statistics
+ * mode [in]
+ * @param sort_on_read Should results be sorted on the first read call? Only
+ * applicable if composition-based statistics is on [in]
  * @param num_queries Number of query sequences in this BLAST search [in]
  */
 BlastHSPStream* 
 Blast_HSPListCollectorInit(EBlastProgramType program, 
                            SBlastHitsParameters* blasthit_params, 
+                           const BlastExtensionOptions* extn_opts,
+                           Boolean sort_on_read,
                            Int4 num_queries);
 
 #ifdef __cplusplus
diff --git a/algo/blast/core/lookup_wrap.c b/algo/blast/core/lookup_wrap.c
index a1d835f3..1759c3a1 100644
--- a/algo/blast/core/lookup_wrap.c
+++ b/algo/blast/core/lookup_wrap.c
@@ -1,4 +1,4 @@
-/* $Id: lookup_wrap.c,v 1.30 2007/03/07 19:25:34 kazimird Exp $
+/* $Id: lookup_wrap.c,v 1.31 2008/01/31 23:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -37,7 +37,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] = 
-    "$Id: lookup_wrap.c,v 1.30 2007/03/07 19:25:34 kazimird Exp $";
+    "$Id: lookup_wrap.c,v 1.31 2008/01/31 23:55:42 kazimird Exp $";
 #endif /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/lookup_wrap.h>
@@ -51,6 +51,7 @@ static char const rcsid[] =
 
 Int2 LookupTableWrapInit(BLAST_SequenceBlk* query, 
         const LookupTableOptions* lookup_options,	
+        const QuerySetUpOptions* query_options,
         BlastSeqLoc* lookup_segments, BlastScoreBlk* sbp, 
         LookupTableWrap** lookup_wrap_ptr, const BlastRPSInfo *rps_info,
         Blast_Message* *error_msg)
@@ -120,7 +121,7 @@ Int2 LookupTableWrapInit(BLAST_SequenceBlk* query,
           else if (lookup_wrap->lut_type == eSmallNaLookupTable) {
              status = BlastSmallNaLookupTableNew(query, lookup_segments,
                             (BlastSmallNaLookupTable* *) &(lookup_wrap->lut), 
-                             lookup_options, lut_width);
+                             lookup_options, query_options, lut_width);
              if (status != 0) {
                 lookup_wrap->lut_type = eNaLookupTable;
                 status = BlastNaLookupTableNew(query, lookup_segments,
diff --git a/algo/blast/core/lookup_wrap.h b/algo/blast/core/lookup_wrap.h
index 614b63c5..98b4cde5 100644
--- a/algo/blast/core/lookup_wrap.h
+++ b/algo/blast/core/lookup_wrap.h
@@ -1,4 +1,4 @@
-/* $Id: lookup_wrap.h,v 1.16 2006/11/21 16:50:02 papadopo Exp $
+/* $Id: lookup_wrap.h,v 1.18 2008/01/31 23:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -62,13 +62,16 @@ typedef struct LookupTableWrap {
  * @param rps_info Structure containing RPS blast setup information [in]
  * @param error_msg message with warning or errors [in|out]
  */
+NCBI_XBLAST_EXPORT
 Int2 LookupTableWrapInit(BLAST_SequenceBlk* query, 
         const LookupTableOptions* lookup_options,	
+        const QuerySetUpOptions* query_options,
         BlastSeqLoc* lookup_segments, BlastScoreBlk* sbp, 
         LookupTableWrap** lookup_wrap_ptr, const BlastRPSInfo *rps_info,
         Blast_Message* *error_msg);
 
 /** Deallocate memory for the lookup table */
+NCBI_XBLAST_EXPORT
 LookupTableWrap* LookupTableWrapFree(LookupTableWrap* lookup);
 
 /** Default size of offset arrays filled in a single ScanSubject call. */
@@ -77,6 +80,7 @@ LookupTableWrap* LookupTableWrapFree(LookupTableWrap* lookup);
 /** Determine the size of the offsets arrays to be filled by
  * the ScanSubject function.
  */
+NCBI_XBLAST_EXPORT
 Int4 GetOffsetArraySize(LookupTableWrap* lookup);
 
 #ifdef __cplusplus
diff --git a/algo/blast/core/na_ungapped.c b/algo/blast/core/na_ungapped.c
index 2d65821c..1421ad5f 100644
--- a/algo/blast/core/na_ungapped.c
+++ b/algo/blast/core/na_ungapped.c
@@ -1,4 +1,4 @@
-/* $Id: na_ungapped.c,v 1.10 2007/03/29 20:55:30 kazimird Exp $
+/* $Id: na_ungapped.c,v 1.13 2008/01/31 23:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -30,7 +30,7 @@
 
 #ifndef SKIP_DOXYGEN_PROCESSING
 static char const rcsid[] =
-    "$Id: na_ungapped.c,v 1.10 2007/03/29 20:55:30 kazimird Exp $";
+    "$Id: na_ungapped.c,v 1.13 2008/01/31 23:55:42 kazimird Exp $";
 #endif                          /* SKIP_DOXYGEN_PROCESSING */
 
 #include <algo/blast/core/na_ungapped.h>
@@ -419,7 +419,7 @@ s_BlastnDiagTableExtendInitialHit(BLAST_SequenceBlk * query,
         hit_ready = 1;
 
     if (hit_ready) {
-        if (word_params->options->ungapped_extension) {
+        if (word_params->ungapped_extension) {
             /* Perform ungapped extension */
             Int4 context = BSearchContextInfo(q_off, query_info);
             cutoffs = word_params->cutoffs + context;
@@ -536,7 +536,7 @@ s_BlastnDiagHashExtendInitialHit(BLAST_SequenceBlk * query,
             hit_ready = 1;
 
         if (hit_ready) {
-            if (word_params->options->ungapped_extension) {
+            if (word_params->ungapped_extension) {
                 /* Perform ungapped extension */
                 Int4 context = BSearchContextInfo(q_off, query_info);
                 cutoffs = word_params->cutoffs + context;
@@ -587,7 +587,7 @@ s_BlastnDiagHashExtendInitialHit(BLAST_SequenceBlk * query,
         /* Save the hit if it already qualifies */
         if (!two_hits) {
             hit_ready = 1;
-            if (word_params->options->ungapped_extension) {
+            if (word_params->ungapped_extension) {
                 /* Perform ungapped extension */
                 Int4 context = BSearchContextInfo(q_off, query_info);
                 cutoffs = word_params->cutoffs + context;
@@ -661,7 +661,7 @@ s_BlastNaExtendDirect(const BlastOffsetPair * offset_pairs, Int4 num_hits,
         lut_word_length = lut->lut_word_length;
         /* When ungapped extension is not performed, the hit will be new only 
            if it is more than scan_step away from the previous hit. */
-        if (!word_params->options->ungapped_extension)
+        if (!word_params->ungapped_extension)
             min_step = lut->scan_step;
         template_length = lut->template_length;
     } 
@@ -669,13 +669,13 @@ s_BlastNaExtendDirect(const BlastOffsetPair * offset_pairs, Int4 num_hits,
         BlastSmallNaLookupTable *lut = 
                         (BlastSmallNaLookupTable *) lookup_wrap->lut;
         lut_word_length = lut->lut_word_length;
-        if (!word_params->options->ungapped_extension)
+        if (!word_params->ungapped_extension)
             min_step = lut->scan_step;
     } 
     else {
         BlastNaLookupTable *lut = (BlastNaLookupTable *) lookup_wrap->lut;
         lut_word_length = lut->lut_word_length;
-        if (!word_params->options->ungapped_extension)
+        if (!word_params->ungapped_extension)
             min_step = lut->scan_step;
     }
 
@@ -757,7 +757,7 @@ s_BlastNaExtend(const BlastOffsetPair * offset_pairs, Int4 num_hits,
         BlastMBLookupTable *lut = (BlastMBLookupTable *) lookup_wrap->lut;
         word_length = lut->word_length;
         lut_word_length = lut->lut_word_length;
-        if (!word_params->options->ungapped_extension)
+        if (!word_params->ungapped_extension)
             min_step = lut->scan_step;
         template_length = lut->template_length;
     } 
@@ -765,7 +765,7 @@ s_BlastNaExtend(const BlastOffsetPair * offset_pairs, Int4 num_hits,
         BlastNaLookupTable *lut = (BlastNaLookupTable *) lookup_wrap->lut;
         word_length = lut->word_length;
         lut_word_length = lut->lut_word_length;
-        if (!word_params->options->ungapped_extension)
+        if (!word_params->ungapped_extension)
             min_step = lut->scan_step;
     }
     extra_bases = word_length - lut_word_length;
@@ -908,7 +908,7 @@ s_BlastNaExtendAligned(const BlastOffsetPair * offset_pairs, Int4 num_hits,
         BlastMBLookupTable *lut = (BlastMBLookupTable *) lookup_wrap->lut;
         word_length = lut->word_length;
         lut_word_length = lut->lut_word_length;
-        if (!word_params->options->ungapped_extension)
+        if (!word_params->ungapped_extension)
             min_step = lut->scan_step;
         template_length = lut->template_length;
     } 
@@ -1098,7 +1098,7 @@ s_BlastSmallNaExtendAlignedOneByte(const BlastOffsetPair * offset_pairs,
     Int4 hits_extended = 0;
     Int4 min_step = 0;
 
-    if (!word_params->options->ungapped_extension)
+    if (!word_params->ungapped_extension)
         min_step = lut->scan_step;
 
     for (i = 0; i < num_hits; i++) {
@@ -1147,10 +1147,10 @@ s_BlastSmallNaExtendAlignedOneByte(const BlastOffsetPair * offset_pairs,
                                            subject, min_step, 0, word_params, 
                                            matrix, query_info,
                                            ewp->hash_table,
-                                           q_off - extended_left,
+                                           q_off,
                                            s_off + lut_word_length +
                                                      extended_right,
-                                           s_off - extended_left,
+                                           s_off,
                                            init_hitlist);
         }
         else {
@@ -1158,16 +1158,47 @@ s_BlastSmallNaExtendAlignedOneByte(const BlastOffsetPair * offset_pairs,
                                            subject, min_step, 0, word_params, 
                                            matrix, query_info,
                                            ewp->diag_table,
-                                           q_off - extended_left,
+                                           q_off,
                                            s_off + lut_word_length +
                                                      extended_right,
-                                           s_off - extended_left,
+                                           s_off,
                                            init_hitlist);
         }
     }
     return hits_extended;
 }
 
+
+/** Check that word just found is not part of a soft-masked region.
+ * This check only happens for soft masking for certain word sizes
+ * @param locations not masked regions [in]
+ * @param offset query offset for for word [in]
+ * @param left_extend how far extended to left by mini-extension [in]
+ * @param right_extend how far extended to right by mini-extension [in]
+ */
+Boolean 
+s_SmallBlastnCheckLocations(BlastSeqLoc* locations,
+                            Int4 offset,
+                            Int4 left_extend,
+                            Int4 right_extend)
+{
+    Boolean retval = FALSE;
+    Int4 q_start = offset - left_extend;
+    Int4 q_end = offset + right_extend;
+    while (locations)
+    {
+       if ((q_end > locations->ssr->left && q_end < locations->ssr->right) ||
+          (q_start > locations->ssr->left && q_start < locations->ssr->right))
+       {
+          retval = TRUE;
+          break;
+       }
+       locations = locations->next;
+    }
+    return retval;
+
+}
+
 /** Perform exact match extensions on the hits retrieved from
  * small-query blastn lookup tables, assuming an arbitrary number of bases 
  * in a lookup and arbitrary start offset of each hit. Also 
@@ -1207,7 +1238,7 @@ s_BlastSmallNaExtend(const BlastOffsetPair * offset_pairs, Int4 num_hits,
     Int4 hits_extended = 0;
     Int4 min_step = 0;
 
-    if (!word_params->options->ungapped_extension)
+    if (!word_params->ungapped_extension)
         min_step = lut->scan_step;
 
     for (i = 0; i < num_hits; i++) {
@@ -1269,21 +1300,27 @@ s_BlastSmallNaExtend(const BlastOffsetPair * offset_pairs, Int4 num_hits,
         if (extended_left + extended_right < word_length)
             continue;
 
+        /* Check that the exact match was not masked out. */
+        if (word_length > lut_word_length && lut->masked_locations)
+            if (s_SmallBlastnCheckLocations(lut->masked_locations, q_off, extended_left, extended_right) == TRUE)
+                continue; 
+        
+
         if (word_params->container_type == eDiagHash) {
             hits_extended += s_BlastnDiagHashExtendInitialHit(query, subject, 
                                                min_step, 0, word_params, matrix,
                                                query_info, ewp->hash_table,
-                                               q_off - extended_left,
+                                               q_off,
                                                s_off + extended_right,
-                                               s_off - extended_left,
+                                               s_off,
                                                init_hitlist);
         } else {
             hits_extended += s_BlastnDiagTableExtendInitialHit(query, subject, 
                                                min_step, 0, word_params, matrix,
                                                query_info, ewp->diag_table,
-                                               q_off - extended_left,
+                                               q_off,
                                                s_off + extended_right,
-                                               s_off - extended_left,
+                                               s_off,
                                                init_hitlist);
         }
     }
@@ -1358,7 +1395,7 @@ Int2 BlastNaWordFinder(BLAST_SequenceBlk * subject,
     Blast_UngappedStatsUpdate(ungapped_stats, total_hits, hits_extended,
                               init_hitlist->total);
 
-    if (word_params->options->ungapped_extension)
+    if (word_params->ungapped_extension)
         Blast_InitHitListSortByScore(init_hitlist);
 
     return 0;
@@ -1394,7 +1431,7 @@ Int2 MB_IndexedWordFinder(
     ASSERT(get_results);
     word_size = get_results(lookup_wrap->lut, oid, chunk, init_hitlist);
 
-    if( word_size > 0 && word_params->options->ungapped_extension ) {
+    if( word_size > 0 && word_params->ungapped_extension ) {
         hash = ir_hash_create();
         new_hsp = hsp = init_hitlist->init_hsp_array;
         hsp_end = hsp + init_hitlist->total;
@@ -1439,7 +1476,7 @@ Int2 MB_IndexedWordFinder(
         hash = ir_hash_destroy( hash );
     }
 
-    if (word_params->options->ungapped_extension)
+    if (word_params->ungapped_extension)
         Blast_InitHitListSortByScore(init_hitlist);
 
     return 0;
diff --git a/api/alignval.c b/api/alignval.c
index 546e346e..e039db2e 100644
--- a/api/alignval.c
+++ b/api/alignval.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/3/99
 *
-* $Revision: 6.64 $
+* $Revision: 6.65 $
 *
 * File Description:  To validate sequence alignment.
 *
@@ -862,25 +862,26 @@ static void ValidateStrandInPack_DenseSeg(Pointer segs, Uint1 segtype, SeqAlignP
 { 
   DenseSegPtr dsp=NULL;
   PackSegPtr psp=NULL;
-  Int2         numseg, aligndim, dimnumseg, i, j, m;
+  Int4         numseg, aligndim, dimnumseg, i, j, m;
   SeqIdPtr     sip=NULL, siptemp;
   Uint1           strand1=0, strand2=0;
   Uint1Ptr strandptr=NULL;
         
   if(!segs)
+  {
     ValMessage (salp, Err_Null_Segs, SEV_ERROR, NULL, NULL, 0);
+  } 
   else if(segtype==2||segtype==4)
-    {
-      if(segtype==2)
+  {
+    if(segtype==2)
     {
       dsp=(DenseSegPtr)segs;
       strandptr=dsp->strands;
       sip=dsp->ids;
       numseg=dsp->numseg;
       aligndim=dsp->dim;
-    }
-      
-      else if(segtype==4)
+    }     
+    else if(segtype==4)
     {
       psp=(PackSegPtr)segs;
       strandptr=psp->strands;
@@ -888,44 +889,46 @@ static void ValidateStrandInPack_DenseSeg(Pointer segs, Uint1 segtype, SeqAlignP
       numseg=psp->numseg;
       aligndim=psp->dim;
     }
-      dimnumseg=numseg*aligndim;
-      if(strandptr)
-    {
-     
+
+    dimnumseg=numseg*aligndim;
+    if(strandptr)
+    {     
       /*go through id for each alignment sequence*/
       for(j=0; j<aligndim; j++)
-        {
-          /* first  strand value for each sequence*/ 
-          strand1=dsp->strands[j];
-          /* go through all strand values for each sequence*/  
-          for(i=j+aligndim; i<dimnumseg; i=i+aligndim)
+      {
+        /* first  strand value for each sequence*/ 
+        strand1=strandptr[j];
+        /* go through all strand values for each sequence*/  
+        for(i=j+aligndim; i<dimnumseg; i=i+aligndim)
         {          
-          strand2=dsp->strands[i];
+          strand2=strandptr[i];
           
           if(strand1==0||strand1==255)
-            {
-              strand1=strand2;
-              continue;
-            }
+          {
+            strand1=strand2;
+            continue;
+          }
           
           /*skip undefined strand*/
-          if(strand2!=0&&strand2!=255)
+          if(strand2!=0&&strand2!=255) 
+          {
             /*strand should be same for a given seq*/ 
             if(strand1!=strand2)
-              {
-            /*find current seqid*/
-            
-            siptemp=sip;
-            for(m=0; m<j&&siptemp!=NULL; m++)
-              siptemp=siptemp->next;
-            ValMessage (salp, Err_Strand_Rev, SEV_ERROR, siptemp, sip, i/aligndim+1);
-        
+            {
+              /*find current seqid*/
             
+              siptemp=sip;
+              for(m=0; m<j&&siptemp!=NULL; m++)
+              {
+                siptemp=siptemp->next;
               }
+              ValMessage (salp, Err_Strand_Rev, SEV_ERROR, siptemp, sip, i/aligndim+1);
+            }
+          }
         }
-        }
-    }
+      }
     }
+  }
 }
 
 
diff --git a/api/asn2gnb1.c b/api/asn2gnb1.c
index 4fe9828a..dd83ce73 100644
--- a/api/asn2gnb1.c
+++ b/api/asn2gnb1.c
@@ -28,11 +28,11 @@
 * Author:  Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans,
 *          Mati Shomrat
 *
-* $Id: asn2gnb1.c,v 1.135 2007/08/23 15:40:43 ludwigf Exp $
+* $Id: asn2gnb1.c,v 1.139 2007/12/04 18:55:29 kans Exp $
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.135 $
+* $Revision: 1.139 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -1020,7 +1020,9 @@ NLM_EXTERN void FFTrim (
 
 NLM_EXTERN int FFNextChar(
   StringItemPtr start_sip,
-  Int4 start_pos) {
+  Int4 start_pos
+)
+{
   if (start_pos < start_sip->pos-1) {
     return start_sip->buf[start_pos+1];
   }
@@ -1034,7 +1036,8 @@ NLM_EXTERN int FFNextChar(
 
 NLM_EXTERN void FFAdvanceChar(
   StringItemPtr* start_sip,
-  Int4* start_pos )
+  Int4* start_pos
+)
 {
   if (*start_pos < (*start_sip)->pos-1) {
     ++(*start_pos);
@@ -2623,8 +2626,8 @@ NLM_EXTERN void DoOneBioseq (
       if (bsp->idx.parenttype == OBJ_BIOSEQSET) {
         bssp = (BioseqSetPtr) bsp->idx.parentptr;
         if (bssp != NULL && bssp->_class == BioseqseqSet_class_nuc_prot) {
-          if (bsp->idx.parenttype == OBJ_BIOSEQSET) {
-            bssp = (BioseqSetPtr) bsp->idx.parentptr;
+          if (bssp->idx.parenttype == OBJ_BIOSEQSET) {
+            bssp = (BioseqSetPtr) bssp->idx.parentptr;
             if (bssp != NULL && bssp->_class == BioseqseqSet_class_gen_prod_set) {
               return;
             }
diff --git a/api/asn2gnb2.c b/api/asn2gnb2.c
index 0190e57c..c493bcc1 100644
--- a/api/asn2gnb2.c
+++ b/api/asn2gnb2.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.88 $
+* $Revision: 1.93 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -71,14 +71,16 @@ static CharPtr strd [4] = {
   "   ", "ss-", "ds-", "ms-"
 };
 
-static CharPtr gnbk_mol [14] = {
-  "    ", "DNA ", "RNA ", "mRNA", "rRNA", "tRNA", "snRNA", "scRNA", " AA ", "DNA ", "DNA ", "cRNA ", "snoRNA", "RNA "
+static CharPtr gnbk_mol [16] = {
+  "    ", "DNA ", "RNA ", "mRNA", "rRNA", "tRNA", "snRNA", "scRNA",
+  " AA ", "DNA ", "DNA ", "cRNA ", "snoRNA", "RNA ", "RNA ", "tmRNA "
 };
 
 /* EMBL_FMT in RELEASE_MODE or ENTREZ_MODE, otherwise use gnbk_mol */
 
-static CharPtr embl_mol [14] = {
-  "xxx", "DNA", "RNA", "RNA", "RNA", "RNA", "RNA", "RNA", "AA ", "DNA", "DNA", "RNA", "RNA", "RNA"
+static CharPtr embl_mol [16] = {
+  "xxx", "DNA", "RNA", "RNA", "RNA", "RNA", "RNA", "RNA",
+  "AA ", "DNA", "DNA", "RNA", "RNA", "RNA", "RNA", "RNA"
 };
 
 static CharPtr embl_divs [18] = {
@@ -86,8 +88,8 @@ static CharPtr embl_divs [18] = {
   "SYN", "UNA", "VRL", "VRT", "PAT", "EST", "STS", "HUM", "HTC"
 };
 
-static Uint1 imolToMoltype [14] = {
-  0, 1, 2, 5, 4, 3, 6, 7, 9, 1, 1, 2, 8, 2
+static Uint1 imolToMoltype [16] = {
+  0, 1, 2, 5, 4, 3, 6, 7, 9, 1, 1, 2, 8, 2, 2, 2
 };
 
 static DatePtr GetBestDate (
@@ -648,7 +650,7 @@ NLM_EXTERN void AddLocusBlock (
 
     mip = (MolInfoPtr) sdp->data.ptrvalue;
     if (mip != NULL) {
-      if (mip->biomol <= MOLECULE_TYPE_TRANSCRIBED_RNA) {
+      if (mip->biomol <= MOLECULE_TYPE_TMRNA) {
         imol = (Int2) mip->biomol;
       }
       tech = mip->tech;
@@ -721,7 +723,8 @@ NLM_EXTERN void AddLocusBlock (
   /* ss=any RNA don't show ss */
 
   if ((bmol > Seq_mol_rna ||
-      (imol >= MOLECULE_TYPE_MRNA && imol <= MOLECULE_TYPE_PEPTIDE)) &&
+      (imol >= MOLECULE_TYPE_MRNA && imol <= MOLECULE_TYPE_PEPTIDE) ||
+      (imol >= MOLECULE_TYPE_CRNA && imol <= MOLECULE_TYPE_TMRNA)) &&
       istrand == 1) {
     istrand = 0;
   }
@@ -1099,6 +1102,9 @@ NLM_EXTERN void AddLocusBlock (
       if (StringCmp (str, "viral cRNA") == 0) {
         str = "other RNA";
       }
+      if (StringICmp (str, "ncRNA") == 0) {
+        str = "RNA";
+      }
       StringNCpy_0 (mol, str, sizeof (mol));
 
       FFStartPrint (ffstring, awp->format, 0, 0, NULL, 0, 5, 0, "ID", FALSE);
@@ -2516,13 +2522,13 @@ static Boolean WriteDbsourceID (
       pfx = prefix;
       rsult = TRUE;
     }
-    if (tsip->version > 0) {
+    if (tsip->version > 0 && sip->choice != SEQID_SWISSPROT) {
       sprintf (tmp, ".%d", (int) tsip->version);
       StringCat (str, tmp);
       sfx = suffix;
       pfx = prefix;
     }
-    if (! StringHasNoText (tsip->release)) {
+    if (! StringHasNoText (tsip->release) && sip->choice != SEQID_SWISSPROT) {
       StringCat (str, pfx);
       StringCat (str, "release ");
       StringCat (str, tsip->release);
@@ -2757,6 +2763,25 @@ static void AddSPBlock (
     } else {
       FFAddOneString (ffstring, ", ", FALSE, FALSE, TILDE_IGNORE);
     }
+
+    str = NULL;
+    if ( oip->str != NULL ) {
+      str = oip->str;
+      if (StringNCmp (str, "GO:", 3) == 0) {
+        str += 3;
+      } else if (StringNCmp (str, "MGI:", 4) == 0) {
+        str += 4;
+      } else if (StringNCmp (str, "HGNC:", 5) == 0) {
+        str += 5;
+      }
+    } else if ( oip->id > 0 ) {
+      sprintf (numbuf, "%d", oip->id);
+      str = numbuf;
+    }
+
+    FF_www_db_xref (ajp, ffstring, db->db, str, bsp);
+
+    /*
     if (StringCmp (db->db, "MGD") == 0 || StringCmp (db->db, "MGI") == 0) {
       FFAddOneString (ffstring, "MGI", FALSE, FALSE, TILDE_IGNORE);
     } else {
@@ -2791,6 +2816,7 @@ static void AddSPBlock (
         FFAddOneString(ffstring, str, FALSE, FALSE, TILDE_IGNORE);
       }
     }
+    */
   }
 }
 
@@ -2958,32 +2984,28 @@ static void AddPRFBlock (
 
     if (extra->host != NULL) {
       FFAddTextToString(ffstring, "host:", extra->host, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
+      prefix = ";\n";
     }
 
     if (extra->part != NULL) {
       FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
       FFAddTextToString(ffstring, "part: ", extra->part, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
+      prefix = ";\n";
     }
     if (extra->state != NULL) {
       FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
       FFAddTextToString(ffstring, "state: ", extra->state, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
+      prefix = ";\n";
     }
     if (extra->strain != NULL) {
       FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
       FFAddTextToString(ffstring, "strain: ", extra->strain, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
+      prefix = ";\n";
     }
     if (extra->taxon != NULL) {
       FFAddOneString(ffstring, prefix, FALSE, FALSE, TILDE_IGNORE);
-      FFAddNewLine(ffstring);
       FFAddTextToString(ffstring, "taxonomy: ", extra->taxon, NULL, FALSE, TRUE, TILDE_IGNORE);
-      prefix = ";";
+      prefix = ";\n";
     }
 
     FFAddOneChar(ffstring, '.', FALSE);
@@ -3683,6 +3705,14 @@ NLM_EXTERN void AddKeywordsBlock (
           }
           ValNodeCopyStr (&head, 0, "BARCODE");
           break;
+        case MI_TECH_tsa :
+          if (head != NULL) {
+            ValNodeCopyStr (&head, 0, "; ");
+          }
+          ValNodeCopyStr (&head, 0, "TSA");
+          ValNodeCopyStr (&head, 0, "; ");
+          ValNodeCopyStr (&head, 0, "Transcriptome Shotgun Assembly");
+          break;
         case MI_TECH_unknown :
         case MI_TECH_standard :
         case MI_TECH_other :
diff --git a/api/asn2gnb3.c b/api/asn2gnb3.c
index b1110614..edd95a04 100644
--- a/api/asn2gnb3.c
+++ b/api/asn2gnb3.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.75 $
+* $Revision: 1.81 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -418,6 +418,7 @@ static CharPtr GetStrForBankit (
 }
 
 static CharPtr reftxt0 = " The reference sequence was derived from ";
+static CharPtr reftxtg = " The reference sequence was generated based on analysis of ";
 static CharPtr reftxt1 = " This record is predicted by genome sequence analysis and is not yet supported by experimental evidence.";
 static CharPtr reftxt2 = " This record has not yet been subject to final NCBI review.";
 static CharPtr reftxt3 = " The mRNA record is supported by experimental evidence; however, the coding sequence is predicted.";
@@ -480,18 +481,19 @@ static void AddStrForRefTrack (
 )
 
 {
-  CharPtr       accn, curator = NULL, source = NULL, st;
+  CharPtr       accn, curator = NULL, name, source = NULL, st;
+  Char          buf [64];
   ObjectIdPtr   oip;
   UserFieldPtr  ufp, tmp, u, urf = NULL;
+  Int4          from, to;
   Int2          i = 0;
-  Int2          review = 0,len;
-  Boolean       is_accn;
+  Int2          review = 0;
+  Boolean       generated = FALSE;
 
   if ( uop == NULL || ffstring == NULL ) return;
   if ((oip = uop->type) == NULL) return;
   if (StringCmp (oip->str, "RefGeneTracking") != 0) return;
 
-  len = StringLen (reftxt0);
   for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
     oip = ufp->label;
     if (StringCmp(oip->str, "Assembly") == 0) {
@@ -516,6 +518,8 @@ static void AddStrForRefTrack (
       } else if (StringICmp (st, "Pipeline") == 0) {
         review = 8;
       }
+    } else if (StringCmp (oip->str, "Generated") == 0) {
+      generated = ufp->data.boolvalue;
     } else if (StringCmp (oip->str, "Collaborator") == 0) {
       st = (CharPtr) ufp->data.ptrvalue;
       if (! StringHasNoText (st)) {
@@ -575,33 +579,58 @@ static void AddStrForRefTrack (
   }
   if (source != NULL) {
     FFAddOneString (ffstring, reftxt9, FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString (ffstring, source, FALSE, FALSE, TILDE_IGNORE);
+    if (GetWWW (ajp) && ValidateAccn (source) == 0) {
+      FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
+      FFAddTextToString(ffstring, "val=", source, ">", FALSE, FALSE, TILDE_IGNORE);
+      FFAddOneString (ffstring, source, FALSE, FALSE, TILDE_IGNORE);
+      FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+    } else {
+      FFAddOneString (ffstring, source, FALSE, FALSE, TILDE_IGNORE);
+    }
     FFAddOneString (ffstring, ").", FALSE, FALSE, TILDE_IGNORE);
   }
   if (i > 0) {
-    FFAddOneString (ffstring, reftxt0, FALSE, FALSE, TILDE_IGNORE);
+    if (generated) {
+      FFAddOneString (ffstring, reftxtg, FALSE, FALSE, TILDE_IGNORE);
+    } else {
+      FFAddOneString (ffstring, reftxt0, FALSE, FALSE, TILDE_IGNORE);
+    }
 
     for (tmp = urf->data.ptrvalue; tmp != NULL; tmp = tmp->next) {
-      is_accn = TRUE;
+      accn = NULL;
+      from = 0;
+      to = 0;
+      name = NULL;
       for (u = tmp->data.ptrvalue; u != NULL; u = u->next) {
         oip = u->label;
-        if (StringCmp (oip->str, "accession") == 0) break;
-        if (StringCmp (oip->str, "name") == 0) {
-          is_accn = FALSE;
-          break;
+        if (oip != NULL && oip->str != NULL) {
+          if (StringICmp (oip->str, "accession") == 0 && u->choice == 1) {
+            accn = (CharPtr) u->data.ptrvalue;
+          } else if (StringICmp (oip->str, "from") == 0 && u->choice == 2) {
+            from = u->data.intvalue;
+          } else if (StringICmp (oip->str, "to") == 0 && u->choice == 2) {
+            to = u->data.intvalue;
+          } else if (StringICmp (oip->str, "name") == 0 && u->choice == 1) {
+            name = (CharPtr) u->data.ptrvalue;
+          }
         }
       }
-      if (u == NULL) continue;
-      accn = (CharPtr) u->data.ptrvalue;
-      if (StringHasNoText (accn)) continue;
-      if (is_accn && GetWWW(ajp) ) {
-        FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
-        FFAddTextToString(ffstring, "val=", accn, ">", FALSE, FALSE, TILDE_IGNORE);
-        FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
-        FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-      } else {
-        FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
-      }
+      if (StringDoesHaveText (accn)) {
+        if (GetWWW (ajp) && ValidateAccn (accn) == 0) {
+          FFAddTextToString(ffstring, "<a href=", link_seq, NULL, FALSE, FALSE, TILDE_IGNORE);
+          FFAddTextToString(ffstring, "val=", accn, ">", FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
+          FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+        } else {
+          FFAddOneString (ffstring, accn, FALSE, FALSE, TILDE_IGNORE);
+        }
+        if (from > 0 && to > 0) {
+          sprintf (buf, " (range: %ld-%ld)", (long) from, (long) to);
+          FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+        }
+      } else if (StringDoesHaveText (name)) {
+        FFAddOneString (ffstring, name, FALSE, FALSE, TILDE_IGNORE);
+      } else continue;
       if (tmp->next != NULL) {
         ufp = tmp->next;
         if (ufp->next != NULL) {
@@ -1491,6 +1520,148 @@ static void AddAltPrimaryBlock (
   FFRecycleString(ajp, ffstring);
 }
 
+static CharPtr GeStrForTSA (
+  UserObjectPtr uop
+)
+
+{
+  Int4          asf, ast, prf, prt;
+  Char          buf [80], tmp [80];
+  UserFieldPtr  curr;
+  Boolean       has_asf, has_ast, has_prf, has_prt;
+  ValNodePtr    head = NULL;
+  ObjectIdPtr   oip;
+  CharPtr       pid;
+  CharPtr       str;
+  UserFieldPtr  ufp;
+
+  if (uop == NULL) return NULL;
+  if ((oip = uop->type) == NULL) return NULL;
+  if (StringCmp (oip->str, "TSA") != 0) return NULL;
+
+  for (curr = uop->data; curr != NULL; curr = curr->next) {
+    if (curr->choice != 11) continue;
+    asf = 0;
+    ast = 0;
+    prf = 0;
+    prt = 0;
+    pid = NULL;
+    has_asf = FALSE;
+    has_ast = FALSE;
+    has_prf = FALSE;
+    has_prt = FALSE;
+    for (ufp = curr->data.ptrvalue; ufp != NULL; ufp = ufp->next) {
+      oip = ufp->label;
+      if (oip == NULL) continue;
+      if (StringICmp (oip->str, "assembly from") == 0 && ufp->choice == 2) {
+        asf = (Int4) ufp->data.intvalue;
+        has_asf = TRUE;
+      } else if (StringICmp (oip->str, "assembly to") == 0 && ufp->choice == 2) {
+        ast = (Int4) ufp->data.intvalue;
+        has_ast = TRUE;
+      } else if (StringICmp (oip->str, "primary from") == 0 && ufp->choice == 2) {
+        prf = (Int4) ufp->data.intvalue;
+        has_prf = TRUE;
+      } else if (StringICmp (oip->str, "primary to") == 0 && ufp->choice == 2) {
+        prt = (Int4) ufp->data.intvalue;
+        has_prt = TRUE;
+      } else if (StringICmp (oip->str, "primary ID") == 0 && ufp->choice == 1) {
+        pid = (CharPtr) ufp->data.ptrvalue;
+      }
+    }
+    if (has_asf && has_ast && has_prf && has_prt && pid != NULL) {
+      if (head == NULL) {
+        ValNodeCopyStr (&head, 0, "TSA_SPAN            PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP");
+      }
+      StringCpy (buf, pid);
+      if (StringNCmp (pid, "gnl|ti|", 7) == 0) {
+        StringCpy (buf, "TI");
+        StringCat (buf, pid + 7);
+      }
+      sprintf (tmp, "~%ld-%ld                                        ",
+               (long) (asf + 1), (long) (ast + 1));
+      tmp [21] = '\0';
+      StringCat (buf, "                                        ");
+      buf [18] = '\0';
+      StringCat (tmp, buf);
+      sprintf (buf, " %ld-%ld                                        ",
+               (long) (prf + 1), (long) (prt + 1));
+      buf [21] = '\0';
+      StringCat (tmp, buf);
+      if (prf > prt) {
+        StringCat (tmp, "c");
+      }
+      ValNodeCopyStr (&head, 0, tmp);
+    }
+  }
+
+  if (head == NULL) return NULL;
+
+  str = MergeFFValNodeStrs (head);
+  ValNodeFreeData (head);
+
+  return str;
+}
+
+static void AddTsaBlock (
+  Asn2gbWorkPtr awp,
+  UserObjectPtr uop
+)
+
+{
+  IntAsn2gbJobPtr  ajp;
+  Asn2gbSectPtr    asp;
+  BaseBlockPtr     bbp = NULL;
+  BioseqPtr        bsp;
+  GBSeqPtr         gbseq;
+  CharPtr          str;
+  StringItemPtr    ffstring;
+
+  if (awp == NULL) return;
+  ajp = awp->ajp;
+  if (ajp == NULL) return;
+  bsp = awp->bsp;
+  if (bsp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
+
+  ffstring = FFGetString(ajp);
+  if ( ffstring == NULL ) return;
+
+  str = GeStrForTSA (uop);
+  if (str != NULL) {
+
+    bbp = (BaseBlockPtr) Asn2gbAddBlock (awp, PRIMARY_BLOCK, sizeof (BaseBlock));
+    if (bbp != NULL) {
+
+      FFStartPrint (ffstring, awp->format, 0, 12, "PRIMARY", 12, 5, 5, "PR", TRUE);
+
+      FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
+
+      bbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12, 5, 5, "PR");
+
+      /* optionally populate gbseq for XML-ized GenBank format */
+
+      if (ajp->gbseq) {
+        gbseq = &asp->gbseq;
+      } else {
+        gbseq = NULL;
+      }
+
+      if (gbseq != NULL) {
+        gbseq->primary = StringSave (str);
+      }
+
+      if (awp->afp != NULL) {
+        DoImmediateFormat (awp->afp, (BaseBlockPtr) bbp);
+      }
+    }
+    MemFree (str);
+  }
+
+  FFRecycleString(ajp, ffstring);
+}
+
 NLM_EXTERN void AddPrimaryBlock (
   Asn2gbWorkPtr awp
 )
@@ -1503,6 +1674,7 @@ NLM_EXTERN void AddPrimaryBlock (
   SeqMgrDescContext  dcontext;
   GBSeqPtr           gbseq;
   Boolean            has_tpa_assembly = FALSE;
+  Boolean            has_tsa = FALSE;
   SeqHistPtr         hist;
   Boolean            isRefSeq = FALSE;
   ObjectIdPtr        oip;
@@ -1527,16 +1699,23 @@ NLM_EXTERN void AddPrimaryBlock (
       if (oip != NULL) {
         if (StringCmp (oip->str, "TpaAssembly") == 0) {
           has_tpa_assembly = TRUE;
+        } else if (StringCmp (oip->str, "TSA") == 0) {
+          has_tsa = TRUE;
         }
       }
     }
-    if (has_tpa_assembly) {
+    if (has_tpa_assembly || has_tsa) {
       sdp = NULL;
     } else {
       sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
     }
   }
 
+  if (has_tsa) {
+    AddTsaBlock (awp, uop);
+    return;
+  }
+
   hist = bsp->hist;
   if ((! IsTpa (bsp, has_tpa_assembly, &isRefSeq)) ||
       hist == NULL || hist->assembly == NULL) {
@@ -1709,6 +1888,7 @@ NLM_EXTERN void AddCommentBlock (
   MolInfoPtr         mip;
   Boolean            mrnaEv = FALSE;
   CharPtr            name = NULL;
+  ObjectIdPtr        ncbifileID = NULL;
   ObjectIdPtr        oip;
   Boolean            okay;
   BioseqPtr          parent;
@@ -2130,6 +2310,8 @@ NLM_EXTERN void AddCommentBlock (
             DoImmediateFormat (awp->afp, (BaseBlockPtr) cbp);
           }
         }
+      } else if (dbt != NULL && StringCmp (dbt->db, "NCBIFILE") == 0 && dbt->tag != NULL) {
+        ncbifileID = dbt->tag;
       }
 
     } else if (sip->choice == SEQID_GI) {
@@ -2181,6 +2363,47 @@ NLM_EXTERN void AddCommentBlock (
     }
   }
 
+  if (ncbifileID != NULL) {
+    if (is_tpa || is_collab) {
+      if (awp->mode == SEQUIN_MODE || awp->mode == DUMP_MODE) {
+        buf [0] = '\0';
+        if (! StringHasNoText (ncbifileID->str)) {
+          if (StringLen (ncbifileID->str) < 1000) {
+            sprintf (buf, "FileID: %s", ncbifileID->str);
+          } else {
+            sprintf (buf, "FileID string too large");
+          }
+        } else {
+          sprintf (buf, "FileID: %ld", (long) ncbifileID->id);
+        }
+
+        cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock));
+        if (cbp != NULL) {
+
+          cbp->entityID = awp->entityID;
+          cbp->first = first;
+          first = FALSE;
+
+          if (cbp->first) {
+            FFStartPrint (ffstring, awp->format, 0, 12, "COMMENT", 12, 5, 5, "CC", TRUE);
+          } else {
+            FFStartPrint (ffstring, awp->format, 0, 12, NULL, 12, 5, 5, "CC", FALSE);
+          }
+
+          FFAddOneString (ffstring, buf, FALSE, FALSE, TILDE_EXPAND);
+
+          cbp->string = FFEndPrint(ajp, ffstring, awp->format, 12, 12,5, 5, "CC");
+          FFRecycleString(ajp, ffstring);
+          ffstring = FFGetString(ajp);
+
+          if (awp->afp != NULL) {
+            DoImmediateFormat (awp->afp, (BaseBlockPtr) cbp);
+          }
+        }
+      }
+    }
+  }
+
   /* RefSeq results in allocated comment string */
 
   sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
@@ -3784,6 +4007,9 @@ NLM_EXTERN void AddSourceFeatBlock (
     }
 
     str = GetMolTypeQual (bsp);
+    if (StringICmp (str, "ncRNA") == 0) {
+      str = "other RNA";
+    }
     if (str == NULL) {
       switch (bsp->mol) {
         case Seq_mol_dna :
diff --git a/api/asn2gnb4.c b/api/asn2gnb4.c
index 7fff07cf..40a640f4 100644
--- a/api/asn2gnb4.c
+++ b/api/asn2gnb4.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.148 $
+* $Revision: 1.159 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -79,6 +79,7 @@ static FtQualType feat_qual_order [] = {
   FTQUAL_operon,
 
   FTQUAL_ncRNA_class,
+  FTQUAL_ncRNA_other,
 
   FTQUAL_product,
 
@@ -191,6 +192,7 @@ static FtQualType feat_note_order [] = {
   FTQUAL_prot_note,
   FTQUAL_prot_comment,
   FTQUAL_prot_method,
+  FTQUAL_ncRNA_note,
   FTQUAL_figure,
   FTQUAL_maploc,
   FTQUAL_prot_conflict,
@@ -281,6 +283,8 @@ static FeaturQual asn2gnbk_featur_quals [ASN2GNBK_TOTAL_FEATUR]  =  {
   { "model_evidence",     Qual_class_model_ev       },
   { "calculated_mol_wt",  Qual_class_mol_wt         },
   { "ncRNA_class",        Qual_class_quote          },
+  { "ncRNA_note",         Qual_class_string         },
+  { "ncRNA_class",        Qual_class_string         },
   { "nomenclature",       Qual_class_nomenclature   },
   { "note",               Qual_class_note           },
   { "number",             Qual_class_number         },
@@ -1055,7 +1059,6 @@ static ValQual legalGbqualList [] = {
   { FEATDEF_misc_recomb , FTQUAL_label },
   { FEATDEF_misc_recomb , FTQUAL_map },
   { FEATDEF_misc_recomb , FTQUAL_old_locus_tag },
-  { FEATDEF_misc_recomb , FTQUAL_organism },
   { FEATDEF_misc_recomb , FTQUAL_standard_name },
 
   { FEATDEF_misc_signal , FTQUAL_allele },
@@ -1135,6 +1138,7 @@ static ValQual legalGbqualList [] = {
   { FEATDEF_protein_bind , FTQUAL_label },
   { FEATDEF_protein_bind , FTQUAL_map },
   { FEATDEF_protein_bind , FTQUAL_old_locus_tag },
+  { FEATDEF_protein_bind , FTQUAL_operon },
   { FEATDEF_protein_bind , FTQUAL_standard_name },
 
   { FEATDEF_RBS , FTQUAL_allele },
@@ -2683,10 +2687,13 @@ static void FormatFeatureBlockQuals (
   UserObjectPtr      uop;
   ValNodePtr         vnp;
   StringItemPtr      unique;
+  Boolean            indexerVersion;
 
   unique = FFGetString(ajp);
   if ( unique == NULL ) return;
 
+  indexerVersion = (Boolean) (GetAppProperty ("InternalNcbiSequin") != NULL);
+
   for (i = 0, idx = feat_qual_order [i]; idx != (FtQualType) 0; i++, idx = feat_qual_order [i]) {
 
     lasttype = NULL;
@@ -4153,7 +4160,11 @@ static void FormatFeatureBlockQuals (
                   }
                 } else if (jdx == FTQUAL_seqfeat_note) {
                   str = StringSave (qvp [jdx].str);
-                  TrimSpacesAndJunkFromEnds (str, TRUE);
+                  if (indexerVersion) {
+                    TrimSpacesAroundString (str);
+                  } else {
+                    TrimSpacesAndJunkFromEnds (str, TRUE);
+                  }
                   if (! IsEllipsis (str))
                     add_period = s_RemovePeriodFromEnd (str);
                   /*  NOTE -- The following function call cleans up some strings
@@ -5050,6 +5061,7 @@ static CharPtr legalInferencePrefixes [] = {
   "nucleotide motif",
   "protein motif",
   "ab initio prediction",
+  "alignment",
   NULL
 };
 
@@ -5184,8 +5196,10 @@ static SeqFeatPtr GetOverlappingGeneInEntity (
         vn.data.ptrvalue = (Pointer) &spt;
         gene = SeqMgrGetOverlappingGene (&vn, gcontext);
 
+      /*
       } else {
         gene = SeqMgrGetOverlappingGene (locforgene, gcontext);
+      */
       }
     }
   } else {
@@ -5199,6 +5213,23 @@ static SeqFeatPtr GetOverlappingGeneInEntity (
   return gene;
 }
 
+static Boolean LocStrandsMatch (SeqLocPtr loc1, SeqLocPtr loc2)
+
+{
+  Uint1  featstrand;
+  Uint1  locstrand;
+
+  if (loc1 == NULL || loc2 == NULL) return FALSE;
+  featstrand = SeqLocStrand (loc1);
+  locstrand = SeqLocStrand (loc2);
+  if (featstrand == locstrand) return TRUE;
+  if (locstrand == Seq_strand_unknown && featstrand != Seq_strand_minus) return TRUE;
+  if (featstrand == Seq_strand_unknown && locstrand != Seq_strand_minus) return TRUE;
+  if (featstrand == Seq_strand_both && locstrand != Seq_strand_minus) return TRUE;
+  if (locstrand == Seq_strand_both) return TRUE;
+  return FALSE;
+}
+
 static CharPtr FormatFeatureBlockEx (
   IntAsn2gbJobPtr ajp,
   Asn2gbSectPtr asp,
@@ -5248,6 +5279,7 @@ static CharPtr FormatFeatureBlockEx (
   ValNodePtr         illegal = NULL;
   ImpFeatPtr         imp = NULL;
   IndxPtr            index;
+  Boolean            is_ed = FALSE;
   Boolean            is_ged = FALSE;
   Boolean            is_gps = FALSE;
   Boolean            is_journalscan = FALSE;
@@ -5259,6 +5291,7 @@ static CharPtr FormatFeatureBlockEx (
   SeqLocPtr          loc = NULL;
   SeqLocPtr          location = NULL;
   SeqLocPtr          locforgene = NULL;
+  SeqLocPtr          locformatpep = NULL;
   SeqMgrFeatContext  mcontext;
   MolInfoPtr         mip;
   SeqFeatPtr         mrna;
@@ -5363,8 +5396,9 @@ static CharPtr FormatFeatureBlockEx (
       locforgene = location;
       */
       if (cds != NULL) {
-        locforgene = cds->location;    /* mat_peptide always gets parent CDS /gene value */
-        grp = SeqMgrGetGeneXref (cds); /* mat_peptide also needs to use CDS gene xref */
+        grp = SeqMgrGetGeneXref (cds); /* mat_peptide first obeys any CDS gene xref */
+        locformatpep = location;       /* mat_peptide next gets exact match for /gene */
+        locforgene = cds->location;    /* mat_peptide last gets parent CDS /gene */
       }
       loc = location;
   
@@ -5441,8 +5475,16 @@ static CharPtr FormatFeatureBlockEx (
             is_journalscan = TRUE;
             break;
           case SEQID_GENBANK :
+            is_ged = TRUE;
+            break;
           case SEQID_EMBL :
+            is_ged = TRUE;
+            is_ed = TRUE;
+            break;
           case SEQID_DDBJ :
+            is_ged = TRUE;
+            is_ed = TRUE;
+            break;
           case SEQID_TPG :
           case SEQID_TPE :
           case SEQID_TPD :
@@ -5656,6 +5698,9 @@ static CharPtr FormatFeatureBlockEx (
           qvp [FTQUAL_operon].gbq = gbq;
         }
       }
+      if (operon->pseudo) {
+        pseudo = TRUE;
+      }
     }
 
   } else if (featdeftype != FEATDEF_operon && featdeftype != FEATDEF_gap) {
@@ -5688,7 +5733,35 @@ static CharPtr FormatFeatureBlockEx (
 
     if (! suppressed) {
 
-      /* if not suppressed, and no gene xref, get gene by overlap */
+      /* first look for gene that exactly matches mat_peptide DNA projection */
+
+      if (gene == NULL && grp == NULL && locformatpep != NULL) {
+        gene = GetOverlappingGeneInEntity (ajp->ajp.entityID, fcontext, &gcontext, locformatpep);
+        if (gene == NULL && ajp->ajp.entityID != sfp->idx.entityID) {
+          gene = GetOverlappingGeneInEntity (sfp->idx.entityID, fcontext, &gcontext, locformatpep);
+        }
+
+        if (gene != NULL) {
+          if (SeqLocCompare (gene->location, locformatpep) == SLC_A_EQ_B &&
+              LocStrandsMatch (gene->location, locformatpep)) {
+            qvp [FTQUAL_gene_note].str = gene->comment;
+
+            grp = (GeneRefPtr) gene->data.value.ptrvalue;
+            if (gene->pseudo) {
+              pseudo = TRUE;
+            }
+            if (grp != NULL && grp->db != NULL) {
+              qvp [FTQUAL_gene_xref].vnp = grp->db;
+            } else {
+              qvp [FTQUAL_gene_xref].vnp = gene->dbxref;
+            }
+          } else {
+            gene = NULL;
+          }
+        }
+      }
+
+      /* otherwise, if not suppressed and no gene xref, get gene by overlap */
 
       if (gene == NULL && grp == NULL) {
         if (featdeftype != FEATDEF_primer_bind) {
@@ -5728,7 +5801,7 @@ static CharPtr FormatFeatureBlockEx (
         pseudo = TRUE;
       }
 
-      if (grp != NULL && (featdeftype != FEATDEF_repeat_region || gene == NULL)) {
+      if (grp != NULL && (featdeftype != FEATDEF_repeat_region || is_ed || gene == NULL)) {
         if (! StringHasNoText (grp->locus)) {
           qvp [FTQUAL_gene].str = grp->locus;
           qvp [FTQUAL_locus_tag].str = grp->locus_tag;
@@ -5775,6 +5848,9 @@ static CharPtr FormatFeatureBlockEx (
               qvp [FTQUAL_operon].gbq = gbq;
             }
           }
+          if (operon->pseudo) {
+            pseudo = TRUE;
+          }
         }
       }
     }
@@ -6261,20 +6337,9 @@ static CharPtr FormatFeatureBlockEx (
               if (rrp->type == 255) {
                 str = (CharPtr) rrp->ext.value.ptrvalue;
                 if (StringICmp (str, "misc_RNA") == 0 ||
-                    StringICmp (str, "ncRNA") == 0) {
+                    StringICmp (str, "ncRNA") == 0 ||
+                    StringICmp (str, "tmRNA") == 0) {
                    /* pick up product from gbqual */
-                 } else if (StringICmp (str, "tmRNA") == 0) {
-                   /* check for product gbqual in new records */
-                   for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
-                     if (StringICmp (gbq->qual, "product") == 0 &&
-                         StringDoesHaveText (gbq->val)) {
-                       break;
-                     }
-                   }
-                   if (gbq == NULL) {
-                     /* old record has no product gbqual, product is tmRNA */
-                     qvp [FTQUAL_product].str = str;
-                   }
                  } else {
                   str = (CharPtr) rrp->ext.value.ptrvalue;
                   qvp [FTQUAL_product].str = str;
@@ -6612,6 +6677,17 @@ static CharPtr FormatFeatureBlockEx (
     }
   }
 
+  if (qvp [FTQUAL_ncRNA_class].gbq != NULL) {
+    gbq = qvp [FTQUAL_ncRNA_class].gbq;
+    if (StringDoesHaveText (gbq->val)) {
+      if (! IsStringInNcRNAClassList (gbq->val)) {
+        qvp [FTQUAL_ncRNA_other].str = "other";
+        qvp [FTQUAL_ncRNA_note].str = gbq->val;
+        qvp [FTQUAL_ncRNA_class].gbq = NULL;
+      }
+    }
+  }
+
   if (ajp->mode != DUMP_MODE) {
     ParseInference (qvp [FTQUAL_inference].gbq, &good_inference, &bad_inference);
     qvp [FTQUAL_inference_good].vnp = good_inference;
diff --git a/api/asn2gnb5.c b/api/asn2gnb5.c
index 4b9b7f6b..1c3457f9 100644
--- a/api/asn2gnb5.c
+++ b/api/asn2gnb5.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.98 $
+* $Revision: 1.115 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -104,18 +104,30 @@ NLM_EXTERN Char ec_ambig [MAX_WWWBUF];
 NLM_EXTERN Char link_tax [MAX_WWWBUF];
 #define DEF_LINK_TAX "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?"
 
-static Char link_ff [MAX_WWWBUF];
-#define DEF_LINK_FF  "/cgi-bin/Entrez/getfeat?"
-
 NLM_EXTERN Char link_muid [MAX_WWWBUF];
 #define DEF_LINK_MUID  "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=pubmed&list_uids="
 
-static Char link_ace [MAX_WWWBUF];
-#define DEF_LINK_ACE  "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=gene&q="
-
 NLM_EXTERN Char link_code [MAX_WWWBUF];
 #define DEF_LINK_CODE "http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?"
 
+NLM_EXTERN Char link_sp [MAX_WWWBUF];
+#define DEF_LINK_SP "http://www.uniprot.org/entry/"
+
+NLM_EXTERN Char link_encode [MAX_WWWBUF];
+#define DEF_LINK_ENCODE  "http://www.nhgri.nih.gov/10005107"
+
+NLM_EXTERN Char link_go [MAX_WWWBUF];
+#define DEF_LINK_GO "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&depth=1&query="
+
+NLM_EXTERN Char link_go_ref [MAX_WWWBUF];
+#define DEF_LINK_GO_REF "http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:"
+
+static Char link_ff [MAX_WWWBUF];
+#define DEF_LINK_FF  "/cgi-bin/Entrez/getfeat?"
+
+static Char link_ace [MAX_WWWBUF];
+#define DEF_LINK_ACE  "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=gene&q="
+
 static Char link_fly [MAX_WWWBUF];
 #define DEF_LINK_FLY "http://flybase.bio.indiana.edu/.bin/fbidq.html?"
 
@@ -143,9 +155,6 @@ static Char link_ck [MAX_WWWBUF];
 static Char link_rice [MAX_WWWBUF];
 #define DEF_LINK_RICE "http://ars-genome.cornell.edu/cgi-bin/WebAce/webace?db=ricegenes&class=Marker&object="
 
-NLM_EXTERN Char link_sp [MAX_WWWBUF];
-#define DEF_LINK_SP "http://www.uniprot.org/entry/"
-
 static Char link_pdb [MAX_WWWBUF];
 #define DEF_LINK_PDB "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId="
 
@@ -230,21 +239,12 @@ static Char link_zfin [MAX_WWWBUF];
 static Char link_rebase [MAX_WWWBUF];
 #define DEF_LINK_REBASE "http://rebase.neb.com/rebase/enz/"
 
-NLM_EXTERN Char link_encode [MAX_WWWBUF];
-#define DEF_LINK_ENCODE  "http://www.nhgri.nih.gov/10005107"
-
 static Char link_pgn [MAX_WWWBUF];
 #define DEF_LINK_PGN  "http://pgn.cornell.edu/cgi-bin/search/seq_search_result.pl?identifier="
 
 static Char link_subtilist [MAX_WWWBUF];
 #define DEF_LINK_SUBTILIST  "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+"
 
-NLM_EXTERN Char link_go [MAX_WWWBUF];
-#define DEF_LINK_GO "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&depth=1&query="
-
-NLM_EXTERN Char link_go_ref [MAX_WWWBUF];
-#define DEF_LINK_GO_REF "http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:"
-
 static Char link_hinvdb [MAX_WWWBUF];
 #define DEF_LINK_HINVDB "http://www.h-invitational.jp"
 
@@ -261,7 +261,7 @@ static Char link_dicty [MAX_WWWBUF];
 #define DEF_LINK_DICTY "http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid="
 
 static Char link_maizegdb [MAX_WWWBUF];
-#define DEF_LINK_MAIZEGDB "http://www.maizegdb.org/"
+#define DEF_LINK_MAIZEGDB "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id="
 
 static Char link_axeldb [MAX_WWWBUF];
 #define DEF_LINK_AXELDB "http://www.dkfz-heidelberg.de/tbi/services/axeldb/clone/xenopus?name="
@@ -284,6 +284,9 @@ static Char link_hgnc [MAX_WWWBUF];
 static Char link_bold [MAX_WWWBUF];
 #define DEF_LINK_BOLD "http://www.boldsystems.org/connectivity/specimenlookup.php?processid="
 
+static Char link_aftol [MAX_WWWBUF];
+#define DEF_LINK_AFTOL "http://aftol.biology.duke.edu/pub/displayTaxonInfo?aftol_id="
+
 static Char link_hprd [MAX_WWWBUF];
 #define DEF_LINK_HPRD "http://www.hprd.org/protein/"
 
@@ -294,7 +297,7 @@ static Char link_cambia [MAX_WWWBUF];
 #define DEF_LINK_CAMBIA "http://www.patentlens.net/patentlens/simple.cgi?patnum="
 
 static Char link_vector [MAX_WWWBUF];
-#define DEF_LINK_VECTOR "http://www.vectorbase.org/Genome/BRCGene/?"
+#define DEF_LINK_VECTOR "http://www.vectorbase.org/Genome/BRCGene/?feature="
 
 static Char link_mirbase [MAX_WWWBUF];
 #define DEF_LINK_MIRBASE "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc="
@@ -318,7 +321,7 @@ static Char link_eric [MAX_WWWBUF];
 #define DEF_LINK_ERIC "http://www.ericbrc.org/genbank/dbxref/"
 
 static Char link_pbr [MAX_WWWBUF];
-#define DEF_LINK_PBR "http://www.poxvirus.org/gene_detail.asp?gene_id="
+#define DEF_LINK_PBR "http://www.poxvirus.org/query.asp?web_id="
 
 static Char link_nmpdr [MAX_WWWBUF];
 #define DEF_LINK_NMPDR "http://www.nmpdr.org/linkin.cgi?id="
@@ -344,11 +347,39 @@ static Char link_apidb_plasmodb [MAX_WWWBUF];
 static Char link_apidb_toxodb [MAX_WWWBUF];
 #define DEF_LINK_APIDB_TOXODB "http://www.toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&project_id=&primary_key="
 
-static Char link_pathema_locus [MAX_WWWBUF];
-#define DEF_LINK_PATHEMA_LOCUS "http://pathema.tigr.org/tigr-scripts/pathema/shared/GenePage.cgi?locus="
+static Char link_pathema [MAX_WWWBUF];
+/* #define DEF_LINK_PATHEMA "http://pathema.tigr.org/tigr-cripts/Burkholderia/shared/GenePage.cgi?all=1&locus=" */
+#define DEF_LINK_PATHEMA "http://pathema.jcvi.org/cgi-bin/Burkholderia/shared/GenePage.cgi?all=1&locus="
+
+/*
+static Char link_pathema_prefix [MAX_WWWBUF];
+#define DEF_LINK_PATHEMA_PREFIX "http://pathema.tigr.org/tigr-scripts/"
+
+static Char link_pathema_suffix [MAX_WWWBUF];
+#define DEF_LINK_PATHEMA_SUFFIX "/shared/GenePage.cgi?all=1&locus="
+*/
+
+static Char link_pfam [MAX_WWWBUF];
+#define DEF_LINK_PFAM "http://pfam.sanger.ac.uk/family?acc="
+
+static Char link_rfam [MAX_WWWBUF];
+#define DEF_LINK_RFAM "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?"
+
+static Char link_xenbase [MAX_WWWBUF];
+#define DEF_LINK_XENBASE "http://www.xenbase.org/gene/showgene.do?method=display&geneId="
+
+static Char link_nrestdb [MAX_WWWBUF];
+#define DEF_LINK_NRESTDB "http://genome.ukm.my/nrestdb/db/single_view_est.php?id="
+
+static Char link_tigrfam [MAX_WWWBUF];
+#define DEF_LINK_TIGRFAM "http://cmr.tigr.org/tigr-scripts/CMR/HmmReport.cgi?hmm_acc="
+
+static Char link_vbrc [MAX_WWWBUF];
+#define DEF_LINK_VBRC "http://vbrc.org/query.asp?web_view=curation&web_id="
+
+static Char link_unigene [MAX_WWWBUF];
+#define DEF_LINK_UNIGENE "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=unigene&Cmd=Search&Term="
 
-static Char link_pathema_taxon_id [MAX_WWWBUF];
-#define DEF_LINK_PATHEMA_TAXON_ID "http://pathema.tigr.org/tigr-scripts/pathema/GenomePage.cgi?taxon_id="
 
 
 /* www utility functions */
@@ -439,6 +470,7 @@ NLM_EXTERN void InitWWW (IntAsn2gbJobPtr ajp)
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_HSSP", DEF_LINK_HSSP, link_hssp, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_HGNC", DEF_LINK_HGNC, link_hgnc, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_BOLD", DEF_LINK_BOLD, link_bold, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_AFTOL", DEF_LINK_AFTOL, link_aftol, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_HPRD", DEF_LINK_HPRD, link_hprd, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_USPTO", DEF_LINK_USPTO, link_uspto, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_CAMBIA", DEF_LINK_CAMBIA, link_cambia, MAX_WWWBUF);
@@ -459,11 +491,20 @@ NLM_EXTERN void InitWWW (IntAsn2gbJobPtr ajp)
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_APIDB_CRYPTODB", DEF_LINK_APIDB_CRYPTODB, link_apidb_cryptodb, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_APIDB_PLASMODB", DEF_LINK_APIDB_PLASMODB, link_apidb_plasmodb, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_APIDB_TOXODB", DEF_LINK_APIDB_TOXODB, link_apidb_toxodb, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_PATHEMA_LOCUS", DEF_LINK_PATHEMA_LOCUS, link_pathema_locus, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_PATHEMA_TAXON_ID", DEF_LINK_PATHEMA_TAXON_ID, link_pathema_taxon_id, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_PATHEMA", DEF_LINK_PATHEMA, link_pathema, MAX_WWWBUF);
+  /*
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_PATHEMA_PREFIX", DEF_LINK_PATHEMA_PREFIX, link_pathema_prefix, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_PATHEMA_SUFFIX", DEF_LINK_PATHEMA_SUFFIX, link_pathema_suffix, MAX_WWWBUF);
+  */
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_PFAM", DEF_LINK_PFAM, link_pfam, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_RFAM", DEF_LINK_RFAM, link_rfam, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_XENBASE", DEF_LINK_XENBASE, link_xenbase, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_NRESTDB", DEF_LINK_NRESTDB, link_nrestdb, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_TIGRFAM", DEF_LINK_TIGRFAM, link_tigrfam, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_VBRC", DEF_LINK_VBRC, link_vbrc, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_UNIGENE", DEF_LINK_UNIGENE, link_unigene, MAX_WWWBUF);
 }
 
-
 NLM_EXTERN void FF_www_featloc(StringItemPtr ffstring, CharPtr loc)
 {
   CharPtr ptr;
@@ -547,10 +588,12 @@ static Boolean IsOnlyDigits (CharPtr str)
 static void FF_www_db_xref_pathema (
   StringItemPtr ffstring,
   CharPtr db, 
-  CharPtr identifier
+  CharPtr identifier,
+  BioseqPtr bsp
 )
 
 {
+  /*
   if ( StringStr (identifier, "SOP_") != NULL ) {
     FFAddTextToString(ffstring, db, ":", identifier, FALSE, FALSE, TILDE_IGNORE);
   } else if ( StringChr (identifier, '_') != NULL ) {
@@ -560,6 +603,30 @@ static void FF_www_db_xref_pathema (
   } else {
     FFAddTextToString(ffstring, db, ":", identifier, FALSE, FALSE, TILDE_IGNORE);
   }
+  */
+
+  /*
+  Char     link [256];
+  CharPtr  ptr;
+  Char     taxname [128];
+
+  if (bsp != NULL && BioseqToGeneticCode (bsp, NULL, NULL, NULL, taxname, sizeof (taxname), NULL)) {
+    ptr = StringChr (taxname, ' ');
+    if (ptr != NULL) {
+      *ptr = '\0';
+    }
+    StringCpy (link, link_pathema_prefix);
+    StringCat (link, taxname);
+    StringCat (link, link_pathema_suffix);
+
+    FF_www_db_xref_std(ffstring, db, identifier, link);
+  } else {
+    FFAddTextToString(ffstring, db, ":", identifier, FALSE, FALSE, TILDE_IGNORE);
+  }
+  */
+
+
+  FF_www_db_xref_std(ffstring, db, identifier, link_pathema);
 }
 
 static void FF_www_db_xref_imgt_gene (
@@ -689,22 +756,6 @@ static void FF_www_db_xref_niaEST(
 }
 
 
-static void FF_www_db_xref_maizegdb(
-  StringItemPtr ffstring,
-  CharPtr db, 
-  CharPtr identifier
-)
-{
-  while (*identifier == ' ')
-    identifier++;
-
-  FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
-  FFAddTextToString(ffstring, "<a href=", link_maizegdb, ">", FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, identifier, FALSE, FALSE, TILDE_IGNORE);
-  FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
-}
-
-
 static void FF_www_db_xref_gdb(
   StringItemPtr ffstring,
   CharPtr db, 
@@ -804,6 +855,7 @@ static void FF_www_db_xref_hprd (
   FF_www_db_xref_std (ffstring, db, identifier, link);
 }
 
+/*
 static void FF_www_db_xref_vector (
   StringItemPtr ffstring,
   CharPtr db, 
@@ -836,6 +888,7 @@ static void FF_www_db_xref_vector (
   StringCat (buf, "gene=");
   FF_www_db_xref_std (ffstring, db, identifier, buf);
 }
+*/
 
 static void FF_www_db_xref_null (
   StringItemPtr ffstring,
@@ -963,7 +1016,7 @@ static void Do_www_db_xref(
   } else if ( StringCmp(db , "dictyBase") == 0) {
     FF_www_db_xref_std(ffstring, db, identifier, link_dicty);
   } else if ( StringCmp(db , "MaizeGDB") == 0) {
-    FF_www_db_xref_maizegdb(ffstring, db, identifier);
+    FF_www_db_xref_std(ffstring, db, identifier, link_maizegdb);
   } else if ( StringCmp(db , "axeldb") == 0) {
     FF_www_db_xref_std(ffstring, db, identifier, link_axeldb);
   } else if ( StringCmp(db , "VBASE2") == 0) {
@@ -980,10 +1033,12 @@ static void Do_www_db_xref(
     FF_www_db_xref_std(ffstring, db, identifier, link_hgnc);
   } else if ( StringCmp(db , "BOLD") == 0) {
     FF_www_db_xref_std(ffstring, db, identifier, link_bold);
+  } else if ( StringCmp(db , "AFTOL") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_aftol);
   } else if ( StringCmp(db , "HPRD") == 0) {
     FF_www_db_xref_hprd(ffstring, db, identifier, link_hprd);
   } else if ( StringCmp(db , "VectorBase") == 0) {
-    FF_www_db_xref_vector(ffstring, db, identifier, bsp, link_vector);
+    FF_www_db_xref_std(ffstring, db, identifier, link_vector);
   } else if ( StringCmp(db , "miRBase") == 0) {
     FF_www_db_xref_std(ffstring, db, identifier, link_mirbase);
   } else if ( StringCmp(db , "dbClone") == 0) {
@@ -1009,7 +1064,7 @@ static void Do_www_db_xref(
   } else if ( StringCmp(db , "TAIR") == 0) {
     FF_www_db_xref_std(ffstring, db, identifier, link_tair);
   } else if ( StringCmp(db , "Pathema") == 0) {
-    FF_www_db_xref_pathema(ffstring, db, identifier);
+    FF_www_db_xref_pathema(ffstring, db, identifier, bsp);
   } else if ( StringCmp(db , "ApiDB") == 0) {
     FF_www_db_xref_std(ffstring, db, identifier, link_apidb);
   } else if ( StringCmp(db , "ApiDB_CryptoDB") == 0) {
@@ -1018,6 +1073,27 @@ static void Do_www_db_xref(
     FF_www_db_xref_std(ffstring, db, identifier, link_apidb_plasmodb);
   } else if ( StringCmp(db , "ApiDB_ToxoDB") == 0) {
     FF_www_db_xref_std(ffstring, db, identifier, link_apidb_toxodb);
+  } else if ( StringCmp(db , "PFAM") == 0 || StringCmp(db , "Pfam") == 0 ) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_pfam);
+  } else if ( StringCmp(db , "RFAM") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_rfam);
+  } else if ( StringCmp(db , "Xenbase") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_xenbase);
+  } else if ( StringCmp(db , "NRESTdb") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_nrestdb);
+  } else if ( StringCmp(db , "TIGRFAM") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_tigrfam);
+  } else if ( StringCmp(db , "VBRC") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_vbrc);
+
+  /* for dbsource */
+  } else if ( StringCmp(db , "UniGene") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_unigene);
+  } else if ( StringCmp(db , "RefSeq") == 0) {
+    FFAddTextToString(ffstring, NULL, db, ":", FALSE, FALSE, TILDE_IGNORE);
+    FFAddTextToString(ffstring, "<a href=", link_seq, "val=", FALSE, FALSE, TILDE_IGNORE);
+    FFAddTextToString(ffstring, identifier, ">", identifier, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
 
   } else {  
     /* default: no link just the text */
@@ -1306,10 +1382,12 @@ NLM_EXTERN CharPtr GetAuthorsString (
 
   if (alp == NULL) return NULL;
 
+  /*
   alp = AsnIoMemCopy ((Pointer) alp,
                       (AsnReadFunc) AuthListAsnRead,
                       (AsnWriteFunc) AuthListAsnWrite);
   if (alp == NULL) return NULL;
+  */
 
   count = 0;
   if (alp->choice == 1) {
@@ -1418,7 +1496,9 @@ NLM_EXTERN CharPtr GetAuthorsString (
 
   ValNodeFreeData (head);
 
+  /*
   AuthListFree (alp);
+  */
 
   return str;
 }
diff --git a/api/asn2gnb6.c b/api/asn2gnb6.c
index 260e6492..7a41cf38 100644
--- a/api/asn2gnb6.c
+++ b/api/asn2gnb6.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.120 $
+* $Revision: 1.136 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -82,7 +82,10 @@ static SourceType source_qual_order [] = {
   SCQUAL_isolation_source,
   SCQUAL_spec_or_nat_host,
   SCQUAL_sub_species,
+
   SCQUAL_specimen_voucher,
+  SCQUAL_culture_collection,
+  SCQUAL_bio_material,
 
   SCQUAL_db_xref,
   SCQUAL_org_xref,
@@ -170,8 +173,6 @@ static SourceType source_desc_note_order [] = {
   SCQUAL_teleomorph,
   SCQUAL_breed,
 
-  SCQUAL_culture_collection,
-  SCQUAL_bio_material,
   SCQUAL_metagenome_source,
   SCQUAL_metagenome_note,
 
@@ -220,8 +221,6 @@ static SourceType source_feat_note_order [] = {
   SCQUAL_teleomorph,
   SCQUAL_breed,
 
-  SCQUAL_culture_collection,
-  SCQUAL_bio_material,
   SCQUAL_metagenome_source,
   SCQUAL_metagenome_note,
 
@@ -298,7 +297,7 @@ NLM_EXTERN SourceQual asn2gnbk_source_quals [ASN2GNBK_TOTAL_SOURCE] = {
   { "isolation_source",         Qual_class_subsource  },
   { "lab_host",                 Qual_class_subsource  },
   { "label",                    Qual_class_label      },
-  { "lat_lon",                  Qual_class_subsource  },
+  { "lat_lon",                  Qual_class_lat_lon    },
   { "macronuclear",             Qual_class_boolean    },
   { "map",                      Qual_class_subsource  },
   { "derived from metagenome",  Qual_class_orgmod     },
@@ -404,6 +403,7 @@ NLM_EXTERN SourceType subSourceToSourceIdx [39] = {
 NLM_EXTERN CharPtr legalDbXrefs [] = {
   "PIDe", "PIDd", "PIDg", "PID",
   "AceView/WormGenes",
+  "AFTOL",
   "ApiDB",
   "ApiDB_CryptoDB",
   "ApiDB_PlasmoDB",
@@ -462,20 +462,24 @@ NLM_EXTERN CharPtr legalDbXrefs [] = {
   "NextDB",
   "niaEST",
   "NMPDR",
+  "NRESTdb",
   "Pathema",
   "PDB",
+  "PFAM",
   "PGN",
   "PIR",
   "PSEUDO",
   "RATMAP",
-  "RiceGenes",
+  "RFAM",
   "RGD",
+  "RiceGenes",
   "RZPD",
   "SEED",
   "SGD",
   "SoyBase",
   "SubtiList",
   "taxon",
+  "TIGRFAM",
   "UniGene",
   "UniProtKB/Swiss-Prot",
   "UniProtKB/TrEMBL",
@@ -484,6 +488,7 @@ NLM_EXTERN CharPtr legalDbXrefs [] = {
   "VectorBase",
   "WorfDB",
   "WormBase",
+  "Xenbase",
   "ZFIN",
   NULL
 };
@@ -497,9 +502,413 @@ NLM_EXTERN CharPtr legalRefSeqDbXrefs [] = {
   "PBR",
   "REBASE",
   "TAIR",
+  "VBRC",
   NULL
 };
 
+
+typedef struct dbxrefval {
+  CharPtr dbval;
+  Uint4   flags;
+} DbxrefValData, PNTR DbxrefValPtr;
+
+#define DBXREF_VAL_FLAG_KNOWN_BAD       0
+#define DBXREF_VAL_FLAG_OK_ON_ANYFEAT   1
+#define DBXREF_VAL_FLAG_OK_ON_CDSFEAT   2
+#define DBXREF_VAL_FLAG_OK_ON_ORGREF    4
+#define DBXREF_VAL_FLAG_OK_ON_ANY       8
+#define DBXREF_VAL_FLAG_OK_ON_NCBI      16
+#define DBXREF_VAL_FLAG_OK_ON_EMBL      32
+#define DBXREF_VAL_FLAG_OK_ON_DDBJ      64
+
+static DbxrefValData validDbxref [] = {
+ {"AceView/WormGenes",        DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"AFTOL",                    DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ApiDB",                    DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ApiDB_CryptoDB",           DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ApiDB_PlasmoDB",           DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ApiDB_ToxoDB",             DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ASAP",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ATCC",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ATCC(dna)",                DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ATCC(in host)",            DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"axeldb",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"BDGP_EST",                 DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"BDGP_INS",                 DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"BOLD",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"CCDS",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"CDD",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"cdd",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"CK",                       DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"CloneID",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"COG",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"dbClone",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"dbCloneLib",               DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"dbEST",                    DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"dbProbe",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"dbSNP",                    DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"dbSTS",                    DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"DDBJ",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"dictyBase",                DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ECOCYC",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"EcoGene",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"EMBL",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"ENSEMBL",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ERIC",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ESTLIB",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"FANTOM_DB",                DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"FLYBASE",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"FlyBase",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"GABI",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"GDB",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"GenBank",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"GeneDB",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"GeneID",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"GI",                       DBXREF_VAL_FLAG_KNOWN_BAD },
+ {"GO",                       DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"GOA",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"GRIN",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"H-InvDB",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"HGNC",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"HPRD",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"HSSP",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"IMGT/GENE-DB",             DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"IMGT/HLA",                 DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"IMGT/LIGM",                DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"InterimID",                DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"InterPro",                 DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ISD",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ISFinder",                 DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"JCM",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"LocusID",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"MaizeGDB",                 DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"MGD",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"MGI",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"MIM",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"miRBASE",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"NBRC",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"NextDB",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"niaEST",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"NID",                      DBXREF_VAL_FLAG_KNOWN_BAD },
+ {"NMPDR",                    DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"NRESTdb",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"Pathema",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"PBR",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"PDB",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"PFAM",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"PGN",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"PID",                      DBXREF_VAL_FLAG_OK_ON_CDSFEAT },
+ {"PIDd",                     DBXREF_VAL_FLAG_OK_ON_CDSFEAT },
+ {"PIDe",                     DBXREF_VAL_FLAG_OK_ON_CDSFEAT },
+ {"PIDg",                     DBXREF_VAL_FLAG_OK_ON_CDSFEAT },
+ {"PIR",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"PSEUDO",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"RATMAP",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"REBASE",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"RFAM",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"RGD",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"RiceGenes",                DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"RZPD",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ORGREF | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"SEED",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"SGD",                      DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"SoyBase",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"SubtiList",                DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"TAIR",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"taxon",                    DBXREF_VAL_FLAG_OK_ON_ORGREF  | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"TIGRFAM",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"UniGene",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"UniProtKB/Swiss-Prot",     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"UniProtKB/TrEMBL",         DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"UniSTS",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"VBASE2",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"VBRC",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT },
+ {"VectorBase",               DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"WorfDB",                   DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"WormBase",                 DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"Xenbase",                  DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY },
+ {"ZFIN",                     DBXREF_VAL_FLAG_OK_ON_ANYFEAT | DBXREF_VAL_FLAG_OK_ON_ANY }
+};
+
+const Int4 cNumValidDbxref = sizeof (validDbxref) / sizeof (DbxrefValData);
+
+
+/* These functions are for testing dbxrefs */
+static ValNodePtr MakeDbxrefList (void)
+{
+  ValNodePtr dbxref_list = NULL;
+  Int4 i;
+  DbtagPtr dbtag;
+  
+  for (i = 0; i < cNumValidDbxref; i++)
+  {
+    dbtag = DbtagNew ();
+    dbtag->db = StringSave (validDbxref[i].dbval);
+    dbtag->tag = ObjectIdNew ();
+    dbtag->tag->id = 42;
+    ValNodeAddPointer (&dbxref_list, 0, dbtag);
+  }
+  return dbxref_list;
+}
+
+static void AddDbxrefsToBioSource (BioSourcePtr biop)
+{
+  if (biop == NULL) return;
+  if (biop->org == NULL)
+  {
+    biop->org = OrgRefNew();
+  }
+
+  ValNodeLink (&(biop->org->db), MakeDbxrefList());
+}
+
+static void AddDbxrefsToSeqFeat (SeqFeatPtr sfp)
+{
+  if (sfp == NULL) return;
+  ValNodeLink (&(sfp->dbxref), MakeDbxrefList());
+}
+
+NLM_EXTERN void AddAllDbxrefsToBioseq (BioseqPtr bsp)
+{
+  SeqDescrPtr sdp;
+  SeqFeatPtr  sfp;
+  SeqMgrDescContext dcontext;
+  SeqMgrFeatContext fcontext;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  if (sdp != NULL) {
+    AddDbxrefsToBioSource (sdp->data.ptrvalue);
+  }
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
+  if (sfp != NULL) {
+    AddDbxrefsToBioSource (sfp->data.value.ptrvalue);
+    AddDbxrefsToSeqFeat (sfp);
+  }
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &fcontext);
+  if (sfp != NULL) {
+    AddDbxrefsToSeqFeat (sfp);
+  }
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_GENE, 0, &fcontext);
+  if (sfp != NULL) {
+    AddDbxrefsToSeqFeat (sfp);
+  }
+}
+
+/* functions for validating dbxrefs */
+
+static CharPtr FormatIllegalMsg (CharPtr db)
+{
+  CharPtr msg_fmt = "Illegal db_xref type %s";
+  CharPtr err = NULL;
+
+  if (StringHasNoText (db)) return NULL;
+  err = (CharPtr) MemNew (sizeof (Char) * (StringLen (msg_fmt) + StringLen (db)));
+  sprintf (err, msg_fmt, db);
+  return err;
+}
+
+
+static CharPtr FormatBadCapMsg (CharPtr db, CharPtr correct)
+{
+  CharPtr msg_fmt = "Illegal db_xref type %s, legal capitalization is %s";
+  CharPtr err = NULL;
+
+  if (StringHasNoText (db) || StringHasNoText (correct)) return NULL;
+  err = (CharPtr) MemNew (sizeof (Char) * (StringLen (msg_fmt) + StringLen (db) + StringLen (correct)));
+  sprintf (err, msg_fmt, db, correct);
+  return err;
+}
+
+
+static CharPtr FormatFlatfileOnlyMsg (CharPtr db)
+{
+  CharPtr msg_fmt = "db_xref type %s is only created by the flatfile generator, and should not be in the record as a separate xref";
+  CharPtr err = NULL;
+
+  if (StringHasNoText (db)) return NULL;
+  err = (CharPtr) MemNew (sizeof (Char) * (StringLen (msg_fmt) + StringLen (db)));
+  sprintf (err, msg_fmt, db);
+  return err;
+}
+
+
+static CharPtr FormatBadOrgDbxrefMsg (CharPtr db)
+{
+  CharPtr msg_fmt = "db_xref type %s should not used on an OrgRef";
+  CharPtr err = NULL;
+
+  if (StringHasNoText (db)) return NULL;
+  err = (CharPtr) MemNew (sizeof (Char) * (StringLen (msg_fmt) * StringLen (db)));
+  sprintf (err, msg_fmt, db);
+  return err;
+}
+  
+
+static CharPtr FormatBadSeqFeatDbxrefMsg (CharPtr db)
+{
+  CharPtr msg_fmt = "db_xref type %s should not used as a feature xref";
+  CharPtr err = NULL;
+
+  if (StringHasNoText (db)) return NULL;
+  err = (CharPtr) MemNew (sizeof (Char) * (StringLen (msg_fmt) * StringLen (db)));
+  sprintf (err, msg_fmt, db);
+  return err;
+}
+
+
+/* returns 1 if found and valid
+ * returns 0 if not found
+ * returns -1 if found but invalid
+ * returns -2 if found and known bad
+ */
+NLM_EXTERN Int4 IsDbxrefValid (CharPtr db, SeqFeatPtr sfp, OrgRefPtr org, Boolean IsRefSeq, CharPtr PNTR errmsg)
+{
+  Int4 imin, imax, i, j;
+  Int4 capmismatch = -1, exactmatch = -1, validmatch;
+  Int4 rval = 0;
+
+  if (StringHasNoText (db)) return 0;
+
+  if (errmsg != NULL) *errmsg = NULL;
+
+  imin = 0;                   /* find in list */
+  imax = cNumValidDbxref - 1;
+  i = (imax + imin) / 2;
+  while (imax > imin)
+  {
+    j = StringICmp (db, validDbxref[i].dbval);
+    if (j < 0)
+      imax = i - 1;
+      else if (j > 0)
+          imin = i + 1;
+      else
+          break;
+      i = (imax + imin)/2;
+  }
+
+  if (i > -1 && StringICmp (db, validDbxref[i].dbval) == 0)
+  {
+    j = StringCmp (db, validDbxref[i].dbval);
+    if (j == 0)
+    {
+      exactmatch = i;
+    }
+    else if (j < 0)
+    {
+      capmismatch = i;
+      i--;
+      while (i > -1 && StringICmp (db, validDbxref[i].dbval) == 0 && exactmatch < 0)
+      {
+        if (StringCmp (db, validDbxref[i].dbval) == 0)
+        {
+          exactmatch = i;
+        }
+        else
+        {
+          i--;
+        }
+      }
+    }
+    else if (j > 0)
+    {
+      capmismatch = i;
+      i++;
+      while (i < cNumValidDbxref && StringICmp (db, validDbxref[i].dbval) == 0 && exactmatch < 0)
+      {
+        if (StringCmp (db, validDbxref[i].dbval) == 0)
+        {
+          exactmatch = i;
+        }
+        else
+        {
+          i--;
+        }
+      }
+    }
+  }
+
+  if (capmismatch > -1 && exactmatch < 0)
+  {
+    validmatch = capmismatch;
+  }
+  else
+  {
+    validmatch = exactmatch;
+  }
+
+  if (validmatch < 0)
+  {
+    rval = 0;
+    if (errmsg != NULL) 
+    {
+      *errmsg = FormatIllegalMsg (db);
+    }
+  } 
+  else 
+  {
+    if (validDbxref[validmatch].flags == DBXREF_VAL_FLAG_KNOWN_BAD)
+    {
+      rval = -2;
+      if (errmsg != NULL)
+      {
+        *errmsg = FormatFlatfileOnlyMsg (db);
+      }
+    }
+    else if (org != NULL && !(validDbxref[validmatch].flags & DBXREF_VAL_FLAG_OK_ON_ORGREF))
+    {
+      rval = -1;
+      if (errmsg != NULL)
+      {
+        *errmsg = FormatBadOrgDbxrefMsg (db);
+      }
+    }
+    else if (sfp != NULL && !(validDbxref[validmatch].flags & DBXREF_VAL_FLAG_OK_ON_ANYFEAT)
+             && (sfp->data.choice != SEQFEAT_CDREGION 
+                 || !(validDbxref[validmatch].flags & DBXREF_VAL_FLAG_OK_ON_CDSFEAT)))
+    {
+      if ((validDbxref[validmatch].flags & DBXREF_VAL_FLAG_OK_ON_CDSFEAT)
+          && !(validDbxref[validmatch].flags & DBXREF_VAL_FLAG_OK_ON_ANYFEAT)
+          && sfp->data.choice != SEQFEAT_CDREGION)
+      {
+        rval = -2;
+        if (errmsg != NULL)
+        {
+          *errmsg = FormatFlatfileOnlyMsg (db);
+        }
+      }
+      else
+      {
+        rval = -1;
+        if (errmsg != NULL)
+        {
+          *errmsg = FormatBadSeqFeatDbxrefMsg (db);
+        }
+      }
+    }
+    else if (IsRefSeq ||(validDbxref[validmatch].flags & DBXREF_VAL_FLAG_OK_ON_ANY))
+    {
+      rval = 1;
+      if (validmatch == capmismatch && errmsg != NULL)
+      {
+        *errmsg = FormatBadCapMsg (db, validDbxref[validmatch].dbval);
+      }
+    }
+    else
+    {
+      rval = -1;
+      if (errmsg != NULL) 
+      {
+        *errmsg = FormatIllegalMsg (db);
+      }
+    }
+  }
+
+  return rval;
+}
+
+
 static CharPtr organellePrefix [] = {
   NULL,
   NULL,
@@ -2498,6 +2907,12 @@ NLM_EXTERN CharPtr GetMolTypeQual (
     case MOLECULE_TYPE_TRANSCRIBED_RNA :
       return "other RNA";
       break;
+    case MOLECULE_TYPE_NCRNA :
+      return "ncRNA";
+      break;
+    case MOLECULE_TYPE_TMRNA :
+      return "tmRNA";
+      break;
     case 255 :
       switch (bsp->mol) {
         case Seq_mol_dna :
@@ -2565,7 +2980,7 @@ static ValNodePtr ParseColonString (
   tmp = StringSave (strs);
   str = tmp;
   len = StringLen (str);
-  if (len > 1 && StringChr (str, ':') != NULL && multiple) {
+  if (len > 1 && StringChr (str, ':') != NULL /* && multiple */) {
     while (StringDoesHaveText (str)) {
       ptr = StringChr (str, ':');
       if (ptr != NULL) {
@@ -2917,6 +3332,113 @@ static void FF_www_specimen_voucher (
   Do_www_specimen_voucher (ffstring, inst, id, vdp);
 }
 
+NLM_EXTERN Char link_lat_lon [MAX_WWWBUF];
+#define DEF_LINK_LAT_LON "http://www.ncbi.nlm.nih.gov/projects/Sequin/latlonview.html?"
+
+static Boolean lat_lon_link_set = FALSE;
+
+static void Do_www_lat_lon (
+  StringItemPtr ffstring,
+  CharPtr lat_lon
+)
+
+{
+  Char     buf [128];
+  Char     ch;
+  CharPtr  ew = "";
+  Int2     i;
+  CharPtr  ns = "";
+  CharPtr  ptr;
+  Char     tmp [128];
+  CharPtr  tokens [6];
+
+  if ( ffstring == NULL || lat_lon == NULL ) return;
+
+  if (! lat_lon_link_set) {
+    GetAppParam ("NCBI", "WWWENTREZ", "LINK_LAT_LON", DEF_LINK_LAT_LON, link_lat_lon, MAX_WWWBUF);
+    lat_lon_link_set = TRUE;
+  }
+
+  MemSet ((Pointer) tokens, 0, sizeof (tokens));
+
+  StringNCpy_0 (buf, lat_lon, sizeof (buf));
+
+  i = 0;
+  ptr = buf;
+  ch = *ptr;
+  tokens [i] = ptr;
+  while (ch != '\0' && i < 5) {
+    if (ch == ' ') {
+      *ptr = '\0';
+      ptr++;
+      ch = *ptr;
+      while (ch == ' ') {
+        ptr++;
+        ch = *ptr;
+      }
+      i++;
+      tokens [i] = ptr;
+    } else {
+      ptr++;
+      ch = *ptr;
+    }
+  }
+
+  ptr = tokens [1];
+  if (ptr != NULL && *ptr == 'S') {
+    ns = "-";
+  }
+  ptr = tokens [3];
+  if (ptr != NULL && *ptr == 'W') {
+    ew = "-";
+  }
+
+  if (tokens [0] == NULL) {
+    tokens [0] = "?";
+  }
+  if (tokens [2] == NULL) {
+    tokens [2] = "?";
+  }
+
+  FFAddOneString (ffstring, "<a href=", FALSE, FALSE, TILDE_IGNORE);
+  FFAddOneString (ffstring, link_lat_lon, FALSE, FALSE, TILDE_IGNORE);
+  sprintf (tmp, "lat=%s%s&lon=%s%s", ns, tokens [0], ew, tokens [2]);
+  FFAddOneString (ffstring, tmp, FALSE, FALSE, TILDE_IGNORE);
+  FFAddTextToString (ffstring, ">", lat_lon, "</a>", FALSE, FALSE, TILDE_IGNORE);
+}
+
+static void FF_www_lat_lon (
+  IntAsn2gbJobPtr ajp,
+  StringItemPtr ffstring,
+  CharPtr lat_lon
+)
+
+{
+  Boolean  format_ok = FALSE;
+  FloatHi  lat = 0.0;
+  FloatHi  lon = 0.0;
+  Boolean  lat_in_range = FALSE;
+  Boolean  lon_in_range = FALSE;
+
+  if ( ffstring == NULL || lat_lon == NULL ) return;
+  if (! GetWWW (ajp)) { /* not in www mode */
+    FFAddTextToString(ffstring, NULL, lat_lon, NULL, FALSE, TRUE, TILDE_TO_SPACES);
+    return;
+  }
+  if (StringDoesHaveText (lat_lon)) {
+    IsCorrectLatLonFormat (lat_lon, &format_ok, &lat_in_range, &lon_in_range);
+    if (format_ok && lat_in_range && lon_in_range) {
+      if (ParseLatLon (lat_lon, &lat, &lon)) {
+        Do_www_lat_lon (ffstring, lat_lon);
+        return;
+      }
+    }
+  }
+
+  /* if any of above tests failed, default print */
+  FFAddTextToString (ffstring, NULL, lat_lon, NULL, FALSE, TRUE, TILDE_TO_SPACES);
+}
+
 NLM_EXTERN CharPtr FormatSourceFeatBlock (
   Asn2gbFormatPtr afp,
   BaseBlockPtr bbp
@@ -3109,6 +3631,9 @@ NLM_EXTERN CharPtr FormatSourceFeatBlock (
   }
 
   str = GetMolTypeQual (bsp);
+  if (StringICmp (str, "ncRNA") == 0) {
+    str = "other RNA";
+  }
   if (str == NULL) {
     switch (bsp->mol) {
       case Seq_mol_dna :
@@ -3272,6 +3797,25 @@ NLM_EXTERN CharPtr FormatSourceFeatBlock (
         }
         break;
 
+      case Qual_class_lat_lon :
+        omp = qvp [idx].omp;
+        if (lastomptype == 0 && omp != NULL) {
+          lastomptype = omp->subtype;
+        }
+        while (omp != NULL && omp->subtype == lastomptype) {
+          if (StringIsJustQuotes (omp->subname)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=\"\"\n",
+                              FALSE, TRUE, TILDE_IGNORE);
+          } else if (! StringHasNoText (omp->subname)) {
+            FFAddTextToString(ffstring, "/", asn2gnbk_source_quals [idx].name, "=\"",
+                              FALSE, TRUE, TILDE_IGNORE);
+            FF_www_lat_lon(ajp, ffstring, omp->subname);
+            FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
+          }
+          omp = omp->next;
+        }
+        break;
+
       case Qual_class_subsource :
         ssp = qvp [idx].ssp;
         if (lastssptype == 0 && ssp != NULL) {
diff --git a/api/asn2gnbi.h b/api/asn2gnbi.h
index 836daf63..ffed723c 100644
--- a/api/asn2gnbi.h
+++ b/api/asn2gnbi.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   12/30/03
 *
-* $Revision: 1.82 $
+* $Revision: 1.85 $
 *
 * File Description:  New GenBank flatfile generator, internal header
 *
@@ -465,6 +465,7 @@ typedef enum {
   Qual_class_pcr,
   Qual_class_mol_wt,
   Qual_class_voucher,
+  Qual_class_lat_lon,
   Qual_class_mobile_element
 }  QualType;
 
@@ -635,6 +636,8 @@ typedef enum {
   FTQUAL_modelev,
   FTQUAL_mol_wt,
   FTQUAL_ncRNA_class,
+  FTQUAL_ncRNA_note,
+  FTQUAL_ncRNA_other,
   FTQUAL_nomenclature,
   FTQUAL_note,
   FTQUAL_number,
@@ -712,6 +715,7 @@ NLM_EXTERN Char ec_link [MAX_WWWBUF];
 NLM_EXTERN Char ec_ambig [MAX_WWWBUF];
 NLM_EXTERN Char link_tax [MAX_WWWBUF];
 NLM_EXTERN Char link_muid [MAX_WWWBUF];
+NLM_EXTERN Char link_lat_lon [MAX_WWWBUF];
 NLM_EXTERN Char link_code [MAX_WWWBUF];
 NLM_EXTERN Char link_encode [MAX_WWWBUF];
 NLM_EXTERN Char link_go [MAX_WWWBUF];
@@ -823,7 +827,16 @@ NLM_EXTERN void FFTrim (
     StringItemPtr line_start,
     Int4 line_pos,
     Int4 line_prefix_len
-);NLM_EXTERN void FFCalculateLineBreak (
+);
+NLM_EXTERN int FFNextChar(
+  StringItemPtr start_sip,
+  Int4 start_pos
+);
+NLM_EXTERN void FFAdvanceChar(
+  StringItemPtr* start_sip,
+  Int4* start_pos
+);
+NLM_EXTERN void FFCalculateLineBreak (
   StringItemPtr PNTR break_sip, Int4 PNTR break_pos,
   Int4 init_indent, Int4 visible
 );
@@ -1071,6 +1084,17 @@ NLM_EXTERN CharPtr goFieldType [];
 NLM_EXTERN CharPtr legalDbXrefs [];
 NLM_EXTERN CharPtr legalRefSeqDbXrefs [];
 
+NLM_EXTERN Int4 IsDbxrefValid (
+  CharPtr    db,
+  SeqFeatPtr sfp,
+  OrgRefPtr  org, 
+  Boolean    IsRefSeq,
+  CharPtr PNTR case_correction
+);
+
+
+NLM_EXTERN void AddAllDbxrefsToBioseq (BioseqPtr bsp);
+
 
 NLM_EXTERN void AddRefStatsBlock (
   Asn2gbWorkPtr awp
diff --git a/api/findrepl.c b/api/findrepl.c
index 641ff677..29855d04 100644
--- a/api/findrepl.c
+++ b/api/findrepl.c
@@ -40,130 +40,6 @@
 *
 * ==========================================================================
 *
-*
-* RCS Modification History:
-* -------------------------
-* $Log: findrepl.c,v $
-* Revision 6.25  2006/10/25 21:38:25  kans
-* adding source qualifier metagenomic
-*
-* Revision 6.24  2006/08/31 16:34:32  kans
-* FindReplAuthor handles consortium, properly replaces pid->data, not pNameStr, for string choices
-*
-* Revision 6.23  2006/07/13 21:06:52  kans
-* SearchForString passes strLen - (ptr - str) to FindSubString when looping for whole_word
-*
-* Revision 6.22  2006/07/13 17:06:38  bollin
-* use Uint4 instead of Uint2 for itemID values
-* removed unused variables
-* resolved compiler warnings
-*
-* Revision 6.21  2006/01/17 17:50:01  bollin
-* allow FindReplaceInEntity to search for a string made up of whitespace, as
-* long as whole_word is not specified
-*
-* Revision 6.20  2006/01/10 18:13:56  kans
-* FindReplAligns does not have case for SAS_DISC, since visit function recursively presents these components separately
-*
-* Revision 6.19  2006/01/09 21:15:03  bollin
-* allow punctuation to terminate a word in find replace
-*
-* Revision 6.18  2006/01/04 21:26:57  kans
-* FSA hit does not need code from validator unstructured source test, cleaned up variable names
-*
-* Revision 6.17  2006/01/04 20:39:41  kans
-* added FindStringsInEntity using finite state machine, general cleanup of code
-*
-* Revision 6.16  2005/12/29 21:42:06  kans
-* only call callback if text was found or replaced
-*
-* Revision 6.15  2005/12/29 20:54:41  kans
-* FindReplaceInEntity takes callback and userdata
-*
-* Revision 6.14  2005/09/21 14:39:09  bollin
-* fixed bug in FindReplace where if the whole-word flag was specified but
-* the substring was found in a not-whole-word context earlier in the string
-* the search terminated early with a null result
-*
-* Revision 6.13  2005/04/26 21:33:52  kans
-* added SEQID_GPIPE
-*
-* Revision 6.12  2004/04/01 13:43:05  lavr
-* Spell "occurred", "occurrence", and "occurring"
-*
-* Revision 6.11  2003/11/21 17:58:46  bollin
-* remove tax ref and common name when changing taxonomy name via ASN Find/Replace
-*
-* Revision 6.10  2003/07/31 20:54:54  kans
-* FindReplaceString does not need do_replace argument
-*
-* Revision 6.9  2003/07/31 18:18:03  kans
-* added FindReplaceString
-*
-* Revision 6.8  2003/05/11 21:12:50  kans
-* FindReplAligns loops through StdSegPtr chain, also does ssp->ids within
-*
-* Revision 6.7  2002/06/11 14:41:20  kans
-* added support for locus_tag
-*
-* Revision 6.6  2002/03/05 21:11:04  kans
-* do not replace ifp->key
-*
-* Revision 6.5  2001/12/12 17:38:38  kans
-* added new subsource qualifiers, four now have empty name
-*
-* Revision 6.4  2001/12/07 13:49:34  kans
-* workingBuffer needs to be large enough for terminal null byte
-*
-* Revision 6.3  2001/08/06 22:13:12  kans
-* using NUM_SEQID, added TPA ids to arrays
-*
-* Revision 6.2  2000/11/03 20:36:00  kans
-* FindReplaceInEntity replaces FindInEntity and FindInEntityX - complete redesign,
-* no longer using AsnExpOptExplore because of the difficulty of replacing with a
-* larger string (TF + JK)
-*
-* Revision 6.1  1999/03/05 23:31:07  kans
-* FindInEntityX was not initializing flen, replen
-*
-* Revision 6.0  1997/08/25 18:05:38  madden
-* Revision changed to 6.0
-*
-* Revision 5.3  1997/06/19 18:37:41  vakatov
-* [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
-*
-* Revision 5.2  1997/03/17 23:44:39  kans
-* added whole_word parameter to FindInEntity and FindInEntityX, and protected
-* against multiple ObjMgrAlsoSelects on a single itemID
-*
-* Revision 5.1  1996/09/06  20:20:41  kans
-* keeps going even if ObjMgrTypeFind returns NULL (e.g., on OBJ_BIOSEQ_SEG),
-* and adds a case_counts parameter for case sensitive/insensitive searches.
-*
-* Revision 5.0  1996/05/28  13:23:23  ostell
-* Set to revision 5.0
-*
-* Revision 1.7  1996/02/28  04:53:06  ostell
-* fix to prevernt recursion on substring replaces
-*
-* Revision 1.6  1996/02/26  20:24:05  kans
-* replace needs MemCopy instead of StringMove (JO), and set dirty flag
-*
-* Revision 1.5  1996/01/03  23:06:32  ostell
-* support for longer replaces, controlled updating
-*
-* Revision 1.3  1996/01/02  18:40:07  ostell
-* simplified code.
-*
-* Revision 1.2  1996/01/01  00:05:14  kans
-* replaced StringStr with StringISearch to ignore case
-*
-* Revision 1.1  1995/12/31  18:13:14  kans
-* Initial revision
-*
-* Revision 1.1.1.1  1995/10/19 18:42:10  sad
-* Initial version
-*
 */
 
 #include <ncbi.h>
@@ -176,7 +52,6 @@
 #include <findrepl.h>
 
 /* callback type for search/replace functions */
-
 typedef void (*FindReplFunc) (CharPtr PNTR strp, Pointer fspdata);
 
 /* internal data structure */
@@ -186,6 +61,7 @@ typedef struct findstruct {
   FindReplFunc  func;
   FindReplProc  callback;
   Pointer       userdata;
+  StringActionFunc string_action;
 
   CharPtr       find_string;
   CharPtr       replace_string;
@@ -1009,7 +885,7 @@ static void FindReplPubdesc (
   }
 }
 
-static void RemoveTaxRef (OrgRefPtr orp)
+extern void RemoveTaxRef (OrgRefPtr orp)
 {
   ValNodePtr      vnp, next;
   ValNodePtr PNTR prev;
@@ -1702,7 +1578,514 @@ static void FindReplSubmitBlock (
   FindReplSendMessages (fsp, ssp->idx.itemID, ssp->idx.itemtype);
 }
 
+
+NLM_EXTERN CharPtr GetSpecialWinCharacterReplacement (unsigned char ch)
+{
+  CharPtr r = "#";
+
+  if (ch == 198 || ch == 196)
+  {
+    r = "Ae";
+  }
+  else if (ch == 230 || ch == 228)
+  {
+    r = "ae";
+  }
+  else if (ch == 197)
+  {
+    r = "Aa";
+  } 
+  else if (ch == 229)
+  {
+    r = "aa";
+  }
+  else if (ch == 220)
+  {
+    r = "Ue";
+  } 
+  else if (ch == 252)
+  {
+    r = "ue";
+  }
+  else if (ch == 214)
+  {
+    r = "Oe";
+  }
+  else if (ch == 246)
+  {
+    r = "oe";
+  }
+  else if (ch == 223)
+  {
+    r = "ss";
+  } 
+  else if (ch == 199)
+  {
+    r = "C";
+  }
+  else if (ch >= 200 && ch <= 203)
+  {
+    r = "E";
+  }
+  else if (ch >= 204 && ch <= 207)
+  {
+    r = "I";
+  }
+  else if (ch == 209)
+  {
+    r = "N";
+  }
+  else if ((ch >= 210 && ch <= 214) || ch == 216)
+  {
+    r = "O";
+  }
+  else if (ch >= 217 && ch <= 220)
+  {
+    r = "U";
+  }
+  else if (ch == 221)
+  {
+    r = "Y";
+  }
+  else if (ch >= 224 && ch <= 229)
+  {
+    r = "a";
+  }
+  else if (ch == 231)
+  {
+    r = "c";
+  }
+  else if (ch >= 232 && ch <= 235)
+  {
+    r = "e";
+  }
+  else if (ch >= 236 && ch <= 239)
+  {
+    r = "i";
+  }
+  else if (ch == 241)
+  {
+    r = "n";
+  }
+  else if ((ch >= 242 && ch <= 246) || ch == 248)
+  {
+    r = "o";
+  }
+  else if (ch >= 249 && ch <= 252)
+  {
+    r = "u";
+  }
+  else if (ch == 253 || ch == 255)
+  {
+    r = "y";
+  }
+  return r;
+}
+
+
+NLM_EXTERN CharPtr GetSpecialMacCharacterReplacement (unsigned char ch)
+{
+  CharPtr r = "#";
+
+  if (ch == 174 || ch == 128)
+  {
+    r = "Ae";
+  }
+  else if (ch == 190 || ch == 138)
+  {
+    r = "ae";
+  }
+  else if (ch == 129)
+  {
+    r = "Aa";
+  } 
+  else if (ch == 140)
+  {
+    r = "aa";
+  }
+  else if (ch == 134)
+  {
+    r = "Ue";
+  } 
+  else if (ch == 159)
+  {
+    r = "ue";
+  }
+  else if (ch == 133)
+  {
+    r = "Oe";
+  }
+  else if (ch == 154)
+  {
+    r = "oe";
+  }
+  else if (ch == 167)
+  {
+    r = "ss";
+  } 
+  else if (ch == 130)
+  {
+    r = "C";
+  }
+  else if (ch == 233 || ch == 131 || ch == 230 || ch == 232)
+  {
+    r = "E";
+  }
+  else if (ch == 237 || ch == 234 || ch == 235 || ch == 236)
+  {
+    r = "I";
+  }
+  else if (ch == 132)
+  {
+    r = "N";
+  }
+  else if (ch == 241 || ch == 238 || ch == 239 || ch == 205 || ch == 133 || ch == 175)
+  {
+    r = "O";
+  }
+  else if (ch == 244 || ch == 242 || ch == 243 || ch == 134)
+  {
+    r = "U";
+  }
+  else if (ch == 136 || ch == 135 || ch == 137 || ch == 139 || ch == 138)
+  {
+    r = "a";
+  }
+  else if (ch == 141)
+  {
+    r = "c";
+  }
+  else if (ch == 143 || ch == 142 || ch == 144 || ch == 145)
+  {
+    r = "e";
+  }
+  else if (ch == 147 || ch == 146 || ch == 148 || ch == 149)
+  {
+    r = "i";
+  }
+  else if (ch == 150)
+  {
+    r = "n";
+  }
+  else if (ch == 152 || ch == 151 || ch == 153 || ch == 155 || ch == 154 || ch == 190)
+  {
+    r = "o";
+  }
+  else if (ch == 157 || ch == 156 || ch == 158 || ch == 159)
+  {
+    r = "u";
+  }
+  else if (ch == 216)
+  {
+    r = "y";
+  }
+  return r;
+}
+
+
+NLM_EXTERN CharPtr GetSpecialCharacterReplacement (unsigned char ch)
+
+{
+#ifdef WIN_MAC
+  return GetSpecialMacCharacterReplacement (ch);
+#endif
+#ifdef WIN_MSWIN
+  return GetSpecialWinCharacterReplacement (ch);
+#endif
+  return NULL;
+}
+
+
+NLM_EXTERN void SpecialCharFind (CharPtr PNTR strp, Pointer userdata, BoolPtr did_find, BoolPtr did_change)
+{
+  CharPtr cp;
+  Boolean found_any = FALSE;
+
+  if (strp == NULL || *strp == NULL) return;
+
+  cp = *strp;
+  while (*cp != 0 && !found_any)
+  {
+    if (*cp < ' ' || *cp > '~')
+    {
+      found_any = TRUE;
+    }
+    cp++;
+  }
+  if (found_any && did_find != NULL)
+  {
+    *did_find = TRUE;
+  }
+}
+
+
+NLM_EXTERN void SpecialCharReplace (CharPtr PNTR strp, Pointer userdata, BoolPtr did_find, BoolPtr did_change)
+{
+  Int4 orig_len, new_len, repl_len;
+  CharPtr cp, cpy, dst, repl;
+  Boolean found_any = FALSE;
+
+  if (strp == NULL || *strp == NULL) return;
+
+  /* count all characters that need two replacement characters */
+  cp = *strp;
+  orig_len = StringLen (cp);
+  new_len = orig_len;
+  while (*cp != 0)
+  {
+    new_len += abs (StringLen (GetSpecialCharacterReplacement ((unsigned char)*cp)) - 1);
+    if (*cp < ' ' || *cp > '~')
+    {
+      found_any = TRUE;
+    }
+    cp++;
+  }
+  if (!found_any)
+  { 
+    return;
+  }
+
+  /* allocate memory for new string if necessary */
+  if (new_len > orig_len)
+  {
+    cpy = (CharPtr) MemNew (sizeof (Char) * (new_len + 1));
+  }
+  else
+  {
+    cpy = *strp;
+  }
+
+  /* copy in with replacements */
+  cp = *strp;
+  dst = cpy;
+  while (*cp != 0)
+  {
+    if ((unsigned char)*cp < ' ')
+    {
+      /* will replace with pound sign */
+      *dst = '#';
+      dst++;
+    }
+    else if ((unsigned char)*cp > '~')
+    {
+#if 0
+      repl = GetSpecialCharacterReplacement ((unsigned char)*cp);
+#else
+      repl = "#";
+#endif
+      repl_len = StringLen (repl);
+      StringNCpy (dst, repl, repl_len);
+      dst += repl_len;
+    }
+    else
+    {
+      *dst = *cp;
+      dst++;
+    }
+    cp++;
+  }
+  *dst = 0;
+
+  /* put new string in place of old string */
+  if (cpy != *strp)
+  {
+    *strp = MemFree (*strp);
+    *strp = cpy;
+  }
+  if (did_find != NULL)
+  {
+    *did_find = TRUE;
+  }
+  if (did_change != NULL)
+  {
+    *did_change = TRUE;
+  }
+}
+
+
+static void StringActionCallback (CharPtr PNTR strp, Pointer fspdata)
+{
+  FindStructPtr fsp;
+  
+  if (strp == NULL || fspdata == NULL) return;
+
+  fsp = (FindStructPtr) fspdata;
+
+  if (fsp->string_action == NULL) return;
+  (fsp->string_action)(strp, fsp->userdata, &(fsp->did_find), &(fsp->dirty));
+}
+
+
 /* EXTERNAL FIND-REPLACE FUNCTIONS */
+NLM_EXTERN void StringActionInEntity (
+  Uint2 entityID,
+  Boolean select_item,
+  Int2 send_update,
+  BoolPtr descFilter,
+  BoolPtr featFilter,
+  BoolPtr seqidFilter,
+  Boolean do_seqid_local,
+  StringActionFunc action_func,
+  FindReplProc callback,
+  Pointer userdata
+)
+
+{
+  FindStruct     fs;
+  ObjMgrDataPtr  omdp;
+  SeqEntryPtr    sep = NULL;
+  SeqSubmitPtr   ssp = NULL;
+
+  if (entityID == 0 || action_func == NULL) return;
+
+  omdp = ObjMgrGetData (entityID);
+  if (omdp != NULL) {
+    switch (omdp->datatype) {
+      case OBJ_SEQSUB :
+        ssp = (SeqSubmitPtr) omdp->dataptr;
+        if (ssp != NULL && ssp->datatype == 1) {
+          sep = (SeqEntryPtr) ssp->data;
+        }
+        break;
+      case OBJ_BIOSEQ :
+        sep = (SeqEntryPtr) omdp->choice;
+      case OBJ_BIOSEQSET :
+        sep = (SeqEntryPtr) omdp->choice;
+      default :
+        break;
+    }
+  }
+  /* sep = GetTopSeqEntryForEntityID (entityID); */
+  if (sep == NULL) return;
+
+  MemSet ((Pointer) &fs, 0, sizeof (FindStruct));
+
+  fs.entityID = entityID;
+  fs.func = StringActionCallback;
+  fs.callback = callback;
+  fs.userdata = userdata;
+  fs.string_action = action_func;
+
+  fs.select_item = select_item;
+  fs.send_update = send_update;
+  fs.dirty = FALSE;
+
+  /* if desc or feat filter arrays not supplied, default to all TRUE */
+
+  if (descFilter != NULL) {
+    MemCopy ((Pointer) &fs.descFilter, (Pointer) descFilter, sizeof (fs.descFilter));
+  } else {
+    MemSet ((Pointer) &fs.descFilter, (int) TRUE, sizeof (fs.descFilter));
+  }
+
+  if (featFilter != NULL) {
+    MemCopy ((Pointer) &fs.featFilter, (Pointer) featFilter, sizeof (fs.featFilter));
+  } else {
+    MemSet ((Pointer) &fs.featFilter, (int) TRUE, sizeof (fs.featFilter));
+  }
+
+  /* if seqid filter array not supplied, default to all FALSE */
+
+  if (seqidFilter != NULL) {
+    MemCopy ((Pointer) &fs.seqidFilter, (Pointer) seqidFilter, sizeof (fs.seqidFilter));
+  } else if (do_seqid_local) {
+    MemSet ((Pointer) &fs.seqidFilter, (int) FALSE, sizeof (fs.seqidFilter));
+    fs.seqidFilter [SEQID_LOCAL] = TRUE;
+  } else {
+    MemSet ((Pointer) &fs.seqidFilter, (int) FALSE, sizeof (fs.seqidFilter));
+  }
+
+  /* ensure feature subtype is set in sfp->idx block */
+
+  AssignIDsInEntity (entityID, 0, NULL);
+
+  /* visit callbacks that find/replace specific fields */
+
+  VisitBioseqsInSep (sep, (Pointer) &fs, FindReplBioseqs);
+
+  VisitFeaturesInSep (sep, (Pointer) &fs, FindReplFeats);
+
+  VisitAlignmentsInSep (sep, (Pointer) &fs, FindReplAligns);
+
+  VisitGraphsInSep (sep, (Pointer) &fs, FindReplGraphs);
+
+  VisitDescriptorsInSep (sep, (Pointer) &fs, FindReplDescs);
+
+  if (ssp != NULL) {
+    FindReplSubmitBlock (ssp, &fs);
+  }
+
+  /* send select message, if applicable */
+
+  if (fs.send_update == UPDATE_ONCE && fs.dirty) {
+    ObjMgrSetDirtyFlag (entityID, TRUE);
+    ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
+  }
+}
+
+NLM_EXTERN void StringActionForObject (
+  Uint2   datatype,
+  Pointer objdata,
+  Uint2 entityID,
+  Boolean select_item,
+  Int2 send_update,
+  StringActionFunc action_func,
+  FindReplProc callback,
+  Pointer userdata
+)
+
+{
+  FindStruct     fs;
+
+  if (objdata == NULL || action_func == NULL) return;
+
+  MemSet ((Pointer) &fs, 0, sizeof (FindStruct));
+
+  fs.entityID = entityID;
+  fs.func = StringActionCallback;
+  fs.callback = callback;
+  fs.userdata = userdata;
+  fs.string_action = action_func;
+
+  fs.select_item = select_item;
+  fs.send_update = send_update;
+  fs.dirty = FALSE;
+
+  MemSet ((Pointer) &fs.descFilter, (int) TRUE, sizeof (fs.descFilter));
+
+  MemSet ((Pointer) &fs.featFilter, (int) TRUE, sizeof (fs.featFilter));
+
+  MemSet ((Pointer) &fs.seqidFilter, (int) FALSE, sizeof (fs.seqidFilter));
+
+  switch (datatype)
+  {
+    case OBJ_BIOSEQ:
+      FindReplBioseqs ((BioseqPtr) objdata, &fs);
+      break;
+    case OBJ_SEQFEAT:
+      FindReplFeats ((SeqFeatPtr) objdata, &fs);
+      break;
+    case OBJ_SEQALIGN:
+      FindReplAligns ((SeqAlignPtr) objdata, &fs);
+      break;
+    case OBJ_SEQGRAPH:
+      FindReplGraphs ((SeqGraphPtr) objdata, &fs);
+      break;
+    case OBJ_SEQDESC:
+      FindReplDescs ((SeqDescrPtr) objdata, &fs);
+      break;
+    case OBJ_SEQSUB:
+      FindReplSubmitBlock ((SeqSubmitPtr) objdata, &fs);
+      break;
+  }
+
+  /* send select message, if applicable */
+
+  if (fs.send_update == UPDATE_ONCE && fs.dirty) {
+    ObjMgrSetDirtyFlag (entityID, TRUE);
+    ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
+  }
+}
 
 /*=======================================================================*/
 /*                                                                       */
diff --git a/api/findrepl.h b/api/findrepl.h
index 9c17a470..3fff5a5b 100644
--- a/api/findrepl.h
+++ b/api/findrepl.h
@@ -41,52 +41,6 @@
 * ==========================================================================
 *
 *
-* RCS Modification History:
-* -------------------------
-* $Log: findrepl.h,v $
-* Revision 6.6  2006/07/13 18:17:17  bollin
-* use Uint4 instead of Uint2 for itemID values
-*
-* Revision 6.5  2006/01/04 20:39:41  kans
-* added FindStringsInEntity using finite state machine, general cleanup of code
-*
-* Revision 6.4  2005/12/29 20:54:41  kans
-* FindReplaceInEntity takes callback and userdata
-*
-* Revision 6.3  2003/07/31 20:54:54  kans
-* FindReplaceString does not need do_replace argument
-*
-* Revision 6.2  2003/07/31 18:18:03  kans
-* added FindReplaceString
-*
-* Revision 6.1  2000/11/03 20:36:00  kans
-* FindReplaceInEntity replaces FindInEntity and FindInEntityX - complete redesign, no longer using AsnExpOptExplore because of the difficulty of replacing with a larger string (TF + JK)
-*
-* Revision 6.0  1997/08/25 18:05:40  madden
-* Revision changed to 6.0
-*
-* Revision 5.3  1997/06/19 18:37:43  vakatov
-* [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
-*
-* Revision 5.2  1997/03/17 23:44:39  kans
-* added whole_word parameter to FindInEntity and FindInEntityX
-*
- * Revision 5.1  1996/09/06  20:20:41  kans
- * keeps going even if ObjMgrTypeFind returns NULL (e.g., on OBJ_BIOSEQ_SEG),
- * and adds a case_counts parameter for case sensitive/insensitive searches.
- *
- * Revision 5.0  1996/05/28  13:23:23  ostell
- * Set to revision 5.0
- *
- * Revision 1.3  1996/01/03  23:06:32  ostell
- * support for longer replaces, controlled updating
- *
- * Revision 1.1  1995/12/31  18:13:14  kans
- * Initial revision
- *
-* Revision 1.1.1.1  1995/10/19 18:42:10  sad
-* Initial version
-*
 */
 
 #ifndef __FINDREPL_H__
@@ -114,6 +68,38 @@ extern "C" {
 
 typedef void (*FindReplProc) (Uint2 entityID, Uint4 itemID, Uint2 itemtype, Pointer userdata);
 
+typedef void (*StringActionFunc) (CharPtr PNTR strp, Pointer userdata, BoolPtr did_find, BoolPtr did_change);
+/* EXTERNAL FIND-REPLACE FUNCTIONS */
+NLM_EXTERN void StringActionInEntity (
+  Uint2 entityID,
+  Boolean select_item,
+  Int2 send_update,
+  BoolPtr descFilter,
+  BoolPtr featFilter,
+  BoolPtr seqidFilter,
+  Boolean do_seqid_local,
+  StringActionFunc action_func,
+  FindReplProc callback,
+  Pointer userdata
+);
+
+NLM_EXTERN void StringActionForObject (
+  Uint2   datatype,
+  Pointer objdata,
+  Uint2 entityID,
+  Boolean select_item,
+  Int2 send_update,
+  StringActionFunc action_func,
+  FindReplProc callback,
+  Pointer userdata
+);
+
+NLM_EXTERN void SpecialCharReplace (CharPtr PNTR strp, Pointer userdata, BoolPtr did_find, BoolPtr did_change);
+NLM_EXTERN void SpecialCharFind (CharPtr PNTR strp, Pointer userdata, BoolPtr did_find, BoolPtr did_change);
+NLM_EXTERN CharPtr GetSpecialCharacterReplacement (unsigned char ch);
+NLM_EXTERN CharPtr GetSpecialWinCharacterReplacement (unsigned char ch);
+NLM_EXTERN CharPtr GetSpecialMacCharacterReplacement (unsigned char ch);
+
 NLM_EXTERN void FindReplaceInEntity (
   Uint2 entityID,
   CharPtr find_string,
@@ -155,6 +141,9 @@ NLM_EXTERN void FindStringsInEntity (
 );
 
 
+extern void RemoveTaxRef (OrgRefPtr orp);
+
+
 #ifdef __cplusplus
 extern "C" }
 #endif	/* __cplusplus */
diff --git a/api/gbftglob.c b/api/gbftglob.c
index c5d1f0c0..be11dd91 100644
--- a/api/gbftglob.c
+++ b/api/gbftglob.c
@@ -247,12 +247,11 @@ static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"misc_recomb", 0, {-1, -1, -1, -1, -1}, 16,
+   {"misc_recomb", 0, {-1, -1, -1, -1, -1}, 15,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_experiment, GBQUAL_inference, GBQUAL_gene, 
-     GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_organism, 
-     GBQUAL_partial, GBQUAL_standard_name, GBQUAL_usedin,
+     GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, GBQUAL_old_locus_tag, GBQUAL_allele,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"misc_RNA",  0, {-1, -1, -1, -1, -1}, 20,
@@ -388,12 +387,12 @@ static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
       GBQUAL_bound_moiety, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"protein_bind",  1, {GBQUAL_bound_moiety, -1, -1, -1, -1}, 16,
+   {"protein_bind",  1, {GBQUAL_bound_moiety, -1, -1, -1, -1}, 17,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_experiment, GBQUAL_inference, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
       GBQUAL_standard_name, GBQUAL_usedin,
       GBQUAL_locus_tag, GBQUAL_old_locus_tag, GBQUAL_allele,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_operon, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"RBS",  0, {-1, -1, -1, -1, -1}, 15,
@@ -486,7 +485,7 @@ static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"source", 1, {GBQUAL_organism, -1, -1, -1, -1}, 59,
+   {"source", 1, {GBQUAL_organism, -1, -1, -1, -1}, 61,
      {GBQUAL_cell_line, GBQUAL_cell_type, GBQUAL_chloroplast, 
       GBQUAL_chromoplast, GBQUAL_chromosome,
       GBQUAL_citation, GBQUAL_clone, GBQUAL_clone_lib, GBQUAL_country, GBQUAL_cultivar,
@@ -503,7 +502,8 @@ static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
       GBQUAL_organelle, GBQUAL_transgenic, GBQUAL_environmental_sample,
       GBQUAL_isolation_source, GBQUAL_serovar, GBQUAL_mol_type, GBQUAL_segment,
       GBQUAL_ecotype, GBQUAL_collected_by, GBQUAL_collection_date, GBQUAL_identified_by,
-      GBQUAL_lat_lon, GBQUAL_PCR_primers, GBQUAL_metagenomic, -1, -1, -1, -1, -1, -1}},
+      GBQUAL_lat_lon, GBQUAL_PCR_primers, GBQUAL_metagenomic, GBQUAL_culture_collection,
+      GBQUAL_bio_material, -1, -1, -1, -1}},
    {"stem_loop",  0, {-1, -1, -1, -1, -1}, 17,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_experiment, GBQUAL_inference, GBQUAL_function,
       GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, 
@@ -535,12 +535,12 @@ static SematicFeat STATIC__ParFlat_GBFeat[ParFlat_TOTAL_GBFEAT] = {
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
-   {"tmRNA",  0, {-1, -1, -1, -1, -1}, 19,
+   {"tmRNA",  0, {-1, -1, -1, -1, -1}, 20,
      {GBQUAL_citation, GBQUAL_db_xref, GBQUAL_evidence, GBQUAL_experiment, GBQUAL_inference, GBQUAL_function, 
      GBQUAL_gene, GBQUAL_label, GBQUAL_map, GBQUAL_note, GBQUAL_partial, GBQUAL_product,
       GBQUAL_pseudo, GBQUAL_standard_name, GBQUAL_usedin,
-      GBQUAL_locus_tag, GBQUAL_old_locus_tag, GBQUAL_allele, GBQUAL_operon,
-      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+      GBQUAL_locus_tag, GBQUAL_old_locus_tag, GBQUAL_allele, GBQUAL_operon, GBQUAL_tag_peptide,
+      -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}},
    {"transit_peptide",  0, {-1, -1, -1, -1, -1}, 18,
diff --git a/api/macroapi.c b/api/macroapi.c
new file mode 100755
index 00000000..28bdf3d3
--- /dev/null
+++ b/api/macroapi.c
@@ -0,0 +1,11254 @@
+/*   macro.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  macro.c
+*
+* Author:  Colleen Bollin
+*
+* Version Creation Date:   11/8/2007
+*
+* $Revision: 1.58 $
+*
+* File Description: 
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* Date     Name        Description of modification
+* -------  ----------  -----------------------------------------------------
+*
+*
+* ==========================================================================
+*/
+
+#include <asn.h>
+#include <objmacro.h>
+#include <objfeat.h>
+#include <subutil.h>
+#include <objmgr.h>
+#include <objfdef.h>
+#include <gbftdef.h>
+#include <sqnutils.h>
+#include <edutil.h>
+#include <gather.h>
+#include <asn2gnbi.h>
+#define NLM_GENERATED_CODE_PROTO
+#include <macroapi.h>
+#include <seqport.h>
+
+/* structure and create/free functions for CGPSet, used for handling CDS-Gene-Prot sets */
+typedef struct cgpset 
+{
+  ValNodePtr cds_list;
+  ValNodePtr gene_list;
+  ValNodePtr prot_list;
+  ValNodePtr mrna_list;
+} CGPSetData, PNTR CGPSetPtr;
+
+
+
+static CGPSetPtr CGPSetNew (void)
+{
+  CGPSetPtr c;
+
+  c = (CGPSetPtr) MemNew (sizeof (CGPSetData));
+  c->cds_list = NULL;
+  c->gene_list = NULL;
+  c->prot_list = NULL;
+  c->mrna_list = NULL;
+  return c;
+}
+
+
+static CGPSetPtr CGPSetFree (CGPSetPtr c)
+{
+  if (c != NULL) {
+    c->cds_list = ValNodeFree (c->cds_list);
+    c->gene_list = ValNodeFree (c->gene_list);
+    c->prot_list = ValNodeFree (c->prot_list);
+    c->mrna_list = ValNodeFree (c->mrna_list);
+    c = MemFree (c);
+  }
+  return c;
+}
+
+
+static ValNodePtr FreeCGPSetList (ValNodePtr vnp)
+{
+  ValNodePtr vnp_next;
+  
+  while (vnp != NULL) {
+    vnp_next = vnp->next;
+    vnp->next = NULL;
+    vnp->data.ptrvalue = CGPSetFree (vnp->data.ptrvalue);
+    vnp = ValNodeFree (vnp);
+    vnp = vnp_next;
+  }
+  return NULL;
+}
+
+
+/* generic functions for mapping constraints */
+
+typedef struct feattypefeatdef {
+  Int4 feattype;
+  Int4 featdef;
+  CharPtr featname;
+} FeatTypeFeatDefData, PNTR FeatTypeFeatDefPtr;
+
+static FeatTypeFeatDefData feattype_featdef[] = {
+ { Feature_type_any , FEATDEF_ANY , "any" } , 
+ { Feature_type_gene , FEATDEF_GENE , "gene" } , 
+ { Feature_type_org , FEATDEF_ORG , "org" } , 
+ { Feature_type_cds , FEATDEF_CDS , "CDS" } , 
+ { Feature_type_prot , FEATDEF_PROT , "Protein" } , 
+ { Feature_type_preRNA , FEATDEF_preRNA , "preRNA" } , 
+ { Feature_type_mRNA , FEATDEF_mRNA , "mRNA" } , 
+ { Feature_type_tRNA , FEATDEF_tRNA , "tRNA" } , 
+ { Feature_type_rRNA , FEATDEF_rRNA , "rRNA" } , 
+ { Feature_type_snRNA , FEATDEF_snRNA , "snRNA" } , 
+ { Feature_type_scRNA , FEATDEF_scRNA , "scRNA" } , 
+ { Feature_type_otherRNA , FEATDEF_otherRNA , "misc_RNA" } , 
+ { Feature_type_pub , FEATDEF_PUB , "pub" } , 
+ { Feature_type_seq , FEATDEF_SEQ , "seq" } , 
+ { Feature_type_imp , FEATDEF_IMP , "imp" } , 
+ { Feature_type_allele , FEATDEF_allele , "allele" } , 
+ { Feature_type_attenuator , FEATDEF_attenuator , "attenuator" } , 
+ { Feature_type_c_region , FEATDEF_C_region , "c_region" } , 
+ { Feature_type_caat_signal , FEATDEF_CAAT_signal , "caat_signal" } , 
+ { Feature_type_imp_CDS , FEATDEF_Imp_CDS , "imp_CDS" } , 
+ { Feature_type_conflict , FEATDEF_conflict , "conflict" } , 
+ { Feature_type_d_loop , FEATDEF_D_loop , "d_loop" } , 
+ { Feature_type_d_segment , FEATDEF_D_segment , "d_segment" } , 
+ { Feature_type_enhancer , FEATDEF_enhancer , "enhancer" } , 
+ { Feature_type_exon , FEATDEF_exon , "exon" } , 
+ { Feature_type_gC_signal , FEATDEF_GC_signal , "gC_signal" } , 
+ { Feature_type_iDNA , FEATDEF_iDNA , "iDNA" } , 
+ { Feature_type_intron , FEATDEF_intron , "intron" } , 
+ { Feature_type_j_segment , FEATDEF_J_segment , "j_segment" } , 
+ { Feature_type_ltr , FEATDEF_LTR , "ltr" } , 
+ { Feature_type_mat_peptide , FEATDEF_mat_peptide , "mat_peptide" } , 
+ { Feature_type_misc_binding , FEATDEF_misc_binding , "misc_binding" } , 
+ { Feature_type_misc_difference , FEATDEF_misc_difference , "misc_difference" } , 
+ { Feature_type_misc_feature , FEATDEF_misc_feature , "misc_feature" } , 
+ { Feature_type_misc_recomb , FEATDEF_misc_recomb , "misc_recomb" } , 
+ { Feature_type_misc_RNA , FEATDEF_misc_RNA , "misc_RNA" } , 
+ { Feature_type_misc_signal , FEATDEF_misc_signal , "misc_signal" } , 
+ { Feature_type_misc_structure , FEATDEF_misc_structure , "misc_structure" } , 
+ { Feature_type_modified_base , FEATDEF_modified_base , "modified_base" } , 
+ { Feature_type_mutation , FEATDEF_mutation , "mutation" } , 
+ { Feature_type_n_region , FEATDEF_N_region , "n_region" } , 
+ { Feature_type_old_sequence , FEATDEF_old_sequence , "old_sequence" } , 
+ { Feature_type_polyA_signal , FEATDEF_polyA_signal , "polyA_signal" } , 
+ { Feature_type_polyA_site , FEATDEF_polyA_site , "polyA_site" } , 
+ { Feature_type_precursor_RNA , FEATDEF_precursor_RNA , "precursor_RNA" } , 
+ { Feature_type_prim_transcript , FEATDEF_prim_transcript , "prim_transcript" } , 
+ { Feature_type_primer_bind , FEATDEF_primer_bind , "primer_bind" } , 
+ { Feature_type_promoter , FEATDEF_promoter , "promoter" } , 
+ { Feature_type_protein_bind , FEATDEF_protein_bind , "protein_bind" } , 
+ { Feature_type_rbs , FEATDEF_RBS , "rbs" } , 
+ { Feature_type_repeat_region , FEATDEF_repeat_region , "repeat_region" } , 
+ { Feature_type_repeat_unit , FEATDEF_repeat_unit , "repeat_unit" } , 
+ { Feature_type_rep_origin , FEATDEF_rep_origin , "rep_origin" } , 
+ { Feature_type_s_region , FEATDEF_S_region , "s_region" } , 
+ { Feature_type_satellite , FEATDEF_satellite , "satellite" } , 
+ { Feature_type_sig_peptide , FEATDEF_sig_peptide , "sig_peptide" } , 
+ { Feature_type_source , FEATDEF_source , "source" } , 
+ { Feature_type_stem_loop , FEATDEF_stem_loop , "stem_loop" } , 
+ { Feature_type_sts , FEATDEF_STS , "sts" } , 
+ { Feature_type_tata_signal , FEATDEF_TATA_signal , "tata_signal" } , 
+ { Feature_type_terminator , FEATDEF_terminator , "terminator" } , 
+ { Feature_type_transit_peptide , FEATDEF_transit_peptide , "transit_peptide" } , 
+ { Feature_type_unsure , FEATDEF_unsure , "unsure" } , 
+ { Feature_type_v_region , FEATDEF_V_region , "v_region" } , 
+ { Feature_type_v_segment , FEATDEF_V_segment , "v_segment" } , 
+ { Feature_type_variation , FEATDEF_variation , "variation" } , 
+ { Feature_type_virion , FEATDEF_virion , "virion" } , 
+ { Feature_type_n3clip , FEATDEF_3clip , "3clip" } , 
+ { Feature_type_n3UTR , FEATDEF_3UTR , "3UTR" } , 
+ { Feature_type_n5clip , FEATDEF_5clip , "5clip" } , 
+ { Feature_type_n5UTR , FEATDEF_5UTR , "5UTR" } , 
+ { Feature_type_n10_signal , FEATDEF_10_signal , "10_signal" } , 
+ { Feature_type_n35_signal , FEATDEF_35_signal , "35_signal" } , 
+ { Feature_type_site_ref , FEATDEF_site_ref , "site_ref" } , 
+ { Feature_type_region , FEATDEF_REGION , "region" } , 
+ { Feature_type_comment , FEATDEF_COMMENT , "comment" } , 
+ { Feature_type_bond , FEATDEF_BOND , "bond" } , 
+ { Feature_type_site , FEATDEF_SITE , "site" } , 
+ { Feature_type_rsite , FEATDEF_RSITE , "rsite" } , 
+ { Feature_type_user , FEATDEF_USER , "user" } , 
+ { Feature_type_txinit , FEATDEF_TXINIT , "txinit" } , 
+ { Feature_type_num , FEATDEF_NUM , "num" } , 
+ { Feature_type_psec_str , FEATDEF_PSEC_STR , "psec_str" } , 
+ { Feature_type_non_std_residue , FEATDEF_NON_STD_RESIDUE , "non_std_residue" } , 
+ { Feature_type_het , FEATDEF_HET , "het" } , 
+ { Feature_type_biosrc , FEATDEF_BIOSRC , "biosrc" } , 
+ { Feature_type_preprotein , FEATDEF_preprotein , "preprotein" } , 
+ { Feature_type_mat_peptide_aa , FEATDEF_mat_peptide_aa , "mat_peptide_aa" } , 
+ { Feature_type_sig_peptide_aa , FEATDEF_sig_peptide_aa , "sig_peptide_aa" } , 
+ { Feature_type_transit_peptide_aa , FEATDEF_transit_peptide_aa , "transit_peptide_aa" } , 
+ { Feature_type_snoRNA , FEATDEF_snoRNA , "snoRNA" } , 
+ { Feature_type_gap , FEATDEF_gap , "gap" } , 
+ { Feature_type_operon , FEATDEF_operon , "operon" } , 
+ { Feature_type_oriT , FEATDEF_oriT , "oriT" } , 
+ { Feature_type_ncRNA , FEATDEF_ncRNA , "ncRNA" } , 
+ { Feature_type_tmRNA , FEATDEF_tmRNA , "tmRNA" }};
+
+#define NUM_feattype_featdef sizeof (feattype_featdef) / sizeof (FeatTypeFeatDefData)
+
+NLM_EXTERN Int4 GetFeatdefFromFeatureType (Int4 feature_type) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_feattype_featdef; i++) {
+    if (feature_type == feattype_featdef[i].feattype) {
+      return feattype_featdef[i].featdef;
+    }
+  }
+  return FEATDEF_BAD;
+}
+
+
+NLM_EXTERN CharPtr GetFeatureNameFromFeatureType (Int4 feature_type)
+{
+  CharPtr str = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_feattype_featdef && str == NULL; i++) {
+    if (feature_type == feattype_featdef[i].feattype) {
+      str = feattype_featdef[feature_type].featname;
+    }
+  } 
+  if (str == NULL) {
+    str = "Unknown feature type";
+  }
+  return str;
+}
+
+
+static Boolean Matchnamestring (CharPtr name1, CharPtr name2)
+{
+  if (name1 == NULL && name2 == NULL) {
+    return TRUE;
+  } else if (name1 == NULL || name2 == NULL) {
+    return FALSE;
+  } else {
+    while (*name1 != 0 && *name2 != 0) {
+      while (*name1 == ' ' || *name1 == '-' || *name1 == '_') {
+        name1++;
+      }
+      while (*name2 == ' ' || *name2 == '-' || *name2 == '_') {
+        name2++;
+      }
+      if (*name1 != *name2) {
+        return FALSE;
+      }
+      name1++;
+      name2++;
+    }
+    if (*name1 == 0 && *name2 == 0) {
+      return TRUE;
+    } else {
+      return FALSE;
+    }
+  }
+}
+
+
+NLM_EXTERN Int4 GetFeatureTypeByName (CharPtr feat_name)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_feattype_featdef; i++) {
+    if (Matchnamestring (feattype_featdef[i].featname, feat_name)) {
+      return feattype_featdef[i].feattype;
+    }
+  }
+  return -1;  
+}
+
+
+NLM_EXTERN void AddImportFeaturesToChoiceList (ValNodePtr PNTR feature_type_list)
+{
+  Int4 i, seqfeattype;
+  CharPtr featname;
+  ValNodePtr tmp_list = NULL;
+
+  for (i = 1; i < NUM_feattype_featdef; i++) {
+    if (feattype_featdef[i].feattype == Feature_type_gap) continue;
+    seqfeattype = FindFeatFromFeatDefType (feattype_featdef[i].featdef);
+    if (seqfeattype == SEQFEAT_IMP) {
+      featname = GetFeatureNameFromFeatureType (feattype_featdef[i].feattype);
+      if (featname != NULL) {
+        ValNodeAddPointer (&tmp_list, feattype_featdef[i].feattype, StringSave (featname));
+      }
+    }
+  }
+  tmp_list = ValNodeSort (tmp_list, SortVnpByString);
+  ValNodeLink (feature_type_list, tmp_list);
+}
+
+
+
+static Boolean IsMostUsedFeature (Uint1 val)
+{
+  if (val == Feature_type_gene
+      || val == Feature_type_cds
+      || val == Feature_type_prot
+      || val == Feature_type_exon
+      || val == Feature_type_intron
+      || val == Feature_type_mRNA
+      || val == Feature_type_rRNA
+      || val == Feature_type_otherRNA) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+
+static int LIBCALLBACK SortVnpByFeatureName (VoidPtr ptr1, VoidPtr ptr2)
+
+{
+  CharPtr     str1;
+  CharPtr     str2;
+  ValNodePtr  vnp1;
+  ValNodePtr  vnp2;
+  Boolean     most_used1, most_used2;
+
+  if (ptr1 != NULL && ptr2 != NULL) {
+    vnp1 = *((ValNodePtr PNTR) ptr1);
+    vnp2 = *((ValNodePtr PNTR) ptr2);
+    if (vnp1 != NULL && vnp2 != NULL) {
+      most_used1 = IsMostUsedFeature (vnp1->choice);
+      most_used2 = IsMostUsedFeature (vnp2->choice);
+      if (most_used1 && !most_used2) {
+        return -1;
+      } else if (!most_used1 && most_used2) {
+        return 1;
+      } else {
+        str1 = (CharPtr) vnp1->data.ptrvalue;
+        str2 = (CharPtr) vnp2->data.ptrvalue;
+        if (str1 != NULL && str2 != NULL) {
+          return StringICmp (str1, str2);
+        }
+      }
+    }
+  }
+  return 0;
+}
+
+
+NLM_EXTERN void AddAllFeaturesToChoiceList (ValNodePtr PNTR feature_type_list)
+{
+  Int4 i;
+  CharPtr featname;
+  ValNodePtr tmp_list = NULL;
+
+  for (i = 1; i < NUM_feattype_featdef; i++) {
+    if (feattype_featdef[i].feattype == Feature_type_gap) continue;
+    featname = GetFeatureNameFromFeatureType (feattype_featdef[i].feattype);
+    if (featname != NULL) {
+      ValNodeAddPointer (&tmp_list, feattype_featdef[i].feattype, StringSave (featname));
+    }
+  }
+  tmp_list = ValNodeSort (tmp_list, SortVnpByFeatureName);
+  ValNodeLink (feature_type_list, tmp_list);
+}
+
+
+typedef struct featqualgbqual {
+  Int4 featqual;
+  Int4 gbqual;
+  CharPtr qualname;
+} FeatQualGBQualData, PNTR FeatQualGBQualPtr;
+
+static FeatQualGBQualData featqual_gbqual[] = {
+ { Feat_qual_legal_allele , GBQUAL_allele , "allele" } , 
+ { Feat_qual_legal_anticodon , GBQUAL_anticodon , "anticodon" } , 
+ { Feat_qual_legal_bound_moiety , GBQUAL_bound_moiety , "bound-moiety" } , 
+ { Feat_qual_legal_chromosome , GBQUAL_chromosome , "chromosome" } , 
+ { Feat_qual_legal_citation , GBQUAL_citation , "citation" } , 
+ { Feat_qual_legal_codon , GBQUAL_codon , "codon" } , 
+ { Feat_qual_legal_codon_start , GBQUAL_codon_start , "codon-start" } , 
+ { Feat_qual_legal_compare , GBQUAL_compare , "compare" } , 
+ { Feat_qual_legal_cons_splice , GBQUAL_cons_splice , "cons-splice" } , 
+ { Feat_qual_legal_db_xref , GBQUAL_db_xref , "db-xref" } , 
+ { Feat_qual_legal_direction , GBQUAL_direction , "direction" } , 
+ { Feat_qual_legal_environmental_sample , GBQUAL_environmental_sample , "environmental-sample" } , 
+ { Feat_qual_legal_evidence , GBQUAL_evidence , "evidence" } , 
+ { Feat_qual_legal_exception , GBQUAL_exception , "exception" } , 
+ { Feat_qual_legal_experiment , GBQUAL_experiment , "experiment" } , 
+ { Feat_qual_legal_focus , GBQUAL_focus , "focus" } , 
+ { Feat_qual_legal_frequency , GBQUAL_frequency , "frequency" } , 
+ { Feat_qual_legal_function , GBQUAL_function , "function" } , 
+ { Feat_qual_legal_gene , GBQUAL_gene , "locus" } , 
+ { Feat_qual_legal_inference , GBQUAL_inference , "inference" } , 
+ { Feat_qual_legal_label , GBQUAL_label , "label" } , 
+ { Feat_qual_legal_locus_tag , GBQUAL_locus_tag , "locus-tag" } , 
+ { Feat_qual_legal_map , GBQUAL_map , "map" } , 
+ { Feat_qual_legal_mobile_element , GBQUAL_mobile_element , "mobile-element" } , 
+ { Feat_qual_legal_mod_base , GBQUAL_mod_base , "mod-base" } , 
+ { Feat_qual_legal_mol_type , GBQUAL_mol_type , "mol-type" } , 
+ { Feat_qual_legal_ncRNA_class , GBQUAL_ncRNA_class , "ncRNA-class" } , 
+ { Feat_qual_legal_note , GBQUAL_note , "note" } , 
+ { Feat_qual_legal_number , GBQUAL_number , "number" } , 
+ { Feat_qual_legal_old_locus_tag , GBQUAL_old_locus_tag , "old-locus-tag" } , 
+ { Feat_qual_legal_operon , GBQUAL_operon , "operon" } , 
+ { Feat_qual_legal_organism , GBQUAL_organism , "organism" } , 
+ { Feat_qual_legal_organelle , GBQUAL_organelle , "organelle" } , 
+ { Feat_qual_legal_partial , GBQUAL_partial , "partial" } , 
+ { Feat_qual_legal_phenotype , GBQUAL_phenotype , "phenotype" } , 
+ { Feat_qual_legal_plasmid , GBQUAL_plasmid , "plasmid" } , 
+ { Feat_qual_legal_product , GBQUAL_product , "product" } , 
+ { Feat_qual_legal_protein_id , GBQUAL_protein_id , "protein-id" } , 
+ { Feat_qual_legal_pseudo , GBQUAL_pseudo , "pseudo" } , 
+ { Feat_qual_legal_rearranged , GBQUAL_rearranged , "rearranged" } , 
+ { Feat_qual_legal_replace , GBQUAL_replace , "replace" } , 
+ { Feat_qual_legal_rpt_family , GBQUAL_rpt_family , "rpt-family" } , 
+ { Feat_qual_legal_rpt_type , GBQUAL_rpt_type , "rpt-type" } , 
+ { Feat_qual_legal_rpt_unit , GBQUAL_rpt_unit , "rpt-unit" } , 
+ { Feat_qual_legal_rpt_unit_seq , GBQUAL_rpt_unit_seq , "rpt-unit-seq" } , 
+ { Feat_qual_legal_rpt_unit_range , GBQUAL_rpt_unit_range , "rpt-unit-range" } , 
+ { Feat_qual_legal_segment , GBQUAL_segment , "segment" } , 
+ { Feat_qual_legal_sequenced_mol , GBQUAL_sequenced_mol , "sequenced-mol" } , 
+ { Feat_qual_legal_standard_name , GBQUAL_standard_name , "standard-name" } , 
+ { Feat_qual_legal_transcript_id , GBQUAL_transcript_id , "transcript-id" } , 
+ { Feat_qual_legal_transgenic , GBQUAL_transgenic , "transgenic" } , 
+ { Feat_qual_legal_translation , GBQUAL_translation , "translation" } , 
+ { Feat_qual_legal_transl_except , GBQUAL_transl_except , "transl-except" } , 
+ { Feat_qual_legal_transl_table , GBQUAL_transl_table , "transl-table" } , 
+ { Feat_qual_legal_usedin , GBQUAL_usedin , "usedin" } };
+
+#define NUM_featqual_gbqual sizeof (featqual_gbqual) / sizeof (FeatQualGBQualData)
+
+
+NLM_EXTERN Int4 GetNumFeatQual (void)
+{
+  return NUM_featqual_gbqual;
+}
+
+
+static Int4 GetGBQualFromFeatQual (Int4 featqual) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_featqual_gbqual; i++) {
+    if (featqual == featqual_gbqual[i].featqual) {
+      return featqual_gbqual[i].gbqual;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN CharPtr GetFeatQualName (Int4 featqual) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_featqual_gbqual; i++) {
+    if (featqual == featqual_gbqual[i].featqual) {
+      return featqual_gbqual[i].qualname;
+    }
+  }
+  return NULL;
+}
+
+
+NLM_EXTERN Int4 GetFeatQualByName (CharPtr qualname) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_featqual_gbqual; i++) {
+    if (Matchnamestring (featqual_gbqual[i].qualname, qualname)) {
+      return featqual_gbqual[i].featqual;
+    }
+  }
+  return -1;  
+}
+
+
+NLM_EXTERN void AddAllFeatureFieldsToChoiceList (ValNodePtr PNTR field_list)
+{
+  Int4 i;
+
+  for (i = 1; i < NUM_featqual_gbqual; i++) {
+    ValNodeAddPointer (field_list, featqual_gbqual[i].featqual, StringSave (featqual_gbqual[i].qualname));
+  }
+}
+
+
+#define IS_ORGMOD 1
+#define IS_SUBSRC 2
+#define IS_OTHER  3
+
+typedef struct srcqualscqual {
+  Int4 srcqual;
+  Int4 subtype;
+  Int4 typeflag;
+  CharPtr qualname;
+} SrcQualSCQualData, PNTR SrcQualSCQualPtr;
+
+static SrcQualSCQualData srcqual_scqual[] = {
+ { Source_qual_acronym , ORGMOD_acronym , IS_ORGMOD , "acronym" } , 
+ { Source_qual_anamorph , ORGMOD_anamorph , IS_ORGMOD , "anamorph" } , 
+ { Source_qual_authority , ORGMOD_authority , IS_ORGMOD , "authority" } , 
+ { Source_qual_bio_material , ORGMOD_bio_material , IS_ORGMOD , "bio-material" } , 
+ { Source_qual_biotype , ORGMOD_biotype , IS_ORGMOD , "biotype" } , 
+ { Source_qual_biovar , ORGMOD_biovar , IS_ORGMOD , "biovar" } , 
+ { Source_qual_breed , ORGMOD_breed , IS_ORGMOD , "breed" } , 
+ { Source_qual_cell_line , SUBSRC_cell_line , IS_SUBSRC , "cell-line" } , 
+ { Source_qual_cell_type , SUBSRC_cell_type , IS_SUBSRC , "cell-type" } , 
+ { Source_qual_chemovar , ORGMOD_chemovar , IS_ORGMOD , "chemovar" } , 
+ { Source_qual_chromosome , SUBSRC_chromosome , IS_SUBSRC , "chromosome" } , 
+ { Source_qual_clone , SUBSRC_clone , IS_SUBSRC , "clone" } , 
+ { Source_qual_clone_lib , SUBSRC_clone_lib , IS_SUBSRC , "clone-lib" } , 
+ { Source_qual_collected_by , SUBSRC_collected_by , IS_SUBSRC , "collected-by" } , 
+ { Source_qual_collection_date , SUBSRC_collection_date , IS_SUBSRC , "collection-date" } , 
+ { Source_qual_common , ORGMOD_common , IS_ORGMOD , "common" } , 
+ { Source_qual_common_name , 0 , IS_OTHER , "common name" } , 
+ { Source_qual_country , SUBSRC_country , IS_SUBSRC , "country" } , 
+ { Source_qual_cultivar , ORGMOD_cultivar , IS_ORGMOD , "cultivar" } , 
+ { Source_qual_culture_collection , ORGMOD_culture_collection , IS_ORGMOD , "culture-collection" } , 
+ { Source_qual_dev_stage , SUBSRC_dev_stage , IS_SUBSRC , "dev-stage" } , 
+ { Source_qual_division , 0 , IS_OTHER, "divistion" } ,
+ { Source_qual_dosage , ORGMOD_dosage , IS_ORGMOD , "dosage" } , 
+ { Source_qual_ecotype , ORGMOD_ecotype , IS_ORGMOD , "ecotype" } , 
+ { Source_qual_endogenous_virus_name , SUBSRC_endogenous_virus_name , IS_SUBSRC , "endogenous-virus-name" } , 
+ { Source_qual_environmental_sample , SUBSRC_environmental_sample , IS_SUBSRC , "environmental-sample" } , 
+ { Source_qual_forma , ORGMOD_forma , IS_ORGMOD , "forma" } , 
+ { Source_qual_forma_specialis , ORGMOD_forma_specialis , IS_ORGMOD , "forma-specialis" } , 
+ { Source_qual_frequency , SUBSRC_frequency , IS_SUBSRC , "frequency" } , 
+ { Source_qual_fwd_primer_name , SUBSRC_fwd_primer_name , IS_SUBSRC , "fwd-primer-name" } , 
+ { Source_qual_fwd_primer_seq , SUBSRC_fwd_primer_seq , IS_SUBSRC , "fwd-primer-seq" } , 
+ { Source_qual_gb_acronym , ORGMOD_gb_acronym , IS_ORGMOD , "gb-acronym" } , 
+ { Source_qual_gb_anamorph , ORGMOD_gb_anamorph , IS_ORGMOD , "gb-anamorph" } , 
+ { Source_qual_gb_synonym , ORGMOD_gb_synonym , IS_ORGMOD , "gb-synonym" } , 
+ { Source_qual_genotype , SUBSRC_genotype , IS_SUBSRC , "genotype" } , 
+ { Source_qual_germline , SUBSRC_germline , IS_SUBSRC , "germline" } , 
+ { Source_qual_group , ORGMOD_group , IS_ORGMOD , "group" } , 
+ { Source_qual_haplotype , SUBSRC_haplotype , IS_SUBSRC , "haplotype" } , 
+ { Source_qual_identified_by , SUBSRC_identified_by , IS_SUBSRC , "identified-by" } , 
+ { Source_qual_insertion_seq_name , SUBSRC_insertion_seq_name , IS_SUBSRC , "insertion-seq-name" } , 
+ { Source_qual_isolate , ORGMOD_isolate , IS_ORGMOD , "isolate" } , 
+ { Source_qual_isolation_source , SUBSRC_isolation_source , IS_SUBSRC , "isolation-source" } , 
+ { Source_qual_lab_host , SUBSRC_lab_host , IS_SUBSRC , "lab-host" } , 
+ { Source_qual_lat_lon , SUBSRC_lat_lon , IS_SUBSRC , "lat-lon" } , 
+ { Source_qual_lineage , 0, IS_OTHER, "lineage" } ,
+ { Source_qual_map , SUBSRC_map , IS_SUBSRC , "map" } , 
+ { Source_qual_metagenome_source , ORGMOD_metagenome_source , IS_ORGMOD , "metagenome-source" } , 
+ { Source_qual_metagenomic , SUBSRC_metagenomic , IS_SUBSRC , "metagenomic" } , 
+ { Source_qual_old_lineage , ORGMOD_old_lineage , IS_ORGMOD , "old-lineage" } , 
+ { Source_qual_old_name , ORGMOD_old_name , IS_ORGMOD , "old-name" } , 
+ { Source_qual_orgmod_note , ORGMOD_other, IS_ORGMOD, "orgmod note" } ,
+ { Source_qual_nat_host , ORGMOD_nat_host , IS_ORGMOD , "nat-host" } , 
+ { Source_qual_pathovar , ORGMOD_pathovar , IS_ORGMOD , "pathovar" } , 
+ { Source_qual_plasmid_name , SUBSRC_plasmid_name , IS_SUBSRC , "plasmid-name" } , 
+ { Source_qual_plastid_name , SUBSRC_plastid_name , IS_SUBSRC , "plastid-name" } , 
+ { Source_qual_pop_variant , SUBSRC_pop_variant , IS_SUBSRC , "pop-variant" } , 
+ { Source_qual_rearranged , SUBSRC_rearranged , IS_SUBSRC , "rearranged" } , 
+ { Source_qual_rev_primer_name , SUBSRC_rev_primer_name , IS_SUBSRC , "rev-primer-name" } , 
+ { Source_qual_rev_primer_seq , SUBSRC_rev_primer_seq , IS_SUBSRC , "rev-primer-seq" } , 
+ { Source_qual_segment , SUBSRC_segment , IS_SUBSRC , "segment" } , 
+ { Source_qual_serogroup , ORGMOD_serogroup , IS_ORGMOD , "serogroup" } , 
+ { Source_qual_serotype , ORGMOD_serotype , IS_ORGMOD , "serotype" } , 
+ { Source_qual_serovar , ORGMOD_serovar , IS_ORGMOD , "serovar" } , 
+ { Source_qual_sex , SUBSRC_sex , IS_SUBSRC , "sex" } , 
+ { Source_qual_specimen_voucher , ORGMOD_specimen_voucher , IS_ORGMOD , "specimen-voucher" } , 
+ { Source_qual_strain , ORGMOD_strain , IS_ORGMOD , "strain" } , 
+ { Source_qual_subclone , SUBSRC_subclone , IS_SUBSRC , "subclone" } , 
+ { Source_qual_subgroup , ORGMOD_subgroup , IS_ORGMOD , "subgroup" } , 
+ { Source_qual_subsource_note , SUBSRC_other , IS_SUBSRC , "subsource note" } ,
+ { Source_qual_sub_species , ORGMOD_sub_species , IS_ORGMOD , "sub-species" } , 
+ { Source_qual_substrain , ORGMOD_substrain , IS_ORGMOD , "substrain" } , 
+ { Source_qual_subtype , ORGMOD_subtype , IS_ORGMOD , "subtype" } , 
+ { Source_qual_synonym , ORGMOD_synonym , IS_ORGMOD , "synonym" } , 
+ { Source_qual_taxname , 0 , IS_OTHER , "taxname" } , 
+ { Source_qual_teleomorph , ORGMOD_teleomorph , IS_ORGMOD , "teleomorph" } , 
+ { Source_qual_tissue_lib , SUBSRC_tissue_lib , IS_SUBSRC , "tissue-lib" } , 
+ { Source_qual_tissue_type , SUBSRC_tissue_type , IS_SUBSRC , "tissue-type" } , 
+ { Source_qual_transgenic , SUBSRC_transgenic , IS_SUBSRC , "transgenic" } , 
+ { Source_qual_transposon_name , SUBSRC_transposon_name , IS_SUBSRC , "transposon-name" } , 
+ { Source_qual_type , ORGMOD_type , IS_ORGMOD , "type" } , 
+ { Source_qual_variety , ORGMOD_variety , IS_ORGMOD , "variety" } };
+
+#define NUM_srcqual_scqual sizeof (srcqual_scqual) / sizeof (SrcQualSCQualData)
+
+static Int4 GetSubSrcQualFromSrcQual (Int4 srcqual) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_srcqual_scqual; i++) {
+    if (srcqual == srcqual_scqual[i].srcqual) {
+      if (srcqual_scqual[i].typeflag == IS_SUBSRC) {
+        return srcqual_scqual[i].subtype;
+      } else {
+        return -1;
+      }
+    }
+  }
+  return -1;
+}
+
+
+static Int4 GetOrgModQualFromSrcQual (Int4 srcqual) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_srcqual_scqual; i++) {
+    if (srcqual == srcqual_scqual[i].srcqual) {
+      if (srcqual_scqual[i].typeflag == IS_ORGMOD) {
+        return srcqual_scqual[i].subtype;
+      } else {
+        return -1;
+      }
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN Boolean IsNonTextSourceQual (Int4 srcqual)
+{
+  if (srcqual == Source_qual_transgenic
+      || srcqual == Source_qual_germline
+      || srcqual == Source_qual_metagenomic
+      || srcqual == Source_qual_environmental_sample
+      || srcqual == Source_qual_rearranged)
+  {
+    return TRUE;  
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+
+NLM_EXTERN CharPtr GetSourceQualName (Int4 srcqual)
+{
+  CharPtr str = NULL;
+  Int4    i;
+
+  for (i = 0; i < NUM_srcqual_scqual && str == NULL; i++) {
+    if (srcqual_scqual[i].srcqual == srcqual) {
+      str = srcqual_scqual[i].qualname;
+    }
+  }
+  if (str == NULL) {
+    str = "Unknown source qualifier";
+  }
+  return str;
+}
+
+
+NLM_EXTERN Int4 GetSourceQualTypeByName (CharPtr qualname)
+{
+  Int4    i;
+
+  for (i = 0; i < NUM_srcqual_scqual; i++) {
+    if (Matchnamestring(srcqual_scqual[i].qualname, qualname)) {
+      return srcqual_scqual[i].srcqual;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN ValNodePtr GetSourceQualList (void)
+{
+  ValNodePtr list = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_srcqual_scqual; i++) {
+    ValNodeAddPointer (&list, 0, StringSave (srcqual_scqual[i].qualname));
+  }
+  return list;
+}
+
+typedef struct srclocgenome {
+  Int4 srcloc;
+  Int4 genome;
+  CharPtr name;
+} SrcLocGenomeData, PNTR SrcLocGenomePtr;
+
+static SrcLocGenomeData srcloc_genome[] = {
+ { Source_location_unknown , GENOME_unknown , "unknown" } ,
+ { Source_location_genomic , GENOME_genomic , "genomic" } ,
+ { Source_location_chloroplast , GENOME_chloroplast , "chloroplast" } ,
+ { Source_location_chromoplast , GENOME_chromoplast , "chromoplast" } ,
+ { Source_location_kinetoplast , GENOME_kinetoplast , "kinetoplast" } ,
+ { Source_location_mitochondrion , GENOME_mitochondrion , "mitochondrion" } ,
+ { Source_location_plastid , GENOME_plastid , "plastid" } ,
+ { Source_location_macronuclear , GENOME_macronuclear , "macronuclear" } ,
+ { Source_location_extrachrom , GENOME_extrachrom , "extrachrom" } ,
+ { Source_location_plasmid , GENOME_plasmid , "plasmid" } ,
+ { Source_location_transposon , GENOME_transposon , "transposon" } ,
+ { Source_location_insertion_seq , GENOME_insertion_seq , "insertion-seq" } ,
+ { Source_location_cyanelle , GENOME_cyanelle , "cyanelle" } ,
+ { Source_location_proviral , GENOME_proviral , "proviral" } ,
+ { Source_location_virion , GENOME_virion , "virion" } ,
+ { Source_location_nucleomorph , GENOME_nucleomorph , "nucleomorph" } ,
+ { Source_location_apicoplast , GENOME_apicoplast , "apicoplast" } ,
+ { Source_location_leucoplast , GENOME_leucoplast , "leucoplast" } ,
+ { Source_location_proplastid , GENOME_proplastid , "proplastid" } ,
+ { Source_location_endogenous_virus , GENOME_endogenous_virus , "endogenous-virus" } ,
+ { Source_location_hydrogenosome , GENOME_hydrogenosome , "hydrogenosome" } ,
+ { Source_location_chromosome , 21 , "chromosome" } ,
+ { Source_location_chromatophore , 22 , "chromatophore" } };
+
+#define NUM_srcloc_genome sizeof (srcloc_genome) / sizeof (SrcLocGenomeData)
+
+NLM_EXTERN Int4 GenomeFromSrcLoc (Int4 srcloc) \
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_srcloc_genome; i++) {
+    if (srcloc_genome[i].srcloc == srcloc) {
+      return srcloc_genome[i].genome;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN CharPtr LocNameFromGenome (Int4 genome) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_srcloc_genome; i++) {
+    if (srcloc_genome[i].genome == genome) {
+      return srcloc_genome[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+static Int4 GenomeFromLocName (CharPtr loc_name)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_srcloc_genome; i++) {
+    if (StringICmp (srcloc_genome[i].name, loc_name) == 0) {
+      return srcloc_genome[i].genome;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN ValNodePtr GetLocationList (Boolean for_remove)
+{
+  ValNodePtr list = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_srcloc_genome; i++) {
+    if (for_remove && srcloc_genome[i].srcloc == Source_location_unknown) {
+      ValNodeAddPointer (&list, srcloc_genome[i].srcloc, StringSave ("any"));
+    } else {
+      ValNodeAddPointer (&list, srcloc_genome[i].srcloc, StringSave (srcloc_genome[i].name));
+    }
+  }
+  return list;
+}
+
+
+typedef struct srcorigorigin {
+  Int4 srcorig;
+  Int4 origin;
+  CharPtr name;
+} SrcOrigOriginData, PNTR SrcrigOriginPtr;
+
+static SrcOrigOriginData srcorig_origin[] = {
+ { Source_origin_unknown , 0 , "unknown" } ,
+ { Source_origin_natural , 1 , "natural" } ,
+ { Source_origin_natmut , 2 , "natmut" } ,
+ { Source_origin_mut , 3 , "mut" } ,
+ { Source_origin_artificial , 4 , "artificial" } ,
+ { Source_origin_synthetic , 5 , "synthetic" } ,
+ { Source_origin_other , 255 , "other" } };
+
+#define NUM_srcorig_origin sizeof (srcorig_origin) / sizeof (SrcOrigOriginData)
+
+NLM_EXTERN Int4 OriginFromSrcOrig (Int4 srcorig) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_srcorig_origin; i++) {
+    if (srcorig_origin[i].srcorig == srcorig) {
+      return srcorig_origin[i].origin;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN CharPtr OriginNameFromOrigin (Int4 origin) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_srcorig_origin; i++) {
+    if (srcorig_origin[i].origin == origin) {
+      return srcorig_origin[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+static Int4 OriginFromOriginName (CharPtr origin_name)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_srcorig_origin; i++) {
+    if (StringCmp (srcorig_origin[i].name, origin_name) == 0) {
+      return srcorig_origin[i].origin;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN ValNodePtr GetOriginList (Boolean for_remove)
+{
+  ValNodePtr list = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_srcorig_origin; i++) {
+    if (for_remove && srcorig_origin[i].srcorig == Source_origin_unknown) {
+      ValNodeAddPointer (&list, srcorig_origin[i].srcorig, StringSave ("any"));
+    } else {
+      ValNodeAddPointer (&list, srcorig_origin[i].srcorig, StringSave (srcorig_origin[i].name));
+    }
+  }
+  return list;
+}
+
+
+typedef struct cdsgeneprotfieldname {
+  Int4 field;
+  CharPtr name;
+} CDSGeneProtFieldNameData, PNTR CDSGeneProtFieldNamePtr;
+
+static CDSGeneProtFieldNameData cdsgeneprotfield_name[] = {
+{ CDSGeneProt_field_cds_comment , "CDS comment" } ,
+{ CDSGeneProt_field_gene_locus , "gene locus" } ,
+{ CDSGeneProt_field_gene_description , "gene description" } ,
+{ CDSGeneProt_field_gene_comment , "gene comment" } ,
+{ CDSGeneProt_field_gene_allele , "allele" } ,
+{ CDSGeneProt_field_gene_maploc , "maploc" } ,
+{ CDSGeneProt_field_gene_locus_tag , "locus tag" } ,
+{ CDSGeneProt_field_gene_synonym , "synonym" } ,
+{ CDSGeneProt_field_gene_old_locus_tag , "old locus tag" } ,
+{ CDSGeneProt_field_mrna_product , "mRNA product" } ,
+{ CDSGeneProt_field_mrna_comment , "mRNA comment" } ,
+{ CDSGeneProt_field_prot_name , "protein name" } ,
+{ CDSGeneProt_field_prot_description , "protein description" } ,
+{ CDSGeneProt_field_prot_ec_number , "protein EC number" } ,
+{ CDSGeneProt_field_prot_activity , "protein activity" } ,
+{ CDSGeneProt_field_prot_comment , "protein comment" } ,
+{ CDSGeneProt_field_mat_peptide_name , "mat-peptide name" } ,
+{ CDSGeneProt_field_mat_peptide_description ,  "mat-peptide description" } ,
+{ CDSGeneProt_field_mat_peptide_ec_number , "mat-peptide EC number" } ,
+{ CDSGeneProt_field_mat_peptide_activity , "mat-peptide activity" } ,
+{ CDSGeneProt_field_mat_peptide_comment , "mat-peptide comment" } };
+
+#define NUM_cdsgeneprotfield_name sizeof (cdsgeneprotfield_name) / sizeof (CDSGeneProtFieldNameData)
+
+NLM_EXTERN CharPtr CDSGeneProtNameFromField (Int4 field) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_cdsgeneprotfield_name; i++) {
+    if (cdsgeneprotfield_name[i].field == field) {
+      return cdsgeneprotfield_name[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+NLM_EXTERN void AddAllCDSGeneProtFieldsToChoiceList (ValNodePtr PNTR field_list)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_cdsgeneprotfield_name; i++) {
+    ValNodeAddPointer (field_list, cdsgeneprotfield_name[i].field, StringSave (cdsgeneprotfield_name[i].name));
+  }
+}
+
+
+typedef struct cdsgeneprotfeatname {
+  Int4 feature_type;
+  CharPtr name;
+} CDSGeneProtFeatNameData, PNTR CDSGeneProtFeatNamePtr;
+
+static CDSGeneProtFeatNameData cdsgeneprotfeat_name[] = {
+{ CDSGeneProt_feature_type_constraint_gene , "gene" } ,
+{ CDSGeneProt_feature_type_constraint_mRNA , "mRNA" } ,
+{ CDSGeneProt_feature_type_constraint_cds , "CDS" } ,
+{ CDSGeneProt_feature_type_constraint_prot , "protein" } ,
+{ CDSGeneProt_feature_type_constraint_mat_peptide , "mat-peptide" }};
+
+#define NUM_cdsgeneprotfeat_name sizeof (cdsgeneprotfeat_name) / sizeof (CDSGeneProtFeatNameData)
+
+NLM_EXTERN CharPtr CDSGeneProtFeatureNameFromFeatureType (Int4 feature_type)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_cdsgeneprotfeat_name; i++) {
+    if (cdsgeneprotfeat_name[i].feature_type == feature_type) {
+      return cdsgeneprotfeat_name[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+NLM_EXTERN void AddAllCDSGeneProtFeaturesToChoiceList (ValNodePtr PNTR field_list)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_cdsgeneprotfeat_name; i++) {
+    ValNodeAddPointer (field_list, cdsgeneprotfeat_name[i].feature_type, StringSave (cdsgeneprotfeat_name[i].name));
+  }
+}
+
+
+NLM_EXTERN FeatureFieldPtr FeatureFieldFromCDSGeneProtField (Uint2 cds_gene_prot_field)
+{
+  FeatureFieldPtr f = NULL;
+
+  switch (cds_gene_prot_field) {
+    case CDSGeneProt_field_cds_comment:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_cds;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_note;
+      break;
+    case CDSGeneProt_field_gene_locus:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_gene;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_gene;
+      break;
+    case CDSGeneProt_field_gene_description:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_gene;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_gene_description;
+      break;
+    case CDSGeneProt_field_gene_comment:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_gene;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_note;
+      break;
+    case CDSGeneProt_field_gene_allele:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_gene;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_allele;
+      break;
+    case CDSGeneProt_field_gene_maploc:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_gene;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_map;
+      break;
+    case CDSGeneProt_field_gene_locus_tag:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_gene;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_locus_tag;
+      break;
+    case CDSGeneProt_field_gene_synonym:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_gene;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_synonym;
+      break;
+    case CDSGeneProt_field_gene_old_locus_tag:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_gene;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_old_locus_tag;
+      break;
+    case CDSGeneProt_field_mrna_product:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_mRNA;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_product;
+      break;
+    case CDSGeneProt_field_mrna_comment:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_mRNA;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_note;
+      break;
+    case CDSGeneProt_field_prot_name:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_prot;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_product;
+      break;
+    case CDSGeneProt_field_prot_description:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_prot;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_description;
+      break;
+    case CDSGeneProt_field_prot_ec_number:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_prot;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_ec_number;
+      break;
+    case CDSGeneProt_field_prot_activity:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_prot;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_activity;
+      break;
+    case CDSGeneProt_field_prot_comment:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_prot;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_note;
+      break;
+    case CDSGeneProt_field_mat_peptide_name:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_mat_peptide;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_product;
+      break;
+    case CDSGeneProt_field_mat_peptide_description:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_mat_peptide;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_description;
+      break;
+    case CDSGeneProt_field_mat_peptide_ec_number:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_mat_peptide;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_ec_number;
+      break;
+    case CDSGeneProt_field_mat_peptide_activity:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_mat_peptide;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_activity;
+      break;
+    case CDSGeneProt_field_mat_peptide_comment:
+      f = FeatureFieldNew ();
+      f->type = Feature_type_mat_peptide;
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FeatQualChoice_legal_qual;
+      f->field->data.intvalue = Feat_qual_legal_note;
+      break;
+  }
+  return f;
+}
+
+
+/* Molinfo fields */
+typedef struct moleculetypebiomol {
+  Int4 molecule_type;
+  Int4 biomol;
+  CharPtr name;
+} MoleculeTypeBiomolData, PNTR MoleculeTypeBiomolPtr;
+
+static MoleculeTypeBiomolData moleculetype_biomol[] = {
+ { Molecule_type_unknown , 0, "unknown" } ,
+ { Molecule_type_genomic , MOLECULE_TYPE_GENOMIC , "genomic" } ,
+ { Molecule_type_precursor_RNA , MOLECULE_TYPE_PRE_MRNA , "precursor RNA" } ,
+ { Molecule_type_mRNA , MOLECULE_TYPE_MRNA , "mRNA" } ,
+ { Molecule_type_rRNA , MOLECULE_TYPE_RRNA , "rRNA" } ,
+ { Molecule_type_tRNA , MOLECULE_TYPE_TRNA , "tRNA" } ,
+ { Molecule_type_snRNA , MOLECULE_TYPE_SNRNA , "snRNA" } ,
+ { Molecule_type_scRNA , MOLECULE_TYPE_SCRNA , "scRNA" } ,
+ { Molecule_type_genomic_mRNA , MOLECULE_TYPE_GENOMIC_MRNA_MIX , "genomic mRNA" } ,
+ { Molecule_type_cRNA , MOLECULE_TYPE_CRNA , "cRNA" } ,
+ { Molecule_type_scRNA , MOLECULE_TYPE_SCRNA , "scRNA" } ,
+ { Molecule_type_scRNA , MOLECULE_TYPE_SCRNA , "scRNA" } ,
+ { Molecule_type_scRNA , MOLECULE_TYPE_SCRNA , "scRNA" } ,
+ { Molecule_type_snoRNA , MOLECULE_TYPE_SNORNA, "snoRNA" } ,
+ { Molecule_type_transcribed_RNA, MOLECULE_TYPE_TRANSCRIBED_RNA, "transcribed RNA" } ,
+ { Molecule_type_ncRNA, MOLECULE_TYPE_NCRNA, "ncRNA" } ,
+ { Molecule_type_transfer_messenger_RNA, MOLECULE_TYPE_TMRNA, "tmRNA" } ,
+ { Molecule_type_other, MOLECULE_TYPE_OTHER_GENETIC_MATERIAL, "other" }
+};
+
+
+#define NUM_moleculetype_biomol sizeof (moleculetype_biomol) / sizeof (MoleculeTypeBiomolData)
+
+NLM_EXTERN Int4 BiomolFromMoleculeType (Int4 molecule_type) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_moleculetype_biomol; i++) {
+    if (moleculetype_biomol[i].molecule_type == molecule_type) {
+      return moleculetype_biomol[i].biomol;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN CharPtr BiomolNameFromBiomol (Int4 biomol) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_moleculetype_biomol; i++) {
+    if (moleculetype_biomol[i].biomol == biomol) {
+      return moleculetype_biomol[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+static Int4 BiomolFromBiomolName (CharPtr biomol_name)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_moleculetype_biomol; i++) {
+    if (StringCmp (moleculetype_biomol[i].name, biomol_name) == 0) {
+      return moleculetype_biomol[i].biomol;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN ValNodePtr GetMoleculeTypeList (void)
+{
+  ValNodePtr list = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_moleculetype_biomol; i++) {
+    ValNodeAddPointer (&list, moleculetype_biomol[i].molecule_type, StringSave (moleculetype_biomol[i].name));
+  }
+  return list;
+}
+
+
+/* Technique fields */
+typedef struct techniquetypetech {
+  Int4 technique_type;
+  Int4 tech;
+  CharPtr name;
+} TechniqueTypeTechData, PNTR TechniqueTypeTechPtr;
+
+static TechniqueTypeTechData techniquetype_tech[] = {
+ { Technique_type_unknown , MI_TECH_unknown , "unknown" } ,
+ { Technique_type_standard , MI_TECH_standard , "standard" } ,
+ { Technique_type_est , MI_TECH_est , "EST" } ,
+ { Technique_type_sts , MI_TECH_sts , "STS" } ,
+ { Technique_type_survey , MI_TECH_survey , "survey" } ,
+ { Technique_type_genetic_map , MI_TECH_genemap , "genetic map" } ,
+ { Technique_type_physical_map , MI_TECH_physmap , "physical map" } ,
+ { Technique_type_derived , MI_TECH_derived , "derived" } ,
+ { Technique_type_concept_trans , MI_TECH_concept_trans , "concept-trans" } ,
+ { Technique_type_seq_pept , MI_TECH_seq_pept , "seq-pept" } ,
+ { Technique_type_both , MI_TECH_both , "both" } ,
+ { Technique_type_seq_pept_overlap , MI_TECH_seq_pept_overlap , "seq-pept-overlap" } ,
+ { Technique_type_seq_pept_homol , MI_TECH_seq_pept_homol, "seq-pept-homol" } ,
+ { Technique_type_concept_trans_a, MI_TECH_concept_trans_a, "concept-trans-a" } ,
+ { Technique_type_htgs_1, MI_TECH_htgs_1, "HTGS-1" } ,
+ { Technique_type_htgs_2, MI_TECH_htgs_2, "HTGS-2" } ,
+ { Technique_type_htgs_3, MI_TECH_htgs_3, "HTGS-3" } ,
+ { Technique_type_fli_cDNA, MI_TECH_fli_cdna, "fli-cDNA" } ,
+ { Technique_type_htgs_0, MI_TECH_htgs_0, "HTGS-0" } ,
+ { Technique_type_htc, MI_TECH_htc, "HTC" } ,
+ { Technique_type_wgs, MI_TECH_wgs, "WGS" } ,
+ { Technique_type_barcode, MI_TECH_barcode, "BARCODE" } ,
+ { Technique_type_composite_wgs_htgs, MI_TECH_composite_wgs_htgs, "composite WGS-HTGS" } ,
+ { Technique_type_tsa, MI_TECH_tsa, "TSA" } ,
+ { Technique_type_other, MI_TECH_other, "other" } 
+};
+
+
+#define NUM_techniquetype_tech sizeof (techniquetype_tech) / sizeof (TechniqueTypeTechData)
+
+NLM_EXTERN Int4 TechFromTechniqueType (Int4 technique_type) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_techniquetype_tech; i++) {
+    if (techniquetype_tech[i].technique_type == technique_type) {
+      return techniquetype_tech[i].tech;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN CharPtr TechNameFromTech (Int4 tech) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_techniquetype_tech; i++) {
+    if (techniquetype_tech[i].tech == tech) {
+      return techniquetype_tech[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+static Int4 TechFromTechName (CharPtr tech_name)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_techniquetype_tech; i++) {
+    if (StringCmp (techniquetype_tech[i].name, tech_name) == 0) {
+      return techniquetype_tech[i].tech;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN ValNodePtr GetTechniqueTypeList (void)
+{
+  ValNodePtr list = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_techniquetype_tech; i++) {
+    ValNodeAddPointer (&list, techniquetype_tech[i].technique_type, StringSave (techniquetype_tech[i].name));
+  }
+  return list;
+}
+
+
+/* Completedness fields */
+typedef struct completednesstypecompleteness {
+  Int4 completedness_type;
+  Int4 completeness;
+  CharPtr name;
+} CompletednessTypeCompletenessData, PNTR CompletednessTypeCompletenessPtr;
+
+static CompletednessTypeCompletenessData completednesstype_completeness[] = {
+ { Completedness_type_unknown, 0, "unknown" } ,
+ { Completedness_type_complete, 1, "complete" } ,
+ { Completedness_type_partial, 2, "partial" } ,
+ { Completedness_type_no_left, 3, "no left" } ,
+ { Completedness_type_no_right, 4, "no right" } ,
+ { Completedness_type_no_ends, 5, "no ends" } ,
+ { Completedness_type_has_left, 6, "has left" } ,
+ { Completedness_type_has_right, 7, "has right" } ,
+ { Completedness_type_other, 255, "other" }
+};
+
+#define NUM_completednesstype_completeness sizeof (completednesstype_completeness) / sizeof (CompletednessTypeCompletenessData)
+
+NLM_EXTERN Int4 CompletenessFromCompletednessType (Int4 completedness_type) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_completednesstype_completeness; i++) {
+    if (completednesstype_completeness[i].completedness_type == completedness_type) {
+      return completednesstype_completeness[i].completeness;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN CharPtr CompletenessNameFromCompleteness (Int4 completeness) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_completednesstype_completeness; i++) {
+    if (completednesstype_completeness[i].completeness == completeness) {
+      return completednesstype_completeness[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+static Int4 CompletenessFromCompletenessName (CharPtr completeness_name)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_completednesstype_completeness; i++) {
+    if (StringCmp (completednesstype_completeness[i].name, completeness_name) == 0) {
+      return completednesstype_completeness[i].completeness;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN ValNodePtr GetCompletednessTypeList (void)
+{
+  ValNodePtr list = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_completednesstype_completeness; i++) {
+    ValNodeAddPointer (&list, completednesstype_completeness[i].completedness_type, StringSave (completednesstype_completeness[i].name));
+  }
+  return list;
+}
+
+
+/* Molecule class fields */
+typedef struct moleculeclasstypemol {
+  Int4 moleculeclass_type;
+  Int4 mol;
+  CharPtr name;
+} MoleculeClassTypeMolData, PNTR MoleculeClassTypeMolPtr;
+
+static MoleculeClassTypeMolData moleculeclasstype_mol[] = {
+ { Molecule_class_type_unknown, 0, "unknown" } ,
+ { Molecule_class_type_dna, MOLECULE_CLASS_DNA, "DNA" } ,
+ { Molecule_class_type_rna, MOLECULE_CLASS_RNA, "RNA" } ,
+ { Molecule_class_type_protein, MOLECULE_CLASS_PROTEIN, "protein" } ,
+ { Molecule_class_type_nucleotide, MOLECULE_CLASS_NUC, "nucleotide" } ,
+ { Molecule_class_type_other, 255, "other" } 
+};
+
+
+#define NUM_moleculeclasstype_mol sizeof (moleculeclasstype_mol) / sizeof (MoleculeClassTypeMolData)
+
+NLM_EXTERN Int4 MolFromMoleculeClassType (Int4 moleculeclass_type) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_moleculeclasstype_mol; i++) {
+    if (moleculeclasstype_mol[i].moleculeclass_type == moleculeclass_type) {
+      return moleculeclasstype_mol[i].mol;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN CharPtr MolNameFromMol (Int4 mol) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_moleculeclasstype_mol; i++) {
+    if (moleculeclasstype_mol[i].mol == mol) {
+      return moleculeclasstype_mol[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+static Int4 MolFromMolName (CharPtr mol_name)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_moleculeclasstype_mol; i++) {
+    if (StringCmp (moleculeclasstype_mol[i].name, mol_name) == 0) {
+      return moleculeclasstype_mol[i].mol;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN ValNodePtr GetMoleculeClassTypeList (void)
+{
+  ValNodePtr list = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_moleculeclasstype_mol; i++) {
+    ValNodeAddPointer (&list, moleculeclasstype_mol[i].moleculeclass_type, StringSave (moleculeclasstype_mol[i].name));
+  }
+  return list;
+}
+
+
+/* Topology fields */
+typedef struct topologytypetopology {
+  Int4 topology_type;
+  Int4 topology;
+  CharPtr name;
+} TopologyTypeTopologyData, PNTR TopologyTypeTopologyPtr;
+
+static TopologyTypeTopologyData topologytype_topology[] = {
+ { Topology_type_unknown, 0, "unknown" } ,
+ { Topology_type_linear, TOPOLOGY_LINEAR, "linear" } ,
+ { Topology_type_circular, TOPOLOGY_CIRCULAR, "circular" } ,
+ { Topology_type_tandem, TOPOLOGY_TANDEM, "tandem" } ,
+ { Topology_type_other, 255, "other" } 
+};
+
+#define NUM_topologytype_topology sizeof (topologytype_topology) / sizeof (TopologyTypeTopologyData)
+
+NLM_EXTERN Int4 TopologyFromTopologyType (Int4 topology_type) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_topologytype_topology; i++) {
+    if (topologytype_topology[i].topology_type == topology_type) {
+      return topologytype_topology[i].topology;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN CharPtr TopologyNameFromTopology (Int4 topology) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_topologytype_topology; i++) {
+    if (topologytype_topology[i].topology == topology) {
+      return topologytype_topology[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+static Int4 TopologyFromTopologyName (CharPtr topology_name)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_topologytype_topology; i++) {
+    if (StringCmp (topologytype_topology[i].name, topology_name) == 0) {
+      return topologytype_topology[i].topology;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN ValNodePtr GetTopologyTypeList (void)
+{
+  ValNodePtr list = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_topologytype_topology; i++) {
+    ValNodeAddPointer (&list, topologytype_topology[i].topology_type, StringSave (topologytype_topology[i].name));
+  }
+  return list;
+}
+
+
+/* strand fields */
+typedef struct strandtypestrand {
+  Int4 strand_type;
+  Int4 strand;
+  CharPtr name;
+} StrandTypeStrandData, PNTR StrandTypeStrandPtr;
+
+static StrandTypeStrandData strandtype_strand[] = {
+ { Strand_type_unknown, 0, "unknown" } ,
+ { Strand_type_single, STRANDEDNESS_SINGLE, "single" } ,
+ { Strand_type_double__, STRANDEDNESS_DOUBLE, "double" } ,
+ { Strand_type_mixed, 3, "mixed" } ,
+ { Strand_type_mixed_rev, 4, "mixed-rev" } ,
+ { Strand_type_other, 255, "other" } 
+};
+
+#define NUM_strandtype_strand sizeof (strandtype_strand) / sizeof (StrandTypeStrandData)
+
+NLM_EXTERN Int4 StrandFromStrandType (Int4 strand_type) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_strandtype_strand; i++) {
+    if (strandtype_strand[i].strand_type == strand_type) {
+      return strandtype_strand[i].strand;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN CharPtr StrandNameFromStrand (Int4 strand) 
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_strandtype_strand; i++) {
+    if (strandtype_strand[i].strand == strand) {
+      return strandtype_strand[i].name;
+    }
+  }
+  return NULL;
+}
+
+
+static Int4 StrandFromStrandName (CharPtr strand_name)
+{
+  Int4 i;
+
+  for (i = 0; i < NUM_strandtype_strand; i++) {
+    if (StringCmp (strandtype_strand[i].name, strand_name) == 0) {
+      return strandtype_strand[i].strand;
+    }
+  }
+  return -1;
+}
+
+
+NLM_EXTERN ValNodePtr GetStrandTypeList (void)
+{
+  ValNodePtr list = NULL;
+  Int4 i;
+
+  for (i = 0; i < NUM_strandtype_strand; i++) {
+    ValNodeAddPointer (&list, strandtype_strand[i].strand_type, StringSave (strandtype_strand[i].name));
+  }
+  return list;
+}
+
+
+static CharPtr GetSequenceQualValName (ValNodePtr field)
+{
+  CharPtr val = NULL;
+
+  if (field == NULL) return NULL;
+  switch (field->choice) {
+    case MolinfoField_molecule:
+      val = BiomolNameFromBiomol (BiomolFromMoleculeType (field->data.intvalue));
+      break;
+    case MolinfoField_technique:
+      val = TechNameFromTech (TechFromTechniqueType (field->data.intvalue));
+      break;
+    case MolinfoField_completedness:
+      val = CompletenessNameFromCompleteness (CompletenessFromCompletednessType (field->data.intvalue));
+      break;
+    case MolinfoField_mol_class:
+      val = MolNameFromMol (MolFromMoleculeClassType (field->data.intvalue));
+      break;
+    case MolinfoField_topology:
+      val = TopologyNameFromTopology (TopologyFromTopologyType (field->data.intvalue));
+      break;
+    case MolinfoField_strand:
+      val = StrandNameFromStrand (StrandFromStrandType (field->data.intvalue));
+      break;
+  }
+  return val;
+}
+
+
+static CharPtr GetSequenceQualName (ValNodePtr field)
+{
+  CharPtr str = NULL, fieldname = "invalid field", val = "invalid value";
+  CharPtr fmt = "%s %s";
+
+  if (field == NULL) return NULL;
+  switch (field->choice) {
+    case MolinfoField_molecule:
+      fieldname = "molecule";
+      val = BiomolNameFromBiomol (BiomolFromMoleculeType (field->data.intvalue));
+      break;
+    case MolinfoField_technique:
+      fieldname = "technique";
+      val = TechNameFromTech (TechFromTechniqueType (field->data.intvalue));
+      break;
+    case MolinfoField_completedness:
+      fieldname = "completeness";
+      val = CompletenessNameFromCompleteness (CompletenessFromCompletednessType (field->data.intvalue));
+      break;
+    case MolinfoField_mol_class:
+      fieldname = "class";
+      val = MolNameFromMol (MolFromMoleculeClassType (field->data.intvalue));
+      break;
+    case MolinfoField_topology:
+      fieldname = "topology";
+      val = TopologyNameFromTopology (TopologyFromTopologyType (field->data.intvalue));
+      break;
+    case MolinfoField_strand:
+      fieldname = "strand";
+      val = StrandNameFromStrand (StrandFromStrandType (field->data.intvalue));
+      break;
+  }
+  if (val == NULL) {
+    val = "Invalid value";
+  }
+  str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (fieldname) + StringLen (val)));
+  sprintf (str, fmt, fieldname, val);
+  return str;
+}
+
+
+/* Simple constraints */
+static Boolean IsWholeWordMatch (CharPtr start, CharPtr found, Int4 match_len)
+{
+  Boolean rval = TRUE;
+  Char    char_after;
+  Char    char_before;
+  
+  if (match_len == 0)
+  {
+    rval = TRUE;
+  }
+  else if (start == NULL || found == NULL)
+  {
+    rval = FALSE;
+  }
+  else
+  {
+	  char_after = *(found + match_len);
+    if (found != start)
+	  {
+	    char_before = *(found - 1);
+	    if (isalpha ((Int4) char_before) || isdigit ((Int4) char_before))
+	    {
+	      rval = FALSE;
+	    }
+	  }
+	  if (char_after != 0 && (isalpha ((Int4) char_after) || isdigit ((Int4)char_after)))
+	  {
+	    rval = FALSE;
+	  }   
+  }
+  return rval;
+}
+
+
+NLM_EXTERN Boolean IsStringConstraintEmpty (StringConstraintPtr scp)
+{
+  if (scp == NULL || StringHasNoText (scp->match_text)) return TRUE;
+  else return FALSE;
+}
+
+
+NLM_EXTERN Boolean DoesSingleStringMatchConstraint (CharPtr str, StringConstraintPtr scp)
+{
+  CharPtr pFound;
+  Boolean rval = FALSE;
+  Char    char_after = 0;
+  
+  if (IsStringConstraintEmpty (scp)) return TRUE;
+  if (StringHasNoText (str)) return FALSE;
+
+  switch (scp->match_location) 
+  {
+    case String_location_contains:
+	    if (scp->case_sensitive)
+	    {
+	      pFound = StringSearch (str, scp->match_text);
+	    }
+	    else
+	    {
+	      pFound = StringISearch (str, scp->match_text);
+	    }
+      if (pFound == NULL) 
+      {
+        rval = FALSE;
+      }
+      else if (scp->whole_word) 
+      {
+        rval = IsWholeWordMatch (str, pFound, StringLen (scp->match_text));
+        while (!rval && pFound != NULL) 
+        {
+	        if (scp->case_sensitive)
+	        {
+	          pFound = StringSearch (pFound + 1, scp->match_text);
+	        }
+	        else
+	        {
+	          pFound = StringISearch (pFound + 1, scp->match_text);
+	        }
+          if (pFound != NULL)
+          {
+            rval = IsWholeWordMatch (str, pFound, StringLen (scp->match_text));
+          }
+        }
+      }
+      else
+      {
+        rval = TRUE;
+      }
+      break;
+    case String_location_starts:
+	    if (scp->case_sensitive)
+	    {
+	      pFound = StringSearch (str, scp->match_text);
+	    }
+	    else
+	    {
+	      pFound = StringISearch (str, scp->match_text);
+	    }
+      if (pFound == str)
+      {
+        if (scp->whole_word) 
+        {
+          rval = IsWholeWordMatch (str, pFound, StringLen (scp->match_text));
+        }
+        else
+        {
+          rval = TRUE;
+        }
+      }
+      break;
+    case String_location_ends:
+	    if (scp->case_sensitive)
+	    {
+	      pFound = StringSearch (str, scp->match_text);
+	    }
+	    else
+	    {
+	      pFound = StringISearch (str, scp->match_text);
+	    }
+      while (pFound != NULL && !rval) {
+  	    char_after = *(pFound + StringLen (scp->match_text));
+        if (char_after == 0)
+        {
+          if (scp->whole_word) 
+          {
+            rval = IsWholeWordMatch (str, pFound, StringLen (scp->match_text));
+          }
+          else
+          {
+            rval = TRUE;
+          }
+          /* stop the search, we're at the end of the string */
+          pFound = NULL;
+        }
+        else
+        {
+	        if (scp->case_sensitive)
+	        {
+	          pFound = StringSearch (pFound + 1, scp->match_text);
+	        }
+	        else
+	        {
+	          pFound = StringISearch (pFound + 1, scp->match_text);
+	        }
+        }
+      }
+      break;
+    case String_location_equals:
+      if (scp->case_sensitive) 
+      {
+        if (StringCmp (str, scp->match_text) == 0) 
+        {
+          rval = TRUE;
+        }
+      }
+      else
+      {
+        if (StringICmp (str, scp->match_text) == 0) 
+        {
+          rval = TRUE;
+        }
+      }
+      break;
+    case String_location_inlist:
+	    if (scp->case_sensitive)
+	    {
+	      pFound = StringSearch (scp->match_text, str);
+	    }
+	    else
+	    {
+	      pFound = StringISearch (scp->match_text, str);
+	    }
+      if (pFound == NULL) 
+      {
+        rval = FALSE;
+      }
+      else
+      {
+        rval = IsWholeWordMatch (scp->match_text, pFound, StringLen (str));
+        while (!rval && pFound != NULL) 
+        {
+	        if (scp->case_sensitive)
+	        {
+	          pFound = StringSearch (pFound + 1, str);
+	        }
+	        else
+	        {
+	          pFound = StringISearch (pFound + 1, str);
+	        }
+          if (pFound != NULL)
+          {
+            rval = IsWholeWordMatch (scp->match_text, pFound, StringLen (str));
+          }
+        }
+      }
+      if (!rval) {
+        /* look for spans */
+        rval = IsStringInSpanInList (str, scp->match_text);
+      }
+      break;
+	}
+	return rval;
+}
+
+
+NLM_EXTERN Boolean DoesStringMatchConstraint (CharPtr str, StringConstraintPtr scp)
+{
+  Boolean rval;
+
+  rval = DoesSingleStringMatchConstraint (str, scp);
+  if (scp != NULL && scp->not_present) {
+    rval = !rval;
+  }
+  return rval;
+}
+
+
+static Boolean DoesStringListMatchConstraint (ValNodePtr list, StringConstraintPtr scp)
+{
+  Int4 len = 1;
+  CharPtr tmp;
+  Boolean rval = FALSE;
+  ValNodePtr vnp;
+
+  if (IsStringConstraintEmpty (scp)) {
+    return TRUE;
+  }
+  if (list == NULL) return FALSE;
+
+  for (vnp = list; vnp != NULL; vnp = vnp->next) {
+    len += StringLen (vnp->data.ptrvalue) + 2;
+  }
+
+  tmp = (CharPtr) MemNew (sizeof (Char) * len);
+  for (vnp = list; vnp != NULL; vnp = vnp->next) {
+    StringCat (tmp, vnp->data.ptrvalue);
+    if (vnp->next != NULL) {
+      StringCat (tmp, "; ");
+    }
+  }
+
+  rval = DoesStringMatchConstraint (tmp, scp);
+  tmp = MemFree (tmp);
+  return rval;  
+}
+
+
+static Boolean DoesStrandMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
+{
+  Uint2 strand;
+  Boolean rval = FALSE;
+  
+  if (slp == NULL)
+  {
+    rval = FALSE;
+  }
+  else if (lcp == NULL || lcp->strand == Strand_constraint_any)
+  {
+    rval = TRUE;
+  }
+  else
+  {
+    strand = SeqLocStrand (slp);
+    if (strand == Seq_strand_minus)
+    {
+      if (lcp->strand == Strand_constraint_minus)
+      {
+        rval = TRUE;
+      }
+      else
+      {
+        rval = FALSE;
+      }
+    }
+    else
+    {
+      if (lcp->strand == Strand_constraint_plus)
+      {
+        rval = TRUE;
+      }
+      else
+      {
+        rval = FALSE;
+      }
+    }
+  }
+  return rval;
+}
+
+
+static Boolean DoesBioseqMatchSequenceType (BioseqPtr bsp, Uint2 seq_type)
+{
+  Boolean rval = FALSE;
+
+  if (bsp == NULL) return FALSE;
+  if (seq_type == Seqtype_constraint_any) return TRUE;
+
+  if (ISA_na (bsp->mol) && seq_type == Seqtype_constraint_nuc)
+  {
+    rval = TRUE;
+  }
+  else if (ISA_aa (bsp->mol) && seq_type == Seqtype_constraint_prot)
+  {
+    rval = TRUE;
+  }
+  return rval;
+}
+
+
+static Boolean DoesSequenceTypeMatchContraint (SeqLocPtr slp, LocationConstraintPtr lcp)
+{
+  Boolean   rval = FALSE;
+  BioseqPtr bsp;
+  
+  if (slp == NULL)
+  {
+    rval = FALSE;
+  }
+  else if (lcp == NULL || lcp->seq_type == Seqtype_constraint_any)
+  {
+    rval = TRUE;
+  }
+  else
+  {
+    bsp = BioseqFindFromSeqLoc (slp);
+    rval = DoesBioseqMatchSequenceType (bsp, lcp->seq_type);
+  }
+  return rval;
+}
+
+static Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
+
+{
+  Boolean rval = FALSE;
+  
+  if (slp == NULL)
+  {
+    rval = FALSE;
+  }  
+  else if (lcp == NULL || (DoesStrandMatchConstraint (slp, lcp) && DoesSequenceTypeMatchContraint (slp, lcp)))
+  {
+    rval = TRUE;
+  }
+  return rval; 
+}
+
+
+static Boolean DoesObjectMatchLocationConstraint (Uint1 choice, Pointer data, LocationConstraintPtr constraint)
+{
+  SeqFeatPtr  sfp;
+  SeqDescrPtr sdp;
+  CGPSetPtr   cgp;
+  BioseqPtr  bsp = NULL;
+  BioseqSetPtr bssp;
+  ValNodePtr    vnp;
+  ObjValNodePtr ovp;
+  SeqMgrFeatContext context;
+
+  if (data == NULL) return FALSE;
+ 
+  if (constraint == NULL 
+      || (constraint->strand == Strand_constraint_any
+          && constraint->seq_type == Seqtype_constraint_any)) {
+    return TRUE;
+  }
+
+  if (choice == OBJ_SEQFEAT) {
+    sfp = (SeqFeatPtr) data;
+    bsp = BioseqFindFromSeqLoc (sfp->location);
+  } else if (choice == OBJ_SEQDESC) {
+    sdp = (SeqDescrPtr) data;
+    if (sdp->extended != 0) {
+      ovp = (ObjValNodePtr) sdp;
+      if (ovp->idx.parenttype == OBJ_BIOSEQSET) {
+        bssp = (BioseqSetPtr) ovp->idx.parentptr;
+        if (bssp != NULL && bssp->seq_set != NULL && IS_Bioseq_set (bssp->seq_set)) {
+          bsp = (BioseqPtr) bssp->seq_set->data.ptrvalue;
+        }
+      } else if (ovp->idx.parenttype == OBJ_BIOSEQ) {
+        bsp = (BioseqPtr) ovp->idx.parentptr;
+      }
+    }
+  } else if (choice == 0) {
+    if (constraint->seq_type != Seqtype_constraint_any) {
+      return FALSE;
+    }
+    cgp = (CGPSetPtr) data;
+    if (cgp->cds_list != NULL && cgp->cds_list->data.ptrvalue != NULL) {
+      sfp = (SeqFeatPtr) cgp->cds_list->data.ptrvalue;
+      bsp = BioseqFindFromSeqLoc (sfp->location);
+    } else if (cgp->gene_list != NULL && cgp->gene_list->data.ptrvalue != NULL) {
+      sfp = (SeqFeatPtr) cgp->gene_list->data.ptrvalue;
+      bsp = BioseqFindFromSeqLoc (sfp->location);
+    } else if (cgp->mrna_list != NULL && cgp->mrna_list->data.ptrvalue != NULL) {
+      sfp = (SeqFeatPtr) cgp->mrna_list->data.ptrvalue;
+      bsp = BioseqFindFromSeqLoc (sfp->location);
+    } else if (cgp->prot_list != NULL && cgp->prot_list->data.ptrvalue != NULL) {
+      sfp = (SeqFeatPtr) cgp->prot_list->data.ptrvalue;
+      bsp = BioseqFindFromSeqLoc (sfp->location);
+    }
+  }
+  if (!DoesBioseqMatchSequenceType(bsp, constraint->seq_type)) {
+    return FALSE;
+  }
+  if (constraint->strand != Strand_constraint_any && ISA_aa (bsp->mol)) {      
+    sfp = SeqMgrGetCDSgivenProduct (bsp, &context);
+    if (constraint->strand == Strand_constraint_minus && context.strand != Seq_strand_minus) {
+      return FALSE;
+    }
+    if (constraint->strand == Strand_constraint_plus && context.strand == Seq_strand_minus) {
+      return FALSE;
+    }
+  } else if (constraint->strand != Strand_constraint_any) {
+    if (choice == 0) {
+      /* strand for CDS-Gene-Prot group */
+      cgp = (CGPSetPtr) data;
+      for (vnp = cgp->cds_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && !DoesStrandMatchConstraint (sfp->location, constraint)) {
+          return FALSE;
+        }
+      }
+      for (vnp = cgp->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && !DoesStrandMatchConstraint (sfp->location, constraint)) {
+          return FALSE;
+        }
+      }
+      for (vnp = cgp->mrna_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && !DoesStrandMatchConstraint (sfp->location, constraint)) {
+          return FALSE;
+        }
+      }
+    } else if (choice == OBJ_SEQFEAT) {
+      sfp = (SeqFeatPtr) data;
+      if (!DoesStrandMatchConstraint (sfp->location, constraint)) {
+        return FALSE;
+      }
+    } else {
+      /* descriptors can't meet strand constraints */
+      return FALSE;
+    }
+  }
+  return TRUE;
+}
+
+
+/* for parsing and editing */
+static CharPtr GetTextPortionFromString (CharPtr str, TextPortionPtr text_portion)
+{
+  CharPtr portion = NULL;
+  CharPtr found_start, found_end;
+  Int4    found_len;
+
+  if (StringHasNoText (str)) {
+    return NULL;
+  }
+  if (text_portion == NULL) {
+    return StringSave (str);
+  }  
+  
+  if (text_portion->left_text == NULL || text_portion->left_text [0] == 0)
+  {
+    found_start = str;
+  }
+  else
+  {
+    if (text_portion->case_sensitive)
+    {
+      found_start = StringSearch (str, text_portion->left_text);
+    }
+    else
+    {
+      found_start = StringISearch (str, text_portion->left_text);
+    }
+    
+    if (text_portion->whole_word && ! IsWholeWordMatch (str, found_start, StringLen (text_portion->left_text)))
+    {
+      found_start = NULL;
+    }
+  }
+  
+  if (found_start == NULL)
+  {
+    return NULL;
+  }
+  
+  if (!text_portion->include_left)
+  {
+    found_start += StringLen (text_portion->left_text);
+  }
+  
+  if (text_portion->right_text == NULL || text_portion->right_text [0] == 0)
+  {
+    found_len = StringLen (found_start);
+  }
+  else
+  {
+    if (text_portion->case_sensitive)
+    {
+      found_end = StringSearch (found_start, text_portion->right_text);
+    }
+    else
+    {
+      found_end = StringISearch (found_start, text_portion->right_text);
+    }
+    if (text_portion->whole_word && ! IsWholeWordMatch (str, found_end, StringLen (text_portion->right_text)))
+    {
+      found_end = NULL;
+    }    
+    
+    if (found_end == NULL)
+    {
+      found_len = 0;
+    }
+    else if (text_portion->include_right)
+    {
+      found_len = (Int4)(found_end - found_start) + StringLen (text_portion->right_text);
+    }
+    else
+    {
+      found_len = found_end - found_start;
+    }
+  }
+
+  if (found_len > 0)
+  {
+    portion = (CharPtr) MemNew (sizeof (Char) * (found_len + 1));
+    StringNCpy (portion, found_start, found_len);
+    portion[found_len] = 0;
+  }
+  return portion;
+}
+
+
+
+static CharPtr FindTextPortionLocationInString (CharPtr str, TextPortionPtr text_portion)
+{
+  CharPtr start, stop;
+
+  if (str == NULL || text_portion == NULL) return FALSE;
+
+  if (text_portion->left_text != NULL) {
+    start = StringSearch (str, text_portion->left_text);
+    if (start != NULL) {
+      if (!text_portion->include_left) {
+        start += StringLen (text_portion->left_text);
+      }
+    }
+  } else {
+    start = str;
+  }
+  if (start != NULL) {
+    if (text_portion->right_text != NULL) { 
+      stop = StringSearch (start, text_portion->right_text);
+      if (stop == NULL) {
+        start = NULL;
+      }
+    }
+  }
+  return start;
+}
+
+
+static void ReplaceStringForParse(CharPtr src_text, TextPortionPtr text_portion)
+{
+  CharPtr         src, dst;
+  
+  if (src_text == NULL || text_portion == NULL) {
+    return;
+  }
+
+  dst = FindTextPortionLocationInString (src_text, text_portion);
+  if (dst == NULL) return;
+  if (text_portion->right_text == NULL) {
+    *dst = 0;
+  } else {
+    src = StringSearch (src_text, text_portion->right_text);
+    if (src != NULL) {
+      if (text_portion->include_right) {
+        src += StringLen (text_portion->right_text);
+      }
+      while (*src != 0) {
+        *dst = *src;
+        dst++;
+        src++;
+      }
+      *dst = 0;
+    }
+  }
+}
+
+
+/* generic functions for getting string values */
+static Int4 GetDbtagStringLen (DbtagPtr db_tag)
+{
+  Int4 len;
+  
+  if (db_tag == NULL)
+  {
+    return 0;
+  }
+  
+  len = StringLen (db_tag->db) + 2;
+  if (db_tag->tag != NULL)
+  {
+    if (db_tag->tag->str != NULL)
+    {
+      len += StringLen (db_tag->tag->str);
+    }
+    else
+    {
+      len += 10;
+    }
+  }
+  return len;
+}
+
+
+static CharPtr GetDbtagString (DbtagPtr db_tag)
+{
+  Int4    len;
+  CharPtr str;
+  
+  if (db_tag == NULL) {
+    return NULL;
+  }
+  
+  len = GetDbtagStringLen (db_tag);
+  if (len == 0) {
+    return NULL;
+  }
+  
+  str = (CharPtr) MemNew (len * sizeof (Char));
+  if (str != NULL) {
+    StringCpy (str, db_tag->db);
+    StringCat (str, ":");
+    if (db_tag->tag != NULL) {
+      if (db_tag->tag->str != NULL) {
+        StringCat (str, db_tag->tag->str);
+      } else {
+        sprintf (str + StringLen (str), "%d", db_tag->tag->id);
+      }
+    }
+  }
+  return str;
+}
+
+
+/* generic functions for setting field values */
+static Boolean SetStringValue (CharPtr PNTR existing_val, CharPtr new_val, Uint2 existing_text)
+{
+  Boolean rval = FALSE;
+  Int4 len;
+  CharPtr tmp;
+
+  if (existing_val == NULL) {
+    return FALSE;
+  }
+
+  if (StringHasNoText (*existing_val)) {
+    *existing_val = MemFree (*existing_val);
+    *existing_val = StringSave (new_val);
+    rval = TRUE;
+  } else {
+    switch (existing_text) {
+      case ExistingTextOption_replace_old :
+        *existing_val = MemFree (*existing_val);
+        *existing_val = StringSave (new_val);
+        rval = TRUE;
+        break;
+      case ExistingTextOption_append_semi :
+        len = StringLen (new_val) + StringLen (*existing_val) + 3;
+        tmp = (CharPtr) MemNew (sizeof (Char) * len);
+        if (tmp != NULL) {
+          sprintf (tmp, "%s; %s", *existing_val, new_val);
+          MemFree (*existing_val);
+          *existing_val = tmp;
+          rval = TRUE;
+        }
+        break;
+      case ExistingTextOption_append_space :
+        len = StringLen (new_val) + StringLen (*existing_val) + 2;
+        tmp = (CharPtr) MemNew (sizeof (Char) * len);
+        if (tmp != NULL) {
+          sprintf (tmp, "%s %s", *existing_val, new_val);
+          MemFree (*existing_val);
+          *existing_val = tmp;
+          rval = TRUE;
+        }
+        break;
+      case ExistingTextOption_append_colon :
+        len = StringLen (new_val) + StringLen (*existing_val) + 3;
+        tmp = (CharPtr) MemNew (sizeof (Char) * len);
+        if (tmp != NULL) {
+          sprintf (tmp, "%s: %s", *existing_val, new_val);
+          MemFree (*existing_val);
+          *existing_val = tmp;
+          rval = TRUE;
+        }
+        break;
+      case ExistingTextOption_append_none :
+        len = StringLen (new_val) + StringLen (*existing_val) + 1;
+        tmp = (CharPtr) MemNew (sizeof (Char) * len);
+        if (tmp != NULL) {
+          sprintf (tmp, "%s%s", *existing_val, new_val);
+          MemFree (*existing_val);
+          *existing_val = tmp;
+          rval = TRUE;
+        }
+        break;
+      case ExistingTextOption_prefix_semi :
+        len = StringLen (new_val) + StringLen (*existing_val) + 3;
+        tmp = (CharPtr) MemNew (sizeof (Char) * len);
+        if (tmp != NULL) {
+          sprintf (tmp, "%s; %s", new_val, *existing_val);
+          MemFree (*existing_val);
+          *existing_val = tmp;
+          rval = TRUE;
+        }
+        break;
+      case ExistingTextOption_prefix_space :
+        len = StringLen (new_val) + StringLen (*existing_val) + 2;
+        tmp = (CharPtr) MemNew (sizeof (Char) * len);
+        if (tmp != NULL) {
+          sprintf (tmp, "%s %s", new_val, *existing_val);
+          MemFree (*existing_val);
+          *existing_val = tmp;
+          rval = TRUE;
+        }
+        break;
+      case ExistingTextOption_prefix_colon :
+        len = StringLen (new_val) + StringLen (*existing_val) + 3;
+        tmp = (CharPtr) MemNew (sizeof (Char) * len);
+        if (tmp != NULL) {
+          sprintf (tmp, "%s: %s", new_val, *existing_val);
+          MemFree (*existing_val);
+          *existing_val = tmp;
+          rval = TRUE;
+        }
+        break;
+      case ExistingTextOption_prefix_none :
+        len = StringLen (new_val) + StringLen (*existing_val) + 1;
+        tmp = (CharPtr) MemNew (sizeof (Char) * len);
+        if (tmp != NULL) {
+          sprintf (tmp, "%s%s", new_val, *existing_val);
+          MemFree (*existing_val);
+          *existing_val = tmp;
+          rval = TRUE;
+        }
+        break;
+      case ExistingTextOption_leave_old :
+        rval = FALSE;
+    }
+  }
+  return rval;
+}
+
+
+static Boolean SetStringsInValNodeStringList (ValNodePtr PNTR list, StringConstraintPtr scp, CharPtr new_val, Uint2 existing_text)
+{
+  ValNodePtr vnp;
+  CharPtr    cp;
+  Boolean rval = FALSE;
+  
+  if (list == NULL)
+  {
+    return FALSE;
+  }
+
+  if (*list == NULL && (scp == NULL || StringHasNoText (scp->match_text))) {
+    ValNodeAddPointer (list, 0, StringSave (new_val));
+    rval = TRUE;
+  } else if (existing_text == ExistingTextOption_append_semi) {
+    if (DoesStringListMatchConstraint (*list, scp)) {
+      ValNodeAddPointer (list, 0, StringSave (new_val));
+      rval = TRUE;
+    }
+  } else if (existing_text == ExistingTextOption_prefix_semi) {
+    if (DoesStringListMatchConstraint (*list, scp)) {
+      vnp = ValNodeNew (NULL);
+      vnp->data.ptrvalue = StringSave (new_val);
+      vnp->next = *list;
+      *list = vnp;
+      rval = TRUE;
+    }
+  } else if (existing_text == ExistingTextOption_replace_old) {
+    if (DoesStringListMatchConstraint (*list, scp)) {
+      *list = ValNodeFreeData (*list);
+      vnp = ValNodeNew (NULL);
+      vnp->data.ptrvalue = StringSave (new_val);
+      *list = vnp;
+      rval = TRUE;
+    }
+  } else if (existing_text == ExistingTextOption_leave_old) {
+    rval = FALSE;
+  } else {
+    for (vnp = *list; vnp != NULL; vnp = vnp->next)
+    {
+      cp = (CharPtr) vnp->data.ptrvalue;
+      if (DoesStringMatchConstraint (cp, scp)) {
+        rval |= SetStringValue (&cp, new_val, existing_text);
+        vnp->data.ptrvalue = cp;
+      }
+    }
+  }
+  return rval;
+}
+
+
+static Boolean SetStringInGBQualList (GBQualPtr PNTR list, ValNodePtr field, StringConstraintPtr scp, CharPtr new_val, Uint2 existing_text)
+{
+  Boolean rval = FALSE;
+  Int4 gbqual;
+  CharPtr qual_name = NULL;
+  GBQualPtr gbq, last_gbq = NULL;
+
+  if (field == NULL) return FALSE;
+
+  if (field->choice == FeatQualChoice_legal_qual) 
+  {
+    gbqual = GetGBQualFromFeatQual (field->data.intvalue);
+    if (gbqual > -1) {
+      qual_name = ParFlat_GBQual_names [gbqual].name;
+      for (gbq = *list; gbq != NULL; gbq = gbq->next) {
+        if (StringCmp (gbq->qual, qual_name) == 0
+            && DoesStringMatchConstraint (gbq->val, scp)) {
+          rval |= SetStringValue (&(gbq->val), new_val, existing_text);
+        }
+        last_gbq = gbq;
+      }
+      if (!rval && (scp == NULL || scp->match_text == NULL)) {
+        gbq = GBQualNew ();
+        gbq->qual = StringSave (qual_name);
+        gbq->val = StringSave (new_val);
+        if (last_gbq == NULL) {
+          *list = gbq;
+        } else {
+          last_gbq->next = gbq;
+        }
+        rval = TRUE;
+      }
+    }
+  } else if (field->choice == FeatQualChoice_illegal_qual) {
+    for (gbq = *list; gbq != NULL; gbq = gbq->next) {
+      if (DoesStringMatchConstraint (gbq->qual, field->data.ptrvalue)
+          && DoesStringMatchConstraint (gbq->val, scp)) {
+        rval |= SetStringValue (&(gbq->val), new_val, existing_text);
+      }
+    }
+  }
+
+  return rval;
+}
+
+
+static Boolean IsAllDigits (CharPtr str)
+{
+  CharPtr cp;
+
+  if (StringHasNoText (str)) return FALSE;
+
+  cp = str;
+  while (*cp != 0 && isdigit (*cp)) {
+    cp++;
+  }
+  if (*cp == 0) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+
+static Boolean SetObjectIdString (ObjectIdPtr oip, CharPtr value, Uint2 existing_text)
+{
+  Boolean rval = FALSE;
+  Char    num[15];
+  CharPtr tmp = NULL;
+
+  if (oip == NULL) {
+    return FALSE;
+  }
+
+  if (oip->id > 0) {
+    sprintf (num, "%d", oip->id);
+    tmp = StringSave (num);
+  } else {
+    tmp = StringSaveNoNull (oip->str);
+  }
+  if (SetStringValue (&tmp, value, existing_text)) {
+    oip->str = MemFree (oip->str);        
+    oip->id = 0;
+    if (IsAllDigits (tmp)) {
+      oip->id = atoi (tmp);
+    } else {
+      oip->str = tmp;
+      tmp = NULL;
+    }
+    rval = TRUE;
+  }
+  tmp = MemFree (tmp);
+  return rval;
+}
+
+
+static Boolean SetDbtagString (DbtagPtr db_tag, CharPtr value, Uint2 existing_text)
+{
+  Boolean rval = FALSE;
+  CharPtr cp;
+  Int4    dbxvalid;
+  CharPtr tmp;
+  CharPtr twoval;
+  
+  if (db_tag == NULL || StringHasNoText (value)) {
+    return FALSE;
+  }
+
+  cp = StringChr (value, ':');
+  if (cp == NULL) {
+    tmp = StringSave (db_tag->db);
+    if (SetStringValue (&tmp, value, existing_text)) {
+      dbxvalid = IsDbxrefValid (tmp, NULL, NULL, TRUE, NULL);
+      if (dbxvalid != 0) {
+        db_tag->db = MemFree (db_tag->db);
+        db_tag->db = tmp;
+        tmp = NULL;
+        rval = TRUE;
+      }
+    }
+    if (!rval) {
+      if (db_tag->tag == NULL) {
+        db_tag->tag = ObjectIdNew();
+      }
+      rval = SetObjectIdString (db_tag->tag, value, existing_text);
+    }
+    tmp = MemFree (tmp);
+  } else {
+    twoval = StringSave (value);
+    cp = StringChr (twoval, ':');
+    *cp = 0;
+    cp++;
+    rval = SetStringValue (&(db_tag->db), twoval, existing_text);
+    if (db_tag->tag == NULL) {
+      db_tag->tag = ObjectIdNew ();
+    }
+    rval |= SetObjectIdString (db_tag->tag, cp, existing_text);
+    twoval = MemFree (twoval);
+  }
+  return rval;
+}
+
+
+static Boolean SetDbxrefString (SeqFeatPtr sfp, StringConstraintPtr scp, CharPtr value, Uint2 existing_text)
+{
+  ValNodePtr vnp;
+  Boolean    rval = FALSE, skip;
+  DbtagPtr   dbtag;
+  CharPtr    cp;
+  
+  if (sfp == NULL) {
+    return FALSE;
+  }
+
+  if ((sfp->dbxref == NULL || existing_text == ExistingTextOption_append_semi) && (scp == NULL || StringHasNoText (scp->match_text))) {
+    dbtag = DbtagNew ();
+    rval = SetDbtagString (dbtag, value, existing_text);
+    if (rval) {
+      ValNodeAddPointer (&(sfp->dbxref), 0, dbtag);
+    } else {
+      dbtag = DbtagFree (dbtag);
+    }
+  } else {
+    for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next) {
+      skip = FALSE;
+      if (scp != NULL) {
+        cp = GetDbtagString (vnp->data.ptrvalue);
+        if (!DoesStringMatchConstraint (cp, scp)) {
+          skip = TRUE;
+        }
+        cp = MemFree (cp);
+      }
+      if (!skip) {
+        rval |= SetDbtagString (vnp->data.ptrvalue, value, existing_text);
+      }
+    }
+  }
+  return rval;
+}
+
+
+
+static CharPtr GetFirstValNodeStringMatch (ValNodePtr vnp, StringConstraintPtr scp)
+{
+  CharPtr str = NULL;
+  while (vnp != NULL && str == NULL) {
+    if (!StringHasNoText (vnp->data.ptrvalue)
+        && DoesStringMatchConstraint (vnp->data.ptrvalue, scp)) {
+      str = StringSave (vnp->data.ptrvalue);
+    } 
+    vnp = vnp->next;
+  }
+  return str;
+}
+
+
+static Boolean RemoveValNodeStringMatch (ValNodePtr PNTR list, StringConstraintPtr scp)
+{
+  ValNodePtr vnp_prev = NULL, vnp_next, vnp;
+  Boolean    rval = FALSE;
+
+  if (list == NULL) return FALSE;
+  vnp = *list;
+  while (vnp != NULL) {
+    vnp_next = vnp->next;
+    if (!StringHasNoText (vnp->data.ptrvalue) 
+        && DoesStringMatchConstraint (vnp->data.ptrvalue, scp)) {
+      if (vnp_prev == NULL) {
+        *list = vnp->next;
+      } else {
+        vnp_prev->next = vnp->next;
+      }
+      vnp->next = NULL;
+      vnp = ValNodeFreeData (vnp);
+      rval = TRUE;
+    } else {
+      vnp_prev = vnp;
+    }
+    vnp = vnp_next;
+  }
+  return rval;
+}
+
+
+static CharPtr GetFirstGBQualMatch (GBQualPtr qual, CharPtr qual_name, StringConstraintPtr scp)
+{
+  CharPtr str = NULL;
+  while (qual != NULL && str == NULL) {
+    if (StringICmp (qual->qual, qual_name) == 0
+        &&!StringHasNoText (qual->val)
+        && DoesStringMatchConstraint (qual->val, scp)) {
+      str = StringSave (qual->val);
+    } 
+    qual = qual->next;
+  }
+  return str;
+}
+
+
+static CharPtr GetFirstGBQualMatchConstraintName (GBQualPtr qual, StringConstraintPtr qual_name, StringConstraintPtr scp)
+{
+  CharPtr str = NULL;
+  while (qual != NULL && str == NULL) {
+    if (DoesStringMatchConstraint (qual->qual, qual_name)
+        &&!StringHasNoText (qual->val)
+        && DoesStringMatchConstraint (qual->val, scp)) {
+      str = StringSave (qual->val);
+    } 
+    qual = qual->next;
+  }
+  return str;
+}
+
+
+static Boolean RemoveGBQualMatch (GBQualPtr PNTR list, CharPtr qual_name, StringConstraintPtr scp)
+{
+  GBQualPtr qual_prev = NULL, qual_next, qual;
+  Boolean   rval = FALSE;
+
+  if (list == NULL) return FALSE;
+  qual = *list;
+  while (qual != NULL) {
+    qual_next = qual->next;
+    if (StringICmp (qual->qual, qual_name) == 0
+        && !StringHasNoText (qual->val) 
+        && DoesStringMatchConstraint (qual->val, scp)) {
+      if (qual_prev == NULL) {
+        *list = qual->next;
+      } else {
+        qual_prev->next = qual->next;
+      }
+      qual->next = NULL;
+      qual = GBQualFree (qual);
+      rval = TRUE;
+    } else {
+      qual_prev = qual;
+    }
+    qual = qual_next;
+  }
+  return rval;
+}
+
+
+static Boolean RemoveGBQualMatchConstraintName (GBQualPtr PNTR list, StringConstraintPtr qual_name, StringConstraintPtr scp)
+{
+  GBQualPtr qual_prev = NULL, qual_next, qual;
+  Boolean   rval = FALSE;
+
+  if (list == NULL) return FALSE;
+  qual = *list;
+  while (qual != NULL) {
+    qual_next = qual->next;
+    if (DoesStringMatchConstraint (qual->qual, qual_name)
+        && !StringHasNoText (qual->val) 
+        && DoesStringMatchConstraint (qual->val, scp)) {
+      if (qual_prev == NULL) {
+        *list = qual->next;
+      } else {
+        qual_prev->next = qual->next;
+      }
+      qual->next = NULL;
+      qual = GBQualFree (qual);
+      rval = TRUE;
+    } else {
+      qual_prev = qual;
+    }
+    qual = qual_next;
+  }
+  return rval;
+}
+
+
+static CharPtr GetDbxrefString (SeqFeatPtr sfp, StringConstraintPtr scp)
+{
+  ValNodePtr vnp;
+  Int4       len = 0;
+  CharPtr    str = NULL, cp;
+  
+  if (sfp == NULL || sfp->dbxref == NULL) {
+    return NULL;
+  }
+  
+  for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next) {
+    cp = GetDbtagString (vnp->data.ptrvalue);
+    if (cp != NULL && DoesStringMatchConstraint(cp, scp)) {
+      len += StringLen (cp) + 1;
+    }
+    cp = MemFree (cp);
+  }
+  
+  if (len == 0) {
+    return NULL;
+  }
+  
+  str = (CharPtr) MemNew ((len + 1) * sizeof (Char));
+  if (str != NULL) {
+    for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next) {
+      cp = GetDbtagString (vnp->data.ptrvalue);
+      if (cp != NULL && DoesStringMatchConstraint(cp, scp)) {
+        StringCat (str, cp);
+        StringCat (str, ";");
+      }
+      cp = MemFree (cp);
+    }
+  }
+  if (StringLen (str) >1) {
+    /* remove final semicolon */
+    str [StringLen (str) - 2] = 0;
+  }
+  return str;
+}
+
+
+static Boolean RemoveDbxrefString (SeqFeatPtr sfp, StringConstraintPtr scp)
+{
+  ValNodePtr vnp, vnp_prev = NULL, vnp_next;
+  CharPtr    cp;
+  Boolean    rval = FALSE;
+  
+  if (sfp == NULL || sfp->dbxref == NULL) {
+    return FALSE;
+  }
+  
+  vnp = sfp->dbxref;
+  while (vnp != NULL) {
+    vnp_next = vnp->next;
+    cp = GetDbtagString (vnp->data.ptrvalue);
+    if (DoesStringMatchConstraint(cp, scp)) {
+      if (vnp_prev == NULL) {
+        sfp->dbxref = vnp->next;
+      } else {
+        vnp_prev->next = vnp->next;
+      }
+      vnp->next = NULL;
+      vnp->data.ptrvalue = DbtagFree (vnp->data.ptrvalue);
+      vnp = ValNodeFree (vnp);
+      rval = TRUE;
+    } else {
+      vnp_prev = vnp;
+    }
+  }
+  return rval;  
+}
+
+
+static CharPtr GetRNAProductString (SeqFeatPtr sfp, StringConstraintPtr scp)
+{
+  RnaRefPtr  rrp;
+  SeqMgrFeatContext context;
+  CharPtr    str = NULL;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL) {
+    return NULL;
+  }
+
+  rrp = sfp->data.value.ptrvalue;
+  if (rrp->ext.choice == 0 
+      || (rrp->ext.choice == 1 && StringHasNoText (rrp->ext.value.ptrvalue))
+      || (rrp->ext.choice == 1 
+          && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0 
+              || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
+              || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))) {
+    str = GetFirstGBQualMatch (sfp->qual, "product", scp);
+  }
+
+  if (str == NULL) {
+    if (rrp->ext.choice == 1 && !StringHasNoText (rrp->ext.value.ptrvalue)
+        && StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0
+        && StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0
+        && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") != 0) {
+      str = StringSave (rrp->ext.value.ptrvalue);        
+    } else if (rrp->ext.choice == 2 && rrp->ext.value.ptrvalue != NULL) {
+      if (SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, 0, 0, sfp, &context) != NULL
+          && !StringHasNoText (context.label)
+          && StringCmp (context.label, "tRNA") != 0) {
+        str = (CharPtr) MemNew (sizeof (Char) + (StringLen (context.label) + 6));
+        sprintf (str, "tRNA-%s", context.label);
+      }
+    }
+    if (!DoesStringMatchConstraint(str, scp)) {
+      str = MemFree (str);
+    }
+  }
+  return str;
+}
+
+
+static Boolean IsParseabletRNAName (CharPtr name_string)
+{
+  if (StringHasNoText(name_string)) 
+  {
+    return TRUE;
+  }
+  else if (StringNICmp (name_string, "trna-", 5) != 0)
+  {
+    return FALSE;
+  }
+  else if (StringLen (name_string) != 8)
+  {
+    return FALSE;
+  }
+  else if (ParseTRnaString (name_string, NULL, NULL, TRUE) == 0)
+  {
+    return FALSE;
+  }
+  else
+  {
+    return TRUE;
+  }
+}
+
+
+static Boolean SetRNAProductString (SeqFeatPtr sfp, StringConstraintPtr scp, CharPtr new_val, Uint2 existing_text)
+{
+  RnaRefPtr  rrp;
+  Boolean rval = FALSE;
+  ValNode vn;
+  CharPtr cp, tmp;
+  tRNAPtr trp;
+  Boolean justTrnaText = FALSE;
+  Uint1   codon [6];
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL) {
+    return FALSE;
+  }
+
+  rrp = sfp->data.value.ptrvalue;
+  if (rrp->ext.choice == 0 
+      || (rrp->ext.choice == 1 && StringHasNoText (rrp->ext.value.ptrvalue))
+      || (rrp->ext.choice == 1 
+          && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0 
+              || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
+              || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))) {
+    vn.choice = FeatQualChoice_legal_qual;
+    vn.data.intvalue = Feat_qual_legal_product;
+
+    rval = SetStringInGBQualList (&(sfp->qual), &vn, scp, new_val, existing_text);
+  }
+
+  if (!rval) {
+    if ((rrp->ext.choice == 0 || (rrp->ext.choice == 1 && StringHasNoText (rrp->ext.value.ptrvalue)))
+        && (scp == NULL || scp->match_text == NULL)) {
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = StringSave (new_val);
+      rrp->ext.choice = 1;
+      rval = TRUE;
+    } else if (rrp->ext.choice == 1 
+                && StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0
+                && StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0
+                && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") != 0
+                && DoesStringMatchConstraint (rrp->ext.value.ptrvalue, scp)) {
+      cp = rrp->ext.value.ptrvalue;
+      rval = SetStringValue (&cp, new_val, existing_text);
+      rrp->ext.value.ptrvalue = cp;
+      rval = TRUE;
+    } else if (rrp->ext.choice == 2) {
+      tmp = GetRNAProductString (sfp, NULL);
+      if (DoesStringMatchConstraint (tmp, scp)
+          && SetStringValue (&tmp, new_val, existing_text)) {
+        trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+        if (trp == NULL) {
+          trp = MemNew (sizeof (tRNA));
+          trp->aatype = 0;
+          MemSet (trp->codon, 255, sizeof (trp->codon));
+          trp->anticodon = NULL;
+          rrp->ext.value.ptrvalue = trp;
+        }
+
+        if (!IsParseabletRNAName(tmp))
+        {
+          if (trp->anticodon == NULL
+              && trp->codon[0] == 255
+              && trp->codon[1] == 255
+              && trp->codon[2] == 255
+              && trp->codon[3] == 255
+              && trp->codon[4] == 255
+              && trp->codon[5] == 255)
+          {
+            trp = MemFree (trp);
+            rrp->ext.choice = 1;
+            rrp->ext.value.ptrvalue = tmp;
+            tmp = NULL;
+            rval = TRUE;
+          }
+          else
+          {
+            vn.choice = FeatQualChoice_legal_qual;
+            vn.data.intvalue = Feat_qual_legal_product;
+            if (SetStringInGBQualList (&(sfp->qual), &vn, scp, new_val, existing_text)) {
+              trp->aa = 0;
+              rval = TRUE;
+            }
+          }
+        }
+        else
+        {
+          trp->aa = ParseTRnaString (tmp, &justTrnaText, codon, TRUE);
+          trp->aatype = 2;
+          rval = TRUE;
+        }
+        tmp = MemFree (tmp);
+      }
+    }
+  }
+  return rval;
+}
+
+
+static Boolean RemoveRNAProductString (SeqFeatPtr sfp, StringConstraintPtr scp)
+{
+  RnaRefPtr  rrp;
+  Boolean    rval = FALSE;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL) {
+    return FALSE;
+  }
+
+  rrp = sfp->data.value.ptrvalue;
+  if (rrp->ext.choice == 0 
+      || (rrp->ext.choice == 1 && StringHasNoText (rrp->ext.value.ptrvalue))
+      || (rrp->ext.choice == 1 
+          && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0 
+              || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
+              || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))) {
+    rval = RemoveGBQualMatch (&(sfp->qual), "product", scp);
+  }
+
+  if (!rval 
+      && rrp->ext.choice == 1 && !StringHasNoText (rrp->ext.value.ptrvalue)
+      && StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0
+      && StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0
+      && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") != 0
+      && DoesStringMatchConstraint(rrp->ext.value.ptrvalue, scp)) {
+    rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+    rrp->ext.choice = 0;
+    rval = TRUE;
+  }
+  return rval;
+}
+
+
+static SeqFeatPtr GetProtFeature (BioseqPtr protbsp)
+{
+  SeqMgrFeatContext fcontext;
+  SeqAnnotPtr sap;
+  SeqFeatPtr prot_sfp;
+  ProtRefPtr prp;
+
+  if (protbsp == NULL) return NULL;
+
+  prot_sfp = SeqMgrGetNextFeature (protbsp, NULL, 0, FEATDEF_PROT, &fcontext);
+  if (prot_sfp == NULL) {
+    sap = protbsp->annot;
+    while (sap != NULL && prot_sfp == NULL) {
+      if (sap->type == 1) {
+        prot_sfp = sap->data;
+        while (prot_sfp != NULL
+               && (prot_sfp->data.choice != SEQFEAT_PROT
+                   || (prp = prot_sfp->data.value.ptrvalue) == NULL
+                   || prp->processed != 0)) {
+          prot_sfp = prot_sfp->next;
+        }
+      }
+      sap = sap->next;
+    }
+  }
+  return prot_sfp;
+}
+
+
+static ProtRefPtr GetProtRefForFeature (SeqFeatPtr sfp)
+{
+  BioseqPtr  protbsp;
+  SeqFeatPtr protsfp;
+  ProtRefPtr prp = NULL;
+  SeqFeatXrefPtr xref;
+
+  if (sfp == NULL) return NULL;
+
+  if (sfp->data.choice == SEQFEAT_PROT) {
+    prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+  } else if (sfp->data.choice == SEQFEAT_CDREGION) {
+    xref = sfp->xref;
+    while (xref != NULL && xref->data.choice != SEQFEAT_PROT) {
+      xref = xref->next;
+    }
+    if (xref != NULL) {
+      prp = xref->data.value.ptrvalue;
+    }
+    if (prp == NULL && sfp->product != NULL) {
+      protbsp = BioseqFindFromSeqLoc (sfp->product);
+      protsfp = GetProtFeature (protbsp);    
+      if (protsfp != NULL) {
+        prp = protsfp->data.value.ptrvalue;
+      }
+    }
+  }
+  return prp;
+}
+
+
+NLM_EXTERN CharPtr GetQualFromFeature (SeqFeatPtr sfp, FeatureFieldPtr field, StringConstraintPtr scp)
+{
+  CharPtr   str = NULL;
+  GeneRefPtr grp = NULL;
+  ProtRefPtr prp = NULL;
+  Int4      gbqual;
+
+  if (sfp == NULL || field == NULL || field->field == NULL)
+  {
+    return NULL;
+  }
+  if (field->type != Feature_type_any && sfp->idx.subtype != GetFeatdefFromFeatureType (field->type))
+  {
+    return NULL;
+  }
+
+  // for gene fields
+  if (sfp->idx.subtype == FEATDEF_GENE) {
+    grp = sfp->data.value.ptrvalue;
+  } else {
+    grp = SeqMgrGetGeneXref (sfp);
+  }
+
+  // for protein fields
+  prp = GetProtRefForFeature (sfp);
+
+  /* fields common to all features */
+  /* note, also known as comment */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_note)
+      || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("note", field->field->data.ptrvalue)))
+  {
+    if (!StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+    {
+      str = StringSave (sfp->comment);
+    }
+  }
+  /* db-xref */
+  if (str == NULL
+      && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_db_xref)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("db_xref", field->field->data.ptrvalue))))
+  {
+    str = GetDbxrefString (sfp, scp);
+  }
+  /* exception */
+  if (str == NULL 
+      && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_exception)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("exception", field->field->data.ptrvalue))))
+  {
+    if (!StringHasNoText (sfp->except_text) && DoesStringMatchConstraint(sfp->except_text, scp))
+    {
+      str = StringSave (sfp->except_text);
+    }
+  }
+  /* evidence */
+  if (str == NULL
+      && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_evidence)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("evidence", field->field->data.ptrvalue))))
+  {
+    if (sfp->exp_ev == 1)
+    {
+      str = StringSave ("experimental");
+    }
+    else if (sfp->exp_ev == 2)
+    {
+      str = StringSave ("non-experimental");
+    }
+    if (!DoesStringMatchConstraint(str, scp)) {
+      str = MemFree (str);
+    }
+  }
+
+  /* fields common to some features */
+  /* product */
+  if (str == NULL
+      && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_product)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("product", field->field->data.ptrvalue))))
+  {
+    if (prp != NULL) {
+      str = GetFirstValNodeStringMatch (prp->name, scp);
+    } else if (sfp->data.choice == SEQFEAT_RNA) {
+      str = GetRNAProductString (sfp, scp);
+    }
+  }
+
+  /* Gene fields */
+  /* locus */
+  if (str == NULL 
+       && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_gene)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("locus", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (!StringHasNoText (grp->locus) && DoesStringMatchConstraint(grp->locus, scp))
+    {
+      str = StringSave (grp->locus);
+    }
+  }
+  /* description */
+  if (str == NULL 
+       && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_gene_description)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("description", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (!StringHasNoText (grp->desc) && DoesStringMatchConstraint(grp->desc, scp))
+    {
+      str = StringSave (grp->desc);
+    }
+  }
+  /* maploc */
+  if (str == NULL 
+       && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_map)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("map", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (!StringHasNoText (grp->maploc) && DoesStringMatchConstraint(grp->maploc, scp))
+    {
+      str = StringSave (grp->maploc);
+    }
+  }
+  /* allele */
+  if (str == NULL 
+       && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_allele)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("allele", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (!StringHasNoText (grp->allele) && DoesStringMatchConstraint(grp->allele, scp))
+    {
+      str = StringSave (grp->allele);
+    }
+  }
+  /* locus_tag */
+  if (str == NULL 
+       && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_locus_tag)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("locus_tag", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (!StringHasNoText (grp->locus_tag) && DoesStringMatchConstraint(grp->locus_tag, scp))
+    {
+      str = StringSave (grp->locus_tag);
+    }
+  }
+  /* synonym */
+  if (str == NULL 
+       && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_synonym)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("synonym", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    str = GetFirstValNodeStringMatch (grp->syn, scp);
+  }
+
+
+  /* protein fields */
+  /* note - product handled above */
+  /* description */
+  if (str == NULL 
+       && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_description)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("description", field->field->data.ptrvalue)))
+       && prp != NULL)
+  {
+    if (!StringHasNoText (prp->desc) && DoesStringMatchConstraint(prp->desc, scp)) {
+      str = StringSave (prp->desc);
+    }
+  }
+  /* ec_number */
+  if (str == NULL 
+       && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_ec_number)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("ec_number", field->field->data.ptrvalue)))
+       && prp != NULL)
+  {
+    str = GetFirstValNodeStringMatch (prp->ec, scp);
+  }
+  /* activity */
+  if (str == NULL 
+       && ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_activity)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("activity", field->field->data.ptrvalue)))
+       && prp != NULL)
+  {
+    str = GetFirstValNodeStringMatch (prp->activity, scp);
+  }
+  
+
+  /* actual GenBank qualifiers */
+  if (str == NULL)
+  {
+    if (field->field->choice == FeatQualChoice_legal_qual) 
+    {
+      gbqual = GetGBQualFromFeatQual (field->field->data.intvalue);
+      if (gbqual > -1) {
+        str = GetFirstGBQualMatch (sfp->qual, ParFlat_GBQual_names [gbqual].name, scp);
+      } else {
+        /* need to do something with non-qualifier qualifiers */
+      }
+    } else {
+      str = GetFirstGBQualMatchConstraintName (sfp->qual, field->field->data.ptrvalue, scp);
+    }
+  }
+  return str;
+}
+
+
+static Boolean RemoveQualFromFeature (SeqFeatPtr sfp, FeatureFieldPtr field, StringConstraintPtr scp)
+{
+  Boolean rval = FALSE;
+  GeneRefPtr grp = NULL;
+  ProtRefPtr prp = NULL;
+  RnaRefPtr  rrp;
+  tRNAPtr trp;
+  Int4      gbqual;
+
+  if (sfp == NULL || field == NULL || field->field == NULL)
+  {
+    return FALSE;
+  }
+  if (field->type != Feature_type_any && sfp->idx.subtype != GetFeatdefFromFeatureType (field->type))
+  {
+    return FALSE;
+  }
+
+  // for gene fields
+  if (sfp->idx.subtype == FEATDEF_GENE) {
+    grp = sfp->data.value.ptrvalue;
+  } else {
+    grp = SeqMgrGetGeneXref (sfp);
+  }
+
+  // for protein fields
+  prp = GetProtRefForFeature (sfp);
+
+  // for RNA fields
+  if (sfp->data.choice == SEQFEAT_RNA) {
+    rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  }
+
+  /* fields common to all features */
+  /* note, also known as comment */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_note)
+      || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("note", field->field->data.ptrvalue)))
+  {
+    if (!StringHasNoText (sfp->comment) && DoesStringMatchConstraint (sfp->comment, scp))
+    {
+      sfp->comment = MemFree (sfp->comment);
+      rval = TRUE;
+    }
+  }
+  /* db-xref */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_db_xref)
+      || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("db_xref", field->field->data.ptrvalue)))
+  {
+    rval = RemoveDbxrefString (sfp, scp);
+  }
+  /* exception */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_exception)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("exception", field->field->data.ptrvalue)))
+  {
+    if (!StringHasNoText (sfp->except_text) && DoesStringMatchConstraint (sfp->except_text, scp))
+    {
+      sfp->except_text = MemFree (sfp->except_text);
+      rval = TRUE;
+    }
+  }
+  /* evidence */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_evidence)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("evidence", field->field->data.ptrvalue)))
+  {
+    if ((sfp->exp_ev == 1 && DoesStringMatchConstraint("experimental", scp))
+        || (sfp->exp_ev == 2 && DoesStringMatchConstraint("non-experimental", scp))) {
+      sfp->exp_ev = 0;
+      rval = TRUE;
+    }
+  }
+
+  /* fields common to some features */
+  /* product */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_product)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("product", field->field->data.ptrvalue)))
+  {
+    if (prp != NULL) {
+      rval = RemoveValNodeStringMatch (&(prp->name), scp);
+    } else if (sfp->data.choice == SEQFEAT_RNA) {
+      rval = RemoveRNAProductString (sfp, scp);
+    }
+  }
+
+  /* Gene fields */
+  /* locus */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_gene)
+       || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("locus", field->field->data.ptrvalue)))
+      && grp != NULL)
+  {
+    if (!StringHasNoText (grp->locus) && DoesStringMatchConstraint (grp->locus, scp)) {
+      grp->locus = MemFree (grp->locus);
+      rval = TRUE;
+    }
+  }
+  /* description */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_gene_description)
+       || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("description", field->field->data.ptrvalue)))
+      && grp != NULL)
+  {
+    if (!StringHasNoText (grp->desc) && DoesStringMatchConstraint(grp->desc, scp))
+    {
+      grp->desc = MemFree (grp->desc);
+      rval = TRUE;
+    }
+  }
+  /* maploc */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_map)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("map", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (!StringHasNoText (grp->maploc) && DoesStringMatchConstraint(grp->maploc, scp))
+    {
+      grp->maploc = MemFree (grp->maploc);
+      rval = TRUE;
+    }
+  }
+  /* allele */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_allele)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("allele", field->field->data.ptrvalue)))
+      && grp != NULL)
+  {
+    if (!StringHasNoText (grp->allele) && DoesStringMatchConstraint(grp->allele, scp))
+    {
+      grp->allele = MemFree (grp->allele);
+      rval = TRUE;
+    }
+  }
+  /* locus_tag */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_locus_tag)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("locus_tag", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (!StringHasNoText (grp->locus_tag) && DoesStringMatchConstraint(grp->locus_tag, scp))
+    {
+      grp->locus_tag = MemFree (grp->locus_tag);
+      rval = TRUE;
+    }
+  }
+  /* synonym */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_synonym)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("synonym", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    rval = RemoveValNodeStringMatch (&(grp->syn), scp);
+  }
+
+  /* protein fields */
+  /* note - product handled above */
+  /* description */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_description)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("description", field->field->data.ptrvalue)))
+       && prp != NULL)
+  {
+    if (!StringHasNoText (prp->desc) && DoesStringMatchConstraint(prp->desc, scp)) {
+      prp->desc = MemFree (prp->desc);
+      rval = TRUE;
+    }
+  }
+  /* ec_number */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_ec_number)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("ec_number", field->field->data.ptrvalue)))
+       && prp != NULL)
+  {
+    rval = RemoveValNodeStringMatch (&(prp->ec), scp);
+  }
+  /* activity */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_activity)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("activity", field->field->data.ptrvalue)))
+       && prp != NULL)
+  {
+    rval = RemoveValNodeStringMatch (&(prp->activity), scp);
+  }
+  
+  /* RNA fields */
+  /* anticodon */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_anticodon)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("anticodon", field->field->data.ptrvalue)))
+       && rrp != NULL && rrp->ext.choice == 2)
+  {
+    trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+    if (trp != NULL && trp->anticodon != NULL) {
+      trp->anticodon = SeqLocFree (trp->anticodon);
+      rval = TRUE;
+    }
+  }
+  /* codons recognized */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_anticodon)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("anticodon", field->field->data.ptrvalue)))
+       && rrp != NULL && rrp->ext.choice == 2)
+  {
+    trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+    if (trp != NULL && (trp->codon[0] != 255 || trp->codon[1] != 255 || trp->codon[2] != 255
+                        || trp->codon[3] != 255 || trp->codon[4] != 255 || trp->codon[5] != 255)) {
+      trp->codon [0] = 255;
+      trp->codon [1] = 255;
+      trp->codon [2] = 255;
+      trp->codon [3] = 255;
+      trp->codon [4] = 255;
+      trp->codon [5] = 255;
+      rval = TRUE;
+    }
+  }
+
+  if (!rval) {
+    /* actual GenBank qualifiers */
+    if (field->field->choice == FeatQualChoice_legal_qual) 
+    {
+      gbqual = GetGBQualFromFeatQual (field->field->data.intvalue);
+      if (gbqual > -1) {
+        rval = RemoveGBQualMatch (&(sfp->qual), ParFlat_GBQual_names [gbqual].name, scp);
+      } else {
+        /* need to do something with non-qualifier qualifiers */
+      }
+    } else {
+      rval = RemoveGBQualMatchConstraintName (&(sfp->qual), field->field->data.ptrvalue, scp);
+    }
+  }
+
+  return rval;
+}
+
+
+static Boolean ChooseBestFrame (SeqFeatPtr sfp)
+{
+  CdRegionPtr  crp;
+  Uint1        new_frame = 0, i, orig_frame;
+  ByteStorePtr bs;
+  Int4         lens [3];
+  Int4         max;
+  Boolean      retval = TRUE;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return FALSE;
+  
+  crp = sfp->data.value.ptrvalue;
+  if (crp == NULL) return FALSE;
+  orig_frame = crp->frame;
+
+  max = 0;
+  for (i = 1; i <= 3; i++) {
+    crp->frame = i;
+    bs = ProteinFromCdRegionEx (sfp, FALSE, FALSE);
+    lens[i - 1] = BSLen (bs);
+    BSFree (bs);
+    if (lens[i - 1] > max) {
+      max = lens[i - 1];
+      new_frame = i;
+    }
+  }
+  for (i = 1; i <= 3; i++) {
+    if (lens [i - 1] == max && i != new_frame) {
+      retval = FALSE;
+    }
+  }
+  if (retval) {
+    crp->frame = new_frame;
+  } else {
+    crp->frame = orig_frame;
+  }
+  return retval;
+}
+
+
+static Boolean SetQualOnFeature (SeqFeatPtr sfp, FeatureFieldPtr field, StringConstraintPtr scp, CharPtr value, Uint2 existing_text)
+{
+  Boolean rval = FALSE;
+  GeneRefPtr grp = NULL;
+  ProtRefPtr prp = NULL;
+  CharPtr    tmp;
+  CdRegionPtr crp;
+
+  if (sfp == NULL || field == NULL || field->field == NULL)
+  {
+    return FALSE;
+  }
+  if (field->type != Feature_type_any && sfp->idx.subtype != GetFeatdefFromFeatureType (field->type))
+  {
+    return FALSE;
+  }
+
+  // for gene fields
+  if (sfp->idx.subtype == FEATDEF_GENE) {
+    grp = sfp->data.value.ptrvalue;
+  } else {
+    grp = SeqMgrGetGeneXref (sfp);
+  }
+
+  // for protein fields
+  prp = GetProtRefForFeature (sfp);
+
+  /* fields common to all features */
+  /* note, also known as comment */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_note)
+      || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("note", field->field->data.ptrvalue)))
+  {
+    if (DoesStringMatchConstraint(sfp->comment, scp))
+    {
+      rval = SetStringValue ( &(sfp->comment), value, existing_text);
+    }
+  }
+  /* db-xref */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_db_xref)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("db_xref", field->field->data.ptrvalue)))
+  {
+    rval = SetDbxrefString (sfp, scp, value, existing_text);
+  }
+  /* exception */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_exception)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("exception", field->field->data.ptrvalue)))
+  {
+    if (DoesStringMatchConstraint(sfp->except_text, scp))
+    {
+      rval = SetStringValue ( &(sfp->except_text), value, existing_text);
+    }
+  }
+  /* evidence */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_evidence)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("evidence", field->field->data.ptrvalue)))
+  {
+    tmp = NULL;
+    if (sfp->exp_ev == 1)
+    {
+      tmp = StringSave ("experimental");
+    }
+    else if (sfp->exp_ev == 2)
+    {
+      tmp = StringSave ("non-experimental");
+    }
+    if (DoesStringMatchConstraint(tmp, scp)) {
+      rval = SetStringValue (&tmp, value, existing_text);
+      if (rval) {
+        rval = FALSE;
+        if (StringICmp (tmp, "experimental") == 0) {
+          sfp->exp_ev = 1;
+          rval = TRUE;
+        } else if (StringICmp (tmp, "non-experimental") == 0) {
+          sfp->exp_ev = 2;
+          rval = TRUE;
+        } else if (StringHasNoText (tmp)) {
+          sfp->exp_ev = 0;
+          rval = TRUE;
+        }
+      }
+    }
+    tmp = MemFree (tmp);
+  }
+  
+
+  /* fields common to some features */
+  /* product */
+  if ((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_product)
+          || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("product", field->field->data.ptrvalue)))
+  {
+    if (prp != NULL) {
+      rval = SetStringsInValNodeStringList (&(prp->name), scp, value, existing_text);
+    } else if (sfp->data.choice == SEQFEAT_RNA) {
+      rval = SetRNAProductString (sfp, scp, value, existing_text);
+    }
+  }
+
+  /* Gene fields */
+  /* locus */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_gene)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("locus", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (DoesStringMatchConstraint(grp->locus, scp))
+    {
+      rval = SetStringValue (&(grp->locus), value, existing_text);
+    }
+  }
+  /* description */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_gene_description)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("description", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (DoesStringMatchConstraint(grp->desc, scp))
+    {
+      rval = SetStringValue (&(grp->desc), value, existing_text);
+    }
+  }
+  /* maploc */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_map)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("map", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (DoesStringMatchConstraint(grp->maploc, scp))
+    {
+      rval = SetStringValue (&(grp->maploc), value, existing_text);
+    }
+  }
+  /* allele */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_allele)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("allele", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (DoesStringMatchConstraint(grp->allele, scp))
+    {
+      rval = SetStringValue (&(grp->allele), value, existing_text);
+    }
+  }
+  /* locus_tag */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_locus_tag)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("locus_tag", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    if (DoesStringMatchConstraint(grp->locus_tag, scp))
+    {
+      rval = SetStringValue (&(grp->locus_tag), value, existing_text);
+    }
+  }
+  /* synonym */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_synonym)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("synonym", field->field->data.ptrvalue)))
+       && grp != NULL)
+  {
+    rval = SetStringsInValNodeStringList (&(grp->syn), scp, value, existing_text);
+  }
+
+
+  /* protein fields */
+  /* note - product handled above */
+  /* description */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_description)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("description", field->field->data.ptrvalue)))
+       && prp != NULL)
+  {
+    if (DoesStringMatchConstraint(prp->desc, scp)) {
+      rval = SetStringValue (&(prp->desc), value, existing_text);
+    }
+  }
+  /* ec_number */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_ec_number)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("ec_number", field->field->data.ptrvalue)))
+       && prp != NULL)
+  {
+    rval = SetStringsInValNodeStringList (&(prp->ec), scp, value, existing_text);
+  }
+  /* activity */
+  if (((field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_activity)
+           || (field->field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("activity", field->field->data.ptrvalue)))
+       && prp != NULL)
+  {
+    rval = SetStringsInValNodeStringList (&(prp->activity), scp, value, existing_text);
+  }
+ 
+  if (field->field->choice == FeatQualChoice_legal_qual && field->field->data.intvalue == Feat_qual_legal_codon_start
+      && sfp->data.choice == SEQFEAT_CDREGION) 
+  {
+    crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+    if (StringICmp (value, "best") == 0)
+    {
+      rval = ChooseBestFrame (sfp);
+    }
+    else if (StringCmp (value, "1") == 0) 
+    {
+      crp->frame = 1;
+      rval = TRUE;
+    }
+    else if (StringCmp (value, "2") == 0) 
+    {
+      crp->frame = 2;
+      rval = TRUE;
+    }
+    else if (StringCmp (value, "3") == 0)
+    {
+      crp->frame = 3;
+      rval = TRUE;
+    } 
+  } 
+
+  /* actual GenBank qualifiers */
+  if (!rval)
+  {
+    rval = SetStringInGBQualList (&(sfp->qual), field->field, scp, value, existing_text);
+  }
+  return rval;
+}
+
+
+NLM_EXTERN CharPtr GetSourceQualFromBioSource (BioSourcePtr biop, SourceQualChoicePtr scp, StringConstraintPtr constraint)
+{
+  CharPtr str = NULL;
+  SubSourcePtr ssp;
+  OrgModPtr mod;
+  Int4 orgmod_subtype = -1, subsrc_subtype = -1;
+
+  if (biop == NULL || scp == NULL) return NULL;
+
+  switch (scp->choice) 
+  {
+    case SourceQualChoice_textqual:
+      if (scp->data.intvalue == Source_qual_taxname) {
+        if (biop->org != NULL && !StringHasNoText (biop->org->taxname)
+            && DoesStringMatchConstraint (biop->org->taxname, constraint)) {
+          str = StringSave (biop->org->taxname);
+        }
+      } else if (scp->data.intvalue == Source_qual_common_name) {
+        if (biop->org != NULL && !StringHasNoText (biop->org->common)
+            && DoesStringMatchConstraint (biop->org->common, constraint)) {
+          str = StringSave (biop->org->common);
+        }
+      } else if (scp->data.intvalue == Source_qual_lineage) {
+        if (biop->org != NULL && biop->org->orgname != NULL && !StringHasNoText (biop->org->orgname->lineage)
+            && DoesStringMatchConstraint (biop->org->orgname->lineage, constraint)) {
+          str = StringSave (biop->org->orgname->lineage);
+        }
+      } else if (scp->data.intvalue == Source_qual_division) {
+        if (biop->org != NULL && biop->org->orgname != NULL  && !StringHasNoText (biop->org->orgname->div)
+            && DoesStringMatchConstraint (biop->org->orgname->div, constraint)) {
+          str = StringSave (biop->org->orgname->div);
+        }
+      } else {
+        orgmod_subtype = GetOrgModQualFromSrcQual (scp->data.intvalue);
+        if (orgmod_subtype == -1) {
+          subsrc_subtype = GetSubSrcQualFromSrcQual (scp->data.intvalue);
+          for (ssp = biop->subtype; ssp != NULL && str == NULL; ssp = ssp->next) {
+            if (ssp->subtype == subsrc_subtype) {
+              if (StringHasNoText (ssp->name)) {
+                if (IsNonTextSourceQual (scp->data.intvalue)
+                    && DoesStringMatchConstraint ("TRUE", constraint)) {
+                  str = StringSave ("TRUE");
+                }
+              } else {
+                if (DoesStringMatchConstraint (ssp->name, constraint)) {
+                  str = StringSave (ssp->name);
+                }
+              }
+            }
+          }
+        } else {
+          if (biop->org != NULL && biop->org->orgname != NULL) {
+            for (mod = biop->org->orgname->mod; mod != NULL && str == NULL; mod = mod->next) {
+              if (mod->subtype == orgmod_subtype) {
+                if (StringHasNoText (mod->subname)) {
+                  if (IsNonTextSourceQual (scp->data.intvalue)
+                      && DoesStringMatchConstraint ("TRUE", constraint)) {
+                    str = StringSave ("TRUE");
+                  }
+                } else {
+                  if (DoesStringMatchConstraint (mod->subname, constraint)) {
+                    str = StringSave (mod->subname);
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+      break;
+    case SourceQualChoice_location:
+      str = LocNameFromGenome (biop->genome);
+      if (DoesStringMatchConstraint (str, constraint)) {
+        str = StringSave (str);
+      } else {
+        str = NULL;
+      }
+      break;
+    case SourceQualChoice_origin:
+      str = OriginNameFromOrigin (biop->origin);
+      if (DoesStringMatchConstraint (str, constraint)) {
+        str = StringSave (str);
+      } else {
+        str = NULL;
+      }
+      break;
+  }
+  return str;
+}
+
+
+static Boolean RemoveSourceQualFromBioSource (BioSourcePtr biop, SourceQualChoicePtr scp, StringConstraintPtr constraint)
+{
+  SubSourcePtr ssp, ssp_prev = NULL, ssp_next;
+  OrgModPtr mod, mod_prev = NULL, mod_next;
+  Int4 orgmod_subtype = -1, subsrc_subtype = -1;
+  CharPtr str;
+  Boolean rval = FALSE;
+
+  if (biop == NULL || scp == NULL) return FALSE;
+
+  switch (scp->choice) 
+  {
+    case SourceQualChoice_textqual:
+      if (scp->data.intvalue == Source_qual_taxname) {
+        if (biop->org != NULL && !StringHasNoText (biop->org->taxname)
+            && DoesStringMatchConstraint (biop->org->taxname, constraint)) {
+          biop->org->taxname = MemFree (biop->org->taxname);
+          rval = TRUE;
+        }
+      } else if (scp->data.intvalue == Source_qual_common_name) {
+        if (biop->org != NULL && !StringHasNoText (biop->org->common)
+            && DoesStringMatchConstraint (biop->org->common, constraint)) {
+          biop->org->common = MemFree (biop->org->common);
+          rval = TRUE;
+        }
+      } else if (scp->data.intvalue == Source_qual_lineage) {
+        if (biop->org != NULL && biop->org->orgname != NULL && !StringHasNoText (biop->org->orgname->lineage)
+            && DoesStringMatchConstraint (biop->org->orgname->lineage, constraint)) {
+          biop->org->orgname->lineage = MemFree (biop->org->orgname->lineage);
+          rval = TRUE;
+        }
+      } else if (scp->data.intvalue == Source_qual_division) {
+        if (biop->org != NULL && biop->org->orgname != NULL  && !StringHasNoText (biop->org->orgname->div)
+            && DoesStringMatchConstraint (biop->org->orgname->div, constraint)) {
+          biop->org->orgname->div = MemFree (biop->org->orgname->div);
+          rval = TRUE;
+        }
+      } else {
+        orgmod_subtype = GetOrgModQualFromSrcQual (scp->data.intvalue);
+        if (orgmod_subtype == -1) {
+          subsrc_subtype = GetSubSrcQualFromSrcQual (scp->data.intvalue);
+          ssp = biop->subtype;
+          while (ssp != NULL) {
+            ssp_next = ssp->next;
+            if (ssp->subtype == subsrc_subtype 
+                && DoesStringMatchConstraint (ssp->name, constraint)) {
+              if (ssp_prev == NULL) {
+                biop->subtype = ssp->next;
+              } else {
+                ssp_prev->next = ssp->next;
+              }
+              ssp->next = NULL;
+              ssp = SubSourceFree (ssp);
+              rval = TRUE;
+            } else {
+              ssp_prev = ssp;
+            }
+            ssp = ssp_next;
+          }
+        } else {
+          if (biop->org != NULL && biop->org->orgname != NULL) {
+            mod = biop->org->orgname->mod;
+            while (mod != NULL) {
+              mod_next = mod->next;
+              if (mod->subtype == orgmod_subtype
+                  && DoesStringMatchConstraint (mod->subname, constraint)) {
+                if (mod_prev == NULL) {
+                  biop->org->orgname->mod = mod->next;
+                } else {
+                  mod_prev->next = mod->next;
+                }
+                mod->next = NULL;
+                mod = OrgModFree (mod);
+                rval = TRUE;
+              } else {
+                mod_prev = mod;
+              }
+              mod = mod_next;
+            }
+          }
+        }
+      }
+      break;
+    case SourceQualChoice_location:
+      str = LocNameFromGenome (biop->genome);
+      if (DoesStringMatchConstraint (str, constraint)) {
+        if (scp->data.intvalue == 0 || biop->genome == GenomeFromSrcLoc (scp->data.intvalue)) {
+          biop->genome = 0;
+          rval = TRUE;
+        }
+      }
+      break;
+    case SourceQualChoice_origin:
+      str = OriginNameFromOrigin (biop->origin);
+      if (DoesStringMatchConstraint (str, constraint)) {
+        if (scp->data.intvalue == 0 || biop->origin == OriginFromSrcOrig (scp->data.intvalue)) {
+          biop->origin = 0;
+          rval = TRUE;
+        }
+      }
+      break; 
+  }
+  return rval;
+}
+
+
+NLM_EXTERN Boolean SetSourceQualInBioSource (BioSourcePtr biop, SourceQualChoicePtr scp, StringConstraintPtr constraint, CharPtr value, Uint2 existing_text)
+{
+  SubSourcePtr ssp, ssp_prev = NULL, ssp_next;
+  OrgModPtr mod, mod_prev = NULL, mod_next;
+  Int4 orgmod_subtype = -1, subsrc_subtype = -1;
+  CharPtr str;
+  Boolean rval = FALSE, found = FALSE;
+
+  if (biop == NULL || scp == NULL) return FALSE;
+
+  switch (scp->choice) 
+  {
+    case SourceQualChoice_textqual:
+      if (scp->data.intvalue == Source_qual_taxname) {
+        if (biop->org != NULL
+            && DoesStringMatchConstraint (biop->org->taxname, constraint)) {
+          rval = SetStringValue (&(biop->org->taxname), value, existing_text);
+        }
+      } else if (scp->data.intvalue == Source_qual_common_name) {
+        if (biop->org != NULL
+            && DoesStringMatchConstraint (biop->org->common, constraint)) {
+          rval = SetStringValue (&(biop->org->common), value, existing_text);
+        }
+      } else if (scp->data.intvalue == Source_qual_lineage) {
+        if (biop->org != NULL && biop->org->orgname != NULL 
+            && DoesStringMatchConstraint (biop->org->orgname->lineage, constraint)) {
+          rval = SetStringValue (&(biop->org->orgname->lineage), value, existing_text);
+        }
+      } else if (scp->data.intvalue == Source_qual_division) {
+        if (biop->org != NULL && biop->org->orgname != NULL
+            && DoesStringMatchConstraint (biop->org->orgname->div, constraint)) {
+          rval = SetStringValue (&(biop->org->orgname->div), value, existing_text);
+        }
+      } else {
+        orgmod_subtype = GetOrgModQualFromSrcQual (scp->data.intvalue);
+        if (orgmod_subtype == -1) {
+          subsrc_subtype = GetSubSrcQualFromSrcQual (scp->data.intvalue);
+          if (subsrc_subtype > -1) {
+            ssp = biop->subtype;
+            while (ssp != NULL) {
+              ssp_next = ssp->next;
+              if (ssp->subtype == subsrc_subtype
+                  && DoesStringMatchConstraint (ssp->name, constraint)) {
+                rval = SetStringValue (&(ssp->name), value, existing_text);
+                found = TRUE;
+                if (rval && StringHasNoText (ssp->name) && !IsNonTextSourceQual(scp->data.intvalue)) {
+                  if (ssp_prev == NULL) {
+                    biop->subtype = ssp->next;
+                  } else {
+                    ssp_prev->next = ssp->next;
+                  }
+                  ssp->next = NULL;
+                  ssp = SubSourceFree (ssp);
+                } else {
+                  ssp_prev = ssp;
+                }
+              } else {
+                ssp_prev = ssp;
+              }
+              ssp = ssp_next;
+            }
+            if (!found && IsStringConstraintEmpty (constraint)) {
+              ssp = SubSourceNew ();
+              ssp->subtype = subsrc_subtype;
+              rval = SetStringValue (&(ssp->name), value, existing_text);
+              if (ssp_prev == NULL) {
+                biop->subtype = ssp;
+              } else {
+                ssp_prev->next = ssp;
+              }
+            }
+          }
+        } else {
+          if (biop->org != NULL && biop->org->orgname != NULL) {
+            mod = biop->org->orgname->mod;
+            while (mod != NULL) {
+              mod_next = mod->next;
+              if (mod->subtype == orgmod_subtype
+                  && DoesStringMatchConstraint (mod->subname, constraint)) {
+                rval = SetStringValue (&(mod->subname), value, existing_text);
+                found = TRUE;
+                if (rval && StringHasNoText (mod->subname) && !IsNonTextSourceQual(scp->data.intvalue)) {
+                  if (mod_prev == NULL) {
+                    biop->org->orgname->mod = mod->next;
+                  } else {
+                    mod_prev->next = mod->next;
+                  }
+                  mod->next = NULL;
+                  mod = OrgModFree (mod);
+                } else {
+                  mod_prev = mod;
+                }
+              } else {
+                mod_prev = mod;
+              }
+              mod = mod_next;
+            }
+          }
+          if (!found && IsStringConstraintEmpty (constraint)) {
+            if (biop->org == NULL) {
+              biop->org = OrgRefNew();
+            }
+            if (biop->org->orgname == NULL) {
+              biop->org->orgname = OrgNameNew();
+            }
+            mod = OrgModNew ();
+            mod->subtype = orgmod_subtype;
+            rval = SetStringValue (&(mod->subname), value, existing_text);
+            if (mod_prev == NULL) {
+              biop->org->orgname->mod = mod;
+            } else {
+              mod_prev->next = mod;
+            }
+          }
+        }
+      }
+      break;
+    case SourceQualChoice_location:
+      str = LocNameFromGenome (biop->genome);
+      if (DoesStringMatchConstraint (str, constraint)) {
+        biop->genome = GenomeFromSrcLoc (scp->data.intvalue);
+        rval = TRUE;
+      }
+      break;
+    case SourceQualChoice_origin:
+      str = OriginNameFromOrigin (biop->origin);
+      if (DoesStringMatchConstraint (str, constraint)) {
+        biop->origin = OriginFromSrcOrig(scp->data.intvalue);
+        rval = TRUE;
+      }
+      break; 
+  }
+  return rval;
+}
+
+
+static BioseqPtr GetSequenceForObject (Uint1 choice, Pointer data)
+{
+  BioseqPtr bsp = NULL;
+  SeqFeatPtr sfp;
+  SeqDescrPtr sdp;
+  ObjValNodePtr ovp;
+  CGPSetPtr cgp;
+  ValNodePtr vnp;
+
+  if (data == NULL) return NULL;
+
+  switch (choice) {
+    case OBJ_BIOSEQ:
+      bsp = (BioseqPtr) data;
+      break;
+    case OBJ_SEQFEAT:
+      sfp = (SeqFeatPtr) data;
+      bsp = BioseqFindFromSeqLoc (sfp->location);
+      break;
+    case OBJ_SEQDESC:
+      sdp = (SeqDescrPtr) data;
+      if (sdp->extended) {
+        ovp = (ObjValNodePtr) sdp;
+        if (ovp->idx.parenttype == OBJ_BIOSEQ && ovp->idx.parentptr != NULL) {
+          bsp = ovp->idx.parentptr;
+        }
+      }
+      break;
+    case 0:
+      cgp = (CGPSetPtr) data;
+      for (vnp = cgp->cds_list; vnp != NULL && bsp == NULL; vnp = vnp->next) {
+        sfp = vnp->data.ptrvalue;
+        if (sfp != NULL) {
+          bsp = BioseqFindFromSeqLoc (sfp->location);
+        }
+      }
+      for (vnp = cgp->mrna_list; vnp != NULL && bsp == NULL; vnp = vnp->next) {
+        sfp = vnp->data.ptrvalue;
+        if (sfp != NULL) {
+          bsp = BioseqFindFromSeqLoc (sfp->location);
+        }
+      }
+      break;
+      for (vnp = cgp->gene_list; vnp != NULL && bsp == NULL; vnp = vnp->next) {
+        sfp = vnp->data.ptrvalue;
+        if (sfp != NULL) {
+          bsp = BioseqFindFromSeqLoc (sfp->location);
+        }
+      }
+      break;
+  }
+  return bsp;
+}
+
+
+NLM_EXTERN BioSourcePtr GetBioSourceFromObject (Uint1 choice, Pointer data)
+{
+  BioSourcePtr biop = NULL;
+  SeqDescrPtr  sdp;
+  SeqFeatPtr   sfp;
+  BioseqPtr    bsp = NULL;
+  SeqMgrDescContext context;
+
+  if (data == NULL) return NULL;
+
+  switch (choice)
+  {
+    case OBJ_SEQDESC:
+      sdp = (SeqDescrPtr) data;
+      if (sdp->choice == Seq_descr_source) {
+        biop = sdp->data.ptrvalue;
+      }
+      break;
+    case OBJ_SEQFEAT:
+      sfp = (SeqFeatPtr) data;
+      if (sfp->data.choice == SEQFEAT_BIOSRC) {
+        biop = sfp->data.value.ptrvalue;
+      }
+      break;
+  }
+  if (biop == NULL) {
+    bsp = GetSequenceForObject (choice, data);
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &context);
+    if (sdp != NULL && sdp->choice == Seq_descr_source) {
+      biop = sdp->data.ptrvalue;
+    }
+  }
+  return biop;
+}
+
+
+/* functions for dealing with CDS-Gene-Prot sets */
+static CharPtr GetFieldValueFromCGPSet (CGPSetPtr c, Uint2 field, StringConstraintPtr scp)
+{
+  CharPtr str = NULL;
+  ValNodePtr vnp;
+  SeqFeatPtr sfp;
+  GeneRefPtr grp;
+  RnaRefPtr  rrp;
+  ProtRefPtr prp;
+  
+  if (c == NULL) return NULL;
+  switch (field) {
+    case CDSGeneProt_field_cds_comment:
+      for (vnp = c->cds_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          str = StringSave (sfp->comment);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_locus:
+      for (vnp = c->gene_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->locus) 
+            && DoesStringMatchConstraint(grp->locus, scp))
+        {
+          str = StringSave (grp->locus);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_description:
+      for (vnp = c->gene_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->desc) 
+            && DoesStringMatchConstraint(grp->desc, scp))
+        {
+          str = StringSave (grp->desc);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_comment:
+      for (vnp = c->gene_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          str = StringSave (sfp->comment);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_allele:
+      for (vnp = c->gene_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->allele) 
+            && DoesStringMatchConstraint(grp->allele, scp))
+        {
+          str = StringSave (grp->allele);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_maploc:
+      for (vnp = c->gene_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->maploc) 
+            && DoesStringMatchConstraint(grp->maploc, scp))
+        {
+          str = StringSave (grp->maploc);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_locus_tag:
+      for (vnp = c->gene_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->locus_tag) 
+            && DoesStringMatchConstraint(grp->locus_tag, scp))
+        {
+          str = StringSave (grp->locus_tag);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_synonym:
+      for (vnp = c->gene_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL)
+        {
+          str = GetFirstValNodeStringMatch (grp->syn, scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_old_locus_tag:
+      for (vnp = c->gene_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL) {
+          str = GetFirstGBQualMatch (sfp->qual, "old-locus-tag", scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mrna_product:
+      for (vnp = c->mrna_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_RNA
+            && (rrp = sfp->data.value.ptrvalue) != NULL
+            && rrp->ext.choice == 1
+            && !StringHasNoText (rrp->ext.value.ptrvalue) 
+            && DoesStringMatchConstraint(rrp->ext.value.ptrvalue, scp))
+        {
+          str = StringSave (rrp->ext.value.ptrvalue);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mrna_comment:
+      for (vnp = c->mrna_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          str = StringSave (sfp->comment);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_name:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          str = GetFirstValNodeStringMatch (prp->name, scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_description:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (prp->desc) && DoesStringMatchConstraint(prp->desc, scp)) {
+          str = StringSave (prp->desc);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_ec_number:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          str = GetFirstValNodeStringMatch (prp->ec, scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_activity:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          str = GetFirstValNodeStringMatch (prp->activity, scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_comment:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->idx.subtype == FEATDEF_PROT
+            && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          str = StringSave (sfp->comment);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_name:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          str = GetFirstValNodeStringMatch (prp->name, scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_description:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (prp->desc) && DoesStringMatchConstraint(prp->desc, scp)) {
+          str = StringSave (prp->desc);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_ec_number:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          str = GetFirstValNodeStringMatch (prp->ec, scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_activity:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          str = GetFirstValNodeStringMatch (prp->activity, scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_comment:
+      for (vnp = c->prot_list; vnp != NULL && str == NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          str = StringSave (sfp->comment);
+        }
+      }
+      break;
+  }
+  return str;
+}
+
+
+static Boolean RemoveFieldValueFromCGPSet (CGPSetPtr c, Uint2 field, StringConstraintPtr scp)
+{
+  Boolean    rval = FALSE;
+  ValNodePtr vnp;
+  SeqFeatPtr sfp;
+  GeneRefPtr grp;
+  RnaRefPtr  rrp;
+  ProtRefPtr prp;
+  
+  if (c == NULL) return FALSE;
+  switch (field) {
+    case CDSGeneProt_field_cds_comment:
+      for (vnp = c->cds_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          sfp->comment = MemFree (sfp->comment);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_locus:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->locus) 
+            && DoesStringMatchConstraint(grp->locus, scp))
+        {
+          grp->locus = MemFree (grp->locus);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_description:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->desc) 
+            && DoesStringMatchConstraint(grp->desc, scp))
+        {
+          grp->desc = MemFree(grp->desc);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_comment:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          sfp->comment = MemFree (sfp->comment);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_allele:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->allele) 
+            && DoesStringMatchConstraint(grp->allele, scp))
+        {
+          grp->allele = MemFree (grp->allele);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_maploc:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->maploc) 
+            && DoesStringMatchConstraint(grp->maploc, scp))
+        {
+          grp->maploc = MemFree (grp->maploc);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_locus_tag:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (grp->locus_tag) 
+            && DoesStringMatchConstraint(grp->locus_tag, scp))
+        {
+          grp->locus_tag = MemFree (grp->locus_tag);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_synonym:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= RemoveValNodeStringMatch (&(grp->syn), scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_old_locus_tag:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL) {
+          rval |= RemoveGBQualMatch (&(sfp->qual), "old-locus-tag", scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mrna_product:
+      for (vnp = c->mrna_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_RNA
+            && (rrp = sfp->data.value.ptrvalue) != NULL
+            && rrp->ext.choice == 1
+            && !StringHasNoText (rrp->ext.value.ptrvalue) 
+            && DoesStringMatchConstraint(rrp->ext.value.ptrvalue, scp))
+        {
+          rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+          rrp->ext.choice = 0;
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_mrna_comment:
+      for (vnp = c->mrna_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          sfp->comment = MemFree (sfp->comment);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_name:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= RemoveValNodeStringMatch (&(prp->name), scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_description:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (prp->desc) && DoesStringMatchConstraint(prp->desc, scp)) {
+          prp->desc = MemFree (prp->desc);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_ec_number:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= RemoveValNodeStringMatch (&(prp->ec), scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_activity:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= RemoveValNodeStringMatch (&(prp->activity), scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_comment:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->idx.subtype == FEATDEF_PROT
+            && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          sfp->comment = MemFree (sfp->comment);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_name:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= RemoveValNodeStringMatch (&(prp->name), scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_description:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL
+            && !StringHasNoText (prp->desc) && DoesStringMatchConstraint(prp->desc, scp)) {
+          prp->desc = MemFree (prp->desc);
+          rval = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_ec_number:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= RemoveValNodeStringMatch (&(prp->ec), scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_activity:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= RemoveValNodeStringMatch (&(prp->activity), scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_comment:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && !StringHasNoText (sfp->comment) && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          sfp->comment = MemFree (sfp->comment);
+          rval = TRUE;
+        }
+      }
+      break;
+  }
+  return rval;
+}
+
+
+static SeqFeatPtr CreateGeneForCGPSet (CGPSetPtr c)
+{
+  SeqFeatPtr gene = NULL, sfp = NULL;
+  BioseqPtr  bsp;
+  ValNodePtr vnp;
+
+  if (c == NULL) return NULL;
+
+  for (vnp = c->cds_list; vnp != NULL && sfp == NULL; vnp = vnp->next) {
+    sfp = vnp->data.ptrvalue;
+  }
+  for (vnp = c->mrna_list; vnp != NULL && sfp == NULL; vnp = vnp->next) {
+    sfp = vnp->data.ptrvalue;
+  }
+  if (sfp != NULL) {
+    bsp = BioseqFindFromSeqLoc (sfp->location);
+    if (bsp != NULL) {
+      gene = CreateNewFeatureOnBioseq (bsp, SEQFEAT_GENE, sfp->location);
+      if (gene != NULL) {
+        gene->data.value.ptrvalue = GeneRefNew();
+      }
+    }
+  }
+  return gene;
+}
+
+
+static Boolean SetFieldValueInCGPSet (CGPSetPtr c, Uint2 field, StringConstraintPtr scp, CharPtr value, Uint2 existing_text)
+{
+  Boolean    rval = FALSE;
+  ValNodePtr vnp;
+  SeqFeatPtr sfp;
+  GeneRefPtr grp;
+  ProtRefPtr prp;
+  
+  if (c == NULL) return FALSE;
+  switch (field) {
+    case CDSGeneProt_field_cds_comment:
+      for (vnp = c->cds_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          rval |= SetStringValue ( &(sfp->comment), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_locus:
+      if (c->gene_list == NULL && scp == NULL) {
+        sfp = CreateGeneForCGPSet (c);
+        if (sfp != NULL) {
+          ValNodeAddPointer (&(c->gene_list), 0, sfp);
+        }
+      }
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && DoesStringMatchConstraint(grp->locus, scp))
+        {
+          rval |= SetStringValue ( &(grp->locus), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_description:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && DoesStringMatchConstraint(grp->desc, scp))
+        {
+          rval |= SetStringValue ( &(grp->desc), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_comment:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          rval |= SetStringValue ( &(sfp->comment), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_allele:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && DoesStringMatchConstraint(grp->allele, scp))
+        {
+          rval |= SetStringValue (&(grp->allele), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_maploc:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && DoesStringMatchConstraint(grp->maploc, scp))
+        {
+          rval |= SetStringValue ( &(grp->maploc), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_locus_tag:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL
+            && DoesStringMatchConstraint(grp->locus_tag, scp))
+        {
+          rval |= SetStringValue ( &(grp->locus_tag), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_synonym:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE
+            && (grp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= SetStringsInValNodeStringList (&(grp->syn), scp, value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_gene_old_locus_tag:
+      for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL) {
+          rval |= RemoveGBQualMatch (&(sfp->qual), "old-locus-tag", scp);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mrna_product:
+      for (vnp = c->mrna_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        rval |= SetRNAProductString (sfp, scp, value, existing_text);
+      }
+      break;
+    case CDSGeneProt_field_mrna_comment:
+      for (vnp = c->mrna_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL&& DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          rval |= SetStringValue ( &(sfp->comment), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_name:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= SetStringsInValNodeStringList (&(prp->name), scp, value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_description:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL
+            && DoesStringMatchConstraint(prp->desc, scp)) {
+          rval |= SetStringValue ( &(prp->desc), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_ec_number:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= SetStringsInValNodeStringList (&(prp->ec), scp, value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_activity:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_PROT
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= SetStringsInValNodeStringList (&(prp->activity), scp, value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_prot_comment:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->idx.subtype == FEATDEF_PROT
+            && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          rval |= SetStringValue ( &(sfp->comment), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_name:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= SetStringsInValNodeStringList (&(prp->name), scp, value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_description:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL
+            && DoesStringMatchConstraint(prp->desc, scp)) {
+          rval |= SetStringValue ( &(prp->desc), value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_ec_number:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= SetStringsInValNodeStringList (&(prp->ec), scp, value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_activity:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->data.choice == SEQFEAT_PROT
+            && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && (prp = sfp->data.value.ptrvalue) != NULL)
+        {
+          rval |= SetStringsInValNodeStringList (&(prp->activity), scp, value, existing_text);
+        }
+      }
+      break;
+    case CDSGeneProt_field_mat_peptide_comment:
+      for (vnp = c->prot_list; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->idx.subtype == FEATDEF_mat_peptide_aa
+            && DoesStringMatchConstraint(sfp->comment, scp))
+        {
+          rval |= SetStringValue ( &(sfp->comment), value, existing_text);
+        }
+      }
+      break;
+  }
+  return rval;
+}
+
+
+static MolInfoPtr GetMolInfoForBioseq (BioseqPtr bsp)
+{
+  MolInfoPtr m = NULL;
+  SeqDescrPtr sdp;
+
+  if (bsp == NULL) return NULL;
+  sdp = bsp->descr;
+  while (sdp != NULL && sdp->choice != Seq_descr_molinfo) {
+    sdp = sdp->next;
+  }
+  if (sdp != NULL) {
+    m = (MolInfoPtr) sdp->data.ptrvalue;
+  }
+  return m;
+}
+  
+
+static CharPtr GetSequenceQualFromBioseq (BioseqPtr bsp, ValNodePtr field)
+{
+  CharPtr rval = NULL;
+  MolInfoPtr m;
+
+  if (bsp == NULL || field == NULL) return NULL;
+
+  switch (field->choice) {
+    case MolinfoField_molecule:
+      m = GetMolInfoForBioseq (bsp);
+      if (m != NULL) {
+        rval = BiomolNameFromBiomol (m->biomol);
+      }
+      break;
+    case MolinfoField_technique:
+      m = GetMolInfoForBioseq (bsp);
+      if (m != NULL) {
+        rval = TechNameFromTech (m->tech);
+      }
+      break;
+    case MolinfoField_completedness:
+      m = GetMolInfoForBioseq (bsp);
+      if (m != NULL) {
+        rval = CompletenessNameFromCompleteness (m->completeness);
+      }
+      break;
+    case MolinfoField_mol_class:
+      rval = MolNameFromMol (bsp->mol);
+      break;
+    case MolinfoField_topology:
+      rval = TopologyNameFromTopology (bsp->topology);
+      break;
+    case MolinfoField_strand:
+      rval = StrandNameFromStrand (bsp->strand);
+      break;
+  }
+  if (rval != NULL) rval = StringSave (rval);
+  return rval;
+}
+
+
+static Boolean RemoveSequenceQualFromBioseq (BioseqPtr bsp, ValNodePtr field)
+{
+  MolInfoPtr m;
+  Boolean    rval = FALSE;
+
+  if (bsp == NULL || field == NULL) return FALSE;
+
+  switch (field->choice) {
+    case MolinfoField_molecule:
+      m = GetMolInfoForBioseq (bsp);
+      if (m != NULL) {
+        m->biomol = 0;
+        rval = TRUE;
+      }
+      break;
+    case MolinfoField_technique:
+      m = GetMolInfoForBioseq (bsp);
+      if (m != NULL) {
+        m->tech = 0;
+        rval = TRUE;
+      }
+      break;
+    case MolinfoField_completedness:
+      m = GetMolInfoForBioseq (bsp);
+      if (m != NULL) {
+        m->completeness = 0;
+        rval = TRUE;
+      }
+      break;
+    case MolinfoField_mol_class:
+      bsp->mol = 0;
+      rval = TRUE;
+      break;
+    case MolinfoField_topology:
+      bsp->topology = 0;
+      rval = TRUE;
+      break;
+    case MolinfoField_strand:
+      bsp->strand = 0;
+      rval = TRUE;
+      break;
+  }
+  return rval;
+}
+
+
+static MolInfoPtr AddMolInfoToBioseq (BioseqPtr bsp)
+{
+  SeqDescrPtr sdp;
+  MolInfoPtr  m;
+
+  sdp = CreateNewDescriptorOnBioseq (bsp, Seq_descr_molinfo);
+  m = MolInfoNew ();
+  sdp->data.ptrvalue = m;
+  return m;
+}
+
+
+static Boolean SetSequenceQualOnBioseq (BioseqPtr bsp, ValNodePtr field)
+{
+  MolInfoPtr m;
+  Boolean    rval = FALSE;
+
+  if (bsp == NULL || field == NULL) return FALSE;
+
+  switch (field->choice) {
+    case MolinfoField_molecule:
+      m = GetMolInfoForBioseq (bsp);
+      if (m == NULL) {
+        m = AddMolInfoToBioseq (bsp);
+      }
+      m->biomol = BiomolFromMoleculeType (field->data.intvalue);
+      rval = TRUE;
+      break;
+    case MolinfoField_technique:
+      m = GetMolInfoForBioseq (bsp);
+      if (m == NULL) {
+        m = AddMolInfoToBioseq (bsp);
+      }
+      m->tech = TechFromTechniqueType (field->data.intvalue);
+      rval = TRUE;
+      break;
+    case MolinfoField_completedness:
+      m = GetMolInfoForBioseq (bsp);
+      if (m == NULL) {
+        m = AddMolInfoToBioseq (bsp);
+      }
+      m->completeness = CompletenessFromCompletednessType (field->data.intvalue);
+      rval = TRUE;
+      break;
+    case MolinfoField_mol_class:
+      bsp->mol = MolFromMoleculeClassType (field->data.intvalue);
+      rval = TRUE;
+      break;
+    case MolinfoField_topology:
+      bsp->topology = TopologyFromTopologyType (field->data.intvalue);
+      rval = TRUE;
+      break;
+    case MolinfoField_strand:
+      bsp->strand = StrandFromStrandType (field->data.intvalue);
+      rval = TRUE;
+      break;
+  }
+  return rval;
+}
+
+
+NLM_EXTERN FieldTypePtr GetFromFieldFromFieldPair (FieldPairTypePtr fieldpair)
+{
+  SourceQualChoicePtr ss = NULL;
+  SourceQualPairPtr sqpp;
+  FeatureFieldPairPtr fp;
+  FeatureFieldPtr fs;
+  FieldTypePtr f = NULL;
+  CDSGeneProtFieldPairPtr cp;
+  MolinfoFieldPairPtr mp;
+  ValNodePtr vnp;
+
+  if (fieldpair == NULL) return NULL;
+  switch (fieldpair->choice) {
+    case FieldPairType_source_qual:
+      sqpp = (SourceQualPairPtr) fieldpair->data.ptrvalue;
+      if (sqpp != NULL) {
+        ss = ValNodeNew (NULL);
+        ss->choice = SourceQualChoice_textqual;
+        ss->data.intvalue = sqpp->field_from;
+        f = ValNodeNew (NULL);
+        f->choice = FieldType_source_qual;
+        f->data.ptrvalue = ss;
+      }
+      break;
+    case FieldPairType_feature_field:
+      fp = (FeatureFieldPairPtr) fieldpair->data.ptrvalue;
+      if (fp != NULL) {
+        fs = FeatureFieldNew ();
+        fs->type = fp->type;
+        fs->field = (FeatQualChoicePtr) AsnIoMemCopy (fp->field_from, (AsnReadFunc) FeatQualChoiceAsnRead, (AsnWriteFunc) FeatQualChoiceAsnWrite);
+        f = ValNodeNew (NULL);
+        f->choice = FieldType_feature_field;
+        f->data.ptrvalue = fs;
+      }
+      break;
+    case FieldPairType_cds_gene_prot:
+      cp = (CDSGeneProtFieldPairPtr) fieldpair->data.ptrvalue;
+      if (cp != NULL) {
+        f = ValNodeNew (NULL);
+        f->choice = FieldType_cds_gene_prot;
+        f->data.intvalue = cp->field_from;
+      }
+      break;
+    case FieldPairType_molinfo_field:
+      mp = (MolinfoFieldPairPtr) fieldpair->data.ptrvalue;
+      if (mp != NULL && mp->data.ptrvalue != NULL) {
+        vnp = NULL;
+        switch (mp->choice) {
+          case MolinfoFieldPair_molecule:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_molecule;
+            vnp->data.intvalue = ((MolinfoMoleculePairPtr)mp->data.ptrvalue)->from;
+            break;
+          case MolinfoFieldPair_technique:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_technique;
+            vnp->data.intvalue = ((MolinfoTechniquePairPtr)mp->data.ptrvalue)->from;
+            break;
+          case MolinfoFieldPair_completedness:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_completedness;
+            vnp->data.intvalue = ((MolinfoCompletednessPairPtr)mp->data.ptrvalue)->from;
+            break;
+          case MolinfoFieldPair_mol_class:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_mol_class;
+            vnp->data.intvalue = ((MolinfoMolClassPairPtr)mp->data.ptrvalue)->from;
+            break;
+          case MolinfoFieldPair_topology:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_topology;
+            vnp->data.intvalue = ((MolinfoTopologyPairPtr)mp->data.ptrvalue)->from;
+            break;
+          case MolinfoFieldPair_strand:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_strand;
+            vnp->data.intvalue = ((MolinfoStrandPairPtr)mp->data.ptrvalue)->from;
+            break;
+        }
+        if (vnp != NULL) {
+          f = ValNodeNew (NULL);
+          f->choice = FieldType_molinfo_field;
+          f->data.ptrvalue = vnp;
+        }
+      }
+      break;     
+  }
+  return f;
+}
+
+
+NLM_EXTERN FieldTypePtr GetToFieldFromFieldPair (FieldPairTypePtr fieldpair)
+{
+  SourceQualChoicePtr ss = NULL;
+  SourceQualPairPtr sqpp;
+  FeatureFieldPairPtr fp;
+  FeatureFieldPtr fs;
+  FieldTypePtr f = NULL;
+  CDSGeneProtFieldPairPtr cp;
+  MolinfoFieldPairPtr     mp;
+  ValNodePtr              vnp;
+
+  if (fieldpair == NULL) return NULL;
+  switch (fieldpair->choice) {
+    case FieldPairType_source_qual:
+      sqpp = (SourceQualPairPtr) fieldpair->data.ptrvalue;
+      if (sqpp != NULL) {
+        ss = ValNodeNew (NULL);
+        ss->choice = SourceQualChoice_textqual;
+        ss->data.intvalue = sqpp->field_to;
+        f = ValNodeNew (NULL);
+        f->choice = FieldType_source_qual;
+        f->data.ptrvalue = ss;
+      }
+      break;
+    case FieldPairType_feature_field:
+      fp = (FeatureFieldPairPtr) fieldpair->data.ptrvalue;
+      if (fp != NULL) {
+        fs = FeatureFieldNew ();
+        fs->type = fp->type;
+        fs->field = (FeatQualChoicePtr) AsnIoMemCopy (fp->field_to, (AsnReadFunc) FeatQualChoiceAsnRead, (AsnWriteFunc) FeatQualChoiceAsnWrite);
+        f = ValNodeNew (NULL);
+        f->choice = FieldType_feature_field;
+        f->data.ptrvalue = fs;
+      }
+      break;
+    case FieldPairType_cds_gene_prot:
+      cp = (CDSGeneProtFieldPairPtr) fieldpair->data.ptrvalue;
+      if (cp != NULL) {
+        f = ValNodeNew (NULL);
+        f->choice = FieldType_cds_gene_prot;
+        f->data.intvalue = cp->field_to;
+      }
+      break;
+    case FieldPairType_molinfo_field:
+      mp = (MolinfoFieldPairPtr) fieldpair->data.ptrvalue;
+      if (mp != NULL && mp->data.ptrvalue != NULL) {
+        vnp = NULL;
+        switch (mp->choice) {
+          case MolinfoFieldPair_molecule:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_molecule;
+            vnp->data.intvalue = ((MolinfoMoleculePairPtr)mp->data.ptrvalue)->to;
+            break;
+          case MolinfoFieldPair_technique:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_technique;
+            vnp->data.intvalue = ((MolinfoTechniquePairPtr)mp->data.ptrvalue)->to;
+            break;
+          case MolinfoFieldPair_completedness:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_completedness;
+            vnp->data.intvalue = ((MolinfoCompletednessPairPtr)mp->data.ptrvalue)->to;
+            break;
+          case MolinfoFieldPair_mol_class:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_mol_class;
+            vnp->data.intvalue = ((MolinfoMolClassPairPtr)mp->data.ptrvalue)->to;
+            break;
+          case MolinfoFieldPair_topology:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_topology;
+            vnp->data.intvalue = ((MolinfoTopologyPairPtr)mp->data.ptrvalue)->to;
+            break;
+          case MolinfoFieldPair_strand:
+            vnp = ValNodeNew (NULL);
+            vnp->choice = MolinfoField_strand;
+            vnp->data.intvalue = ((MolinfoStrandPairPtr)mp->data.ptrvalue)->to;
+            break;
+        }
+        if (vnp != NULL) {
+          f = ValNodeNew (NULL);
+          f->choice = FieldType_molinfo_field;
+          f->data.ptrvalue = vnp;
+        }
+      }
+      break;     
+  }
+  return f;
+}
+
+
+static Uint1 FieldTypeChoiceFromFieldPairTypeChoice (Uint1 field_pair_choice)
+{
+  Uint1 field_type_choice = 0;
+
+  switch (field_pair_choice) {
+    case FieldPairType_source_qual:
+      field_type_choice = FieldType_source_qual;
+      break;
+    case FieldPairType_feature_field:
+      field_type_choice = FieldType_feature_field;
+      break;
+    case FieldPairType_cds_gene_prot:
+      field_type_choice = FieldType_cds_gene_prot;
+      break;
+    case FieldPairType_molinfo_field:
+      field_type_choice = FieldType_molinfo_field;
+      break;
+  }
+
+  return field_type_choice;
+}
+
+
+NLM_EXTERN Uint1 FieldTypeFromAECRAction (AECRActionPtr action)
+{
+  Uint1 field_type = 0;
+  ApplyActionPtr a;
+  EditActionPtr  e;
+  ConvertActionPtr v;
+  CopyActionPtr c;
+  SwapActionPtr s;
+  RemoveActionPtr r;
+  AECRParseActionPtr p;
+
+  if (action == NULL || action->action == NULL || action->action->data.ptrvalue == NULL) {
+    return 0;
+  }
+  switch (action->action->choice) {
+    case ActionChoice_apply:
+      a = (ApplyActionPtr) action->action->data.ptrvalue;
+      if (a->field != NULL) {
+        field_type = a->field->choice;
+      }
+      break;
+    case ActionChoice_edit:
+      e = (EditActionPtr) action->action->data.ptrvalue;
+      if (e->field != NULL) {
+        field_type = e->field->choice;
+      }
+      break;
+    case ActionChoice_convert:
+      v = (ConvertActionPtr) action->action->data.ptrvalue;
+      field_type = FieldTypeChoiceFromFieldPairTypeChoice (v->fields->choice);
+      break;
+    case ActionChoice_copy:
+      c = (CopyActionPtr) action->action->data.ptrvalue;
+      field_type = FieldTypeChoiceFromFieldPairTypeChoice (c->fields->choice);
+      break;
+    case ActionChoice_swap:
+      s = (SwapActionPtr) action->action->data.ptrvalue;
+      field_type = FieldTypeChoiceFromFieldPairTypeChoice (s->fields->choice);
+      break;
+    case ActionChoice_remove:
+      r = (RemoveActionPtr) action->action->data.ptrvalue;
+      if (r->field != NULL) {
+        field_type = r->field->choice;
+      }
+      break;
+    case ActionChoice_parse:
+      p = (AECRParseActionPtr) action->action->data.ptrvalue;
+      field_type = FieldTypeChoiceFromFieldPairTypeChoice (p->fields->choice);
+      break;
+  }
+  return field_type;
+}
+
+
+static CharPtr GetFieldValueForObject (Uint1 choice, Pointer data, FieldTypePtr field, StringConstraintPtr scp)
+{
+  CharPtr str = NULL;
+  FeatureFieldPtr feature_field;
+
+  if (data == NULL || field == NULL || field->data.ptrvalue == NULL) return FALSE;
+
+  switch (field->choice) {
+    case FieldType_source_qual :
+      str = GetSourceQualFromBioSource (GetBioSourceFromObject (choice, data), (SourceQualChoicePtr) field->data.ptrvalue, scp);
+      break;
+    case FieldType_feature_field :
+      if (choice == OBJ_SEQFEAT) {
+        str = GetQualFromFeature ((SeqFeatPtr) data, (FeatureFieldPtr) field->data.ptrvalue, scp);
+      }
+      break;
+    case FieldType_cds_gene_prot :
+      if (choice == 0) {
+        str = GetFieldValueFromCGPSet ((CGPSetPtr) data, field->data.intvalue, scp);
+      } else if (choice == OBJ_SEQFEAT) {
+        feature_field = FeatureFieldFromCDSGeneProtField (field->data.intvalue);
+        str = GetQualFromFeature ((SeqFeatPtr) data, feature_field, scp);
+        feature_field = FeatureFieldFree (feature_field);
+      }
+      break;
+    case FieldType_molinfo_field :
+      if (choice == OBJ_BIOSEQ) {
+        str = GetSequenceQualFromBioseq ((BioseqPtr) data, field->data.ptrvalue);
+      }
+      break;
+  }
+  return str;
+}
+
+
+static Boolean RemoveFieldValueForObject (Uint1 choice, Pointer data, FieldTypePtr field, StringConstraintPtr scp)
+{
+  Boolean rval = FALSE;
+  FeatureFieldPtr feature_field;
+
+  if (data == NULL || field == NULL || field->data.ptrvalue == NULL) return FALSE;
+
+  switch (field->choice) {
+    case FieldType_source_qual :
+      rval = RemoveSourceQualFromBioSource (GetBioSourceFromObject (choice, data), (SourceQualChoicePtr) field->data.ptrvalue, scp);
+      break;
+    case FieldType_feature_field :
+      if (choice == OBJ_SEQFEAT) {
+        rval = RemoveQualFromFeature ((SeqFeatPtr) data, (FeatureFieldPtr) field->data.ptrvalue, scp);
+      }
+      break;
+    case FieldType_cds_gene_prot:
+      if (choice == 0) {
+        rval = RemoveFieldValueFromCGPSet ((CGPSetPtr) data, field->data.intvalue, scp);
+      } else if (choice == OBJ_SEQFEAT) {
+        feature_field = FeatureFieldFromCDSGeneProtField (field->data.intvalue);
+        rval = RemoveQualFromFeature ((SeqFeatPtr) data, feature_field, scp);
+        feature_field = FeatureFieldFree (feature_field);
+      }
+      break;
+    case FieldType_molinfo_field :
+      if (choice == OBJ_BIOSEQ) {
+        rval = RemoveSequenceQualFromBioseq ((BioseqPtr) data, field->data.ptrvalue);
+      }
+      break;
+  }
+  return rval;
+}
+
+
+static Boolean SetFieldValueForObject (Uint1 choice, Pointer data, FieldTypePtr field, StringConstraintPtr scp, CharPtr value, Uint2 existing_text)
+{
+  Boolean rval = FALSE;
+  FeatureFieldPtr feature_field;
+
+  if (data == NULL || field == NULL || field->data.ptrvalue == NULL) return FALSE;
+
+  switch (field->choice) {
+    case FieldType_source_qual :
+      rval = SetSourceQualInBioSource (GetBioSourceFromObject (choice, data), (SourceQualChoicePtr) field->data.ptrvalue, scp, value, existing_text);
+      break;
+    case FieldType_feature_field :
+      if (choice == OBJ_SEQFEAT) {
+        rval = SetQualOnFeature ((SeqFeatPtr) data, (FeatureFieldPtr) field->data.ptrvalue, scp, value, existing_text);
+      }
+      break;
+    case FieldType_cds_gene_prot:
+      if (choice == 0) {
+        rval = SetFieldValueInCGPSet ((CGPSetPtr) data, field->data.intvalue, scp, value, existing_text);
+      } else if (choice == OBJ_SEQFEAT) {
+        feature_field = FeatureFieldFromCDSGeneProtField (field->data.intvalue);
+        rval = SetQualOnFeature ((SeqFeatPtr) data, feature_field, scp, value, existing_text);
+        feature_field = FeatureFieldFree (feature_field);
+      }
+      break;
+    case FieldType_molinfo_field:
+      if (choice == OBJ_BIOSEQ) {
+        rval = SetSequenceQualOnBioseq ((BioseqPtr) data, field->data.ptrvalue);
+      }
+      break;
+  }
+  return rval;
+}
+
+
+static Boolean IsObjectAppropriateForFieldValue (Uint1 choice, Pointer data, FieldTypePtr field)
+{
+  SeqFeatPtr        sfp;
+  SeqDescrPtr       sdp;
+  FeatureFieldPtr   fp;
+  Boolean rval = FALSE;
+
+  if (data == NULL || field == NULL) return FALSE;
+
+  switch (field->choice) {
+    case FieldType_source_qual :
+      if (choice == OBJ_SEQFEAT) {
+        sfp = (SeqFeatPtr) data;
+        if (sfp->data.choice == SEQFEAT_BIOSRC) {
+          rval = TRUE;
+        }
+      } else if (choice == OBJ_SEQDESC) {
+        sdp = (SeqDescrPtr) data;
+        if (sdp->choice == Seq_descr_source) {
+          rval = TRUE;
+        }
+      }
+      break;
+    case FieldType_feature_field :
+      if (choice == OBJ_SEQFEAT) {
+        sfp = (SeqFeatPtr) data;
+        fp = (FeatureFieldPtr) field->data.ptrvalue;
+        if (fp != NULL && (fp->type == Feature_type_any || GetFeatdefFromFeatureType (fp->type) == sfp->idx.subtype)) {
+          rval = TRUE;
+        }
+      }
+      break;
+    case FieldType_cds_gene_prot :
+      if (choice == 0) {
+        rval = TRUE;
+      }
+      break;
+    case FieldType_molinfo_field :
+      if (choice == OBJ_BIOSEQ) {
+        rval = TRUE;
+      }
+      break;
+  }
+  return rval;
+}
+
+
+static Boolean IsObjectAppropriateForFieldPair (Uint1 choice, Pointer data, FieldPairTypePtr fieldpair)
+{
+  FieldTypePtr f;
+  Boolean rval;
+
+  f = GetFromFieldFromFieldPair(fieldpair);
+  rval = IsObjectAppropriateForFieldValue(choice, data, f);
+  f = FieldTypeFree (f);
+  return rval;
+}
+
+
+static Boolean DoFieldTypesMatch (FieldTypePtr field1, FieldTypePtr field2)
+{
+  Boolean rval = FALSE;
+  SourceQualChoicePtr scp1, scp2;
+  FeatureFieldPtr fp1, fp2;
+
+  if (field1 == NULL || field2 == NULL) return FALSE;
+  if (field1->choice != field2->choice) return FALSE;
+
+  switch (field1->choice) {
+    case FieldType_source_qual :
+      scp1 = (SourceQualChoicePtr) field1->data.ptrvalue;
+      scp2 = (SourceQualChoicePtr) field2->data.ptrvalue;
+      if (scp1 != NULL && scp2 != NULL && scp1->choice == scp2->choice) {
+        switch (scp1->choice) {
+          case SourceQualChoice_textqual:
+            if (scp1->data.intvalue == scp2->data.intvalue) {
+              rval = TRUE;
+            }
+            break;
+          case SourceQualChoice_location:
+          case SourceQualChoice_origin:
+            rval = TRUE;
+            break;
+        }
+      }
+      break;
+    case FieldType_feature_field :
+      fp1 = (FeatureFieldPtr) field1->data.ptrvalue;
+      fp2 = (FeatureFieldPtr) field2->data.ptrvalue;
+      if (fp1 != NULL && fp2 != NULL
+          && (fp1->type == fp2->type || fp1->type == Feature_type_any || fp2->type == Feature_type_any)
+          && fp1->field != NULL && fp2->field != NULL
+          && fp1->field->choice == FeatQualChoice_legal_qual && fp2->field->choice == FeatQualChoice_legal_qual
+          && fp1->field->data.intvalue == fp2->field->data.intvalue) {
+        rval = TRUE;
+      }
+      break;
+    case FieldType_cds_gene_prot :
+      if (field1->data.intvalue == field2->data.intvalue) {
+        rval = TRUE;
+      }
+      break;
+  }
+  return rval;
+}
+
+
+static Boolean IsNonTextSourceQualPresent (BioSourcePtr biop, Int4 srcqual)
+{
+  Int4 orgmod_subtype, subsrc_subtype;
+  OrgModPtr mod;
+  SubSourcePtr ssp;
+  Boolean      rval = FALSE;
+
+  if (biop == NULL) return FALSE;
+
+  orgmod_subtype = GetOrgModQualFromSrcQual (srcqual);
+  if (orgmod_subtype == -1) {
+    subsrc_subtype = GetSubSrcQualFromSrcQual (srcqual);
+    for (ssp = biop->subtype; ssp != NULL && !rval; ssp = ssp->next) {
+      if (ssp->subtype == subsrc_subtype) {
+        rval = TRUE;
+      }
+    }
+  } else {
+    if (biop->org != NULL && biop->org->orgname != NULL) {
+      for (mod = biop->org->orgname->mod; mod != NULL && !rval; mod = mod->next) {
+        if (mod->subtype == orgmod_subtype) {
+          rval = TRUE;
+        }
+      }
+    }
+  }
+  return rval;
+}
+
+
+static Boolean IsSourceQualPresent (BioSourcePtr biop, SourceQualChoicePtr scp)
+{
+  Boolean rval = FALSE;
+  CharPtr   str;
+
+  if (biop == NULL) return FALSE;
+  if (scp == NULL) return TRUE;
+
+  switch (scp->choice) {
+    case SourceQualChoice_textqual:
+      if (IsNonTextSourceQual (scp->data.intvalue)) {
+        rval = IsNonTextSourceQualPresent (biop, scp->data.intvalue);
+      } else {
+        str = GetSourceQualFromBioSource (biop, scp, NULL);
+        if (!StringHasNoText (str)) {
+          rval = TRUE;
+        }
+        str = MemFree (str);
+      }
+      break;
+    case SourceQualChoice_location:
+      if (biop->genome != 0) {
+        rval = TRUE;
+      }
+      break;
+    case SourceQualChoice_origin:
+      if (biop->origin != 0) {
+        rval = TRUE;
+      }
+      break;
+  }
+  return rval;
+}
+
+
+typedef struct objecthasstring
+{
+  StringConstraintPtr scp;
+  Boolean             found;
+} ObjectHasStringData, PNTR ObjectHasStringPtr;
+
+
+static void LIBCALLBACK AsnWriteConstraintCallBack (AsnExpOptStructPtr pAEOS)
+
+{
+  CharPtr            pchSource;
+  ObjectHasStringPtr ohsp;
+
+  ohsp = (ObjectHasStringPtr) pAEOS->data;
+  if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp))) 
+  {
+	  pchSource = (CharPtr) pAEOS->dvp->ptrvalue;
+	  ohsp->found |= DoesSingleStringMatchConstraint (pchSource, ohsp->scp);
+  }
+}
+
+
+static Boolean DoesObjectMatchStringConstraint (Uint1 choice, Pointer data, StringConstraintPtr scp)
+
+{
+  ObjMgrPtr         omp;
+  ObjMgrTypePtr     omtp;
+  AsnIoPtr          aip;
+  AsnExpOptPtr      aeop;
+  ObjectHasStringData ohsd;
+  SeqFeatPtr          sfp, prot;
+  SeqMgrFeatContext   fcontext;
+  CharPtr             search_txt;
+  CGPSetPtr           c;
+  ValNodePtr          vnp;
+  Boolean             all_match = TRUE, any_match = FALSE, rval;
+  BioseqPtr           protbsp;
+
+  if (data == NULL) return FALSE;
+  if (scp == NULL) return TRUE;
+
+  if (choice == 0) {
+    /* CDS-Gene-Prot set */
+    c = (CGPSetPtr) data;
+    for (vnp = c->gene_list; vnp != NULL && (!any_match || all_match); vnp = vnp->next) {
+      if (DoesObjectMatchStringConstraint (OBJ_SEQFEAT, vnp->data.ptrvalue, scp)) {
+        any_match = TRUE;
+      } else {
+        all_match = FALSE;
+      }
+    }
+    for (vnp = c->cds_list; vnp != NULL && (!any_match || all_match); vnp = vnp->next) {
+      if (DoesObjectMatchStringConstraint (OBJ_SEQFEAT, vnp->data.ptrvalue, scp)) {
+        any_match = TRUE;
+      } else {
+        all_match = FALSE;
+      }
+    }
+    for (vnp = c->mrna_list; vnp != NULL && (!any_match || all_match); vnp = vnp->next) {
+      if (DoesObjectMatchStringConstraint (OBJ_SEQFEAT, vnp->data.ptrvalue, scp)) {
+        any_match = TRUE;
+      } else {
+        all_match = FALSE;
+      }
+    }
+    for (vnp = c->prot_list; vnp != NULL && (!any_match || all_match); vnp = vnp->next) {
+      if (DoesObjectMatchStringConstraint (OBJ_SEQFEAT, vnp->data.ptrvalue, scp)) {
+        any_match = TRUE;
+      } else {
+        all_match = FALSE;
+      }
+    }
+    if (scp->not_present) {
+      rval = all_match;
+    } else {
+      rval = any_match;
+    }        
+  } else {
+    omp = ObjMgrGet ();
+    omtp = ObjMgrTypeFind (omp, choice, NULL, NULL);
+    if (omtp == NULL) return FALSE;
+    aip = AsnIoNullOpen ();
+    aeop = AsnExpOptNew (aip, NULL, NULL, AsnWriteConstraintCallBack);
+    ohsd.found = FALSE;
+    ohsd.scp = scp;
+    if (aeop != NULL) {
+      aeop->user_data = (Pointer) &ohsd;
+    }
+    
+    (omtp->asnwrite) (data, aip, NULL);
+    
+    if (!ohsd.found && omtp->datatype == OBJ_SEQFEAT)
+    {
+      sfp = (SeqFeatPtr) data;
+      if (sfp->data.choice == SEQFEAT_CDREGION) {
+        protbsp = BioseqFindFromSeqLoc (sfp->product);
+        prot = SeqMgrGetNextFeature (protbsp, NULL, 0, FEATDEF_PROT, &fcontext);
+        if (prot != NULL) {
+          (omtp->asnwrite) (prot, aip, NULL);
+        }
+      } else {
+        if (SeqMgrFeaturesAreIndexed(sfp->idx.entityID) == 0) {
+          SeqMgrIndexFeatures (sfp->idx.entityID, NULL);
+        }
+        if (sfp->idx.subtype == FEATDEF_tRNA) {
+          sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, sfp->idx.itemID, 0, sfp, &fcontext);
+          ohsd.found = DoesSingleStringMatchConstraint (fcontext.label, ohsd.scp);
+          if (!ohsd.found && sfp != NULL && sfp->idx.subtype == FEATDEF_tRNA)
+          {
+            search_txt = (CharPtr) MemNew ((StringLen (fcontext.label) + 6) * sizeof (Char));
+            if (search_txt != NULL)
+            {
+              sprintf (search_txt, "tRNA-%s", fcontext.label);
+              ohsd.found = DoesSingleStringMatchConstraint (search_txt, ohsd.scp);
+              search_txt = MemFree (search_txt);
+            }
+          }
+        }
+      }
+    }
+    AsnIoClose (aip);
+    if (scp->not_present) {
+      rval = !ohsd.found;
+    } else {
+      rval = ohsd.found;
+    }
+  }
+  return rval;
+}
+
+
+NLM_EXTERN Boolean IsSourceConstraintEmpty (SourceConstraintPtr scp)
+{
+  if (scp == NULL) return TRUE;
+
+  if (scp->field1 == NULL
+      && scp->field2 == NULL
+      && IsStringConstraintEmpty(scp->constraint)) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+NLM_EXTERN Boolean DoesBiosourceMatchConstraint (BioSourcePtr biop, SourceConstraintPtr scp)
+{
+  Boolean rval = FALSE;
+  CharPtr str1, str2;
+  ValNode vn;
+
+  if (biop == NULL) return FALSE;
+  if (scp == NULL) return TRUE;
+
+  if (IsStringConstraintEmpty(scp->constraint)) {
+    /* looking for qual present */
+    if (scp->field1 != NULL && scp->field2 == NULL) {
+      rval = IsSourceQualPresent (biop, scp->field1);
+    } else if (scp->field2 != NULL && scp->field1 == NULL) {
+      rval = IsSourceQualPresent (biop, scp->field2);
+    /* looking for quals to match */
+    } else if (scp->field1 != NULL && scp->field2 != NULL) {
+      str1 = GetSourceQualFromBioSource (biop, scp->field1, NULL);
+      str2 = GetSourceQualFromBioSource (biop, scp->field2, NULL);
+      if (StringCmp (str1, str2) == 0) {
+        rval = TRUE;
+      }
+      str1 = MemFree (str1);
+      str2 = MemFree (str2);
+    } else {
+      /* nothing specified, automatic match */
+      rval = TRUE;
+    }
+  } else {
+    if (scp->field1 != NULL && scp->field2 == NULL) {
+      str1 = GetSourceQualFromBioSource (biop, scp->field1, scp->constraint);
+      if (str1 == NULL) {
+        if (scp->constraint->not_present) {
+          str1 = GetSourceQualFromBioSource (biop, scp->field1, NULL);
+          if (str1 == NULL) {
+            rval = TRUE;
+          }
+        }
+      } else if (!StringHasNoText (str1)) {
+        rval = TRUE;
+      }
+      str1 = MemFree (str1);
+    } else if (scp->field2 != NULL && scp->field1 == NULL) {
+      str2 = GetSourceQualFromBioSource (biop, scp->field2, scp->constraint);
+      if (str2 == NULL) {
+        if (scp->constraint->not_present) {
+          str2 = GetSourceQualFromBioSource (biop, scp->field2, NULL);
+          if (str2 == NULL) {
+            rval = TRUE;
+          }
+        }
+      } else if (!StringHasNoText (str2)) {
+        rval = TRUE;
+      }
+      str2 = MemFree (str2);
+    } else if (scp->field1 != NULL && scp->field2 != NULL) {
+      str1 = GetSourceQualFromBioSource (biop, scp->field1, scp->constraint);
+      str2 = GetSourceQualFromBioSource (biop, scp->field2, scp->constraint);
+      if (StringCmp (str1, str2) == 0) {
+        rval = TRUE;
+      }
+      str1 = MemFree (str1);
+      str2 = MemFree (str2);
+    } else {
+      /* generic string constraint */
+      vn.choice = Seq_descr_source;
+      vn.next = NULL;
+      vn.extended = 0;
+      vn.data.ptrvalue = biop;
+      rval = DoesObjectMatchStringConstraint (OBJ_SEQDESC, &vn, scp->constraint);
+    }
+  }
+  return rval;
+}
+
+
+static Boolean DoesCGPSetMatchPseudoConstraint (CGPSetPtr c, CDSGeneProtPseudoConstraintPtr constraint)
+{
+  Boolean    any_pseudo = FALSE;
+  ValNodePtr vnp;
+  SeqFeatPtr sfp;
+  Boolean    rval = FALSE;
+
+  if (c == NULL) return FALSE;
+  if (constraint == NULL) return TRUE;
+
+  switch (constraint->feature) {
+    case CDSGeneProt_feature_type_constraint_gene :
+      for (vnp = c->gene_list; vnp != NULL && !any_pseudo; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->pseudo) {
+          any_pseudo = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_feature_type_constraint_mRNA :
+      for (vnp = c->mrna_list; vnp != NULL && !any_pseudo; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->pseudo) {
+          any_pseudo = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_feature_type_constraint_cds :
+      for (vnp = c->mrna_list; vnp != NULL && !any_pseudo; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->pseudo) {
+          any_pseudo = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_feature_type_constraint_prot :
+      for (vnp = c->mrna_list; vnp != NULL && !any_pseudo; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->pseudo && sfp->idx.subtype == FEATDEF_PROT) {
+          any_pseudo = TRUE;
+        }
+      }
+      break;
+    case CDSGeneProt_feature_type_constraint_mat_peptide :
+      for (vnp = c->mrna_list; vnp != NULL && !any_pseudo; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp != NULL && sfp->pseudo && sfp->idx.subtype == FEATDEF_mat_peptide_aa) {
+          any_pseudo = TRUE;
+        }
+      }
+      break;
+  }
+
+  if ((any_pseudo && constraint->is_pseudo)
+      || (!any_pseudo && !constraint->is_pseudo)) {
+    rval = TRUE;
+  }
+  return rval;
+}
+
+
+NLM_EXTERN Boolean IsCDSGeneProtQualConstraintEmpty (CDSGeneProtQualConstraintPtr constraint)
+{
+  if (constraint == NULL) return TRUE;
+  if (constraint->field1 == NULL && constraint->field2 == NULL && IsStringConstraintEmpty (constraint->constraint)) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+
+static Boolean DoesCGPSetMatchQualConstraint (CGPSetPtr c, CDSGeneProtQualConstraintPtr constraint)
+{
+  Boolean rval = FALSE, any_match = FALSE, all_match = TRUE;
+  CharPtr str, str1, str2;
+
+  if (c == NULL) return FALSE;
+  if (constraint == NULL) return TRUE;
+
+  if (IsStringConstraintEmpty (constraint->constraint)) {
+    /* looking for qual present */
+    if (constraint->field1 != NULL && constraint->field2 == NULL) {
+      str = GetFieldValueFromCGPSet (c, constraint->field1->data.intvalue, NULL);
+      if (str != NULL) {
+        rval = TRUE;
+        str = MemFree (str);
+      }
+    } else if (constraint->field2 != NULL && constraint->field1 == NULL) {
+      str = GetFieldValueFromCGPSet (c, constraint->field2->data.intvalue, NULL);
+      if (str == NULL) {
+        rval = FALSE;
+      } else {
+        str = MemFree (str);
+      }
+    /* looking for quals to match */
+    } else if (constraint->field1 != NULL && constraint->field2 != NULL) {
+      str1 = GetFieldValueFromCGPSet (c, constraint->field1->data.intvalue, NULL);
+      str2 = GetFieldValueFromCGPSet (c, constraint->field2->data.intvalue, NULL);
+      if (StringCmp (str1, str2) == 0) {
+        rval = TRUE;
+      }
+      str1 = MemFree (str1);
+      str2 = MemFree (str2);
+    } else {
+      /* nothing specified, automatic match */
+      rval = TRUE;
+    }
+  } else {
+    if (constraint->field1 != NULL && constraint->field2 == NULL) {
+      str1 = GetFieldValueFromCGPSet (c, constraint->field1->data.intvalue, constraint->constraint);
+      if (str1 == NULL) {
+        if (constraint->constraint->not_present) {
+          str1 = GetFieldValueFromCGPSet (c, constraint->field1->data.intvalue, NULL);
+          if (str1 == NULL) {
+            rval = TRUE;
+          }
+        }
+      } else if (!StringHasNoText (str1)) {
+        rval = TRUE;
+      }
+      str1 = MemFree (str1);
+    } else if (constraint->field2 != NULL && constraint->field1 == NULL) {
+      str2 = GetFieldValueFromCGPSet (c, constraint->field2->data.intvalue, constraint->constraint);
+      if (str2 == NULL) {
+        if (constraint->constraint->not_present) {
+          str2 = GetFieldValueFromCGPSet (c, constraint->field2->data.intvalue, NULL);
+          if (str2 == NULL) {
+            rval = TRUE;
+          }
+        }
+      } else if (!StringHasNoText (str2)) {
+        rval = TRUE;
+      }
+      str2 = MemFree (str2);
+    } else if (constraint->field1 != NULL && constraint->field2 != NULL) {
+      str1 = GetFieldValueFromCGPSet (c, constraint->field1->data.intvalue, constraint->constraint);
+      str2 = GetFieldValueFromCGPSet (c, constraint->field2->data.intvalue, constraint->constraint);
+      if (StringCmp (str1, str2) == 0) {
+        rval = TRUE;
+      }
+      str1 = MemFree (str1);
+      str2 = MemFree (str2);
+    } else {
+      /* generic string constraint */
+      rval = DoesObjectMatchStringConstraint (0, c, constraint->constraint);
+    }
+  }
+  return rval;
+}
+
+
+NLM_EXTERN Boolean IsSequenceConstraintEmpty (SequenceConstraintPtr constraint)
+{
+  if (constraint == NULL) return TRUE;
+  if (constraint->seqtype != NULL && constraint->seqtype->choice != SequenceConstraintMolTypeConstraint_any) return FALSE;
+  if (constraint->feature != Feature_type_any) return FALSE;
+  if (!IsStringConstraintEmpty (constraint->id)) return FALSE;
+  return TRUE;
+}
+
+
+extern Boolean DoesSeqIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr string_constraint)
+{
+  Char       id [41];
+  CharPtr    cp, cp_dst;
+  SeqIdPtr   tmp;
+  Boolean    match, changed;
+
+  if (sip == NULL) 
+  {
+    return FALSE;
+  }
+  if (string_constraint == NULL)
+  {
+    return TRUE;
+  }
+  
+  while (sip != NULL)
+  {
+    /* temporary disconnect ID from list */
+    tmp = sip->next;
+    sip->next = NULL;
+    id [0] = '\0';
+    SeqIdWrite (sip, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
+    match = DoesSingleStringMatchConstraint (id, string_constraint);
+    if (!match) 
+    {
+      changed = FALSE;
+      /* remove terminating pipe character */
+      if (id[StringLen(id) - 1] == '|') 
+      {
+        id[StringLen(id) - 1] = 0;
+        changed = TRUE;
+      }
+      /* remove leading pipe identifier */
+      cp = StringChr (id, '|');
+      if (cp != NULL)
+      {
+        changed = TRUE;
+        cp++;
+        cp_dst = id;
+        while (*cp != 0) 
+        {
+          *cp_dst = *cp;
+          cp_dst++;
+          cp++;
+        }
+        *cp_dst = 0;
+      }  
+      if (changed) 
+      {
+        match = DoesSingleStringMatchConstraint (id, string_constraint);
+      }
+
+      /* if search text doesn't have ., try ID without version */
+      if (!match && StringChr (string_constraint->match_text, '.') == NULL) 
+      {
+        cp = StringChr (id, '.');
+        if (cp != NULL) 
+        {
+          *cp = 0;
+          match = DoesSingleStringMatchConstraint (id, string_constraint);
+        }
+      }       
+    }
+    sip->next = tmp;
+
+    if (match)
+    {
+      if (string_constraint->not_present)
+      {
+        return FALSE;
+      }
+      else
+      {
+        return TRUE;
+      }
+    }
+    sip = sip->next;
+  }
+  if (string_constraint->not_present)
+  {
+    return TRUE;
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+
+typedef struct rnatypebiomol {
+  Int4 rnatype;
+  Uint1 biomol;
+  CharPtr rnamolname;
+} RnaTypeBiomolData, PNTR RnaTypeBiomolPtr;
+
+static RnaTypeBiomolData rna_type_biomol[] = {
+{ Sequence_constraint_rnamol_genomic , MOLECULE_TYPE_GENOMIC, "Genomic RNA" } ,
+{ Sequence_constraint_rnamol_precursor_RNA , MOLECULE_TYPE_PRE_MRNA , "Precursor RNA" } ,
+{ Sequence_constraint_rnamol_mRNA , MOLECULE_TYPE_MRNA , "mRNA [cDNA]" } ,
+{ Sequence_constraint_rnamol_rRNA , MOLECULE_TYPE_RRNA , "Ribosomal RNA" } ,
+{ Sequence_constraint_rnamol_tRNA , MOLECULE_TYPE_TRNA , "Transfer RNA" } ,
+{ Sequence_constraint_rnamol_snRNA , MOLECULE_TYPE_SNRNA , "Small nuclear RNA" } ,
+{ Sequence_constraint_rnamol_scRNA , MOLECULE_TYPE_SCRNA , "Small cytoplasmic RNA" } ,
+{ Sequence_constraint_rnamol_genomic_mRNA , MOLECULE_TYPE_GENOMIC_MRNA_MIX , "Genomic-mRNA" } ,
+{ Sequence_constraint_rnamol_cRNA , MOLECULE_TYPE_CRNA , "cRNA" } ,
+{ Sequence_constraint_rnamol_snoRNA , MOLECULE_TYPE_SNORNA , "Small nucleolar RNA" } ,
+{ Sequence_constraint_rnamol_transcribed_RNA , MOLECULE_TYPE_TRANSCRIBED_RNA , "Transcribed RNA" } ,
+{ Sequence_constraint_rnamol_ncRNA , MOLECULE_TYPE_NCRNA , "Non-coding  RNA" } ,
+{ Sequence_constraint_rnamol_transfer_messenger_RNA , MOLECULE_TYPE_TMRNA , "Transfer-messenger RNA" } } ;
+
+#define NUM_rna_type_biomol sizeof (rna_type_biomol) / sizeof (RnaTypeBiomolData)
+
+
+NLM_EXTERN Uint1 GetBiomolForRnaType (Int4 rnatype) 
+{
+  Int4 i;
+
+  for (i = 0; i <  NUM_rna_type_biomol; i++) {
+    if (rna_type_biomol[i].rnatype == rnatype) {
+      return rna_type_biomol[i].biomol;
+    }
+  }
+  return 0;
+}
+
+
+NLM_EXTERN CharPtr GetBiomolNameForRnaType (Int4 rnatype)
+{
+  Int4 i;
+
+  for (i = 0; i <  NUM_rna_type_biomol; i++) {
+    if (rna_type_biomol[i].rnatype == rnatype) {
+      return rna_type_biomol[i].rnamolname;
+    }
+  }
+  return "invalid RNA type";
+}
+
+NLM_EXTERN void AddAllRNASubtypesToChoiceList (ValNodePtr PNTR field_list)
+{
+  Int4 i;
+
+  if (field_list == NULL) return;
+
+  ValNodeAddPointer (field_list, Sequence_constraint_rnamol_any, StringSave ("Any RNA"));
+  for (i = 0; i < NUM_rna_type_biomol; i++) {
+    ValNodeAddPointer (field_list, rna_type_biomol[i].rnatype, StringSave (rna_type_biomol[i].rnamolname));
+  }
+}
+
+
+static Boolean DoesSequenceMatchSequenceConstraint (BioseqPtr bsp, SequenceConstraintPtr constraint)
+{
+  SeqFeatPtr sfp;
+  SeqMgrFeatContext fcontext;
+  SeqDescrPtr sdp;
+  SeqMgrDescContext dcontext;
+  MolInfoPtr mip;
+  
+  if (bsp == NULL) return FALSE;
+  if (IsSequenceConstraintEmpty (constraint)) return TRUE;
+
+  if (constraint->seqtype != NULL && constraint->seqtype->choice != SequenceConstraintMolTypeConstraint_any) {
+    switch (constraint->seqtype->choice) {
+      case SequenceConstraintMolTypeConstraint_nucleotide :
+        if (ISA_aa (bsp->mol)) {
+          return FALSE;
+        }
+        break;
+      case SequenceConstraintMolTypeConstraint_dna :
+        if (bsp->mol != Seq_mol_dna) {
+          return FALSE;
+        }
+        break;
+      case SequenceConstraintMolTypeConstraint_rna :
+        if (bsp->mol != Seq_mol_rna) {
+          return FALSE;
+        }
+        if (constraint->seqtype->data.intvalue != Sequence_constraint_rnamol_any) {
+          sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+          if (sdp == NULL || sdp->data.ptrvalue == NULL || sdp->choice != Seq_descr_molinfo) {
+            return FALSE;
+          }
+          mip = (MolInfoPtr) sdp->data.ptrvalue;
+          if (GetBiomolForRnaType (constraint->seqtype->data.intvalue) != mip->biomol) {
+            return FALSE;
+          }
+        }
+        break;
+      case SequenceConstraintMolTypeConstraint_protein :
+        if (!ISA_aa (bsp->mol)) {
+          return FALSE;
+        }
+        break;
+    }
+  }
+
+  if (constraint->feature != Feature_type_any) {
+    sfp = SeqMgrGetNextFeature (bsp, NULL, 0, GetFeatdefFromFeatureType (constraint->feature), &fcontext);
+    if (sfp == NULL) {
+      return FALSE;
+    }
+  }
+
+  if (!IsStringConstraintEmpty (constraint->id) && !DoesSeqIDListMeetStringConstraint (bsp->id, constraint->id)) {
+    return FALSE;
+  }
+  return TRUE;
+}
+
+static Boolean DoesSequenceInSetMatchSequenceConstraint (BioseqSetPtr bssp, SequenceConstraintPtr constraint)
+{
+  Boolean       rval = FALSE;
+  SeqEntryPtr   sep;
+
+  if (bssp == NULL) return FALSE;
+  if (IsSequenceConstraintEmpty (constraint)) return TRUE;
+  
+  for (sep = bssp->seq_set; sep != NULL && !rval; sep = sep->next) {
+    if (IS_Bioseq (sep)) {
+      rval = DoesSequenceMatchSequenceConstraint ((BioseqPtr) sep->data.ptrvalue, constraint);
+    } else if (IS_Bioseq_set (sep)) {
+      rval = DoesSequenceInSetMatchSequenceConstraint ((BioseqSetPtr) sep->data.ptrvalue, constraint);
+    }
+  }
+  return rval;
+}
+
+
+static Boolean DoesObjectMatchSequenceConstraint (Uint1 choice, Pointer data, SequenceConstraintPtr constraint)
+{
+  BioseqPtr bsp;
+  SeqDescrPtr sdp;
+  ObjValNodePtr ovp;
+  Boolean       rval = FALSE;
+
+  if (data == NULL) return FALSE;
+  if (IsSequenceConstraintEmpty (constraint)) return TRUE;
+
+  bsp = GetSequenceForObject (choice, data);
+  if (bsp == NULL) {
+    if (choice == OBJ_SEQDESC) {
+      sdp = (SeqDescrPtr) data;
+      if (sdp->extended) {
+        ovp = (ObjValNodePtr) sdp;
+        if (ovp->idx.parenttype == OBJ_BIOSEQSET && ovp->idx.parentptr != NULL) {
+          rval = DoesSequenceInSetMatchSequenceConstraint ((BioseqSetPtr) ovp->idx.parentptr, constraint);
+        }
+      }
+    }
+  } else {
+    rval = DoesSequenceMatchSequenceConstraint (bsp, constraint);
+  }
+  return rval; 
+}
+
+
+static Boolean DoesObjectMatchConstraint (Uint1 choice, Pointer data, ConstraintChoicePtr constraint)
+{
+  Boolean rval = TRUE;
+
+  if (data == NULL) return FALSE;
+  if (constraint == NULL) return TRUE;
+
+  switch (constraint->choice) {
+    case ConstraintChoice_string :
+      rval = DoesObjectMatchStringConstraint (choice, data, constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_location :
+      rval = DoesObjectMatchLocationConstraint (choice, data, constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_source :
+      rval = DoesBiosourceMatchConstraint (GetBioSourceFromObject (choice, data), constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_cdsgeneprot_qual :
+      if (choice == 0) {
+        rval = DoesCGPSetMatchQualConstraint (data, constraint->data.ptrvalue);
+      } else {
+        rval = FALSE;
+      }
+      break;
+    case ConstraintChoice_cdsgeneprot_pseudo :
+      if (choice == 0) {
+        rval = DoesCGPSetMatchPseudoConstraint (data, constraint->data.ptrvalue);
+      } else {
+        rval = FALSE;
+      }
+      break;
+    case ConstraintChoice_sequence :
+      rval = DoesObjectMatchSequenceConstraint (choice, data, constraint->data.ptrvalue);
+      break;
+  }
+  return rval;
+}
+
+
+static Boolean DoesObjectMatchConstraintChoiceSet (Uint1 choice, Pointer data, ConstraintChoiceSetPtr csp)
+{
+  Boolean rval = TRUE;
+
+  if (data == NULL) return FALSE;
+
+  while (csp != NULL && rval) {
+    rval = DoesObjectMatchConstraint (choice, data, csp);
+    csp = csp->next;
+  }
+  return rval;
+}
+
+
+NLM_EXTERN StringConstraintPtr FindStringConstraintInConstraintSetForField (FieldTypePtr field, ConstraintChoiceSetPtr csp)
+{
+  StringConstraintPtr scp = NULL;
+  ConstraintChoicePtr constraint;
+  SourceConstraintPtr source_constraint;
+  CDSGeneProtQualConstraintPtr cgp_constraint;
+
+  while (csp != NULL) {
+    constraint = (ConstraintChoicePtr) csp->data.ptrvalue;
+    switch (constraint->choice) {
+      case ConstraintChoice_string :
+        scp = constraint->data.ptrvalue;
+        break;
+      case ConstraintChoice_source :
+        source_constraint = (SourceConstraintPtr) constraint->data.ptrvalue;
+        if (source_constraint != NULL && source_constraint->constraint != NULL
+            && ((source_constraint->field1 != NULL
+                 && DoFieldTypesMatch (field, source_constraint->field1))
+                || (source_constraint->field2 != NULL
+                 && DoFieldTypesMatch (field, source_constraint->field2)))) {
+            scp = source_constraint->constraint;
+        } 
+      break;
+      case ConstraintChoice_cdsgeneprot_qual :
+        cgp_constraint = (CDSGeneProtQualConstraintPtr) field->data.ptrvalue;
+        if (field->choice == FieldType_cds_gene_prot
+            && cgp_constraint != NULL && cgp_constraint->constraint != NULL
+            && ((cgp_constraint->field1 != NULL && cgp_constraint->field1->data.intvalue == field->data.intvalue)
+                || (cgp_constraint->field2 != NULL && cgp_constraint->field2->data.intvalue == field->data.intvalue))) {
+          scp = cgp_constraint->constraint;
+        }
+        break;
+    }
+    csp = csp->next;
+  }
+  return scp;
+}
+
+
+NLM_EXTERN StringConstraintPtr FindStringConstraintInConstraintSetForFieldPair (FieldPairTypePtr fieldpair, ConstraintChoiceSetPtr csp)
+{
+  StringConstraintPtr scp;
+  FieldTypePtr f;
+
+  f = GetFromFieldFromFieldPair (fieldpair);
+  scp = FindStringConstraintInConstraintSetForField (f, csp);
+  f = FieldTypeFree (f);
+  return scp;
+}
+ 
+
+NLM_EXTERN StringConstraintPtr StringConstraintFromFieldEdit (FieldEditPtr edit)
+{
+  StringConstraintPtr scp;
+
+  if (edit == NULL || edit->find_txt == NULL) return NULL;
+  scp = StringConstraintNew ();
+  scp->match_text = StringSave (edit->find_txt);
+
+  switch (edit->location) {
+    case Field_edit_location_anywhere :
+      scp->match_location = String_location_contains;
+      break;
+    case Field_edit_location_beginning :
+      scp->match_location = String_location_starts;
+      break;
+    case Field_edit_location_end :
+      scp->match_location = String_location_ends;
+      break;
+  }
+
+  scp->case_sensitive = TRUE;
+  scp->whole_word = FALSE;
+  scp->not_present = FALSE;
+
+  return scp;
+}
+
+
+static CharPtr ApplyEditToString (CharPtr str, FieldEditPtr edit)
+{
+  CharPtr cp_found, new_str;
+  Int4 found_len, replace_len, new_len;
+
+  if (edit == NULL) return StringSave (str);
+
+  str = StringSave (str);
+  cp_found = StringISearch (str, edit->find_txt);
+
+  found_len = StringLen (edit->find_txt);
+  replace_len = StringLen (edit->repl_txt);
+  if (edit->location == Field_edit_location_beginning
+      && cp_found != str) {
+    cp_found = NULL;
+  } 
+  while (cp_found != NULL)
+  {
+    if (edit->location == Field_edit_location_end
+        && cp_found != str + StringLen (str) - found_len) {
+      cp_found = StringISearch (cp_found + found_len, edit->find_txt);
+    } else {
+      new_len = StringLen (str) + 1 - found_len + replace_len;
+      new_str = (CharPtr) MemNew (new_len * sizeof (Char));
+      if (new_str != NULL)
+      {
+        if (cp_found != str)
+        {
+          StringNCpy (new_str, str, cp_found - str);
+        }
+        StringCat (new_str, edit->repl_txt);
+        StringCat (new_str, cp_found + found_len);
+        cp_found = new_str + (cp_found - str) + replace_len;
+        str = MemFree (str);
+        str = new_str;
+      }
+      cp_found = StringISearch (cp_found, edit->find_txt);
+    }
+  }
+  return str;
+}
+
+
+typedef struct objectcollection {
+  AECRActionPtr action;
+  ValNodePtr object_list;
+} ObjectCollectionData, PNTR ObjectCollectionPtr;
+
+
+static void AECRActionObjectCollectionItemCallback (Uint1 objecttype, Pointer objectdata, ObjectCollectionPtr o)
+{
+  ApplyActionPtr a;
+  EditActionPtr e;
+  ConvertActionPtr v;
+  CopyActionPtr c;
+  SwapActionPtr s;
+  RemoveActionPtr r;
+  AECRParseActionPtr p;
+  CharPtr str, portion;
+  StringConstraintPtr scp;
+  FieldTypePtr field_from = NULL, field_to = NULL;
+
+  if (objectdata == NULL || o == NULL) return;
+
+  /* check to make sure object is appropriate for field and meets filter */
+  switch (o->action->action->choice) {
+    case ActionChoice_apply :
+      a = (ApplyActionPtr) o->action->action->data.ptrvalue;
+      if (a != NULL
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, a->field)
+          && DoesObjectMatchConstraintChoiceSet (objecttype, objectdata, o->action->constraint)) {
+        ValNodeAddPointer (&(o->object_list), objecttype, objectdata);
+      }
+      break;
+    case ActionChoice_edit :
+      e = (EditActionPtr) o->action->action->data.ptrvalue;
+      if (e != NULL
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, e->field)
+          && DoesObjectMatchConstraintChoiceSet (objecttype, objectdata, o->action->constraint)) {
+        scp = StringConstraintFromFieldEdit (e->edit);
+        str = GetFieldValueForObject (objecttype, objectdata, e->field, scp);
+        if (!StringHasNoText (str)) {
+          ValNodeAddPointer (&(o->object_list), objecttype, objectdata);
+        }
+        str = MemFree (str);
+      }
+      break;
+    case ActionChoice_convert :
+      v = (ConvertActionPtr) o->action->action->data.ptrvalue;
+      if (v != NULL
+          && (field_from = GetFromFieldFromFieldPair(v->fields)) != NULL
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, field_from)
+          && DoesObjectMatchConstraintChoiceSet (objecttype, objectdata, o->action->constraint)) {
+        scp = FindStringConstraintInConstraintSetForField (field_from, o->action->constraint);
+        str = GetFieldValueForObject (objecttype, objectdata, field_from, scp);
+        if (!StringHasNoText (str)) {
+          ValNodeAddPointer (&(o->object_list), objecttype, objectdata);
+        }
+        str = MemFree (str);
+      }
+      field_from = FieldTypeFree (field_from);
+      break;
+    case ActionChoice_copy :
+      c = (CopyActionPtr) o->action->action->data.ptrvalue;
+      if (c != NULL
+          && (field_from = GetFromFieldFromFieldPair(c->fields)) != NULL
+          && (field_to = GetFromFieldFromFieldPair(c->fields)) != NULL
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, field_from)
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, field_to)
+          && DoesObjectMatchConstraintChoiceSet (objecttype, objectdata, o->action->constraint)) {
+        ValNodeAddPointer (&(o->object_list), objecttype, objectdata);
+      }
+      field_from = FieldTypeFree (field_from);
+      field_to = FieldTypeFree (field_to);
+      break;
+    case ActionChoice_swap :
+      s = (SwapActionPtr) o->action->action->data.ptrvalue;
+      if (s != NULL
+          && (field_from = GetFromFieldFromFieldPair(s->fields)) != NULL
+          && (field_to = GetFromFieldFromFieldPair(s->fields)) != NULL
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, field_from)
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, field_to)
+          && DoesObjectMatchConstraintChoiceSet (objecttype, objectdata, o->action->constraint)) {
+        ValNodeAddPointer (&(o->object_list), objecttype, objectdata);
+      }
+      field_from = FieldTypeFree (field_from);
+      field_to = FieldTypeFree (field_to);
+      break;
+    case ActionChoice_remove :
+      r = (RemoveActionPtr) o->action->action->data.ptrvalue;
+      if (r != NULL
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, r->field)
+          && DoesObjectMatchConstraintChoiceSet (objecttype, objectdata, o->action->constraint)) {
+        ValNodeAddPointer (&(o->object_list), objecttype, objectdata);
+      }
+      break;
+    case ActionChoice_parse :
+      p = (AECRParseActionPtr) o->action->action->data.ptrvalue;
+      if (p != NULL
+          && (field_from = GetFromFieldFromFieldPair(p->fields)) != NULL
+          && (field_to = GetFromFieldFromFieldPair(p->fields)) != NULL
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, field_from)
+          && IsObjectAppropriateForFieldValue (objecttype, objectdata, field_to)
+          && DoesObjectMatchConstraintChoiceSet (objecttype, objectdata, o->action->constraint)) {
+        scp = FindStringConstraintInConstraintSetForField (field_from, o->action->constraint);
+        str = GetFieldValueForObject (objecttype, objectdata, field_from, scp);
+        portion = GetTextPortionFromString (str, p->portion);
+        if (!StringHasNoText (portion)) {
+          ValNodeAddPointer (&(o->object_list), objecttype, objectdata);
+        }
+        portion = MemFree (portion);
+        str = MemFree (str);
+      }
+      field_from = FieldTypeFree (field_from);
+      field_to = FieldTypeFree (field_to);
+      break;
+  }
+
+}
+
+
+static void AECRActionObjectCollectionFeatureCallback (SeqFeatPtr sfp, Pointer data)
+{
+  ObjectCollectionPtr o;
+  if (sfp == NULL || data == NULL) return;
+
+  o = (ObjectCollectionPtr) data;
+  AECRActionObjectCollectionItemCallback (OBJ_SEQFEAT, sfp, o);
+
+}
+
+
+static void AECRActionObjectCollectionDescriptorCallback (SeqDescrPtr sdp, Pointer data)
+{
+  ObjectCollectionPtr o;
+
+  if (sdp == NULL || data == NULL) return;
+
+  o = (ObjectCollectionPtr) data;
+  AECRActionObjectCollectionItemCallback (OBJ_SEQDESC, sdp, o);
+}
+
+
+static void AECRObjectCollectionBioseqCallback (BioseqPtr bsp, Pointer data)
+{
+  ObjectCollectionPtr o;
+
+  if (bsp == NULL || data == NULL) return;
+
+  o = (ObjectCollectionPtr) data;
+  AECRActionObjectCollectionItemCallback (OBJ_BIOSEQ, bsp, o);
+}
+
+
+NLM_EXTERN ValNodePtr GetObjectListForAECRAction (SeqEntryPtr sep, AECRActionPtr action)
+{
+  ObjectCollectionData ocd;
+
+  ocd.action = action;
+  ocd.object_list = NULL;
+
+  if (action == NULL) return NULL;
+  if (FieldTypeFromAECRAction (action) == FieldType_molinfo_field) {
+    VisitBioseqsInSep (sep, &ocd, AECRObjectCollectionBioseqCallback);
+  } else {
+    VisitFeaturesInSep (sep, &ocd, AECRActionObjectCollectionFeatureCallback);
+    VisitDescriptorsInSep (sep, &ocd, AECRActionObjectCollectionDescriptorCallback);
+  }
+  return ocd.object_list;
+}
+
+
+typedef struct buildcgpset
+{
+  ValNodePtr cds_list;
+  ValNodePtr mrna_list;
+  ValNodePtr gene_list;
+} BuildCGPSetData, PNTR BuildCGPSetPtr;
+
+static void BuildCGPSetCallback (SeqFeatPtr sfp, Pointer userdata)
+{
+  BuildCGPSetPtr b;
+
+  if (sfp == NULL || sfp->idx.deleteme || userdata == NULL) return;
+  b = (BuildCGPSetPtr) userdata;
+  if (sfp->data.choice == SEQFEAT_CDREGION)
+  {
+    ValNodeAddPointer (&(b->cds_list), OBJ_SEQFEAT, sfp);
+  }
+  else if (sfp->data.choice == SEQFEAT_GENE)
+  {
+    ValNodeAddPointer (&(b->gene_list), OBJ_SEQFEAT, sfp);
+  }
+  else if (sfp->idx.subtype == FEATDEF_mRNA)
+  {
+    ValNodeAddPointer (&(b->mrna_list), OBJ_SEQFEAT, sfp);
+  }
+  else if (SeqMgrGetGeneXref (sfp) != NULL)
+  {
+    ValNodeAddPointer (&(b->gene_list), OBJ_SEQFEAT, sfp);
+  }
+}
+
+
+static CGPSetPtr BuildCGPSetFromCodingRegion (SeqFeatPtr cds, BoolPtr indexing_needed)
+{
+  SeqMgrFeatContext fcontext;
+  SeqFeatPtr        gene = NULL, mrna, prot;
+  BioseqPtr         protbsp;
+  CGPSetPtr         cdsp;
+  ProtRefPtr        prp;
+
+  if (cds == NULL || cds->data.choice != SEQFEAT_CDREGION) return NULL;
+
+  cdsp = (CGPSetPtr) MemNew (sizeof (CGPSetData));
+  ValNodeAddPointer (&(cdsp->cds_list), 0, cds);
+
+  gene = GetGeneForFeature (cds);
+  if (gene != NULL)
+  {
+    ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
+    /* mark gene, so that we'll know it isn't lonely */
+    gene->idx.deleteme = TRUE;
+  }
+
+  mrna = SeqMgrGetOverlappingmRNA (cds->location, &fcontext);
+  if (mrna != NULL)
+  {
+    ValNodeAddPointer (&(cdsp->mrna_list), 0, mrna);
+    /* mark mrna, so that we'll know it's already in a set */
+    mrna->idx.deleteme = TRUE;
+  }
+
+  if (cds->product != NULL)
+  {
+    protbsp = BioseqFindFromSeqLoc (cds->product);
+    if (protbsp != NULL)
+    {
+      prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
+      /* if there is no full-length protein feature, make one */
+      if (prot == NULL)
+      {
+        prp = ProtRefNew ();
+        prot = CreateNewFeatureOnBioseq (protbsp, SEQFEAT_PROT, NULL);
+        if (prot != NULL)
+        {
+          prot->data.value.ptrvalue = prp;
+          if (indexing_needed != NULL)
+          {
+            *indexing_needed = TRUE;
+          }
+        }
+      }
+      if (prot != NULL)
+      {
+        ValNodeAddPointer (&(cdsp->prot_list), 0, prot);
+      }
+      
+      /* also add in mat_peptides from protein feature */
+      prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext);
+      while (prot != NULL)
+      {
+        ValNodeAddPointer (&(cdsp->prot_list), 0, prot);
+        prot = SeqMgrGetNextFeature (protbsp, prot, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext);
+      }
+    }
+  }  
+  return cdsp;
+}
+
+
+static CGPSetPtr BuildCGPSetFrommRNA (SeqFeatPtr mrna)
+{
+  SeqFeatPtr        gene;
+  CGPSetPtr          cdsp;
+
+  if (mrna == NULL || mrna->idx.deleteme || mrna->idx.subtype != FEATDEF_mRNA) return NULL;
+
+  cdsp = (CGPSetPtr) MemNew (sizeof (CGPSetData));
+  ValNodeAddPointer (&(cdsp->mrna_list), 0, mrna);
+
+  gene = GetGeneForFeature (mrna);
+  if (gene != NULL)
+  {
+    ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
+    /* mark gene, so that we'll know it isn't lonely */
+    gene->idx.deleteme = TRUE;
+  }
+
+  return cdsp;
+}
+
+
+static void UnmarkFeatureList (ValNodePtr list)
+{
+  SeqFeatPtr sfp;
+
+  while (list != NULL)
+  {
+    sfp = list->data.ptrvalue;
+    if (sfp != NULL)
+    {
+      sfp->idx.deleteme = FALSE;
+    }
+    list = list->next;
+  }
+}
+
+
+static ValNodePtr BuildCGPSetList (Uint2 entityID, ValNodePtr constraint)
+{
+  SeqEntryPtr    sep;
+  BuildCGPSetData b;
+  CGPSetPtr       cdsp;
+  ValNodePtr     vnp, vnp_next, vnp_prev;
+  ValNodePtr     cdset_list = NULL;
+  SeqFeatPtr     cds, gene, mrna;
+  Boolean        need_indexing = FALSE;
+  
+  sep = GetTopSeqEntryForEntityID (entityID);
+
+  b.cds_list = NULL;
+  b.gene_list = NULL;
+  b.mrna_list = NULL;
+  
+  VisitFeaturesInSep (sep, &b, BuildCGPSetCallback);
+
+  /* build cdsets that have coding regions */
+  for (vnp = b.cds_list; vnp != NULL; vnp = vnp->next)
+  {
+    cds = (SeqFeatPtr) vnp->data.ptrvalue;
+    if (cds == NULL) continue;
+    cdsp = BuildCGPSetFromCodingRegion (cds, &need_indexing);
+    if (cdsp != NULL)
+    {
+      ValNodeAddPointer (&cdset_list, 0, cdsp);
+    }
+  }
+  if (need_indexing)
+  {
+    /* indexing because we have created full-length protein features */
+    SeqMgrIndexFeatures (entityID, NULL);
+  }
+
+  /* build cdsets for mrna features that don't have coding regions */
+  for (vnp = b.mrna_list; vnp != NULL; vnp = vnp->next)
+  {
+    mrna = (SeqFeatPtr) vnp->data.ptrvalue;
+    if (mrna == NULL || mrna->idx.deleteme) continue;
+    cdsp = BuildCGPSetFrommRNA (mrna);
+    if (cdsp != NULL)
+    {
+      ValNodeAddPointer (&cdset_list, 0, cdsp);
+    }
+  }
+
+  /* build cdsets for lonely genes / features with gene xrefs that are not coding regions or mrnas */
+  for (vnp = b.gene_list; vnp != NULL; vnp = vnp->next)
+  {
+    gene = (SeqFeatPtr) vnp->data.ptrvalue;
+    if (gene == NULL || gene->idx.deleteme) continue;
+    cdsp = CGPSetNew ();
+    ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
+    ValNodeAddPointer (&cdset_list, 0, cdsp);
+  }
+
+  /* now unmark features */
+  UnmarkFeatureList (b.cds_list);
+  UnmarkFeatureList (b.mrna_list);
+  UnmarkFeatureList (b.gene_list);
+
+  b.cds_list = ValNodeFree (b.cds_list);
+  b.mrna_list = ValNodeFree (b.mrna_list);
+  b.gene_list = ValNodeFree (b.gene_list);
+
+  /* now remove sets that don't match our choice constraint */
+  vnp_prev = NULL;
+  for (vnp = cdset_list; vnp != NULL; vnp = vnp_next)
+  {
+    vnp_next = vnp->next;
+    if (!DoesObjectMatchConstraintChoiceSet (0, vnp->data.ptrvalue, constraint))
+    {
+      if (vnp_prev == NULL)
+      {
+        cdset_list = vnp->next;
+      }
+      else
+      {
+        vnp_prev->next = vnp->next;
+      }
+      vnp->next = NULL;
+      FreeCGPSetList (vnp);     
+    }
+    else
+    {
+      vnp_prev = vnp;
+    }
+  }
+  
+  return cdset_list;
+}
+
+
+NLM_EXTERN Int4 DoApplyActionToObjectList (ApplyActionPtr action, ValNodePtr object_list, StringConstraintPtr scp)
+{
+  ValNodePtr vnp;
+  Int4       num_succeed = 0, num_fail = 0;
+
+  if (action == NULL || object_list == NULL) return 0;
+
+  for (vnp = object_list; vnp != NULL; vnp = vnp->next) {
+    if (SetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, action->field, scp, action->value, action->existing_text)) {
+      num_succeed ++;
+    } else {
+      num_fail++;
+    }
+  }
+  return num_succeed;
+}
+
+
+NLM_EXTERN Int4 DoEditActionToObjectList (EditActionPtr action, ValNodePtr object_list)
+{
+  ValNodePtr vnp;
+  Int4       num_succeed = 0, num_fail = 0;
+  StringConstraintPtr scp;
+  CharPtr    str, new_str;
+
+  if (action == NULL || object_list == NULL) return 0;
+  scp = StringConstraintFromFieldEdit (action->edit);
+
+  for (vnp = object_list; vnp != NULL; vnp = vnp->next) {
+    str = GetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, action->field, scp);
+    new_str = ApplyEditToString (str, action->edit);
+    if (StringCmp (str, new_str) != 0
+        && SetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, action->field, scp, new_str, ExistingTextOption_replace_old)) {
+      num_succeed ++;
+    } else {
+      num_fail++;
+    }
+    new_str = MemFree (new_str);
+    str = MemFree (str);
+  }
+  return num_succeed;
+}
+
+
+NLM_EXTERN Int4 DoConvertActionToObjectList (ConvertActionPtr action, ValNodePtr object_list, StringConstraintPtr scp)
+{
+  ValNodePtr vnp;
+  Int4       num_succeed = 0, num_fail = 0;
+  CharPtr    str, from_val;
+  FieldTypePtr field_from, field_to;
+
+  if (action == NULL || object_list == NULL || action->fields == NULL) return 0;
+
+  field_from = GetFromFieldFromFieldPair (action->fields);
+  field_to = GetToFieldFromFieldPair (action->fields);
+
+  if (action->fields->choice == FieldPairType_molinfo_field) {
+    for (vnp = object_list; vnp != NULL; vnp = vnp->next) {
+      str = GetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_from, NULL);
+      from_val = GetSequenceQualValName (field_from->data.ptrvalue);
+      if (StringCmp (str, from_val) == 0
+          && SetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_to, NULL, str, ExistingTextOption_replace_old)) {
+        num_succeed ++;
+      }
+      str = MemFree (str);
+    }
+  } else {
+    for (vnp = object_list; vnp != NULL; vnp = vnp->next) {
+      str = GetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_from, scp);
+      if (SetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_to, NULL, str, action->existing_text)
+          && RemoveFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_from, scp)) {
+        num_succeed ++;
+      } else {
+        num_fail++;
+      }
+      str = MemFree (str);
+    }
+  }
+
+  field_from = FieldTypeFree (field_from);
+  field_to = FieldTypeFree (field_to);
+
+  return num_succeed;
+}
+
+
+NLM_EXTERN Int4 DoCopyActionToObjectList (CopyActionPtr action, ValNodePtr object_list, StringConstraintPtr scp)
+{
+  ValNodePtr vnp;
+  Int4       num_succeed = 0, num_fail = 0;
+  CharPtr    str;
+  FieldTypePtr field_from, field_to;
+
+  if (action == NULL || object_list == NULL) return 0;
+  field_from = GetFromFieldFromFieldPair (action->fields);
+  field_to = GetToFieldFromFieldPair (action->fields);
+
+  for (vnp = object_list; vnp != NULL; vnp = vnp->next) {
+    str = GetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_from, scp);
+    if (SetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_to, NULL, str, action->existing_text)) {
+      num_succeed ++;
+    } else {
+      num_fail++;
+    }
+    str = MemFree (str);
+  }
+
+  field_from = FieldTypeFree (field_from);
+  field_to = FieldTypeFree (field_to);
+  return num_succeed;
+}
+
+
+NLM_EXTERN Int4 DoSwapActionToObjectList (SwapActionPtr action, ValNodePtr object_list, StringConstraintPtr scp)
+{
+  ValNodePtr vnp;
+  Int4       num_succeed = 0, num_fail = 0;
+  CharPtr    str1, str2;
+  FieldTypePtr field_from, field_to;
+
+  if (action == NULL || object_list == NULL) return 0;
+  field_from = GetFromFieldFromFieldPair (action->fields);
+  field_to = GetToFieldFromFieldPair (action->fields);
+
+  for (vnp = object_list; vnp != NULL; vnp = vnp->next) {
+    str1 = GetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_from, scp);
+    str2 = GetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_to, NULL);
+    if (SetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_to, NULL, str1, ExistingTextOption_replace_old)
+        && SetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_from, scp, str2, ExistingTextOption_replace_old)) {
+      num_succeed ++;
+    } else {
+      num_fail++;
+    }
+    str1 = MemFree (str1);
+    str2 = MemFree (str2);
+  }
+  field_from = FieldTypeFree (field_from);
+  field_to = FieldTypeFree (field_to);
+  return num_succeed;
+}
+
+
+NLM_EXTERN Int4 DoRemoveActionToObjectList (RemoveActionPtr action, ValNodePtr object_list, StringConstraintPtr scp)
+{
+  ValNodePtr vnp;
+  Int4       num_succeed = 0, num_fail = 0;
+
+  if (action == NULL || object_list == NULL) return 0;
+
+  for (vnp = object_list; vnp != NULL; vnp = vnp->next) {
+    if (RemoveFieldValueForObject (vnp->choice, vnp->data.ptrvalue, action->field, scp)) {
+      num_succeed ++;
+    } else {
+      num_fail++;
+    }
+  }
+  return num_succeed;
+}
+
+
+NLM_EXTERN Int4 DoParseActionToObjectList (AECRParseActionPtr action, ValNodePtr object_list, StringConstraintPtr scp)
+{
+  ValNodePtr vnp;
+  CharPtr    str1, str2, cp;
+  Int4       len, num_succeed = 0;
+  FieldTypePtr field_from, field_to;
+
+  if (action == NULL || object_list == NULL) return 0;
+  field_from = GetFromFieldFromFieldPair (action->fields);
+  field_to = GetToFieldFromFieldPair (action->fields);
+
+  for (vnp = object_list; vnp != NULL; vnp = vnp->next) {
+    str1 = GetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_from, scp);
+    str2 = GetTextPortionFromString (str1, action->portion);    
+    if (str2 != NULL) {
+      if (action->remove_from_parsed) {
+        cp = StringSearch (str1, str2);
+        len = StringLen (str2);
+        StringCpy (cp, cp + len);
+        SetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_from, scp, str1, ExistingTextOption_replace_old);
+      }
+      if (SetFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_to, NULL, str1, action->existing_text)) {
+        num_succeed++;
+      }
+    }
+    str1 = MemFree (str1);
+    str2 = MemFree (str2);
+  }
+  field_from = FieldTypeFree (field_from);
+  field_to = FieldTypeFree (field_to);
+  return num_succeed;
+}
+
+
+static Int4 ApplyAECRActionToSeqEntry (AECRActionPtr act, SeqEntryPtr sep)
+{
+  StringConstraintPtr scp;
+  ApplyActionPtr      a;
+  ValNodePtr          object_list = NULL;
+  Uint1               field_type;
+  Uint2               entityID;
+  Int4                num_succeed = 0;
+
+  if (act == NULL || act->action == NULL) return 0;
+  field_type = FieldTypeFromAECRAction (act);
+  if (field_type == FieldType_cds_gene_prot) {
+    entityID = ObjMgrGetEntityIDForChoice(sep);
+    object_list = BuildCGPSetList (entityID, act->constraint);
+  } else {
+    object_list = GetObjectListForAECRAction (sep, act);
+  }
+
+  switch (act->action->choice) {
+    case ActionChoice_apply:
+      a = (ApplyActionPtr) act->action->data.ptrvalue;
+      scp = FindStringConstraintInConstraintSetForField (a->field, act->constraint);
+      num_succeed = DoApplyActionToObjectList (act->action->data.ptrvalue, object_list, scp);
+      scp = StringConstraintFree (scp);
+      break;
+    case ActionChoice_edit:
+      num_succeed = DoEditActionToObjectList (act->action->data.ptrvalue, object_list);
+      break;
+    case ActionChoice_convert:
+      num_succeed = DoConvertActionToObjectList (act->action->data.ptrvalue, object_list, NULL);
+      break;
+    case ActionChoice_swap:
+      num_succeed = DoSwapActionToObjectList (act->action->data.ptrvalue, object_list, NULL);
+      break;
+    case ActionChoice_copy:
+      num_succeed = DoCopyActionToObjectList (act->action->data.ptrvalue, object_list, NULL);
+      break;
+    case ActionChoice_remove:
+      num_succeed = DoRemoveActionToObjectList (act->action->data.ptrvalue, object_list, NULL);
+      break;
+    case ActionChoice_parse:
+      num_succeed = DoRemoveActionToObjectList (act->action->data.ptrvalue, object_list, NULL);
+      break;
+  }
+  object_list = ValNodeFree (object_list);  
+  return num_succeed;
+}
+
+
+/* This section handles parsing where the source field and destination field may not be on the same
+ * group of objects. */
+typedef struct parsesourceinfo 
+{
+  BioseqPtr   bsp;
+  SeqFeatPtr  sfp;
+  SeqDescrPtr sdp;
+  SeqIdPtr    sip;
+  ValNodePtr  dest_list;
+  CharPtr     parse_src_txt;
+} ParseSourceInfoData, PNTR ParseSourceInfoPtr;
+
+static ParseSourceInfoPtr ParseSourceInfoNew (BioseqPtr bsp, SeqFeatPtr sfp, SeqDescrPtr sdp, SeqIdPtr sip, CharPtr parse_src_txt)
+{
+  ParseSourceInfoPtr psip;
+
+  psip = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
+  if (psip != NULL) {
+    psip->bsp = bsp;
+    psip->sdp = sdp;
+    psip->sfp = sfp;
+    psip->sip = sip;
+    psip->dest_list = NULL;
+    psip->parse_src_txt = parse_src_txt;
+  } 
+  return psip;
+}
+
+
+static ParseSourceInfoPtr ParseSourceInfoFree (ParseSourceInfoPtr psip)
+{
+  if (psip != NULL)
+  {
+    psip->dest_list = ValNodeFree (psip->dest_list);
+    psip->parse_src_txt = MemFree (psip->parse_src_txt);
+    psip = MemFree (psip);
+  }
+  return psip;
+}
+
+static ParseSourceInfoPtr ParseSourceInfoCopy (ParseSourceInfoPtr psip)
+{
+  ParseSourceInfoPtr pcopy = NULL;
+  
+  if (psip != NULL) 
+  {
+    pcopy = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
+    if (pcopy != NULL) {
+      pcopy->bsp = psip->bsp;
+      pcopy->sfp = psip->sfp;
+      pcopy->sdp = psip->sdp;
+      pcopy->sip = psip->sip;
+      pcopy->dest_list = NULL;
+      pcopy->parse_src_txt = NULL;
+    }
+  }
+  return pcopy;
+}
+
+static ValNodePtr ParseSourceListFree (ValNodePtr vnp)
+{
+  ValNodePtr vnp_next;
+  while (vnp != NULL) {
+    vnp_next = vnp->next;
+    vnp->next = NULL;
+    vnp->data.ptrvalue = ParseSourceInfoFree (vnp->data.ptrvalue);
+    vnp = ValNodeFree (vnp);
+    vnp = vnp_next;
+  }
+  return vnp;
+}
+
+
+static void 
+GetDeflineSourcesForBioseq 
+(BioseqPtr              bsp,
+ TextPortionPtr         portion,
+ ValNodePtr PNTR source_list)
+{
+  SeqDescrPtr        sdp;
+  SeqMgrDescContext  dcontext;
+  CharPtr            str;
+  ParseSourceInfoPtr psip;
+  
+  if (bsp == NULL || source_list == NULL)
+  {
+    return;
+  }
+  
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_title, &dcontext);
+  while (sdp != NULL)
+  {
+    str = GetTextPortionFromString (sdp->data.ptrvalue, portion);    
+    if (str != NULL) {
+      psip = ParseSourceInfoNew (bsp, NULL, sdp, NULL, str);
+      if (psip != NULL) {
+        ValNodeAddPointer (source_list, 0, psip);
+      } else {
+        str = MemFree (str);
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_title, &dcontext);
+  }
+}
+
+
+static CharPtr GetIDSrc (SeqIdPtr sip, Uint1 id_type, CharPtr tag)
+{
+  DbtagPtr    dbt = NULL;
+  ObjectIdPtr oip = NULL;
+  Char        id_str[128];
+  CharPtr     str_src = NULL;
+
+  if (sip == NULL || sip->choice != id_type) return NULL;
+
+  if (id_type == SEQID_GENERAL)
+  {
+    dbt = (DbtagPtr) sip->data.ptrvalue;
+    if (dbt == NULL || (tag != NULL && StringCmp (dbt->db, tag) != 0)) return NULL;
+    oip = dbt->tag;
+  }
+  else if (id_type == SEQID_LOCAL)
+  {
+    oip = sip->data.ptrvalue;
+  }
+
+  if (oip == NULL)
+  {
+    SeqIdWrite (sip, id_str, PRINTID_REPORT, sizeof (id_str));
+    str_src = StringSave (id_str);
+  }
+  else
+  {
+    if (oip->str == NULL)
+    {
+      sprintf (id_str, "%d", oip->id);
+      str_src = StringSave (id_str);
+    }
+    else
+    {
+      str_src = StringSave (oip->str);
+    }
+  }
+  return str_src;
+}
+
+
+static void
+GetIDSourcesForBioseq
+(BioseqPtr       bsp,
+ TextPortionPtr  portion,
+ Uint1           id_type,
+ CharPtr         tag,
+ ValNodePtr PNTR source_list)
+{
+  SeqIdPtr           sip;
+  ParseSourceInfoPtr psip;
+  CharPtr            src_str = NULL, str;
+  
+  if (bsp == NULL || source_list == NULL)
+  {
+    return;
+  }
+  
+  sip = bsp->id;
+  while (sip != NULL)
+  {
+    if ((src_str = GetIDSrc (sip, id_type, tag)) != NULL) { 
+      str = GetTextPortionFromString (src_str, portion); 
+      if (str != NULL) {
+        psip = ParseSourceInfoNew (bsp, NULL, NULL, sip, str);
+        if (psip != NULL) {
+          ValNodeAddPointer (source_list, 0, psip);
+        } else {
+          str = MemFree (str);
+        }
+      }
+      src_str = MemFree (src_str);
+    }
+    sip = sip->next;
+  }
+}
+
+
+static void
+GetLocalIDSourcesForBioseq
+(BioseqPtr       bsp,
+ TextPortionPtr  tp,
+ ValNodePtr PNTR source_list)
+{
+  GetIDSourcesForBioseq (bsp, tp, SEQID_LOCAL, NULL, source_list);
+}
+
+
+static void GetNcbiFileSourceForBioseq
+(BioseqPtr       bsp,
+ TextPortionPtr  tp,
+ ValNodePtr PNTR source_list)
+{
+  GetIDSourcesForBioseq (bsp, tp, SEQID_GENERAL, "NCBIFILE", source_list);
+}
+
+
+static void StripBankitCommentForParse (SeqDescrPtr sdp, TextPortionPtr tp)
+{
+  UserObjectPtr      uop;
+  ObjectIdPtr        oip;
+  UserFieldPtr       ufp;
+  
+  if (sdp == NULL || sdp->choice != Seq_descr_user || tp == NULL) {
+    return;
+  }
+  
+  /* Bankit Comments */
+  uop = (UserObjectPtr) sdp->data.ptrvalue;
+  if (uop != NULL && StringCmp (uop->_class, "SMART_V1.0") != 0) {
+    oip = uop->type;
+    if (oip != NULL && StringCmp (oip->str, "Submission") == 0) {
+      for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+        oip = ufp->label;
+        if (oip != NULL && StringCmp (oip->str, "AdditionalComment") == 0) {
+          ReplaceStringForParse (ufp->data.ptrvalue, tp);
+        }
+      }
+    }
+  }
+}
+
+
+static void StripStructuredCommentForParse (SeqDescrPtr sdp, CharPtr comment_field, TextPortionPtr tp)
+{
+  UserObjectPtr      uop;
+  ObjectIdPtr        oip;
+  UserFieldPtr       ufp;
+
+  if (sdp == NULL || sdp->choice != Seq_descr_user || tp == NULL || StringHasNoText (comment_field)) {
+    return;
+  }
+    
+  uop = (UserObjectPtr) sdp->data.ptrvalue;
+  oip = uop->type;
+  if (oip != NULL && StringCmp (oip->str, "StructuredComment") == 0) {
+    for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+      oip = ufp->label;
+      if (oip != NULL && StringCmp (oip->str, comment_field) == 0) {
+        ReplaceStringForParse (ufp->data.ptrvalue, tp);
+      }
+    }
+  }
+}
+
+
+static void
+GetBankitCommentSourcesForBioseq 
+(BioseqPtr       bsp,
+ TextPortionPtr  tp,
+ ValNodePtr PNTR source_list)
+{
+  SeqDescrPtr        sdp;
+  SeqMgrDescContext  dcontext;
+  ParseSourceInfoPtr psip;
+  UserObjectPtr      uop;
+  ObjectIdPtr        oip;
+  UserFieldPtr       ufp;
+  CharPtr            str = NULL;
+  
+  if (bsp == NULL || source_list == NULL) {
+    return;
+  }
+  
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {
+    if (sdp->extended != 0) {
+      /* Bankit Comments */
+      uop = (UserObjectPtr) sdp->data.ptrvalue;
+      if (uop != NULL && StringCmp (uop->_class, "SMART_V1.0") != 0) {
+        oip = uop->type;
+        if (oip != NULL && StringCmp (oip->str, "Submission") == 0) {
+          for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+            oip = ufp->label;
+            if (oip != NULL && StringCmp (oip->str, "AdditionalComment") == 0) {
+              str = GetTextPortionFromString (ufp->data.ptrvalue, tp);
+              if (str != NULL) {
+                psip = ParseSourceInfoNew (bsp, NULL, sdp, NULL, str);
+                if (psip == NULL) {
+                  str = MemFree (str);
+                } else {
+                  ValNodeAddPointer (source_list, 0, psip);
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+  }
+}
+
+
+static void 
+GetCommentSourcesForBioseq 
+(BioseqPtr       bsp,
+ TextPortionPtr  tp,
+ ValNodePtr PNTR source_list)
+{
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  SeqMgrFeatContext  fcontext;
+  SeqMgrDescContext  dcontext;
+  ParseSourceInfoPtr psip;
+  CharPtr            str;
+  
+  if (bsp == NULL || source_list == NULL) {
+    return;
+  }
+  
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_comment, &dcontext);
+  while (sdp != NULL) {
+    str = GetTextPortionFromString (sdp->data.ptrvalue, tp);
+    if (str != NULL) {
+      psip = ParseSourceInfoNew (bsp, NULL, sdp, NULL, str);
+      if (psip == NULL) {
+        str = MemFree (str);
+      } else {
+        ValNodeAddPointer (source_list, 0, psip);
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_comment, &dcontext);
+  }
+  
+  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_COMMENT, 0, &fcontext);
+  while (sfp != NULL) {
+    str = GetTextPortionFromString (sfp->data.value.ptrvalue, tp);
+    if (str != NULL) {
+      psip = ParseSourceInfoNew (bsp, sfp, NULL, NULL, str);
+      if (psip == NULL) {
+        str = MemFree (str);
+      } else {
+        ValNodeAddPointer (source_list, 0, psip);
+      }
+    }
+    sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_COMMENT, 0, &fcontext);
+  }
+  GetBankitCommentSourcesForBioseq (bsp, tp, source_list);
+}
+
+
+static void 
+GetStructuredCommentSourcesForBioseq 
+(BioseqPtr       bsp,
+ TextPortionPtr  tp,
+ CharPtr         comment_field,
+ ValNodePtr PNTR source_list)
+{
+  SeqDescrPtr        sdp;
+  UserObjectPtr      uop;
+  ObjectIdPtr        oip;
+  UserFieldPtr       ufp;
+  SeqMgrDescContext  dcontext;
+  CharPtr            str;
+  ParseSourceInfoPtr psip;
+  
+  if (bsp == NULL || source_list == NULL)
+  {
+    return;
+  }
+  
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
+  while (sdp != NULL) {  
+    if (sdp->extended != 0
+        && sdp->data.ptrvalue != NULL) {
+      uop = (UserObjectPtr) sdp->data.ptrvalue;
+      oip = uop->type;
+      if (oip != NULL && StringCmp (oip->str, "StructuredComment") == 0) {
+        for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
+          oip = ufp->label;
+          if (oip != NULL && StringCmp (oip->str, comment_field) == 0) {
+            str = GetTextPortionFromString (ufp->data.ptrvalue, tp);
+            if (str != NULL) {
+              psip = ParseSourceInfoNew (bsp, NULL, sdp, NULL, str);
+              if (psip == NULL) {
+                str = MemFree (str);
+              } else {
+                ValNodeAddPointer (source_list, 0, psip);
+              }
+            }
+          }
+        }
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext);
+  }
+}
+
+
+const CharPtr nomial_keywords[] = {
+"f. sp. ",
+"var.",
+"pv.",
+"bv.",
+"serovar",
+"subsp." };
+
+const Int4 num_nomial_keywords = sizeof(nomial_keywords) / sizeof (CharPtr);
+
+static CharPtr GetTextAfterNomial (CharPtr taxname)
+
+{
+  CharPtr ptr, nomial_end;
+  Int4    i;
+  Boolean found_keyword = TRUE;
+  
+  ptr = StringChr (taxname, ' ');
+  if (ptr == NULL) return NULL;
+  /* skip over the first word and the spaces after it. */
+  while (*ptr == ' ') {
+    ptr++;
+  }
+  ptr = StringChr (ptr, ' ');
+  /* if there are only two words, give up. */
+  if (ptr == NULL) {
+    return NULL;
+  }
+  nomial_end = ptr;
+  while (*ptr == ' ') {
+    ptr++;
+  }
+  
+  while (found_keyword) {
+    found_keyword = FALSE;
+    /* if the next word is a nomial keyword, skip that plus the first word that follows it. */
+    for (i = 0; i < num_nomial_keywords && *nomial_end != 0; i++) {
+      if (StringNCmp (ptr, nomial_keywords[i], StringLen(nomial_keywords[i])) == 0) {
+        ptr += StringLen(nomial_keywords[i]);
+        while (*ptr == ' ' ) {
+          ptr++;
+        }
+        nomial_end = StringChr (ptr, ' ');
+        if (nomial_end == NULL) {
+          nomial_end = ptr + StringLen (ptr);
+        } else {          
+          ptr = nomial_end;
+          while (*ptr == ' ') {
+            ptr++;
+          }
+          found_keyword = TRUE;
+        }
+      }
+    }
+  }
+  return nomial_end;
+}
+
+
+static void 
+GetOrgParseSourcesForBioSource 
+(BioSourcePtr    biop,
+ BioseqPtr       bsp,
+ SeqDescrPtr     sdp,
+ SeqFeatPtr      sfp,
+ ParseSrcOrgPtr  o,
+ TextPortionPtr  tp,
+ ValNodePtr PNTR source_list)
+{
+  CharPtr str = NULL, portion, tmp;
+  ValNode vn;
+  ParseSourceInfoPtr psip;
+
+  if (biop == NULL || o == NULL || o->field == NULL || source_list == NULL) return;
+
+  switch (o->field->choice) {
+    case ParseSrcOrgChoice_source_qual :
+      vn.choice = SourceQualChoice_textqual;
+      vn.data.intvalue = o->field->data.intvalue;
+      vn.next = NULL;
+      str = GetSourceQualFromBioSource (biop, &vn, NULL);
+      break;
+    case ParseSrcOrgChoice_taxname_after_binomial :
+      vn.choice = SourceQualChoice_textqual;
+      vn.data.intvalue = Source_qual_taxname;
+      vn.next = NULL;
+      str = GetSourceQualFromBioSource (biop, &vn, NULL);
+      tmp = GetTextAfterNomial (str);
+      tmp = StringSave (tmp);
+      str = MemFree (str);
+      str = tmp;
+      break;
+  }
+  portion = GetTextPortionFromString (str, tp);
+  if (portion != NULL) {
+    psip = ParseSourceInfoNew (bsp, sfp, sdp, NULL, portion);
+    if (psip == NULL) {
+      portion = MemFree (portion);
+    } else {
+      ValNodeAddPointer (source_list, 0, psip);
+    }
+  }
+  str = MemFree (str);
+}
+
+
+static void GetOrgParseSourcesForBioseq (BioseqPtr bsp, ParseSrcOrgPtr o, TextPortionPtr tp, ValNodePtr PNTR source_list)
+{
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  SeqMgrFeatContext  fcontext;
+  SeqMgrDescContext  dcontext;
+
+  if (bsp == NULL || o == NULL || source_list == NULL) return;
+
+  if (o->type == Object_type_constraint_any || o->type == Object_type_constraint_descriptor) {
+    for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+         sdp != NULL;
+         sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext)) {
+      GetOrgParseSourcesForBioSource (sdp->data.ptrvalue, bsp, sdp, NULL, o, tp, source_list);
+    }
+  }
+
+  if (o->type == Object_type_constraint_any || o->type == Object_type_constraint_feature) {
+    for (sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
+         sfp != NULL;
+         sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext)) {
+      GetOrgParseSourcesForBioSource (sfp->data.value.ptrvalue, bsp, NULL, sfp, o, tp, source_list);
+    }
+  }
+}
+
+
+typedef struct parsesrccollection {
+  ParseSrcPtr src;
+  TextPortionPtr portion;
+  ValNodePtr src_list;
+} ParseSrcCollectionData, PNTR ParseSrcCollectionPtr;
+
+
+static void FindParseSourceBioseqCallback (BioseqPtr bsp, Pointer userdata)
+{
+  ParseSrcCollectionPtr psp;
+  
+  if (bsp == NULL || userdata == NULL)
+  {
+    return;
+  }
+  
+  psp = (ParseSrcCollectionPtr) userdata;
+  if (psp->src == NULL) return;
+
+  switch (psp->src->choice)
+  {
+    case ParseSrc_defline:
+      if (!ISA_aa (bsp->mol)) {
+        GetDeflineSourcesForBioseq (bsp, psp->portion, &(psp->src_list));
+      }
+      break;
+    case ParseSrc_local_id:
+      if (! ISA_aa (bsp->mol) && bsp->repr != Seq_repr_seg) {
+        GetLocalIDSourcesForBioseq (bsp, psp->portion, &(psp->src_list));
+      }
+      break;
+    case ParseSrc_file_id:
+      GetNcbiFileSourceForBioseq (bsp, psp->portion, &(psp->src_list));
+      break;
+    case ParseSrc_org:
+      GetOrgParseSourcesForBioseq (bsp, psp->src->data.ptrvalue, psp->portion, &(psp->src_list));
+      break;
+    case ParseSrc_comment:
+      GetCommentSourcesForBioseq (bsp, psp->portion, &(psp->src_list));
+      break;
+    case ParseSrc_structured_comment:
+      GetStructuredCommentSourcesForBioseq(bsp, psp->portion, psp->src->data.ptrvalue, &(psp->src_list));
+      break;
+    case ParseSrc_bankit_comment:
+      if (!ISA_aa (bsp->mol)) {
+        GetBankitCommentSourcesForBioseq (bsp, psp->portion, &(psp->src_list));
+      }
+      break;
+  }
+}
+
+
+static void GetOrgNamesInRecordCallback (BioSourcePtr biop, Pointer userdata)
+{
+  ValNodePtr PNTR org_names;
+  
+  if (biop == NULL || biop->org == NULL || StringHasNoText (biop->org->taxname)
+      || userdata == NULL)
+  {
+    return;
+  }
+  
+  org_names = (ValNodePtr PNTR) userdata;
+  
+  ValNodeAddPointer (org_names, 0, biop->org->taxname);
+}
+
+
+static void SetToUpper (CharPtr cp)
+{
+  if (cp == NULL) return;
+  while (*cp != 0) {
+    if (isalpha (*cp)) {
+      *cp = toupper (*cp);
+    }
+    cp++;
+  }
+}
+
+
+static void 
+FixCapitalizationInString 
+(CharPtr PNTR pTitle,
+ Uint2 capitalization,
+ ValNodePtr   org_names)
+{
+  if (pTitle == NULL || capitalization == Cap_change_none) return;
+
+  switch (capitalization) {
+    case Cap_change_tolower:
+      ResetCapitalization (FALSE, *pTitle);
+      FixAbbreviationsInElement (pTitle);
+      FixOrgNamesInString (*pTitle, org_names);
+      break;
+    case Cap_change_toupper:
+      SetToUpper (*pTitle);
+      FixAbbreviationsInElement (pTitle);
+      FixOrgNamesInString (*pTitle, org_names);
+      break;
+    case Cap_change_firstcap:
+      ResetCapitalization (TRUE, *pTitle);
+      FixAbbreviationsInElement (pTitle);
+      FixOrgNamesInString (*pTitle, org_names);
+      break;
+  }
+}
+
+
+static void AddDeflineDestinationsForBioseq (BioseqPtr bsp, ValNodePtr PNTR dest_list)
+{
+  SeqDescrPtr        sdp;
+  SeqMgrDescContext  dcontext;
+
+  if (bsp == NULL || dest_list == NULL) {
+    return;
+  }
+  
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_title, &dcontext);
+  while (sdp != NULL) {
+    ValNodeAddPointer (dest_list, OBJ_SEQDESC, sdp);
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_title, &dcontext);
+  }
+}
+
+
+static void AddFeatureDestinationsForBioseq (BioseqPtr bsp, FeatureFieldLegalPtr featfield, ValNodePtr PNTR dest_list)
+{
+  SeqFeatPtr        sfp;
+  SeqMgrFeatContext fcontext;
+  Int4             featdef;
+
+  if (bsp == NULL || featfield == NULL || dest_list == NULL) return;
+
+  featdef = GetFeatdefFromFeatureType (featfield->type);
+  for (sfp = SeqMgrGetNextFeature (bsp, NULL, 0, featdef, &fcontext);
+       sfp != NULL;
+       sfp = SeqMgrGetNextFeature (bsp, sfp, 0, featdef, &fcontext)) {
+    ValNodeAddPointer (dest_list, OBJ_SEQFEAT, sfp);
+  }
+}
+
+
+static void GetBioSourceDestinationsForBioseq (BioseqPtr bsp, Uint2 object_type, ValNodePtr PNTR dest_list)
+{
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  SeqMgrFeatContext  fcontext;
+  SeqMgrDescContext  dcontext;
+
+  if (bsp == NULL || dest_list == NULL)
+  {
+    return;
+  }
+  
+  if (object_type == Object_type_constraint_any || object_type == Object_type_constraint_descriptor) 
+  {
+    sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+    while (sdp != NULL)
+    {
+      ValNodeAddPointer (dest_list, OBJ_SEQDESC, sdp);
+      sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext);
+    }
+  }
+  
+  if (object_type == Object_type_constraint_any || object_type == Object_type_constraint_feature)
+  {
+    sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
+    while (sfp != NULL)
+    {
+      ValNodeAddPointer (dest_list, OBJ_SEQFEAT, sfp);
+      sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext);
+    }  
+  }
+}
+
+
+static void AddParseDestinations (ParseSourceInfoPtr psip, ParseDestPtr dst)
+{
+  ParseDstOrgPtr o;
+
+  if (psip == NULL || dst == NULL) return;
+
+  switch (dst->choice) {
+    case ParseDest_defline :
+      AddDeflineDestinationsForBioseq (psip->bsp, &(psip->dest_list));
+      break;
+    case ParseDest_org :
+      o = (ParseDstOrgPtr) dst->data.ptrvalue;
+      if ((o->type == Object_type_constraint_any || o->type == Object_type_constraint_descriptor)
+          && psip->sdp != NULL && psip->sdp->choice == Seq_descr_source) {
+        ValNodeAddPointer (&(psip->dest_list), OBJ_SEQDESC, psip->sdp);
+      } else if ((o->type == Object_type_constraint_any || o->type == Object_type_constraint_feature)
+                 && psip->sfp != NULL && psip->sfp->data.choice == SEQFEAT_BIOSRC) {
+        ValNodeAddPointer (&(psip->dest_list), OBJ_SEQFEAT, psip->sfp);
+      } else {
+        GetBioSourceDestinationsForBioseq (psip->bsp, o->type, &(psip->dest_list));
+      }
+      break;
+    case ParseDest_featqual :
+      AddFeatureDestinationsForBioseq (psip->bsp, dst->data.ptrvalue, &(psip->dest_list));
+      break;
+    case ParseDest_dbxref :
+      GetBioSourceDestinationsForBioseq (psip->bsp, Object_type_constraint_any, &(psip->dest_list));
+      break;
+  }
+}
+
+
+static Boolean SourceHasOneUndeletedDestination (ParseSourceInfoPtr source)
+{
+  Int4       num_seen = 0;
+  ValNodePtr vnp;
+  
+  if (source == NULL
+      || source->dest_list == NULL)
+  {
+    return FALSE;
+  }
+  
+  vnp = source->dest_list;
+  while (vnp != NULL && num_seen < 2)
+  {
+    if (vnp->choice > 1)
+    {
+      num_seen ++;
+    }
+    vnp = vnp->next;
+  }
+  if (num_seen == 1)
+  {
+    return TRUE;
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+
+static void CombineSourcesForDestinations (ValNodePtr PNTR source_list)
+{
+  ValNodePtr         source1_vnp, source2_vnp, dest1_vnp, dest2_vnp;
+  ValNodePtr         source_new, del_vnp;
+  ParseSourceInfoPtr psip1, psip2, new_psip;
+  CharPtr            comb_txt;
+  
+  for (source1_vnp = *source_list;
+       source1_vnp != NULL; 
+       source1_vnp = source1_vnp->next)
+  {
+    psip1 = (ParseSourceInfoPtr) source1_vnp->data.ptrvalue;
+    if (psip1 == NULL || psip1->dest_list == NULL)
+    {
+      continue;
+    }
+    for (source2_vnp = source1_vnp->next;
+         source2_vnp != NULL; 
+         source2_vnp = source2_vnp->next)
+    {
+      if (source2_vnp->choice > 0) 
+      {
+        /* already marked for deletion */
+        continue;
+      }
+      psip2 = (ParseSourceInfoPtr) source2_vnp->data.ptrvalue;
+      if (psip2 == NULL || psip2->dest_list == NULL)
+      {
+        continue;
+      }
+      for (dest1_vnp = psip1->dest_list;
+           dest1_vnp != NULL; 
+           dest1_vnp = dest1_vnp->next)
+      {
+        if (dest1_vnp->choice == 0)
+        {
+          /* already marked for deletion */
+          continue;
+        }
+        for (dest2_vnp = psip2->dest_list;
+             dest2_vnp != NULL;
+             dest2_vnp = dest2_vnp->next)
+        {
+          if (dest2_vnp->choice == 0)
+          {
+            /* already marked for deletion */
+            continue;
+          }
+          if (dest1_vnp->choice == dest2_vnp->choice
+              && dest1_vnp->data.ptrvalue == dest2_vnp->data.ptrvalue)
+          {
+            comb_txt = (CharPtr) (MemNew (sizeof (Char) 
+                                  * (StringLen (psip1->parse_src_txt)
+                                     + StringLen (psip2->parse_src_txt)
+                                     + 2)));
+            StringCpy (comb_txt, psip1->parse_src_txt);
+            StringCat (comb_txt, ";");
+            StringCat (comb_txt, psip2->parse_src_txt);
+            
+            /* If the first source has a single destination, then we can 
+             * add the text from the second source to the first and remove
+             * the destination from the second source.
+             */
+            if (SourceHasOneUndeletedDestination (psip1))
+            {
+              
+              psip1->parse_src_txt = MemFree (psip1->parse_src_txt);
+              psip1->parse_src_txt = comb_txt;
+              dest2_vnp->choice = 0;
+            }             
+            /* If the first source has more than one destination and
+             * the second source has a single destination, then we can 
+             * remove the repeated desination from the first source
+             * and add the text from the first source to the second source.
+             */
+            else if (SourceHasOneUndeletedDestination (psip2))
+            {
+              psip2->parse_src_txt = MemFree (psip2->parse_src_txt);
+              psip2->parse_src_txt = comb_txt;
+              dest1_vnp->choice = 0;
+            }
+            /* If the first and second sources have multiple destinations,
+             * we need to remove the repeated destination from both the first
+             * and second source and create a new source with the combined 
+             * text for just the repeated destination.
+             */
+            else
+            {
+              new_psip = ParseSourceInfoNew (NULL, NULL, NULL, NULL, comb_txt);
+              ValNodeAddPointer (&(new_psip->dest_list), 
+                                 dest1_vnp->choice, 
+                                 dest1_vnp->data.ptrvalue);
+              dest1_vnp->choice = 0;
+              dest2_vnp->choice = 0;
+              source_new = ValNodeNew (NULL);
+              source_new->choice = 0;
+              source_new->data.ptrvalue = new_psip;
+              source_new->next = source1_vnp->next;
+              source1_vnp->next = source_new;
+            }
+          }
+        }
+      }
+      
+      del_vnp = ValNodeExtractList (&(psip1->dest_list), 0);
+      del_vnp = ValNodeFree (del_vnp);
+      if (psip1->dest_list == NULL)
+      {
+        source1_vnp->choice = 1;
+      }
+      del_vnp = ValNodeExtractList (&(psip2->dest_list), 0);
+      del_vnp = ValNodeFree (del_vnp);
+      if (psip2->dest_list == NULL)
+      {
+        source2_vnp->choice = 1;
+      }
+    }
+  }
+
+  /* now remove sources deleted */
+  del_vnp = ValNodeExtractList (source_list, 1);
+  del_vnp = ParseSourceListFree (del_vnp); 
+}
+
+
+static BioseqSetPtr GetPartsForSourceDescriptorOnSegSet (SeqDescrPtr sdp)
+{
+  ObjValNodePtr ovp;
+  BioseqSetPtr  bssp;
+  SeqEntryPtr   sep;
+  
+  if (sdp == NULL || sdp->extended != 1) {
+    return NULL;
+  }
+  ovp = (ObjValNodePtr) sdp;
+  if (ovp->idx.parenttype != OBJ_BIOSEQSET || ovp->idx.parentptr == NULL) {
+    return NULL;
+  }
+  bssp = (BioseqSetPtr) ovp->idx.parentptr;
+  
+  if (bssp->_class == BioseqseqSet_class_nuc_prot
+      && IS_Bioseq_set (bssp->seq_set)
+      && bssp->seq_set->data.ptrvalue != NULL) {
+    bssp = (BioseqSetPtr) bssp->seq_set->data.ptrvalue;
+  }
+  
+  if (bssp->_class == BioseqseqSet_class_segset) {
+    sep = bssp->seq_set;
+    while (sep != NULL) {
+      if (IS_Bioseq_set (sep) && sep->data.ptrvalue != NULL) {
+        bssp = (BioseqSetPtr) sep->data.ptrvalue;
+        if (bssp->_class == BioseqseqSet_class_parts) {
+          return bssp;
+        }
+      }
+      sep = sep->next;
+    }
+  }
+
+  return NULL;
+}
+
+
+static SeqDescrPtr FindSourceDescriptorInSeqEntry (SeqEntryPtr sep)
+{
+  BioseqPtr    bsp;
+  BioseqSetPtr bssp;
+  SeqDescrPtr  sdp = NULL;
+  
+  if (sep != NULL && sep->data.ptrvalue != NULL) {
+    if (IS_Bioseq (sep)) {
+      bsp = (BioseqPtr) sep->data.ptrvalue;
+      sdp = bsp->descr;
+    } else if (IS_Bioseq_set (sep)) {
+      bssp = (BioseqSetPtr) sep->data.ptrvalue;
+      sdp = bssp->descr;
+    }
+    while (sdp != NULL && sdp->choice != Seq_descr_source)
+    {
+      sdp = sdp->next;
+    }
+  }
+  return sdp;
+}
+
+
+static SeqDescrPtr PropagateToSeqEntry (SeqEntryPtr sep, SeqDescrPtr sdp)
+{
+  BioseqPtr    bsp;
+  BioseqSetPtr bssp;
+  SeqDescrPtr  new_sdp = NULL;
+  
+  if (sep != NULL && sep->data.ptrvalue != NULL) {
+    if (IS_Bioseq (sep)) {
+      bsp = (BioseqPtr) sep->data.ptrvalue;
+      new_sdp = AsnIoMemCopy ((Pointer) sdp,
+                              (AsnReadFunc) SeqDescrAsnRead,
+                              (AsnWriteFunc) SeqDescrAsnWrite);
+      ValNodeLink (&(bsp->descr), new_sdp);
+    } else if (IS_Bioseq_set (sep)) {
+      bssp = (BioseqSetPtr) sep->data.ptrvalue;
+      new_sdp = AsnIoMemCopy ((Pointer) sdp,
+                              (AsnReadFunc) SeqDescrAsnRead,
+                              (AsnWriteFunc) SeqDescrAsnWrite);
+      ValNodeLink (&(bssp->descr), new_sdp);
+    }
+  }
+  return new_sdp;
+}
+
+
+static void PropagateSourceOnSegSetForParse (ValNodePtr parse_source_list)
+{
+  ParseSourceInfoPtr psip;
+  ValNodePtr         vnp_src, vnp_dst;
+  SeqDescrPtr        sdp, other_sdp;
+  SeqEntryPtr        sep;
+  ValNodePtr         extra_dests = NULL;
+  BioseqSetPtr       parts_bssp;
+  
+  for (vnp_src = parse_source_list; vnp_src != NULL; vnp_src = vnp_src->next) {
+    psip = (ParseSourceInfoPtr) vnp_src->data.ptrvalue;
+    if (psip != NULL) {
+      for (vnp_dst = psip->dest_list; vnp_dst != NULL; vnp_dst = vnp_dst->next) {
+        if (vnp_dst->choice == OBJ_SEQDESC) {
+          sdp = (SeqDescrPtr) vnp_dst->data.ptrvalue;
+          if (sdp != NULL && sdp->choice == Seq_descr_source) {
+            parts_bssp = GetPartsForSourceDescriptorOnSegSet (sdp);
+            if (parts_bssp != NULL) {
+              for (sep = parts_bssp->seq_set; sep != NULL; sep = sep->next) {
+                if (IS_Bioseq(sep) && sep->data.ptrvalue == psip->bsp) {
+                  other_sdp = FindSourceDescriptorInSeqEntry (sep);
+                  if (other_sdp == NULL) {
+                    other_sdp = PropagateToSeqEntry (sep, sdp);
+                    ValNodeAddPointer (&extra_dests, OBJ_SEQDESC, other_sdp);
+                  }
+                }
+              }
+            
+              /* set choice to 0 so master won't be a destination */
+              vnp_dst->choice = 0;
+            
+            }
+          }
+        }
+      }
+      /* add extra destinations to list */
+      ValNodeLink (&psip->dest_list, extra_dests);
+      extra_dests = NULL;
+    }
+  }
+  
+}
+
+
+static Boolean SetDBxrefForBioSource (BioSourcePtr biop, CharPtr db_name, CharPtr str, Uint2 existing_text)
+{
+  ValNodePtr    dbx;
+  DbtagPtr      dbtag;
+  Boolean       found = FALSE;
+  Char          buf[20];
+  Boolean       rval = FALSE;
+
+  if (biop == NULL || StringHasNoText (db_name) || StringHasNoText (str)) {
+    return FALSE;
+  }
+
+  if (biop->org == NULL)
+  {
+    biop->org = OrgRefNew();
+  }
+  dbx = biop->org->db;
+  while (dbx != NULL && !found)
+  {
+    dbtag = (DbtagPtr) dbx->data.ptrvalue;
+    if (dbtag != NULL && dbtag->tag != NULL
+        && StringCmp (dbtag->db, db_name) == 0)
+    {
+      found = TRUE;
+    }
+    if (!found)
+    {
+      dbx = dbx->next;
+    }
+  }
+  if (!found)
+  {
+    dbtag = DbtagNew();
+    dbtag->db = StringSave (db_name);      
+    ValNodeAddPointer (&(biop->org->db), 0, dbtag);
+  }
+  if (dbtag->tag == NULL)
+  {
+    dbtag->tag = ObjectIdNew();
+  }
+  /* if it was a number before, make it a string now */
+  if (dbtag->tag->id > 0 && dbtag->tag->str == NULL)
+  {
+    sprintf (buf, "%s", dbtag->tag->id);
+    dbtag->tag->id = 0;
+    dbtag->tag->str = StringSave (buf);
+  }
+  rval = SetStringValue (&(dbtag->tag->str), str, existing_text);
+  return rval;
+}
+
+
+static Int4 SetFieldForDestList (ValNodePtr dest_list, ParseDestPtr field, CharPtr str, Uint2 existing_text)
+{
+  ValNodePtr vnp;
+  SeqDescrPtr sdp;
+  CharPtr     cp;
+  BioSourcePtr biop;
+  ParseDstOrgPtr o;
+  FeatureFieldLegalPtr fl;
+  FeatureField f;
+  Int4         num_succeeded = 0;
+
+  if (dest_list == NULL || field == NULL) return 0;
+
+  switch (field->choice) {
+    case ParseDest_defline :
+      for (vnp = dest_list; vnp != NULL; vnp = vnp->next) {
+        if (vnp->choice == OBJ_SEQDESC && vnp->data.ptrvalue != NULL) {
+          sdp = (SeqDescrPtr) vnp->data.ptrvalue;
+          if (sdp->choice == Seq_descr_title) {
+            cp = sdp->data.ptrvalue;
+            if (SetStringValue (&cp, str, existing_text)) {
+              num_succeeded++;
+            }
+            sdp->data.ptrvalue = cp;
+          }
+        }
+      }
+      break;
+    case ParseDest_org :
+      o = (ParseDstOrgPtr) field->data.ptrvalue;
+      if (o != NULL) {
+        for (vnp = dest_list; vnp != NULL; vnp = vnp->next) {
+          biop = GetBioSourceFromObject (vnp->choice, vnp->data.ptrvalue);
+          if (SetSourceQualInBioSource (biop, o->field, NULL, str, existing_text)) {
+            num_succeeded++;
+          }
+        }
+      }
+      break;
+    case ParseDest_featqual:
+      fl = (FeatureFieldLegalPtr) field->data.ptrvalue;
+      if (fl != NULL) {
+        f.type = fl->type;
+        f.field = ValNodeNew(NULL);
+        f.field->next = NULL;
+        f.field->choice = FeatQualChoice_legal_qual;
+        f.field->data.intvalue = fl->field;        
+        for (vnp = dest_list; vnp != NULL; vnp = vnp->next) {
+          if (SetQualOnFeature (vnp->data.ptrvalue, &f, NULL, str, existing_text)) {
+            num_succeeded++;
+          }
+        }
+        f.field = ValNodeFree (f.field);
+      }
+      break;
+    case ParseDest_dbxref:
+      if (!StringHasNoText (field->data.ptrvalue)) {
+        for (vnp = dest_list; vnp != NULL; vnp = vnp->next) {
+          biop = GetBioSourceFromObject (vnp->choice, vnp->data.ptrvalue);
+          if (SetDBxrefForBioSource (biop, field->data.ptrvalue, str, existing_text)) {
+            num_succeeded++;
+          }
+        }
+      }
+      break;
+  }
+  return num_succeeded;
+}
+
+
+static void StripFieldForSrcList (ParseSourceInfoPtr psip, ParseSrcPtr field, TextPortionPtr text_portion)
+{
+  CharPtr     str;
+  ParseSrcOrgPtr o;
+  BioSourcePtr biop;
+
+  if (psip == NULL || field == NULL || text_portion == NULL) return;
+
+  switch (field->choice) {
+    case ParseSrc_defline :
+      if (psip->sdp != NULL && psip->sdp->choice == Seq_descr_title) {
+        ReplaceStringForParse (psip->sdp->data.ptrvalue, text_portion);
+      }
+      break;
+    case ParseSrc_org :
+      o = (ParseSrcOrgPtr) field->data.ptrvalue;
+      if (o != NULL) {
+        if (psip->sdp != NULL && psip->sdp->choice == Seq_descr_source) {
+          biop = (BioSourcePtr) psip->sdp->data.ptrvalue;
+          str = GetSourceQualFromBioSource (biop, o->field, NULL);
+          ReplaceStringForParse (str, text_portion);
+          SetSourceQualInBioSource (biop, o->field, NULL, str, ExistingTextOption_replace_old);
+          str = MemFree (str);
+        } else if (psip->sfp != NULL && psip->sfp->data.choice == SEQFEAT_BIOSRC) {
+          biop = (BioSourcePtr) psip->sfp->data.value.ptrvalue;
+          str = GetSourceQualFromBioSource (biop, o->field, NULL);
+          ReplaceStringForParse (str, text_portion);
+          SetSourceQualInBioSource (biop, o->field, NULL, str, ExistingTextOption_replace_old);
+          str = MemFree (str);
+        }
+      }
+      break;
+    case ParseSrc_comment:
+      if (psip->sdp != NULL) {
+        if (psip->sdp->choice == Seq_descr_user) {
+          StripBankitCommentForParse (psip->sdp, text_portion);
+        } else if (psip->sdp->choice == Seq_descr_comment) {
+          ReplaceStringForParse (psip->sdp->data.ptrvalue, text_portion);
+        }
+      }
+      if (psip->sfp != NULL && psip->sfp->data.choice == SEQFEAT_COMMENT) {
+        ReplaceStringForParse (psip->sfp->data.value.ptrvalue, text_portion);
+      }
+      break;
+    case ParseSrc_bankit_comment:
+      if (psip->sdp != NULL && psip->sdp->choice == Seq_descr_user) {
+        StripBankitCommentForParse (psip->sdp, text_portion);
+      }
+      break;
+    case ParseSrc_structured_comment:
+      if (psip->sdp != NULL && psip->sdp->choice == Seq_descr_user) {
+        StripStructuredCommentForParse (psip->sdp, field->data.ptrvalue, text_portion);
+      }
+      break;
+  }
+}
+
+
+static Int4 ApplyParseActionToSeqEntry (ParseActionPtr action, SeqEntryPtr sep)
+{
+  ParseSrcCollectionData psd;
+  ParseSourceInfoPtr     psip;
+  ValNodePtr             orgnames = NULL, source_list_for_removal = NULL, vnp;
+  Int4                   num_succeeded = 0;
+
+  if (action == NULL || sep == NULL) return 0;
+
+  psd.src = action->src;
+  psd.portion = action->portion;
+  psd.src_list = NULL;
+
+  /* first, we need to get a list of the parse sources */  
+  VisitBioseqsInSep (sep, &psd, FindParseSourceBioseqCallback);
+
+  if (action->capitalization != Cap_change_none) {
+    /* if we will be fixing capitalization, get org names to use in fixes */
+    VisitBioSourcesInSep (sep, &orgnames, GetOrgNamesInRecordCallback);
+  }
+
+  /* for each parse source, we need to get a list of the destinations */
+  for (vnp = psd.src_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->data.ptrvalue == NULL) continue;
+    psip = (ParseSourceInfoPtr) vnp->data.ptrvalue;
+    if (action->remove_from_parsed) {
+        ValNodeAddPointer (&source_list_for_removal, 0, ParseSourceInfoCopy (psip));
+    }
+    /* fix source text */
+    FixCapitalizationInString (&(psip->parse_src_txt), action->capitalization, orgnames);
+
+    /* find destinations */
+    AddParseDestinations (psip, action->dest);
+
+  }
+
+  /* free orgname list if we created it */
+  orgnames = ValNodeFree (orgnames);
+
+  CombineSourcesForDestinations (&(psd.src_list));
+
+  if (action->dest->choice == ParseDest_org) {
+    PropagateSourceOnSegSetForParse (psd.src_list);
+  }
+  
+  /* now do the parsing */
+  for (vnp = psd.src_list; vnp != NULL; vnp = vnp->next) {
+    psip = (ParseSourceInfoPtr) vnp->data.ptrvalue;
+    num_succeeded += SetFieldForDestList (psip->dest_list, action->dest, psip->parse_src_txt, action->existing_text);
+  }
+
+  /* now remove strings from sources */
+  for (vnp = source_list_for_removal; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->data.ptrvalue == NULL) continue;
+    psip = (ParseSourceInfoPtr) vnp->data.ptrvalue;
+    StripFieldForSrcList (psip, action->src, action->portion);
+  }
+  return num_succeeded;
+}
+
+
+static void SetCdRegionGeneticCode (SeqFeatPtr cds)
+{
+  CdRegionPtr crp;
+  SeqEntryPtr parent_sep;
+  BioseqPtr   bsp;
+  Int4        genCode;
+  ValNodePtr  code, vnp;
+
+  if (cds == NULL || cds->data.choice != SEQFEAT_CDREGION) return;
+  if (cds->data.value.ptrvalue == NULL) {
+    cds->data.value.ptrvalue = CdRegionNew();
+  }
+  crp = (CdRegionPtr) cds->data.value.ptrvalue;
+  bsp = BioseqFindFromSeqLoc (cds->location);
+  if (bsp == NULL) return;
+  parent_sep = GetBestTopParentForData (bsp->idx.entityID, bsp);
+  genCode = SeqEntryToGeneticCode (parent_sep, NULL, NULL, 0);
+
+  code = ValNodeNew (NULL);
+  if (code != NULL) {
+    code->choice = 254;
+    vnp = ValNodeNew (NULL);
+    code->data.ptrvalue = vnp;
+    if (vnp != NULL) {
+      vnp->choice = 2;
+      vnp->data.intvalue = genCode;
+    }
+  }
+  crp->genetic_code = code;
+}
+
+  
+static void CreateDataForFeature (SeqFeatPtr sfp, Int4 feature_type)
+{
+  Int4 featdef, seqfeattype;
+  CharPtr    label = NULL;
+  RnaRefPtr  rrp;
+  GBQualPtr  gbq;
+  ImpFeatPtr ifp;
+
+  featdef = GetFeatdefFromFeatureType (feature_type);
+  sfp->idx.subtype = featdef;
+  seqfeattype = FindFeatFromFeatDefType (featdef);
+  switch (seqfeattype) {
+    case SEQFEAT_GENE:
+      sfp->data.value.ptrvalue = GeneRefNew();
+      break;
+    case SEQFEAT_CDREGION:
+      sfp->data.value.ptrvalue = CdRegionNew();
+      SetCdRegionGeneticCode (sfp);
+      break;
+    case SEQFEAT_RNA:
+      rrp = RnaRefNew();
+      rrp->ext.choice = 0;
+      sfp->data.value.ptrvalue = rrp;
+      switch (featdef) {
+        case FEATDEF_preRNA:
+          rrp->type = RNA_TYPE_premsg;
+          break;
+        case FEATDEF_mRNA:
+          rrp->type = RNA_TYPE_mRNA;
+          break;
+        case FEATDEF_tRNA:
+          rrp->type = RNA_TYPE_tRNA;
+          break;
+        case FEATDEF_rRNA:
+          rrp->type = RNA_TYPE_rRNA;
+          break;
+        case FEATDEF_snRNA:
+          rrp->type = RNA_TYPE_other;
+          rrp->ext.choice = 1;
+          rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+          gbq = GBQualNew ();
+          gbq->qual = StringSave ("ncRNA_class");
+          gbq->val = StringSave ("snRNA");
+          break;
+        case FEATDEF_scRNA:
+          rrp->type = RNA_TYPE_other;
+          rrp->ext.choice = 1;
+          rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+          gbq = GBQualNew ();
+          gbq->qual = StringSave ("ncRNA_class");
+          gbq->val = StringSave ("scRNA");
+          break;
+        case FEATDEF_tmRNA:
+          rrp->type = RNA_TYPE_other;
+          rrp->ext.choice = 1;
+          rrp->ext.value.ptrvalue = StringSave ("tmRNA");
+          break;
+        case FEATDEF_ncRNA:
+          rrp->type = RNA_TYPE_other;
+          rrp->ext.choice = 1;
+          rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+          break;
+      }
+      break;
+    case SEQFEAT_IMP:
+      ifp = ImpFeatNew();
+      sfp->data.value.ptrvalue = ifp;
+      label = GetFeatureNameFromFeatureType (feature_type);
+      ifp->key = StringSave (label);
+      break;
+  }
+}
+
+
+static void ExtraCDSCreationActions (SeqFeatPtr cds, SeqEntryPtr parent_sep)
+{
+  ByteStorePtr       bs;
+  CharPtr            prot, ptr;
+  BioseqPtr          bsp;
+  Char               ch;
+  Int4               i;
+  SeqEntryPtr        psep, nsep;
+  MolInfoPtr         mip;
+  ValNodePtr         vnp, descr;
+  SeqFeatPtr         prot_sfp;
+  ProtRefPtr         prp;
+  Boolean            partial5, partial3;
+
+  if (cds == NULL) return;
+
+  CheckSeqLocForPartial (cds->location, &partial5, &partial3);
+
+  /* Create corresponding protein sequence data for the CDS */
+
+  bs = ProteinFromCdRegionEx (cds, TRUE, FALSE);
+  if (NULL == bs)
+    return;
+
+  prot = BSMerge (bs, NULL);
+  bs = BSFree (bs);
+  if (NULL == prot)
+    return;
+
+  ptr = prot;
+  ch = *ptr;
+  while (ch != '\0') {
+    *ptr = TO_UPPER (ch);
+    ptr++;
+    ch = *ptr;
+  }
+  i = StringLen (prot);
+  if (i > 0 && prot [i - 1] == '*') {
+    prot [i - 1] = '\0';
+  }
+  bs = BSNew (1000);
+  if (bs != NULL) {
+    ptr = prot;
+    BSWrite (bs, (VoidPtr) ptr, (Int4) StringLen (ptr));
+  }
+
+  /* Create the product protein Bioseq */
+  
+  bsp = BioseqNew ();
+  if (NULL == bsp)
+    return;
+  
+  bsp->repr = Seq_repr_raw;
+  bsp->mol = Seq_mol_aa;
+  bsp->seq_data_type = Seq_code_ncbieaa;
+  bsp->seq_data = (SeqDataPtr) bs;
+  bsp->length = BSLen (bs);
+  bs = NULL;
+  bsp->id = MakeNewProteinSeqId (cds->location, NULL);
+  SeqMgrAddToBioseqIndex (bsp);
+  
+  /* Create a new SeqEntry for the Prot Bioseq */
+  
+  psep = SeqEntryNew ();
+  if (NULL == psep)
+    return;
+  
+  psep->choice = 1;
+  psep->data.ptrvalue = (Pointer) bsp;
+  SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, psep);
+  
+  /* Add a descriptor to the protein Bioseq */
+  
+  mip = MolInfoNew ();
+  if (NULL == mip)
+    return;
+  
+  mip->biomol = 8;
+  mip->tech = 8;
+  if (partial5 && partial3) {
+    mip->completeness = 5;
+  } else if (partial5) {
+    mip->completeness = 3;
+  } else if (partial3) {
+    mip->completeness = 4;
+  }
+  vnp = CreateNewDescriptor (psep, Seq_descr_molinfo);
+  if (NULL == vnp)
+    return;
+  
+  vnp->data.ptrvalue = (Pointer) mip;
+  
+  /**/
+  
+  descr = ExtractBioSourceAndPubs (parent_sep);
+
+  AddSeqEntryToSeqEntry (parent_sep, psep, TRUE);
+  nsep = FindNucSeqEntry (parent_sep);
+  ReplaceBioSourceAndPubs (parent_sep, descr);
+  SetSeqFeatProduct (cds, bsp);
+  
+  prp = ProtRefNew ();
+  
+  if (prp != NULL) {
+    prot_sfp = CreateNewFeature (psep, NULL, SEQFEAT_PROT, NULL);
+    if (prot_sfp != NULL) {
+      prot_sfp->data.value.ptrvalue = (Pointer) prp;
+      SetSeqLocPartial (prot_sfp->location, partial5, partial3);
+      prot_sfp->partial = (partial5 || partial3);
+    }
+  }
+}
+
+
+static SeqLocPtr LocationFromApplyFeatureAction (BioseqPtr bsp, ApplyFeatureActionPtr action)
+{
+  LocationIntervalPtr l;
+  SeqLocPtr slp = NULL;
+  Uint1 strand = Seq_strand_plus;
+  Int4  from, to;
+
+  if (bsp == NULL || action == NULL || action->location == NULL) return NULL;
+
+  if (!action->plus_strand) {
+    strand = Seq_strand_minus;
+  }
+  if (action->location->choice == LocationChoice_interval) {
+    l = (LocationIntervalPtr) action->location->data.ptrvalue;
+    if (l != NULL) {
+      from = MIN (l->from, l->to);
+      to = MAX (l->from, l->to);
+      slp = SeqLocIntNew (from, to, strand, SeqIdFindWorst (bsp->id));
+    }
+  } else if (action->location->choice == LocationChoice_whole_sequence) {
+    slp = SeqLocIntNew (0, bsp->length - 1, strand, SeqIdFindWorst (bsp->id));
+  }
+  SetSeqLocPartial (slp, action->partial5, action->partial3);
+  return slp;
+}
+
+
+static Boolean OkToApplyToBioseq (ApplyFeatureActionPtr action, BioseqPtr bsp)
+{
+  SeqFeatPtr sfp;
+  SeqMgrFeatContext context;
+  Int4 featdef;
+  Boolean rval = TRUE;
+
+  if (action == NULL || bsp == NULL) return FALSE;
+
+  if (!action->add_redundant) {
+    featdef = GetFeatdefFromFeatureType (action->type);
+    sfp = SeqMgrGetNextFeature (bsp, NULL, 0, featdef, &context);
+    if (sfp != NULL) {
+      rval = FALSE;
+    }
+  }
+  return rval;
+} 
+
+static void AddParts (ApplyFeatureActionPtr action, BioseqSetPtr parts, ValNodePtr PNTR bsp_list)
+{
+  SeqEntryPtr sep;
+  Int4         seg_num;
+
+  if (action == NULL || !action->apply_to_parts
+      || parts == NULL || parts->_class != BioseqseqSet_class_parts
+      || bsp_list == NULL) {
+    return;
+  }
+
+  if (action->only_seg_num > -1) {
+    seg_num = 0;
+    sep = parts->seq_set;
+    while (seg_num < action->only_seg_num && sep != NULL) {
+      sep = sep->next;
+      seg_num++;
+    }
+    if (sep != NULL && IS_Bioseq (sep) && OkToApplyToBioseq (action, sep->data.ptrvalue)) {
+      ValNodeAddPointer (bsp_list, OBJ_BIOSEQ, sep->data.ptrvalue);
+    }
+  } else {
+    for (sep = parts->seq_set; sep != NULL; sep = sep->next) {
+      if (IS_Bioseq (sep) && OkToApplyToBioseq (action, sep->data.ptrvalue)) {
+        ValNodeAddPointer (bsp_list, OBJ_BIOSEQ, sep->data.ptrvalue);
+      }
+    }
+  }  
+}
+
+
+static void AddSequenceOrParts (ApplyFeatureActionPtr action, BioseqPtr bsp, ValNodePtr PNTR bsp_list)
+{
+  BioseqSetPtr bssp, parts;
+  SeqEntryPtr sep;
+
+  if (action == NULL || bsp == NULL || bsp_list == NULL) return;
+
+  if (bsp->idx.parenttype == OBJ_BIOSEQSET && bsp->idx.parentptr != NULL) {
+    bssp = (BioseqSetPtr) bsp->idx.parentptr;
+    if (bssp->_class == BioseqseqSet_class_segset) {
+      if (action->apply_to_parts) {
+        sep = bssp->seq_set;
+        while (sep != NULL && !IS_Bioseq_set (sep)) {
+          sep = sep->next;
+        }
+        if (sep != NULL) {
+          AddParts (action, sep->data.ptrvalue, bsp_list);
+        }
+      } else {
+        if (OkToApplyToBioseq (action, bsp)) {
+          ValNodeAddPointer (bsp_list, OBJ_BIOSEQ, bsp);
+        }
+      }       
+    } else if (bssp->_class == BioseqseqSet_class_parts) {
+      if (action->apply_to_parts) {
+        AddParts (action, bssp, bsp_list);
+      } else {
+        parts = bssp;
+        if (parts->idx.parenttype == OBJ_BIOSEQSET && parts->idx.parentptr != NULL) {
+          bssp = (BioseqSetPtr) parts->idx.parentptr;
+          if (IS_Bioseq (bssp->seq_set) && OkToApplyToBioseq (action, bssp->seq_set->data.ptrvalue)) {
+            ValNodeAddPointer (bsp_list, OBJ_BIOSEQ, bsp_list);
+          }
+        }
+      }
+    } else {
+      if (OkToApplyToBioseq (action, bsp)) {
+        ValNodeAddPointer (bsp_list, OBJ_BIOSEQ, bsp);
+      }
+    }
+  } else {
+    if (OkToApplyToBioseq (action, bsp)) {
+      ValNodeAddPointer (bsp_list, OBJ_BIOSEQ, bsp);
+    }
+  }
+}
+
+static void AddSequenceOrPartsFromSeqEntry (ApplyFeatureActionPtr action, SeqEntryPtr sep, ValNodePtr PNTR bsp_list)
+{
+  BioseqSetPtr bssp;
+  SeqEntryPtr  seq_set;
+
+  if (action == NULL || sep == NULL) return;
+
+  while (sep != NULL) {
+    if (IS_Bioseq (sep)) {
+      AddSequenceOrParts (action, sep->data.ptrvalue, bsp_list);
+    } else if (IS_Bioseq_set (sep)) {
+      bssp = (BioseqSetPtr) sep->data.ptrvalue;
+      if (bssp->_class == BioseqseqSet_class_segset) {
+        /* find master segment */
+        seq_set = bssp->seq_set;
+        while (seq_set != NULL && !IS_Bioseq (seq_set)) {
+          seq_set = seq_set->next;
+        }
+        if (seq_set != NULL) {
+          AddSequenceOrParts (action, seq_set->data.ptrvalue, bsp_list);
+        }
+      } else if (bssp->_class == BioseqseqSet_class_nuc_prot) {
+        /* find nucleotide sequence */
+        seq_set = bssp->seq_set;
+        if (seq_set != NULL) {
+          if (IS_Bioseq_set (seq_set)) {
+            /* nucleotide is segmented set */
+            bssp = (BioseqSetPtr) seq_set->data.ptrvalue;
+            if (bssp != NULL && bssp->_class == BioseqseqSet_class_segset
+                && bssp->seq_set != NULL && IS_Bioseq (bssp->seq_set)) {
+              AddSequenceOrParts (action, bssp->seq_set->data.ptrvalue, bsp_list);
+            }
+          } else if (IS_Bioseq (seq_set)) {
+            AddSequenceOrParts (action, seq_set->data.ptrvalue, bsp_list);
+          }
+        }
+      } else {
+        /* add from set members */
+        AddSequenceOrPartsFromSeqEntry (action, bssp->seq_set, bsp_list);
+      }
+    }
+    sep = sep->next;
+  }  
+}  
+  
+
+static void AdjustProteinSequenceForReadingFrame (SeqFeatPtr cds)
+{
+  BioseqPtr protbsp, bsp;
+  ByteStorePtr bs;
+  SeqFeatPtr   prot_sfp;
+  Boolean      partial5, partial3;
+
+  if (cds == NULL || cds->data.choice != SEQFEAT_CDREGION) return;
+
+  protbsp = BioseqFindFromSeqLoc (cds->product);
+
+  if (protbsp == NULL) {
+    bsp = BioseqFindFromSeqLoc (cds->location);
+    if (bsp != NULL) {
+      ExtraCDSCreationActions (cds, GetBestTopParentForData (bsp->idx.entityID, bsp));
+    }
+  } else {
+    bs = ProteinFromCdRegionExWithTrailingCodonHandling (cds,
+                                              TRUE,
+                                              FALSE,
+                                              FALSE);
+    protbsp->seq_data = (SeqDataPtr) BSFree ((ByteStorePtr)(protbsp->seq_data));
+    protbsp->seq_data = (SeqDataPtr) bs;
+    protbsp->length = BSLen (bs);
+    prot_sfp = GetProtFeature (protbsp);
+    if (prot_sfp == NULL) {
+      CheckSeqLocForPartial (cds->location, &partial5, &partial3);
+      prot_sfp = CreateNewFeatureOnBioseq (protbsp, SEQFEAT_PROT, NULL);
+      prot_sfp->data.value.ptrvalue = ProtRefNew ();
+      SetSeqLocPartial (prot_sfp->location, partial5, partial3);
+      prot_sfp->partial = (partial5 || partial3);
+    } else {
+      if (SeqLocLen (prot_sfp->location) != protbsp->length) {
+        prot_sfp->location = SeqLocFree (prot_sfp->location);
+        prot_sfp->location = SeqLocIntNew (0, protbsp->length - 1, Seq_strand_plus, SeqIdFindWorst (protbsp->id));   
+      }
+    }
+  }
+}
+
+
+static Int4 ApplyApplyFeatureActionToSeqEntry (ApplyFeatureActionPtr action, SeqEntryPtr sep)
+{
+  ValNodePtr bsp_list = NULL, vnp, field_vnp;
+  Int4       featdef, seqfeattype;
+  BioseqPtr  bsp;
+  SeqFeatPtr sfp;
+  SeqLocPtr  slp;
+  FeatQualLegalValPtr q;
+  FeatureField f;
+  SeqIdPtr   sip;
+  SeqFeatPtr gene;
+  Int4       num_created = 0;
+
+  if (sep == NULL || action == NULL) return 0;
+
+  /* first, get list of Bioseqs to apply features to */
+  /* relevant values : seq_list, add_redundant, apply_to_parts, only_seg_num */
+  if (action->seq_list != NULL && action->seq_list->choice == SequenceListChoice_list) {
+    for (vnp = action->seq_list->data.ptrvalue; vnp != NULL; vnp = vnp->next) {
+      sip = CreateSeqIdFromText (vnp->data.ptrvalue, sep);
+      bsp = BioseqFind (sip);
+      if (bsp != NULL) {
+        AddSequenceOrParts (action, bsp, &bsp_list);
+      }
+    }  
+  } else {
+    AddSequenceOrPartsFromSeqEntry (action, sep, &bsp_list);
+  }
+
+  /* now add feature to each bioseq in list */
+  for (vnp = bsp_list; vnp != NULL; vnp = vnp->next) {
+    bsp = vnp->data.ptrvalue;
+    if (bsp == NULL) continue;
+    featdef = GetFeatdefFromFeatureType (action->type);
+    seqfeattype = FindFeatFromFeatDefType (featdef);
+    slp = LocationFromApplyFeatureAction (bsp, action);
+    sfp = CreateNewFeatureOnBioseq (bsp, seqfeattype, slp);
+    if (sfp == NULL) continue;
+    CreateDataForFeature (sfp, action->type);
+    /* any extra actions */
+    switch (action->type) {
+      case (Feature_type_cds) :
+        ExtraCDSCreationActions (sfp, GetBestTopParentForData (bsp->idx.entityID, bsp));
+        break;
+    }
+    gene = NULL;
+    for (field_vnp = action->fields; field_vnp != NULL; field_vnp = field_vnp->next) {
+      q = (FeatQualLegalValPtr) field_vnp->data.ptrvalue;
+      if (q != NULL) {
+        f.field = ValNodeNew(NULL);
+        f.field->next = NULL;
+        f.field->choice = FeatQualChoice_legal_qual;
+        f.field->data.intvalue = q->qual;        
+        if (sfp->data.choice != SEQFEAT_GENE
+            && (q->qual == Feat_qual_legal_gene || q->qual == Feat_qual_legal_gene_description)) {
+          if (gene == NULL) {
+            gene = CreateNewFeatureOnBioseq (bsp, SEQFEAT_GENE, slp);
+            CreateDataForFeature (gene, Feature_type_gene);
+          }
+          f.type = Feature_type_gene;
+          SetQualOnFeature (gene, &f, NULL, q->val, ExistingTextOption_replace_old);
+        } else {
+          f.type = action->type;
+          SetQualOnFeature (sfp, &f, NULL, q->val, ExistingTextOption_replace_old);
+        }
+      }
+    }
+    if (action->type == Feature_type_cds) {
+      /* retranslate, to account for change in reading frame */
+      AdjustProteinSequenceForReadingFrame (sfp);
+      /* after the feature has been created, then adjust it for gaps */
+      /* Note - this step may result in multiple coding regions being created. */
+      AdjustCDSLocationsForUnknownGapsCallback (sfp, NULL);
+    }
+    num_created++;
+  }  
+  return num_created;
+}
+
+
+typedef struct convertandremovefeaturecollection {
+  Uint1 featdef;
+  ValNodePtr constraint_set;
+  ValNodePtr feature_list;
+} ConvertAndRemoveFeatureCollectionData, PNTR ConvertAndRemoveFeatureCollectionPtr;
+
+static void ConvertAndRemoveFeatureCollectionCallback (SeqFeatPtr sfp, Pointer data)
+{
+  ConvertAndRemoveFeatureCollectionPtr p;  
+
+  if (sfp == NULL || data == NULL) return;
+
+  p = (ConvertAndRemoveFeatureCollectionPtr) data;
+  if (sfp->idx.subtype == p->featdef && DoesObjectMatchConstraintChoiceSet (OBJ_SEQFEAT, sfp, p->constraint_set)) {
+    ValNodeAddPointer (&(p->feature_list), OBJ_SEQFEAT, sfp);
+  }
+}
+
+
+static Int4 ApplyRemoveFeatureActionToSeqEntry (RemoveFeatureActionPtr action, SeqEntryPtr sep)
+{
+  ConvertAndRemoveFeatureCollectionData d;
+  ValNodePtr vnp;
+  SeqFeatPtr sfp;
+  Int4       num_deleted = 0;
+
+  if (action == NULL) return 0;
+
+  d.featdef = GetFeatdefFromFeatureType (action->type);
+  d.constraint_set = action->constraint;
+  d.feature_list = NULL;
+
+  VisitFeaturesInSep (sep, &d, ConvertAndRemoveFeatureCollectionCallback);
+  for (vnp = d.feature_list; vnp != NULL; vnp = vnp->next) {
+    sfp = vnp->data.ptrvalue;
+    if (sfp != NULL) {
+      sfp->idx.deleteme = TRUE;
+      num_deleted ++;
+    }
+  }
+  DeleteMarkedObjects (ObjMgrGetEntityIDForChoice(sep), 0, NULL);
+  return num_deleted;
+}
+
+
+static Boolean DoesStrandMatch (Int4 strand_choice, Uint1 strand_val)
+{
+  Boolean rval = FALSE;
+  
+  switch (strand_choice)
+  {
+    case Feature_location_strand_from_any:
+      rval = TRUE;
+      break;
+    case Feature_location_strand_from_unknown:
+      if (strand_val == Seq_strand_unknown)
+      {
+        rval = TRUE;
+      }
+      break;
+    case Feature_location_strand_from_plus:
+      if (strand_val != Seq_strand_minus)
+      {
+        rval = TRUE;
+      }
+      break;
+    case Feature_location_strand_from_minus:
+      if (strand_val == Seq_strand_minus)
+      {
+        rval = TRUE;
+      }
+      break;
+    case Feature_location_strand_from_both:
+      if (strand_val == Seq_strand_both)
+      {
+        rval = TRUE;
+      }
+      break;
+  }
+  return rval;
+}
+
+
+static Uint1 GetNewStrandValue (Int4 strand_choice, Uint1 strand_val)
+{
+  Uint1 rval = Seq_strand_unknown;
+  
+  switch (strand_choice)
+  {
+    case Feature_location_strand_to_reverse:
+      switch (strand_val)
+      {
+        case Seq_strand_plus:
+        case Seq_strand_unknown:
+          rval = Seq_strand_minus;
+          break;
+        case Seq_strand_minus:
+          rval = Seq_strand_plus;
+          break;
+        default:
+          rval = strand_val;
+          break;
+      }
+      break;
+    case Feature_location_strand_to_unknown:
+      rval = Seq_strand_unknown;
+      break;
+    case Feature_location_strand_to_plus:
+      rval = Seq_strand_plus;
+      break;
+    case Feature_location_strand_to_minus:
+      rval = Seq_strand_minus;
+      break;
+    case Feature_location_strand_to_both:
+      rval = Seq_strand_both;
+      break;
+  }  
+  return rval;
+}
+
+
+static Boolean ConvertLocationStrand (SeqLocPtr slp, Int4 fromStrand, Int4 toStrand)
+{
+  SeqLocPtr      loc;
+  PackSeqPntPtr  psp;
+  SeqBondPtr     sbp;
+  SeqIntPtr      sinp;
+  SeqPntPtr      spp;
+  Boolean        rval = FALSE;
+  Uint1          strand_orig;
+
+  while (slp != NULL) {
+    switch (slp->choice) {
+      case SEQLOC_NULL :
+        break;
+      case SEQLOC_EMPTY :
+      case SEQLOC_WHOLE :
+        break;
+      case SEQLOC_INT :
+        sinp = (SeqIntPtr) slp->data.ptrvalue;
+        if (sinp != NULL && DoesStrandMatch (fromStrand, sinp->strand)) 
+        {
+          strand_orig = sinp->strand;
+          sinp->strand = GetNewStrandValue (toStrand, sinp->strand);
+          if (strand_orig != sinp->strand) {
+            rval = TRUE;
+          }
+        }
+        break;
+      case SEQLOC_PNT :
+        spp = (SeqPntPtr) slp->data.ptrvalue;
+        if (spp != NULL && DoesStrandMatch (fromStrand, spp->strand))
+        {
+          strand_orig = spp->strand;
+          spp->strand = GetNewStrandValue (toStrand, spp->strand);
+          if (strand_orig != spp->strand) {
+            rval = TRUE;
+          }
+        }
+        break;
+      case SEQLOC_PACKED_PNT :
+        psp = (PackSeqPntPtr) slp->data.ptrvalue;
+        if (psp != NULL && DoesStrandMatch (fromStrand, psp->strand)) 
+        {
+          strand_orig = psp->strand;
+          psp->strand = GetNewStrandValue (toStrand, psp->strand);
+          if (strand_orig != psp->strand) {
+            rval = TRUE;
+          }
+        }
+        break;
+      case SEQLOC_PACKED_INT :
+      case SEQLOC_MIX :
+      case SEQLOC_EQUIV :
+        loc = (SeqLocPtr) slp->data.ptrvalue;
+        while (loc != NULL) {
+          rval |= ConvertLocationStrand (loc, fromStrand, toStrand);
+          loc = loc->next;
+        }
+        break;
+      case SEQLOC_BOND :
+        sbp = (SeqBondPtr) slp->data.ptrvalue;
+        if (sbp != NULL) {
+          spp = (SeqPntPtr) sbp->a;
+          if (spp != NULL && DoesStrandMatch (fromStrand, spp->strand)) 
+          {
+            strand_orig = spp->strand;
+            spp->strand = GetNewStrandValue (toStrand, spp->strand);
+            if (strand_orig != spp->strand) {
+              rval = TRUE;
+            }
+          }
+          spp = (SeqPntPtr) sbp->b;
+          if (spp != NULL && DoesStrandMatch (fromStrand, spp->strand)) 
+          {
+            strand_orig = spp->strand;
+            spp->strand = GetNewStrandValue (toStrand, spp->strand);
+            if (strand_orig != spp->strand) {
+              rval = TRUE;
+            }
+          }
+        }
+        break;
+      case SEQLOC_FEAT :
+        break;
+      default :
+        break;
+    }
+    slp = slp->next;
+  }
+  return rval;
+}
+
+
+static Boolean ApplyEditLocationStrandToSeqFeat (EditLocationStrandPtr edit, SeqFeatPtr sfp)
+{
+  Boolean rval = FALSE;
+
+  if (edit == NULL || sfp == NULL) {
+    return FALSE;
+  }
+
+  rval = ConvertLocationStrand (sfp->location, edit->strand_from, edit->strand_to);  
+  return rval;
+}
+
+
+static Boolean At5EndOfSequence (SeqLocPtr slp, BioseqPtr bsp)
+{
+  Uint1 strand;
+  Int4  start;
+  Boolean at_end = FALSE;
+
+  if (slp == NULL || bsp == NULL) return FALSE;
+
+  strand = SeqLocStrand (slp);
+
+  if (strand == Seq_strand_minus) {
+    start = SeqLocStop (slp);
+    if (start == bsp->length - 1) {
+      at_end = TRUE;
+    }
+  } else {
+    start = SeqLocStart (slp);
+    if (start == 0) {
+      at_end = TRUE;
+    }
+  }
+  return at_end;
+}
+
+
+static Boolean HasGoodStartCodon (SeqFeatPtr sfp)
+{
+  ByteStorePtr bs;
+  CharPtr      prot;
+  Boolean     has_start = FALSE;
+
+  if (sfp != NULL && sfp->data.choice == SEQFEAT_CDREGION) {
+    bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
+    if (bs != NULL) {
+      prot = BSMerge (bs, NULL);
+      bs = BSFree (bs);
+      if (prot != NULL && *prot == 'M') {
+        has_start = TRUE;
+      }
+      prot = MemFree (prot);
+    }
+  }
+  return has_start;
+}
+
+
+static Boolean ApplyPartial5SetActionToSeqFeat (Partial5SetActionPtr action, SeqFeatPtr sfp)
+{
+  Boolean      rval = FALSE;
+  Boolean      make_partial = FALSE;
+  Uint1        strand;
+  BioseqPtr    bsp;
+  CdRegionPtr  crp;
+  Boolean      partial5, partial3;
+
+  if (action == NULL || sfp == NULL) return FALSE;
+  bsp = BioseqFindFromSeqLoc (sfp->location);
+  strand = SeqLocStrand (sfp->location);
+
+  switch (action->constraint) {
+    case Partial_5_set_constraint_all:
+      make_partial = TRUE;
+      break;
+    case Partial_5_set_constraint_at_end:
+      make_partial = At5EndOfSequence (sfp->location, bsp);
+      break;
+    case Partial_5_set_constraint_bad_start:
+      make_partial = HasGoodStartCodon (sfp);
+      break;
+    case Partial_5_set_constraint_frame_not_one:
+      if (sfp->data.choice == SEQFEAT_CDREGION
+          && (crp = sfp->data.value.ptrvalue) != NULL
+          && crp->frame != 0 && crp->frame != 1) {
+        make_partial = TRUE;
+      }
+      break;
+  }
+
+  if (make_partial) {
+    CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+    if (!partial5) {
+      SetSeqLocPartial (sfp->location, TRUE, partial3);
+      if (action->extend && bsp != NULL) {
+        ExtendSeqLocToEnd (sfp->location, bsp, TRUE);
+      }
+      rval = TRUE; 
+    }
+  }
+  return rval;
+}
+
+
+static Boolean ApplyClear5PartialToSeqFeat (Int4 action, SeqFeatPtr sfp)
+{
+  Boolean rval = FALSE, clear_partial = FALSE;
+  Boolean partial5, partial3;
+
+  if (sfp == NULL) return FALSE;
+
+  switch (action) {
+    case Partial_5_clear_constraint_all:
+      clear_partial = TRUE;
+      break;
+    case Partial_5_clear_constraint_not_at_end:
+      clear_partial = !At5EndOfSequence(sfp->location, BioseqFindFromSeqLoc (sfp->location));
+      break;
+    case Partial_5_clear_constraint_good_start:
+      clear_partial = !HasGoodStartCodon(sfp);
+      break;
+  }
+  if (clear_partial) {
+    CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+    if (partial5) {
+      SetSeqLocPartial (sfp->location, FALSE, partial3);
+      rval = TRUE;
+    }
+  }
+  return rval;
+}
+
+
+static Boolean At3EndOfSequence (SeqLocPtr slp, BioseqPtr bsp)
+{
+  Uint1 strand;
+  Int4  stop;
+  Boolean at_end = FALSE;
+
+  if (slp == NULL || bsp == NULL) return FALSE;
+
+  strand = SeqLocStrand (slp);
+
+  if (strand == Seq_strand_minus) {
+    stop = SeqLocStart (slp);
+    if (stop == 0) {
+      at_end = TRUE;
+    }
+  } else {
+    stop = SeqLocStop (slp);
+    if (stop == bsp->length - 1) {
+      at_end = TRUE;
+    }
+  }
+  return at_end;
+}
+
+
+static Boolean HasGoodStopCodon (SeqFeatPtr sfp)
+{
+  ByteStorePtr bs;
+  CharPtr      prot;
+  Boolean      has_stop = FALSE;
+
+  if (sfp != NULL && sfp->data.choice == SEQFEAT_CDREGION) {
+    bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
+    if (bs != NULL) {
+      prot = BSMerge (bs, NULL);
+      bs = BSFree (bs);
+      if (prot != NULL && prot[StringLen (prot) - 1] == '*') {
+        has_stop = TRUE;
+      }
+      prot = MemFree (prot);
+    }
+  }
+  return has_stop;
+}
+
+
+static Boolean ApplyPartial3SetActionToSeqFeat (Partial3SetActionPtr action, SeqFeatPtr sfp)
+{
+  Boolean      rval = FALSE;
+  Boolean      make_partial = FALSE;
+  Uint1        strand;
+  BioseqPtr    bsp;
+  Boolean      partial5, partial3;
+
+  if (action == NULL || sfp == NULL) return FALSE;
+  bsp = BioseqFindFromSeqLoc (sfp->location);
+  strand = SeqLocStrand (sfp->location);
+
+  switch (action->constraint) {
+    case Partial_3_set_constraint_all:
+      make_partial = TRUE;
+      break;
+    case Partial_3_set_constraint_at_end:
+      make_partial = At3EndOfSequence (sfp->location, bsp);
+      break;
+    case Partial_3_set_constraint_bad_end:
+      make_partial = HasGoodStopCodon (sfp);
+      break;
+  }
+
+  if (make_partial) {
+    CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+    if (!partial3) {
+      SetSeqLocPartial (sfp->location, partial5, TRUE);
+      if (action->extend && bsp != NULL) {
+        ExtendSeqLocToEnd (sfp->location, bsp, FALSE);
+      }
+      rval = TRUE; 
+    }
+  }
+  return rval;
+}
+
+
+static Boolean ApplyClear3PartialToSeqFeat (Int4 action, SeqFeatPtr sfp)
+{
+  Boolean rval = FALSE, clear_partial = FALSE;
+  Boolean partial5, partial3;
+
+  if (sfp == NULL) return FALSE;
+
+  switch (action) {
+    case Partial_3_clear_constraint_all:
+      clear_partial = TRUE;
+      break;
+    case Partial_3_clear_constraint_not_at_end:
+      clear_partial = !At3EndOfSequence(sfp->location, BioseqFindFromSeqLoc (sfp->location));
+      break;
+    case Partial_3_clear_constraint_good_end:
+      clear_partial = !HasGoodStopCodon(sfp);
+      break;
+  }
+  if (clear_partial) {
+    CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+    if (partial3) {
+      SetSeqLocPartial (sfp->location, partial5, FALSE);
+      rval = TRUE;
+    }
+  }
+  return rval;
+}
+
+
+static Boolean ApplyConvertLocationToSeqFeat (Int4 convert_location, SeqFeatPtr sfp)
+{
+  Boolean hasNulls, rval = FALSE;
+  SeqLocPtr slp;
+  BioseqPtr bsp;
+  Boolean   partial5, partial3;
+
+  if (sfp == NULL || (bsp = BioseqFindFromSeqLoc (sfp->location))== NULL) {
+    return FALSE;
+  }
+
+  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+	hasNulls = LocationHasNullsBetween (sfp->location);
+	switch (convert_location) 
+	{
+	  case Convert_location_type_join :
+	    if (hasNulls) 
+	    {
+	      slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, FALSE, FALSE);
+		    sfp->location = SeqLocFree (sfp->location);
+		    sfp->location = slp;
+		    if (bsp->repr == Seq_repr_seg) 
+		    {
+		      slp = SegLocToPartsEx (bsp, sfp->location, FALSE);
+		      sfp->location = SeqLocFree (sfp->location);
+		      sfp->location = slp;
+		      hasNulls = LocationHasNullsBetween (sfp->location);
+		      sfp->partial = (sfp->partial || hasNulls);
+		    }
+		    FreeAllFuzz (sfp->location);
+		    SetSeqLocPartial (sfp->location, partial5, partial3);
+        rval = TRUE;
+	    }
+	    break;
+  	case Convert_location_type_order :
+	    if (!hasNulls) 
+	    {
+		    slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, FALSE, TRUE);
+        sfp->location = SeqLocFree (sfp->location);
+		    sfp->location = slp;
+		    if (bsp->repr == Seq_repr_seg) 
+		    {
+		      slp = SegLocToPartsEx (bsp, sfp->location, TRUE);
+		      sfp->location = SeqLocFree (sfp->location);
+		      sfp->location = slp;
+		      hasNulls = LocationHasNullsBetween (sfp->location);
+		      sfp->partial = (sfp->partial || hasNulls);
+		    }
+		    FreeAllFuzz (sfp->location);
+		    SetSeqLocPartial (sfp->location, partial5, partial3);
+        rval = TRUE;
+	    }
+	    break;
+	  case Convert_location_type_merge :
+      if (sfp->location->choice != SEQLOC_INT) {
+	      slp = SeqLocMerge (bsp, sfp->location, NULL, TRUE, FALSE, FALSE);
+	      sfp->location = SeqLocFree (sfp->location);
+	      sfp->location = slp;
+		    SetSeqLocPartial (sfp->location, partial5, partial3);
+        rval = TRUE;
+      }
+	  default:
+	    break;
+	}
+  return rval;
+}
+
+
+static Boolean ApplyLocationEditTypeToSeqFeat (ValNodePtr action, SeqFeatPtr sfp)
+{
+  Boolean rval = FALSE;
+
+  if (action == NULL || sfp == NULL) {
+    return FALSE;
+  }
+
+  switch (action->choice) {
+    case LocationEditType_strand:
+      rval = ApplyEditLocationStrandToSeqFeat (action->data.ptrvalue, sfp);
+      break;
+    case LocationEditType_set_5_partial:
+      rval = ApplyPartial5SetActionToSeqFeat (action->data.ptrvalue, sfp);
+      break;
+    case LocationEditType_clear_5_partial:
+      rval = ApplyClear5PartialToSeqFeat (action->data.intvalue, sfp);
+      break;
+    case LocationEditType_set_3_partial:
+      rval = ApplyPartial3SetActionToSeqFeat (action->data.ptrvalue, sfp);
+      break;
+    case LocationEditType_clear_3_partial:
+      rval = ApplyClear3PartialToSeqFeat (action->data.intvalue, sfp);
+      break;
+    case LocationEditType_convert:
+      rval = ApplyConvertLocationToSeqFeat (action->data.intvalue, sfp);
+      break;
+  }
+  return rval;
+}
+
+
+static Int4 ApplyEditFeatureLocationActionToSeqEntry (EditFeatureLocationActionPtr action, SeqEntryPtr sep)
+{
+  ConvertAndRemoveFeatureCollectionData d;
+  ValNodePtr vnp;
+  SeqFeatPtr sfp;
+  Int4       num_affected = 0;
+
+  if (action == NULL) return 0;
+
+  d.featdef = GetFeatdefFromFeatureType (action->type);
+  d.constraint_set = action->constraint;
+  d.feature_list = NULL;
+
+  VisitFeaturesInSep (sep, &d, ConvertAndRemoveFeatureCollectionCallback);
+  for (vnp = d.feature_list; vnp != NULL; vnp = vnp->next) {
+    sfp = vnp->data.ptrvalue;
+    if (sfp != NULL && ApplyLocationEditTypeToSeqFeat (action->action, sfp)) {
+      num_affected++;
+    }
+  }
+  return num_affected;
+}
+
+
+NLM_EXTERN void ApplyMacroToSeqEntry (SeqEntryPtr sep, ValNodePtr macro, Int4Ptr pNumFields, Int4Ptr pNumFeat)
+{
+  Int4 num_AECR = 0, num_parse = 0, num_feature = 0, num_fields = 0;
+
+  while (macro != NULL) {
+    switch (macro->choice) {
+      case MacroActionChoice_aecr:
+        num_AECR += ApplyAECRActionToSeqEntry ((AECRActionPtr) macro->data.ptrvalue, sep);
+        break;
+      case MacroActionChoice_parse:
+        num_parse += ApplyParseActionToSeqEntry ((ParseActionPtr) macro->data.ptrvalue, sep);
+        break;
+      case MacroActionChoice_add_feature:
+        num_feature += ApplyApplyFeatureActionToSeqEntry ((ApplyFeatureActionPtr) macro->data.ptrvalue, sep);
+        SeqMgrIndexFeatures (ObjMgrGetEntityIDForChoice(sep), NULL);
+        break;
+      case MacroActionChoice_remove_feature:
+        num_feature += ApplyRemoveFeatureActionToSeqEntry ((RemoveFeatureActionPtr) macro->data.ptrvalue, sep);
+        break;
+      case MacroActionChoice_edit_location:
+        num_fields += ApplyEditFeatureLocationActionToSeqEntry ((EditFeatureLocationActionPtr) macro->data.ptrvalue, sep);
+        break;
+    }
+    macro = macro->next;
+  }
+  if (pNumFields != NULL) {
+    *pNumFields = num_AECR + num_parse + num_fields;
+  }
+  if (pNumFeat != NULL) {
+    *pNumFeat = num_feature;
+  }
+}
+
+
+/* for generating text descriptions of macro objects */
+NLM_EXTERN CharPtr SummarizeSourceQual (ValNodePtr field)
+{
+  CharPtr summ = NULL, locname, origname;
+  Int4    genome, origin;
+  CharPtr loc_fmt = "location %s";
+  CharPtr orig_fmt = "origin %s";
+
+  if (field == NULL) return NULL;
+  switch (field->choice) {
+    case SourceQualChoice_textqual:
+      summ = StringSave (GetSourceQualName (field->data.intvalue));
+      break;
+    case SourceQualChoice_location:
+      genome = GenomeFromSrcLoc (field->data.intvalue);
+      locname = LocNameFromGenome (genome);
+      summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (loc_fmt) + StringLen (locname)));
+      sprintf (summ, loc_fmt, locname);
+      break;
+    case SourceQualChoice_origin:
+      origin = OriginFromSrcOrig (field->data.intvalue);
+      origname = OriginNameFromOrigin (origin);
+      summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (orig_fmt) + StringLen (origname)));
+      sprintf (summ, orig_fmt, origname);
+      break;
+  }
+  return summ;
+}
+
+
+NLM_EXTERN CharPtr FeatureFieldLabel (CharPtr feature_name, ValNodePtr field)
+{
+  CharPtr cp;
+  CharPtr label = NULL;
+  CharPtr legal_fmt = "%s %s";
+  CharPtr illegal_fmt = "constrained field on %s";
+  
+  if (feature_name == NULL) {
+    feature_name = "Unknown feature";
+  }
+
+  if (field == NULL) {
+    return StringSave ("missing field");
+  } else if (field->choice == FeatQualChoice_legal_qual) {
+    cp = GetFeatQualName (field->data.intvalue);
+    if (cp == NULL) cp = "Unknown field type";
+    label = (CharPtr) MemNew (sizeof (Char) * (StringLen (legal_fmt) + StringLen (feature_name) + StringLen (cp)));
+    sprintf (label, legal_fmt, feature_name, cp);
+  } else if (field->choice == FeatQualChoice_illegal_qual) {
+    label = (CharPtr) MemNew (sizeof (Char) * (StringLen (illegal_fmt) + StringLen (feature_name)));
+    sprintf (label, illegal_fmt, feature_name);
+  } else {
+    label = StringSave ("illegal field value");
+  }
+  return label;
+}
+
+
+NLM_EXTERN Boolean IsFeatureFieldEmpty (FeatureFieldPtr field)
+{
+  if (field == NULL) return TRUE;
+  if (field->field == NULL) return TRUE;
+  return FALSE;
+}
+
+
+NLM_EXTERN Boolean IsFieldTypeEmpty (FieldTypePtr field)
+{
+  Boolean rval = TRUE;
+
+  if (field == NULL) return TRUE;
+  switch (field->choice) {
+    case FieldType_source_qual:
+      if (field->data.ptrvalue != NULL) {
+        rval = FALSE;
+      }
+      break;
+    case FieldType_feature_field:
+      if (!IsFeatureFieldEmpty (field->data.ptrvalue)) {
+        rval = FALSE;
+      }
+      break;
+    case FieldType_cds_gene_prot:
+      rval = FALSE;
+      break;
+  }
+  return rval;
+}
+
+
+NLM_EXTERN CharPtr SummarizeFieldType (ValNodePtr vnp)
+{
+  FeatureFieldPtr ffp;
+  CharPtr str = NULL;
+  CharPtr    label = NULL;
+
+  if (vnp == NULL) {
+    str = StringSave ("missing field");
+  } else {
+    switch (vnp->choice) {
+      case FieldType_source_qual:
+        str = SummarizeSourceQual (vnp->data.ptrvalue);
+        break;
+      case FieldType_feature_field:
+        ffp = (FeatureFieldPtr) vnp->data.ptrvalue;
+        if (ffp == NULL || ffp->field == NULL) {
+          str = StringSave ("missing field");
+        } else {
+          label = GetFeatureNameFromFeatureType (ffp->type);
+          str = FeatureFieldLabel (label, ffp->field);
+        }
+        break;
+      case FieldType_cds_gene_prot:
+        str = StringSaveNoNull (CDSGeneProtNameFromField (vnp->data.intvalue));
+        if (str == NULL) {
+          str = StringSave ("Invalid CDS-Gene-Prot Field");
+        }
+        break;
+      case FieldType_molinfo_field:
+        str = GetSequenceQualName (vnp->data.ptrvalue);
+        if (str == NULL) {
+          str = StringSave ("Invalid Sequence Qual Field");
+        }
+        break;
+      default:
+        str = StringSave ("Invalid field type");
+        break;
+    }
+  }
+  return str;
+}
+
+
+/* for table readers that use the macro language functions */
+NLM_EXTERN TabColumnConfigPtr TabColumnConfigNew (void)
+{
+  TabColumnConfigPtr t;
+
+  t = (TabColumnConfigPtr) MemNew (sizeof (TabColumnConfigData));
+  t->field = NULL;
+  t->existing_text = ExistingTextOption_replace_old;
+  t->skip_blank = TRUE;
+  return t;
+}
+
+
+
+NLM_EXTERN TabColumnConfigPtr TabColumnConfigFree (TabColumnConfigPtr t)
+{
+  if (t != NULL) {
+    t->field = FieldTypeFree (t->field);
+    t = MemFree (t);
+  }
+  return t;
+}
+
+
+NLM_EXTERN TabColumnConfigPtr TabColumnConfigCopy (TabColumnConfigPtr orig)
+{
+  TabColumnConfigPtr t = NULL;
+
+  if (orig != NULL) {
+    t = TabColumnConfigNew ();
+    t->match_type = orig->match_type;
+    t->existing_text = orig->existing_text;
+    t->skip_blank = orig->skip_blank;
+    t->match_mrna = orig->match_mrna;
+    t->field = AsnIoMemCopy (orig->field, (AsnReadFunc) FieldTypeAsnRead, (AsnWriteFunc) FieldTypeAsnWrite);
+  }
+  return t;
+}
+
+
+NLM_EXTERN ValNodePtr TabColumnConfigListFree (ValNodePtr columns)
+{
+  ValNodePtr vnp_next;
+
+  while (columns != NULL) {
+    vnp_next = columns->next;
+    columns->data.ptrvalue = TabColumnConfigFree (columns->data.ptrvalue);
+    columns->next = NULL;
+    columns = ValNodeFree (columns);
+    columns = vnp_next;
+  }
+  return columns;
+}
+
+
+NLM_EXTERN ValNodePtr TabColumnConfigListCopy (ValNodePtr orig)
+{
+  ValNodePtr new_list = NULL;
+  TabColumnConfigPtr t;
+
+  while (orig != NULL) {
+    t = TabColumnConfigCopy (orig->data.ptrvalue);
+    ValNodeAddPointer (&new_list, 0, t);
+    orig = orig->next;
+  }
+  return new_list;
+}
+
+
+
+/* This checks the column names and returns a list of the feature fields */
+NLM_EXTERN ValNodePtr ValidateFeatureFieldColumnNames (ValNodePtr header_line, ValNodePtr PNTR perr_list)
+{
+  ValNodePtr         header_vnp;
+  ValNodePtr         err_list = NULL, col_list = NULL;
+  Boolean            rval = TRUE;
+  TabColumnConfigPtr t;
+  FeatureFieldPtr    field;
+  Int4               featqual, feat_type;
+  CharPtr            first_space;
+  
+  if (header_line == NULL)
+  {
+    return FALSE;
+  }
+  
+  header_vnp = header_line->data.ptrvalue;
+  if (header_vnp == NULL || header_vnp->next == NULL)
+  {
+    return FALSE;
+  }
+  
+  /* skip ID column */
+  header_vnp = header_vnp->next;
+  while (header_vnp != NULL && rval)
+  {
+    first_space = StringChr (header_vnp->data.ptrvalue, ' ');
+    if (first_space != NULL) {
+      *first_space = 0;
+      feat_type = GetFeatureTypeByName (header_vnp->data.ptrvalue);
+      featqual = GetFeatQualByName (first_space + 1);
+      *first_space = ' ';
+      if (feat_type < 0 || featqual < 0) {
+        /* unable to recognize column name */
+        ValNodeAddPointer (&err_list, 0, StringSave (header_vnp->data.ptrvalue));
+        /* if we're not able to send back a list of errors, just quit now */
+        if (perr_list == NULL) {
+          rval = FALSE;
+        }
+      } else if (err_list == NULL) {
+        /* if we've already found errors, don't bother collecting more fields */
+        field = FeatureFieldNew ();
+        field->type = feat_type;
+        field->field = ValNodeNew (NULL);
+        field->field->choice = FeatQualChoice_legal_qual;
+        field->field->data.intvalue = featqual;
+        t = TabColumnConfigNew ();
+        t->field = ValNodeNew (NULL);
+        t->field->choice = FieldType_feature_field;
+        t->field->data.ptrvalue = field;
+        ValNodeAddPointer (&col_list, 0, t);
+      }
+    } else {
+      featqual = GetFeatQualByName (header_vnp->data.ptrvalue);
+      if (featqual < 0) {
+        /* unable to recognize column name */
+        ValNodeAddPointer (&err_list, 0, StringSave (header_vnp->data.ptrvalue));
+        /* if we're not able to send back a list of errors, just quit now */
+        if (perr_list == NULL) {
+          rval = FALSE;
+        }
+      } else if (err_list == NULL) {
+        /* if we've already found errors, don't bother collecting more fields */
+        field = FeatureFieldNew ();
+        field->type = Feature_type_any;
+        field->field = ValNodeNew (NULL);
+        field->field->choice = FeatQualChoice_legal_qual;
+        field->field->data.intvalue = featqual;
+        t = TabColumnConfigNew ();
+        t->field = ValNodeNew (NULL);
+        t->field->choice = FieldType_feature_field;
+        t->field->data.ptrvalue = field;
+        ValNodeAddPointer (&col_list, 0, t);
+      }
+    }
+    header_vnp = header_vnp->next;
+  }
+  if (err_list != NULL) {
+    col_list = TabColumnConfigListFree (col_list);
+    if (perr_list != NULL) {
+      *perr_list = err_list;
+    } else {
+      err_list = ValNodeFreeData (err_list);
+    }
+  }
+  return col_list;
+}
+
+typedef struct findgenelocustag {
+  CharPtr locus_tag;
+  ValNodePtr gene_list;
+} FindGeneLocusTagData, PNTR FindGeneLocusTagPtr;
+
+static void FindGeneByLocusTagBioseqCallback (BioseqPtr bsp, Pointer userdata)
+{
+  FindGeneLocusTagPtr p;
+  SeqFeatPtr          gene;
+  SeqMgrFeatContext   fcontext;
+
+  if (bsp == NULL || userdata == NULL || !ISA_na (bsp->mol)) {
+    return;
+  }
+
+  p = (FindGeneLocusTagPtr) userdata;
+
+  gene = SeqMgrGetGeneByLocusTag (bsp, p->locus_tag, &fcontext);
+  if (gene != NULL) {
+    ValNodeAddPointer (&p->gene_list, OBJ_SEQFEAT, gene);
+  }
+}
+
+
+typedef struct objbystr {
+  ValNodePtr obj_list;
+  CharPtr    str;
+} ObjByStrData, PNTR ObjByStrPtr;
+
+static void GetFeaturesByDbxrefCallback (SeqFeatPtr sfp, Pointer userdata)
+{
+  ObjByStrPtr p;
+  ValNodePtr    vnp;
+  DbtagPtr      dbt;
+  Char          buf[20];
+  Boolean       found = FALSE;
+
+  if (sfp == NULL || sfp->dbxref == NULL || userdata == NULL) return;
+  p = (ObjByStrPtr) userdata;
+
+  if (StringHasNoText (p->str)) return;
+
+  for (vnp = sfp->dbxref; vnp != NULL && !found; vnp = vnp->next) {
+    dbt = (DbtagPtr) vnp->data.ptrvalue;
+    if (dbt != NULL && dbt->tag != NULL) {
+      if (dbt->tag->id > 0) {
+        sprintf (buf, "%d", dbt->tag->id);
+        if (StringCmp (buf, p->str) == 0) {
+          found = TRUE;
+        }
+      } else if (StringCmp (dbt->tag->str, p->str) == 0) {
+        found = TRUE;
+      }
+    }
+  }
+  if (found) {
+    ValNodeAddPointer (&(p->obj_list), OBJ_SEQFEAT, sfp);
+  }
+
+}
+
+
+static ValNodePtr GetFeaturesByDbxref (SeqEntryPtr sep, CharPtr dbxref)
+{
+  ObjByStrData d;
+
+  d.str = dbxref;
+  d.obj_list = NULL;
+  VisitFeaturesInSep (sep, &d, GetFeaturesByDbxrefCallback);
+  return d.obj_list;
+}
+
+
+static void GetBioSourcesByTaxNameDescriptorCallback (SeqDescrPtr sdp, Pointer userdata)
+{
+  ObjByStrPtr p;
+  BioSourcePtr biop;
+
+  if (sdp == NULL || sdp->choice != Seq_descr_source || userdata == NULL) return;
+  p = (ObjByStrPtr) userdata;
+
+  if (StringHasNoText (p->str)) return;
+
+  biop = (BioSourcePtr) sdp->data.ptrvalue;
+  if (biop != NULL && biop->org != NULL && StringCmp (biop->org->taxname, p->str) == 0) {
+    ValNodeAddPointer (&(p->obj_list), OBJ_SEQDESC, sdp);
+  }
+
+}
+
+
+static void GetBioSourcesByTaxNameFeatureCallback (SeqFeatPtr sfp, Pointer userdata)
+{
+  ObjByStrPtr p;
+  BioSourcePtr biop;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || userdata == NULL) return;
+  p = (ObjByStrPtr) userdata;
+
+  if (StringHasNoText (p->str)) return;
+
+  biop = (BioSourcePtr) sfp->data.value.ptrvalue;
+  if (biop != NULL && biop->org != NULL && StringCmp (biop->org->taxname, p->str) == 0) {
+    ValNodeAddPointer (&(p->obj_list), OBJ_SEQFEAT, sfp);
+  }
+
+}
+
+
+static ValNodePtr GetBioSourcesByTaxName (SeqEntryPtr sep, CharPtr taxname)
+{
+  ObjByStrData d;
+
+  d.str = taxname;
+  d.obj_list = NULL;
+  VisitDescriptorsInSep (sep, &d, GetBioSourcesByTaxNameDescriptorCallback);
+
+  VisitFeaturesInSep (sep, &d, GetBioSourcesByTaxNameFeatureCallback);
+  return d.obj_list;
+}
+
+
+
+static ValNodePtr 
+FindMatchForRow 
+(ValNodePtr  match_type,
+ Uint2       entityID,
+ SeqEntryPtr sep)
+{
+  ValNodePtr match_list = NULL;
+  SeqIdPtr   sip;
+  BioseqPtr  bsp, nbsp = NULL;
+  FindGeneLocusTagData fd;
+  SeqFeatPtr           sfp;
+  SeqMgrFeatContext    fcontext;
+
+  if (match_type == NULL || sep == NULL) return NULL;
+
+  switch (match_type->choice) {
+    case eTableMatchFeatureID:
+      sfp = SeqMgrGetFeatureByFeatID (entityID, NULL, match_type->data.ptrvalue, NULL, &fcontext);
+      if (sfp != NULL) {
+        ValNodeAddPointer (&match_list, OBJ_SEQFEAT, sfp);
+      }
+      break;
+    case eTableMatchGeneLocusTag:
+      fd.locus_tag = match_type->data.ptrvalue;
+      fd.gene_list = NULL;
+      VisitBioseqsInSep (sep, &fd, FindGeneByLocusTagBioseqCallback);
+      ValNodeLink (&match_list, fd.gene_list);
+      break;
+    case eTableMatchProteinID:
+    case eTableMatchNucID:
+      sip = CreateSeqIdFromText (match_type->data.ptrvalue, sep);
+      bsp = BioseqFind (sip);
+      sip = SeqIdFree (sip);
+      if (bsp != NULL) 
+      {
+        ValNodeAddPointer (&match_list, OBJ_BIOSEQ, bsp);
+      }
+      break;
+    case eTableMatchDbxref:
+      match_list = GetFeaturesByDbxref (sep, match_type->data.ptrvalue);
+      break;
+    case eTableMatchBioSource:
+      match_list = GetBioSourcesByTaxName (sep, match_type->data.ptrvalue);
+      break;
+  }
+  return match_list;
+}
+
+
+static ValNodePtr GetFeatureListForProteinBioseq (Uint1 featdef, BioseqPtr bsp)
+{
+  ValNodePtr feat_list = NULL;
+  SeqFeatPtr sfp, cds;
+  SeqMgrFeatContext fcontext;
+  Int4              seqfeattype;
+
+  if (bsp == NULL || !ISA_aa (bsp->mol)) 
+  {
+    return NULL;
+  }
+
+  seqfeattype = FindFeatFromFeatDefType (featdef);
+  if (seqfeattype == SEQFEAT_PROT)
+  {
+    for (sfp = SeqMgrGetNextFeature (bsp, NULL, 0, featdef, &fcontext);
+         sfp != NULL;
+         sfp = SeqMgrGetNextFeature (bsp, sfp, 0, featdef, &fcontext))
+    {
+      ValNodeAddPointer (&feat_list, OBJ_SEQFEAT, sfp);
+    }
+  }
+  else
+  {
+    cds = SeqMgrGetCDSgivenProduct (bsp, NULL);
+    if (cds != NULL) 
+    {
+      if (featdef == FEATDEF_CDS)
+      {
+        sfp = cds;
+      }
+      else if (featdef == FEATDEF_GENE)
+      {
+        sfp = GetGeneForFeature (cds);
+      }
+      else if (featdef == FEATDEF_mRNA)
+      {
+        sfp = SeqMgrGetOverlappingmRNA (cds->location, &fcontext);
+      }
+      if (sfp != NULL)
+      {
+        ValNodeAddPointer (&feat_list, OBJ_SEQFEAT, sfp);
+      }
+    }
+  }
+  return feat_list;
+}
+
+
+static ValNodePtr GetFeatureListForNucleotideBioseq (Uint1 featdef, BioseqPtr bsp)
+{
+  ValNodePtr feat_list = NULL;
+  SeqFeatPtr sfp;
+  SeqMgrFeatContext fcontext;
+  Int4              seqfeattype;
+  BioseqPtr         prot_bsp;
+
+  if (bsp == NULL || ISA_aa (bsp->mol)) 
+  {
+    return NULL;
+  }
+
+  seqfeattype = FindFeatFromFeatDefType (featdef);
+  if (seqfeattype == SEQFEAT_PROT)
+  {
+    for (sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_CDS, &fcontext);
+         sfp != NULL;
+         sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_CDS, &fcontext))
+    {
+      prot_bsp = BioseqFindFromSeqLoc (sfp->product);
+      ValNodeLink (&feat_list, GetFeatureListForProteinBioseq (featdef, prot_bsp));
+    }
+  }
+  else
+  {
+    for (sfp = SeqMgrGetNextFeature (bsp, NULL, 0, featdef, &fcontext);
+         sfp != NULL;
+         sfp = SeqMgrGetNextFeature (bsp, sfp, 0, featdef, &fcontext))
+    {
+      ValNodeAddPointer (&feat_list, OBJ_SEQFEAT, sfp);
+    }
+  }
+  return feat_list;
+}
+
+
+static ValNodePtr GetFeaturesForGene (SeqFeatPtr gene, Uint1 featdef)
+{
+  BioseqPtr bsp;
+  SeqFeatPtr sfp;
+  ValNodePtr feat_list = NULL;
+  SeqMgrFeatContext fcontext;
+  Int4              start, stop, swap;
+
+  if (gene == NULL) return NULL;
+
+  bsp = BioseqFindFromSeqLoc (gene->location);
+  start = SeqLocStart (gene->location);
+  stop = SeqLocStop (gene->location);
+  if (stop < start) 
+  {
+    swap = start;
+    start = stop;
+    stop = swap;
+  }
+  for (sfp = SeqMgrGetNextFeature (bsp, NULL, 0, featdef, &fcontext);
+       sfp != NULL && fcontext.left < stop;
+       sfp = SeqMgrGetNextFeature (bsp, sfp, 0, featdef, &fcontext))
+  {
+    if (fcontext.right >= start && gene == GetGeneForFeature (sfp))
+    {
+      ValNodeAddPointer (&feat_list, OBJ_SEQFEAT, sfp);
+    }
+  }
+  return feat_list;
+}
+
+
+static ValNodePtr GetFeatureListForGene (Uint1 featdef, SeqFeatPtr gene)
+{
+  ValNodePtr feat_list = NULL, cds_list, vnp;
+  SeqFeatPtr sfp, cds;
+  SeqMgrFeatContext fcontext;
+  BioseqPtr         protbsp;
+
+  if (gene == NULL) 
+  {
+    return NULL;
+  }
+
+  if (featdef == FEATDEF_GENE)
+  {
+    ValNodeAddPointer (&feat_list, OBJ_SEQFEAT, gene);
+  }
+  else if (FindFeatFromFeatDefType (featdef == SEQFEAT_PROT))
+  {
+    cds_list = GetFeaturesForGene (gene, FEATDEF_CDS);
+    for (vnp = cds_list; vnp != NULL; vnp = vnp->next) 
+    {
+      cds = vnp->data.ptrvalue;
+      if (cds != NULL)
+      {
+        protbsp = BioseqFindFromSeqLoc (cds->product);
+        for (sfp = SeqMgrGetNextFeature (protbsp, NULL, 0, featdef, &fcontext);
+             sfp != NULL;
+             sfp = SeqMgrGetNextFeature (protbsp, sfp, 0, featdef, &fcontext))
+        {
+          ValNodeAddPointer (&feat_list, OBJ_SEQFEAT, sfp);
+        }
+      }
+    }
+    cds_list = ValNodeFree (cds_list);
+  }
+  else
+  {
+    feat_list = GetFeaturesForGene (gene, featdef);
+  }
+
+  return feat_list;
+}
+
+
+static ValNodePtr AddFeaturesFromBioseqSet (BioseqSetPtr bssp, Uint1 featdef)
+{
+  SeqEntryPtr sep;
+  BioseqPtr   bsp;
+  Int4        seqfeattype;
+  ValNodePtr  item_list = NULL;
+
+  if (bssp == NULL) return NULL;
+
+  seqfeattype = FindFeatFromFeatDefType (featdef);
+  for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
+    if (sep->data.ptrvalue == NULL) continue;
+    if (IS_Bioseq (sep)) {
+      bsp = sep->data.ptrvalue;
+      if (seqfeattype == SEQFEAT_PROT) {
+        if (ISA_aa (bsp->mol)) {
+          ValNodeLink (&item_list, GetFeatureListForProteinBioseq (featdef, bsp));
+        }
+      } else if (!ISA_aa (bsp->mol)) {
+        ValNodeLink (&item_list, GetFeatureListForNucleotideBioseq (featdef, bsp));
+      }
+    } else if (IS_Bioseq_set (sep)) {
+      ValNodeLink (&item_list, AddFeaturesFromBioseqSet (sep->data.ptrvalue, featdef));
+    }
+  }
+  return item_list;
+}
+
+
+static ValNodePtr GetFeatureListForBioSourceObjects (ValNodePtr item_list, FeatureFieldPtr field)
+{
+  ValNodePtr vnp;
+  SeqFeatPtr sfp;
+  SeqDescrPtr sdp;
+  BioseqPtr   bsp;
+  ObjValNodePtr ovp;
+  ValNodePtr  feature_list = NULL;
+
+  if (item_list == NULL || field == NULL) return NULL;
+
+  for (vnp = item_list; vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == OBJ_SEQFEAT) {
+      sfp = vnp->data.ptrvalue;
+      if (sfp != NULL) {
+        bsp = BioseqFindFromSeqLoc (sfp->location);
+        ValNodeLink (&feature_list, GetFeatureListForNucleotideBioseq (GetFeatdefFromFeatureType(field->type), bsp));
+      }
+    } else if (vnp->choice == OBJ_SEQDESC) {
+      sdp = vnp->data.ptrvalue;
+      if (sdp != NULL && sdp->extended != 0) {
+        ovp = (ObjValNodePtr) sdp;
+        if (ovp->idx.parenttype == OBJ_BIOSEQSET) {
+          ValNodeLink (&feature_list, AddFeaturesFromBioseqSet (ovp->idx.parentptr, GetFeatdefFromFeatureType(field->type)));
+        } else if (ovp->idx.parenttype == OBJ_BIOSEQ) {
+          bsp = (BioseqPtr) ovp->idx.parentptr;
+          ValNodeLink (&feature_list, GetFeatureListForNucleotideBioseq (GetFeatdefFromFeatureType(field->type), bsp));
+        }
+      }
+    }
+  }
+  return feature_list;
+}
+
+
+static ValNodePtr ValNodeCopyPtr (ValNodePtr orig)
+{
+  ValNodePtr new_list = NULL, last_vnp = NULL, vnp;
+
+  while (orig != NULL) {
+    vnp = ValNodeNew (NULL);
+    vnp->choice = orig->choice;
+    vnp->data.ptrvalue = orig->data.ptrvalue;
+    if (last_vnp == NULL) {
+      new_list = vnp;
+    } else {
+      last_vnp->next = vnp;
+    }
+    last_vnp = vnp;
+    orig = orig->next;
+  }
+  return new_list;
+}
+
+
+static ValNodePtr GetFeatureListForRowAndColumn (Uint1 match_type, ValNodePtr match_list, FeatureFieldPtr field)
+{
+  ValNodePtr feature_list = NULL, vnp;
+
+  if (match_list == NULL || field == NULL) return NULL;
+
+  switch (match_type) {
+    case eTableMatchFeatureID:
+      feature_list = ValNodeCopyPtr (match_list);
+      break;
+    case eTableMatchGeneLocusTag:
+      for (vnp = match_list; vnp != NULL; vnp = vnp->next) {
+        ValNodeLink (&feature_list, GetFeatureListForGene (GetFeatdefFromFeatureType(field->type), vnp->data.ptrvalue));
+      }
+      break;
+    case eTableMatchProteinID:
+      for (vnp = match_list; vnp != NULL; vnp = vnp->next) {
+        ValNodeLink (&feature_list, GetFeatureListForProteinBioseq (GetFeatdefFromFeatureType(field->type), vnp->data.ptrvalue));
+      }
+      break;
+    case eTableMatchDbxref:
+      feature_list = ValNodeCopyPtr (match_list);
+      break;
+    case eTableMatchNucID:
+      for (vnp = match_list; vnp != NULL; vnp = vnp->next) {
+        ValNodeLink (&feature_list, GetFeatureListForNucleotideBioseq (GetFeatdefFromFeatureType(field->type), vnp->data.ptrvalue));
+      }
+      break;
+    case eTableMatchBioSource:
+      ValNodeLink (&feature_list, GetFeatureListForBioSourceObjects (match_list, field));
+      break;
+  }
+  return feature_list;
+}
+
+
+static void AddBioSourcesForBioseq (BioseqPtr bsp, ValNodePtr PNTR feature_list)
+{
+  SeqDescrPtr sdp;
+  SeqMgrDescContext context;
+
+  if (feature_list == NULL) return;
+  for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &context);
+        sdp != NULL;
+        sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &context)) {
+    ValNodeAddPointer (feature_list, OBJ_SEQDESC, sdp);
+  }
+}
+
+static void AddBioSourcesForFeature (SeqFeatPtr sfp, ValNodePtr PNTR feature_list)
+{
+  BioseqPtr bsp;
+
+  if (sfp == NULL || feature_list == NULL) return;
+
+  if (sfp->data.choice == SEQFEAT_BIOSRC) {
+    ValNodeAddPointer (feature_list, OBJ_SEQFEAT, sfp);
+  } else {
+    bsp = BioseqFindFromSeqLoc (sfp->location);
+    AddBioSourcesForBioseq (bsp, feature_list);
+  }
+}
+
+
+static ValNodePtr GetBioSourceListForRowAndColumn (Uint1 match_type, ValNodePtr match_list, FeatureFieldPtr field)
+{
+  ValNodePtr feature_list = NULL, vnp;
+
+  if (match_list == NULL || field == NULL) return NULL;
+
+  switch (match_type) {
+    case eTableMatchFeatureID:
+      for (vnp = match_list; vnp != NULL; vnp = vnp->next) {
+        if (vnp->choice == OBJ_SEQFEAT && vnp->data.ptrvalue != NULL) {
+          AddBioSourcesForFeature (vnp->data.ptrvalue, &feature_list);
+        }
+      }
+      break;
+    case eTableMatchGeneLocusTag:
+      for (vnp = match_list; vnp != NULL; vnp = vnp->next) {
+        if (vnp->choice == OBJ_SEQFEAT && vnp->data.ptrvalue != NULL) {
+          AddBioSourcesForFeature (vnp->data.ptrvalue, &feature_list);
+        }
+      }
+      break;
+    case eTableMatchProteinID:
+    case eTableMatchNucID:
+      for (vnp = match_list; vnp != NULL; vnp = vnp->next) {
+        if (vnp->choice == OBJ_BIOSEQ) {
+          AddBioSourcesForBioseq (vnp->data.ptrvalue, &feature_list);
+        }
+      }
+      break;
+    case eTableMatchDbxref:
+      for (vnp = match_list; vnp != NULL; vnp = vnp->next) {
+        if (vnp->choice == OBJ_SEQFEAT && vnp->data.ptrvalue != NULL) {
+          AddBioSourcesForFeature (vnp->data.ptrvalue, &feature_list);
+        }
+      }
+      break;
+    case eTableMatchBioSource:
+      feature_list = ValNodeCopyPtr (match_list);
+      break;
+  }
+  return feature_list;
+}
+
+
+static ValNodePtr GetTargetListForRowAndColumn (Uint1 match_type, ValNodePtr match_list, FieldTypePtr field)
+{
+  ValNodePtr target_list = NULL;
+  FeatureFieldPtr feature_field;
+
+  if (field == NULL) return NULL;
+  switch (field->choice) {
+    case FieldType_source_qual:
+      target_list = GetBioSourceListForRowAndColumn (match_type, match_list, field->data.ptrvalue);
+      break;
+    case FieldType_feature_field:
+      target_list = GetFeatureListForRowAndColumn (match_type, match_list, field->data.ptrvalue);
+      break;
+    case FieldType_cds_gene_prot:
+      feature_field = FeatureFieldFromCDSGeneProtField (field->data.intvalue);
+      target_list = GetFeatureListForRowAndColumn (match_type, match_list, feature_field);
+      feature_field = FeatureFieldFree (feature_field);
+      break;
+  }
+  return target_list;
+}
+
+
+static void ReportMissingTargets (ValNodePtr PNTR perr_list, FieldTypePtr ft, CharPtr match_val, Int4 col_num, Int4 line_num)
+{
+  CharPtr            feat_name;
+  FeatureFieldPtr    field;
+  CharPtr            no_feat_fmt = "No %s feature for %s (column %d, line %d)";
+  CharPtr            no_src_fmt = "No biosource for %s (column %d, line %d)";
+  CharPtr            err_msg;
+
+  if (perr_list == NULL || ft == NULL || match_val == NULL) return;
+
+  switch (ft->choice) {
+    case FieldType_source_qual:
+      err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (no_feat_fmt) 
+                                                    + StringLen (match_val)
+                                                    + 30));
+      sprintf (err_msg, no_src_fmt, match_val, col_num, line_num);
+      ValNodeAddPointer (perr_list, 0, err_msg);
+      break;
+    case FieldType_feature_field:
+      field = (FeatureFieldPtr) ft->data.ptrvalue;
+      if (field != NULL) {
+        feat_name = GetFeatureNameFromFeatureType (field->type);
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (no_feat_fmt) 
+                                                      + StringLen (feat_name)
+                                                      + StringLen (match_val)
+                                                      + 30));
+        sprintf (err_msg, no_feat_fmt, feat_name, match_val, col_num, line_num);
+        ValNodeAddPointer (perr_list, 0, err_msg);
+      }
+      break;
+    case FieldType_cds_gene_prot:
+      field = FeatureFieldFromCDSGeneProtField (ft->data.intvalue);
+      if (field != NULL) {
+        feat_name = GetFeatureNameFromFeatureType (field->type);
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (no_feat_fmt) 
+                                                      + StringLen (feat_name)
+                                                      + StringLen (match_val)
+                                                      + 30));
+        sprintf (err_msg, no_feat_fmt, feat_name, match_val, col_num, line_num);
+        ValNodeAddPointer (perr_list, 0, err_msg);
+      }
+      field = FeatureFieldFree (field);
+      break;
+  }
+}
+
+
+static void ReportEmptyIDColumn (ValNodePtr PNTR perr_list, Int4 line_num)
+{
+  CharPtr            err_msg;
+  CharPtr            missing_id_fmt = "No ID for line %d";
+
+  err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (missing_id_fmt) + 15));
+  sprintf (err_msg, missing_id_fmt, line_num);
+  ValNodeAddPointer (perr_list, 0, err_msg);
+}
+
+static ValNodePtr FindMatchChoiceInLine (ValNodePtr val_vnp, ValNodePtr col_vnp)
+{
+  TabColumnConfigPtr t;
+
+  while (val_vnp != NULL && col_vnp != NULL) {
+    t = (TabColumnConfigPtr) col_vnp->data.ptrvalue;
+    if (t != NULL && t->match_type > 0) {
+      val_vnp->choice = (Uint1) t->match_type;
+      return val_vnp;
+    }
+    val_vnp = val_vnp->next;
+    col_vnp = col_vnp->next;
+  }
+  return NULL;
+}
+
+
+NLM_EXTERN SeqFeatPtr GetmRNAForFeature (SeqFeatPtr sfp)
+{
+  SeqMgrFeatContext fcontext;
+  BioseqPtr         pbsp;
+
+  if (sfp == NULL) return NULL;
+  if (sfp->data.choice == SEQFEAT_PROT) 
+  { 
+    pbsp = BioseqFindFromSeqLoc (sfp->location);
+    sfp = SeqMgrGetCDSgivenProduct (pbsp, NULL);
+    if (sfp == NULL) return NULL;
+  }
+  return SeqMgrGetOverlappingmRNA (sfp->location, &fcontext);
+}
+
+
+NLM_EXTERN Boolean AdjustmRNAProductToMatchProteinProduct (SeqFeatPtr sfp)
+{
+  SeqFeatPtr mrna;
+  ProtRefPtr prp;
+  RnaRefPtr  rrp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT) return FALSE;
+
+  prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+  mrna = GetmRNAForFeature (sfp);
+
+  if (mrna == NULL) return FALSE;
+
+  rrp = (RnaRefPtr) mrna->data.value.ptrvalue;
+  if (rrp == NULL) 
+  {
+    rrp = RnaRefNew();
+    mrna->data.value.ptrvalue = rrp;
+  }
+
+  rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+  if (prp == NULL || prp->name == NULL || StringHasNoText (prp->name->data.ptrvalue))
+  {
+    rrp->ext.choice = 0;
+  }
+  else
+  {
+    rrp->ext.choice = 1;
+    rrp->ext.value.ptrvalue = StringSave (prp->name->data.ptrvalue);
+  }
+  return TRUE;
+}
+
+
+NLM_EXTERN Boolean IsFieldTypeCDSProduct (FieldTypePtr ft)
+{
+  FeatureFieldPtr field;
+  Boolean         rval = FALSE;
+
+  if (ft == NULL) return FALSE;
+  if (ft->choice == FieldType_feature_field) {
+    field = (FeatureFieldPtr) ft->data.ptrvalue;
+    if (field != NULL && field->type == Feature_type_cds
+        && field->field != NULL
+        && field->field->choice == FeatQualChoice_legal_qual
+        && field->field->data.intvalue == Feat_qual_legal_product) {
+      rval = TRUE;
+    }
+  } else if (ft->choice == FieldType_cds_gene_prot) {
+    if (ft->data.intvalue == CDSGeneProt_field_prot_name) {
+      rval = TRUE;
+    }
+  }
+  return rval;
+}
+
+
+static Boolean IsFieldTypeGeneLocusTag (FieldTypePtr ft)
+{
+  FeatureFieldPtr field;
+  Boolean         rval = FALSE;
+
+  if (ft == NULL) return FALSE;
+  if (ft->choice == FieldType_feature_field) {
+    field = (FeatureFieldPtr) ft->data.ptrvalue;
+    if (field != NULL && field->type == Feature_type_gene
+        && field->field != NULL
+        && field->field->choice == FeatQualChoice_legal_qual
+        && field->field->data.intvalue == Feat_qual_legal_locus_tag) {
+      rval = TRUE;
+    }
+  } else if (ft->choice == FieldType_cds_gene_prot) {
+    if (ft->data.intvalue == CDSGeneProt_field_gene_locus_tag) {
+      rval = TRUE;
+    }
+  }
+  return rval;
+}
+
+
+
+NLM_EXTERN ValNodePtr ValidateTabTableValues (ValNodePtr table, ValNodePtr columns)
+{
+  ValNodePtr err_list = NULL;
+  ValNodePtr line_vnp, col_vnp, val_vnp;
+  Int4       line_num, col_num;
+  TabColumnConfigPtr t;
+  ValNodePtr locus_tag_values = NULL, bad_locus_tags = NULL, vnp;
+  CharPtr    bad_format_fmt = "Locus tag %s has incorrect format";
+  CharPtr    dup_fmt = "Locus tag %s appears in the table more than once";
+  CharPtr    inconsistent_fmt = "Locus tag prefix for %s is inconsistent";
+  CharPtr    err_msg;
+
+  if (table == NULL || columns == NULL) {
+    return NULL;
+  }
+
+  for (line_vnp = table, line_num = 1;
+       line_vnp != NULL;
+       line_vnp = line_vnp->next, line_num++) {
+    for (val_vnp = line_vnp->data.ptrvalue, col_vnp = columns, col_num = 1;
+         val_vnp != NULL && col_vnp != NULL;
+         val_vnp = val_vnp->next, col_vnp = col_vnp->next, col_num++) {
+      t = (TabColumnConfigPtr) col_vnp->data.ptrvalue;
+      if (t == NULL || t->match_type > 0 || val_vnp == NULL || StringHasNoText (val_vnp->data.ptrvalue)) {
+        continue;
+      }
+      if (IsFieldTypeGeneLocusTag (t->field)) {
+        ValNodeAddPointer (&locus_tag_values, 0, val_vnp->data.ptrvalue);
+      }
+    }
+  }
+
+  bad_locus_tags = FindBadLocusTagsInList (locus_tag_values);
+  for (vnp = bad_locus_tags; vnp != NULL; vnp = vnp->next) {
+    switch (vnp->choice) {
+      case eLocusTagErrorBadFormat:
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (bad_format_fmt) + StringLen (vnp->data.ptrvalue)));
+        sprintf (err_msg, bad_format_fmt, vnp->data.ptrvalue);
+        ValNodeAddPointer (&err_list, 0, err_msg);
+        break;
+      case eLocusTagErrorDuplicate:
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (dup_fmt) + StringLen (vnp->data.ptrvalue)));
+        sprintf (err_msg, dup_fmt, vnp->data.ptrvalue);
+        ValNodeAddPointer (&err_list, 0, err_msg);
+        break;
+      case eLocusTagErrorInconsistentPrefix:
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (inconsistent_fmt) + StringLen (vnp->data.ptrvalue)));
+        sprintf (err_msg, inconsistent_fmt, vnp->data.ptrvalue);
+        ValNodeAddPointer (&err_list, 0, err_msg);
+        break;
+    }
+  }
+  locus_tag_values = ValNodeFree (locus_tag_values);
+  return err_list;
+}
+
+
+NLM_EXTERN ValNodePtr GetObjectTableForTabTable (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns, ValNodePtr PNTR p_err_list)
+{
+  ValNodePtr err_list = NULL;
+  ValNodePtr line_vnp, val_vnp, col_vnp;
+  ValNodePtr obj_table = NULL, obj_row;
+  Int4       line_num = 1, col_num;
+  Uint2      entityID;
+  ValNodePtr match_list, match_choice, target_list;
+  TabColumnConfigPtr t;
+  CharPtr            err_msg;
+  CharPtr            no_match_fmt = "No match for %s, line %d";
+  CharPtr            bad_col_val_fmt = "Did not set value for column %d, line %d";
+  CharPtr            num_affected_fmt = "%d fields affected";
+  Int4               num_fields_affected = 0;
+
+  if (sep == NULL) {
+    ValNodeAddPointer (&err_list, 0, StringSave ("No SeqEntry"));
+  }
+  if (table == NULL) {
+    ValNodeAddPointer (&err_list, 0, StringSave ("No table"));
+  }
+  if (columns == NULL) {
+    ValNodeAddPointer (&err_list, 0, StringSave ("No column information"));
+  }
+  if (err_list != NULL) {
+    if (p_err_list == NULL) {
+      err_list = ValNodeFreeData (err_list);
+    } else {
+      *p_err_list = err_list;
+    }
+    return NULL;
+  }
+
+  entityID = SeqMgrGetEntityIDForSeqEntry (sep);
+
+  for (line_vnp = table, line_num = 1; line_vnp != NULL; line_vnp = line_vnp->next, line_num++) {
+    obj_row = NULL;
+    match_choice = FindMatchChoiceInLine (line_vnp->data.ptrvalue, columns);
+    if (match_choice == NULL || StringHasNoText (match_choice->data.ptrvalue)) {
+      ReportEmptyIDColumn (&err_list, line_num);
+    } else {
+      match_list = FindMatchForRow (match_choice, entityID, sep);
+      if (match_list == NULL) {
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (no_match_fmt) + StringLen (match_choice->data.ptrvalue) + 15));
+        sprintf (err_msg, no_match_fmt, match_choice->data.ptrvalue, line_num);
+        ValNodeAddPointer (&err_list, 0, err_msg);
+      } else {
+        for (val_vnp = line_vnp->data.ptrvalue, col_vnp = columns, col_num = 1;
+             col_vnp != NULL;
+             col_vnp = col_vnp->next, col_num++) {
+          target_list = NULL;
+          t = (TabColumnConfigPtr) col_vnp->data.ptrvalue;
+          if (t == NULL || t->match_type > 0 
+              || (t->skip_blank && (val_vnp == NULL || StringHasNoText (val_vnp->data.ptrvalue)))) {
+            /* no targets */
+          } else {         
+            target_list = GetTargetListForRowAndColumn (match_choice->choice, match_list, t->field);
+            if (target_list == NULL) {
+              ReportMissingTargets (&err_list, t->field, match_choice->data.ptrvalue, col_num, line_num); 
+            }
+          }
+          ValNodeAddPointer (&obj_row, 0, target_list);
+          if (val_vnp != NULL) {
+            val_vnp = val_vnp->next;
+          }
+        }
+      }
+    }
+    ValNodeAddPointer (&obj_table, 0, obj_row);
+  }
+
+  if (err_list != NULL) {
+    if (p_err_list == NULL) {
+      err_list = ValNodeFreeData (err_list);
+    } else {
+      *p_err_list = err_list;
+    }
+  }  
+  return obj_table;
+}
+
+
+NLM_EXTERN ValNodePtr FreeObjectTableForTabTable (ValNodePtr table)
+{
+  ValNodePtr vnp_next, vnp_row, vnp_row_next;
+
+  while (table != NULL) {
+    vnp_next = table->next;
+    table->next = NULL;
+    vnp_row = table->data.ptrvalue;
+    while (vnp_row != NULL) {
+      vnp_row_next = vnp_row->next;
+      vnp_row->next = NULL;
+      vnp_row->data.ptrvalue = ValNodeFree (vnp_row->data.ptrvalue);
+      vnp_row = ValNodeFree (vnp_row);
+      vnp_row = vnp_row_next;
+    }
+    table = ValNodeFree (table);
+    table = vnp_next;
+  }
+  return table;
+}
+
+
+typedef struct countfeat {
+  Uint1 featdef;
+  Int4 num;
+} CountFeatData, PNTR CountFeatPtr;
+
+
+static void CountFeaturesCallback (SeqFeatPtr sfp, Pointer userdata)
+{
+  CountFeatPtr p;
+
+  if (sfp == NULL || userdata == NULL) return;
+
+  p = (CountFeatPtr) userdata;
+  if (sfp->idx.subtype == p->featdef) {
+    p->num++;
+  }
+}
+
+static void CountBioSourceDescriptorsCallback (SeqDescrPtr sdp, Pointer userdata)
+{
+  Int4Ptr p;
+
+  p = (Int4Ptr) userdata;
+  if (sdp != NULL && p != NULL && sdp->choice == Seq_descr_source) {
+    (*p)++;
+  }
+}
+
+
+static ValNodePtr CountObjectsForColumnFields (SeqEntryPtr sep, ValNodePtr columns)
+{
+  ValNodePtr count_list = NULL, vnp;
+  TabColumnConfigPtr t;
+  CountFeatData d;
+  FeatureFieldPtr f;
+  Int4 num;
+  Uint1 featdef = 0;
+
+  d.featdef = 0;
+  d.num = 0;
+  for (vnp = columns; vnp != NULL; vnp = vnp->next) {
+    num = 0;
+    t = (TabColumnConfigPtr) vnp->data.ptrvalue;
+    if (t != NULL && t->match_type == 0 && t->field != NULL) {
+      switch (t->field->choice) {
+        case FieldType_source_qual:
+          if (featdef != FEATDEF_BIOSRC) {
+            d.featdef = FEATDEF_BIOSRC;
+            d.num = 0;
+            VisitFeaturesInSep (sep, &d, CountFeaturesCallback);
+            VisitDescriptorsInSep (sep, &(d.num), CountBioSourceDescriptorsCallback);
+          }
+          num = d.num;
+          break;
+        case FieldType_feature_field:
+          f = (FeatureFieldPtr) t->field->data.ptrvalue;
+          if (f != NULL) {
+            featdef = GetFeatdefFromFeatureType(f->type);
+            if (featdef != d.featdef) {
+              d.featdef = featdef;
+              d.num = 0;
+              VisitFeaturesInSep (sep, &d, CountFeaturesCallback);
+            }
+            num = d.num;
+          }
+          break;
+        case FieldType_cds_gene_prot:
+          f = FeatureFieldFromCDSGeneProtField (t->field->data.intvalue);
+          if (f != NULL) {
+            featdef = GetFeatdefFromFeatureType(f->type);
+            if (featdef != d.featdef) {
+              d.featdef = featdef;
+              d.num = 0;
+              VisitFeaturesInSep (sep, &d, CountFeaturesCallback);
+            }
+            num = d.num;
+          }
+          f = FeatureFieldFree (f);
+          break;
+      }
+    }
+    ValNodeAddInt (&count_list, 0, num);
+  }
+  return count_list;
+}
+
+
+NLM_EXTERN ValNodePtr ApplyTableValuesToObjectTable (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns, ValNodePtr obj_table)
+{
+  ValNodePtr val_line_vnp, obj_line_vnp;
+  ValNodePtr val_vnp, obj_vnp, col_vnp;
+  ValNodePtr target_vnp;
+  TabColumnConfigPtr t;
+  CharPtr val, qual_name;
+  ValNodePtr         err_list = NULL, count_list, count_affected_list = NULL, count_vnp, count_tot_vnp;
+  CharPtr            err_msg;
+  CharPtr            bad_col_val_fmt = "Did not set value for column %d, line %d";
+  CharPtr            num_affected_fmt = "%d fields affected";
+  CharPtr            col_num_affected_fmt = "For %s (column %d), %d items were affected out of %d total";
+  Int4 num_fields_affected = 0, col_num, line_num, num_this_column;
+  Boolean success;
+  ValNodePtr count_msg = NULL;
+
+  count_list = CountObjectsForColumnFields (sep, columns);
+
+  for (val_line_vnp = table, obj_line_vnp = obj_table, line_num = 1;
+       val_line_vnp != NULL && obj_line_vnp != NULL;
+       val_line_vnp = val_line_vnp->next, obj_line_vnp = obj_line_vnp->next, line_num++) {
+    val_vnp = val_line_vnp->data.ptrvalue;
+    obj_vnp = obj_line_vnp->data.ptrvalue;
+    col_vnp = columns;
+    col_num = 1;
+    count_vnp = count_affected_list;
+    while (obj_vnp != NULL && col_vnp != NULL) {
+      num_this_column = 0;
+      if (obj_vnp->data.ptrvalue != NULL) {
+        t = (TabColumnConfigPtr) col_vnp->data.ptrvalue;
+        if (t == NULL || t->match_type > 0 
+            || (t->skip_blank && (val_vnp == NULL || StringHasNoText (val_vnp->data.ptrvalue)))) {
+          /* ignore column or skip blank value */
+        } else {
+          if (val_vnp == NULL || val_vnp->data.ptrvalue == NULL) {
+            val = "";
+          } else {
+            val = val_vnp->data.ptrvalue;
+          }
+          for (target_vnp = obj_vnp->data.ptrvalue; target_vnp != NULL; target_vnp = target_vnp->next) {
+            if (val[0] == 0) {
+              success = RemoveFieldValueForObject (target_vnp->choice, target_vnp->data.ptrvalue, t->field, NULL);
+            } else {
+              success = SetFieldValueForObject (target_vnp->choice, target_vnp->data.ptrvalue, t->field, NULL,
+                                                val_vnp->data.ptrvalue, t->existing_text);
+            }
+            if (success) {
+              num_fields_affected++;
+              num_this_column++;
+              if (t->match_mrna && IsFieldTypeCDSProduct (t->field)
+                  && target_vnp->choice == OBJ_SEQFEAT) {
+                if (AdjustmRNAProductToMatchProteinProduct (target_vnp->data.ptrvalue)) {
+                  num_fields_affected++;
+                }
+              }
+            } else {
+              err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (bad_col_val_fmt) + 30));
+              sprintf (err_msg, bad_col_val_fmt, col_num, line_num);
+              ValNodeAddPointer (&err_list, 0, err_msg);
+            }
+          }
+        }
+      }
+      if (val_vnp != NULL) {
+        val_vnp = val_vnp->next;
+      }
+      if (count_vnp == NULL) {
+        ValNodeAddInt (&count_affected_list, 0, num_this_column);
+      } else {
+        count_vnp->data.intvalue ++;
+        count_vnp = count_vnp->next;
+      }
+      obj_vnp = obj_vnp->next;
+      col_vnp = col_vnp->next;
+      col_num++;
+    }
+  }
+
+  /* put message at top of list for number of fields affected */
+  err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (num_affected_fmt) + 15));
+  sprintf (err_msg, num_affected_fmt, num_fields_affected);
+  ValNodeAddPointer (&count_msg, 0, err_msg);
+
+  /* if any affected, list number of fields per column, and the total in the record */
+  if (num_fields_affected > 0) {
+    for (count_vnp = count_affected_list, count_tot_vnp = count_list, col_vnp = columns, col_num = 1;
+         count_vnp != NULL && count_tot_vnp != NULL && col_vnp != NULL;
+         count_vnp = count_vnp->next, count_tot_vnp = count_tot_vnp->next, col_vnp = col_vnp->next, col_num++) {
+      t = (TabColumnConfigPtr) col_vnp->data.ptrvalue;
+      if (t != NULL && t->match_type == 0) {
+        qual_name = SummarizeFieldType (t->field);
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (col_num_affected_fmt) + StringLen (qual_name) + 45));
+        sprintf (err_msg, col_num_affected_fmt, qual_name, col_num, count_vnp->data.intvalue, count_tot_vnp->data.intvalue);      
+        ValNodeAddPointer (&count_msg, 0, err_msg);
+        qual_name = MemFree (qual_name);
+      }
+    }
+  }
+
+  ValNodeLink (&count_msg, err_list);
+
+  count_list = ValNodeFree (count_list);
+  count_affected_list = ValNodeFree (count_affected_list);
+
+  return count_msg;
+}
+
+
+static int LIBCALLBACK SortVnpByChoiceAndPtrvalue (VoidPtr ptr1, VoidPtr ptr2)
+
+{
+  ValNodePtr  vnp1;
+  ValNodePtr  vnp2;
+
+  if (ptr1 != NULL && ptr2 != NULL) {
+    vnp1 = *((ValNodePtr PNTR) ptr1);
+    vnp2 = *((ValNodePtr PNTR) ptr2);
+    if (vnp1 != NULL && vnp2 != NULL) {
+      if (vnp1->choice > vnp2->choice) {
+        return 1;
+      } else if (vnp1->choice < vnp2->choice) {
+        return -1;
+      } else if (vnp1->data.ptrvalue > vnp2->data.ptrvalue) {
+        return 1;
+      } else if (vnp2->data.ptrvalue < vnp2->data.ptrvalue) {
+        return -1;
+      } else {
+        return 0;
+      }
+    }
+  }
+  return 0;
+}
+
+
+NLM_EXTERN ValNodePtr CheckObjTableForRowsThatApplyToTheSameDestination (ValNodePtr obj_table)
+{
+  Int4 col_num;
+  ValNodePtr line_vnp, col_vnp, obj_vnp, vnp;
+  ValNodePtr col_list = NULL, col_obj_list;
+  Boolean any_column_values_left;
+  ValNodePtr err_list = NULL;
+  Boolean found_multi;
+  CharPtr multi_fmt = "Multiple rows apply to the same object for column %d";
+  CharPtr err_msg;
+  
+  /* now, for each row, get pointer to first column */
+  for (line_vnp = obj_table; line_vnp != NULL; line_vnp = line_vnp->next) {
+    ValNodeAddPointer (&col_list, 0, line_vnp->data.ptrvalue);
+  }
+
+  /* now for each column, make a list of all features in the column, then sort to see if there are duplicates */
+  any_column_values_left = TRUE;
+  col_num = 1;
+  while (any_column_values_left) {
+    any_column_values_left = FALSE;
+    col_obj_list = NULL;
+    for (vnp = col_list; vnp != NULL; vnp = vnp->next) {
+      col_vnp = vnp->data.ptrvalue;
+      if (col_vnp != NULL) {
+        obj_vnp = col_vnp->data.ptrvalue;
+        ValNodeLink (&col_obj_list, ValNodeCopyPtr (obj_vnp));
+        vnp->data.ptrvalue = col_vnp->next;
+        any_column_values_left = TRUE;
+      }
+    }
+    if (col_obj_list != NULL) {
+      found_multi = FALSE;
+      col_obj_list = ValNodeSort (col_obj_list, SortVnpByChoiceAndPtrvalue);
+      for (vnp = col_obj_list; vnp != NULL && vnp->next != NULL && !found_multi; vnp = vnp->next) {
+        if (vnp->choice == vnp->next->choice
+            && vnp->data.ptrvalue == vnp->next->data.ptrvalue) {
+          found_multi = TRUE;
+        }
+      }
+      if (found_multi) {
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (multi_fmt)
+                                                      + 30));
+        sprintf (err_msg, multi_fmt, col_num);
+        ValNodeAddPointer (&err_list, col_num, err_msg);
+      }
+      col_obj_list = ValNodeFree (col_obj_list);
+    }
+    col_num++;
+  }
+  col_list = ValNodeFree (col_list);
+  return err_list;
+}
+
+
+NLM_EXTERN ValNodePtr CheckObjTableForExistingText (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns, ValNodePtr obj_table)
+{
+  ValNodePtr err_list = NULL, vnp;
+  ValNodePtr val_line_vnp, obj_line_vnp;
+  ValNodePtr val_vnp, obj_vnp, col_vnp;
+  Int4       line_num = 1, col_num, num_existing_text = 0;
+  Uint2      entityID;
+  TabColumnConfigPtr t;
+  CharPtr            err_msg, str, qual_name, val;
+  CharPtr            already_has_val_fmt = "%s already has value '%s' (column %d), line %d.  Replacement is '%s'";
+  CharPtr            num_existing_text_fmt = "%d fields already have text.";
+  CharPtr            mrna_warn_fmt = "%d coding region features have mRNAs, but %d do not.";
+  ValNodePtr         target_list, feat_vnp;
+  Int4               num_with_mrna = 0, num_without_mrna = 0;
+
+  if (sep == NULL) {
+    ValNodeAddPointer (&err_list, 1, StringSave ("No SeqEntry"));
+  }
+  if (table == NULL) {
+    ValNodeAddPointer (&err_list, 1, StringSave ("No table"));
+  }
+  if (columns == NULL) {
+    ValNodeAddPointer (&err_list, 1, StringSave ("No column information"));
+  }
+  if (err_list != NULL) {
+    return err_list;
+  }
+
+  entityID = SeqMgrGetEntityIDForSeqEntry (sep);
+
+  for (val_line_vnp = table, obj_line_vnp = obj_table, line_num = 1;
+       val_line_vnp != NULL && obj_line_vnp != NULL;
+       val_line_vnp = val_line_vnp->next, obj_line_vnp = obj_line_vnp->next, line_num++) {
+    val_vnp = val_line_vnp->data.ptrvalue;
+    obj_vnp = obj_line_vnp->data.ptrvalue;
+    col_vnp = columns;
+    if (val_vnp == NULL || obj_vnp == NULL) continue;
+    col_num = 1;
+    while (obj_vnp != NULL && col_vnp != NULL) {
+      if (obj_vnp->data.ptrvalue != NULL) {
+        t = (TabColumnConfigPtr) col_vnp->data.ptrvalue;
+        if (t == NULL || t->match_type > 0 
+            || (t->skip_blank && (val_vnp == NULL || StringHasNoText (val_vnp->data.ptrvalue)))) {
+          /* ignore column or skip blank value */
+        } else {
+          target_list = obj_vnp->data.ptrvalue;
+          if (val_vnp == NULL || val_vnp->data.ptrvalue == NULL) {
+            val = "";
+          } else {
+            val = val_vnp->data.ptrvalue;
+          }
+          for (feat_vnp = target_list; feat_vnp != NULL; feat_vnp = feat_vnp->next) {
+            /* check for existing text */
+            str = GetFieldValueForObject (feat_vnp->choice, feat_vnp->data.ptrvalue, t->field, NULL);
+            if (!StringHasNoText (str)) {
+              qual_name = SummarizeFieldType (t->field);
+              err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (already_has_val_fmt)
+                                                          + StringLen (qual_name) + StringLen (str)  
+                                                          + StringLen (val)
+                                                          + 30));
+              sprintf (err_msg, already_has_val_fmt, qual_name, str, col_num, line_num, val);
+              ValNodeAddPointer (&err_list, col_num, err_msg);
+              num_existing_text ++;
+            }
+            str = MemFree (str);
+            /* check for mrna if changing CDS product */
+            if (IsFieldTypeCDSProduct (t->field) && feat_vnp->choice == OBJ_SEQFEAT) {
+              if (GetmRNAForFeature (feat_vnp->data.ptrvalue) != NULL) {
+                num_with_mrna++;
+              } else {
+                num_without_mrna++;
+              }
+            }
+          }
+        }
+      }
+      if (val_vnp != NULL) {
+        val_vnp = val_vnp->next;
+      }
+      obj_vnp = obj_vnp->next;
+      col_vnp = col_vnp->next;
+      col_num++;
+    }
+  }          
+  if (num_existing_text > 0) {
+    err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (num_existing_text_fmt)
+                                                + 15));
+    sprintf (err_msg, num_existing_text_fmt, num_existing_text);
+    vnp = ValNodeNew (NULL);
+    vnp->choice = 0;
+    vnp->data.ptrvalue = err_msg;
+    vnp->next = err_list;
+    err_list = vnp;
+  }
+  if (num_with_mrna > 0 && num_without_mrna > 0) {
+    err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (mrna_warn_fmt)
+                                                + 30));
+    sprintf (err_msg, mrna_warn_fmt, num_with_mrna, num_without_mrna);
+    vnp = ValNodeNew (NULL);
+    vnp->choice = 0;
+    vnp->data.ptrvalue = err_msg;
+    vnp->next = err_list;
+    err_list = vnp;
+  }    
+
+  return err_list;
+}
+
+
+NLM_EXTERN ValNodePtr ApplyTableToFeatures (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns)
+{
+  ValNodePtr err_list = NULL;
+  ValNodePtr line_vnp, val_vnp, col_vnp;
+  Int4       line_num = 1, col_num;
+  Uint2      entityID;
+  ValNodePtr match_list, match_choice, target_list, feat_vnp, vnp;
+  TabColumnConfigPtr t;
+  CharPtr            err_msg;
+  CharPtr            no_match_fmt = "No match for %s, line %d";
+  CharPtr            bad_col_val_fmt = "Did not set value for column %d, line %d";
+  CharPtr            num_affected_fmt = "%d fields affected";
+  Int4               num_fields_affected = 0;
+  CharPtr            val;
+  Boolean            success;
+
+  if (sep == NULL) {
+    ValNodeAddPointer (&err_list, 0, StringSave ("No SeqEntry"));
+  }
+  if (table == NULL) {
+    ValNodeAddPointer (&err_list, 0, StringSave ("No table"));
+  }
+  if (columns == NULL) {
+    ValNodeAddPointer (&err_list, 0, StringSave ("No column information"));
+  }
+  if (err_list != NULL) {
+    return err_list;
+  }
+
+  entityID = SeqMgrGetEntityIDForSeqEntry (sep);
+
+  for (line_vnp = table, line_num = 1; line_vnp != NULL; line_vnp = line_vnp->next, line_num++) {
+    match_choice = FindMatchChoiceInLine (line_vnp->data.ptrvalue, columns);
+    if (match_choice == NULL || StringHasNoText (match_choice->data.ptrvalue)) {
+      ReportEmptyIDColumn (&err_list, line_num);
+    } else {
+      match_list = FindMatchForRow (match_choice, entityID, sep);
+      if (match_list == NULL) {
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (no_match_fmt) + StringLen (match_choice->data.ptrvalue) + 15));
+        sprintf (err_msg, no_match_fmt, match_choice->data.ptrvalue, line_num);
+        ValNodeAddPointer (&err_list, 0, err_msg);
+      } else {
+        for (val_vnp = line_vnp->data.ptrvalue, col_vnp = columns, col_num = 1;
+             col_vnp != NULL;
+             col_vnp = col_vnp->next, col_num++) {
+          t = (TabColumnConfigPtr) col_vnp->data.ptrvalue;
+          if (t == NULL || t->match_type > 0 
+              || (t->skip_blank && (val_vnp == NULL || StringHasNoText (val_vnp->data.ptrvalue)))) {
+            if (val_vnp != NULL) {
+              val_vnp = val_vnp->next;
+            }            
+            continue;
+          }
+          
+          target_list = GetTargetListForRowAndColumn (match_choice->choice, match_list, t->field);
+          if (target_list == NULL) {
+            ReportMissingTargets (&err_list, t->field, match_choice->data.ptrvalue, col_num, line_num); 
+          } else {
+            if (val_vnp == NULL || val_vnp->data.ptrvalue == NULL) {
+              val = "";
+            } else {
+              val = val_vnp->data.ptrvalue;
+            }
+            for (feat_vnp = target_list; feat_vnp != NULL; feat_vnp = feat_vnp->next) {
+              if (val[0] == 0) {
+                success = RemoveFieldValueForObject (feat_vnp->choice, feat_vnp->data.ptrvalue, t->field, NULL);
+              } else {
+                success = SetFieldValueForObject (feat_vnp->choice, feat_vnp->data.ptrvalue, t->field, NULL,
+                                                  val_vnp->data.ptrvalue, t->existing_text);
+              }
+              if (success) {
+                num_fields_affected++;
+                if (t->match_mrna && IsFieldTypeCDSProduct (t->field)
+                    && feat_vnp->choice == OBJ_SEQFEAT) {
+                  if (AdjustmRNAProductToMatchProteinProduct (feat_vnp->data.ptrvalue)) {
+                    num_fields_affected++;
+                  }
+                }
+              } else {
+                err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (bad_col_val_fmt) + 30));
+                sprintf (err_msg, bad_col_val_fmt, col_num, line_num);
+                ValNodeAddPointer (&err_list, 0, err_msg);
+              }
+            }
+          }
+          target_list = ValNodeFree (target_list);
+          if (val_vnp != NULL) {
+            val_vnp = val_vnp->next;
+          }
+        }
+      }
+      match_list = ValNodeFree (match_list);
+    }
+  }
+  
+  err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (num_affected_fmt) + 15));
+  sprintf (err_msg, num_affected_fmt, num_fields_affected);
+  vnp = ValNodeNew (NULL);
+  vnp->data.ptrvalue = err_msg;
+  vnp->next = err_list;
+  err_list = vnp;
+
+  return err_list;
+}
+
+
+NLM_EXTERN ValNodePtr CheckTableForExistingText (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns)
+{
+  ValNodePtr err_list = NULL, vnp;
+  ValNodePtr line_vnp, val_vnp, col_vnp;
+  Int4       line_num = 1, col_num, num_existing_text = 0;
+  Uint2      entityID;
+  TabColumnConfigPtr t;
+  CharPtr            err_msg, str, qual_name, val;
+  CharPtr            no_match_fmt = "No match for %s, line %d";
+  CharPtr            no_feat_fmt = "No %s feature for %s (column %d, line %d)";
+  CharPtr            already_has_val_fmt = "%s already has value '%s' (column %d), line %d.  Replacement is '%s'";
+  CharPtr            num_existing_text_fmt = "%d fields already have text.";
+  ValNodePtr         match_choice, match_list;
+  ValNodePtr         target_list, feat_vnp;
+
+  if (sep == NULL) {
+    ValNodeAddPointer (&err_list, 1, StringSave ("No SeqEntry"));
+  }
+  if (table == NULL) {
+    ValNodeAddPointer (&err_list, 1, StringSave ("No table"));
+  }
+  if (columns == NULL) {
+    ValNodeAddPointer (&err_list, 1, StringSave ("No column information"));
+  }
+  if (err_list != NULL) {
+    return err_list;
+  }
+
+  entityID = SeqMgrGetEntityIDForSeqEntry (sep);
+
+  for (line_vnp = table, line_num = 1; line_vnp != NULL; line_vnp = line_vnp->next, line_num++) {
+    match_choice = FindMatchChoiceInLine (line_vnp->data.ptrvalue, columns);
+    if (match_choice == NULL || StringHasNoText (match_choice->data.ptrvalue)) {
+      ReportEmptyIDColumn (&err_list, line_num);
+    } else {
+      match_list = FindMatchForRow (match_choice, entityID, sep);
+      if (match_list == NULL) {
+        err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (no_match_fmt) + StringLen (match_choice->data.ptrvalue) + 15));
+        sprintf (err_msg, no_match_fmt, match_choice->data.ptrvalue, line_num);
+        ValNodeAddPointer (&err_list, 0, err_msg);
+      } else {
+        for (val_vnp = line_vnp->data.ptrvalue, col_vnp = columns, col_num = 1;
+             col_vnp != NULL;
+             col_vnp = col_vnp->next, col_num++) {
+          t = (TabColumnConfigPtr) col_vnp->data.ptrvalue;
+          if (t == NULL || t->match_type > 0 
+              || (t->skip_blank && (val_vnp == NULL || StringHasNoText (val_vnp->data.ptrvalue)))) {
+            if (val_vnp != NULL) {
+              val_vnp = val_vnp->next;
+            }            
+            continue;
+          }
+          target_list = GetTargetListForRowAndColumn (match_choice->choice, match_list, t->field);
+          if (target_list == NULL) {
+            ReportMissingTargets (&err_list, t->field, match_choice->data.ptrvalue, col_num, line_num); 
+          } else {
+            if (val_vnp == NULL || val_vnp->data.ptrvalue == NULL) {
+              val = "";
+            } else {
+              val = val_vnp->data.ptrvalue;
+            }
+            for (feat_vnp = target_list; feat_vnp != NULL; feat_vnp = feat_vnp->next) {
+              str = GetFieldValueForObject (feat_vnp->choice, feat_vnp->data.ptrvalue, t->field, NULL);
+              if (!StringHasNoText (str)) {
+                qual_name = SummarizeFieldType (t->field);
+                err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (already_has_val_fmt)
+                                                            + StringLen (qual_name) + StringLen (str)  
+                                                            + StringLen (val)
+                                                            + 30));
+                sprintf (err_msg, already_has_val_fmt, qual_name, str, col_num, line_num, val);
+                ValNodeAddPointer (&err_list, col_num, err_msg);
+                num_existing_text ++;
+              }
+              str = MemFree (str);
+            }
+          }
+          target_list = ValNodeFree (target_list);
+          if (val_vnp != NULL) {
+            val_vnp = val_vnp->next;
+          }
+        }
+      }
+      match_list = ValNodeFree (match_list);
+    }
+  }          
+  if (num_existing_text > 0) {
+    err_msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (num_existing_text_fmt)
+                                                + 15));
+    sprintf (err_msg, num_existing_text_fmt, num_existing_text);
+    vnp = ValNodeNew (NULL);
+    vnp->choice = 0;
+    vnp->data.ptrvalue = err_msg;
+    vnp->next = err_list;
+    err_list = vnp;
+  }
+
+  return err_list;
+}
+
+
+
+
+
diff --git a/api/macroapi.h b/api/macroapi.h
new file mode 100644
index 00000000..dbd90472
--- /dev/null
+++ b/api/macroapi.h
@@ -0,0 +1,184 @@
+/*   macro_i.h
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  macro_i.h
+*
+* Author:  Colleen Bollin
+*
+* Version Creation Date:   11/15/2007
+*
+* $Revision: 1.31 $
+*
+* File Description: 
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* Date     Name        Description of modification
+* -------  ----------  -----------------------------------------------------
+*
+*
+* ==========================================================================
+*/
+
+#ifndef _macroapi_h_
+#define _macroapi_h_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+NLM_EXTERN Int4 GetFeatdefFromFeatureType (Int4 feature_type);
+NLM_EXTERN CharPtr GetFeatureNameFromFeatureType (Int4 feature_type);
+NLM_EXTERN Int4 GetFeatureTypeByName (CharPtr feat_name);
+NLM_EXTERN void AddImportFeaturesToChoiceList (ValNodePtr PNTR feature_type_list);
+NLM_EXTERN void AddAllFeaturesToChoiceList (ValNodePtr PNTR feature_type_list);
+NLM_EXTERN CharPtr GetFeatQualName (Int4 featqual); 
+NLM_EXTERN Int4 GetFeatQualByName (CharPtr qualname); 
+NLM_EXTERN Int4 GetNumFeatQual (void);
+NLM_EXTERN void AddAllFeatureFieldsToChoiceList (ValNodePtr PNTR field_list);
+NLM_EXTERN CharPtr GetSourceQualName (Int4 srcqual);
+NLM_EXTERN Int4 GetSourceQualTypeByName (CharPtr qualname);
+NLM_EXTERN ValNodePtr GetSourceQualList (void);
+NLM_EXTERN Boolean IsNonTextSourceQual (Int4 srcqual);
+NLM_EXTERN Int4 GenomeFromSrcLoc (Int4 srcloc);
+NLM_EXTERN CharPtr LocNameFromGenome (Int4 genome);
+NLM_EXTERN ValNodePtr GetLocationList (Boolean for_remove); 
+NLM_EXTERN Int4 OriginFromSrcOrig (Int4 srcorig);
+NLM_EXTERN CharPtr OriginNameFromOrigin (Int4 origin);
+NLM_EXTERN ValNodePtr GetOriginList (Boolean for_remove);
+NLM_EXTERN BioSourcePtr GetBioSourceFromObject (Uint1 choice, Pointer data);
+NLM_EXTERN CharPtr CDSGeneProtNameFromField (Int4 field); 
+NLM_EXTERN CharPtr CDSGeneProtFeatureNameFromFeatureType (Int4 feature_type);
+NLM_EXTERN void AddAllCDSGeneProtFieldsToChoiceList (ValNodePtr PNTR field_list);
+NLM_EXTERN void AddAllCDSGeneProtFeaturesToChoiceList (ValNodePtr PNTR field_list);
+NLM_EXTERN FeatureFieldPtr FeatureFieldFromCDSGeneProtField (Uint2 cds_gene_prot_field);
+
+NLM_EXTERN CharPtr BiomolNameFromBiomol (Int4 biomol);
+NLM_EXTERN Int4 BiomolFromMoleculeType (Int4 molecule_type);
+NLM_EXTERN ValNodePtr GetMoleculeTypeList (void);
+NLM_EXTERN CharPtr TechNameFromTech (Int4 tech);
+NLM_EXTERN Int4 TechFromTechniqueType (Int4 technique_type);
+NLM_EXTERN ValNodePtr GetTechniqueTypeList (void);
+NLM_EXTERN Int4 CompletenessFromCompletednessType (Int4 completedness_type);
+NLM_EXTERN CharPtr CompletenessNameFromCompleteness (Int4 completeness); 
+NLM_EXTERN ValNodePtr GetCompletednessTypeList (void);
+NLM_EXTERN Int4 MolFromMoleculeClassType (Int4 moleculeclass_type);
+NLM_EXTERN CharPtr MolNameFromMol (Int4 mol); 
+NLM_EXTERN ValNodePtr GetMoleculeClassTypeList (void);
+NLM_EXTERN Int4 TopologyFromTopologyType (Int4 topology_type);
+NLM_EXTERN CharPtr TopologyNameFromTopology (Int4 topology);
+NLM_EXTERN ValNodePtr GetTopologyTypeList (void);
+NLM_EXTERN Int4 StrandFromStrandType (Int4 strand_type);
+NLM_EXTERN CharPtr StrandNameFromStrand (Int4 strand);
+NLM_EXTERN ValNodePtr GetStrandTypeList (void);
+
+
+
+NLM_EXTERN FieldTypePtr GetFromFieldFromFieldPair (FieldPairTypePtr fieldpair);
+NLM_EXTERN FieldTypePtr GetToFieldFromFieldPair (FieldPairTypePtr fieldpair);
+NLM_EXTERN Uint1 FieldTypeFromAECRAction (AECRActionPtr action);
+NLM_EXTERN Uint1 GetBiomolForRnaType (Int4 rnatype);
+NLM_EXTERN CharPtr GetBiomolNameForRnaType (Int4 rnatype);
+NLM_EXTERN void AddAllRNASubtypesToChoiceList (ValNodePtr PNTR field_list);
+
+NLM_EXTERN CharPtr GetSourceQualFromBioSource (BioSourcePtr biop, SourceQualChoicePtr scp, StringConstraintPtr constraint);
+NLM_EXTERN CharPtr GetQualFromFeature (SeqFeatPtr sfp, FeatureFieldPtr field, StringConstraintPtr scp);
+NLM_EXTERN Boolean SetSourceQualInBioSource (BioSourcePtr biop, SourceQualChoicePtr scp, StringConstraintPtr constraint, CharPtr value, Uint2 existing_text);
+
+
+NLM_EXTERN Boolean IsStringConstraintEmpty (StringConstraintPtr scp);
+NLM_EXTERN Boolean DoesSingleStringMatchConstraint (CharPtr str, StringConstraintPtr scp);
+NLM_EXTERN Boolean DoesStringMatchConstraint (CharPtr str, StringConstraintPtr scp);
+NLM_EXTERN Boolean IsSourceConstraintEmpty (SourceConstraintPtr scp);
+NLM_EXTERN Boolean DoesBiosourceMatchConstraint (BioSourcePtr biop, SourceConstraintPtr scp);
+NLM_EXTERN Boolean IsSequenceConstraintEmpty (SequenceConstraintPtr constraint);
+NLM_EXTERN Boolean IsCDSGeneProtQualConstraintEmpty (CDSGeneProtQualConstraintPtr constraint);
+NLM_EXTERN ValNodePtr GetObjectListForAECRAction (SeqEntryPtr sep, AECRActionPtr action);
+NLM_EXTERN Int4 DoApplyActionToObjectList (ApplyActionPtr action, ValNodePtr object_list, StringConstraintPtr scp);
+NLM_EXTERN Int4 DoEditActionToObjectList (EditActionPtr action, ValNodePtr object_list);
+NLM_EXTERN Int4 DoConvertActionToObjectList (ConvertActionPtr action, ValNodePtr object_list, StringConstraintPtr scp);
+NLM_EXTERN Int4 DoCopyActionToObjectList (CopyActionPtr action, ValNodePtr object_list, StringConstraintPtr scp);
+NLM_EXTERN Int4 DoSwapActionToObjectList (SwapActionPtr action, ValNodePtr object_list, StringConstraintPtr scp);
+NLM_EXTERN Int4 DoRemoveActionToObjectList (RemoveActionPtr action, ValNodePtr object_list, StringConstraintPtr scp);
+NLM_EXTERN Int4 DoParseActionToObjectList (AECRParseActionPtr action, ValNodePtr object_list, StringConstraintPtr scp);
+NLM_EXTERN StringConstraintPtr FindStringConstraintInConstraintSetForField (FieldTypePtr field, ConstraintChoiceSetPtr csp);
+NLM_EXTERN StringConstraintPtr StringConstraintFromFieldEdit (FieldEditPtr edit);
+
+
+
+
+NLM_EXTERN void ApplyMacroToSeqEntry (SeqEntryPtr sep, ValNodePtr macro, Int4Ptr pNumFields, Int4Ptr pNumFeat);
+
+/* for generating text representations of macro objects */
+NLM_EXTERN CharPtr SummarizeSourceQual (ValNodePtr field);
+NLM_EXTERN CharPtr FeatureFieldLabel (CharPtr feature_name, ValNodePtr field);
+NLM_EXTERN Boolean IsFieldTypeEmpty (FieldTypePtr field);
+NLM_EXTERN CharPtr SummarizeFieldType (ValNodePtr vnp);
+
+typedef enum {
+  eTableMatchFeatureID = 1,
+  eTableMatchGeneLocusTag,
+  eTableMatchProteinID,
+  eTableMatchDbxref,
+  eTableMatchNucID,
+  eTableMatchBioSource
+} ETableMatchType;
+
+
+
+typedef struct tabcolumnconfig {
+  Uint2 match_type;
+  FieldTypePtr field;
+  Uint2 existing_text;
+  Boolean skip_blank;
+  Boolean match_mrna;
+} TabColumnConfigData, PNTR TabColumnConfigPtr;
+
+NLM_EXTERN TabColumnConfigPtr TabColumnConfigNew (void);
+NLM_EXTERN TabColumnConfigPtr TabColumnConfigFree (TabColumnConfigPtr t);
+NLM_EXTERN TabColumnConfigPtr TabColumnConfigCopy (TabColumnConfigPtr orig);
+NLM_EXTERN ValNodePtr TabColumnConfigListFree (ValNodePtr columns);
+NLM_EXTERN ValNodePtr TabColumnConfigListCopy (ValNodePtr orig);
+NLM_EXTERN ValNodePtr ValidateTabTableValues (ValNodePtr table, ValNodePtr columns);
+NLM_EXTERN ValNodePtr ValidateFeatureFieldColumnNames (ValNodePtr header_line, ValNodePtr PNTR perr_list);
+NLM_EXTERN ValNodePtr FreeObjectTableForTabTable (ValNodePtr table);
+NLM_EXTERN ValNodePtr GetObjectTableForTabTable (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns, ValNodePtr PNTR p_err_list);
+NLM_EXTERN ValNodePtr ApplyTableValuesToObjectTable (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns, ValNodePtr obj_table);
+NLM_EXTERN ValNodePtr CheckObjTableForRowsThatApplyToTheSameDestination (ValNodePtr obj_table);
+NLM_EXTERN ValNodePtr CheckObjTableForExistingText (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns, ValNodePtr obj_table);
+
+NLM_EXTERN ValNodePtr ApplyTableToFeatures (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns);
+NLM_EXTERN ValNodePtr CheckTableForExistingText (SeqEntryPtr sep, ValNodePtr table, ValNodePtr columns);
+
+NLM_EXTERN SeqFeatPtr GetmRNAForFeature (SeqFeatPtr sfp);
+NLM_EXTERN Boolean AdjustmRNAProductToMatchProteinProduct (SeqFeatPtr sfp);
+NLM_EXTERN Boolean IsFieldTypeCDSProduct (FieldTypePtr ft);
+
+
+#ifdef __cplusplus 
+} 
+#endif
+
+#endif
diff --git a/api/seqmgr.c b/api/seqmgr.c
index ca7ff20e..4f918cd0 100644
--- a/api/seqmgr.c
+++ b/api/seqmgr.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 9/94
 *
-* $Revision: 6.291 $
+* $Revision: 6.293 $
 *
 * File Description:  Manager for Bioseqs and BioseqSets
 *
@@ -8318,6 +8318,32 @@ static void SeqMgrBestOverlapSetContext (
   }
 }
 
+static Boolean TransSplicedStrandsMatch (Uint1 locstrand, SeqLocPtr slp, SMFeatItemPtr feat)
+
+{
+  Uint1       featstrand;
+  SeqLocPtr   loc;
+  SeqFeatPtr  sfp;
+
+  if (slp == NULL || feat == NULL) return FALSE;
+  sfp = feat->sfp;
+  if (sfp == NULL) return FALSE;
+
+  if (! sfp->excpt) return FALSE;
+  if (StringISearch (sfp->except_text, "trans-splicing") == NULL) return FALSE;
+
+  loc = SeqLocFindNext (sfp->location, NULL);
+  while (loc != NULL) {
+    if (SeqLocAinB (slp, loc) >= 0) {
+      featstrand = SeqLocStrand (loc);
+      if (StrandsMatch (featstrand, locstrand)) return TRUE;
+    }
+    loc = SeqLocFindNext (sfp->location, loc);
+  }
+
+  return FALSE;
+}
+
 static SeqFeatPtr SeqMgrGetBestOverlappingFeat (
   SeqLocPtr slp,
   Uint2 subtype,
@@ -8349,6 +8375,7 @@ static SeqFeatPtr SeqMgrGetBestOverlappingFeat (
   Int4            left;
   SeqLocPtr       loc;
   Int4            max = INT4_MAX;
+  Boolean         may_be_trans_spliced;
   Int4            mid;
   Int2            numivals = 0;
   SeqEntryPtr     oldscope;
@@ -8514,14 +8541,15 @@ static SeqFeatPtr SeqMgrGetBestOverlappingFeat (
 
       /* requires feature to be contained within gene, etc. */
 
-      if (special && (feat->bad_order || feat->mixed_strand)) {
+      may_be_trans_spliced = (Boolean) (special && (feat->bad_order || feat->mixed_strand));
+      if (may_be_trans_spliced) {
         diff = TestForOverlap (feat, slp, left, right, LOCATION_SUBSET, numivals, ivals);
       } else {
         diff = TestForOverlap (feat, slp, left, right, overlapType, numivals, ivals);
       }
       if (diff >= 0) {
 
-        if (StrandsMatch (feat->strand, strand)) {
+        if (StrandsMatch (feat->strand, strand) || (may_be_trans_spliced && TransSplicedStrandsMatch (strand, slp, feat))) {
 
           if (userfunc != NULL && context != NULL && goOn) {
             SeqMgrBestOverlapSetContext (feat, omdp, userdata, context);
@@ -8553,14 +8581,15 @@ static SeqFeatPtr SeqMgrGetBestOverlappingFeat (
     feat = array [hier];
     if (feat != NULL && ((! feat->ignore) || userfunc == NULL)) {
 
-      if (special && (feat->bad_order || feat->mixed_strand)) {
+      may_be_trans_spliced = (Boolean) (special && (feat->bad_order || feat->mixed_strand));
+      if (may_be_trans_spliced) {
         diff = TestForOverlap (feat, slp, left, right, LOCATION_SUBSET, numivals, ivals);
       } else {
         diff = TestForOverlap (feat, slp, left, right, overlapType, numivals, ivals);
       }
       if (diff >= 0) {
 
-        if (StrandsMatch (feat->strand, strand)) {
+        if (StrandsMatch (feat->strand, strand) || (may_be_trans_spliced && TransSplicedStrandsMatch (strand, slp, feat))) {
 
           if (userfunc != NULL && context != NULL && goOn) {
             SeqMgrBestOverlapSetContext (feat, omdp, userdata, context);
diff --git a/api/seqport.c b/api/seqport.c
index b9eed095..989af547 100644
--- a/api/seqport.c
+++ b/api/seqport.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/13/91
 *
-* $Revision: 6.169 $
+* $Revision: 6.172 $
 *
 * File Description:  Ports onto Bioseqs
 *
@@ -39,6 +39,15 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: seqport.c,v $
+* Revision 6.172  2008/02/12 18:56:52  bollin
+* Made ReverseSeqData and ComplementSeqData extern
+*
+* Revision 6.171  2007/12/28 16:27:58  kans
+* in SeqPortStreamSetup, on failure, return -1 if count was 0 to ensure failure signal
+*
+* Revision 6.170  2007/12/04 19:00:21  kans
+* SeqPortStreamSeqLoc uses scope to get local (segset) components while allowing multiple simultaneous StreamCache objects
+*
 * Revision 6.169  2007/05/30 18:10:06  kans
 * added KNOWN_GAP_AS_PLUS to distinguish known-length from unknown-length gaps, use for validation
 *
@@ -2647,6 +2656,7 @@ typedef struct streamdata {
   CharPtr            tmp;
   Boolean            failed;
   Int2               depth;
+  SeqEntryPtr        scope;
 } StreamData, PNTR StreamDataPtr;
 
 /* prototype for main internal recursive processing function */
@@ -3065,15 +3075,16 @@ static Int4 SeqPortStreamSeqLoc (
 )
 
 {
-  BioseqPtr bsp;
-  Char      buf [64];
-  Int4      count = 0;
-  Char      pid [64];
-  SeqIdPtr  sip;
+  BioseqPtr    bsp;
+  Char         buf [64];
+  Int4         count = 0;
+  SeqEntryPtr  oldscope = NULL;
+  Char         pid [64];
+  SeqIdPtr     sip;
 #ifdef OS_UNIX
-  Int2      attempts;
-  CharPtr   str;
-  int       val = 0;
+  Int2         attempts;
+  CharPtr      str;
+  int          val = 0;
 #endif
 
   if (slp == NULL || sdp == NULL) return 0;
@@ -3098,7 +3109,9 @@ static Int4 SeqPortStreamSeqLoc (
     return 0;
   }
 
+  oldscope = SeqEntrySetScope (sdp->scope);
   bsp = BioseqLockById (sip);
+  SeqEntrySetScope (oldscope);
 
 #ifdef OS_UNIX
   if (bsp == NULL) {
@@ -3134,7 +3147,9 @@ static Int4 SeqPortStreamSeqLoc (
           sleep (stream_retry_sleep);
         }
 
+        oldscope = SeqEntrySetScope (sdp->scope);
         bsp = BioseqLockById (sip);
+        SeqEntrySetScope (oldscope);
         attempts++;
       }
       if (bsp != NULL) {
@@ -3612,6 +3627,7 @@ static Int4 SeqPortStreamSetup (
   Char        ch, lttr;
   CharPtr     complementBase = " TVGH  CD  M KN   YSAABW R ";
   Int4        count = 0, from, to;
+  Uint2       entityID;
   Int2        i;
   StreamData  sd;
   SeqLocPtr   slp;
@@ -3658,10 +3674,15 @@ static Int4 SeqPortStreamSetup (
 
   if (bsp != NULL) {
 
+    entityID = ObjMgrGetEntityIDForPointer (bsp);
+    sd.scope = GetTopSeqEntryForEntityID (entityID);
+
     count += SeqPortStreamWork (bsp, start, stop, strand, &sd);
 
   } else if (loc != NULL) {
 
+    sd.scope = SeqEntryGetScope ();
+
     slp = SeqLocFindNext (loc, NULL);
     while (slp != NULL) {
 
@@ -3678,6 +3699,7 @@ static Int4 SeqPortStreamSetup (
   /* return number of bases or residues streamed to callback */
 
   if (sd.failed) {
+    if (count  < 1) return -1;
     return -count;
   }
 
@@ -5216,7 +5238,7 @@ NLM_EXTERN Boolean LIBCALL BioseqRevComp (BioseqPtr bsp)
 	return retval;
 }
 
-static Boolean ComplementSeqData (Uint1 seqtype, Int4 seqlen, SeqDataPtr sdp)
+NLM_EXTERN Boolean ComplementSeqData (Uint1 seqtype, Int4 seqlen, SeqDataPtr sdp)
 {
 	SeqCodeTablePtr sctp;
 	ByteStorePtr    bysp;
@@ -5393,7 +5415,7 @@ NLM_EXTERN Boolean LIBCALL BioseqComplement (BioseqPtr bsp)
 } /* BioseqComplement */
 
 
-static Boolean LIBCALL ReverseSeqData (Uint1 seqtype, Int4 seqlen, SeqDataPtr sdp)
+NLM_EXTERN Boolean LIBCALL ReverseSeqData (Uint1 seqtype, Int4 seqlen, SeqDataPtr sdp)
 {
 	ByteStorePtr 	bysp1, bysp2 = '\0';
 	long 		readbyte, bslen = 0;
diff --git a/api/seqport.h b/api/seqport.h
index 3e1269cb..9928a18e 100644
--- a/api/seqport.h
+++ b/api/seqport.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/13/91
 *
-* $Revision: 6.58 $
+* $Revision: 6.59 $
 *
 * File Description:  Ports onto Bioseqs
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: seqport.h,v $
+* Revision 6.59  2008/02/12 18:56:52  bollin
+* Made ReverseSeqData and ComplementSeqData extern
+*
 * Revision 6.58  2007/05/30 18:10:06  kans
 * added KNOWN_GAP_AS_PLUS to distinguish known-length from unknown-length gaps, use for validation
 *
@@ -1059,6 +1062,11 @@ NLM_EXTERN FloatHi MolWtForBsp (BioseqPtr bsp);
 NLM_EXTERN FloatHi MolWtForStr (CharPtr str);
 
 
+
+NLM_EXTERN Boolean LIBCALL ReverseSeqData (Uint1 seqtype, Int4 seqlen, SeqDataPtr sdp);
+NLM_EXTERN Boolean ComplementSeqData (Uint1 seqtype, Int4 seqlen, SeqDataPtr sdp);
+
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/api/sequtil.c b/api/sequtil.c
index e802ade2..efad56a8 100644
--- a/api/sequtil.c
+++ b/api/sequtil.c
@@ -29,918 +29,15 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.225 $
+* $Revision: 6.241 $
 *
 * File Description:  Sequence Utilities for objseq and objsset
 *
 * Modifications:  
 * --------------------------------------------------------------------------
-* $Log: sequtil.c,v $
-* Revision 6.225  2007/08/08 15:59:04  kans
-* added EW to WHICH_db_accession as NCBI EST
+* Date       Name        Description of modification
+* -------  ----------  -----------------------------------------------------
 *
-* Revision 6.224  2007/07/03 16:41:30  kans
-* use EV for NCBI EST
-*
-* Revision 6.223  2007/06/21 19:15:22  kans
-* EU is NCBI direct submission prefix
-*
-* Revision 6.222  2007/05/30 15:45:57  kans
-* WHICH_db_accession uses ET for NCBI GSS
-*
-* Revision 6.221  2007/05/08 19:01:43  kans
-* set uninitialized variables, changed tabs to spaces
-*
-* Revision 6.220  2007/05/07 13:28:35  kans
-* added casts for Seq-data.gap (SeqDataPtr, SeqGapPtr, ByteStorePtr)
-*
-* Revision 6.219  2007/04/05 13:43:36  kans
-* DDBJ uses DI for patents
-*
-* Revision 6.218  2007/03/20 19:18:04  kans
-* added ES to WHICH_db_accession
-*
-* Revision 6.217  2007/03/13 18:03:45  kans
-* added FreeSeqLocSetComponents to free sequence records referenced in a chain of SeqLocs
-*
-* Revision 6.216  2007/03/06 16:06:20  kans
-* added ER to WHICH_db_accession as ncbi gss
-*
-* Revision 6.215  2007/03/05 20:01:19  kans
-* added new wgs scaffold segmented parent prefixes to WHICH_db_accession
-*
-* Revision 6.214  2007/02/21 17:23:59  bollin
-* Added IsSkippableDbtag function, to use when TMSMART, BankIt, and NCBIFILE
-* IDs should be ignored (for displays, formatting, etc.)
-*
-* Revision 6.213  2007/02/01 17:19:19  kans
-* added EL to WHICH_db_accession as NCBI EST
-*
-* Revision 6.212  2007/01/04 16:43:56  kans
-* added EJ and EK to WHICH_db_accession as NCBI GSS
-*
-* Revision 6.211  2006/12/20 14:55:40  kans
-* added DH for DDBJ GSS
-*
-* Revision 6.210  2006/11/22 15:24:22  kans
-* WHICH_db_accession uses EI for NCBI GSS
-*
-* Revision 6.209  2006/11/15 18:01:22  kans
-* added SeqLocPartialCheckEx to control fetching of far location
-*
-* Revision 6.208  2006/11/03 19:06:03  kans
-* another accession prefix in WHICH_db_accession
-*
-* Revision 6.207  2006/09/28 20:19:26  bollin
-* fixed buffer overrun problem in SeqPointWriteEx, increased size of buffer used
-* by SeqLocPrintProc
-*
-* Revision 6.206  2006/09/20 14:53:18  kans
-* ExtendSingleGeneOnMRNA and CorrectGeneFeatLocation look for origin artificial and taxname synthetic construct, do not extend gene
-*
-* Revision 6.205  2006/09/18 17:58:41  kans
-* added EG to WHICH_db_accession
-*
-* Revision 6.204  2006/08/21 20:02:31  kans
-* assign EF to NCBI dirsub in WHICH_db_accession
-*
-* Revision 6.203  2006/07/13 17:06:39  bollin
-* use Uint4 instead of Uint2 for itemID values
-* removed unused variables
-* resolved compiler warnings
-*
-* Revision 6.202  2006/07/06 15:05:02  kans
-* added EE to WHICH_db_accession as NCBI EST
-*
-* Revision 6.201  2006/06/29 20:31:19  kans
-* only AH may be segmented protein, CH, CM, DS are nucleotide
-*
-* Revision 6.200  2006/06/29 14:24:05  kans
-* added ED to WHICH_db_accession as NCBI GSS
-*
-* Revision 6.199  2006/06/20 20:49:21  kans
-* added CU to WHICH_db_accession as EMBL genome project data
-*
-* Revision 6.198  2006/05/30 14:54:06  kans
-* added EC as NCBI EST prefix
-*
-* Revision 6.197  2006/05/11 17:08:13  bollin
-* corrected problem in GetThePointForOffset for SeqLocStart and SeqLocStop for
-* all-minus strand interval locations
-*
-* Revision 6.196  2006/04/06 15:41:19  kans
-* added DG to WHICH_db_accession
-*
-* Revision 6.195  2006/04/05 16:45:01  bollin
-* special left-right end handling for circular topology in GetThePointForOffset
-*
-* Revision 6.194  2006/03/30 17:04:53  kans
-* DF is DDBJ CON accession prefix
-*
-* Revision 6.193  2006/03/23 18:31:32  kans
-* added EB as NCBI EST
-*
-* Revision 6.192  2006/03/10 17:27:14  bollin
-* make sure parentptr is BioseqSet in GetEarlierSeqIdPtr
-*
-* Revision 6.191  2006/03/10 17:13:45  bollin
-* changes to GetEarlierSeqIdPtr to handle the situation where one of the Bioseqs
-* has not been indexed.  Fixes bug reported by Serge Bazhin
-*
-* Revision 6.190  2006/02/16 17:19:14  kans
-* better handling of trans splicing in GetThePointForOffset, SeqLocStart (CB)
-*
-* Revision 6.189  2006/02/07 17:50:53  kans
-* support for pgp instead of pat for pre-grant publication in SeqIdWrite and SeqIdParse
-*
-* Revision 6.188  2006/02/01 21:53:44  kans
-* DZ and EA for ncbi patent in WHICH_db_accession
-*
-* Revision 6.187  2006/01/24 17:59:26  kans
-* use DY for NCBI EST
-*
-* Revision 6.186  2006/01/05 14:11:56  bollin
-* added SeqLocPrintUseBestID function, which prints out the sequence location
-* but uses the "best" sequence ID instead of the one actually stored in the
-* SeqLoc.
-*
-* Revision 6.185  2006/01/03 15:49:36  kans
-* added DX as ncbi gss to WHICH_db_accession
-*
-* Revision 6.184  2005/12/09 19:43:43  kans
-* added DW as NCBI EST
-*
-* Revision 6.183  2005/09/20 21:11:34  kans
-* added DV as NCBI EST
-*
-* Revision 6.182  2005/08/09 20:04:17  kans
-* added NW_ with 6 or 9 digits to WHICH_db_accession
-*
-* Revision 6.181  2005/07/28 18:33:31  kans
-* in WHICH_db_accession, DT is NCBI EST and DU is NCBI GSS
-*
-* Revision 6.180  2005/07/18 14:49:53  kans
-* fixed minor xcode compiler warnings
-*
-* Revision 6.179  2005/07/06 14:31:19  kans
-* DS is ncbi segmented set header (WGS CON scaffolds) in WHICH_db_accession
-*
-* Revision 6.178  2005/06/17 19:25:58  coulouri
-* correct pdb accession output
-*
-* Revision 6.177  2005/06/15 17:22:39  kans
-* added CT as embl genome to WHICH_db_accession
-*
-* Revision 6.176  2005/05/18 20:33:45  bollin
-* changed BSConvertSeq to handle transitions from nucleotide to protein and
-* protein to nucleotide
-*
-* Revision 6.175  2005/04/28 19:24:45  kans
-* DR prefix moved from STS to EST
-*
-* Revision 6.174  2005/04/27 17:24:21  kans
-* support seqid_gpipe in combination with a more public accession type
-*
-* Revision 6.173  2005/04/26 21:33:52  kans
-* added SEQID_GPIPE
-*
-* Revision 6.172  2005/04/05 15:25:30  kans
-* added DR as NCBI STS
-*
-* Revision 6.171  2005/03/29 14:46:42  papadopo
-* use a different start point when changing StdSeg-type seqalign offsets, if the underlying SeqLoc specifes the minus strand
-*
-* Revision 6.170  2005/03/22 20:42:03  kans
-* added DP and DQ accession prefixes
-*
-* Revision 6.169  2005/02/01 13:28:55  kans
-* added DN as NCBI EST accession prefix
-*
-* Revision 6.168  2005/01/25 18:13:47  kans
-* added CS as EMBL patent
-*
-* Revision 6.167  2004/12/08 19:44:52  kans
-* added CZ as NCBI GSS
-*
-* Revision 6.166  2004/12/08 15:14:51  kans
-* added ACCN_DDBJ_GSS, accession prefix DE
-*
-* Revision 6.165  2004/12/02 19:02:47  kans
-* added CY accession prefix
-*
-* Revision 6.164  2004/11/22 20:50:15  kans
-* added CX as NCBI EST
-*
-* Revision 6.163  2004/11/12 14:45:39  kans
-* added DD as DDBJ patent prefix
-*
-* Revision 6.162  2004/11/08 18:19:44  madden
-* GetScoreAndEvalue change to return number of hsps (in linked set) for most significant set.
-*
-* Revision 6.161  2004/10/13 16:46:52  kans
-* added DA, DB, DC as DDBJ_EST
-*
-* Revision 6.160  2004/09/21 22:34:36  dondosha
-* Get the number of linked HSPs for a DenDiag from the first segment, not from the largest linked set
-*
-* Revision 6.159  2004/09/15 13:02:02  kans
-* added CW to WHICH_db_accession as NCBI GSS
-*
-* Revision 6.158  2004/08/20 18:55:27  kans
-* SeqLocStrand skips NULL or EMPTY components of MIX to avoid giving incorrect unknown result
-*
-* Revision 6.157  2004/08/17 19:35:44  kans
-* BSPack uses BSRead instead of BSGetByte for significant speed increase
-*
-* Revision 6.156  2004/08/06 17:15:50  kans
-* added CV as NCBI EST
-*
-* Revision 6.155  2004/08/04 17:15:16  kans
-* added AccnInUniProt - still need AccnIsSWISSPROT for old style
-*
-* Revision 6.154  2004/07/21 18:05:00  rsmith
-* SeqLocStart and SeqLocStop were not handling SEQLOC_PACKED_PNTs properly
-*
-* Revision 6.153  2004/07/14 22:55:04  dondosha
-* Add version in GetAccessionVersionFromSeqId only if it is > 0
-*
-* Revision 6.152  2004/07/14 22:46:08  dondosha
-* Added GetAccessionVersionFromSeqId function to extract Accession.version from a Seq-id
-*
-* Revision 6.151  2004/07/14 19:09:19  kans
-* added CP for ACCN_NCBI_GENOME in WHICH_db_accession
-*
-* Revision 6.150  2004/06/04 17:31:34  kans
-* added CN and CO accession prefixes
-*
-* Revision 6.149  2004/05/27 15:37:31  kans
-* fixed typo in WHICH_db_accession - new 12-character RefSeq test used wrong comparison for underscore test
-*
-* Revision 6.148  2004/05/25 20:46:18  kans
-* WHICH_db_accession handles 12-character RefSeq accessions
-*
-* Revision 6.147  2004/03/30 20:29:33  kans
-* in static std_order array within SeqIdBestRank, demoted gibbsq, gibbmt, and patent
-*
-* Revision 6.146  2004/03/16 22:08:31  kans
-* added CL to WHICH_db_accession as NCBI EST
-*
-* Revision 6.145  2004/03/15 18:42:59  coulouri
-* Handle memory allocation failure gracefully with BSRebuildDNA_4na
-*
-* Revision 6.144  2004/01/16 16:37:01  kans
-* added CM as scaffold/CON record
-*
-* Revision 6.143  2003/12/18 19:35:53  kans
-* added CQ and CR prefixes
-*
-* Revision 6.142  2003/12/16 16:03:04  kans
-* added CL as ncbi gss
-*
-* Revision 6.141  2003/11/10 16:12:33  kans
-* added CK as genbank est
-*
-* Revision 6.140  2003/10/31 20:51:24  kans
-* added CI and CJ as DDBJ ESTs to WHICH_db_accession
-*
-* Revision 6.139  2003/10/24 14:36:12  kans
-* added CH as GenBank CONN to WHICH_db_accession
-*
-* Revision 6.138  2003/09/09 20:08:18  kans
-* SeqLocPartialCheck locks bioseq if seqloc_whole and far
-*
-* Revision 6.137  2003/09/02 15:11:50  kans
-* WHICH_db_accession takes ZP_ with 8 digits as refseq_prot_predicted
-*
-* Revision 6.136  2003/08/11 13:45:18  kans
-* added CG as ncbi gss
-*
-* Revision 6.135  2003/07/14 20:17:53  kans
-* added CF as ncbi est to WHICH_db_accession
-*
-* Revision 6.134  2003/07/02 14:35:21  kans
-* added CE as ncbi gss
-*
-* Revision 6.133  2003/05/20 22:15:24  yaschenk
-* SeqIdSelect loops indefinitely on corrupted memory
-*
-* Revision 6.132  2003/04/30 16:40:41  kans
-* added CD as GenBank EST
-*
-* Revision 6.131  2003/03/25 13:32:22  kans
-* added CC as ncbi gss accession prefix
-*
-* Revision 6.130  2003/03/24 19:41:56  kans
-* added tmsmart_order, use in SeqIdWrite to prevent TMSMART temporary ID from being used
-*
-* Revision 6.129  2003/02/20 19:05:31  ford
-* Modified MakeNewProteinSeqIdExMT() to create an ID of maximum length 30 instead of 20.
-*
-* Revision 6.128  2003/01/21 17:06:57  kans
-* implement PRINTID_FASTA_ALL SeqIdWrite
-*
-* Revision 6.127  2003/01/13 18:15:35  kans
-* added CB as NCBI EST prefix
-*
-* Revision 6.126  2002/11/05 18:50:31  kans
-* fixed bug in SeqLocPartialCheck
-*
-* Revision 6.125  2002/10/19 19:11:21  kans
-* added CA as GenBank EST
-*
-* Revision 6.124  2002/10/03 16:18:35  kans
-* added BZ as NCBI GSS
-*
-* Revision 6.123  2002/09/20 20:47:51  kans
-* added BY as DDBJ EST prefix
-*
-* Revision 6.122  2002/08/28 13:28:54  kans
-* added BX prefix
-*
-* Revision 6.121  2002/08/26 20:38:26  kans
-* added BW as ddbj est prefix
-*
-* Revision 6.120  2002/08/19 15:57:28  kans
-* BV is NCBI STS prefix
-*
-* Revision 6.119  2002/08/19 15:54:47  kans
-* added BU as NCBI EST prefix
-*
-* Revision 6.118  2002/07/12 18:47:46  kans
-* WHICH_db_accession was using the result of AccnIsSWISSPROT incorrectly
-*
-* Revision 6.117  2002/07/08 20:25:45  kans
-* added BT as FLI_cDNA type
-*
-* Revision 6.116  2002/06/28 14:48:03  kans
-* added BS as ddbj genome project prefix
-*
-* Revision 6.115  2002/06/20 18:38:43  kans
-* added FAA and GAA, ACCN_NCBI_WGS_PROT, ACCN_EMBL_WGS_PROT, ACCN_DDBJ_WGS_PROT, and ACCN_IS_WGS
-*
-* Revision 6.114  2002/06/19 17:13:48  kans
-* added ACCN_PDB, support for PDB in SeqIdFromAccessionDotVersion
-*
-* Revision 6.113  2002/06/10 18:06:16  kans
-* SeqLocLen use of smp->seq_len_lookup_func first checks sip for NULL
-*
-* Revision 6.112  2002/06/10 14:07:12  kans
-* SeqLocLen on whole tries new smp->seq_len_lookup_func registered function
-*
-* Revision 6.111  2002/05/29 19:19:53  bazhin
-* Added support for new EAA-EZZ protein's WGS accessions.
-*
-* Revision 6.110  2002/04/24 17:11:03  kans
-* added BR as DDBJ TPA accession prefix
-*
-* Revision 6.109  2002/04/02 18:19:56  kans
-* SeqLocPartialCheck fixes
-*
-* Revision 6.108  2002/03/26 18:11:26  kans
-* WHICH_db_accession WGS assignments - A*** NCBI, B*** DDBJ, C*** EMBL
-*
-* Revision 6.107  2002/03/12 17:08:32  kans
-* added BQ as NCBI EST
-*
-* Revision 6.106  2002/02/14 18:30:27  kans
-* SeqIdFromAccessionDotVersion defaults version to INT2_MIN
-*
-* Revision 6.105  2002/01/29 19:28:16  kans
-* SeqIdParse can parse type|accession.ver with no trailing vertical bars for RefSeq and DNA database types
-*
-* Revision 6.104  2002/01/22 18:49:15  kans
-* added ACCN_NCBI_WGS, ACCN_EMBL_WGS, and ACCN_DDBJ_WGS
-*
-* Revision 6.103  2002/01/17 13:49:32  kans
-* BP added as DDBJ EST accession prefix
-*
-* Revision 6.102  2002/01/16 16:59:38  camacho
-* Changed the type of buflen parameter in SeqIdWrite from Int2 to Uint4
-*
-* Revision 6.101  2001/11/29 14:04:29  kans
-* reverted GetThePointForOffset, deal with trans-splicing in feature indexing left/right extreme calculation itself
-*
-* Revision 6.100  2001/11/14 13:55:45  kans
-* added BN accession
-*
-* Revision 6.99  2001/11/08 13:49:45  kans
-* GetThePointForOffset on left or right end now handles trans-spliced mixed strands properly - still need to fix SeqLocMerge
-*
-* Revision 6.98  2001/10/23 14:04:18  kans
-* added BM and BL accession prefixes
-*
-* Revision 6.97  2001/09/28 22:42:49  vakatov
-* Renamed "new" to "x_new" -- to avoid clash with the C++ "operator new"
-*
-* Revision 6.96  2001/09/28 14:31:00  madden
-* Added functions BSCompressDNANew and GenericCompressDNAEx for long sequences with ambiguity
-*
-* Revision 6.95  2001/09/20 18:53:28  kans
-* changed SeqLocCompare matrices to handle artificial frameshifts
-*
-* Revision 6.94  2001/08/07 18:12:05  kans
-* added macros for EMBL and DDBJ TPA and TPA_PROT prefixes
-*
-* Revision 6.93  2001/08/06 22:13:12  kans
-* using NUM_SEQID, added TPA ids to arrays
-*
-* Revision 6.92  2001/08/06 20:07:53  ostell
-* added support for SEQID_TPG, TPE, TPD types
-*
-* Revision 6.91  2001/08/01 17:56:24  kans
-* in SeqLocGetSegLens on mix or equiv, ctr += changed to ctr = to avoid multiple increments
-*
-* Revision 6.90  2001/07/03 21:42:01  kans
-* added macros and accession prefixes for TPA (third-party annotation) records
-*
-* Revision 6.89  2001/06/06 17:53:42  kans
-* added BI and BJ accession prefixes
-*
-* Revision 6.88  2001/06/05 16:28:40  kans
-* restored logic of GetThePointForOffset, with comment that SeqLocStart returns sintp->from even on minus strand, different behavior than SEQLOC_START
-*
-* Revision 6.87  2001/06/04 19:31:14  kans
-* PDB lower case chain now represented by double upper case letter, modified SeqIdWrite, SeqIdParse, SeqIdComp, removed DeltaSeqsToSeqLoc call and variables from CheckPointInBioseq
-*
-* Revision 6.86  2001/06/04 19:07:48  kans
-* fixed buggy logic for minus strand LEFT_END/RIGHT_END in GetThePointForOffset
-*
-* Revision 6.85  2001/06/01 21:11:45  kans
-* CheckPointInBioseq now works for far delta sequences, calls SeqMgrMapPartToSegmentedBioseq, allowing NG propagation onto NT genomic records
-*
-* Revision 6.84  2001/05/30 22:47:23  kans
-* fixed Mac compiler warnings about unwanted assignments, moved function prototypes to header, removed unused variables
-*
-* Revision 6.83  2001/05/30 20:30:31  shoemake
-* Fixed bug in SeqIdParse for VB chain in SEQID_PDBs.
-*
-* Revision 6.82  2001/05/14 19:42:37  sicotte
-* Added BH prefix for ncbi GSS
-*
-* Revision 6.81  2001/05/04 22:09:45  dondosha
-* Small modification in GetAccessionFromSeqId for local id
-*
-* Revision 6.80  2001/04/27 15:46:20  madden
-* Add function RebuildDNA_4na
-*
-* Revision 6.79  2001/03/23 16:56:26  dondosha
-* Correction in function GetAccessionFromSeqId
-*
-* Revision 6.78  2001/01/30 18:11:13  kans
-* SeqIdParse for general and local counts digits, and any number > INT4_MAX will be stored as a string
-*
-* Revision 6.77  2000/12/20 20:59:58  sicotte
-* bug fix for AccnnIsSWISSPROT
-*
-* Revision 6.76  2000/12/07 16:34:42  sicotte
-* Updated WHICH_db_accession and corresponding macros: I* accessions can no longer be proteins (they were PIR) and have completed hardcoding of N000?? accessions which can belong to twoDB. Added SeqIdFromAccessionEx, ACCN_PIR_FORMAT, and AccnIsSWISSPROT functions
-*
-* Revision 6.75  2000/12/05 23:10:29  kans
-* SeqIdParse does not override default pdb chain if no tokens[1] content
-*
-* Revision 6.74  2000/11/20 17:13:47  kans
-* SeqIdParse uses SEQID_PARSE_BUF_SIZE instead of 40 character limit - needed to handle humongously long local IDs in genome annotation models, which will be removed when loaded into ID, but still need to be dealt with during processing
-*
-* Revision 6.73  2000/11/16 17:23:26  sicotte
-* IS_protdb_accession is now true for any 3 letter accession and IS_ntdb_accession is now also true for any unknown accession-looking accession number
-*
-* Revision 6.72  2000/11/14 20:49:48  sicotte
-* add XM_ refseq prefix
-*
-* Revision 6.71  2000/10/31 21:20:05  vakatov
-* [WIN32] DLL'zation
-*
-* Revision 6.70  2000/10/27 20:10:57  shavirin
-* Added new function MakeNewProteinSeqIdExMT for MT save operation.
-*
-* Revision 6.69  2000/10/26 15:28:58  dondosha
-* Do not adjust offsets for empty SeqLocs in AdjustOffSetsInSeqAlign
-*
-* Revision 6.68  2000/10/24 19:04:18  dondosha
-* Moved function UniqueLocalId from blast.c
-*
-* Revision 6.67  2000/10/11 21:59:35  kans
-* added PRINTID_FASTA_GENERAL
-*
-* Revision 6.66  2000/10/11 18:33:36  kans
-* SeqIdWrite fasta_order prefers SEQID_OTHER, then SEQID_GENERAL, then SEQID_LOCAL
-*
-* Revision 6.65  2000/10/03 16:51:07  cavanaug
-* Added BF accession prefix to WHICH_db_accession
-*
-* Revision 6.64  2000/10/02 14:30:48  sicotte
-* Added BE prefix for NCBI EST to WHICH_db_accession
-*
-* Revision 6.63  2000/10/02 14:29:16  sicotte
-* Added BE prefix for NCBI EST to WHICH_db_accession
-*
-* Revision 6.62  2000/09/28 15:08:31  dondosha
-* Corrected local id handling in GetAccessionFromSeqid - used in Mega BLAST
-*
-* Revision 6.61  2000/09/19 15:22:07  sicotte
-* fix BD and BE prefix
-*
-* Revision 6.60  2000/09/12 20:20:13  cavanaug
-* WHICH_db_accession : fixed missing paren
-*
-* Revision 6.59  2000/09/12 19:54:22  cavanaug
-* WHICH_db_accession now knows about BE accessions
-*
-* Revision 6.58  2000/08/02 21:26:15  kans
-* SeqIdWrite will not print version if release is used
-*
-* Revision 6.57  2000/07/11 15:01:50  kans
-* added SeqIdFromAccessionDotVersion for genome mapping project
-*
-* Revision 6.56  2000/06/08 14:30:07  dondosha
-* Fixed bug in GetAccessionFromSeqId for general id
-*
-* Revision 6.55  2000/05/22 17:37:01  sicotte
-* add BD prefix to WHICH_db_accession
-*
-* Revision 6.54  2000/05/17 17:20:43  dondosha
-* Added function GetAccessionFromSeqId, used in standalone programs blastclust and megablast
-*
-* Revision 6.53  2000/05/10 16:56:33  kans
-* SeqIdParse stops looking for expected_tokens when done is TRUE, avoids reading past end of string for ref|xxx| with two bars
-*
-* Revision 6.52  2000/05/05 13:24:50  kans
-* For SEQID_OTHER (RefSeq), SeqIdWrite will not print third vertical bar (originally for when there would be periodic releases - obsolete now that RefSeq is part of Entrez), and SeqIdParse will not upper case the tsip->name (LOCUS)
-*
-* Revision 6.51  2000/05/04 15:07:54  kans
-* SeqIdParse sends SEV_INFO, not SEV_ERROR, since blast uses it to test IDs for validity
-*
-* Revision 6.50  2000/05/03 17:56:05  sicotte
-* Added BC prefix ; changed refseq SeqID
-*
-* Revision 6.49  2000/03/29 15:53:50  sicotte
-* Added BB predix for DDBJ EST to WHICH_db_accession
-*
-* Revision 6.48  2000/02/17 17:29:52  sicotte
-* Added BA prefix for DDBJ CON division
-*
-* Revision 6.47  2000/02/11 21:09:52  madden
-* Check for NULL SeqAlignPtr before dereferencing
-*
-* Revision 6.46  2000/02/04 16:13:16  kans
-* added prefix parameter to MakeNewProteinSeqIdEx
-*
-* Revision 6.45  1999/12/22 15:46:19  sicotte
-* Added prefix AZ
-*
-* Revision 6.44  1999/11/22 17:28:01  kans
-* allow RefSeq ID to have two or (expected) three tokens
-*
-* Revision 6.43  1999/10/12 13:46:42  kans
-* AX and AY added to WHICH_db_accession
-*
-* Revision 6.42  1999/08/31 20:49:03  shavirin
-* Added case 5 (discontinous alignment) in function TxGetIdFromSeqAlign().
-*
-* Revision 6.41  1999/08/11 15:49:21  sicotte
-* Add AW prefix for NCBI EST in WHICH_db_accession
-*
-* Revision 6.40  1999/08/05 20:52:25  sicotte
-* fix in SeqIdFindBestAccession
-*
-* Revision 6.39  1999/08/03 20:00:34  sicotte
-* Add SeqIdFindBestAccession
-*
-* Revision 6.38  1999/07/30 09:28:17  sicotte
-* Transfered fns from salutil.c(chappey) AddSeqId,SeqIdDupList,SeqIdDupBestList,SeqIdListfromSeqLoc
-*
-* Revision 6.37  1999/06/24 20:39:21  kans
-* SeqIdPrint just calls SeqIdWrite, PRINTID_TEXTID_LOCUS uses accession (no version) if no locus name
-*
-* Revision 6.36  1999/05/24 22:22:25  sicotte
-* SeqIdFromAccession: Fix bug for embl/ddbj accessions
-*
-* Revision 6.35  1999/05/20 14:33:13  sicotte
-* SeqIdFromAccession: remove tsp->name to accomodate LOCUS names
-*
-* Revision 6.34  1999/04/22 14:52:34  tatiana
-* changes in MuskSeqIdWrite to print human chromosome Ids
-*
-* Revision 6.33  1999/04/20 14:34:53  sicotte
-* Add AV accession prefix for DDBJ EST in WHICH_db_accession
-*
-* Revision 6.32  1999/04/08 14:11:16  sicotte
-* Add SeqIdOrderInBioseqIdList (consider synomymous SeqIds)
-*
-* Revision 6.31  1999/04/02 17:31:59  vakatov
-* Added NLM_EXTERN for FindNuc() and FindProt() proto
-*
-* Revision 6.30  1999/04/01 17:41:20  sicotte
-* Added SeqIdInSeqLocList : Check if the Bioseq of SeqId sip is in list: may try to fetch the Bioseq
-*
-* Revision 6.29  1999/04/01 13:54:47  sicotte
-* Added SeqIdOrderInList(To find the position of a SeqId in a Chain)
-*       ExtractAccession ( To parse an accession into it's version and acc.)
-*       SeqIdFromAccession (To make the proper type of SeqId given an
-*                           accession string. (uses WHICH_db_accession)
-*       moved IS_ntdb_accession, IS_protdb_accession, WHICH_db_accession
-*          from accutils.ch to sequtil.ch
-*
-* Revision 6.28  1999/03/31 16:53:40  madden
-* Added FindNuc and FindProt functions for SeqEntryExplore
-*
-* Revision 6.27  1999/03/11 23:32:06  kans
-* sprintf casts
-*
-* Revision 6.26  1999/03/04 17:10:14  kans
-* check for tsip->release == NULL for showversion (JO)
-*
-* Revision 6.25  1999/02/22 15:34:22  kans
-* print version if > 0 (had erroneously been > 1)
-*
-* Revision 6.24  1999/02/09 20:15:00  kans
-* initialized version, release, in stack textseqid (JO)
-*
-* Revision 6.23  1999/02/02 21:38:12  kans
-* moved SHOWVERSION to header, SeqMgrAddIndexElement with and without version (JO)
-*
-* Revision 6.22  1999/02/01 18:41:02  ostell
-* added SHOWVER define to stop printing versions until ready
-*
-* Revision 6.21  1999/02/01 16:24:45  ostell
-* check for accession.version >0 not just non-zero
-*
-* Revision 6.20  1999/02/01 16:17:12  ostell
-* added version support for SeqIdWrite and SeqIdParse
-*
-* Revision 6.19  1999/01/12 18:00:18  kans
-* SeqIdComp now ignores version if < 1, and added PRINTID_TEXTID_ACC_VER and PRINTID_TEXTID_ACC_ONLY formats for SeqIdWrite
-*
-* Revision 6.18  1999/01/11 17:11:22  kans
-* SeqIdComp now checks version numbers
-*
-* Revision 6.17  1999/01/05 18:30:26  kans
-* SeqLocId ignores SEQLOC_NULL (Tatiana)
-*
-* Revision 6.16  1998/12/14 20:56:26  kans
-* dnaLoc_to_aaLoc takes allowTerminator parameter to handle stop codons created by polyA tail
-*
-* Revision 6.15  1998/11/24 20:15:05  kans
-* seqid other has better priority than local so refgene id is used preferentially
-*
-* Revision 6.14  1998/11/12 15:48:35  kans
-* SEQID_OTHER now prints as "ref" instead of "oth", though the latter is still detected by SeqIdParse as a special case
-*
-* Revision 6.13  1998/10/19 15:49:08  kans
-* SeqIdWrite now writes three fields for SEQID_OTHER in FASTA_SHORT
-*
-* Revision 6.12  1998/08/26 20:56:06  kans
-* got SeqIdComp test for general ID db strings wrong the first time
-*
-* Revision 6.11  1998/08/26 20:29:45  kans
-* SeqIdComp allows multiple general IDs with different db names
-*
-* Revision 6.10  1998/08/18 21:42:44  kans
-* SeqIdIn does not return on SIC_NO in order to handle multiple IDs of the same class (e.g., general)
-*
-* Revision 6.9  1998/08/13 22:31:48  kans
-* SeqMgrMapPartToSegmentedBioseq to speed up GetOffsetInBioseq, start of indexing segments, also index biosource by location for binary search (Wheelan)
-*
-* Revision 6.8  1998/07/28 16:41:08  kans
-* added MakeNewProteinSeqIdEx for faster creation of many new protein products
-*
-* Revision 6.7  1998/05/05 15:54:39  kans
-* SeqIdMatch now handles SEQID_OTHER (JO)
-*
-* Revision 6.6  1998/04/22 18:07:22  egorov
-* Make possible the second paramter (SeqLocPtr slp2) of AdjustOffSetsInSeqAlign to be NULL
-*
-* Revision 6.5  1998/02/27 17:10:01  vakatov
-* [WIN32 DLL]  Declared some functions as NLM_EXTERN(DLL-exportable)
-*
-* Revision 6.4  1998/02/26 19:14:03  madden
-* Added AdjustOffSetsInSeqAlign
-*
-* Revision 6.3  1998/01/26 17:25:30  madden
-* Added TxGetQueryIdFromSeqAlign function
-*
-* Revision 6.2  1997/10/15 14:43:18  ostell
-* changed SeqIdPrint, SeqIdWrite, SeqIdParse to convert PDB chain id '|' into VB
-*
-* Revision 6.1  1997/10/06 14:01:23  zjing
-* move TxGetSubjectId, GetScoreAndEvalue to sequtil.ch
-*
-* Revision 6.0  1997/08/25 18:07:20  madden
-* Revision changed to 6.0
-*
-* Revision 5.43  1997/08/19 17:07:09  kans
-* EntrezASN1Detected now explores all components
-*
-* Revision 5.42  1997/07/17 18:46:21  kans
-* SeqLocStrand now treats mixed unknown and plus as plus
-*
-* Revision 5.41  1997/06/19 18:38:56  vakatov
-* [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
-*
-* Revision 5.40  1997/05/19 19:25:26  shavirin
-* Added function CorrectGeneFeatLocation()
-*
- * Revision 5.39  1997/04/09  18:43:01  tatiana
- * a typo in MolTypeForGi description fixed
- *
- * Revision 5.38  1997/04/09  18:00:10  tatiana
- * added MolTypeForGI()
- *
- * Revision 5.37  1997/04/08  17:27:51  shavirin
- * Fixed typecast warnings.
- *
- * Revision 5.36  1997/04/04  17:24:44  shavirin
- * Fixed position calculation in BSRebuildDNA_4na() function
- *
- * Revision 5.35  1997/03/28  21:18:10  shavirin
- * Added function BSRebuildDNA_4na()
- *
- * Revision 5.34  1997/03/18  23:22:25  kans
- * changed return NULL to return FALSE in GenericCompressDNA (detected by
- * CodeWarrior)
- *
- * Revision 5.33  1997/03/18  19:16:30  shavirin
- * Added error handling in GenericCompressDNA() function
- *
- * Revision 5.32  1997/03/18  15:26:31  ostell
- * made SeqIdComp case insensitive
- *
- * Revision 5.31  1997/03/06  22:56:31  kans
- * added include <seqport.h> for dnaLoc_to_aaLoc
- *
- * Revision 5.30  1997/03/06  22:46:50  shavirin
- * Moved SPCompress functions to seqport.c
- *
- * Revision 5.29  1997/03/06  21:27:30  shavirin
- * Added new set of functions: SPCompressDNA(), SPRebuildDNA(), SPCompressNew(),
- * SPCompressFree()
- *
- * Revision 5.28  1997/03/04  21:58:48  shavirin
- * Added function GenericCompressDNA()
- *
- * Revision 5.27  1997/03/04  19:57:03  epstein
- * fix minus strand problem for gatherCodingRegions()
- *
- * Revision 5.26  1997/03/04  03:51:32  shavirin
- * Fixed memory leak in BSCompressDNA()
- *
- * Revision 5.25  1997/03/03  22:34:09  shavirin
- * Changed IO Buffer from 100/1 to 1024/1024 in BSCompressDNA
- *
- * Revision 5.23  1997/02/26  20:14:16  shavirin
- * Removed RandomSeed initialization in SeqMapTableFind()
- *
- * Revision 5.22  1997/02/26  19:24:16  shavirin
- * Optimized by increasing IO buffers function BSConvertSeq()
- *
- * Revision 5.21  1997/02/03  20:56:24  ostell
- * added additional check to MakeNewProteinSeqId() for an existing id in
- * GenBank locus form.
- *
- * Revision 5.20  1997/01/08  22:24:26  zjing
- * changes in MuskSeqIdWrite to Print THC Ids
- *
- * Revision 5.19  1996/12/10  19:17:39  kans
- * *** empty log message ***
- *
- * Revision 5.18  1996/11/18  20:37:37  shavirin
- * "Pack" set of functions now will produce ncbieaa Seq_code
- * for proteins.
- *
- * Revision 5.17  1996/10/15  15:44:08  shavirin
- * *** empty log message ***
- *
- * Revision 5.16  1996/10/15  14:47:18  shavirin
- * Added new functions: BSCompressDNA() and BSRebuildDNA() to handle
- * ambiguity characters.
- *
- * Revision 5.15  1996/10/11  21:08:28  chappey
- * backed out changes to add extra byte at end of bytestore
- *
- * Revision 5.14  1996/10/10  21:06:01  shavirin
- * Implemented random conversion of ASCII and ncbi4na encoding
- * to ncbi2na in case of ambiguous bases.
- *
- * Revision 5.13  1996/10/09  19:01:37  shavirin
- * Changed format of last byte in BSConvertSeq() function.
- *
- * Revision 5.12  1996/10/04  19:07:31  shavirin
- * Rewritten function BSPack() with more efficient algorithm
- *
- * Revision 5.11  1996/09/26  01:51:37  ostell
- * fixed logic error in BioseqConvert()
- *
- * Revision 5.10  1996/08/26  14:07:52  madden
- * Changed try to tax_try in for compatability with DEC OS.
- *
- * Revision 5.9  1996/08/07  20:13:04  epstein
- * move MuskSeqIdWrite, seqid_name, local_id_make and update_seq_loc from jzmisc to sequtil, to untangle the desktop and tools libraries from one another
- *
- * Revision 5.8  1996/07/15  19:03:57  epstein
- * adapt to dnaLoc_to_aaLoc() change
- *
- * Revision 5.7  1996/07/15  15:57:23  kans
- * fixed a call to ISA_na, removed an unused variable
- *
- * Revision 5.6  1996/07/15  14:41:53  epstein
- * add SeqEntryContainsSeqIdOfMolType() and FindCodingRegion() and add performance improvements to FindSpliceSites()
- *
- * Revision 5.5  1996/07/11  16:25:31  kans
- * MakeNewProteinSeqId default string is now tmpseq_
- *
- * Revision 5.4  1996/06/27  19:58:39  epstein
- * return NULL from FindSpliceSites if there are no splice sites
- *
- * Revision 5.3  1996/06/24  18:38:24  epstein
- * move splicing functionality to sequtil.c
- *
- * Revision 5.2  1996/06/16  15:19:31  ostell
- * added delta seq support to SeqEntryPack
- *
- * Revision 5.1  1996/06/12  18:29:14  epstein
- * move SeqLocIntNew() and SeqLocPntNew() from edutil to sequtil
- *
- * Revision 5.0  1996/05/28  13:23:23  ostell
- * Set to revision 5.0
- *
- * Revision 4.18  1996/03/25  22:18:32  tatiana
- * *** empty log message ***
- *
- * Revision 4.17  1996/03/11  19:06:43  ostell
- * added MakeNewProteinSeqId()
- *
- * Revision 4.16  1996/02/28  04:53:06  ostell
- * fix for SeqLocFindNext and ..Part for head haveing next pointer
- *
- * Revision 4.15  1996/02/26  03:44:33  ostell
- * added support for SEQLOC_BOND to SeqLocStart, SeqLocStop, SeqLocID, SeqLocStrand
- *
- * Revision 4.14  1996/02/24  03:11:40  ostell
- * made GetResidueForSymbol ruturn INVALID=-RESIDUE when letter is 0
- *
- * Revision 4.13  1996/01/31  16:08:16  tatiana
- * StringForSeqTech() added by Tatiana
- *
- * Revision 4.12  1995/12/27  22:30:21  ostell
- * added support for delta seqs in BioseqGetSegs, ..GetGaps
- *
- * Revision 4.11  1995/12/22  20:18:10  ostell
- * fix to SeqIdWrite to fall though PRINTID_FASTA_LONG when no gi is present
- *
- * Revision 4.10  1995/12/05  21:43:13  ostell
- * changed SeqIdWrite to format a little nicer
- *
- * Revision 4.9  1995/10/19  02:30:31  ostell
- * fixed SeqLocFindNext() bug that caused early termination at the
- * end of nested locations.
- *
- * Revision 4.8  1995/10/17  04:15:37  ostell
- * added SeqLocFindPart()
- * made SeqLocFindNext() call it
- * added equiv_is_one to IS_one_loc()
- *
- * Revision 4.7  1995/10/12  18:11:23  kans
- * corrected SeqLocLen for SEQLOC_MIX (JO)
- *
- * Revision 4.6  1995/09/29  15:03:06  ostell
- * changed SeqIdParse() to retain first Seqid if failure only on second
- *
- * Revision 4.5  1995/09/28  20:51:13  tatiana
- * SeqLocLen changed to handle case SEQLOC_EQUIV
- *
- * Revision 4.3  1995/09/06  21:06:28  ostell
- * fixed logical condition in SeqLocPartialCheck() that looked at Int-fuzz
- * lim type >= 0 || <= 2 (for unk, gt, lt).. changed || to &&
- *
- * Revision 4.2  1995/08/24  20:15:31  tatiana
- * bug fixed in sequtil.c
- *
- * Revision 4.1  1995/08/09  17:00:15  tatiana
- * bug fixed in SeqIdWrite()
- *
- * Revision 2.80  1995/07/20  22:08:39  tatiana
- * change SeqIdprint to SeqIdWrite
- *
- * Revision 2.79  1995/07/18  19:53:22  tatiana
- * add SeqIdWrite() to replace SeqIdPrint()
- *
- * Revision 2.78  1995/06/27  20:39:58  kans
- * SeqIdForSameBioseq no longer fetches
- *
- * Revision 2.77  1995/06/14  16:31:59  kans
- * EntrezASN1Detected function added (to be used by Sequin and ID)
- *
- * Revision 2.76  1995/06/06  16:25:38  ostell
- * added support for MolInfo in SeqLocPartialCheck()
- *
- * Revision 2.75  1995/05/19  04:02:08  ostell
- * added SeqLocAinB()
- *
- * Revision 2.74  1995/05/09  18:10:09  ostell
- * changed to using NUM_SEQID
- *
- * Revision 2.74  1995/05/09  18:10:09  ostell
- * changed to using NUM_SEQID
 * ==========================================================================
 */
 
@@ -1506,7 +603,11 @@ NLM_EXTERN Boolean BioseqPack (BioseqPtr bsp)
   
   if (Bioseq_repr(bsp) != Seq_repr_delta)
     return FALSE;
+
+  /* not set up to compress delta proteins */
   
+  if (ISA_aa (bsp->mol)) return FALSE;
+
   /* go through the delta chain */
   
   for (vnp = (ValNodePtr)(bsp->seq_ext); vnp != NULL; vnp = vnp->next) {
@@ -3632,6 +2733,7 @@ NLM_EXTERN CharPtr SeqIdWrite (SeqIdPtr isip, CharPtr buf, Uint1 format, Uint4 b
     Char chainbuf[3];
     Char versionbuf[10];
     Int2 version = 0;
+    CharPtr release = NULL;
 
     buf[0] = '\0';
     buflen--;
@@ -3779,6 +2881,10 @@ NLM_EXTERN CharPtr SeqIdWrite (SeqIdPtr isip, CharPtr buf, Uint1 format, Uint4 b
             case SEQID_TPD:
             case SEQID_GPIPE:
                 tsip = (TextSeqIdPtr)sip->data.ptrvalue;
+                release = tsip->release;
+                if (sip->choice == SEQID_SWISSPROT) {
+                  release = NULL;
+                }
                 if ((format == PRINTID_TEXTID_LOCUS) && (tsip->name != NULL)) {
                     Nlm_LabelCopyNext(&tmp, tsip->name, &buflen);
                     return tmp;
@@ -3788,7 +2894,7 @@ NLM_EXTERN CharPtr SeqIdWrite (SeqIdPtr isip, CharPtr buf, Uint1 format, Uint4 b
                     return tmp;
                 } else if ((format == PRINTID_TEXTID_ACC_VER) 
                     && (tsip->accession != NULL)) {
-                    if (tsip->version > 0 && tsip->release == NULL) {
+                    if (tsip->version > 0 && release == NULL) {
                         sprintf(localbuf, "%s.%d", tsip->accession,
                             (int)(tsip->version));
                     } else {
@@ -3807,6 +2913,12 @@ NLM_EXTERN CharPtr SeqIdWrite (SeqIdPtr isip, CharPtr buf, Uint1 format, Uint4 b
     {
         if (sip->choice == SEQID_PATENT && is_us_pre_grant) {
             Nlm_LabelCopyNext(&tmp, "pgp", &buflen);
+        } else if (sip->choice == SEQID_SWISSPROT) {
+            tsip = (TextSeqIdPtr)sip->data.ptrvalue;
+            if (tsip->release && StringCmp(tsip->release, "unreviewed") == 0)
+                Nlm_LabelCopyNext(&tmp, "tr", &buflen);
+            else
+                Nlm_LabelCopyNext(&tmp, txtid[sip->choice], &buflen);
         } else {
             Nlm_LabelCopyNext(&tmp, txtid[sip->choice], &buflen);
         }
@@ -3844,12 +2956,16 @@ NLM_EXTERN CharPtr SeqIdWrite (SeqIdPtr isip, CharPtr buf, Uint1 format, Uint4 b
         case SEQID_TPE:
         case SEQID_TPD:
         case SEQID_GPIPE:
+        case SEQID_SWISSPROT:
            tsip = (TextSeqIdPtr)(sip->data.ptrvalue);
-       if (((tsip->version > 0) && (tsip->release == NULL)) && SHOWVERSION)
-        version = tsip->version;  /* show versions */
-       sprintf(versionbuf, ".%d", (int)version);
+            release = tsip->release;
+            if (sip->choice == SEQID_SWISSPROT) {
+              release = NULL;
+            }
+           if (((tsip->version > 0) && (release == NULL)) && SHOWVERSION)
+             version = tsip->version;  /* show versions */
+           sprintf(versionbuf, ".%d", (int)version);
         case SEQID_PIR:
-        case SEQID_SWISSPROT:
         case SEQID_PRF:
             tsip = (TextSeqIdPtr)sip->data.ptrvalue;
             if (tsip->accession != NULL)
@@ -4101,6 +3217,7 @@ NLM_EXTERN SeqIdPtr SeqIdParse(CharPtr buf)
     d = *delim;   /* delimiter */
     while (! done)
     {
+        Boolean sp_prelim = FALSE;  /* Used to set release field in Swissprot TextSeqId */
                         /* set all tokens pointing to \0 */
         localbuf[SEQID_PARSE_BUF_SIZE + 1] = '\0';
         for (i = 0; i < 6; i++)
@@ -4134,6 +3251,12 @@ NLM_EXTERN SeqIdPtr SeqIdParse(CharPtr buf)
             is_us_pre_grant = TRUE;
         }
 
+        /* Trembl ID is really Swissprot with release field of TextSeqId set to "unreviewed" */
+        if ((! type) && (! StringCmp(localbuf, "tr"))) {
+            type = SEQID_SWISSPROT;
+            sp_prelim = TRUE;
+        }
+
         if (! type) goto erret;
 
                         /* copy and tokenize - token\0token\0\n */
@@ -4261,6 +3384,13 @@ NLM_EXTERN SeqIdPtr SeqIdParse(CharPtr buf)
                         }
                     }
                 }
+                if (type == SEQID_SWISSPROT)
+                {
+                     if (sp_prelim)
+                        tsip->release = StringSave("unreviewed");
+                     else
+                        tsip->release = StringSave("reviewed");
+                }
                 break;
             case SEQID_PATENT:
                 if ((*tokens[0] == '\0') || (*tokens[1] == '\0')) goto erret;
@@ -9542,7 +8672,12 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
           (StringICmp(temp,"EL") == 0) || 
           (StringICmp(temp,"ES") == 0) || 
           (StringICmp(temp,"EV") == 0) || 
-          (StringICmp(temp,"EW") == 0) ) {                /* NCBI EST */
+          (StringICmp(temp,"EW") == 0) || 
+          (StringICmp(temp,"EX") == 0) || 
+          (StringICmp(temp,"EY") == 0) || 
+          (StringICmp(temp,"FC") == 0) || 
+          (StringICmp(temp,"FD") == 0) || 
+          (StringICmp(temp,"FE") == 0) ) {                /* NCBI EST */
               retcode = ACCN_NCBI_EST;
           } else if ((StringICmp(temp,"BV") == 0)) {      /* NCBI STS */
               retcode = ACCN_NCBI_STS;
@@ -9567,7 +8702,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
                      (StringICmp(temp,"EM") == 0) ||
                      (StringICmp(temp,"EN") == 0) ||
                      (StringICmp(temp,"EP") == 0) ||
-                     (StringICmp(temp,"EQ") == 0)) {      /* NCBI segmented set header Bioseq */
+                     (StringICmp(temp,"EQ") == 0) ||
+                     (StringICmp(temp,"FA") == 0)) {      /* NCBI segmented set header Bioseq */
               retcode = ACCN_NCBI_SEGSET;
           } else if ((StringICmp(temp,"AS") == 0)) {      /* NCBI "other" */
               retcode = ACCN_NCBI_OTHER;
@@ -9603,12 +8739,15 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
           } else if((StringICmp(temp,"BK")==0) ||         /* NCBI third-party annotation */
                     (StringICmp(temp,"BL") == 0)) {
               retcode = ACCN_NCBI_TPA;
+          } else if((StringICmp(temp,"EZ") == 0)) {
+              retcode = ACCN_NCBI_TSA;
           } else if ((StringICmp(temp,"BN") == 0)) {      /* EMBL third-party annotation */
               retcode = ACCN_EMBL_TPA;
           } else if ((StringICmp(temp,"BR") == 0)) {      /* DDBJ third-party annotation */
               retcode = ACCN_DDBJ_TPA;
           } else if ((StringICmp(temp,"AJ") == 0) ||
-                     (StringICmp(temp,"AM") == 0)) {     /* EMBL direct submission */
+                     (StringICmp(temp,"AM") == 0) ||
+                     (StringICmp(temp,"FM") == 0)) {     /* EMBL direct submission */
               retcode = ACCN_EMBL_DIRSUB;
           } else if ((StringICmp(temp,"AL") == 0) ||
                      (StringICmp(temp,"BX") == 0)||
@@ -9620,7 +8759,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
               retcode = ACCN_EMBL_CON;
           } else if ((StringICmp(temp,"AX") == 0) ||
                      (StringICmp(temp,"CQ") == 0) ||
-                     (StringICmp(temp,"CS") == 0)) {      /* EMBL patent division */
+                     (StringICmp(temp,"CS") == 0) ||
+                     (StringICmp(temp,"FB") == 0)) {      /* EMBL patent division */
               retcode = ACCN_EMBL_PATENT;
           } else if ((StringICmp(temp,"AT") == 0) || 
                      (StringICmp(temp,"AU") == 0) ||
@@ -9650,7 +8790,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
               retcode = ACCN_DDBJ_CON;
           } else if ((StringICmp(temp,"BD") == 0) ||
                      (StringICmp(temp,"DD") == 0) || 
-                     (StringICmp(temp,"DI") == 0)) {      /* DDBJ patent division */
+                     (StringICmp(temp,"DI") == 0) || 
+                     (StringICmp(temp,"DJ") == 0)) {      /* DDBJ patent division */
               retcode = ACCN_DDBJ_PATENT;
           } else if ((StringICmp(temp,"DE") == 0) ||
                      (StringICmp(temp,"DH") == 0)) {      /* DDBJ GSS */
@@ -9683,7 +8824,7 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
       temp[1] = *s; s++;
       temp[2] = NULLB; s++;
       
-      if ((StringICmp(temp,"NP") == 0)) { 
+      if ((StringICmp(temp,"NP") == 0) || (StringICmp(temp,"AP") == 0)) { 
           retcode = ACCN_REFSEQ_PROT;
       } else if ((StringICmp(temp,"NM") == 0)) { 
           retcode = ACCN_REFSEQ_mRNA;
@@ -9697,8 +8838,10 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
           retcode = ACCN_REFSEQ_mRNA_PREDICTED;
       } else if ((StringICmp(temp,"XP") == 0)) { 
           retcode = ACCN_REFSEQ_PROT_PREDICTED;
-      } else if ((StringICmp(temp,"NG") == 0)) { 
+      } else if ((StringICmp(temp,"NG") == 0) || (StringICmp(temp,"AC") == 0)) { 
           retcode = ACCN_REFSEQ_GENOMIC;
+      } else if ((StringICmp(temp,"NS") == 0)) { 
+          retcode = ACCN_REFSEQ_ARTIFICIAL_ASSEMBLY;
       } else if (IS_ALPHA(*temp) && IS_ALPHA(*(temp+1))) {
           retcode =ACCN_REFSEQ | ACCN_AMBIGOUS_MOL;
       } else
diff --git a/api/sequtil.h b/api/sequtil.h
index 470c7b23..5d0f0b8f 100644
--- a/api/sequtil.h
+++ b/api/sequtil.h
@@ -29,13 +29,19 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.52 $
+* $Revision: 6.54 $
 *
 * File Description:  Sequence Utilities for objseq and objsset
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: sequtil.h,v $
+* Revision 6.54  2008/02/12 16:30:29  kans
+* added ACCN_REFSEQ_ARTIFICIAL_ASSEMBLY for NS_
+*
+* Revision 6.53  2008/01/25 22:31:48  kans
+* added ACCN_XXXX_TSA and ACCN_XXXX_TSA_PROT, EZ as NCBI TSA accession
+*
 * Revision 6.52  2007/03/13 18:03:45  kans
 * added FreeSeqLocSetComponents to free sequence records referenced in a chain of SeqLocs
 *
@@ -1218,6 +1224,15 @@ NLM_EXTERN Boolean LIBCALL NAccnIsDDBJ (CharPtr s);
 
 #define ACCN_DDBJ_GSS 61
 
+#define ACCN_NCBI_TSA 62
+#define ACCN_NCBI_TSA_PROT 63
+#define ACCN_EMBL_TSA 64
+#define ACCN_EMBL_TSA_PROT 65
+#define ACCN_DDBJ_TSA 66
+#define ACCN_DDBJ_TSA_PROT 67
+
+#define ACCN_REFSEQ_ARTIFICIAL_ASSEMBLY 68
+
 
 /* Some accessions prefix can be either protein or nucleotide 
    such as NCBI PATENT I, AR .. or segmented set Bioseqs 'AH'
@@ -1247,18 +1262,20 @@ NLM_EXTERN Boolean LIBCALL NAccnIsDDBJ (CharPtr s);
    Define to detect Genbank's accessions: Genbank-subsumed GSDB accession numbers
    are defined to be Genbank's as well as GSDB DIRSUB records.
 */
-#define ACCN_IS_GENBANK(c) ((((c)&65535) == ACCN_NCBI_GSDB) ||  (((c)&65535)==ACCN_GSDB_DIRSUB) || (((c)&65535) == ACCN_NCBI_EST) ||  (((c)&65535) == ACCN_NCBI_DIRSUB) ||  (((c)&65535) == ACCN_NCBI_GENOME) ||  (((c)&65535) == ACCN_NCBI_PATENT) ||  (((c)&65535) == ACCN_NCBI_HTGS) ||  (((c)&65535) == ACCN_NCBI_GSS) ||  (((c)&65535) == ACCN_NCBI_STS) ||  (((c)&65535) == ACCN_NCBI_BACKBONE) ||  (((c)&65535) == ACCN_NCBI_SEGSET)  ||  (((c)&65535) == ACCN_NCBI_WGS) ||  (((c)&65535) == ACCN_NCBI_OTHER)  || (((c)&65535) == ACCN_NCBI_PROT) || (((c)&65535) == ACCN_NCBI_cDNA) || (((c)&65535) == ACCN_EMBL_GB) || (((c)&65535) == ACCN_EMBL_GB_DDBJ || (((c)&65535) == ACCN_GB_DDBJ)) )
+#define ACCN_IS_GENBANK(c) ((((c)&65535) == ACCN_NCBI_GSDB) ||  (((c)&65535)==ACCN_GSDB_DIRSUB) || (((c)&65535) == ACCN_NCBI_EST) ||  (((c)&65535) == ACCN_NCBI_DIRSUB) ||  (((c)&65535) == ACCN_NCBI_GENOME) ||  (((c)&65535) == ACCN_NCBI_PATENT) ||  (((c)&65535) == ACCN_NCBI_HTGS) ||  (((c)&65535) == ACCN_NCBI_GSS) ||  (((c)&65535) == ACCN_NCBI_STS) ||  (((c)&65535) == ACCN_NCBI_BACKBONE) ||  (((c)&65535) == ACCN_NCBI_SEGSET)  ||  (((c)&65535) == ACCN_NCBI_WGS) ||  (((c)&65535) == ACCN_NCBI_OTHER)  || (((c)&65535) == ACCN_NCBI_PROT) || (((c)&65535) == ACCN_NCBI_cDNA) || (((c)&65535) == ACCN_NCBI_TSA) || (((c)&65535) == ACCN_NCBI_TSA_PROT) || (((c)&65535) == ACCN_EMBL_GB) || (((c)&65535) == ACCN_EMBL_GB_DDBJ || (((c)&65535) == ACCN_GB_DDBJ)) )
 
 /* XM_,NP_,NM_,NT_,NC_ reference sequence records created and curated by NCBI 
    REFSEQ project
 */
-#define ACCN_IS_REFSEQ(c) (((c)== ACCN_REFSEQ_PROT) || ((c)== ACCN_REFSEQ_mRNA) || ((c)== ACCN_REFSEQ_CONTIG) || ((c)== ACCN_REFSEQ_CHROMOSOME) || ((c)== ACCN_REFSEQ_mRNA_PREDICTED) || ((c)== ACCN_REFSEQ_PROT_PREDICTED) || ((c)== ACCN_REFSEQ_GENOMIC) || (((c)&65535)== ACCN_REFSEQ) )
+#define ACCN_IS_REFSEQ(c) (((c)== ACCN_REFSEQ_PROT) || ((c)== ACCN_REFSEQ_mRNA) || ((c)== ACCN_REFSEQ_CONTIG) || ((c)== ACCN_REFSEQ_CHROMOSOME) || ((c)== ACCN_REFSEQ_mRNA_PREDICTED) || ((c)== ACCN_REFSEQ_PROT_PREDICTED) || ((c)== ACCN_REFSEQ_GENOMIC) || ((c)== ACCN_REFSEQ_ARTIFICIAL_ASSEMBLY) || (((c)&65535)== ACCN_REFSEQ) )
 
 #define ACCN_IS_TPA(c) (((c)== ACCN_NCBI_TPA) || ((c)== ACCN_NCBI_TPA_PROT) || ((c)== ACCN_EMBL_TPA) || ((c)== ACCN_EMBL_TPA_PROT) || ((c)== ACCN_DDBJ_TPA) || ((c)== ACCN_DDBJ_TPA_PROT))
 
 #define ACCN_IS_WGS(c) (((c)== ACCN_NCBI_WGS) || ((c)== ACCN_NCBI_WGS_PROT) || ((c)== ACCN_EMBL_WGS) || ((c)== ACCN_EMBL_WGS_PROT) || ((c)== ACCN_DDBJ_WGS) || ((c)== ACCN_DDBJ_WGS_PROT))
 
-#define ACCN_IS_NCBI(c) (ACCN_IS_REFSEQ((c)) || ACCN_IS_GENBANK((c)) || ((c)== ACCN_NCBI_TPA) || ((c)== ACCN_NCBI_TPA_PROT) || ((c)== ACCN_NCBI_WGS) || ((c)== ACCN_NCBI_WGS_PROT))
+#define ACCN_IS_TSA(c) (((c)== ACCN_NCBI_TSA) || ((c)== ACCN_NCBI_TSA_PROT) || ((c)== ACCN_EMBL_TSA) || ((c)== ACCN_EMBL_TSA_PROT) || ((c)== ACCN_DDBJ_TSA) || ((c)== ACCN_DDBJ_TSA_PROT))
+
+#define ACCN_IS_NCBI(c) (ACCN_IS_REFSEQ((c)) || ACCN_IS_GENBANK((c)) || ((c)== ACCN_NCBI_TPA) || ((c)== ACCN_NCBI_TPA_PROT) || ((c)== ACCN_NCBI_WGS) || ((c)== ACCN_NCBI_WGS_PROT) || ((c)== ACCN_NCBI_TSA))
 
 /*
   Macro to detect EMBL accession numbers  (can also belong to another DB)
diff --git a/api/sqnutil1.c b/api/sqnutil1.c
index 623c5750..cf854efb 100644
--- a/api/sqnutil1.c
+++ b/api/sqnutil1.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.415 $
+* $Revision: 6.433 $
 *
 * File Description: 
 *
@@ -1976,7 +1976,7 @@ NLM_EXTERN void PromoteXrefsExEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID,
     sfp = first;
     while (sfp != NULL) {
       if (sfp->data.choice == SEQFEAT_RNA &&
-          sfp->idx.subtype != FEATDEF_tRNA &&
+          /* sfp->idx.subtype != FEATDEF_tRNA && */
           sfp->product == NULL && (! sfp->pseudo)) {
         gbq = sfp->qual;
         prevqual = (GBQualPtr PNTR) &(sfp->qual);
@@ -2090,6 +2090,12 @@ NLM_EXTERN void PromoteXrefsExEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID,
                       case FEATDEF_snoRNA :
                         mip->biomol = MOLECULE_TYPE_SNORNA;
                         break;
+                      case FEATDEF_ncRNA :
+                        mip->biomol = MOLECULE_TYPE_NCRNA;
+                        break;
+                      case FEATDEF_tmRNA :
+                        mip->biomol = MOLECULE_TYPE_TMRNA;
+                        break;
                       default :
                         mip->biomol = 0;
                         break;
@@ -3516,6 +3522,7 @@ static Boolean HandledGBQualOnCDS (SeqFeatPtr sfp, GBQualPtr gbq, ValNodePtr PNT
   return FALSE;
 }
 
+
 static Boolean HandledGBQualOnRNA (SeqFeatPtr sfp, GBQualPtr gbq, Boolean isEmblOrDdbj)
 
 {
@@ -3612,10 +3619,7 @@ static Boolean HandledGBQualOnRNA (SeqFeatPtr sfp, GBQualPtr gbq, Boolean isEmbl
           return TRUE;
         }
       }
-      if (rrp->type == 255 &&
-          (StringICmp (name, "misc_RNA") == 0 ||
-           StringICmp (name, "ncRNA") == 0 ||
-           StringICmp (name, "tmRNA") == 0)) {
+      if (rrp->type == 255) {
         /* new convention follows ASN.1 spec comments, allows new RNA types */
         return FALSE;
       }
@@ -4314,12 +4318,12 @@ static void CleanupFeatureGBQuals (SeqFeatPtr sfp, Boolean isEmblOrDdbj)
         sfp->comment = str;
       }
     } else if (StringICmp (gbq->qual, "db_xref") == 0) {
-      vnp = ValNodeNew (NULL);
-      db = DbtagNew ();
-      vnp->data.ptrvalue = db;
       tag = gbq->val;
       ptr = StringChr (tag, ':');
       if (ptr != NULL) {
+        vnp = ValNodeNew (NULL);
+        db = DbtagNew ();
+        vnp->data.ptrvalue = db;
         *ptr = '\0';
         ptr++;
         db->db = StringSave (tag);
@@ -4760,13 +4764,54 @@ static OrgModPtr SortOrgModList (OrgModPtr list)
   return list;
 }
 
-static void CleanOrgModList (OrgModPtr PNTR ompp)
 
+static void RemoveSpaceBeforeAndAfterColon (CharPtr str)
 {
+  CharPtr pColon, cp, src, dst;
+
+  if (StringHasNoText (str)) {
+    return;
+  }
+
+  pColon = StringChr (str, ':');
+  while (pColon != NULL) {
+    cp = pColon - 1;
+    while (cp > str && isspace (*cp)) {
+      cp--;
+    }
+    if (cp < str || !isspace (*cp)) {
+      cp++;
+    }
+    *cp = ':';
+    dst = cp + 1;
+    cp = pColon + 1;
+    while (isspace (*cp)) {
+      cp++;
+    }
+    src = cp;
+    pColon = dst - 1;
+    if (src != dst) {
+      while (*src != 0) {
+        *dst = *src;
+        dst++; src++;
+      }
+      *dst = 0;
+    }
+    pColon = StringChr (pColon + 1, ':');
+  }
+}
+
+
+NLM_EXTERN void CleanOrgModList (OrgModPtr PNTR ompp)
+
+{
+  Char            ch;
   OrgModPtr       last = NULL;
   OrgModPtr       next;
   OrgModPtr       omp;
   OrgModPtr PNTR  prev;
+  CharPtr         ptr;
+  CharPtr         tmp;
   Boolean         unlink;
 
   if (ompp == NULL) return;
@@ -4793,6 +4838,8 @@ static void CleanOrgModList (OrgModPtr PNTR ompp)
         omp->subname = NULL;
         unlink = TRUE;
       }
+    } else if (HasNoText (omp->subname)) {
+      unlink = TRUE;
     } else {
       last = omp;
     }
@@ -4806,6 +4853,28 @@ static void CleanOrgModList (OrgModPtr PNTR ompp)
     }
     omp = next;
   }
+
+  for (omp = *ompp; omp != NULL; omp = omp->next) {
+    if (omp->subtype != ORGMOD_specimen_voucher &&
+        omp->subtype != ORGMOD_culture_collection &&
+        omp->subtype != ORGMOD_bio_material) continue;
+    if (StringHasNoText (omp->subname)) continue;
+    RemoveSpaceBeforeAndAfterColon (omp->subname);
+    ptr = StringStr (omp->subname, "::");
+    if (ptr == NULL) continue;
+    ptr++;
+    tmp = ptr;
+    tmp++;
+    ch = *tmp;
+    while (ch != '\0') {
+      *ptr = ch;
+      ptr++;
+      tmp++;
+      ch = *tmp;
+    }
+    *ptr = '\0';
+    
+  }
 }
 
 static int LIBCALLBACK SortBySubSourceSubtype (VoidPtr ptr1, VoidPtr ptr2)
@@ -4936,7 +5005,29 @@ static CharPtr CombineSplitQual (CharPtr origval, CharPtr newval)
   return str;
 }
 
-static void CleanSubSourceList (SubSourcePtr PNTR sspp)
+static Uint1 LocationForPlastidText (CharPtr plastid_name)
+{
+  if (StringICmp (plastid_name, "chloroplast") == 0) {
+    return GENOME_chloroplast;
+  } else if (StringICmp (plastid_name, "chromoplast") == 0) {
+    return GENOME_chromoplast;
+  } else if (StringICmp (plastid_name, "kinetoplast") == 0) {
+    return GENOME_kinetoplast;
+  } else if (StringICmp (plastid_name, "plastid") == 0) {
+    return GENOME_plastid;
+  } else if (StringICmp (plastid_name, "apicoplast") == 0) {
+    return GENOME_apicoplast;
+  } else if (StringICmp (plastid_name, "leucoplast") == 0) {
+    return GENOME_leucoplast;
+  } else if (StringICmp (plastid_name, "proplastid") == 0) {
+    return GENOME_proplastid;
+  } else {
+    return 0;
+  }
+}
+
+
+extern void CleanSubSourceList (SubSourcePtr PNTR sspp, Uint1 location)
 
 {
   Char               ch;
@@ -5059,6 +5150,17 @@ static void CleanSubSourceList (SubSourcePtr PNTR sspp)
         ssp->name = NULL;
         unlink = TRUE;
       }
+    } else if (HasNoText (ssp->name) &&
+               ssp->subtype != SUBSRC_germline &&
+               ssp->subtype != SUBSRC_rearranged &&
+               ssp->subtype != SUBSRC_transgenic &&
+               ssp->subtype != SUBSRC_environmental_sample &&
+               ssp->subtype != SUBSRC_metagenomic) {
+      unlink = TRUE;
+    } else if (ssp->subtype == SUBSRC_plastid_name &&
+               location != 0
+               && location == LocationForPlastidText (ssp->name)) {
+      unlink = TRUE;
     } else {
       last = ssp;
     }
@@ -5412,7 +5514,6 @@ Nlm_QualNameAssoc current_subsource_subtype_alist[] = {
   {"Map",                   SUBSRC_map},
   {"Metagenomic",           SUBSRC_metagenomic},
   {"Plasmid-name",          SUBSRC_plasmid_name},
-  {"Plastid-name",          SUBSRC_plastid_name},
   {"Pop-variant",           SUBSRC_pop_variant},
   {"Rearranged",            SUBSRC_rearranged},
   {"Rev-PCR-primer-name",   SUBSRC_rev_primer_name},
@@ -5426,6 +5527,7 @@ Nlm_QualNameAssoc current_subsource_subtype_alist[] = {
   { NULL, 0 } };
 
 Nlm_QualNameAssoc discouraged_subsource_subtype_alist[] = {
+  {"Plastid-name",          SUBSRC_plastid_name},
   { NULL, 0 } };
 
 Nlm_QualNameAssoc discontinued_subsource_subtype_alist[] = {
@@ -6673,10 +6775,13 @@ static void NormalizePubdesc (PubdescPtr pdp, Boolean stripSerial, ValNodePtr PN
 {
   Char             buf1 [121];
   Char             buf2 [121];
+  CitArtPtr        cap;
   CitGenPtr        cgp;
+  CitJourPtr       cjp;
   Boolean          fixInitials = TRUE;
   Boolean          hasArt = FALSE;
   Boolean          hasUid = FALSE;
+  ImprintPtr       imp;
   ValNodePtr       next;
   ValNodePtr PNTR  prev;
   ValNodePtr       vnp;
@@ -6735,6 +6840,23 @@ static void NormalizePubdesc (PubdescPtr pdp, Boolean stripSerial, ValNodePtr PN
     buf1 [0] = '\0';
     PubLabelUnique (vnp, buf1, sizeof (buf1) - 1, OM_LABEL_CONTENT, TRUE);
     NormalizeAPub (vnp, stripSerial, fixInitials);
+    if (vnp->choice == PUB_Article) {
+      cap = (CitArtPtr) vnp->data.ptrvalue;
+      if (cap != NULL && cap->from == 1) {
+        cjp = (CitJourPtr) cap->fromptr;
+        if (cjp != NULL) {
+          imp = cjp->imp;
+          if (imp != NULL) {
+            if (imp->pubstatus == PUBSTATUS_aheadofprint && imp->prepub != 2) {
+              imp->prepub = 2;
+            }
+            if (imp->pubstatus == PUBSTATUS_epublish && imp->prepub == 2) {
+              imp->prepub = 0;
+            }
+          }
+        }
+      }
+    }
     if (vnp->choice == PUB_Gen && empty_citgen ((CitGenPtr) vnp->data.ptrvalue)) {
       *prev = vnp->next;
       vnp->next = NULL;
@@ -7534,11 +7656,13 @@ static void CleanupFeatureStrings (SeqFeatPtr sfp, Boolean stripSerial, ValNodeP
   BioSourcePtr  biop;
   Char          ch;
   Uint1         codon [6];
+  GBQualPtr     gbq;
   GeneRefPtr    grp;
   ImpFeatPtr    ifp;
   Boolean       is_fMet = FALSE;
   Int2          j;
   Boolean       justTrnaText;
+  GBQualPtr     last;
   size_t        len;
   CharPtr       name;
   OrgNamePtr    onp;
@@ -7923,9 +8047,14 @@ static void CleanupFeatureStrings (SeqFeatPtr sfp, Boolean stripSerial, ValNodeP
             name++;
             ch = *name;
           }
+          /*
           if (ch == 's' && StringCmp (name, "s ribosomal RNA") == 0) {
             *name = 'S';
           }
+          */
+          if (ch == 's' && name [1] == ' ') {
+            *name = 'S';
+          }
         }
         StrStripSpaces ((CharPtr) rrp->ext.value.ptrvalue);
         name = (CharPtr) rrp->ext.value.ptrvalue;
@@ -8049,6 +8178,41 @@ static void CleanupFeatureStrings (SeqFeatPtr sfp, Boolean stripSerial, ValNodeP
           rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
           rrp->ext.value.ptrvalue = StringSave ("internal transcribed spacer 3");
         }
+
+        name = (CharPtr) rrp->ext.value.ptrvalue;
+        if (StringNICmp (name, "internal transcribed spacer", 27) == 0) {
+          gbq = GBQualNew ();
+          if (gbq != NULL) {
+            rrp->ext.value.ptrvalue = StringSave ("misc_RNA");
+            gbq->qual = StringSave ("product");
+            gbq->val = name;
+            if (sfp->qual == NULL) {
+              sfp->qual = gbq;
+            } else {
+              last = sfp->qual;
+              while (last->next != NULL) {
+                last = last->next;
+              }
+              last->next = gbq;
+            }
+          }
+        }
+
+        for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
+          if (StringCmp (gbq->qual, "product") != 0) continue;
+          name = gbq->val;
+          if (StringHasNoText (name)) continue;
+          if (StringICmp (name, "its1") == 0 || StringICmp (name, "its 1") == 0) {
+            gbq->val = MemFree (gbq->val);
+            gbq->val = StringSave ("internal transcribed spacer 1");
+          } else if (StringICmp (name, "its2") == 0 || StringICmp (name, "its 2") == 0) {
+            gbq->val = MemFree (gbq->val);
+            gbq->val = StringSave ("internal transcribed spacer 2");
+          } else if (StringICmp (name, "its3") == 0 || StringICmp (name, "its 3") == 0) {
+            gbq->val = MemFree (gbq->val);
+            gbq->val = StringSave ("internal transcribed spacer 3");
+          }
+        }
       }
       break;
     case SEQFEAT_PUB :
@@ -8099,8 +8263,8 @@ static void CleanupFeatureStrings (SeqFeatPtr sfp, Boolean stripSerial, ValNodeP
         CleanVisStringList (&(orp->mod));
         OrpModToSubSource (&(orp->mod), &(biop->subtype));
       }
-      CleanSubSourceList (&(biop->subtype));
       biop->subtype = SortSubSourceList (biop->subtype);
+      CleanSubSourceList (&(biop->subtype), biop->genome);
       break;
     default :
       break;
@@ -8245,8 +8409,8 @@ static void CleanupDescriptorStrings (ValNodePtr sdp, Boolean stripSerial, ValNo
         CleanVisStringList (&(orp->mod));
         OrpModToSubSource (&(orp->mod), &(biop->subtype));
       }
-      CleanSubSourceList (&(biop->subtype));
       biop->subtype = SortSubSourceList (biop->subtype);
+      CleanSubSourceList (&(biop->subtype), biop->genome);
       break;
     case Seq_descr_molinfo :
       break;
@@ -8603,6 +8767,7 @@ static CodeBreakPtr SortCodeBreaks (SeqFeatPtr sfp, CodeBreakPtr list)
     if (head [i].pos < pos) {
       out_of_order = TRUE;
     }
+    pos = head [i].pos;
   }
 
   if (out_of_order) {
@@ -8655,6 +8820,195 @@ static void CleanupDuplicatedCodeBreaks (CodeBreakPtr PNTR prevcbp)
   }
 }
 
+
+CharPtr ncrnaClassList[] = {
+"antisense_RNA",
+"autocatalytically_spliced_intron",
+"hammerhead_ribozyme",
+"RNase_P_RNA",
+"RNase_MRP_RNA",
+"telomerase_RNA",
+"guide_RNA",
+"rasiRNA",
+"scRNA",
+"siRNA",
+"miRNA",
+"piRNA",
+"snoRNA",
+"snRNA",
+"SRP_RNA",
+"vault_RNA",
+"Y_RNA",
+"other",
+NULL};
+
+Int4 NcrnaOTHER = sizeof (ncrnaClassList) / sizeof (CharPtr) - 1;
+
+
+extern Boolean IsStringInNcRNAClassList (CharPtr str)
+{
+  CharPtr PNTR p;
+
+  if (StringHasNoText (str)) return FALSE;
+  for (p = ncrnaClassList; *p != NULL; p++)
+  {
+    if (StringICmp (str, *p) == 0)
+    {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+
+static void AddNonCopiedQual (SeqFeatPtr sfp, CharPtr qual, CharPtr class_val)
+{
+  GBQualPtr gbq;
+
+  if (sfp == NULL || StringHasNoText (qual) || StringHasNoText (class_val)) 
+  {
+    return;
+  }
+  gbq = sfp->qual;
+  while (gbq != NULL 
+          && (StringCmp (gbq->qual, qual) != 0
+              || StringCmp (gbq->val, class_val) != 0))
+  {
+    gbq = gbq->next;
+  }
+  if (gbq == NULL)
+  {
+    gbq = GBQualNew ();
+    gbq->qual = StringSave (qual);
+    gbq->val = StringSave (class_val);
+    gbq->next = sfp->qual;
+    sfp->qual = gbq;
+  }
+
+}
+
+
+static CharPtr GetMiRNAProduct (CharPtr str)
+{
+  Int4    len;
+  CharPtr product = NULL;
+
+  if (StringHasNoText (str)) return NULL;
+  if (StringNCmp (str, "miRNA ", 6) == 0)
+  {
+    product = StringSave (str + 6);
+  }
+  else if (StringNCmp (str, "microRNA ", 9) == 0)
+  {
+    product = StringSave (str + 9);
+  }
+  else
+  {
+    len = StringLen (str);
+    if (len > 6 && StringCmp (str + len - 6, " miRNA") == 0
+        && (len < 15 || StringCmp (str - 15, "precursor miRNA") != 0))
+    {
+      product = (CharPtr) MemNew (sizeof (Char) * (len - 5));
+      StringNCpy (product, str, len - 6);
+      product[len - 6] = 0;
+    }
+    else if (len > 9 && StringCmp (str + len - 9, " microRNA") == 0
+             && (len < 21 || StringCmp (str - 21, "precursor microRNA") != 0))
+    {
+      product = (CharPtr) MemNew (sizeof (Char) * (len - 8));
+      StringNCpy (product, str, len - 9);
+      product[len - 9] = 0;
+    }
+  }
+  return product;
+}
+
+
+static Boolean ConvertToNcRNA (SeqFeatPtr sfp)
+{
+  GBQualPtr gbq;
+  RnaRefPtr rrp;
+  Boolean was_converted = FALSE;
+  CharPtr miRNAproduct = NULL;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL)
+  {
+    return FALSE;
+  }
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (rrp->type == 5 || rrp->type == 6 || rrp->type == 7)
+  {
+    if (rrp->type == 5)
+    {
+      AddNonCopiedQual (sfp, "ncRNA_class", "snRNA");
+    }
+    else if (rrp->type == 6)
+    {
+      AddNonCopiedQual (sfp, "ncRNA_class", "scRNA");
+    }
+    else if (rrp->type == 7)
+    {
+      AddNonCopiedQual (sfp, "ncRNA_class", "snoRNA");
+    }
+    if (rrp->ext.choice == 1)
+    {
+      AddNonCopiedQual (sfp, "product", rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+    }
+    rrp->ext.choice = 1;
+    rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+    rrp->type = 255;
+    was_converted = TRUE;
+  }
+  else if (rrp->type == 255 && rrp->ext.choice == 1)
+  {
+    if (IsStringInNcRNAClassList (rrp->ext.value.ptrvalue)) 
+    {
+      AddNonCopiedQual (sfp, "ncRNA_class", rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+      was_converted = TRUE;
+    }
+    else if ((miRNAproduct = GetMiRNAProduct (rrp->ext.value.ptrvalue)) != NULL)
+    {
+      AddNonCopiedQual (sfp, "ncRNA_class", "miRNA");
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+      AddNonCopiedQual (sfp, "product", miRNAproduct);
+      miRNAproduct = MemFree (miRNAproduct);
+      was_converted = TRUE;
+    }
+    else if (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0
+             && StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0
+             && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") != 0)
+    {
+      AddNonCopiedQual (sfp, "product", rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = StringSave ("misc_RNA");
+    }
+  }
+  if (rrp->type == 255 && rrp->ext.choice == 0) {
+    rrp->ext.choice = 1;
+    rrp->ext.value.ptrvalue = StringSave ("misc_RNA");
+  }
+  if (rrp->type == 255 && rrp->ext.choice == 1 &&
+      StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0) {
+    for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
+      if (StringCmp (gbq->qual, "ncRNA_class") == 0) {
+        rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+        rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+        was_converted = TRUE;
+      } else if (StringCmp (gbq->qual, "tag_peptide") == 0) {
+        rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+        rrp->ext.value.ptrvalue = StringSave ("tmRNA");
+        was_converted = TRUE;
+      }
+    }
+  }
+  return was_converted;
+}
+
+
 NLM_EXTERN void CleanUpSeqFeat (
   SeqFeatPtr sfp,
   Boolean isEmblOrDdbj,
@@ -8843,6 +9197,9 @@ NLM_EXTERN void CleanUpSeqFeat (
         }
       }
     }
+    if (ConvertToNcRNA (sfp)) {
+      sfp->idx.subtype = FindFeatDefType (sfp);
+    }
   } else if (sfp->data.choice == SEQFEAT_REGION ||
              sfp->data.choice == SEQFEAT_SITE ||
              sfp->data.choice == SEQFEAT_BOND ||
@@ -8926,6 +9283,8 @@ static void BasicSeqEntryCleanupInternal (SeqEntryPtr sep, ValNodePtr PNTR publi
             case MOLECULE_TYPE_CRNA :
             case MOLECULE_TYPE_SNORNA :
             case MOLECULE_TYPE_TRANSCRIBED_RNA :
+            case MOLECULE_TYPE_NCRNA :
+            case MOLECULE_TYPE_TMRNA :
               bsp->mol = Seq_mol_rna;
               break;
             case MOLECULE_TYPE_PEPTIDE :
diff --git a/api/sqnutil2.c b/api/sqnutil2.c
index 6164be8f..5a439145 100644
--- a/api/sqnutil2.c
+++ b/api/sqnutil2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.290 $
+* $Revision: 6.310 $
 *
 * File Description: 
 *
@@ -54,6 +54,8 @@
 #include <tofasta.h>
 #include <simple.h>
 #include <validerr.h>
+#include <findrepl.h>
+#include <alignmgr2.h>
 
 static CharPtr SqnTrimSpacesAroundString (CharPtr str)
 
@@ -1962,7 +1964,7 @@ NLM_EXTERN BioSourcePtr ParseTitleIntoBioSource (
 static CharPtr molinfo_biomol_list [] = {
   "?", "genomic", "precursor RNA", "mRNA", "rRNA", "tRNA", "snRNA",
   "scRNA", "peptide", "other-genetic", "genomic-mRNA", "cRNA", "snoRNA",
-  "transcribed RNA", NULL
+  "transcribed RNA", "non-coding RNA", "transfer-messenger RNA", NULL
 };
 
 static CharPtr molinfo_tech_list [] = {
@@ -5219,6 +5221,7 @@ static CharPtr okayInferencePrefixes [] = {
   "nucleotide motif",
   "protein motif",
   "ab initio prediction",
+  "alignment",
   NULL
 };
 
@@ -5793,14 +5796,15 @@ static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val,
             sfp->comment = str;
           }
         }
-      } else {
+        return;
+      } else if (rrp->type != 255) {
         if (rrp->ext.choice == 1) {
           rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
         }
         rrp->ext.choice = 1;
         rrp->ext.value.ptrvalue = StringSave (val);
+        return;
       }
-      return;
     } else if (qnum == GBQUAL_anticodon) {
       if (ParseAnticodon (sfp, val, offset)) return;
     }
@@ -6052,6 +6056,7 @@ static SeqAnnotPtr ReadFeatureTable (FileCachePtr fcp, CharPtr seqid, CharPtr an
   GeneRefPtr     grp;
   Int2           idx;
   ImpFeatPtr     ifp;
+  Boolean        inquals = FALSE;
   Boolean        isminus;
   Boolean        isnote;
   Boolean        ispoint;
@@ -6210,13 +6215,32 @@ static SeqAnnotPtr ReadFeatureTable (FileCachePtr fcp, CharPtr seqid, CharPtr an
                 } else if (StringCmp (feat, "rRNA") == 0) {
                   rnatype = 4;
                 } else if (StringCmp (feat, "snRNA") == 0) {
-                  rnatype = 5;
+                  rnatype = 255;
+                  rrp->ext.choice = 1;
+                  rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+                  AddQualifierToFeatureEx (sfp, "ncRNA_class", feat, offset, lin_num);
                 } else if (StringCmp (feat, "scRNA") == 0) {
-                  rnatype = 6;
+                  rnatype = 255;
+                  rrp->ext.choice = 1;
+                  rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+                  AddQualifierToFeatureEx (sfp, "ncRNA_class", feat, offset, lin_num);
                 } else if (StringCmp (feat, "snoRNA") == 0) {
-                  rnatype = 7;
+                  rnatype = 255;
+                  rrp->ext.choice = 1;
+                  rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+                  AddQualifierToFeatureEx (sfp, "ncRNA_class", feat, offset, lin_num);
                 } else if (StringCmp (feat, "misc_RNA") == 0) {
                   rnatype = 255;
+                  rrp->ext.choice = 1;
+                  rrp->ext.value.ptrvalue = StringSave ("misc_RNA");
+                } else if (StringCmp (feat, "ncRNA") == 0) {
+                  rnatype = 255;
+                  rrp->ext.choice = 1;
+                  rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+                } else if (StringCmp (feat, "tmRNA") == 0) {
+                  rnatype = 255;
+                  rrp->ext.choice = 1;
+                  rrp->ext.value.ptrvalue = StringSave ("tmRNA");
                 }
                 rrp->type = rnatype;
               }
@@ -6329,12 +6353,21 @@ static SeqAnnotPtr ReadFeatureTable (FileCachePtr fcp, CharPtr seqid, CharPtr an
             }
           }
 
+          inquals = FALSE;
+
         } else if (start >= 0 && stop >= 0 && feat == NULL && qual == NULL && val == NULL && sfp != NULL) {
 
-          sfp->location = AddIntervalToLocation (sfp->location, sip, start, stop, partial5, partial3);
+          if (inquals) {
 
-          if (partial5 || partial3) {
-            sfp->partial = TRUE;
+            ErrPostEx (SEV_ERROR, ERR_SEQ_FEAT_ImpFeatBadLoc, "Unexpected intervals after qualifiers (start %ld, stop %ld)", (long) start, (long) stop);
+
+          } else {
+
+            sfp->location = AddIntervalToLocation (sfp->location, sip, start, stop, partial5, partial3);
+
+            if (partial5 || partial3) {
+              sfp->partial = TRUE;
+            }
           }
 
         } else if (sfp != NULL && qual != NULL &&
@@ -6348,6 +6381,8 @@ static SeqAnnotPtr ReadFeatureTable (FileCachePtr fcp, CharPtr seqid, CharPtr an
           }
           AddQualifierToFeatureEx (sfp, qual, val, offset, lin_num);
 
+          inquals = TRUE;
+
         } else if (sfp != NULL && qual != NULL && val == NULL) {
 
           label = (CharPtr) FeatDefTypeLabel (sfp);
@@ -8898,7 +8933,7 @@ NLM_EXTERN TextFsaPtr TextFsaFree (TextFsaPtr tbl)
   if (stateTable != NULL) {
     highState = tbl->highState;
 
-    for (state = 0; state < highState; state++) {
+    for (state = 0; state <= highState; state++) {
       sp = stateTable [state];
       if (sp == NULL) continue;
 
@@ -8909,14 +8944,15 @@ NLM_EXTERN TextFsaPtr TextFsaFree (TextFsaPtr tbl)
         gp = nxtgp;
       }
 
-      ValNodeFreeData (sp->matchfound);
-      MemFree (sp);
+      sp->matchfound = ValNodeFreeData (sp->matchfound);
+      sp = MemFree (sp);
+      stateTable[state] = NULL;
     }
 
-    MemFree (stateTable);
+    stateTable = MemFree (stateTable);
   }
 
-  ValNodeFreeData (tbl->siteList);
+  tbl->siteList = ValNodeFreeData (tbl->siteList);
 
   return MemFree (tbl);
 }
@@ -10258,3 +10294,2348 @@ NLM_EXTERN SeqAnnotPtr PhrapGraphForContig (
   return sap;
 }
 
+/* Functions for correcting capitalization */
+
+typedef struct replaceitempair {
+  CharPtr FindString;
+  CharPtr ReplaceString;
+} ReplaceItemPair, PNTR ReplaceItemPairPtr;
+
+
+ReplaceItemPair AbbreviationList[] = {
+ { "arabidopsis thaliana", "Arabidopsis thaliana" },
+ { "adp", "ADP" },
+ { "adp-", "ADP-" },
+ { "atp", "ATP" },
+ { "atp-", "ATP-" },
+ { "bac", "BAC" },
+ { "caenorhabditis elegans", "Caenorhabditis elegans" },
+ { "cdna", "cDNA" },
+ { "cdnas", "cDNAs" },
+ { "coa", "CoA" },
+ { "coi", "COI" },
+ { "coii", "COII" },
+ { "danio rerio", "Danio rerio" },
+ { "dna", "DNA" },
+ { "dna-", "DNA-" },
+ { "drosophila melanogaster", "Drosophila melanogaster" },
+ { "dsrna", "dsRNA" },
+ { "escherichia coli", "Escherichia coli" },
+ { "hiv", "HIV" },
+ { "hiv-1", "HIV-1" },
+ { "hiv-2", "HIV-2" },
+ { "hnrna", "hnRNA" },
+ { "homo sapiens", "Homo sapiens" },
+ { "mhc", "MHC" },
+ { "mrna", "mRNA" },
+ { "mtdna", "mtDNA" },
+ { "mus musculus", "Mus musculus" },
+ { "nadh", "NADH" },
+ { "nov.", "nov." },
+ { "nov..", "nov.." },
+ { "pcr", "PCR" },
+ { "pcr-", "PCR-" },
+ { "rattus norvegicus", "Rattus norvegicus" },
+ { "rapd", "RAPD" },
+ { "rdna", "rDNA" },
+ { "rna", "RNA" },
+ { "rna-", "RNA-" },
+ { "rrna", "rRNA" },
+ { "rt-pcr", "RT-PCR" },
+ { "saccharomyces cerevisiae", "Saccharomyces cerevisiae" },
+ { "scrna", "scRNA" },
+ { "siv-1", "SIV-1" },
+ { "snp", "SNP"     },
+ { "snps", "SNPs"   },
+ { "snrna", "snRNA" },
+ { "sp.", "sp." },
+ { "sp..", "sp.." },
+ { "ssp.", "ssp." },
+ { "ssp..", "ssp.." },
+ { "ssrna", "ssRNA" },
+ { "subsp.", "subsp." },
+ { "subsp..", "subsp.." },
+ { "trna", "tRNA" },
+ { "trna-", "tRNA-" },
+ { "var.", "var." },
+ { "var..", "var.." },
+ { "usa", "USA" },
+ { "U.S.A.", "USA" },
+ { "U.S.A", "USA" },
+ { "United States of America", "USA" },
+ {"(hiv)", "(HIV)" },
+ {"(hiv1)", "(HIV1)" },
+ {"(hiv-1)", "(HIV-1)" }
+};
+
+ReplaceItemPair SpecialAbbreviationList[] = {
+ { "sp.", "sp." },
+ { "nov.", "nov." },
+ { "ssp.", "ssp." },
+ { "var.", "var." },
+ { "subsp.", "subsp." }
+};
+
+NLM_EXTERN void FixAbbreviationsInElement (CharPtr PNTR pEl)
+{
+  int i;
+  CharPtr NewPtr;
+  Boolean whole_word;
+
+  if (pEl == NULL) return;
+  if (*pEl == NULL) return;
+
+  for (i = 0; i < sizeof (AbbreviationList) / sizeof (ReplaceItemPair); i++)
+  {
+    if (AbbreviationList[i].FindString[StringLen (AbbreviationList[i].FindString) - 1] == '-')
+    {
+      whole_word = FALSE;
+    }
+    else
+    {
+      whole_word = TRUE;
+    }
+    FindReplaceString (pEl, AbbreviationList[i].FindString,
+			AbbreviationList[i].ReplaceString, FALSE, whole_word);
+  }
+  for (i = 0; i < sizeof (SpecialAbbreviationList) / sizeof (ReplaceItemPair); i++)
+  {
+    FindReplaceString (pEl, SpecialAbbreviationList[i].FindString,
+			SpecialAbbreviationList[i].ReplaceString, FALSE, TRUE);
+    if (StringLen (*pEl) >= StringLen (SpecialAbbreviationList[i].ReplaceString)
+      && StringCmp ((*pEl) + StringLen (*pEl) - StringLen (SpecialAbbreviationList[i].ReplaceString), SpecialAbbreviationList[i].ReplaceString) == 0)
+    {
+      NewPtr = MemNew (StringLen (*pEl) + 2);
+      if (NewPtr == NULL) return;
+      StringCpy (NewPtr, *pEl);
+      StringCat (NewPtr, ".");
+      MemFree (*pEl);
+      *pEl = NewPtr;
+    }
+  }
+}
+
+ReplaceItemPair ShortWordList[] = {
+ { "A", "a" },
+ { "About", "about" },
+ { "And", "and" },
+ { "At", "at" },
+ { "But", "but" },
+ { "By", "by" },
+ { "For", "for" },
+ { "In", "in" },
+ { "Is", "is" },
+ { "Of", "of" },
+ { "On", "on" },
+ { "Or", "or" },
+ { "The", "the" },
+ { "To", "to" },
+ { "With", "with" }
+};
+
+static void FixShortWordsInElement (CharPtr PNTR pEl)
+{
+  Int2 i;
+
+  if (pEl == NULL) return;
+  if (*pEl == NULL) return;
+
+  for (i = 0; i < sizeof (ShortWordList) / sizeof (ReplaceItemPair); i++)
+  {
+    FindReplaceString (pEl, ShortWordList[i].FindString,
+			ShortWordList[i].ReplaceString, FALSE, TRUE);
+  }
+  if (isalpha ((Int4)((*pEl)[0])))
+  {
+    (*pEl)[0] = toupper ((*pEl)[0]);
+  }
+}
+
+NLM_EXTERN void 
+FixCapitalizationInElement 
+(CharPtr PNTR pEl,
+ Boolean      bAbbrev, 
+ Boolean      bShortWords,
+ Boolean      bApostrophes)
+{
+  CharPtr pCh;
+  Boolean bSendToLower;
+ 
+  if(pEl == NULL) return; 
+  if(*pEl == NULL) return; 
+
+  bSendToLower = FALSE;
+  for(pCh = *pEl; *pCh != 0; pCh++)
+  {
+    if(isalpha((Int4)(*pCh)))
+    {
+      if(bSendToLower)
+      {
+        *pCh = tolower(*pCh);
+      }
+      else
+      {
+        *pCh = toupper(*pCh);
+        bSendToLower = TRUE;
+      }
+    }
+    else if (bApostrophes || *pCh != '\'')
+    {
+      bSendToLower = FALSE;
+    }
+  }
+  if (bShortWords)
+    FixShortWordsInElement (pEl);
+  if (bAbbrev)
+    FixAbbreviationsInElement (pEl);
+}
+
+
+NLM_EXTERN void FixOrgNamesInString (CharPtr str, ValNodePtr org_names)
+{
+  ValNodePtr vnp;
+  CharPtr    cp, taxname;
+  Int4       taxname_len;
+  
+  if (StringHasNoText (str) || org_names == NULL) return;
+  for (vnp = org_names; vnp != NULL; vnp = vnp->next)
+  {
+    taxname = (CharPtr) org_names->data.ptrvalue;
+    taxname_len = StringLen (taxname);
+    cp = StringISearch (str, taxname);
+    while (cp != NULL)
+    {
+      StringNCpy (cp, taxname, taxname_len);
+      cp = StringISearch (cp + taxname_len, taxname);
+    }
+  }
+}
+
+
+NLM_EXTERN void ResetCapitalization (Boolean first_is_upper, CharPtr pString)
+{
+  CharPtr pCh;
+  Boolean was_digit = FALSE;
+
+  pCh = pString;
+  if (pCh == NULL) return;
+  if (*pCh == '\0') return;
+  
+  if (first_is_upper)
+  {
+    /* Set first character to upper */
+    *pCh = toupper (*pCh);	
+  }
+  else
+  {
+    /* set first character to lower */
+    *pCh = tolower (*pCh);	
+  }
+  
+  if (isdigit ((Int4)(*pCh)))
+  {
+  	was_digit = TRUE;
+  }
+  pCh++;
+  /* Set rest of characters to lower */
+  while (*pCh != '\0')
+  {
+    if (was_digit 
+        && (*pCh == 'S' || *pCh == 's') 
+        && (isspace ((Int4)(*(pCh + 1))) || *(pCh + 1) == 0))
+    {
+      *pCh = toupper (*pCh);
+      was_digit = FALSE;
+    }
+    else if (isdigit ((Int4)(*pCh)))
+    {
+      was_digit = TRUE;
+    }
+    else
+    {
+      was_digit = FALSE;
+      *pCh = tolower (*pCh);
+    }
+    pCh++;
+  }  
+}
+
+
+static Boolean IsAllDigits (CharPtr str)
+{
+  CharPtr cp;
+
+  if (StringHasNoText (str)) return FALSE;
+
+  cp = str;
+  while (*cp != 0 && isdigit (*cp)) {
+    cp++;
+  }
+  if (*cp == 0) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+
+NLM_EXTERN SeqIdPtr CreateSeqIdFromText (CharPtr id_str, SeqEntryPtr sep)
+{
+  BioseqPtr   bsp = NULL;
+  CharPtr     tmpstr;
+  SeqIdPtr    sip = NULL;
+  SeqEntryPtr scope;
+  
+  if (StringStr (id_str, "|") == NULL) {
+    tmpstr = (CharPtr) MemNew (sizeof (Char) * (StringLen (id_str) + 20));
+    sprintf (tmpstr, "lcl|%s", id_str);
+    sip = SeqIdParse (tmpstr);
+    if (sip != NULL) {
+      scope = SeqEntrySetScope (sep);
+      bsp = BioseqFind (sip);
+      SeqEntrySetScope (scope);
+      if (bsp == NULL) {
+        sip = SeqIdFree (sip);
+      }
+    } 
+    if (bsp == NULL) {
+      sprintf (tmpstr, "gb|%s", id_str);
+      sip = SeqIdParse (tmpstr);
+      if (sip != NULL) {
+        scope = SeqEntrySetScope (sep);
+        bsp = BioseqFind (sip);
+        SeqEntrySetScope (scope);
+        if (bsp == NULL) {
+          sip = SeqIdFree (sip);
+        }
+      }
+    }
+    if (bsp == NULL) {
+      sprintf (tmpstr, "gnl|%s", id_str);
+      sip = SeqIdParse (tmpstr);
+      if (sip != NULL) {
+        scope = SeqEntrySetScope (sep);
+        bsp = BioseqFind (sip);
+        SeqEntrySetScope (scope);
+        if (bsp == NULL) {
+          sip = SeqIdFree (sip);
+        }
+      }
+    }
+    if (bsp == NULL) {
+      if (StringNICmp (id_str, "bankit", 6) == 0) {
+        sprintf (tmpstr, "gnl|BankIt|%s", id_str + 6);
+      } else {
+        sprintf (tmpstr, "gnl|BankIt|%s", id_str);
+      }
+      sip = SeqIdParse (tmpstr);
+      if (sip != NULL) {
+        scope = SeqEntrySetScope (sep);
+        bsp = BioseqFind (sip);
+        SeqEntrySetScope (scope);
+        if (bsp == NULL) {
+          sip = SeqIdFree (sip);
+        }
+      }
+    }
+
+    if (bsp == NULL) {
+      sprintf (tmpstr, "gnl|NCBIFILE|%s", id_str);
+      sip = SeqIdParse (tmpstr);
+      if (sip != NULL) {
+        scope = SeqEntrySetScope (sep);
+        bsp = BioseqFind (sip);
+        SeqEntrySetScope (scope);
+        if (bsp == NULL) {
+          sip = SeqIdFree (sip);
+        }
+      }
+    }
+
+    if (bsp == NULL && IsAllDigits (id_str)) {
+      sprintf (tmpstr, "gi|%s", id_str);
+      sip = SeqIdParse (tmpstr);
+      if (sip != NULL) {
+        scope = SeqEntrySetScope (sep);
+        bsp = BioseqFind (sip);
+        SeqEntrySetScope (scope);
+        if (bsp == NULL) {
+          sip = SeqIdFree (sip);
+        }
+      }
+    }
+    MemFree (tmpstr);
+  } else {
+    sip = SeqIdParse (id_str);
+    if (sip != NULL) {
+      scope = SeqEntrySetScope (sep);
+      bsp = BioseqFind (sip);
+      SeqEntrySetScope (scope);
+      if (bsp == NULL) {
+        sip = SeqIdFree (sip);
+      }
+    }
+  }        
+  return sip;
+}
+
+
+NLM_EXTERN SeqLocPtr SeqLocWholeNew (BioseqPtr bsp)
+{
+  ValNodePtr vnp;
+
+  if (bsp == NULL) return NULL;
+
+  vnp = ValNodeNew (NULL);
+
+  if (vnp == NULL) return NULL;
+
+  vnp->choice = SEQLOC_WHOLE;
+  vnp->data.ptrvalue = (Pointer) SeqIdDup (SeqIdFindBest (bsp->id, 0));
+  return (SeqLocPtr)vnp;
+}
+
+
+NLM_EXTERN Int4 GetDeltaSeqLen (DeltaSeqPtr dsp)
+{
+  Int4 len = 0;
+  SeqLitPtr slp;
+
+  if (dsp == NULL || dsp->data.ptrvalue == NULL) {
+    /* do nothing, empty */
+  } else if (dsp->choice == 1) {
+    len = SeqLocLen ((SeqLocPtr)(dsp->data.ptrvalue));
+  } else if (dsp->choice == 2) {
+    slp = (SeqLitPtr) dsp->data.ptrvalue;
+    len = slp->length;
+  }
+  return len;
+}
+
+
+/* The following section of code is used for retranslating a CDS and updating
+ * the protein features based on an alignment between the old and new protein
+ * sequences.
+ */
+static Int4 SeqEdRemapCoord (SeqAlignPtr salp, Int4 coord, Boolean move_up, Int4 len)
+
+{
+  Int4 aln_pos;
+  
+  if (salp == NULL) return -1;
+  aln_pos = AlnMgr2MapBioseqToSeqAlign (salp, coord, 1);
+  while (aln_pos == -1)
+  {
+  	if (move_up)
+  	{
+  	  if (coord >= len - 1)
+  	  {
+  	  	return len - 1;
+  	  }
+  	  else
+  	  {
+  	  	coord ++;
+  	  }
+  	}
+  	else
+  	{
+  	  if (coord <= 0)
+  	  {
+  	  	return 0;
+  	  }
+  	  else
+  	  {
+  	  	coord --;
+  	  }
+  	}
+  	aln_pos = AlnMgr2MapBioseqToSeqAlign (salp, coord, 1);
+  }
+  return AlnMgr2MapSeqAlignToBioseq (salp, aln_pos, 2);
+}
+
+
+static void SeqEdRemapSeqIntLoc (SeqAlignPtr salp, SeqIntPtr sintp, Int4 seq_len)
+
+{  
+  if (salp == NULL || sintp == NULL) return;
+  sintp->from = SeqEdRemapCoord (salp, sintp->from, TRUE, seq_len);
+  sintp->to = SeqEdRemapCoord (salp, sintp->to, FALSE, seq_len); 
+}
+
+static void SeqEdRemapSeqPntLoc (SeqAlignPtr salp, SeqPntPtr spp, Int4 seq_len)
+
+{  
+  if (salp == NULL || spp == NULL) return;
+  
+  spp->point = SeqEdRemapCoord (salp, spp->point, FALSE, seq_len);
+}
+
+
+static void SeqEdRemapPackSeqPnt (SeqAlignPtr salp, PackSeqPntPtr pspp, Int4 seq_len)
+
+{
+  Uint1          used;
+
+  if (salp == NULL || pspp == NULL) return;
+  for (used = 0; used < pspp->used; used++) 
+  {
+    pspp->pnts [used] = SeqEdRemapCoord (salp, pspp->pnts [used], FALSE, seq_len);
+  }
+}
+
+
+NLM_EXTERN void SeqEdRemapLocation (SeqAlignPtr salp, SeqLocPtr slp, Int4 seq_len)
+
+{
+
+  if (slp == NULL) return;
+  switch (slp->choice) {
+    case SEQLOC_INT :
+      SeqEdRemapSeqIntLoc (salp, slp->data.ptrvalue, seq_len);
+      break;
+    case SEQLOC_PNT :
+      SeqEdRemapSeqPntLoc (salp, slp->data.ptrvalue, seq_len);
+      break;
+    case SEQLOC_PACKED_PNT :
+      SeqEdRemapPackSeqPnt (salp, slp->data.ptrvalue, seq_len);
+      break;
+    default :
+      break;
+  }
+}
+
+
+static void MakeLocationMatchEntireSequence (SeqLocPtr slp, BioseqPtr bsp)
+{
+  SeqIntPtr sip;
+  
+  if (slp == NULL || bsp == NULL) return;
+  
+  if (slp->choice == SEQLOC_WHOLE)
+  {
+  	SeqIdFree (slp->data.ptrvalue);
+  	slp->data.ptrvalue = SeqIdDup (bsp->id);
+  }
+  else if (slp->choice == SEQLOC_INT)
+  {
+    sip = (SeqIntPtr) slp->data.ptrvalue;
+    if (sip == NULL)
+    {
+      sip = SeqIntNew ();
+      slp->data.ptrvalue = sip;
+    }
+    if (sip != NULL)
+    {
+      sip->from = 0;
+      sip->to = bsp->length - 1;
+    }
+  }
+}
+
+
+NLM_EXTERN Boolean SeqEdFixProteinFeatures (BioseqPtr oldbsp, BioseqPtr newbsp, Boolean force_fix, GlobalAlignFunc align_func)
+{
+  SeqAlignPtr       salp = NULL;
+  Boolean           revcomp = FALSE;
+  SeqFeatPtr        sfp;
+  Boolean           tried_to_get_alignment = FALSE;
+  Boolean           unmappable_feats = FALSE;
+  SeqLocPtr         slp_tmp = NULL;
+  SeqAnnotPtr       sap;
+  ProtRefPtr        prp;
+  
+  if (oldbsp == NULL || newbsp == NULL) return FALSE;
+
+  /* get alignment between old and new proteins */
+
+  if (ISA_na (oldbsp->mol) != ISA_na (newbsp->mol)) return FALSE;
+
+  /* iterate through the features on the old protein.  Full length features
+   * should be set to the new length.  Other features should be mapped through
+   * the alignment (if possible), otherwise warn the user that they could not
+   * be remapped. */      
+
+  if (!force_fix)
+  {
+    for (sap = oldbsp->annot; sap != NULL && !unmappable_feats; sap = sap->next) {
+      if (sap->type == 1) {
+        for (sfp = sap->data; sfp != NULL && !unmappable_feats; sfp = sfp->next) {
+          if (sfp->data.choice != SEQFEAT_PROT || sfp->data.value.ptrvalue == NULL) {
+            continue;
+          }
+          prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+          if (prp->processed != 0)
+          {
+            if (salp == NULL)
+            {
+              if (align_func != NULL)
+              {
+                salp = align_func (oldbsp, newbsp, &revcomp);
+              }
+            }
+            if (salp == NULL)
+            {
+              unmappable_feats = TRUE;
+            } 
+            else
+            {
+              slp_tmp = (SeqLocPtr) AsnIoMemCopy (sfp->location,
+                                                  (AsnReadFunc) SeqLocAsnRead,
+                                                  (AsnWriteFunc) SeqLocAsnWrite);
+              SeqEdRemapLocation (salp, slp_tmp, newbsp->length);	  	  	
+              if (slp_tmp == NULL)
+              {
+                unmappable_feats = TRUE;
+              }
+              else
+              {
+                slp_tmp = SeqLocFree (slp_tmp);
+              }
+            }
+          }
+        }
+      }
+    }
+    if (unmappable_feats)
+    {
+      return FALSE;
+    }
+  }
+
+  for (sap = oldbsp->annot; sap != NULL && !unmappable_feats; sap = sap->next) {
+    if (sap->type == 1) {
+      for (sfp = sap->data; sfp != NULL && !unmappable_feats; sfp = sfp->next) {
+        if (sfp->data.choice != SEQFEAT_PROT || sfp->data.value.ptrvalue == NULL) {
+          continue;
+        }
+        prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+        if (prp->processed == 0)
+        {
+          /* make new location match new sequence length */
+          MakeLocationMatchEntireSequence (sfp->location, newbsp);
+        }
+        else
+        {
+          if (salp == NULL && !tried_to_get_alignment && align_func != NULL)
+          {
+            salp = align_func (oldbsp, newbsp, &revcomp);
+            tried_to_get_alignment = TRUE;
+          }
+          if (salp != NULL)
+          {
+            SeqEdRemapLocation (salp, sfp->location, newbsp->length);	  	  	
+          }
+          else
+          {
+            unmappable_feats = TRUE;
+          }
+        }
+      }
+    }
+  } 
+        
+  if (salp != NULL)
+  {
+    SeqAlignFree (salp);
+  }
+  if (unmappable_feats)
+  {
+    return FALSE;
+  }
+  else
+  {
+    return TRUE;
+  }
+}
+
+
+NLM_EXTERN void SeqEdTranslateOneCDS (SeqFeatPtr sfp, BioseqPtr featbsp, Uint2 entityID, GlobalAlignFunc align_func)
+{
+  ByteStorePtr  bs;
+  Char          ch;
+  CharPtr       prot;
+  CharPtr       ptr;
+  Int4          star_at_end = 0;
+  BioseqPtr     old_prot;
+  SeqIdPtr      new_prot_id;
+  SeqEntryPtr   parent, new_prot_sep;
+  SeqLocPtr     slp;
+  Uint1         seq_data_type;
+  Int4          old_length;
+  BioseqPtr     newbsp;
+  ProtRefPtr    prp;
+  SeqFeatPtr    prot_sfp;
+  SeqDataPtr    sdp;
+  
+  if (featbsp == NULL || sfp == NULL || sfp->location == NULL 
+      || sfp->data.choice != SEQFEAT_CDREGION) 
+  {
+  	return;
+  }
+  
+  old_prot = BioseqFindFromSeqLoc (sfp->product);
+  new_prot_id = SeqIdDup (SeqLocId (sfp->product));
+  if (new_prot_id == NULL)
+  {
+  	new_prot_id = MakeNewProteinSeqId (sfp->location, featbsp->id);
+  }
+  	
+  bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
+  if (bs != NULL) {
+    prot = BSMerge (bs, NULL);
+    bs = BSFree (bs);
+    if (prot != NULL) {
+      ptr = prot;
+      ch = *ptr;
+      while (ch != '\0') {
+        *ptr = TO_UPPER (ch);
+        if (ch == '*') {
+          star_at_end = 1;
+        } else {
+          star_at_end = 0;
+        }
+        ptr++;
+        ch = *ptr;
+      }
+      if (star_at_end)
+      {
+      	*(ptr - 1) = 0;
+      }
+      bs = BSNew (1000);
+      if (bs != NULL) {
+        ptr = prot;
+        BSWrite (bs, (VoidPtr) ptr, (Int4) StringLen (ptr));
+      }
+      MemFree (prot);
+    }
+    newbsp = BioseqNew ();
+    if (newbsp != NULL) {
+      newbsp->id = SeqIdParse ("lcl|CdRgnTransl");
+      newbsp->repr = Seq_repr_raw;
+      newbsp->mol = Seq_mol_aa;
+      newbsp->seq_data_type = Seq_code_ncbieaa;
+      newbsp->seq_data = (SeqDataPtr) bs;
+      newbsp->length = BSLen (bs);
+      
+      if (old_prot == NULL)
+      {
+  	    /* need to create a new protein sequence */
+  	    SeqIdFree (newbsp->id);
+  	    newbsp->id = new_prot_id;
+  	    new_prot_sep = SeqEntryNew ();
+  	    new_prot_sep->choice = 1;
+  	    new_prot_sep->data.ptrvalue = newbsp;
+  	    parent = GetBestTopParentForData (entityID, featbsp);
+  	    if (parent != NULL)
+  	    {
+  	      AddSeqEntryToSeqEntry (parent, new_prot_sep, TRUE);
+  	    }
+  	    slp = ValNodeNew (NULL);
+  	    if (slp != NULL)
+  	    {
+  	      slp->choice = SEQLOC_WHOLE;
+  	      slp->data.ptrvalue = SeqIdDup (new_prot_id);
+  	    }
+  	    sfp->product = slp;
+  	    
+  	    /* create full length protein feature */
+        prp = ProtRefNew ();
+        prot_sfp = CreateNewFeature (new_prot_sep, NULL, SEQFEAT_PROT, NULL);
+        if (prot_sfp != NULL) {
+          prot_sfp->data.value.ptrvalue = (Pointer) prp;
+        }
+      }
+      else
+      {
+        /* propagate features to new protein */
+        if (!SeqEdFixProteinFeatures (old_prot, newbsp, TRUE, align_func))
+        {
+          Message (MSG_ERROR, "Unable to construct alignment between old and new "
+                  "proteins - you will need to adjust the protein features "
+                  "manually.");
+        }
+             	
+      	/* then replace old protein with new */
+      	seq_data_type = old_prot->seq_data_type;
+      	sdp = old_prot->seq_data;
+      	old_length = old_prot->length;
+      	old_prot->seq_data_type = newbsp->seq_data_type;
+      	old_prot->seq_data = newbsp->seq_data;
+      	old_prot->length = newbsp->length;
+      	newbsp->seq_data_type = seq_data_type;
+      	newbsp->seq_data = sdp;
+      	newbsp->length = old_length;
+      	BioseqFree (newbsp);
+      }
+    }
+  }
+}
+
+
+static SeqLocPtr RemoveGapsFromSegmentedLocation (SeqLocPtr slp, BioseqPtr bsp)
+{
+  SeqLocPtr loc_slp, slp_new, slp_tmp, loc_list = NULL, loc_last = NULL;
+  SeqIdPtr  sip;
+  Uint1     strand;
+  Int4      seq_offset, start_pos, end_pos, piece_len;
+  
+  if (slp == NULL || bsp == NULL || bsp->repr != Seq_repr_seg)
+  {
+    return slp;
+  }
+  
+  loc_slp = SeqLocFindNext (slp, NULL);
+
+  while (loc_slp != NULL)
+  {
+    strand = SeqLocStrand (loc_slp);
+    start_pos = SeqLocStart (loc_slp);
+    end_pos = SeqLocStop (loc_slp);
+  
+    /* create list of locations */
+    slp_tmp = bsp->seq_ext;
+    seq_offset = 0;
+    while (slp_tmp != NULL)
+    {
+      piece_len = SeqLocLen (slp_tmp);
+      
+      if (seq_offset < end_pos
+          && seq_offset + piece_len >= start_pos)
+      {
+        sip = SeqLocId (slp_tmp);
+      
+        slp_new = SeqLocIntNew (MAX (0, start_pos - seq_offset),
+                                MIN (piece_len, end_pos - seq_offset),
+                                strand, sip);
+
+        if (slp_new != NULL)
+        {
+          if (loc_last == NULL)
+          {
+            loc_list = slp_new;
+          }
+          else
+          {
+            loc_last->next = slp_new;
+          }
+          loc_last = slp_new;
+        }
+      }
+      seq_offset += piece_len;
+      slp_tmp = slp_tmp->next;
+    }
+    loc_slp = SeqLocFindNext (slp, loc_slp);
+  }
+  
+  if (loc_list == NULL)
+  {
+    /* failed to convert - do not change */
+  }
+  else if (loc_list->next == NULL)
+  {
+    /* only found one piece */
+    slp = SeqLocFree (slp);
+    slp = loc_list;
+  }
+  else
+  {
+    /* make mixed location */
+    slp_new = ValNodeNew (NULL);
+    if (slp_new != NULL)
+    {
+      slp_new->choice = SEQLOC_MIX;
+      slp_new->data.ptrvalue = loc_list;
+      slp = SeqLocFree (slp);
+      slp = slp_new;
+    }
+  }
+  return slp;
+}
+
+static Boolean PointInInterval (Int4 interval_start, Int4 interval_length, Int4 point)
+{
+  if (point >= interval_start && point < interval_start + interval_length) 
+  {
+    return TRUE;
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+NLM_EXTERN Boolean GapInLocation (Int4 seq_offset, Int4 length, SeqLocPtr loc)
+{
+  SeqLocPtr slp;
+  Int4      start, stop;
+  Boolean   gap_in_location = FALSE;
+  
+  slp = SeqLocFindNext (loc, NULL);
+  
+  while (slp != NULL && ! gap_in_location)
+  {
+    start = SeqLocStart (slp);
+    stop = SeqLocStop (slp);
+    
+    if (PointInInterval (seq_offset, length, start)
+        || PointInInterval (seq_offset, length, stop)
+        || PointInInterval (start, stop - start + 1, seq_offset)
+        || PointInInterval (start, stop - start + 1, seq_offset + length))
+    {
+      gap_in_location = TRUE;
+    }
+    
+    slp = SeqLocFindNext (loc, slp);
+  }
+  return gap_in_location;
+}
+
+
+NLM_EXTERN void
+LocationContainsGaps
+(SeqLocPtr slp,
+ BioseqPtr bsp,
+ Boolean   unknown_gaps,
+ Boolean   known_gaps,
+ BoolPtr   terminal_gaps,
+ BoolPtr   internal_gaps,
+ BoolPtr   entirely_in_gap)
+{
+  DeltaSeqPtr dsp;
+  Int4        seq_offset = 0;
+  Int4        dsp_len;
+  Boolean     has_terminal_gaps = FALSE;
+  Boolean     has_internal_gaps = FALSE;
+  Boolean     all_sublocs_in_gap = TRUE, this_subloc_in_gap = FALSE, this_subloc_start_gap = FALSE, this_subloc_stop_gap = FALSE;
+  Boolean     right_sublocs_in_gap = FALSE;
+  SeqLocPtr   tmp_slp;
+  Int4        start, stop;
+
+  if (slp == NULL || bsp == NULL 
+      || bsp->repr != Seq_repr_delta
+      || bsp->seq_ext_type != 4
+      || bsp->seq_ext == NULL)
+  {
+    return;
+  }
+    
+  for (tmp_slp = SeqLocFindNext (slp, NULL); 
+       tmp_slp != NULL;
+       tmp_slp = SeqLocFindNext (slp, tmp_slp))
+  {
+    seq_offset = 0;
+    start = SeqLocStart (tmp_slp);
+    stop = SeqLocStop (tmp_slp);
+    this_subloc_in_gap = FALSE;
+    this_subloc_start_gap = FALSE;
+    this_subloc_stop_gap = FALSE;
+    for (dsp = (DeltaSeqPtr) bsp->seq_ext;
+         dsp != NULL && seq_offset <= stop && !this_subloc_in_gap;
+         dsp = dsp->next)
+    {
+      dsp_len = GetDeltaSeqLen(dsp);
+      if (IsDeltaSeqGap (dsp) && !DoesDeltaSeqHaveGapTypeOrLinkage(dsp)
+          && ((unknown_gaps && IsDeltaSeqUnknownGap (dsp))
+              || (known_gaps && IsDeltaSeqKnownGap (dsp)))
+          && GapInLocation (seq_offset, dsp_len, tmp_slp))
+      {
+        if (PointInInterval (seq_offset, dsp_len, start)
+            && PointInInterval (seq_offset, dsp_len, stop))
+        {
+          this_subloc_in_gap = TRUE;
+        }
+        else if (PointInInterval (seq_offset, dsp_len, start))
+        {
+          this_subloc_start_gap = TRUE;
+        }
+        else if (PointInInterval (seq_offset, dsp_len, stop)) 
+        {
+          this_subloc_stop_gap = TRUE;
+        }
+        else 
+        {
+          has_internal_gaps = TRUE;
+        }
+      }
+      seq_offset += dsp_len;
+    }
+
+    if (this_subloc_in_gap)
+    {
+      /* all sublocs up to this point have been in the gap, so still part of left gap */
+      if (all_sublocs_in_gap)
+      {
+        has_terminal_gaps = TRUE;
+      }
+      /* could be part of chain of sublocs on the right in gap */
+      right_sublocs_in_gap = TRUE;
+    }
+    else
+    {
+      if (right_sublocs_in_gap && !all_sublocs_in_gap)
+      {
+        /* a chain of prior gapped sublocs has ended that did not start at the left end */
+        has_internal_gaps = TRUE;
+      }
+
+      if (this_subloc_start_gap)
+      { 
+        if (all_sublocs_in_gap)
+        {
+          has_terminal_gaps = TRUE;
+        }
+        else
+        {
+          /* gap on left, not part of chain of sublocs on left in gap */
+          has_internal_gaps = TRUE;
+        }
+      } 
+      
+      if (this_subloc_stop_gap)
+      {
+        /* could be start of chain of sublocs on the right in gap */
+        right_sublocs_in_gap = TRUE;
+      }
+      else
+      {
+        right_sublocs_in_gap = FALSE;
+      }
+      /* at least this subloc is not completely contained in a gap */
+      all_sublocs_in_gap = FALSE;
+    }
+  }
+
+  if (right_sublocs_in_gap)
+  {
+    has_terminal_gaps = TRUE;
+  }
+
+  if (all_sublocs_in_gap)
+  {
+    has_terminal_gaps = FALSE;
+    has_internal_gaps = FALSE;
+  }
+
+  if (terminal_gaps != NULL)
+  {
+    *terminal_gaps = has_terminal_gaps;
+  }
+
+  if (internal_gaps != NULL)
+  {
+    *internal_gaps = has_internal_gaps;
+  }
+
+  if (entirely_in_gap != NULL)
+  {
+    *entirely_in_gap = all_sublocs_in_gap;
+  }
+}
+
+
+static SeqLocPtr 
+RemoveGapsFromDeltaLocation 
+(SeqLocPtr slp,
+ BioseqPtr bsp,
+ Boolean   unknown_gaps,
+ Boolean   known_gaps,
+ Boolean   trim_ends,
+ Boolean   split_internal,
+ Boolean   set_partial_ends,
+ BoolPtr   split)
+{
+  DeltaSeqPtr dsp;
+  Int4        seq_offset = 0;
+  Int4        dsp_len;
+  SeqLocPtr   loc_list = NULL, prev_loc = NULL;
+  SeqIdPtr    sip, before_sip, after_sip;
+  Boolean     changed, partial5, partial3;
+  SeqLocPtr   before = NULL, after = NULL;
+  Int4        start, stop;
+  Boolean     delete_for_this_gap;
+  Uint1       strand;
+
+  if (slp == NULL || bsp == NULL 
+      || bsp->repr != Seq_repr_delta
+      || bsp->seq_ext_type != 4
+      || bsp->seq_ext == NULL)
+  {
+    return slp;
+  }
+  
+  sip = SeqLocId (slp);
+  if (sip == NULL)
+  {
+    return slp;
+  }
+  
+  CheckSeqLocForPartial (slp, &partial5, &partial3);
+  
+  seq_offset = 0;
+  before = SeqLocCopy (slp);
+  loc_list = before;
+  
+  for (dsp = (DeltaSeqPtr) bsp->seq_ext;
+       dsp != NULL;
+       dsp = dsp->next)
+  {
+    dsp_len = GetDeltaSeqLen(dsp);
+    if (IsDeltaSeqGap (dsp) && !DoesDeltaSeqHaveGapTypeOrLinkage(dsp)
+        && ((unknown_gaps && IsDeltaSeqUnknownGap (dsp))
+            || (known_gaps && IsDeltaSeqKnownGap (dsp)))
+        && GapInLocation (seq_offset, dsp_len, before))
+    {
+      delete_for_this_gap = TRUE;
+      start = SeqLocStart (before);
+      stop = SeqLocStop (before);
+      if (PointInInterval (seq_offset, dsp_len, start)
+          && PointInInterval (seq_offset, dsp_len, stop))
+      {
+        loc_list = SeqLocFree (loc_list);
+        before = NULL;
+        after = NULL;
+        break;
+      }
+      else if (!PointInInterval (seq_offset, dsp_len, start) 
+          && !PointInInterval (seq_offset, dsp_len, stop)) 
+      {
+        if (!split_internal) 
+        {
+          delete_for_this_gap = FALSE;
+        }
+        else
+        {
+          if (split != NULL)
+          {
+            *split = TRUE;
+          }
+        }
+      }
+      else if (!trim_ends)
+      {
+        delete_for_this_gap = FALSE;
+      }
+
+      if (delete_for_this_gap)
+      {
+        /* get strand - determines direction of partials */
+        strand = SeqLocStrand (before);
+
+        /* we make a copy of the original location */
+        after = SeqLocCopy (before);
+        
+        /* note - we need to use duplicates of the SeqID returned by
+         * SeqLocId, just in case the first location in a mixed location 
+         * is deleted, which would free the result from SeqLocId 
+         */
+        after_sip = SeqIdDup (SeqLocId (after));
+        before_sip = SeqIdDup (SeqLocId (before));
+        /* in the "after" location, we free everything before the 
+         * end of the gap.
+         */
+        after = SeqLocDeleteEx (after, after_sip,
+                          0, seq_offset + dsp_len - 1,
+                          FALSE, &changed, &partial5, &partial3);
+                          
+        /* in the "before" location, we free everything after the
+         * beginning of the gap.
+         */
+        before = SeqLocDeleteEx (before, before_sip, 
+                          seq_offset, bsp->length,
+                          FALSE, &changed, &partial5, &partial3);
+        
+        /* handle partialness for ends */
+        CheckSeqLocForPartial (after, &partial5, &partial3);
+        if (strand == Seq_strand_minus) 
+        {
+          if (before == NULL)
+          {
+            /* truncated at 3' end */
+            SetSeqLocPartial (after, partial5, set_partial_ends);
+          }
+          else
+          {
+            SetSeqLocPartial (after, partial5, TRUE);
+          }
+
+        }
+        else
+        {        
+          if (before == NULL)
+          {
+            /* truncated at 5' end*/
+            SetSeqLocPartial (after, set_partial_ends, partial3);
+          }
+          else
+          {
+            SetSeqLocPartial (after, TRUE, partial3);
+          }
+        }
+       
+        CheckSeqLocForPartial (before, &partial5, &partial3);
+        if (strand == Seq_strand_minus)
+        {
+          if (after == NULL) 
+          {
+            /* truncated at 5' end*/
+            SetSeqLocPartial (before, set_partial_ends, partial3);
+          } else {
+            SetSeqLocPartial (before, TRUE, partial3);
+          }
+        }
+        else
+        {
+          if (after == NULL) 
+          {
+            /* truncated */
+            SetSeqLocPartial (before, partial5, set_partial_ends);
+          } else {
+            SetSeqLocPartial (before, partial5, TRUE);
+          }
+        }
+        
+        /* we're done with these IDs now */                  
+        after_sip = SeqIdFree (after_sip);
+        before_sip = SeqIdFree (before_sip);                          
+                          
+        if (before == NULL)
+        {
+          if (prev_loc == NULL)
+          {
+            loc_list = after;
+          }
+          else
+          {
+            prev_loc->next = after;
+          }
+        }
+        else
+        {
+          before->next = after;
+          prev_loc = before;
+        }        
+        before = after;
+      }
+    }
+    seq_offset += dsp_len;
+  }
+
+  slp = SeqLocFree (slp);
+  return loc_list;  
+}
+
+
+static SeqLocPtr 
+RemoveGapsFromLocation 
+(SeqLocPtr slp, 
+ Boolean   unknown_gaps,
+ Boolean   known_gaps,
+ Boolean   trim_ends,
+ Boolean   split_internal,
+ Boolean   set_partial_ends,
+ BoolPtr   split)
+{
+  BioseqPtr   bsp;
+  SeqIdPtr    sip;
+  
+  if (slp == NULL)
+  {
+    return slp;
+  }
+  
+  sip = SeqLocId (slp);
+  if (sip == NULL)
+  {
+    return slp;
+  }
+  
+  bsp = BioseqFind (sip);
+  if (bsp == NULL)
+  {
+    return slp;
+  }
+  else if (bsp->repr == Seq_repr_seg)
+  {
+    if (!split_internal) {
+      return slp;
+    } else {
+      return RemoveGapsFromSegmentedLocation (slp, bsp);
+    }
+  }
+  else if (bsp->repr == Seq_repr_delta
+          && bsp->seq_ext_type == 4
+          && bsp->seq_ext != NULL)
+  {
+    return RemoveGapsFromDeltaLocation (slp, bsp, unknown_gaps, known_gaps, trim_ends, split_internal, set_partial_ends, split);
+  }
+  else
+  {
+    return slp;
+  }
+}
+
+NLM_EXTERN void AdjustFrame (SeqFeatPtr sfp, BioseqPtr oldprot)
+{
+  ByteStorePtr bs;
+  CdRegionPtr  crp;
+  CharPtr      oldprot_str, newprot_str;
+  Uint1        orig_frame, best_frame = 0;
+  
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION
+      || sfp->data.value.ptrvalue == NULL
+      || oldprot == NULL)
+  {
+    return;
+  }
+  
+  crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+  
+  oldprot_str = GetSequenceByBsp (oldprot);
+  
+  orig_frame = crp->frame;
+  for (crp->frame = 1; crp->frame <= 3 && best_frame == 0; crp->frame++)
+  {
+    newprot_str = NULL;
+    bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
+    if (bs != NULL) 
+    {
+      newprot_str = BSMerge (bs, NULL);
+      bs = BSFree (bs);
+    }
+    
+    if (StringHasNoText (newprot_str))
+    {
+      newprot_str = MemFree (newprot_str);
+      continue;
+    }
+    if (StringSearch (oldprot_str, newprot_str) != NULL
+        || StringSearch (oldprot_str, newprot_str + 1) != NULL)
+    {
+      best_frame = crp->frame;
+    }
+    else
+    {
+      newprot_str [StringLen (newprot_str) - 1] = 0;
+      if (StringSearch (oldprot_str, newprot_str) != NULL
+          || StringSearch (oldprot_str, newprot_str + 1) != NULL)
+      {
+        best_frame = crp->frame;
+      }
+    }
+    newprot_str = MemFree (newprot_str);
+  }
+  oldprot_str = MemFree (oldprot_str);
+  if (best_frame > 0)
+  {
+    crp->frame = best_frame;
+  }
+  else
+  {
+    crp->frame = orig_frame;
+  }
+
+}
+
+
+NLM_EXTERN AdjustFeatForGapPtr AdjustFeatForGapFree (AdjustFeatForGapPtr agp)
+{
+  if (agp != NULL) {
+    agp->feature_list = ValNodeFree (agp->feature_list);
+    agp->features_in_gap = ValNodeFree (agp->features_in_gap);
+    agp = MemFree (agp);
+  }
+  return agp;
+}
+ 
+
+NLM_EXTERN Boolean FeatureOkForFeatureList (SeqFeatPtr sfp, ValNodePtr feature_list)
+{
+  ValNodePtr vnp;
+  Boolean    rval = FALSE;
+
+  if (sfp == NULL) return FALSE;
+  if (feature_list == NULL) return TRUE;
+  for (vnp = feature_list; vnp != NULL && !rval; vnp = vnp->next) {
+    if (vnp->choice == 255 || vnp->choice == sfp->idx.subtype) {
+      rval = TRUE;
+    }
+  }
+  return rval;
+}
+
+
+NLM_EXTERN SeqFeatPtr GetGeneForFeature (SeqFeatPtr sfp)
+{
+  GeneRefPtr grp;
+  SeqFeatPtr overlap_gene;
+  Boolean    is_suppressed;
+  SeqMgrFeatContext fcontext;
+
+  grp = SeqMgrGetGeneXref (sfp);
+  is_suppressed = SeqMgrGeneIsSuppressed (grp);
+  if (is_suppressed) return NULL;
+
+  if (grp != NULL) {
+    overlap_gene = SeqMgrGetGeneByLocusTag (BioseqFindFromSeqLoc(sfp->location), grp->locus_tag, &fcontext);
+  } else {
+    overlap_gene = SeqMgrGetOverlappingGene(sfp->location, &fcontext);
+  }
+  return overlap_gene;
+}
+
+
+const char *cds_gap_comment = "coding region disrupted by sequencing gap";
+
+NLM_EXTERN void AddCDSGapComment (SeqFeatPtr sfp)
+{
+  CharPtr new_comment = NULL;
+  
+  if (sfp == NULL || StringSearch (sfp->comment, cds_gap_comment) != NULL)
+  {
+    return;
+  }
+  
+  if (StringHasNoText (sfp->comment))
+  {
+    sfp->comment = MemFree (sfp->comment);
+    sfp->comment = StringSave (cds_gap_comment);
+  }
+  else
+  {
+    new_comment = (CharPtr) MemNew ((StringLen (sfp->comment) 
+                                     + StringLen (cds_gap_comment)
+                                     + 4) * sizeof (Char));
+    StringCpy (new_comment, sfp->comment);
+    StringCat (new_comment, "; ");
+    StringCat (new_comment, cds_gap_comment);
+    sfp->comment = MemFree (sfp->comment);
+    sfp->comment = new_comment;
+  }
+}
+
+
+NLM_EXTERN BioseqPtr 
+AddProteinSequenceCopy 
+(BioseqPtr  protbsp, 
+ BioseqPtr  featbsp,
+ SeqFeatPtr new_sfp,
+ Uint2      entityID)
+{
+  Char        str [128];
+  SeqIdPtr    new_id;
+  BioseqPtr   new_protbsp;
+  SeqEntryPtr prot_sep, parent_sep;
+  SeqFeatPtr  prot_sfp, prot_cpy;
+  SeqAnnotPtr sap;
+  SeqLocPtr   slp;
+
+  if (protbsp == NULL || featbsp == NULL || new_sfp == NULL)
+  {
+    return NULL;
+  }
+  
+  parent_sep = GetBestTopParentForData (entityID, featbsp);
+  if (parent_sep == NULL 
+      || !IS_Bioseq_set (parent_sep) 
+      || parent_sep->data.ptrvalue == NULL)
+  {
+    return NULL;
+  }
+  
+  SeqIdWrite (protbsp->id, str, PRINTID_REPORT, sizeof (str) - 1);    
+  new_id = MakeUniqueSeqID (str);                                            
+  new_protbsp = BioseqCopyEx (new_id, protbsp, 0, protbsp->length - 1,
+                                      Seq_strand_plus, TRUE);
+  ValNodeLink (&(new_protbsp->descr),
+               AsnIoMemCopy ((Pointer) protbsp->descr,
+                             (AsnReadFunc) SeqDescrAsnRead,
+                             (AsnWriteFunc) SeqDescrAsnWrite));
+                                      
+  prot_sep = SeqEntryNew ();
+  if (prot_sep != NULL)
+  {
+    prot_sep->choice = 1;
+    prot_sep->data.ptrvalue = new_protbsp;
+    SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) new_protbsp, prot_sep);
+    AddSeqEntryToSeqEntry (parent_sep, prot_sep, TRUE);
+  }
+  
+  SeqMgrAddToBioseqIndex (new_protbsp);           
+  new_sfp->product = SeqLocWholeNew (new_protbsp); 
+
+  for (sap = protbsp->annot; sap != NULL; sap = sap->next) {
+    if (sap->type == 1) {
+      for (prot_sfp = sap->data; prot_sfp != NULL; prot_sfp = prot_sfp->next) {
+        slp = SeqLocCopy (prot_sfp->location);
+        slp = SeqLocReplaceID (slp, new_protbsp->id);
+        prot_cpy = CreateNewFeatureOnBioseq (new_protbsp, SEQFEAT_PROT, slp);
+        prot_cpy->data.value.ptrvalue = AsnIoMemCopy (prot_sfp->data.value.ptrvalue, (AsnReadFunc) ProtRefAsnRead, (AsnWriteFunc) ProtRefAsnWrite);
+      }
+    }
+  }
+  SeqMgrIndexFeatures (entityID, NULL);
+  return new_protbsp;
+}
+
+
+NLM_EXTERN void SetProductSequencePartials (BioseqPtr protbsp, Boolean partial5, Boolean partial3)
+{
+  SeqFeatPtr  prot_sfp;
+  SeqMgrFeatContext context;
+  SeqMgrDescContext dcontext;
+  SeqDescrPtr       sdp;
+  MolInfoPtr        mip;
+
+  if (protbsp == NULL)
+  {
+    return;
+  }
+        
+  /* set partials on product */
+  prot_sfp = SeqMgrGetNextFeature (protbsp, NULL, 
+                                          SEQFEAT_PROT, FEATDEF_PROT, &context);
+  if (prot_sfp != NULL)
+  {
+    SetSeqLocPartial (prot_sfp->location, partial5, partial3);
+    prot_sfp->partial = partial5 || partial3;
+  }
+        
+  sdp = SeqMgrGetNextDescriptor (protbsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp != NULL)
+  {
+    mip = (MolInfoPtr) sdp->data.ptrvalue;
+    if (partial5 && partial3) {
+      mip->completeness = 5;
+    } else if (partial5) {
+      mip->completeness = 3;
+    } else if (partial3) {
+      mip->completeness = 4;
+    } else if (prot_sfp != NULL && prot_sfp->partial) {
+      mip->completeness = 2;
+    } else {
+      mip->completeness = 0;
+    }
+  }  
+}
+
+
+static SeqLocPtr MakeMixedLocFromLocList (SeqLocPtr loc_list)
+{
+  SeqLocPtr   slp_mix, tmp_slp, prev_slp = NULL, next_slp;
+
+  /* make location mixed */    
+  slp_mix = ValNodeNew(NULL);
+  slp_mix->choice = SEQLOC_MIX;
+  slp_mix->data.ptrvalue = loc_list;
+  tmp_slp = loc_list;
+  while (tmp_slp != NULL) {
+    next_slp = tmp_slp->next;
+    if (tmp_slp->choice == SEQLOC_MIX) {
+      if (tmp_slp->data.ptrvalue == NULL) {
+        /* empty mixed loc, just remove it */
+        if (prev_slp == NULL) {
+          slp_mix->data.ptrvalue = tmp_slp->next;
+        } else {
+          prev_slp->next = tmp_slp->next;
+        }
+        tmp_slp->next = NULL;
+        tmp_slp = SeqLocFree (tmp_slp);
+      } else {
+        /* take sublocations and promote them */
+        if (prev_slp == NULL) {
+          slp_mix->data.ptrvalue = tmp_slp->data.ptrvalue;
+        } else {
+          prev_slp->next = tmp_slp->data.ptrvalue;
+        }
+        prev_slp = tmp_slp->data.ptrvalue;
+        while (prev_slp->next != NULL) {
+          prev_slp = prev_slp->next;
+        }
+        prev_slp->next = next_slp;
+        tmp_slp->next = NULL;
+        tmp_slp->data.ptrvalue = NULL;
+        tmp_slp = SeqLocFree (tmp_slp);
+      }
+    } else {
+      prev_slp = tmp_slp;
+    }
+    tmp_slp = next_slp;
+  }
+  return slp_mix;
+}
+
+
+NLM_EXTERN void AdjustFeatureForGapsCallback (SeqFeatPtr sfp, Pointer data)
+{
+  AdjustFeatForGapPtr afgp;
+  BioseqPtr   protbsp = NULL, new_protbsp;
+  SeqFeatPtr  new_sfp, tmp, gene, mrna;
+  Boolean     partial5, partial3;
+  Uint2       entityID;
+  SeqLocPtr   slp_new;
+  Boolean     split;
+  Boolean     split_internal;
+  ValNodePtr  tmp_list;
+  BioseqPtr   gapped_bioseq;
+  SeqMgrFeatContext fcontext;
+  Boolean           set_partial_ends;
+
+  if (sfp == NULL || data == NULL) return;
+
+  afgp = (AdjustFeatForGapPtr) data;
+
+  if (!FeatureOkForFeatureList(sfp, afgp->feature_list)) return;
+
+  gapped_bioseq = BioseqFind (SeqLocId (sfp->location));
+  
+  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+  slp_new = (SeqLocPtr) AsnIoMemCopy (sfp->location, 
+                                      (AsnReadFunc) SeqLocAsnRead, 
+                                      (AsnWriteFunc) SeqLocAsnWrite);                                         
+  split = FALSE;
+  set_partial_ends = afgp->make_partial;
+  if (set_partial_ends && ! afgp->partial_for_pseudo) {
+    if (sfp->pseudo) {
+      set_partial_ends = FALSE;
+    } else {
+      gene = GetGeneForFeature (sfp);
+      if (gene != NULL && gene->pseudo) {
+        set_partial_ends = FALSE;
+      }
+    }
+  }
+
+  /* handle overlapping features if coding region */
+  if (sfp->data.choice == SEQFEAT_CDREGION) 
+  {    
+    split_internal = afgp->split_internal;
+    afgp->split_internal = FALSE;
+    tmp_list = afgp->feature_list;
+    afgp->feature_list = NULL;
+    gene = GetGeneForFeature (sfp);
+    AdjustFeatureForGapsCallback (gene, afgp);
+    mrna = SeqMgrGetOverlappingmRNA (sfp->location, &fcontext);
+    afgp->split_internal = split_internal;
+    AdjustFeatureForGapsCallback (mrna, afgp);
+    afgp->feature_list = tmp_list;
+  }
+
+  slp_new = RemoveGapsFromLocation (slp_new, afgp->unknown_gaps, afgp->known_gaps, afgp->trim_ends, afgp->split_internal, set_partial_ends, &split);
+  if (slp_new == NULL) {
+    ValNodeAddPointer (&(afgp->features_in_gap), OBJ_SEQFEAT, sfp);
+    return;
+  } else if (SeqLocCompare (slp_new, sfp->location) == SLC_A_EQ_B) {
+    slp_new = SeqLocFree (slp_new);
+    return;
+  }
+
+  if (split) {
+    AddCDSGapComment(sfp);
+  }
+
+  sfp->location = SeqLocFree (sfp->location);
+  sfp->location = slp_new;
+
+  if (gapped_bioseq != NULL && gapped_bioseq->repr == Seq_repr_delta)
+  {
+    entityID = gapped_bioseq->idx.entityID;
+   
+    while (sfp->location->next != NULL)
+    {
+      /* create a copy of the feature for each interval between gaps */
+      tmp = sfp->next;
+      sfp->next = NULL;
+      new_sfp = (SeqFeatPtr) AsnIoMemCopy (sfp, 
+                                          (AsnReadFunc) SeqFeatAsnRead, 
+                                          (AsnWriteFunc) SeqFeatAsnWrite);
+      sfp->next = new_sfp;
+      new_sfp->next = tmp;
+
+      new_sfp->location = sfp->location->next;
+      new_sfp->comment = StringSave (sfp->comment);
+
+      sfp->location->next = NULL;
+        
+      /* fix partials */
+      CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+      sfp->partial = partial5 || partial3;
+
+      if (sfp->data.choice == SEQFEAT_CDREGION) {
+        protbsp = BioseqFindFromSeqLoc (sfp->product);        
+        if (protbsp != NULL)
+        {
+          new_protbsp = AddProteinSequenceCopy (protbsp, gapped_bioseq, new_sfp, entityID);                                                  
+        }
+                
+        /* adjust frame */
+        AdjustFrame (sfp, protbsp);
+
+        /* retranslate coding region */
+        SeqEdTranslateOneCDS (sfp, gapped_bioseq, entityID, afgp->align_func);
+        
+        /* set partials on product */
+        if (protbsp == NULL)
+        {
+          protbsp = BioseqFindFromSeqLoc (sfp->product);
+        }
+        SetProductSequencePartials (protbsp, partial5, partial3);
+        protbsp = new_protbsp;
+      }    
+      partial5 = TRUE;
+      sfp = new_sfp;
+    }
+    /* fix partials for last feature */
+    CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+    sfp->partial = partial5 || partial3;
+
+    if (sfp->data.choice == SEQFEAT_CDREGION) 
+    {    
+      /* adjust frame */
+      protbsp = BioseqFindFromSeqLoc (sfp->product);
+      AdjustFrame (sfp, protbsp);
+
+      /* retranslate coding region */
+      SeqEdTranslateOneCDS (sfp, gapped_bioseq, entityID, afgp->align_func);
+      /* set partials on product */
+      SetProductSequencePartials (protbsp, partial5, partial3);
+    }
+  }
+  else 
+  {
+    /* make location mixed */
+    sfp->location = MakeMixedLocFromLocList (sfp->location);
+  }
+}
+
+
+NLM_EXTERN void MarkFeaturesInGapsForDeletion (AdjustFeatForGapPtr afgp)
+{
+  ValNodePtr vnp;
+  SeqFeatPtr sfp;
+  BioseqPtr  product_bsp;
+
+  if (afgp == NULL || afgp->features_in_gap == NULL)
+  {
+    return;
+  }
+  
+  for (vnp = afgp->features_in_gap; vnp != NULL; vnp = vnp->next)
+  {
+    sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+    sfp->idx.deleteme = TRUE;
+    if (sfp->data.choice == SEQFEAT_CDREGION && sfp->product != NULL)
+    {
+      product_bsp = BioseqFindFromSeqLoc (sfp->product);
+      if (product_bsp != NULL)
+      {
+        product_bsp->idx.deleteme = TRUE;
+      }
+    }
+  }
+  afgp->features_in_gap = ValNodeFree (afgp->features_in_gap);
+}
+
+NLM_EXTERN void AdjustCDSLocationsForUnknownGapsCallback (SeqFeatPtr sfp, Pointer data)
+{
+  AdjustFeatForGapData agd;
+
+  agd.feature_list = NULL;
+
+  agd.unknown_gaps = TRUE;
+  agd.known_gaps = FALSE;
+  agd.make_partial = TRUE;
+  agd.partial_for_pseudo = FALSE;
+  agd.split_internal = TRUE;
+  agd.trim_ends = TRUE;
+  agd.align_func = data;
+
+  agd.features_in_gap = NULL;
+
+  AdjustFeatureForGapsCallback (sfp, &agd);
+  MarkFeaturesInGapsForDeletion (&agd);
+}
+
+
+static Boolean GetNumberInNthColumn (CharPtr line, Int4 n, Int4Ptr pVal)
+{
+  CharPtr cp, col_start;
+  Int4    col = 1, val = 0;
+  Boolean rval = FALSE;
+
+  if (line == NULL || pVal == NULL) return FALSE;
+
+  col_start = line;
+  cp = StringChr (col_start, '\t');
+  while (n > col && cp != NULL) {
+    col++;
+    col_start = cp + 1;
+    cp = StringChr (col_start, '\t');
+  }
+  if (n == col) {
+    if (cp != NULL) {
+      *cp = 0;
+    }
+    val = atoi (col_start);
+    if (cp != NULL) {
+      *cp = '\t';
+    }
+    *pVal = val;
+    rval = TRUE;
+  }
+  return rval;
+}
+
+
+
+static UserFieldPtr AddTranscriptomeNumberUserField (Int4 value, CharPtr label)
+{
+  UserFieldPtr ufp;
+  ObjectIdPtr  oip;
+
+  ufp = UserFieldNew ();
+  oip = ObjectIdNew ();
+  oip->str = StringSave (label);
+  ufp->label = oip;
+  ufp->choice = 2; /* int */
+  ufp->data.intvalue = value;
+  return ufp;
+}
+
+
+static UserFieldPtr AddTranscriptomeStringUserField (CharPtr value, CharPtr label)
+{
+  UserFieldPtr ufp;
+  ObjectIdPtr  oip;
+
+  ufp = UserFieldNew ();
+  oip = ObjectIdNew ();
+  oip->str = StringSave (label);
+  ufp->label = oip;
+  ufp->choice = 1; /* visible string */
+  ufp->data.ptrvalue = (Pointer) StringSave (value);
+  return ufp;
+}
+
+const CharPtr TSA_assembly_from = "assembly from";
+const CharPtr TSA_assembly_to = "assembly to";
+const CharPtr TSA_primary_id = "primary ID";
+const CharPtr TSA_primary_from = "primary from";
+const CharPtr TSA_primary_to = "primary to";
+
+NLM_EXTERN UserFieldPtr AddLineToTranscriptomeTable (Int4 assembly_from, Int4 assembly_to, CharPtr primary_id, Int4 primary_from, Int4 primary_to)
+{
+  UserFieldPtr row, list, ufp, prev = NULL;
+  ObjectIdPtr oip;
+
+  row = UserFieldNew ();
+  oip = ObjectIdNew ();
+  oip->id = 0;
+  row->label = oip;
+  row->choice = 11; /* user fields */
+
+  ufp = AddTranscriptomeNumberUserField (assembly_from, TSA_assembly_from);
+
+  list = ufp;
+  prev = list;
+
+  ufp = AddTranscriptomeNumberUserField (assembly_to, TSA_assembly_to);
+  prev->next = ufp;
+  prev = ufp;
+
+  ufp = AddTranscriptomeStringUserField (primary_id, TSA_primary_id);
+  prev->next = ufp;
+  prev = ufp;
+
+  ufp = AddTranscriptomeNumberUserField (primary_from, TSA_primary_from);
+  prev->next = ufp;
+  prev = ufp;
+
+  ufp = AddTranscriptomeNumberUserField (primary_to, TSA_primary_to);
+  prev->next = ufp;
+  prev = ufp;
+
+  row->data.ptrvalue = list;
+
+  return row;  
+}
+
+
+NLM_EXTERN Boolean AddTranscriptomeTable (BioseqPtr bsp, FILE *fp)
+{
+  ReadBufferData    rbd;
+  Int4 assembly_from, assembly_to, primary_from, primary_to;
+  CharPtr first_tab;
+  Int4    line_num = 1;
+  UserFieldPtr row_list = NULL, prev = NULL, ufp;
+  UserObjectPtr uop;
+  ObjectIdPtr   oip;
+  Boolean       rval = FALSE;
+  CharPtr line;
+
+  if (bsp == NULL || fp == NULL) return FALSE;
+
+  rbd.fp = fp;
+  rbd.current_data = NULL;
+
+  line = AbstractReadFunction (&rbd);
+  while (line != NULL) {
+    if (line[0] != ';') {
+      first_tab = StringChr (line, '\t');
+      if (first_tab == NULL
+          || !GetNumberInNthColumn (line, 7, &primary_from)
+          || !GetNumberInNthColumn (line, 8, &primary_to)
+          || !GetNumberInNthColumn (line, 3, &assembly_from)
+          || !GetNumberInNthColumn (line, 4, &assembly_to)) {
+        Message (MSG_POST, "Line %d could not be read", line_num);
+      } else {
+        *first_tab = 0;
+        ufp = AddLineToTranscriptomeTable (assembly_from, assembly_to, line, primary_from, primary_to);
+        *first_tab = '\t';
+        if (prev == NULL) {
+          row_list = ufp;
+        } else {
+          prev->next = ufp;
+        }
+        prev = ufp;
+      }
+    }
+    line = AbstractReadFunction (&rbd);
+    line++;
+  }
+
+  if (row_list == NULL) {
+    Message (MSG_POST, "No rows found for table");
+  } else {
+    uop = UserObjectNew ();
+    oip = ObjectIdNew ();
+    oip->str = StringSave ("TSA");
+    uop->type = oip;
+    uop->data = row_list;
+    SeqDescrAddPointer (&(bsp->descr), Seq_descr_user, (Pointer) uop);
+    rval = TRUE;
+  }
+  return rval;
+}
+
+
+static Int4 ReadNumberFromPortionOfString (CharPtr str, Int4 len)
+{
+  CharPtr num_buf;
+  Int4    val;
+
+  if (str == NULL) return -1;
+  num_buf = (CharPtr) MemNew (sizeof (Char) * (len + 1));
+  StringNCpy (num_buf, str, len);
+  num_buf[len] = 0;
+  val = atoi (num_buf);
+  num_buf = MemFree (num_buf);
+  return val;
+}
+
+
+NLM_EXTERN Boolean IsStringInSpanInList (CharPtr str, CharPtr list)
+{
+  CharPtr cp, hyphen;
+  Int4    prefix_len = 0;
+  CharPtr num_start, range_start;
+  Int4    start_val, end_val, swap_val, str_val;
+  Boolean rval = FALSE;
+
+  if (StringHasNoText (list) || StringHasNoText (str)) {
+    return FALSE;
+  }
+
+  cp = str;
+  while (isalpha (*cp)) {
+    prefix_len++;
+    cp++;
+  }
+  if (*cp == 0) {
+    return FALSE;
+  }
+
+  num_start = cp;
+  while (isdigit (*cp)) {
+    cp++;
+  }
+  if (*cp != 0) {
+    return FALSE;
+  }
+
+  /* find ranges */
+
+  hyphen = StringChr (list, '-');
+  while (hyphen != NULL && !rval) {
+    if (hyphen == list) {
+      hyphen = StringChr (hyphen + 1, '-');
+    } else {
+      /* is the second part of the range what we're looking for? */
+      if ((prefix_len == 0 || isdigit (*(hyphen + 1)) || StringNCmp (hyphen + 1, str, prefix_len) == 0)
+          && isdigit (*(hyphen + 1 + prefix_len))) {
+        cp = hyphen + 1 + prefix_len;
+        while (isdigit (*cp)) {
+          cp++;
+        }
+        if (*cp == 0 || ispunct (*cp) || isspace (*cp)) {
+          end_val = ReadNumberFromPortionOfString (hyphen + 1 + prefix_len, cp - hyphen - 1 - prefix_len);
+          if (end_val > -1) {
+            range_start = hyphen - 1;
+            while (range_start > list && isdigit (*range_start)) {
+              range_start --;
+            }
+            if (!isdigit (*range_start)) {
+              range_start++;
+            }
+            if (range_start - list >= prefix_len
+                /* make sure prefix matches */
+                && (prefix_len == 0 || StringNCmp (range_start - prefix_len, str, prefix_len) == 0)
+                /* make sure the prefix is at the beginning of the list, or else the character before is punctuation or space */
+                && (list == range_start - prefix_len 
+                    || ispunct (*(range_start - prefix_len - 1))
+                    || isspace (*(range_start - prefix_len - 1)))) {
+              start_val = ReadNumberFromPortionOfString (range_start, hyphen - range_start);
+              if (start_val > end_val) {
+                swap_val = start_val;
+                start_val = end_val;
+                end_val = swap_val;
+              }
+              str_val = ReadNumberFromPortionOfString (str + prefix_len, StringLen (str + prefix_len));
+              if (str_val > start_val && str_val <= end_val) {
+                rval = TRUE;
+              }
+            }
+          }
+        }
+      }
+      hyphen = StringChr (hyphen + 1, '-');
+    }
+  }
+  
+  return rval;
+}
+
+
+static void ParseGoTermsFromFieldsSfp (UserObjectPtr uop, Pointer userdata)
+{
+  ObjectIdPtr  oip;
+  UserFieldPtr ufp_process, ufp_new, ufp2, ufp, ufp_last = NULL, new_list = NULL, last_new = NULL;
+  CharPtr      cp;
+
+  if (uop == NULL) return;
+  oip = uop->type;
+  if (oip == NULL) return;
+  if (StringCmp (oip->str, "GeneOntology") == 0) {
+    for (ufp_process = uop->data; ufp_process != NULL; ufp_process = ufp_process->next) {
+      if (ufp_process->label == NULL 
+          || (StringCmp (ufp_process->label->str, "Process") != 0
+              && StringCmp (ufp_process->label->str, "Function") != 0
+              && StringCmp (ufp_process->label->str, "Component") != 0)) {
+        continue;
+      }
+      for (ufp2 = ufp_process->data.ptrvalue; ufp2 != NULL; ufp2 = ufp2->next) {
+        if (ufp2->choice != 11) continue;
+        new_list = NULL;
+        ufp_last = NULL;
+        last_new = NULL;
+        for (ufp = ufp2->data.ptrvalue; ufp != NULL; ufp = ufp->next) {
+          ufp_last = ufp;
+          if (ufp->label != NULL && StringCmp (ufp->label->str, "text string") == 0
+              && (cp = StringISearch (ufp->data.ptrvalue, "GO:")) != NULL) {
+            ufp_new = UserFieldNew ();
+            ufp_new->label = ObjectIdNew ();
+            ufp_new->label->str = StringSave ("go id");
+            ufp_new->choice = 1; /* visible string - need to keep leading zeroes */
+            ufp_new->data.ptrvalue = StringSave (cp + 3);
+            *cp = 0;
+            cp--;
+            while (cp > (CharPtr) ufp->data.ptrvalue && isspace (*cp)) {
+              *cp = 0;
+              cp--;
+            }
+            if (last_new == NULL) {
+              new_list = ufp_new;
+            } else {
+              last_new->next = ufp_new;
+            }
+            last_new = ufp_new;
+          }
+        }
+        if (new_list != NULL) {
+          if (ufp_last == NULL) {
+            uop->data = new_list;
+          } else {
+            ufp_last->next = new_list;
+          }
+        }
+      }
+    }
+  }
+}
+
+
+static void ParseGoTermsFromFieldsCallback (SeqFeatPtr sfp, Pointer data)
+{
+  if (sfp == NULL || sfp->ext == NULL) return;
+
+  VisitUserObjectsInUop (sfp->ext, NULL, ParseGoTermsFromFieldsSfp);
+
+}
+
+
+NLM_EXTERN void ParseGoTermsFromFields (SeqEntryPtr sep)
+{
+  VisitFeaturesInSep (sep, NULL, ParseGoTermsFromFieldsCallback);
+}
+
+
+static ValNodePtr ReadOneColumnList (CharPtr line)
+{
+  CharPtr p_start, p_end;
+  Int4    plen;
+  Boolean found_end;
+  ValNodePtr col_list = NULL;
+
+  if (StringHasNoText (line)) return NULL;
+  p_start = line;
+  found_end = FALSE;
+  while (*p_start != 0 && !found_end)
+  {
+    plen = StringCSpn (p_start, "\t\n");
+    if (plen == 0)
+    {
+      if (col_list != NULL)
+      {
+        ValNodeAddStr (&col_list, 0, StringSave (""));
+      }
+      p_start++;
+      if (*p_start == 0) {
+        if (col_list != NULL)
+        {
+          ValNodeAddStr (&col_list, 0, StringSave (""));
+        }
+      }
+      continue;
+    }
+    if (plen == StringLen (p_start))
+    {
+      found_end = TRUE;
+    }
+    else
+    {
+      p_end = p_start + plen;
+      *p_end = 0;
+    }
+    TrimSpacesAroundString (p_start);
+    ValNodeAddStr (&col_list, 0, StringSave (p_start));
+    if (!found_end)
+    {
+      p_start = p_end + 1;
+    }
+  }
+  return col_list;  
+}
+
+NLM_EXTERN ValNodePtr ReadTabTableFromFile (FILE *fp)
+{
+  Int4          max_columns, num_cols;
+  ValNodePtr    header_line;
+  ValNodePtr    line_list, column_list;
+  ValNodePtr    vnp;
+  ReadBufferData rbd;
+  CharPtr        line;
+
+  if (fp == NULL) return NULL;
+  rbd.fp = fp;
+  rbd.current_data = NULL;
+
+  line_list = NULL;
+  max_columns = 0;
+  header_line = NULL;
+  line = AbstractReadFunction (&rbd);
+  while (line != NULL) 
+  {
+    column_list = ReadOneColumnList (line);
+    if (column_list != NULL)
+    {
+      vnp = ValNodeAddPointer (&line_list, 0, column_list);
+      num_cols = ValNodeLen (column_list);
+      if (num_cols > max_columns)
+      {
+        max_columns = num_cols;
+        header_line = vnp;
+      }
+    }
+    line = MemFree (line);
+    line = AbstractReadFunction (&rbd);
+  }
+  FileClose (rbd.fp);
+  /* throw out all lines before header line */
+  if (header_line != line_list)
+  {
+    vnp = line_list;
+    while (vnp != NULL && vnp->next != header_line)
+    {
+      vnp = vnp->next;
+    }
+    vnp->next = NULL;
+    ValNodeFreeData (line_list);
+    line_list = NULL;
+  }
+  return header_line;
+}
+
+
+NLM_EXTERN ValNodePtr FreeTabTable (ValNodePtr row_list)
+{
+  ValNodePtr row_vnp, column_list;
+  
+  if (row_list != NULL)
+  {
+    /* free table text */
+    for (row_vnp = row_list; row_vnp != NULL; row_vnp = row_vnp->next)
+    {
+      column_list = (ValNodePtr) row_vnp->data.ptrvalue;
+      row_vnp->data.ptrvalue = ValNodeFreeData (column_list);
+    }
+    row_list = ValNodeFree (row_list);
+  }
+  return row_list;
+}
+
+
+NLM_EXTERN ValNodePtr CountTabTableBlanks (ValNodePtr row_list)
+{
+  ValNodePtr   line_vnp, col_vnp, blank_vnp;
+  Int4         num_rows = 0;
+  ValNodePtr   blank_list = NULL;
+  
+  if (row_list == NULL) return NULL;  
+
+  for (line_vnp = row_list; line_vnp != NULL; line_vnp = line_vnp->next)
+  {
+    col_vnp = line_vnp->data.ptrvalue;
+    blank_vnp = blank_list;
+    while (col_vnp != NULL || blank_vnp != NULL) {
+      if (blank_vnp == NULL) {
+        /* for all rows prior to this one, this column was blank */
+        blank_vnp = ValNodeAddInt (&blank_list, 0, num_rows);
+      }
+      if (col_vnp == NULL || StringHasNoText (col_vnp->data.ptrvalue)) {
+        blank_vnp->data.intvalue ++;
+      }
+      if (col_vnp != NULL) {
+        col_vnp = col_vnp->next;
+      }
+      blank_vnp = blank_vnp->next;
+    }
+    num_rows ++;
+  }
+  return blank_list;
+}
+
+
+static void AddToContextList (Char ch, CharPtr PNTR strp, ValNodePtr PNTR search_list)
+{
+  ValNodePtr vnp, vnp_last = NULL, vnp2, clist;
+
+  if (strp == NULL || search_list == NULL) return;
+
+  /* group contexts for the same character together */
+  vnp = *search_list;
+  while (vnp != NULL && vnp->choice != (Uint1)ch)
+  {
+    vnp_last = vnp;
+    vnp = vnp->next;
+  }
+  if (vnp == NULL)
+  {
+    vnp = ValNodeNew(NULL);
+    if (vnp_last == NULL) 
+    {
+      *search_list = vnp;
+    }
+    else
+    {
+      vnp_last->next = vnp;
+    }
+  }
+  vnp->choice = (Uint1) ch;
+  clist = vnp->data.ptrvalue;
+  /* don't add the same string twice for the same character */
+  vnp2 = clist;
+  vnp_last = NULL;
+  while (vnp2 != NULL && vnp2->data.ptrvalue != strp)
+  {
+    vnp_last = vnp2;
+    vnp2 = vnp2->next;
+  }
+  if (vnp2 == NULL)
+  {
+    vnp2 = ValNodeNew (NULL);
+    vnp2->data.ptrvalue = strp;
+    if (vnp_last == NULL)
+    {
+      clist = vnp2;
+    }
+    else
+    {
+      vnp_last->next = vnp2;
+    }
+  }
+  vnp->data.ptrvalue = clist;
+}
+
+
+NLM_EXTERN ValNodePtr FreeContextList (ValNodePtr context_list)
+{
+  ValNodePtr vnp;
+
+  for (vnp = context_list; vnp != NULL; vnp = vnp->next)
+  {
+    vnp->data.ptrvalue = ValNodeFree (vnp->data.ptrvalue);
+  }
+  context_list = ValNodeFree (context_list);
+  return context_list;
+}
+
+
+NLM_EXTERN void SpecialCharFindWithContext (CharPtr PNTR strp, Pointer userdata, BoolPtr did_find, BoolPtr did_change)
+{
+  CharPtr cp;
+  Boolean found_any = FALSE;
+
+  if (strp == NULL || *strp == NULL || userdata == NULL) return;
+
+  cp = *strp;
+  while (*cp != 0)
+  {
+    if (*cp < ' ' || *cp > '~')
+    {
+      found_any = TRUE;
+      AddToContextList (*cp, strp, (ValNodePtr PNTR) userdata);
+    }
+    cp++;
+  }
+  if (found_any && did_find != NULL)
+  {
+    *did_find = TRUE;
+  }
+}
+
+
+NLM_EXTERN ValNodePtr ScanTabTableForSpecialCharacters (ValNodePtr row_list)
+{
+  ValNodePtr special_list = NULL, line_vnp, col_vnp;
+
+  if (row_list == NULL) return NULL;  
+
+  for (line_vnp = row_list; line_vnp != NULL; line_vnp = line_vnp->next)
+  {
+    col_vnp = line_vnp->data.ptrvalue;
+    while (col_vnp != NULL) {
+      SpecialCharFindWithContext ((CharPtr PNTR)&(col_vnp->data.ptrvalue), &special_list, NULL, NULL);
+      col_vnp = col_vnp->next;
+    }
+  }
+  return special_list;
+}
diff --git a/api/sqnutil3.c b/api/sqnutil3.c
index 4735f56b..e208570c 100644
--- a/api/sqnutil3.c
+++ b/api/sqnutil3.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   2/7/00
 *
-* $Revision: 6.183 $
+* $Revision: 6.231 $
 *
 * File Description: 
 *
@@ -61,6 +61,7 @@
 #include <salpedit.h>
 #include <alignmgr2.h>
 #include <actutils.h>
+#include <utilpub.h>
 /* included for discrepancy report */
 #include <asn2gnbk.h>
 #include <asn2gnbp.h>
@@ -1235,29 +1236,6 @@ static Int2 FindStr (CharPtr PNTR array, Int2 array_num, CharPtr str)
   return -1;
 }
 
-static ValNodePtr remove_node (ValNodePtr head, ValNodePtr x)
-
-{
-  ValNodePtr  v, p;
-  
-  if (head == NULL) return NULL;
-  if (x == head) {
-    head = x->next;
-    x->next = NULL;
-    ValNodeFree (x);
-    return head;
-  }
-  for (v = head; v != NULL && v != x; v = v->next) {
-    p = v;
-  }
-  if (v != NULL) {
-    p->next = x->next;
-    x->next = NULL;
-    ValNodeFree (x);
-  }
-  return head;
-}
-
 static SeqLocPtr fake_bond_loc (SeqLocPtr slp)
 
 {
@@ -1446,25 +1424,7 @@ static void MergeAdjacentAnnotsCallback (SeqEntryPtr sep, Pointer mydata, Int4 i
   }
 }
 
-static Boolean empty_citgen (CitGenPtr  cit)
-
-{
-  if (cit == NULL) return TRUE;
-  if (cit->cit) return FALSE;
-  if (cit->authors) return FALSE;
-  if (cit->muid > 0) return FALSE;
-  if (cit->journal) return FALSE;
-  if (cit->volume) return FALSE;
-  if (cit->issue) return FALSE;
-  if (cit->pages) return FALSE;
-  if (cit->date) return FALSE;
-  if (cit->serial_number > 0) return FALSE;
-  if (cit->title) return FALSE;
-  if (cit->pmid > 0) return FALSE;
-  return TRUE;
-}
-
-static Boolean PubIsEffectivelyEmpty (PubdescPtr pdp)
+NLM_EXTERN Boolean PubIsEffectivelyEmpty (PubdescPtr pdp)
 
 {
   ValNodePtr  vnp;
@@ -1627,7 +1587,7 @@ static void ConvertPubFeatDescProc (SeqFeatPtr sfp, Pointer userdata)
   }
 }
 
-static void ConvertSourceFeatDescProc (SeqFeatPtr sfp, Pointer userdata)
+extern void ConvertSourceFeatDescProc (SeqFeatPtr sfp, Pointer userdata)
 
 {
   BioSourcePtr   biop;
@@ -1639,6 +1599,7 @@ static void ConvertSourceFeatDescProc (SeqFeatPtr sfp, Pointer userdata)
   SeqIdPtr       sip;
   SubSourcePtr   ssp;
   ValNode        vn;
+  ValNodePtr     last_dbxref;
 
   /* look for biosource features */
   if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC) return;
@@ -1686,6 +1647,23 @@ static void ConvertSourceFeatDescProc (SeqFeatPtr sfp, Pointer userdata)
     }
     lastssp->next = ssp;
   }
+
+  /* move dbxrefs on feature to source */
+  if (sfp->dbxref != NULL) {
+    if (biop->org == NULL) {
+      biop->org = OrgRefNew();
+    }
+    last_dbxref = biop->org->db;
+    while (last_dbxref != NULL && last_dbxref->next != NULL) {
+      last_dbxref = last_dbxref->next;
+    }
+    if (last_dbxref == NULL) {    
+      biop->org->db = sfp->dbxref;
+    } else {
+      last_dbxref->next = sfp->dbxref;
+    }
+    sfp->dbxref = NULL;
+  }
 }
 
 static void PromoteOrgRefDescToBioSource (SeqDescrPtr sdp, Pointer userdata)
@@ -4783,7 +4761,7 @@ static SeqAlignPtr RemoveOneSequenceFromAlignment (SeqIdPtr sip, SeqAlignPtr sal
   SeqIdPtr    tmpsip;
   SeqAlignPtr salp, salp_next, prev_salp, remove_salp, last_remove;
   
-  if (!FindSeqIdinSeqAlign (salphead, sip)) return NULL;
+  if (!FindSeqIdinSeqAlign (salphead, sip)) return salphead;
   
   salp = salphead;
   prev_salp = NULL;
@@ -4943,20 +4921,64 @@ static CharPtr inferencePrefix [] = {
   "nucleotide motif",
   "protein motif",
   "ab initio prediction",
+  "alignment",
   NULL
 };
 
+static Int2 ValidateInferenceAccession (CharPtr str, Char chr, Boolean fetchAccn, Boolean has_fetch_function)
+
+{
+  Int2      accnv, rsult;
+  ErrSev    sev;
+  SeqIdPtr  sip;
+  CharPtr   tmp;
+
+  if (StringHasNoText (str)) return EMPTY_INFERENCE_STRING;
+
+  rsult = VALID_INFERENCE;
+
+  tmp = StringChr (str, chr);
+  if (tmp != NULL) {
+    *tmp = '\0';
+    tmp++;
+    TrimSpacesAroundString (str);
+    TrimSpacesAroundString (tmp);
+    if (StringDoesHaveText (tmp)) {
+      if (StringICmp (str, "INSD") == 0 || StringICmp (str, "RefSeq") == 0) {
+        accnv = ValidateAccnDotVer (tmp);
+        if (accnv == -5 || accnv == -6) {
+          rsult = BAD_INFERENCE_ACC_VERSION;
+        } else if (accnv != 0) {
+          rsult = BAD_INFERENCE_ACCESSION;
+        } else if (fetchAccn) {
+          sip = SeqIdFromAccessionDotVersion (tmp);
+          sev = ErrGetMessageLevel ();
+          ErrSetMessageLevel (SEV_ERROR);
+          if (has_fetch_function && GetGIForSeqId (sip) == 0) {
+            rsult = ACC_VERSION_NOT_PUBLIC;
+          }
+          ErrSetMessageLevel (sev);
+          SeqIdFree (sip);
+        }
+      }
+    }
+    if (StringChr (tmp, ' ') != NULL) rsult = SPACES_IN_INFERENCE;
+  } else {
+    rsult = SINGLE_INFERENCE_FIELD;
+  }
+
+  return rsult;
+}
+
 NLM_EXTERN Int2 ValidateInferenceQualifier (CharPtr val, Boolean fetchAccn)
 
 {
-  Int2           accnv, best, j, rsult;
+  Int2           best, j, rsult, tmprsult;
   Char           ch;
   Boolean        has_fetch_function, same_species;
   size_t         len;
+  CharPtr        nxt, ptr, rest, str;
   ObjMgrProcPtr  ompp = NULL;
-  CharPtr        rest, str, tmp;
-  ErrSev         sev;
-  SeqIdPtr       sip;
 
   if (StringHasNoText (val)) return EMPTY_INFERENCE_STRING;
 
@@ -4996,45 +5018,35 @@ NLM_EXTERN Int2 ValidateInferenceQualifier (CharPtr val, Boolean fetchAccn)
     rsult = SAME_SPECIES_MISUSED;
   }
 
+  has_fetch_function = FALSE;
+  while ((ompp = ObjMgrProcFindNext(NULL, OMPROC_FETCH, OBJ_SEQID, OBJ_SEQID, ompp)) != NULL) {
+    if ((ompp->subinputtype == 0) && (ompp->suboutputtype == SEQID_GI)) {
+      has_fetch_function = TRUE;
+    }
+  }
+
   str = StringSave (rest);
 
-  tmp = StringChr (str, ':');
-  if (tmp != NULL) {
-    *tmp = '\0';
-    tmp++;
-    TrimSpacesAroundString (str);
-    TrimSpacesAroundString (tmp);
-    if (StringDoesHaveText (tmp)) {
-      if (StringICmp (str, "INSD") == 0 || StringICmp (str, "RefSeq") == 0) {
-        accnv = ValidateAccnDotVer (tmp);
-        if (accnv == -5 || accnv == -6) {
-          rsult = BAD_INFERENCE_ACC_VERSION;
-        } else if (accnv != 0) {
-          rsult = BAD_INFERENCE_ACCESSION;
-        } else if (fetchAccn) {
-          sip = SeqIdFromAccessionDotVersion (tmp);
-          has_fetch_function = FALSE;
-          while ((ompp = ObjMgrProcFindNext(NULL, OMPROC_FETCH, OBJ_SEQID, OBJ_SEQID, ompp)) != NULL) {
-            if ((ompp->subinputtype == 0) && (ompp->suboutputtype == SEQID_GI)) {
-              has_fetch_function = TRUE;
-            }
-          }
-          sev = ErrGetMessageLevel ();
-          ErrSetMessageLevel (SEV_ERROR);
-          if (has_fetch_function && GetGIForSeqId (sip) == 0) {
-            rsult = ACC_VERSION_NOT_PUBLIC;
-          }
-          ErrSetMessageLevel (sev);
-          SeqIdFree (sip);
-        }
+  if (best >= 1 && best <= 7) {
+    tmprsult = ValidateInferenceAccession (str, ':', fetchAccn, has_fetch_function);
+    if (tmprsult != VALID_INFERENCE) {
+      rsult = tmprsult;
+    }
+  } else if (best == 12) {
+    ptr = StringRChr (str, ':');
+    while (ptr != NULL) {
+      *ptr = '\0';
+      ptr++;
+      nxt = StringChr (ptr, ',');
+      if (nxt != NULL) {
+        *nxt = '\0';
       }
+      tmprsult = ValidateInferenceAccession (ptr, '|', fetchAccn, has_fetch_function);
+      if (tmprsult != VALID_INFERENCE) {
+        rsult = tmprsult;
+      }
+      ptr = nxt;
     }
-    /*
-    if (StringChr (str, ' ') != NULL) rsult = SPACES_IN_INFERENCE;
-    */
-    if (StringChr (tmp, ' ') != NULL) rsult = SPACES_IN_INFERENCE;
-  } else {
-    rsult = SINGLE_INFERENCE_FIELD;
   }
 
   MemFree (str);
@@ -5185,6 +5197,76 @@ extern void ExtendSingleGeneOnMRNA (BioseqPtr bsp, Pointer userdata)
 
 /* Functions for the Discrepancy Report */
 
+
+static Boolean IsmRNASequenceInGenProdSet (BioseqPtr bsp)
+{
+  SeqMgrDescContext dcontext;
+  BioseqSetPtr      bssp;
+  SeqDescrPtr sdp;
+  MolInfoPtr  mip;
+  Boolean rval = FALSE;
+
+  if (bsp != NULL && bsp->mol == Seq_mol_rna && bsp->idx.parentptr != NULL && bsp->idx.parenttype == OBJ_BIOSEQSET) {
+    bssp = (BioseqSetPtr) bsp->idx.parentptr;
+    if (bssp->_class == BioseqseqSet_class_gen_prod_set) {
+      sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+      if (sdp != NULL && sdp->data.ptrvalue != NULL && sdp->choice == Seq_descr_molinfo) {
+        mip = (MolInfoPtr) sdp->data.ptrvalue;
+        if (mip->biomol == MOLECULE_TYPE_MRNA) {
+          rval = TRUE;
+        }
+      }
+    } else if (bssp->_class == BioseqseqSet_class_nuc_prot && bssp->idx.parentptr != NULL && bssp->idx.parenttype == OBJ_BIOSEQSET) {
+      bssp = (BioseqSetPtr) bssp->idx.parentptr;
+      if (bssp->_class == BioseqseqSet_class_gen_prod_set) {
+        sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+        if (sdp != NULL && sdp->data.ptrvalue != NULL && sdp->choice == Seq_descr_molinfo) {
+          mip = (MolInfoPtr) sdp->data.ptrvalue;
+          if (mip->biomol == MOLECULE_TYPE_MRNA) {
+            rval = TRUE;
+          }
+        }
+      }
+    }
+  }
+  return rval;
+}
+
+
+typedef struct skipmrnafeaturesingenprodset {
+  Pointer userdata;
+  VisitFeaturesFunc callback;
+} SkipmRNAFeaturesInGenProdSetData, PNTR SkipmRNAFeaturesInGenProdSetPtr;
+
+static void VisitGenProdSetFeaturesCallback (SeqFeatPtr sfp, Pointer userdata)
+{
+  SkipmRNAFeaturesInGenProdSetPtr p;
+
+  if (sfp == NULL || userdata == NULL) {
+    return;
+  }
+
+  p = (SkipmRNAFeaturesInGenProdSetPtr) userdata;
+  if (p->callback == NULL) {
+    return;
+  }
+
+  if (!IsmRNASequenceInGenProdSet(BioseqFindFromSeqLoc (sfp->location))) {
+    (p->callback) (sfp, p->userdata);
+  }
+}
+
+
+extern void VisitGenProdSetFeatures (SeqEntryPtr sep, Pointer userdata, VisitFeaturesFunc callback)
+{
+  SkipmRNAFeaturesInGenProdSetData d;
+
+  d.callback = callback;
+  d.userdata = userdata;
+  VisitFeaturesInSep (sep, &d, VisitGenProdSetFeaturesCallback);
+}
+
+
 extern ClickableItemPtr 
 NewClickableItem 
 (Uint4           clickable_item_type,
@@ -5211,28 +5293,32 @@ NewClickableItem
 }
 
 
+extern ClickableItemPtr ClickableItemFree (ClickableItemPtr cip)
+{
+  if (cip != NULL)
+  {
+    cip->description = MemFree (cip->description);
+    if (cip->datafree_func != NULL)
+    {
+      (cip->datafree_func) (cip->callback_data);
+    }
+    cip->item_list = ValNodeFree (cip->item_list);
+  
+    cip->subcategories = FreeClickableList (cip->subcategories);
+    cip = MemFree (cip);
+  }
+  return cip;
+}
+
+
 extern ValNodePtr FreeClickableList (ValNodePtr list)
 {
-  ClickableItemPtr cip;
   ValNodePtr       list_next;
   
   while (list != NULL) {
     list_next = list->next;
     list->next = NULL;
-    cip = (ClickableItemPtr) list->data.ptrvalue;
-    if (cip != NULL)
-    {
-      cip->description = MemFree (cip->description);
-      if (cip->datafree_func != NULL)
-      {
-        (cip->datafree_func) (cip->callback_data);
-      }
-      cip->item_list = ValNodeFree (cip->item_list);
-    
-      cip->subcategories = FreeClickableList (cip->subcategories);
-      cip = MemFree (cip);
-      list->data.ptrvalue = NULL;
-    }
+    list->data.ptrvalue = ClickableItemFree (list->data.ptrvalue);
     list = ValNodeFree (list);
     list = list_next;
   }
@@ -5287,6 +5373,434 @@ static ValNodePtr ItemListFromSubcategories (ValNodePtr subcategories)
   return item_list;
 }
 
+
+extern GlobalDiscrepancyPtr 
+GlobalDiscrepancyNew (CharPtr str, Uint1 data_choice, Pointer data)
+{
+  GlobalDiscrepancyPtr g;
+
+  g = (GlobalDiscrepancyPtr) MemNew (sizeof (GlobalDiscrepancyData));
+  g->str = StringSave (str);
+  g->data_choice = data_choice;
+  if (g->data_choice == 0) {
+    g->data = StringSave (data);
+  } else {
+    g->data = data;
+  }
+  return g;
+}
+
+
+extern GlobalDiscrepancyPtr GlobalDiscrepancyFree (GlobalDiscrepancyPtr g)
+{
+  if (g != NULL) {
+    g->str = MemFree (g->str);
+    if (g->data_choice == 0) {
+      g->data = MemFree (g->data);
+    }
+    g = MemFree (g);
+  }
+  return g;
+}
+
+
+extern ValNodePtr FreeGlobalDiscrepancyList (ValNodePtr vnp)
+{
+  ValNodePtr vnp_next;
+
+  while (vnp != NULL) {
+    vnp_next = vnp->next;
+    vnp->next = NULL;
+    vnp->data.ptrvalue = GlobalDiscrepancyFree (vnp->data.ptrvalue);
+    vnp = ValNodeFree (vnp);
+    vnp = vnp_next;
+  }
+  return vnp;
+}
+
+
+extern void ConvertGlobalDiscrepancyToText (GlobalDiscrepancyPtr g, Boolean use_feature_fmt)
+{
+  ValNode vn;
+  ValNodePtr list_copy;
+
+  if (g == NULL || g->data_choice == 0) return;
+  
+  vn.choice = g->data_choice;
+  vn.data.ptrvalue = g->data;
+  vn.next = NULL;
+
+  g->data_choice = 0;
+  if (use_feature_fmt) {  
+    list_copy = ReplaceDiscrepancyItemWithFeatureTableStrings (&vn);
+    g->data = list_copy->data.ptrvalue;
+    list_copy = ValNodeFree (list_copy);
+  } else {
+    g->data = GetDiscrepancyItemText (&vn);
+  }
+}
+
+
+extern void ConvertGlobalDiscrepancyListToText (ValNodePtr vnp, Boolean use_feature_fmt)
+{
+  while (vnp != NULL) {
+    ConvertGlobalDiscrepancyToText (vnp->data.ptrvalue, use_feature_fmt);
+    vnp = vnp->next;
+  }
+}
+
+
+extern ValNodePtr GetGlobalDiscrepancyItem (GlobalDiscrepancyPtr g)
+{
+  ValNodePtr rval = NULL;
+  if (g != NULL) {
+    rval = ValNodeNew (NULL);
+    rval->choice = g->data_choice;
+    if (rval->choice == 0) {
+      rval->data.ptrvalue = StringSave (g->data);
+    } else {
+      rval->data.ptrvalue = g->data;
+    }
+  }
+  return rval;
+}
+
+
+extern CharPtr GetGlobalDiscrepancyStr (GlobalDiscrepancyPtr g)
+{
+  CharPtr rval = NULL;
+  if (g != NULL) {
+    rval = g->str;
+  }
+  return rval;
+}
+
+
+NLM_EXTERN int LIBCALLBACK SortVnpByGlobalDiscrepancyString (VoidPtr ptr1, VoidPtr ptr2)
+
+{
+  ValNodePtr  vnp1;
+  ValNodePtr  vnp2;
+  GlobalDiscrepancyPtr g1, g2;
+
+  if (ptr1 != NULL && ptr2 != NULL) {
+    vnp1 = *((ValNodePtr PNTR) ptr1);
+    vnp2 = *((ValNodePtr PNTR) ptr2);
+    if (vnp1 != NULL && vnp2 != NULL) {
+      g1 = (GlobalDiscrepancyPtr) vnp1->data.ptrvalue;
+      g2 = (GlobalDiscrepancyPtr) vnp2->data.ptrvalue;
+      if (g1 != NULL && g2 != NULL && g1->str != NULL && g2->str != NULL) {
+        return StringICmp (g1->str, g2->str);
+      }
+    }
+  }
+  return 0;
+}
+
+
+static Int4 CountDupGlobalDiscrepancy (ValNodePtr vnp)
+{
+  GlobalDiscrepancyPtr g1, g2;
+  Int4                 num_dup = 1;
+
+  if (vnp == NULL 
+      || (g1 = (GlobalDiscrepancyPtr) vnp->data.ptrvalue) == NULL
+      || StringHasNoText (g1->str)) {
+    return 0;
+  } else if (vnp->next == NULL) {
+    return 1;
+  }
+  vnp = vnp->next;
+  while (vnp != NULL
+         && (g2 = (GlobalDiscrepancyPtr) vnp->data.ptrvalue) != NULL 
+         && StringICmp (g1->str, g2->str) == 0) {
+    num_dup++;
+    vnp = vnp->next;
+  }
+  return num_dup;
+}
+
+
+extern ClickableItemPtr
+ReportNonUniqueGlobalDiscrepancy 
+(ValNodePtr vnp, 
+ CharPtr    label_fmt,
+ CharPtr    ind_cat_fmt,
+ Uint4      clickable_item_type,
+ Boolean    keep_top_category)
+
+{
+  Boolean       print_heading = TRUE;
+  Int4          num_dup, total_dup = 0, i;
+  ValNodePtr       item_list;
+  ClickableItemPtr cip = NULL;
+  ValNodePtr       subcategories = NULL;
+  CharPtr          str;
+
+  while (vnp != NULL) {
+    num_dup = CountDupGlobalDiscrepancy (vnp);
+    if (num_dup > 1) {
+      total_dup += num_dup;
+      str = GetGlobalDiscrepancyStr (vnp->data.ptrvalue);
+      if (str == NULL) str = "";
+      item_list = NULL;
+      i = num_dup;
+      while (i > 0) {
+        ValNodeLink (&item_list, GetGlobalDiscrepancyItem (vnp->data.ptrvalue));
+        vnp = vnp->next;
+        i--;
+      }
+      cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+      cip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (ind_cat_fmt) + StringLen (str) + 15));
+      sprintf (cip->description, ind_cat_fmt, num_dup, str);
+      cip->clickable_item_type = clickable_item_type;
+      cip->item_list = item_list;
+      ValNodeAddPointer (&subcategories, 0, cip);
+    } else {
+      vnp = vnp->next;
+    }
+  }
+  if (subcategories != NULL) {
+    if (subcategories->next == NULL && !keep_top_category) {
+      cip = subcategories->data.ptrvalue;
+      subcategories = ValNodeFree (subcategories);
+    } else {
+      cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+      cip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (label_fmt) + 15));
+      sprintf (cip->description, label_fmt, total_dup);
+      cip->clickable_item_type = clickable_item_type;
+      cip->subcategories = subcategories;
+    }
+  }
+  return cip;
+}
+
+
+static Boolean IsLocusTagFormatBad (CharPtr locus_tag)
+{
+  CharPtr cp;
+  Boolean after_underscore = FALSE;
+  
+  if (StringHasNoText (locus_tag))
+  {
+    return FALSE;
+  }
+  
+  cp = locus_tag;
+  if (!isalpha (*cp))
+  {
+    return TRUE;
+  }
+  cp++;
+  while (*cp != 0)
+  {
+    if (*cp == '_')
+    {
+      if (after_underscore)
+      {
+        return TRUE;
+      }
+      else
+      {
+        after_underscore = TRUE;
+        if (*(cp + 1) == 0)
+        {
+          return TRUE;
+        }
+      }
+    }
+    else if (!isalpha (*cp) && !isdigit (*cp))
+    {
+      return TRUE;
+    }
+    cp++;
+  }
+  if (after_underscore)
+  {
+    return FALSE;
+  }
+  else
+  {
+    return TRUE;
+  }
+}
+
+
+extern ClickableItemPtr ReportBadLocusTagFormat (ValNodePtr list)
+{
+  ValNodePtr vnp, item_list = NULL;
+  ClickableItemPtr cip = NULL;
+
+  for (vnp = list; vnp != NULL; vnp = vnp->next) {
+    if (IsLocusTagFormatBad (GetGlobalDiscrepancyStr (vnp->data.ptrvalue))) {
+      ValNodeLink (&item_list, GetGlobalDiscrepancyItem (vnp->data.ptrvalue));
+    }
+  }
+  if (item_list != NULL) {
+    cip = NewClickableItem (DISC_GENE_LOCUS_TAG_BAD_FORMAT, "%d locus tags are incorrectly formatted.", item_list);
+  }
+  return cip;
+}
+
+
+static CharPtr GetGlobalDiscrepancyPrefix (GlobalDiscrepancyPtr g)
+{
+  CharPtr cp, prefix = NULL;
+  Int4    len;
+
+  if (g == NULL) return NULL;
+  cp = StringChr (g->str, '_');
+  if (cp != NULL) {
+    len = cp - g->str;
+    prefix = MemNew (sizeof (Char) * (len + 1));
+    StringNCpy (prefix, g->str, len);
+    prefix[len] = 0;
+  }
+  return prefix;
+}
+
+
+static Int4 CountDupGlobalDiscrepancyPrefix (ValNodePtr vnp)
+{
+  GlobalDiscrepancyPtr g1, g2;
+  CharPtr              cp;
+  Int4                 len;
+  Int4                 num_dup = 1;
+
+  if (vnp == NULL 
+      || (g1 = (GlobalDiscrepancyPtr) vnp->data.ptrvalue) == NULL
+      || StringHasNoText (g1->str)
+      || (cp = StringChr (g1->str, '_')) == NULL) {
+    return 0;
+  } else if (vnp->next == NULL) {
+    return 1;
+  }
+  len = cp - g1->str + 1;
+  vnp = vnp->next;
+  while (vnp != NULL
+         && (g2 = (GlobalDiscrepancyPtr) vnp->data.ptrvalue) != NULL 
+         && StringNCmp (g1->str, g2->str, len) == 0) {
+    num_dup++;
+    vnp = vnp->next;
+  }
+  return num_dup;
+}
+
+
+extern ValNodePtr ReportInconsistentGlobalDiscrepancyPrefixes
+(ValNodePtr vnp, 
+ CharPtr    label_fmt,
+ Uint4      clickable_item_type)
+
+{
+  Boolean       print_heading = TRUE;
+  Int4          num_dup;
+  CharPtr       prefix;
+  ValNodePtr    disc_list = NULL;
+  ClickableItemPtr cip;
+
+  if (vnp == NULL) return NULL;
+
+  num_dup = CountDupGlobalDiscrepancyPrefix (vnp);
+  if (num_dup < ValNodeLen (vnp)) {
+    while (vnp != NULL) {
+      prefix = GetGlobalDiscrepancyPrefix (vnp->data.ptrvalue);
+      num_dup = CountDupGlobalDiscrepancyPrefix (vnp);
+      if (num_dup < 1) {
+        vnp = vnp->next;
+      } else if (prefix != NULL) {
+        cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+        cip->clickable_item_type = clickable_item_type;
+        cip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (label_fmt) + StringLen (prefix) + 15));
+        sprintf (cip->description, label_fmt, num_dup, prefix);
+        /* skip duplicates without printing */
+        while (num_dup > 0) {
+          ValNodeLink (&cip->item_list, GetGlobalDiscrepancyItem (vnp->data.ptrvalue));
+          vnp = vnp->next;
+          num_dup--;
+        }
+        prefix = MemFree (prefix);
+        ValNodeAddPointer (&disc_list, 0, cip);
+      } else {
+        /* skip items without prefix */
+        while (num_dup > 0) {
+          vnp = vnp->next;
+          num_dup--;
+        }
+      }
+    }
+  } 
+  return disc_list;
+}
+
+
+extern ValNodePtr ReportInconsistentGlobalDiscrepancyStrings
+(ValNodePtr vnp, 
+ CharPtr    label_fmt,
+ Uint4      clickable_item_type)
+
+{
+  Boolean       print_heading = TRUE;
+  Int4          num_dup;
+  CharPtr       prefix;
+  ValNodePtr    disc_list = NULL;
+  ClickableItemPtr cip;
+
+  if (vnp == NULL) return NULL;
+
+  num_dup = CountDupGlobalDiscrepancy (vnp);
+  if (num_dup < ValNodeLen (vnp)) {
+    while (vnp != NULL) {
+      prefix = GetGlobalDiscrepancyStr (vnp->data.ptrvalue);
+      num_dup = CountDupGlobalDiscrepancy (vnp);
+      if (num_dup < 1) {
+        vnp = vnp->next;
+      } else if (prefix != NULL) {
+        cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+        cip->clickable_item_type = clickable_item_type;
+        cip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (label_fmt) + StringLen (prefix) + 15));
+        sprintf (cip->description, label_fmt, num_dup, prefix);
+        /* skip duplicates without printing */
+        while (num_dup > 0) {
+          ValNodeLink (&cip->item_list, GetGlobalDiscrepancyItem (vnp->data.ptrvalue));
+          vnp = vnp->next;
+          num_dup--;
+        }
+        ValNodeAddPointer (&disc_list, 0, cip);
+      } else {
+        /* skip items without prefix */
+        while (num_dup > 0) {
+          vnp = vnp->next;
+          num_dup--;
+        }
+      }
+    }
+  } 
+  return disc_list;
+}
+
+
+extern ClickableItemPtr ReportMissingFields (ValNodePtr list, CharPtr label_fmt, Uint4 clickable_item_type)
+{
+  ClickableItemPtr cip;
+
+  if (list == NULL) return NULL;
+
+  cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+  cip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (label_fmt) + 15));
+  sprintf (cip->description, label_fmt, ValNodeLen (list));
+  cip->clickable_item_type = clickable_item_type;
+  while (list != NULL) {
+    ValNodeLink (&(cip->item_list), GetGlobalDiscrepancyItem (list->data.ptrvalue));
+    list = list->next;
+  }
+  return cip;  
+}
+
+
+
+
+
 /* declarations for discrepancy tests */
 extern void AddMissingAndSuperfluousGeneDiscrepancies (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list);
 extern void AddDiscrepanciesForMissingOrNonUniqueGeneLocusTags (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list);
@@ -5318,6 +5832,7 @@ extern void FindTranslExceptNotes (ValNodePtr PNTR discrepancy_list, ValNodePtr
 extern void FindCDSOverlappingtRNAs (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list);
 extern int LIBCALLBACK SortVnpByClickableItemDescription (VoidPtr ptr1, VoidPtr ptr2);
 extern void CountProteins (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list);
+extern void FindFeaturesOverlappingSrcFeatures (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list);
 
 /* functions for the missing and superfluous gene tests */
 extern Boolean GeneRefMatch (GeneRefPtr grp1, GeneRefPtr grp2)
@@ -5701,7 +6216,7 @@ static ClickableItemPtr InconsistentPrefix (PrefixCheckPtr pcp, CharPtr bad_fmt,
   dip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
   if (dip != NULL)
   {
-    dip->clickable_item_type = DISC_GENE_LOCUS_TAG_INCONSISTENT_PREFIX;
+    dip->clickable_item_type = disc_type;
     dip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (bad_fmt) + StringLen (pcp->prefix)+ 15));
     sprintf (dip->description, bad_fmt, ValNodeLen (pcp->feature_list), pcp->prefix);
     dip->callback_func = NULL;
@@ -5714,44 +6229,29 @@ static ClickableItemPtr InconsistentPrefix (PrefixCheckPtr pcp, CharPtr bad_fmt,
 }
 
 
-static ClickableItemPtr InconsistentLocusTagPrefix (PrefixCheckPtr pcp)
-{
-  CharPtr            bad_fmt = "%d features have locus tag prefix %s."; 
-
-  return InconsistentPrefix (pcp, bad_fmt, DISC_GENE_LOCUS_TAG_INCONSISTENT_PREFIX);
-}
-
+extern CharPtr discReportInconsistentLocusTagPrefixFmt = "%d features have locus tag prefix %s.";
+extern CharPtr discReportInconsistentProteinIDPrefixFmt = "%d sequences have protein ID prefix %s.";
+extern CharPtr discReportBadProteinIdFmt = "%d proteins have invalid IDs.";
 
-static ClickableItemPtr InconsistentProteinIDPrefix (PrefixCheckPtr pcp)
+static ClickableItemPtr InconsistentLocusTagPrefix (PrefixCheckPtr pcp)
 {
-  CharPtr            bad_fmt = "%d sequences have protein ID prefix %s."; 
-
-  return InconsistentPrefix (pcp, bad_fmt, DISC_INCONSISTENT_PROTEIN_ID_PREFIX);
+  return InconsistentPrefix (pcp, discReportInconsistentLocusTagPrefixFmt, DISC_GENE_LOCUS_TAG_INCONSISTENT_PREFIX);
 }
 
 
-typedef struct missinconstprotids 
+extern void FindProteinIDCallback (BioseqPtr bsp, Pointer userdata)
 {
-  ValNodePtr missing_list;
-  ValNodePtr inconsistent_list;
-} MissInconstProtIDsData, PNTR MissInconstProtIDsPtr;
-
+  ProtIdListsPtr pip;
+  SeqIdPtr       sip;
+  DbtagPtr       dbt = NULL;
 
-static void FindMissingAndInconsistentProteinIDsCallback (BioseqPtr bsp, Pointer userdata)
-{
-  SeqIdPtr              sip;
-  MissInconstProtIDsPtr mipip;
-  DbtagPtr              dbt = NULL;
-  PrefixCheckPtr        pcp;
-  ValNodePtr            vnp;
-  
   if (bsp == NULL || ! ISA_aa (bsp->mol) || userdata == NULL)
   {
     return;
   }
-  
-  mipip = (MissInconstProtIDsPtr) userdata;
-  
+
+  pip = (ProtIdListsPtr) userdata;
+
   for (sip = bsp->id; sip != NULL && dbt == NULL; sip = sip->next)
   {
     if (sip->choice == SEQID_GENERAL)
@@ -5765,90 +6265,47 @@ static void FindMissingAndInconsistentProteinIDsCallback (BioseqPtr bsp, Pointer
   }
   if (dbt == NULL)
   {
-    ValNodeAddPointer (&(mipip->missing_list), OBJ_BIOSEQ, bsp);
+    ValNodeAddPointer (&(pip->missing_gnl_list), 0, GlobalDiscrepancyNew (NULL, OBJ_BIOSEQ, bsp));
   }
   else
   {  
-    /* look for inconsistent prefixes */
-    pcp = NULL;
-    for (vnp = mipip->inconsistent_list; vnp != NULL && pcp == NULL; vnp = vnp->next)
-    {
-      pcp = (PrefixCheckPtr) vnp->data.ptrvalue;
-      if (pcp != NULL && StringCmp (pcp->prefix, dbt->db) == 0)
-      {
-        ValNodeAddPointer (&pcp->feature_list, OBJ_BIOSEQ, bsp);
-      }
-      else
-      {
-        pcp = NULL;
-      }
-    }
-    if (pcp == NULL)
-    {
-      pcp = (PrefixCheckPtr) MemNew (sizeof (PrefixCheckData));
-      if (pcp != NULL)
-      {
-        pcp->prefix = StringSave (dbt->db);
-        pcp->feature_list = ValNodeNew (NULL);
-        pcp->feature_list->choice = OBJ_BIOSEQ;
-        pcp->feature_list->data.ptrvalue = bsp;
-        pcp->feature_list->next = NULL;
-        ValNodeAddPointer (&(mipip->inconsistent_list), 0, pcp);
-      }
-    }
-  }  
+    ValNodeAddPointer (&(pip->gnl_list), 0, GlobalDiscrepancyNew (dbt->db, OBJ_BIOSEQ, bsp));
+  }
 }
 
 
+
 extern void FindMissingProteinIDs (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list)
 {
-  CharPtr                bad_fmt = "%d proteins have invalid IDs.";
-  ClickableItemPtr     dip;
-  MissInconstProtIDsData mipid;
-  ValNodePtr             vnp;
+  ClickableItemPtr dip;
+  ProtIdListsData  pid;
+  ValNodePtr       vnp;
   
   if (discrepancy_list == NULL) return;
   
-  mipid.missing_list = NULL;
-  mipid.inconsistent_list = NULL;
+  MemSet (&pid, 0, sizeof (ProtIdListsData));
   
   for (vnp = sep_list; vnp != NULL; vnp = vnp->next) {
-    VisitBioseqsInSep (vnp->data.ptrvalue, &mipid, FindMissingAndInconsistentProteinIDsCallback);
+    VisitBioseqsInSep (vnp->data.ptrvalue, &pid, FindProteinIDCallback);
   }
   
-  if (mipid.missing_list != NULL)
+  if (pid.missing_gnl_list != NULL)
   {
-    dip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
-    if (dip != NULL)
-    {
-      dip->clickable_item_type = DISC_MISSING_PROTEIN_ID;
-      dip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (bad_fmt) + 15));
-      sprintf (dip->description, bad_fmt, ValNodeLen (mipid.missing_list));
-      dip->callback_func = NULL;
-      dip->callback_data = NULL;
-      dip->datafree_func = NULL;
-      dip->item_list = mipid.missing_list;
+    dip = ReportMissingFields (pid.missing_gnl_list, discReportBadProteinIdFmt, DISC_MISSING_PROTEIN_ID);
+    if (dip != NULL) {
       ValNodeAddPointer (discrepancy_list, 0, dip);
     }
+    pid.missing_gnl_list = FreeGlobalDiscrepancyList (pid.missing_gnl_list);
   }
-  
-
-  if (mipid.inconsistent_list != NULL)
+  if (pid.gnl_list != NULL)
   {
-    if (mipid.inconsistent_list->next != NULL)
-    {
-      for (vnp = mipid.inconsistent_list; vnp != NULL; vnp = vnp->next)
-      {
-        dip = InconsistentProteinIDPrefix (vnp->data.ptrvalue);
-        if (dip != NULL)
-        {
-          ValNodeAddPointer (discrepancy_list, 0, dip);
-        }
-      }
-    }
-    mipid.inconsistent_list = FreePrefixCheckList (mipid.inconsistent_list);
-  }
-    
+    pid.gnl_list = ValNodeSort (pid.gnl_list, SortVnpByGlobalDiscrepancyString);
+    ValNodeLink (discrepancy_list, 
+                 ReportInconsistentGlobalDiscrepancyStrings (pid.gnl_list,
+                                                             discReportInconsistentProteinIDPrefixFmt,
+                                                             DISC_INCONSISTENT_PROTEIN_ID_PREFIX));
+    pid.gnl_list = FreeGlobalDiscrepancyList (pid.gnl_list);
+  } 
 }
 
 
@@ -5856,9 +6313,6 @@ typedef struct locustagcheck
 {
   ValNodePtr locus_tags_list;
   ValNodePtr missing_list;
-  ValNodePtr duplicate_list;
-  ValNodePtr bad_format_list;
-  ValNodePtr inconsistent_prefix;
 } LocusTagCheckData, PNTR LocusTagCheckPtr;
 
 static void GeneLocusTagDiscrepancyCallback (ValNodePtr item_list, Pointer userdata)
@@ -5866,46 +6320,39 @@ static void GeneLocusTagDiscrepancyCallback (ValNodePtr item_list, Pointer userd
   Message (MSG_OK, "I could launch the editor for the individual gene...");
 }
 
-static Boolean IsLocusTagFormatBad (CharPtr locus_tag)
+static void CheckGeneLocusTag (SeqFeatPtr sfp, Pointer userdata)
 {
-  CharPtr cp;
-  Boolean after_underscore = FALSE;
+  GeneRefPtr         grp;
+  LocusTagCheckPtr   ltcp;
   
-  if (StringHasNoText (locus_tag))
+  if (sfp == NULL || userdata == NULL || sfp->data.choice != SEQFEAT_GENE || sfp->data.value.ptrvalue == NULL)
   {
-    return FALSE;
+    return;
   }
   
-  cp = locus_tag;
-  if (!isalpha (*cp))
-  {
-    return TRUE;
+  ltcp = (LocusTagCheckPtr) userdata;
+
+  grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+  if (grp != NULL) {
+    if (grp->pseudo) return;
+    if (StringDoesHaveText (grp->locus_tag)) {
+      ValNodeAddPointer (&(ltcp->locus_tags_list), 0, 
+                          GlobalDiscrepancyNew (grp->locus_tag, OBJ_SEQFEAT, sfp));
+    } else {
+      ValNodeAddPointer (&(ltcp->missing_list), 0,
+                          GlobalDiscrepancyNew (NULL, OBJ_SEQFEAT, sfp));
+    }
   }
-  cp++;
-  while (*cp != 0)
+
+}
+
+static Boolean AlreadyInList (ValNodePtr vnp, SeqFeatPtr sfp)
+{
+  while (vnp != NULL && vnp->data.ptrvalue != sfp)
   {
-    if (*cp == '_')
-    {
-      if (after_underscore)
-      {
-        return TRUE;
-      }
-      else
-      {
-        after_underscore = TRUE;
-        if (*(cp + 1) == 0)
-        {
-          return TRUE;
-        }
-      }
-    }
-    else if (!isalpha (*cp) && !isdigit (*cp))
-    {
-      return TRUE;
-    }
-    cp++;
+    vnp = vnp->next;
   }
-  if (after_underscore)
+  if (vnp == NULL)
   {
     return FALSE;
   }
@@ -5915,288 +6362,215 @@ static Boolean IsLocusTagFormatBad (CharPtr locus_tag)
   }
 }
 
-static CharPtr GetLocusTagPrefix (CharPtr locus_tag)
+
+static SeqFeatPtr GetNextGene (SeqFeatPtr sfp)
 {
-  Int4    prefix_len;
-  CharPtr prefix;
-  
-  if (StringHasNoText (locus_tag))
-  {
-    return NULL;
-  }
-  
-  prefix_len = StringCSpn (locus_tag, "_");
-  if (prefix_len == 0 || prefix_len == StringLen (locus_tag))
-  {
-    return NULL;
-  }
-  else
+  BioseqPtr bsp;
+  SeqFeatPtr sfp_next;
+  SeqMgrFeatContext fcontext;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_GENE) return NULL;
+
+  bsp = BioseqFindFromSeqLoc (sfp->location);
+  if (bsp == NULL) return NULL;
+  /* initialize fcontext for search */
+  sfp_next = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_GENE, FEATDEF_GENE, &fcontext);
+  while (sfp_next != sfp && sfp_next != NULL)
   {
-    prefix = (CharPtr) MemNew ((prefix_len + 1) * sizeof (Char));
-    StringNCpy (prefix, locus_tag, prefix_len);
-    prefix [prefix_len] = 0;
-    return prefix;
+    sfp_next = SeqMgrGetNextFeature (bsp, sfp_next, SEQFEAT_GENE, FEATDEF_GENE, &fcontext);
   }
+  if (sfp_next != sfp) return NULL;
+
+  sfp_next = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_GENE, FEATDEF_GENE, &fcontext);
+  return sfp_next;
 }
 
-static void CheckGeneLocusTag (SeqFeatPtr sfp, Pointer userdata)
+
+static ValNodePtr FindValNodeForGlobalDiscrepancyFeature (ValNodePtr start_search, Int4 len_search, SeqFeatPtr sfp)
 {
-  GeneRefPtr         grp, dup_grp;
-  LocusTagCheckPtr   ltcp;
-  ValNodePtr         vnp;
-  Boolean            found_duplicate;
-  SeqFeatPtr         dup_sfp = NULL;
-  CharPtr            prefix;
-  PrefixCheckPtr     pcp;
-  
-  if (sfp == NULL || userdata == NULL || sfp->data.choice != SEQFEAT_GENE || sfp->data.value.ptrvalue == NULL)
-  {
-    return;
-  }
-  
-  ltcp = (LocusTagCheckPtr) userdata;
-  
-  grp = (GeneRefPtr) sfp->data.value.ptrvalue;
-  if (StringHasNoText (grp->locus_tag))
-  {
-    ValNodeAddPointer (&(ltcp->missing_list), OBJ_SEQFEAT, sfp);
-  }
-  else
-  {
-    /* look for badly formatted locus tags */
-    if (IsLocusTagFormatBad (grp->locus_tag))
-    {
-      ValNodeAddPointer (&(ltcp->bad_format_list), OBJ_SEQFEAT, sfp);
-    }
-    
-    /* look for inconsistent locus tag prefixes */
-    prefix = GetLocusTagPrefix (grp->locus_tag);
-    if (prefix != NULL)
-    {
-      pcp = NULL;
-      for (vnp = ltcp->inconsistent_prefix; vnp != NULL && pcp == NULL; vnp = vnp->next)
-      {
-        pcp = (PrefixCheckPtr) vnp->data.ptrvalue;
-        if (pcp != NULL && StringCmp (pcp->prefix, prefix) == 0)
-        {
-          ValNodeAddPointer (&pcp->feature_list, OBJ_SEQFEAT, sfp);
-          prefix = MemFree (prefix);
-        }
-        else
-        {
-          pcp = NULL;
-        }
-      }
-      if (pcp == NULL)
-      {
-        pcp = (PrefixCheckPtr) MemNew (sizeof (PrefixCheckData));
-        if (pcp != NULL)
-        {
-          pcp->prefix = prefix;
-          pcp->feature_list = ValNodeNew (NULL);
-          pcp->feature_list->choice = OBJ_SEQFEAT;
-          pcp->feature_list->data.ptrvalue = sfp;
-          pcp->feature_list->next = NULL;
-          ValNodeAddPointer (&(ltcp->inconsistent_prefix), 0, pcp);
-        }
-      }
+  GlobalDiscrepancyPtr g;
+
+  while (start_search != NULL && len_search > 0) {
+    g = (GlobalDiscrepancyPtr) start_search->data.ptrvalue;
+    if (g != NULL && g->data_choice == OBJ_SEQFEAT && g->data == sfp) {
+      return start_search;
+    } else {
+      start_search = start_search->next;
+      len_search--;
     }
-    
+  }
+  return NULL;
+}
+
+
+static ValNodePtr FindAdjacentGenesInSubList (ValNodePtr sub_list, Int4 list_len)
+{
+  GlobalDiscrepancyPtr g;
+  SeqFeatPtr           sfp, sfp_next;
+  ValNodePtr           vnp, found_match, adj_list = NULL;
+  Int4                 len;
   
-    dup_sfp = NULL;
-    for (vnp = ltcp->locus_tags_list, found_duplicate = FALSE;
-         vnp != NULL && !found_duplicate;
-         vnp = vnp->next)
-    { 
-      dup_sfp = (SeqFeatPtr) vnp->data.ptrvalue;
-      if (dup_sfp != NULL && dup_sfp->data.choice == SEQFEAT_GENE)
-      {
-        dup_grp = (GeneRefPtr) dup_sfp->data.value.ptrvalue;
-        if (dup_grp != NULL && StringCmp (dup_grp->locus_tag, grp->locus_tag) == 0)
-        {
-          found_duplicate = TRUE;
-          if (vnp->choice != 0)
-          {
-            dup_sfp = NULL;
-          }
-          else
-          {
+  vnp = sub_list;
+  len = list_len;
+  while (vnp != NULL && len > 0) {
+    g = (GlobalDiscrepancyPtr) vnp->data.ptrvalue;
+    if (g->data_choice == OBJ_SEQFEAT && g->data != NULL) {
+      sfp = g->data;
+      sfp_next = GetNextGene (sfp);
+      if (sfp_next != NULL) {
+        found_match = FindValNodeForGlobalDiscrepancyFeature (sub_list, list_len, sfp_next);
+        if (found_match != NULL) {
+          if (vnp->choice == 0) {
+            ValNodeAddPointer (&adj_list, OBJ_SEQFEAT, sfp);
             vnp->choice = 1;
           }
-        }
-        else
-        {
-          dup_sfp = NULL;
+          if (found_match->choice == 0) {
+            ValNodeAddPointer (&adj_list, OBJ_SEQFEAT, sfp_next);
+            found_match->choice = 1;
+          }
         }
       }
-      else
-      {
-        dup_sfp = NULL;
-      }
-    }
-    if (!found_duplicate)
-    {
-      ValNodeAddPointer (&(ltcp->locus_tags_list), 0, sfp);
-    }
-    else
-    {
-      if (dup_sfp != NULL)
-      {
-        ValNodeAddPointer (&(ltcp->duplicate_list), OBJ_SEQFEAT, dup_sfp);
-      }
-      ValNodeAddPointer (&(ltcp->duplicate_list), OBJ_SEQFEAT, sfp);
     }
+    vnp = vnp->next;
+    len --;
+  }
+  /* set choices back to zero */
+  for (vnp = sub_list, len = 0; vnp != NULL && len < list_len; vnp = vnp->next, len++) {
+    vnp->choice = 0;
   }
+  return adj_list;
 }
+ 
 
-static Boolean AlreadyInList (ValNodePtr vnp, SeqFeatPtr sfp)
+extern ClickableItemPtr FindAdjacentDuplicateLocusTagGenes (ValNodePtr locus_tag_list)
 {
-  while (vnp != NULL && vnp->data.ptrvalue != sfp)
-  {
-    vnp = vnp->next;
-  }
-  if (vnp == NULL)
-  {
-    return FALSE;
+  ValNodePtr       vnp, adjacent_list = NULL;
+  ClickableItemPtr cip = NULL;
+  Int4             num_dup;
+  CharPtr          duplicate_adjacent_fmt = "%d genes are adjacent to another gene with the same locus tag.";
+
+  vnp = locus_tag_list;
+  while (vnp != NULL) {
+    num_dup = CountDupGlobalDiscrepancy (vnp);
+    if (num_dup > 1) {
+      ValNodeLink (&adjacent_list, FindAdjacentGenesInSubList (vnp, num_dup));      
+      while (num_dup > 0) {
+        vnp = vnp->next;
+        num_dup--;
+      }
+    } else {
+      vnp = vnp->next;
+    }
   }
-  else
-  {
-    return TRUE;
+
+  if (adjacent_list != NULL) {
+    cip = NewClickableItem (DISC_GENE_DUPLICATE_LOCUS_TAG, duplicate_adjacent_fmt, adjacent_list);
   }
+  return cip;
 }
 
 
-static ValNodePtr FindAdjacentDuplicateLocusTagGenes (ValNodePtr duplicate_list)
+NLM_EXTERN ValNodePtr ValNodeDupStringList (ValNodePtr vnp)
 {
-  ValNodePtr vnp, adjacent_list = NULL;
-  SeqFeatPtr sfp, sfp_next;
-  BioseqPtr  bsp;
-  SeqMgrFeatContext fcontext;
-  GeneRefPtr grp, grp_next;
+  ValNodePtr cpy = NULL, last = NULL, tmp;
 
-  for (vnp = duplicate_list; vnp != NULL; vnp = vnp->next)
+  while (vnp != NULL)
   {
-    sfp = (SeqFeatPtr) vnp->data.ptrvalue;
-    if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE && sfp->data.value.ptrvalue != NULL)
+    tmp = ValNodeNew (NULL);
+    tmp->choice = vnp->choice;
+    tmp->data.ptrvalue = StringSave (vnp->data.ptrvalue);
+    if (last == NULL)
     {
-      bsp = BioseqFindFromSeqLoc (sfp->location);
-      if (bsp == NULL) continue;
-      /* initialize fcontext for search */
-      sfp_next = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_GENE, FEATDEF_GENE, &fcontext);
-      while (sfp_next != sfp && sfp_next != NULL)
-      {
-        sfp_next = SeqMgrGetNextFeature (bsp, sfp_next, SEQFEAT_GENE, FEATDEF_GENE, &fcontext);
-      }
-      if (sfp_next != sfp) continue;
+      cpy = tmp;
+    }
+    else
+    {
+      last->next = tmp;
+    }
+    last = tmp;
+    vnp = vnp->next;
+  }
+  return cpy;
+}
+      
 
-      sfp_next = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_GENE, FEATDEF_GENE, &fcontext);
-      if (sfp_next != NULL && sfp_next->data.choice == SEQFEAT_GENE && sfp_next->data.value.ptrvalue != NULL)
-      {
-        grp = sfp->data.value.ptrvalue;
-        grp_next = sfp_next->data.value.ptrvalue;
-        if (StringCmp (grp->locus_tag, grp_next->locus_tag) == 0 && !StringHasNoText (grp->locus_tag))
-        {
-          if (!AlreadyInList (adjacent_list, sfp))
-          {
-            ValNodeAddPointer (&adjacent_list, OBJ_SEQFEAT, sfp);
-          }
-          if (!AlreadyInList (adjacent_list, sfp_next))
-          {
-            ValNodeAddPointer (&adjacent_list, OBJ_SEQFEAT, sfp_next);
-          }
-        }
-      }
+NLM_EXTERN ValNodePtr FindBadLocusTagsInList (ValNodePtr list)
+{
+  ValNodePtr       bad_list = NULL, list_copy;
+  Boolean          reported_last = FALSE;
+  ValNodePtr       vnp;
+  
+  list_copy = ValNodeDupStringList (list);
+  list_copy = ValNodeSort (list_copy, SortVnpByString);
+
+  for (vnp = list_copy; vnp != NULL; vnp = vnp->next) {
+    /* look for badly formatted locus tags */
+    if (IsLocusTagFormatBad (vnp->data.ptrvalue)) {
+      ValNodeAddPointer(&bad_list, eLocusTagErrorBadFormat, StringSave (vnp->data.ptrvalue));
     }
   }
-  return adjacent_list;
+  list_copy = ValNodeFreeData (list_copy);
+  return bad_list;  
 }
 
 
+extern CharPtr discReportDuplicateLocusTagFmt = "%d genes have duplicate locus tags.";
+extern CharPtr discReportOneDuplicateLocusTagFmt = "%d genes have locus tag %s.";
+extern CharPtr discReportMissingLocusTags = "%d genes have no locus tags.";
+
 extern void AddDiscrepanciesForMissingOrNonUniqueGeneLocusTags (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list)
 {
   LocusTagCheckData  ltcd;
-  ClickableItemPtr dip = NULL;
-  CharPtr            missing_fmt = "%d genes have no locus tags.";
-  CharPtr            duplicate_fmt = "%d genes have duplicate locus tags.";
-  CharPtr            duplicate_adjacent_fmt = "%d genes are adjacent to another gene with the same locus tag.";
+  ClickableItemPtr dip = NULL, dip_sub;
+  ValNodePtr         duplicate_list = NULL;
   CharPtr            bad_fmt = "%d locus tags are incorrectly formatted.";
-  ValNodePtr         vnp, adjacent_list = NULL;
+  ValNodePtr         vnp;
   
   if (discrepancy_list == NULL) return;
   ltcd.locus_tags_list = NULL;
   ltcd.missing_list = NULL;
-  ltcd.duplicate_list = NULL;
-  ltcd.bad_format_list = NULL;
-  ltcd.inconsistent_prefix = NULL;
   
   for (vnp = sep_list; vnp != NULL; vnp = vnp->next) {
-    VisitFeaturesInSep (vnp->data.ptrvalue, &ltcd, CheckGeneLocusTag);
+    VisitGenProdSetFeatures (vnp->data.ptrvalue, &ltcd, CheckGeneLocusTag);
   }
-  ltcd.locus_tags_list = ValNodeFree (ltcd.locus_tags_list);
   
-  if (ltcd.missing_list != NULL)
-  {
-    dip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
-    if (dip != NULL)
-    {
-      dip->clickable_item_type = DISC_GENE_MISSING_LOCUS_TAG;
-      dip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (missing_fmt) + 15));
-      sprintf (dip->description, missing_fmt, ValNodeLen (ltcd.missing_list));
-      dip->callback_func = NULL;
-      dip->datafree_func = NULL;
-      dip->callback_data = NULL;
-      dip->item_list = ltcd.missing_list;
+  if (ltcd.locus_tags_list != NULL) {
+    ltcd.locus_tags_list = ValNodeSort (ltcd.locus_tags_list, SortVnpByGlobalDiscrepancyString);
+    ltcd.missing_list = ValNodeSort (ltcd.missing_list, SortVnpByGlobalDiscrepancyString);
+    
+    if (ltcd.missing_list != NULL) {
+      dip = ReportMissingFields (ltcd.missing_list, discReportMissingLocusTags, DISC_GENE_MISSING_LOCUS_TAG);
+      if (dip != NULL) {
+        ValNodeAddPointer (discrepancy_list, 0, dip);
+      }
+    }
+    dip = ReportNonUniqueGlobalDiscrepancy (ltcd.locus_tags_list, 
+                                            discReportDuplicateLocusTagFmt, 
+                                            discReportOneDuplicateLocusTagFmt,
+                                            DISC_GENE_DUPLICATE_LOCUS_TAG,
+                                            FALSE);
+    if (dip != NULL) {
+      dip_sub = FindAdjacentDuplicateLocusTagGenes (ltcd.locus_tags_list);
+      if (dip_sub != NULL) {
+        ValNodeAddPointer (&(dip->subcategories), 0, dip_sub);
+      }
       ValNodeAddPointer (discrepancy_list, 0, dip);
     }
-  }
-  
-  if (ltcd.duplicate_list != NULL)
-  {
-    adjacent_list = FindAdjacentDuplicateLocusTagGenes (ltcd.duplicate_list);
 
-    dip = NewClickableItem (DISC_GENE_DUPLICATE_LOCUS_TAG, duplicate_fmt, ltcd.duplicate_list);
-    if (dip != NULL)
-    {
-      ValNodeAddPointer (discrepancy_list, 0, dip);
-
-      if (adjacent_list != NULL)
-      {
-        ValNodeAddPointer (&(dip->subcategories), 0, NewClickableItem (DISC_GENE_DUPLICATE_LOCUS_TAG, duplicate_adjacent_fmt, adjacent_list));
-      }
-    }
-  } 
-  
-  if (ltcd.bad_format_list != NULL)
-  {
-    dip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
-    if (dip != NULL)
-    {
-      dip->clickable_item_type = DISC_GENE_LOCUS_TAG_BAD_FORMAT;
-      dip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (bad_fmt) + 15));
-      sprintf (dip->description, bad_fmt, ValNodeLen (ltcd.bad_format_list));
-      dip->callback_func = NULL;
-      dip->datafree_func = NULL;
-      dip->callback_data = NULL;
-      dip->item_list = ltcd.bad_format_list;
+    /* inconsistent locus tags */
+    ValNodeLink (discrepancy_list,
+                 ReportInconsistentGlobalDiscrepancyPrefixes (ltcd.locus_tags_list,
+                                                              discReportInconsistentLocusTagPrefixFmt,
+                                                              DISC_GENE_LOCUS_TAG_INCONSISTENT_PREFIX));
+    /* bad formats */
+    dip = ReportBadLocusTagFormat (ltcd.locus_tags_list);
+    if (dip != NULL) {
       ValNodeAddPointer (discrepancy_list, 0, dip);
     }
   }
-  
-  if (ltcd.inconsistent_prefix != NULL)
-  {
-    if (ltcd.inconsistent_prefix->next != NULL)
-    {
-      for (vnp = ltcd.inconsistent_prefix; vnp != NULL; vnp = vnp->next)
-      {
-        dip = InconsistentLocusTagPrefix (vnp->data.ptrvalue);
-        if (dip != NULL)
-        {
-          ValNodeAddPointer (discrepancy_list, 0, dip);
-        }
-      }
-    }
-    ltcd.inconsistent_prefix = FreePrefixCheckList (ltcd.inconsistent_prefix);
-  }
+
+  ltcd.locus_tags_list = FreeGlobalDiscrepancyList (ltcd.locus_tags_list);
+  ltcd.missing_list = FreeGlobalDiscrepancyList (ltcd.missing_list);
 }
 
 static void AddDiscrepancyForNonGeneLocusTag (SeqFeatPtr sfp, Pointer userdata)
@@ -6353,7 +6727,7 @@ CheckFeatureTypeForLocationDiscrepancies
   SeqFeatPtr        sfp, gene_sfp;
   Boolean           found_match;
   
-  if (bsp == NULL || ISA_aa (bsp->mol) || discrepancy_list == NULL)
+  if (bsp == NULL || ISA_aa (bsp->mol) || discrepancy_list == NULL || IsmRNASequenceInGenProdSet(bsp))
   {
     return;
   }
@@ -6574,7 +6948,7 @@ extern void FindCDSGeneProductConflicts (ValNodePtr PNTR discrepancy_list, ValNo
   ValNodePtr         item_list = NULL, cds_vnp;
   
   for (vnp = sep_list; vnp != NULL; vnp = vnp->next) {
-    VisitFeaturesInSep (vnp->data.ptrvalue, &cds_list, FindCDSGeneProductConflictsCallback);
+    VisitGenProdSetFeatures (vnp->data.ptrvalue, &cds_list, FindCDSGeneProductConflictsCallback);
   }
 
   /* remove CDSs without conflicts */
@@ -6715,7 +7089,7 @@ extern void FindDuplicateGeneLocus (ValNodePtr PNTR discrepancy_list, ValNodePtr
   ClickableItemPtr dip;
   
   for (vnp = sep_list; vnp != NULL; vnp = vnp->next) {
-    VisitFeaturesInSep (vnp->data.ptrvalue, &gene_list, DuplicateGeneLocusCallback);
+    VisitGenProdSetFeatures (vnp->data.ptrvalue, &gene_list, DuplicateGeneLocusCallback);
   }
 
   /* remove Genes without conflicts */
@@ -7361,6 +7735,8 @@ typedef struct cdsrnaoverlap {
   ValNodePtr cds_in_rna;
   ValNodePtr rna_in_cds;
   ValNodePtr exact_match;
+  ValNodePtr overlap_same_strand;
+  ValNodePtr overlap_opp_strand;
   ValNodePtr overlap;
   ValNodePtr all;
 } CDSRNAOverlapData, PNTR CDSRNAOverlapPtr;
@@ -7372,6 +7748,7 @@ static void FindCDSRNAOverlaps (BioseqPtr bsp, Pointer data)
   ValNodePtr        rna_list = NULL, vnp;
   SeqMgrFeatContext fcontext;
   Int2              cmp;
+  Uint1             strand1, strand2;
 
   if (bsp == NULL || data == NULL) return;
 
@@ -7418,6 +7795,19 @@ static void FindCDSRNAOverlaps (BioseqPtr bsp, Pointer data)
       }
       else if (cmp != SLC_NO_MATCH)
       {
+        strand1 = SeqLocStrand (sfp->location);
+        strand2 = SeqLocStrand (rna->location);
+        if ((strand1 == Seq_strand_minus && strand2 != Seq_strand_minus)
+          || (strand2 == Seq_strand_minus && strand1 != Seq_strand_minus))
+        {
+          ValNodeAddPointer (&(p->overlap_opp_strand), OBJ_SEQFEAT, sfp);
+          ValNodeAddPointer (&(p->overlap_opp_strand), OBJ_SEQFEAT, rna);
+        }
+        else
+        {
+          ValNodeAddPointer (&(p->overlap_same_strand), OBJ_SEQFEAT, sfp);
+          ValNodeAddPointer (&(p->overlap_same_strand), OBJ_SEQFEAT, rna);
+        }
         ValNodeAddPointer (&(p->overlap), OBJ_SEQFEAT, sfp);
         ValNodeAddPointer (&(p->overlap), OBJ_SEQFEAT, rna);
         ValNodeAddPointer (&(p->all), OBJ_SEQFEAT, sfp);
@@ -7436,7 +7826,7 @@ static ClickableItemPtr DiscrepancyForPairs (Uint4 item_type, CharPtr bad_fmt, V
 
   if (StringHasNoText (bad_fmt)) return NULL;
   dip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
-  dip->clickable_item_type = DISC_RNA_CDS_OVERLAP;
+  dip->clickable_item_type = item_type;
   dip->item_list = item_list;
   num_feat = ValNodeLen (dip->item_list) / 2;
   dip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (bad_fmt) + 15));
@@ -7447,8 +7837,8 @@ static ClickableItemPtr DiscrepancyForPairs (Uint4 item_type, CharPtr bad_fmt, V
 
 extern void AddRNACDSOverlapDiscrepancies (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list)
 {
-  ClickableItemPtr dip;
-  ValNodePtr       overlap_feat = NULL, vnp;
+  ClickableItemPtr dip, overlap_dip;
+  ValNodePtr       vnp;
   CDSRNAOverlapData d;
 
   if (discrepancy_list == NULL)
@@ -7487,10 +7877,22 @@ extern void AddRNACDSOverlapDiscrepancies (ValNodePtr PNTR discrepancy_list, Val
     }
     if (d.overlap != NULL)
     {
-      ValNodeAddPointer (&(dip->subcategories), 0, 
-                         DiscrepancyForPairs (DISC_RNA_CDS_OVERLAP, 
-                                              "%d coding regions overlap RNAs (no containment)",
-                                              d.overlap));
+      overlap_dip = DiscrepancyForPairs (DISC_RNA_CDS_OVERLAP, 
+                                          "%d coding regions overlap RNAs (no containment)",
+                                          d.overlap);
+      if (d.overlap_same_strand != NULL) {
+        ValNodeAddPointer (&(overlap_dip->subcategories), 0, 
+                            DiscrepancyForPairs (DISC_RNA_CDS_OVERLAP, 
+                                              "%d coding regions overlap RNAs on the same strand (no containment)",
+                                              d.overlap_same_strand));
+      }
+      if (d.overlap_same_strand != NULL) {
+        ValNodeAddPointer (&(overlap_dip->subcategories), 0, 
+                            DiscrepancyForPairs (DISC_RNA_CDS_OVERLAP, 
+                                              "%d coding regions overlap RNAs on the opposite strand (no containment)",
+                                              d.overlap_opp_strand));                                                   
+      }
+      ValNodeAddPointer (&(dip->subcategories), 0, overlap_dip);
     }
     
     ValNodeAddPointer (discrepancy_list, 0, dip);
@@ -7502,8 +7904,11 @@ static void FindShortContigsCallback (BioseqPtr bsp, Pointer userdata)
 {
   ValNodePtr PNTR bioseq_list;
   
-  if (bsp == NULL || !ISA_na (bsp->mol) || userdata == NULL || bsp->length >= 200)
-  {
+  if (bsp == NULL || !ISA_na (bsp->mol) || userdata == NULL || bsp->length >= 200) {
+    return;
+  }
+
+  if (IsmRNASequenceInGenProdSet (bsp)) {
     return;
   }
   
@@ -7546,7 +7951,8 @@ static void FindShortSequencesCallback (BioseqPtr bsp, Pointer userdata)
   ValNodePtr PNTR bioseq_list;
   BioseqSetPtr    bssp;
   
-  if (bsp == NULL || !ISA_na (bsp->mol) || userdata == NULL || bsp->length >= 50)
+  if (bsp == NULL || !ISA_na (bsp->mol) || userdata == NULL || bsp->length >= 50
+      || IsmRNASequenceInGenProdSet (bsp))
   {
     return;
   }
@@ -7809,7 +8215,7 @@ static CharPtr suspect_product_names[] =
 "ttg start",
 "domain protein domain protein",
 "deletion",
-"truncated"
+"truncat"
 };
 
 const int num_suspect_product_names = sizeof (suspect_product_names) / sizeof (CharPtr);
@@ -8018,7 +8424,7 @@ static void FindSuspectProductNamesCallback (SeqFeatPtr sfp, Pointer userdata)
 }
 
 
-static ClickableItemPtr SuspectPhrase (CharPtr phrase, CharPtr feat_type, ValNodePtr feature_list)
+static ClickableItemPtr SuspectPhrase (Uint4 clickable_item_type, CharPtr phrase, CharPtr feat_type, ValNodePtr feature_list)
 {
   ClickableItemPtr dip = NULL;
   CharPtr            bad_fmt = "%d %ss contain %s";
@@ -8031,7 +8437,7 @@ static ClickableItemPtr SuspectPhrase (CharPtr phrase, CharPtr feat_type, ValNod
   dip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
   if (dip != NULL)
   {
-    dip->clickable_item_type = DISC_SUSPECT_PRODUCT_NAME;
+    dip->clickable_item_type = clickable_item_type;
     dip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (bad_fmt) + StringLen (phrase) + StringLen (feat_type) + 15));
     sprintf (dip->description, bad_fmt, ValNodeLen (feature_list), feat_type, phrase);
     dip->callback_func = NULL;
@@ -8063,14 +8469,14 @@ extern void FindSuspectProductNames (ValNodePtr PNTR discrepancy_list, ValNodePt
   
   for (vnp = sep_list; vnp != NULL; vnp = vnp->next) 
   {
-    VisitFeaturesInSep (vnp->data.ptrvalue, feature_list, FindSuspectProductNamesCallback);
+    VisitGenProdSetFeatures (vnp->data.ptrvalue, feature_list, FindSuspectProductNamesCallback);
   }
   
   for (k = 0; k < num_suspect_product_names; k++)
   {
     if (feature_list[k] != NULL)
     {
-      dip = SuspectPhrase (suspect_product_names[k], "product name", feature_list[k]);
+      dip = SuspectPhrase (DISC_SUSPECT_PRODUCT_NAME, suspect_product_names[k], "product name", feature_list[k]);
       if (dip != NULL)
       {
         ValNodeAddPointer (&subcategories, 0, dip);
@@ -8081,7 +8487,7 @@ extern void FindSuspectProductNames (ValNodePtr PNTR discrepancy_list, ValNodePt
   
   if (master_list != NULL)
   {
-    dip = SuspectPhrase ("suspect phrase or characters", "product_name", master_list);
+    dip = SuspectPhrase (DISC_SUSPECT_PRODUCT_NAME, "suspect phrase or characters", "product_name", master_list);
     if (dip != NULL)
     {
       dip->subcategories = subcategories;
@@ -8146,7 +8552,7 @@ extern void FindSuspectPhrases (ValNodePtr PNTR discrepancy_list, ValNodePtr sep
     VisitFeaturesInSep (vnp->data.ptrvalue, &feature_list, FindSuspectPhrasesCallback);
   }
   
-  dip = SuspectPhrase ("fragment or frameshift", "cds comments or protein description", feature_list);
+  dip = SuspectPhrase (DISC_SUSPECT_PHRASES, "fragment or frameshift", "cds comments or protein description", feature_list);
   if (dip != NULL)
   {
     ValNodeAddPointer (discrepancy_list, 0, dip);
@@ -9206,6 +9612,195 @@ extern void FindCDSOverlappingtRNAs (ValNodePtr PNTR discrepancy_list, ValNodePt
 }
 
 
+static void FindFeaturesOverlappingSrcFeaturesBioseqCallback (BioseqPtr bsp, Pointer data)
+{
+  ClickableItemPtr  cip;
+  SeqMgrFeatContext fcontext;
+  SeqFeatPtr        sfp;
+  ValNodePtr        this_list, src_vnp;
+
+  if (bsp == NULL || data == NULL) return;
+
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_BIOSRC, &fcontext);
+  while (sfp != NULL)
+  {
+    this_list = ListFeaturesOverlappingLocation (bsp, sfp->location, 0, 0);
+    if (this_list != NULL)
+    {
+      cip = NewClickableItem (DISC_FEAT_OVERLAP_SRCFEAT, "%d features overlap a source feature", this_list);
+      /* insert source feature at beginning of item list */
+      src_vnp = ValNodeNew (NULL);     
+      src_vnp->choice = OBJ_SEQFEAT;
+      src_vnp->data.ptrvalue = sfp;
+      src_vnp->next = cip->item_list;
+      cip->item_list = src_vnp;
+      ValNodeAddPointer ((ValNodePtr PNTR) data, 0, cip);
+    }
+    sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_BIOSRC, &fcontext);
+  }
+}
+
+
+extern void FindFeaturesOverlappingSrcFeatures (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list)
+{
+  ValNodePtr       vnp;
+  SeqEntryPtr      sep;
+
+  for (vnp = sep_list; vnp != NULL; vnp = vnp->next) {
+    sep = vnp->data.ptrvalue;
+    VisitBioseqsInSep (sep, discrepancy_list, FindFeaturesOverlappingSrcFeaturesBioseqCallback);
+  }
+}
+
+
+extern CharPtr discReportDuplicateProteinIDFmt = "%d coding regions have non-unique protein IDs";
+extern CharPtr discReportOneDuplicateProteinIDFmt = "%d coding regions have protein ID %s";
+extern CharPtr discReportMissingProteinIDFmt = "%d coding regions have missing protein IDs";
+extern CharPtr discReportDuplicateTranscriptIdFmt = "%d mRNAs have non-unique transcript IDs";
+extern CharPtr discReportOneDuplicateTranscriptIdFmt = "%d mRNAs have non-unique transcript ID %s";
+extern CharPtr discReportMissingTranscriptIDFmt = "%d mRNAs have missing transcript IDs";
+
+
+/* look for duplicate protein IDs and duplicate transcript IDs */
+/* every coding region should have a protein ID and a transcript ID */
+/* RNA should have a transcript ID to match. */
+static void CheckGenProdSetBioseq (BioseqPtr bsp, GenProdSetDiscrepancyListsPtr lists)
+{
+  SeqFeatPtr sfp;
+  SeqMgrFeatContext fcontext;
+  SeqIdPtr          sip;
+  Char              buf [96];
+
+  if (bsp == NULL || !ISA_na (bsp->mol) || lists == NULL) {
+    return;
+  }
+
+  /* look for missing protein IDs and duplicate protein IDs on coding regions */
+  for (sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &fcontext);
+       sfp != NULL;
+       sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_CDREGION, 0, &fcontext)) {
+    if (sfp->product == NULL) {
+      if (!sfp->pseudo) {
+        ValNodeAddPointer (&(lists->missing_protein_id), 0,
+                           GlobalDiscrepancyNew (NULL, OBJ_SEQFEAT, sfp));
+      }
+    } else {
+      sip = SeqLocId (sfp->product);
+      SeqIdWrite (sip, buf, PRINTID_REPORT, sizeof (buf) - 1);
+      ValNodeAddPointer (&(lists->cds_product_list), 0,
+                         GlobalDiscrepancyNew (buf, OBJ_SEQFEAT, sfp));
+    }
+  }
+
+  /* look for missing transcript IDs and duplicate transcript IDs on mRNAs */
+  for (sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_mRNA, &fcontext);
+       sfp != NULL;
+       sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_mRNA, &fcontext)) {
+    if (sfp->product == NULL) {
+      ValNodeAddPointer (&(lists->missing_mrna_product), 0, 
+                         GlobalDiscrepancyNew (NULL, OBJ_SEQFEAT, sfp));
+    } else {
+      sip = SeqLocId (sfp->product);
+      SeqIdWrite (sip, buf, PRINTID_REPORT, sizeof (buf) - 1);
+      ValNodeAddPointer (&(lists->mrna_product_list), 0,
+                         GlobalDiscrepancyNew (buf, OBJ_SEQFEAT, sfp));
+    }
+  }
+}
+
+
+extern void CheckGenProdSetsInSeqEntry (SeqEntryPtr sep, GenProdSetDiscrepancyListsPtr lists)
+{
+  BioseqSetPtr bssp;
+
+  if (sep == NULL || !IS_Bioseq_set (sep) || sep->data.ptrvalue == NULL || lists == NULL) return;
+  bssp = (BioseqSetPtr) sep->data.ptrvalue;
+  if (bssp->_class == BioseqseqSet_class_gen_prod_set) {
+    if (IS_Bioseq (bssp->seq_set)) {
+      CheckGenProdSetBioseq(bssp->seq_set->data.ptrvalue, lists);
+    }
+  } else {
+    sep = bssp->seq_set;
+    while (sep != NULL) {
+      CheckGenProdSetsInSeqEntry (sep, lists);
+      sep = sep->next;
+    }
+  }
+}
+
+
+static void CheckListForGenProdSets (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list)
+{
+  ValNodePtr       vnp, disc_list = NULL;
+  ClickableItemPtr cip;
+  GenProdSetDiscrepancyListsData lists;
+
+  MemSet (&lists, 0, sizeof (GenProdSetDiscrepancyListsData));
+  for (vnp = sep_list; vnp != NULL; vnp = vnp->next) {
+    CheckGenProdSetsInSeqEntry (vnp->data.ptrvalue, &lists);
+  }
+
+  if (lists.missing_protein_id != NULL) {
+    cip = ReportMissingFields (lists.missing_protein_id, discReportMissingProteinIDFmt, DISC_MISSING_GENPRODSET_PROTEIN);
+    if (cip != NULL) {
+      ValNodeAddPointer (&disc_list, 0, cip);
+    }
+    lists.missing_protein_id = FreeGlobalDiscrepancyList (lists.missing_protein_id);
+  }
+
+  if (lists.cds_product_list != NULL) {
+    lists.cds_product_list = ValNodeSort (lists.cds_product_list, SortVnpByGlobalDiscrepancyString);
+    cip = ReportNonUniqueGlobalDiscrepancy (lists.cds_product_list, 
+                                            discReportDuplicateProteinIDFmt,
+                                            discReportOneDuplicateProteinIDFmt,
+                                            DISC_DUP_GENPRODSET_PROTEIN,
+                                            FALSE);
+    if (cip != NULL) {
+      ValNodeAddPointer (&disc_list, 0, cip);
+    }
+    lists.cds_product_list = FreeGlobalDiscrepancyList (lists.cds_product_list);
+  }
+  
+  
+  if (lists.missing_mrna_product != NULL) {
+    cip = ReportMissingFields (lists.missing_mrna_product, discReportMissingTranscriptIDFmt, DISC_MISSING_GENPRODSET_TRANSCRIPT_ID);
+    if (cip != NULL) {
+      ValNodeAddPointer (&disc_list, 0, cip);
+    }
+    lists.missing_mrna_product = FreeGlobalDiscrepancyList (lists.missing_mrna_product);
+  }
+
+
+  if (lists.mrna_product_list != NULL) {
+    lists.mrna_product_list = ValNodeSort (lists.mrna_product_list, SortVnpByGlobalDiscrepancyString);
+    cip = ReportNonUniqueGlobalDiscrepancy (lists.mrna_product_list, 
+                                            discReportDuplicateTranscriptIdFmt,
+                                            discReportOneDuplicateTranscriptIdFmt,
+                                            DISC_DUP_GENPRODSET_TRANSCRIPT_ID,
+                                            FALSE);
+    if (cip != NULL) {
+      ValNodeAddPointer (&disc_list, 0, cip);
+    }
+    lists.mrna_product_list = FreeGlobalDiscrepancyList (lists.mrna_product_list);
+  }
+  
+    
+
+
+  if (disc_list != NULL) {
+    if (disc_list->next == NULL) {
+      ValNodeLink (discrepancy_list, disc_list);
+    } else {
+      cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+      cip->description = StringSave ("GenProdSet Errors");
+      cip->subcategories = disc_list;
+      ValNodeAddPointer (discrepancy_list, 0, cip);
+    }
+  }
+}
+
+
 static void CountProteinsBioseqCallback (BioseqPtr bsp, Pointer userdata)
 {
   if (bsp != NULL && ISA_aa (bsp->mol) && userdata != NULL) {
@@ -9300,7 +9895,7 @@ typedef struct discrepancyinfo
 static DiscrepancyInfoData discrepancy_info_list[] = 
 {
   { "Missing Genes", "MISSING_GENES", AddMissingAndSuperfluousGeneDiscrepancies },
-  { "Extra Genes", "EXTRA_GENES", AddDiscrepanciesForMissingOrNonUniqueGeneLocusTags },
+  { "Extra Genes", "EXTRA_GENES", AddMissingAndSuperfluousGeneDiscrepancies },
   { "Missing Locus Tags", "MISSING_LOCUS_TAGS", AddDiscrepanciesForMissingOrNonUniqueGeneLocusTags },
   { "Duplicate Locus Tags", "DUPLICATE_LOCUS_TAGS", AddDiscrepanciesForMissingOrNonUniqueGeneLocusTags },
   { "Bad Locus Tag Format", "BAD_LOCUS_TAG_FORMAT", AddDiscrepanciesForMissingOrNonUniqueGeneLocusTags },
@@ -9339,7 +9934,13 @@ static DiscrepancyInfoData discrepancy_info_list[] =
   { "Note without Transl_except", "NOTE_NO_TRANSL", FindTranslExceptNotes },
   { "Transl_except longer than 3", "TRANSL_TOO_LONG", FindTranslExceptNotes },
   { "CDS tRNA overlaps", "CDS_TRNA_OVERLAP", FindCDSOverlappingtRNAs },
-  { "Count Proteins", "COUNT_PROTEINS", CountProteins }
+  { "Count Proteins", "COUNT_PROTEINS", CountProteins },
+  { "Features Intersecting Source Features", "DISC_FEAT_OVERLAP_SRCFEAT", FindFeaturesOverlappingSrcFeatures },
+  { "CDS on GenProdSet without protein", "MISSING_GENPRODSET_PROTEIN", CheckListForGenProdSets},
+  { "Multiple CDS on GenProdSet, same protein", "DUP_GENPRODSET_PROTEIN", CheckListForGenProdSets},
+  { "mRNA on GenProdSet without transcript ID", "MISSING_GENPRODSET_TRANSCRIPT_ID", CheckListForGenProdSets},
+  { "mRNA on GenProdSet with duplicate ID", "DISC_DUP_GENPRODSET_TRANSCRIPT_ID", CheckListForGenProdSets}
+
 };
 
 extern CharPtr GetDiscrepancyTestConfName (DiscrepancyType dtype) 
@@ -9583,6 +10184,47 @@ extern CharPtr GetDiscrepancyItemText (ValNodePtr vnp)
   return row_text;
 }
 
+extern CharPtr GetParentLabelForDiscrepancyItem (ValNodePtr vnp)
+{
+  CharPtr label = NULL;
+  SeqFeatPtr sfp;
+  SeqDescrPtr sdp;
+  ObjValNodePtr ovn;
+  BioseqPtr  bsp;
+
+  if (vnp == NULL || vnp->data.ptrvalue == NULL) return NULL;
+
+  switch (vnp->choice)
+  {
+    case OBJ_SEQFEAT:
+      sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+      bsp = BioseqFindFromSeqLoc (sfp->location);
+      label = GetBioseqLabel (bsp);
+      break;
+    case OBJ_SEQDESC:
+      sdp = (SeqDescrPtr) vnp->data.ptrvalue;
+      if (sdp != NULL)
+      {
+        if (sdp->extended != 0) {
+          ovn = (ObjValNodePtr) sdp;
+          if (ovn->idx.parenttype == OBJ_BIOSEQ) {
+            label = GetBioseqLabel ((BioseqPtr) ovn->idx.parentptr);
+          } else if (ovn->idx.parenttype == OBJ_BIOSEQSET) {
+            label = GetBioseqSetLabel ((BioseqSetPtr) ovn->idx.parentptr);
+          }
+        }
+      }
+      break;
+    case OBJ_BIOSEQ:
+      label = GetBioseqLabel (vnp->data.ptrvalue);
+      break;
+    case OBJ_BIOSEQSET:
+      label = GetBioseqSetLabel (vnp->data.ptrvalue);
+      break;
+  }
+  return label;
+}
+
 
 static ValNodePtr ValNodePointerDup (ValNodePtr vnp)
 {
@@ -9598,7 +10240,36 @@ static ValNodePtr ValNodePointerDup (ValNodePtr vnp)
   return vnp_new;
 }
 
-static ValNodePtr ReplaceDiscrepancyItemWithFeatureTableStrings (ValNodePtr feat_list)
+
+typedef struct ftstrings {
+  CharPtr header;
+  CharPtr desc;
+} FTStringsData, PNTR FTStringsPtr;
+
+
+static FTStringsPtr FTStringsNew (CharPtr header, CharPtr desc)
+{
+  FTStringsPtr f;
+
+  f = (FTStringsPtr) MemNew (sizeof (FTStringsData));
+  f->header = header;
+  f->desc = desc;
+  return f;
+}
+
+
+static FTStringsPtr FTStringsFree (FTStringsPtr f)
+{
+  if (f != NULL) {
+    f->header = MemFree (f->header);
+    f->desc = MemFree (f->desc);
+    f = MemFree (f);
+  }
+  return f;
+}
+
+
+extern ValNodePtr ReplaceDiscrepancyItemWithFeatureTableStrings (ValNodePtr feat_list)
 {
   BioseqPtr       bsp, prot_bsp;
   CstType         custom_flags = 0;
@@ -9608,6 +10279,7 @@ static ValNodePtr ReplaceDiscrepancyItemWithFeatureTableStrings (ValNodePtr feat
   SeqFeatPtr      sfp, cds;
   ValNodePtr      vnp, list_copy = NULL, list_vnp;
   CharPtr         feature_table_header = NULL, feat_desc;
+  FTStringsPtr    fts;
   
   if (feat_list == NULL) return NULL;
   
@@ -9663,14 +10335,7 @@ static ValNodePtr ReplaceDiscrepancyItemWithFeatureTableStrings (ValNodePtr feat
             /* replace list feature with description, change choice */
             list_vnp->choice = 0;
             feat_desc = asn2gnbk_format (ajp, (Int4) index);
-            if (feature_table_header == NULL) {                   
-              list_vnp->data.ptrvalue = feat_desc;
-            } else {
-              list_vnp->data.ptrvalue = (CharPtr) MemNew (sizeof (Char) * (StringLen (feature_table_header) + StringLen (feat_desc) + 2));
-              StringCpy (list_vnp->data.ptrvalue, feature_table_header);
-              StringCat (list_vnp->data.ptrvalue, feat_desc);
-              feature_table_header = MemFree (feature_table_header);
-            }
+            list_vnp->data.ptrvalue = FTStringsNew (StringSave (feature_table_header), feat_desc);
           }
         }
       }
@@ -9678,6 +10343,26 @@ static ValNodePtr ReplaceDiscrepancyItemWithFeatureTableStrings (ValNodePtr feat
     asn2gnbk_cleanup (ajp);
     feature_table_header = MemFree (feature_table_header);
   }
+
+  /* now remove redundant headers */
+  for (list_vnp = list_copy; list_vnp != NULL; list_vnp = list_vnp->next) {
+    if (list_vnp->choice != 0) continue;
+    fts = (FTStringsPtr) list_vnp->data.ptrvalue;
+    if (feature_table_header == NULL
+        || StringCmp (feature_table_header, fts->header) != 0) {
+      feature_table_header = MemFree (feature_table_header);
+      feature_table_header = fts->header;
+      fts->header = NULL;
+      list_vnp->data.ptrvalue = (CharPtr) MemNew (sizeof (Char) * (StringLen (feature_table_header) + StringLen (fts->desc) + 2));
+      StringCpy (list_vnp->data.ptrvalue, feature_table_header);
+      StringCat (list_vnp->data.ptrvalue, fts->desc);
+    } else {
+      list_vnp->data.ptrvalue = fts->desc;
+      fts->desc = NULL;
+    }
+    fts = FTStringsFree (fts);
+  }
+  feature_table_header = MemFree (feature_table_header);
   return list_copy;
 }
 
@@ -9759,7 +10444,7 @@ extern void WriteDiscrepancyEx (FILE *fp, ClickableItemPtr dip, Boolean use_feat
   while (vnp != NULL)
   {
     filename = NULL;
-    if (vnp->choice == 0 && use_feature_table_fmt)
+    if (vnp->choice == 0)
     {
       row_text = vnp->data.ptrvalue;
     }
@@ -9895,6 +10580,321 @@ extern void SaveDiscrepancyConfig (DiscrepancyConfigPtr dcp)
 }
 
 
+extern CharPtr SetDiscrepancyReportTestsFromString (CharPtr list, Boolean enable, DiscrepancyConfigPtr dcp)
+{
+  CharPtr         ptr, tmp, name_start, err_msg;
+  DiscrepancyType test_type;
+  CharPtr         err_fmt = "%s is an unrecognized test name";
+  
+  if (dcp == NULL) return StringSave ("Unable to configure");
+
+  if (!StringDoesHaveText (list)) {
+      return StringSave ("No tests specified!");
+  }
+
+  tmp = StringSave (list);
+  name_start = tmp;
+  while (name_start != NULL && StringDoesHaveText (name_start)) {
+    ptr = StringChr (name_start, ',');
+    if (ptr != NULL) {
+      *ptr = 0;
+    }
+    TrimSpacesAroundString (name_start);
+    test_type = GetDiscrepancyTypeFromSettingName (name_start);
+    if (test_type == MAX_DISC_TYPE) {
+      err_msg = (CharPtr) MemNew (StringLen (err_fmt) + StringLen (name_start));
+      sprintf (err_msg, err_fmt, name_start);
+      tmp = MemFree (tmp);
+      return err_msg;
+    }
+    dcp->conf_list[test_type] = enable;
+    if (ptr == NULL) {
+      name_start = NULL;
+    } else {
+      name_start = ptr + 1;
+    }
+  }
+  tmp = MemFree (tmp);
+  return NULL;  
+}
+
+
+/* functions for writing discrepancy report to file */
+extern void WriteAsnDiscReport (ValNodePtr discrepancy_list, FILE *ofp, DiscReportOutputConfigPtr oc, Boolean use_flag)
+{
+  ValNodePtr       vnp;
+  ClickableItemPtr cip;
+  CharPtr          setting_name, prefix;
+  CharPtr          prefix_fmt = "DiscRep:%s:";
+
+  if (ofp == NULL || oc == NULL) return;
+
+  for (vnp = discrepancy_list; vnp != NULL; vnp = vnp->next) {
+    cip = (ClickableItemPtr) vnp->data.ptrvalue;
+    if (cip != NULL) {
+      prefix = NULL;
+      if (use_flag) {
+        setting_name = GetDiscrepancyTestSettingName (cip->clickable_item_type);
+        if (StringHasNoText (setting_name)) {
+          prefix = StringSave ("DiscRep:");
+        } else {
+          prefix = (CharPtr) MemNew (sizeof (Char) * (StringLen (prefix_fmt) + StringLen (setting_name)));
+          sprintf (prefix, prefix_fmt, setting_name);
+        }
+      }
+      if (oc->summary_report) {
+        fprintf (ofp, "%s%s\n", prefix == NULL ? "" : prefix, cip->description);           
+      } else {
+        WriteDiscrepancyEx (ofp, cip, oc->use_feature_table_format, oc->filename_list, prefix);
+      }
+      prefix = MemFree (prefix);
+      if ((cip->item_list == NULL || oc->expand_report_categories[cip->clickable_item_type]) && cip->subcategories != NULL) {
+        if (use_flag && cip->clickable_item_type == DISC_INCONSISTENT_BIOSRC_DEFLINE) {
+          WriteAsnDiscReport (cip->subcategories, ofp, oc, FALSE);
+        } else {
+          WriteAsnDiscReport (cip->subcategories, ofp, oc, use_flag);
+        }
+      }
+    }
+  }
+
+}
+
+
+static int LIBCALLBACK SortVnpByDiscrepancyType (VoidPtr ptr1, VoidPtr ptr2)
+
+{
+  ValNodePtr  vnp1;
+  ValNodePtr  vnp2;
+  ClickableItemPtr c1, c2;
+  CharPtr          cp1, cp2;
+
+  if (ptr1 != NULL && ptr2 != NULL) {
+    vnp1 = *((ValNodePtr PNTR) ptr1);
+    vnp2 = *((ValNodePtr PNTR) ptr2);
+    if (vnp1 != NULL && vnp2 != NULL) {
+      c1 = (ClickableItemPtr) vnp1->data.ptrvalue;
+      c2 = (ClickableItemPtr) vnp2->data.ptrvalue;
+      if (c1 != NULL && c2 != NULL) {
+        if (c1->clickable_item_type < c2->clickable_item_type) {
+          return -1;
+        } else if (c1->clickable_item_type > c2->clickable_item_type) {
+          return 1;
+        } else {
+          if (c1->description == NULL && c2->description == NULL) {
+            return 0;
+          } else if (c1->description == NULL) {
+            return -1;
+          } else if (c2->description == NULL) {
+            return 1;
+          } else {
+            cp1 = c1->description;
+            while (isdigit (*cp1)) {
+              cp1++;
+            }
+            cp2 = c2->description;
+            while (isdigit (*cp2)) {
+              cp2++;
+            }
+            return StringCmp (cp1, cp2);
+          }
+        }
+      }
+    }
+  }
+  return 0;
+}
+
+
+static ClickableItemPtr CombineDiscrepancyReports (ClickableItemPtr cip1, ClickableItemPtr cip2)
+{
+  CharPtr cp1, cp2, num_start1, num_start2, num_buf;
+  Char    fixed_buf[15];
+  Int4    common_start_len = 0, common_len_end = 0;
+  Int4    num_len1, num_len2, num_items1, num_items2;
+  ClickableItemPtr combined = NULL;
+  
+
+  if (cip1 == NULL || cip2 == NULL || cip1->clickable_item_type != cip2->clickable_item_type
+      || StringHasNoText (cip1->description) || StringHasNoText (cip2->description)) {
+    return NULL;
+  }
+
+  cp1 = cip1->description;
+  cp2 = cip2->description;
+    
+  while (*cp1 == *cp2 && *cp1 != 0 && *cp2 != 0 && !isdigit (*cp1)) {
+    cp1++;
+    cp2++;
+    common_start_len++;
+  }
+  if (*cp1 == 0 && *cp2 == 0) {
+    /* entire description matches */
+    combined = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+    combined->clickable_item_type = cip1->clickable_item_type;
+    combined->description = StringSave (cip1->description);
+    combined->item_list = cip1->item_list;
+    cip1->item_list = NULL;
+    combined->subcategories = cip1->subcategories;
+    cip1->subcategories = NULL;
+    ValNodeLink (&(combined->item_list), cip2->item_list);
+    cip2->item_list = NULL;
+    ValNodeLink (&(combined->subcategories), cip2->subcategories);
+    cip2->subcategories = NULL;
+  } else if (isdigit (*cp1) && isdigit (*cp2) && (cp1 == cip1->description || isspace (*(cp1 - 1)))) {
+    num_start1 = cp1;
+    num_len1 = 0;
+    while (isdigit (*cp1)) {
+      cp1++;
+      num_len1++;
+    }
+    num_start2 = cp2;
+    num_len2 = 0;
+    while (isdigit (*cp2)) {
+      cp2++;
+      num_len2++;
+    }
+    if ((*cp1 == 0 || isspace (*cp1)) && StringCmp (cp1, cp2) == 0) {
+      /* matches on the other side of the number */
+      /* build combined description */
+      if (num_len1 < sizeof (fixed_buf)) {
+        StringNCpy (fixed_buf, num_start1, num_len1);
+        fixed_buf[num_len1] = 0;
+        num_items1 = atoi(fixed_buf);
+      } else {
+        num_buf = (CharPtr) MemNew (sizeof (Char) * (num_len1 + 1));
+        StringNCpy (num_buf, num_start1, num_len1);
+        num_buf[num_len1] = 0;
+        num_items1 = atoi (num_buf);
+        num_buf = MemFree (num_buf);
+      }
+      if (num_len2 < sizeof (fixed_buf) - 1) {
+        StringNCpy (fixed_buf, num_start2, num_len2);
+        fixed_buf[num_len2] = 0;
+        num_items2 = atoi(fixed_buf);
+      } else {
+        num_buf = (CharPtr) MemNew (sizeof (Char) * (num_len2 + 1));
+        StringNCpy (num_buf, num_start2, num_len2);
+        num_buf[num_len2] = 0;
+        num_items2 = atoi (num_buf);
+        num_buf = MemFree (num_buf);
+      }
+      
+      combined = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+
+      combined->description = (CharPtr) MemNew (sizeof (Char) * (common_start_len + sizeof (fixed_buf) + StringLen (cp1) + 1));
+      StringNCpy (combined->description, cip1->description, common_start_len);
+      sprintf (fixed_buf, "%d", num_items1 + num_items2);
+      StringCat (combined->description, fixed_buf);
+      StringCat (combined->description, cp1);
+
+      combined->clickable_item_type = cip1->clickable_item_type;  
+      combined->item_list = cip1->item_list;
+      cip1->item_list = NULL;
+      combined->subcategories = cip1->subcategories;
+      cip1->subcategories = NULL;
+      ValNodeLink (&(combined->item_list), cip2->item_list);
+      cip2->item_list = NULL;
+      ValNodeLink (&(combined->subcategories), cip2->subcategories);
+      cip2->subcategories = NULL;
+    } else {
+      combined = NULL;
+    }
+  }
+  if (combined != NULL && combined->subcategories != NULL) {
+    CollateDiscrepancyReports (&(combined->subcategories));
+  }
+  return combined;
+}
+
+
+extern void CollateDiscrepancyReports (ValNodePtr PNTR discrepancy_reports)
+{
+  ValNodePtr vnp, tmp;
+  ClickableItemPtr combined;
+
+  *discrepancy_reports = ValNodeSort (*discrepancy_reports, SortVnpByDiscrepancyType);
+
+  vnp = *discrepancy_reports;
+  while (vnp != NULL && vnp->next != NULL) {
+    combined = CombineDiscrepancyReports (vnp->data.ptrvalue, vnp->next->data.ptrvalue);
+    if (combined != NULL) {
+      vnp->data.ptrvalue = ClickableItemFree (vnp->data.ptrvalue);
+      vnp->next->data.ptrvalue = ClickableItemFree (vnp->next->data.ptrvalue);
+      tmp = vnp->next;
+      vnp->next = vnp->next->next;
+      tmp->next = NULL;
+      tmp = ValNodeFree (tmp);
+      vnp->data.ptrvalue = combined;
+    } else {
+      vnp = vnp->next;
+    }
+  }
+}
+
+
+extern CharPtr ExpandDiscrepancyReportTestsFromString (CharPtr list, Boolean expand, DiscReportOutputConfigPtr dcp)
+{
+  CharPtr         ptr, tmp, name_start, err_msg;
+  Int4            i;
+  DiscrepancyType test_type;
+  CharPtr         err_fmt = "%s is an unrecognized test name";
+  
+  if (dcp == NULL) return StringSave ("Unable to configure");
+
+  if (!StringDoesHaveText (list)) {
+    return NULL;
+  } else if (StringICmp (list, "all") == 0) {
+    for (i = 0; i < MAX_DISC_TYPE; i++) {
+      dcp->expand_report_categories[i] = expand;
+    }
+  } else {
+    tmp = StringSave (list);
+    name_start = tmp;
+    while (name_start != NULL && StringDoesHaveText (name_start)) {
+      ptr = StringChr (name_start, ',');
+      if (ptr != NULL) {
+        *ptr = 0;
+      }
+      TrimSpacesAroundString (name_start);
+      test_type = GetDiscrepancyTypeFromSettingName (name_start);
+      if (test_type == MAX_DISC_TYPE) {
+        err_msg = (CharPtr) MemNew (StringLen (err_fmt) + StringLen (name_start));
+        sprintf (err_msg, err_fmt, name_start);
+        tmp = MemFree (tmp);
+        return err_msg;
+      }
+      dcp->expand_report_categories[test_type] = expand;
+      if (ptr == NULL) {
+        name_start = NULL;
+      } else {
+        name_start = ptr + 1;
+      }
+    }
+    tmp = MemFree (tmp);
+  }
+  return NULL;  
+}
+
+
+extern ValNodePtr FreeFilenameList (ValNodePtr filename_list)
+{
+  ValNodePtr vnp_next;
+  
+  while (filename_list != NULL) {
+    vnp_next = filename_list->next;
+    filename_list->next = NULL;
+    if (filename_list->choice == FILENAME_LIST_FILENAME_ITEM) {
+      filename_list = ValNodeFreeData (filename_list);
+    } else {
+      filename_list = ValNodeFree (filename_list);
+    }
+    filename_list = vnp_next;
+  }
+  return filename_list;
+}
+
+
 /* Barcode Discrepancy Function */
 
 /* 
@@ -10261,7 +11261,6 @@ BarcodeTestForSeqEntry
  CharPtr              fmt,
  BarcodeTestConfigPtr cfg)
 {
-  ValNodePtr  bsp_list = NULL;
   BarcodeSearchData bsd;
 
   bsd.bioseq_list = NULL;
@@ -10529,6 +11528,52 @@ extern CharPtr BarcodeTestGenbankIdString (BioseqPtr bsp)
 }
 
 
+
+static CharPtr GetBarcodeTestFailureReasons (BarcodeTestResultsPtr res)
+{
+  Int4             i, msg_len = 0;
+  Boolean          any_failed = FALSE;
+  CharPtr          msg;
+  Char             pct[5];
+
+  if (res == NULL || res->bsp == NULL) return NULL;
+
+  for (i = 0; i < eBarcodeTest_LAST; i++)
+  {
+    if (res->failed_tests[i]) 
+    {
+      msg_len += StringLen (GetBarcodeTestName (i)) + 2;
+      if (i == eBarcodeTest_PercentN)
+      {
+        msg_len += 5;
+      }
+      any_failed = TRUE;
+    }
+  }
+  if (!any_failed) return NULL;
+   
+  msg = (CharPtr) MemNew (sizeof (Char) * msg_len);
+  for (i = 0; i < eBarcodeTest_LAST; i++)
+  {
+    if (res->failed_tests[i])
+    {
+      StringCat (msg, GetBarcodeTestName(i));
+      if (i == eBarcodeTest_PercentN) 
+      {
+        sprintf (pct, ":%.1f", res->n_percent);
+        StringCat (msg, pct);
+      }
+      StringCat (msg, ",");
+    }
+  }
+  /* remove trailing comma */
+  msg[StringLen(msg) - 1] = 0;
+          
+  return msg;
+
+}
+
+
 static CharPtr SummaryTextFromBarcodeTestResults (BarcodeTestResultsPtr res)
 {
   Int4             i, msg_len = 0;
@@ -10742,6 +11787,33 @@ extern void WriteBarcodeTestCompliance (FILE *fp, ValNodePtr results_list)
 }
 
 
+/* Report lists each Bioseq and whether the Bioseq passed all tests
+ * or failed at least one.
+ */
+extern void WriteBarcodeTestComprehensive (FILE *fp, ValNodePtr results_list)
+{
+  BarcodeTestResultsPtr res;
+  ValNodePtr            vnp;
+  CharPtr               barcode_id, genbank_id, reason;
+
+  if (fp == NULL) return;
+
+  for (vnp = results_list; vnp != NULL; vnp = vnp->next)
+  {
+    res = (BarcodeTestResultsPtr) vnp->data.ptrvalue;
+    barcode_id = BarcodeTestBarcodeIdString (res->bsp);
+    genbank_id = BarcodeTestGenbankIdString (res->bsp);
+    reason = GetBarcodeTestFailureReasons (res);
+    fprintf (fp, "%s\t%s\t%s\t%s\n", barcode_id, genbank_id, 
+                                 PassBarcodeTests (res) ? "PASS" : "FAIL",
+                                 reason == NULL ? "" : reason);
+    barcode_id = MemFree (barcode_id);
+    genbank_id = MemFree (genbank_id);
+    reason = MemFree (reason);
+  }
+}
+
+
 /* Create a tag table for updates */
 extern void WriteBarcodeTagTable (FILE *fp, ValNodePtr results_list)
 {
@@ -10879,6 +11951,61 @@ extern void AbstractReportError (
 }
 
 
+
+extern Boolean ParseLatLon (
+  CharPtr lat_lon,
+  FloatHi PNTR latP,
+  FloatHi PNTR lonP
+)
+
+{
+  char    ew;
+  double  lat;
+  double  lon;
+  char    ns;
+
+  if (latP != NULL) {
+    *latP = 0.0;
+  }
+  if (lonP != NULL) {
+    *lonP = 0.0;
+  }
+
+  if (StringHasNoText (lat_lon)) return FALSE;
+
+  if (sscanf (lat_lon, "%lf %c %lf %c", &lat, &ns, &lon, &ew) == 4) {
+    if (lon < -180.0) {
+      lon = -180.0;
+    }
+    if (lat < -90.0) {
+      lat = -90.0;
+    }
+    if (lon > 180.0) {
+      lon = 180.0;
+    }
+    if (lat > 90.0) {
+      lat = 90.0;
+    }
+    if (ew == 'W') {
+      lon = -lon;
+    }
+    if (ns == 'S') {
+      lat = -lat;
+    }
+
+    if (latP != NULL) {
+      *latP = (FloatHi) lat;
+    }
+    if (lonP != NULL) {
+      *lonP = (FloatHi) lon;
+    }
+
+    return TRUE;
+  }
+
+  return FALSE;
+}
+
 static CharPtr print_lat_lon_fmt = "%.*f %c %.*f %c";
 
 extern void IsCorrectLatLonFormat (CharPtr lat_lon, BoolPtr format_correct, BoolPtr lat_in_range, BoolPtr lon_in_range)
@@ -11820,10 +12947,12 @@ typedef struct  countrystatelist {
   CharPtr country_name;
 } CountryStateListData, PNTR CountryStateListPtr;
 
-static Boolean IsMatchInSecondChoiceLists (CharPtr find_str, Int4 match_len, CountryStateListPtr second_choice_lists)
+static Boolean IsMatchInSecondChoiceLists (CharPtr find_str, Int4 match_len, CountryStateListPtr second_choice_lists, CharPtr whole_string)
 {
   Int4    i, j;
   Boolean in_lists = FALSE;
+  CharPtr cp;
+  Int4 len_second_choice;
 
   if (StringHasNoText (find_str) || match_len < 1 || second_choice_lists == NULL) return FALSE;
 
@@ -11831,7 +12960,14 @@ static Boolean IsMatchInSecondChoiceLists (CharPtr find_str, Int4 match_len, Cou
   {
     for (j = 0; second_choice_lists[i].state_list[j] != NULL && !in_lists; j++) 
     {
-      if (StringNCmp (find_str, second_choice_lists[i].state_list[j], match_len) == 0) 
+      len_second_choice = StringLen (second_choice_lists[i].state_list[j]);      
+      if (len_second_choice == match_len 
+          &&StringNCmp (find_str, second_choice_lists[i].state_list[j], match_len) == 0) 
+      {
+        in_lists = TRUE;
+      }
+      else if ((cp = StringSearch (second_choice_lists[i].state_list[j], find_str)) != NULL
+               && StringSearch (whole_string, second_choice_lists[i].state_list[j]) != NULL)
       {
         in_lists = TRUE;
       }
@@ -11841,81 +12977,187 @@ static Boolean IsMatchInSecondChoiceLists (CharPtr find_str, Int4 match_len, Cou
 }
 
 
-static CharPtr FindBestStringMatch (CharPtr PNTR list, CharPtr find_str, Int4Ptr pMatchLen, CountryStateListPtr second_choice_lists)
+static Boolean IsBodyOfWater (CharPtr str)
+{
+  if (StringHasNoText (str)) return FALSE;
+  if (StringSearch (str, "Ocean") != NULL) return TRUE;
+  if (StringSearch (str, "Gulf") != NULL) return TRUE;
+  if (StringSearch (str, "Sea") != NULL) return TRUE;
+  return FALSE;
+}
+
+
+static Boolean IsSubstringOfStringInList (CharPtr whole_str, CharPtr match_p, CharPtr match_str, CharPtr PNTR list)
+{
+  CharPtr cp;
+  Int4    context_len, find_len;
+  Boolean rval = FALSE;
+
+  if (list == NULL || StringHasNoText (whole_str) || match_p == NULL || match_p < whole_str) {
+    return FALSE;
+  }
+  find_len = StringLen (match_str);
+  while (*list != NULL && !rval) {
+    context_len = StringLen (*list);
+    if (find_len < context_len) {
+      cp = StringSearch (whole_str, *list);
+      while (cp != NULL && !rval) {
+        if (match_p < cp) {
+          cp = NULL;
+        } else if (cp + context_len > match_p) {
+          rval = TRUE;
+        } else {
+          cp = StringSearch (cp + 1, *list);
+        }
+      }
+    }
+    list++;
+  }
+  return rval;
+}
+
+
+static CharPtr bad_context_names[] = {
+ "Gibraltar Range National Park",
+ "Western Australia",
+ "WSW Chihuahua",
+ "Mississippi River",
+ NULL };
+
+static Boolean IsBadContextName (CharPtr whole_str, CharPtr match_p, CharPtr match_str)
+{
+  Boolean rval;
+  Int4    len;
+
+  rval = IsSubstringOfStringInList (whole_str, match_p, match_str, bad_context_names);
+  if (!rval) {
+    len = StringLen (match_str);
+    if (StringCmp (match_p + len, " River") == 0) {
+      rval = TRUE;
+    } else if (StringCmp (match_p + len, " State University") == 0) {
+      rval = TRUE;
+    }
+  }
+  return rval;
+}
+
+
+static Boolean IsPartOfStateName (CharPtr whole_str, CharPtr match_p, CharPtr match_str, CountryStateListPtr second_choice_lists)
+{
+  Boolean rval = FALSE;
+  Int4    i;
+
+  if (second_choice_lists == NULL) return FALSE;
+
+  for (i = 0; second_choice_lists[i].state_list != NULL && !rval; i++) {    
+    rval = IsSubstringOfStringInList (whole_str, match_p, match_str, second_choice_lists[i].state_list);
+  }
+  return rval;
+}
+
+
+static CharPtr
+FindStringInStringWithContext
+(CharPtr search_str, CharPtr look_for, CharPtr PNTR list, CountryStateListPtr second_choice_lists)
 {
-  CharPtr PNTR  ptr;
   Int4          len_match;
+  CharPtr       cp;
+
+  if (StringHasNoText (search_str) || StringHasNoText (look_for)) {
+    return NULL;
+  }
+
+  cp = StringISearch (search_str, look_for);
+  len_match = StringLen (look_for);
+  while (cp != NULL) {
+    /* if character after match is alpha, continue */
+    if (isalpha ((Int4)(cp [len_match]))
+        /* if character before match is alpha, continue */
+        || (cp > search_str && isalpha ((Int4)(*(cp - 1))))
+        /* if match is part of a known "bad context", continue */
+        || IsBadContextName (search_str, cp, look_for)
+        /* if is shorter match for other item, continue */
+        || IsSubstringOfStringInList (search_str, cp, look_for, list)
+        || IsPartOfStateName (search_str, cp, look_for, second_choice_lists)) {
+      cp = StringSearch (cp + len_match, look_for);
+    } else {
+      return cp;
+    }
+  }
+  return cp;
+}
+ 
+
+static ValNodePtr FindBestStringMatch (CharPtr PNTR list, CharPtr find_str, CountryStateListPtr second_choice_lists)
+{
+  CharPtr PNTR  ptr;
   Int4          len_find;
-  Int4          best_len = 0;
-  CharPtr       best_match = NULL;
   CharPtr       cp;
-  CharPtr       ocean_best, ocean_this;
+  Boolean       ocean_best, ocean_this;
   Boolean       best_in_second, this_in_second;
+  ValNodePtr    match_list = NULL, vnp, best_vnp;
   
   if (list == NULL || find_str == NULL) return NULL;
   
   len_find = StringLen (find_str);
   
+  /* first, find all matches */
   for (ptr = list; ptr != NULL && *ptr != NULL; ptr++)
   {
-    len_match = StringLen (*ptr);
-    cp = StringISearch (find_str, *ptr);
-    /* if no match at all, continue */
-    if (cp == NULL) continue;
-    /* if character after match is alpha, continue */
-    if (isalpha ((Int4)(cp [len_match]))) continue;
+    cp = FindStringInStringWithContext (find_str, *ptr, list, second_choice_lists);
+    if (cp != NULL) {
+      ValNodeAddPointer (&match_list, 1, *ptr);
+    }
+  } 
+
+  if (match_list == NULL) return NULL;
 
-    if (best_match != NULL)
+  /* now eliminate matches where we know we have a preference */
+  best_vnp = match_list;
+  for (vnp = match_list->next; vnp != NULL; vnp = vnp->next) 
+  {
+    if (StringSearch (vnp->data.ptrvalue, best_vnp->data.ptrvalue) != NULL)
     {
+      /* best is inside this one */
+      best_vnp->choice = 0;
+      best_vnp = vnp;
+    } else if (StringSearch (best_vnp->data.ptrvalue, vnp->data.ptrvalue) != NULL) {
+      /* this is inside best */
+      vnp->choice = 0;
+    } else {
       /* prefer non-ocean to ocean */
-      ocean_best = StringStr (best_match, "Ocean");
-      ocean_this = StringStr (*ptr, "Ocean");
+      ocean_best = IsBodyOfWater (best_vnp->data.ptrvalue);
+      ocean_this = IsBodyOfWater (vnp->data.ptrvalue);
       if (ocean_this && !ocean_best)
       {
+        /* disregard this one */
+        vnp->choice = 0;
         continue;
       }
       else if (!ocean_this && ocean_best) 
       {
         /* definitely take this to replace best */
+        best_vnp->choice = 0;
+        best_vnp = vnp;     
       }
-      else if (second_choice_lists == NULL)
-      {
-        if (len_match < best_len) continue;
-      }
-      else
+      else if (second_choice_lists != NULL)
       {
-        best_in_second = IsMatchInSecondChoiceLists (best_match, best_len, second_choice_lists);
-        this_in_second = IsMatchInSecondChoiceLists (cp, len_match, second_choice_lists);
+        best_in_second = IsMatchInSecondChoiceLists (best_vnp->data.ptrvalue, StringLen (best_vnp->data.ptrvalue), second_choice_lists, find_str);
+        this_in_second = IsMatchInSecondChoiceLists (vnp->data.ptrvalue, StringLen (vnp->data.ptrvalue), second_choice_lists, find_str);
         /* if this choice is a second choice, but the previous best wasn't, don't bother with this */
-        if (this_in_second && !best_in_second) continue;
-        /* if both choices are in the secondary lists, or neither are, choose the longer choice */
-        if (((!this_in_second && !best_in_second) || (this_in_second && best_in_second)) && len_match < best_len) continue;
+        if (this_in_second && !best_in_second) {
+          vnp->choice = 0;
+        } else if (!this_in_second && best_in_second) {
+          /* if previous choice was in the secondary lists, prefer this and ignore previous */
+          best_vnp->choice = 0;
+          best_vnp = vnp;
+        }
       }
     }
-
-    if (cp == find_str)
-    {
-      best_len = len_match;
-      best_match = *ptr;
-    }
-    else if (!isalpha ((Int4)(*(cp - 1))))
-    {
-      best_len = len_match;
-      best_match = *ptr;
-    }
-  }
-  if (pMatchLen != NULL)
-  {
-    if (best_match == NULL) 
-    {
-      *pMatchLen = 0;
-    } 
-    else
-    {
-      *pMatchLen = best_len;
-    }
   }
-  return best_match;
+  vnp = ValNodeExtract (&match_list, 0);
+  vnp = ValNodeFree (vnp);
+  return match_list;
 }
 
 static CharPtr usa_state_list[] = 
@@ -12070,10 +13312,11 @@ static CountryStateListData country_state_list[] = {
 };
 
 
-static CharPtr FindStateMatch (CharPtr search, CharPtr PNTR country, Int4Ptr state_len)
+static CharPtr FindStateMatch (CharPtr search, CharPtr PNTR country, Int4Ptr state_len, BoolPtr pMulti)
 {
-  CharPtr state_match = NULL, best_match = NULL;
-  Int4    i, match_len, best_len = 0;
+  CharPtr best_match = NULL;
+  Int4    i;
+  ValNodePtr state_matches;
 
   if (StringHasNoText (search)) return NULL;
   if (country != NULL) {
@@ -12081,20 +13324,51 @@ static CharPtr FindStateMatch (CharPtr search, CharPtr PNTR country, Int4Ptr sta
   }
 
   for (i = 0; country_state_list[i].state_list != NULL; i++) {    
-    state_match = FindBestStringMatch (country_state_list[i].state_list, search, &match_len, NULL);
-    if (state_match != NULL && (best_match == NULL || match_len > best_len)) {
-      *country = country_state_list[i].country_name;
-      best_len = match_len;
-      best_match = state_match;
+    state_matches = FindBestStringMatch (country_state_list[i].state_list, search, NULL);
+    if (state_matches != NULL) {
+      if (state_matches->next == NULL && best_match == NULL) {
+        best_match = state_matches->data.ptrvalue;
+        *country = country_state_list[i].country_name;
+      } else {
+        *pMulti = TRUE;
+        return NULL;
+      }
+      state_matches = ValNodeFree (state_matches);
     }
   }
   if (best_match != NULL && state_len != NULL) {
-    *state_len = best_len;
+    *state_len = StringLen (best_match);
   }
   return best_match;
 }
 
 
+static CharPtr FindStateMatchForCountry (CharPtr search, CharPtr country, BoolPtr pMulti)
+{
+  ValNodePtr state_matches;
+  CharPtr state_match = NULL;
+  Int4    i;
+
+  if (StringHasNoText (search) || StringHasNoText (country)) return NULL;
+
+  for (i = 0; country_state_list[i].state_list != NULL; i++) {    
+    if (StringCmp (country, country_state_list[i].country_name) == 0) {
+      state_matches = FindBestStringMatch (country_state_list[i].state_list, search, NULL);
+      if (state_matches != NULL) {
+        if (state_matches->next == NULL) {
+          state_match = state_matches->data.ptrvalue;
+        } else {
+          *pMulti = TRUE;
+        }
+        state_matches = ValNodeFree (state_matches);
+        return state_match;
+      }
+    }
+  }
+  return NULL;
+}
+
+
 static void FixCountryStringForStateName (CharPtr PNTR pCountry, CharPtr state_name, CharPtr country_name)
 {
   CharPtr cp;
@@ -12164,19 +13438,35 @@ static void FixCountryStringForStateName (CharPtr PNTR pCountry, CharPtr state_n
 }
 
 
+static CharPtr FindCountryMatch (CharPtr search_str, CharPtr PNTR country_list, BoolPtr isMulti)
+{
+  ValNodePtr match_list;
+  CharPtr best_match = NULL;
+
+  if (StringSearch (search_str, "Yugoslavia")) {
+    *isMulti = TRUE;
+    return NULL;
+  }
+
+  match_list = FindBestStringMatch (country_list, search_str, country_state_list);
+  if (match_list != NULL) {
+    if (match_list->next == NULL) {
+      best_match = match_list->data.ptrvalue;
+    } else {
+      *isMulti = TRUE;
+    }
+    match_list = ValNodeFree (match_list);
+  }
+  return best_match;
+}
+
+
 static ReplacePairData country_name_fixes[] = {
  {"Vietnam", "Viet Nam"},
  {"Ivory Coast", "Cote d'Ivoire"},
- {"UK", "United Kingdom"},
  {"United States of America", "USA"},
- {"United States", "USA"},
  {"U.S.A.", "USA"},
  {"The Netherlands", "Netherlands"},
- {"New Guinea", "Papua New Guinea"},
- {"British Guiana", "Guyana"},
- {"Aleutian Island", "Aleutian Islands"},
- {"Aleutian Is.", "Aleutian Islands"},
- {"Washington, D.C.", "Washington, DC"},
  {NULL, NULL}
 };
 
@@ -12192,13 +13482,14 @@ static void FixCountryNames (CharPtr PNTR pCountry)
   fix = country_name_fixes;
   while (fix->find != NULL) 
   {
-    if (StringStr (*pCountry, fix->replace) == NULL) {
+    if (StringStr (*pCountry, fix->replace) == NULL || StringSearch (fix->find, fix->replace) != NULL) {
       FindReplaceString (pCountry, fix->find, fix->replace, FALSE, TRUE);
     }
     fix++;
   }
 }
 
+
 static ReplacePairData us_state_abbrev_fixes[] = {
  {"AL", "Alabama"},
  {"AK", "Alaska"},
@@ -12226,7 +13517,7 @@ static ReplacePairData us_state_abbrev_fixes[] = {
  {"MS", "Mississippi"},
  {"MO", "Missouri"},
  {"MT", "Montana"},
- {"NB", "Nebraska"},
+ {"NE", "Nebraska"},
  {"NV", "Nevada"},
  {"NH", "New Hampshire"},
  {"NJ", "New Jersey"},
@@ -12253,6 +13544,23 @@ static ReplacePairData us_state_abbrev_fixes[] = {
  {NULL, NULL}
 };
 
+
+NLM_EXTERN CharPtr GetStateAbbreviation (CharPtr state)
+{
+  ReplacePairPtr fix;
+  CharPtr        abbrev = NULL;
+
+  fix = us_state_abbrev_fixes;
+  while (fix->find != NULL && abbrev == NULL) {
+    if (StringICmp (fix->replace, state) == 0) {
+      abbrev = fix->find;
+    } 
+    fix++;
+  }
+  return abbrev;
+}
+
+
 static void FixUSStateAbbreviations (CharPtr PNTR pCountry)
 {
   ReplacePairPtr fix;
@@ -12421,49 +13729,79 @@ static void FixForNamedRegions (CharPtr PNTR pCountry)
 
 static void FindCountryName (CharPtr PNTR pCountry, CharPtr PNTR country_list)
 {
-  CharPtr       best_match, state_match, state_country = NULL;
+  CharPtr       best_match = NULL, state_match, state_country = NULL;
   CharPtr       cp, before, newname, after;
   Int4          len_cntry = 0, len_state = 0, len_qual, len_name;
+  Boolean       state_multi = FALSE, country_multi = FALSE;
 
   if (pCountry == NULL || StringHasNoText (*pCountry))
   {
     return;
   }
   
-  state_match = FindStateMatch (*pCountry, &state_country, &len_state);
+  best_match = FindCountryMatch (*pCountry, country_list, &country_multi);
+  if (country_multi) {
+    *pCountry = MemFree (*pCountry);
+    return;
+  }
+  state_match = FindStateMatch (*pCountry, &state_country, &len_state, &state_multi);
 
-  best_match = FindBestStringMatch (country_list, *pCountry, &len_cntry, country_state_list);
+  if ((best_match == NULL && state_match == NULL) || (best_match == NULL && state_multi)) {
+    *pCountry = MemFree (*pCountry);
+    return;
+  } else if (best_match != NULL && state_match != NULL && StringCmp (best_match, state_country) != 0) {
+    state_match = NULL;
+  }
 
   /* if match could be a country or a state, treat it as a country */
   if (StringCmp (best_match, state_match) == 0) {
     state_match = NULL;
   }
 
-  if (StringStr (state_match, best_match) != NULL)
+  if (IsBodyOfWater (best_match) && state_match != NULL)
   {
-    /* if we found the country in the state, use the state (i.e., Jersey vs. New Jersey)*/
+    /* prefer state to body of water */
     best_match = NULL;
   }
 
   /* if we have a country and a state, but the state is for a different country, drop the state */
   if (state_match != NULL && best_match != NULL && StringNCmp (state_country, best_match, len_cntry) != 0)
   {
-    state_match = NULL;
+    state_multi = FALSE;
+    state_match = FindStateMatchForCountry (*pCountry, best_match, &state_multi);
+    if (state_multi) {
+      *pCountry = MemFree (*pCountry);
+      return;
+    }
   }
 
-  if (best_match != NULL && StringNCmp (best_match, "USA", 3) == 0 && state_match == NULL) 
+  if (best_match != NULL && StringCmp (best_match, "USA") == 0 && StringLen (*pCountry) > 3 && state_match == NULL) 
   {
     FixUSStateAbbreviations (pCountry);
-    FindReplaceString (pCountry, "USA:", "", TRUE, TRUE);
-    best_match = NULL;
-    state_match = FindStateMatch (*pCountry, &state_country, &len_state);
+    state_multi = FALSE;
+    state_match = FindStateMatchForCountry (*pCountry, best_match, &state_multi);
+    if (state_multi)
+    {
+      *pCountry = MemFree (*pCountry);
+      return;
+    }
+    if (state_match != NULL) {
+      FindReplaceString (pCountry, "USA:", "", TRUE, TRUE);
+      FindReplaceString (pCountry, "USA", "", TRUE, TRUE);
+      best_match = NULL;
+      state_country = "USA";
+    }
   }
   
-  if (best_match == NULL && state_match != NULL)
+  if (best_match == NULL && state_match == NULL) {
+    *pCountry = MemFree (*pCountry);
+    return;
+  }
+  else if (best_match == NULL && state_match != NULL)
   {
     FixCountryStringForStateName (pCountry, state_match, state_country);
   }
-  else if (best_match != NULL)
+  else
   { 	
   	cp = StringISearch (*pCountry, best_match);
   	len_cntry = StringLen (best_match);
@@ -12515,12 +13853,12 @@ static void FindCountryName (CharPtr PNTR pCountry, CharPtr PNTR country_list)
              || newname [len_name - 1] == ':'
              || newname [len_name - 1] == ';')
       {
-    	  newname [len_name - 1] = 0;
-   	    len_name --;
- 	  	}                        	      	
-   	  MemFree (*pCountry);
-   	  *pCountry = newname;
-  	}
+        newname [len_name - 1] = 0;
+        len_name --;
+      }                        	      	
+      MemFree (*pCountry);
+      *pCountry = newname;
+    }
   }    
 }
 
@@ -12598,17 +13936,254 @@ static void RemoveDoubleCommas (CharPtr PNTR country_str)
 }
 
 
+static Boolean ContainsMultipleCountryNames (CharPtr PNTR list, CharPtr search_str)
+{
+  CharPtr PNTR  ptr;
+  Int4          len_match;
+  CharPtr       cp;
+  Boolean       found_one = FALSE;
+  
+  if (list == NULL || search_str == NULL) return FALSE;
+  
+  for (ptr = list; ptr != NULL && *ptr != NULL; ptr++)
+  {
+    cp = StringISearch (search_str, *ptr);
+    len_match = StringLen (*ptr);
+    while (cp != NULL) {
+      /* if character after match is alpha, continue */
+      if (isalpha ((Int4)(cp [len_match]))
+          /* if character before match is alpha, continue */
+          || (cp > search_str && isalpha ((Int4)(*(cp - 1))))
+        /* if is shorter match for other item, continue */
+        || IsSubstringOfStringInList (search_str, cp, *ptr, list)) {
+        cp = StringSearch (cp + len_match, *ptr);
+      } else if (found_one) {
+        return TRUE;
+      } else {
+        found_one = TRUE;
+        cp = StringSearch (cp + len_match, *ptr);
+      }
+    }
+  }
+  return FALSE;
+}
+
+
+static CharPtr NewFixCountry (CharPtr country, CharPtr PNTR country_list)
+{
+  CharPtr cp, next_sep, start_after;
+  CharPtr valid_country = NULL, new_country = NULL, tmp;
+  Char    ch;
+  CharPtr separator_list = ",:";
+  Boolean too_many_countries = FALSE;
+  Int4    len_country, len_before, len_after, len_diff;
+  ReplacePairPtr fix;
+  Boolean fix_found;
+
+  country = StringSave (country);
+  cp = country;
+  while (*cp != 0 && !too_many_countries) {
+    next_sep = cp + StringCSpn (cp, separator_list);
+    ch = *next_sep;
+    *next_sep = 0;
+    
+    if (CountryIsValid (cp, NULL)) {
+      if (valid_country == NULL) {
+        valid_country = cp;
+      } else {
+        too_many_countries = TRUE;
+      }
+    } else {
+      /* see if this is a fixable country */
+      fix = country_name_fixes;
+      fix_found = FALSE;
+      while (fix->find != NULL && !fix_found) {
+        if (StringCmp (fix->find, cp) == 0) {
+          fix_found = TRUE;
+          if (valid_country == NULL) {
+            len_before = cp - country;
+            if (ch == 0) {
+              len_after = 0;
+            } else {
+              len_after = StringLen (next_sep + 1) + 1;
+            }
+            len_diff = StringLen (fix->replace) - StringLen (fix->find);
+            len_country = StringLen (country) + len_diff + len_after + 1;       
+            tmp = (CharPtr) MemNew (sizeof (Char) * len_country);
+            if (len_before > 0) {
+              StringNCpy (tmp, country, len_before);
+            }
+            StringCpy (tmp + len_before, fix->replace);
+            if (len_after > 0) {
+              StringCpy (tmp + len_before + StringLen (fix->replace) + 1, next_sep + 1);
+            }
+            cp = tmp + len_before;
+            valid_country = cp;
+            next_sep = tmp + (next_sep - country) + len_diff;
+            country = MemFree (country);
+            country = tmp;
+          } else {
+            too_many_countries = TRUE;
+          }
+        }
+        fix++;
+      }
+    }
+
+    *next_sep = ch;
+    if (*next_sep == 0) {
+      cp = next_sep;
+    } else {
+      cp = next_sep + 1;
+      while (isspace (*cp)) {
+        cp++;
+      }
+    }
+  }
+  if (valid_country != NULL && !too_many_countries) {
+    too_many_countries = ContainsMultipleCountryNames (country_list, country);
+  }
+
+  if (valid_country != NULL && !too_many_countries) {
+    len_country = StringCSpn (valid_country, separator_list);
+    len_before = valid_country - country;
+
+    while (len_before > 0 
+           && (isspace (country [len_before - 1]) 
+               || StringChr (separator_list, country [len_before - 1]) != NULL)) {
+      len_before--;
+    }
+    start_after = valid_country + len_country;
+    while (*start_after != 0 
+           && (isspace (*start_after)
+               || StringChr (separator_list, *start_after) != NULL)) {
+      start_after++;
+    }
+
+    len_after = StringLen (start_after);
+
+    new_country = MemNew (sizeof (Char) * (len_country + len_before + len_after + 5));
+    
+    StringNCpy (new_country, valid_country, len_country);
+    if (len_before > 0 || len_after > 0) {
+      StringCat (new_country, ": ");
+      if (len_before > 0) {
+        StringNCat (new_country, country, len_before);
+        if (len_after > 0) {
+          StringCat (new_country, ", ");
+        }
+      }
+      if (len_after > 0) {
+        StringCat (new_country, start_after);
+      }
+    }
+  }
+  country = MemFree (country);
+  return new_country;
+}
+
+
 extern CharPtr GetCountryFix (CharPtr country, CharPtr PNTR country_list)
 {
   CharPtr new_country;
 
   if (StringHasNoText (country)) return NULL;
+#if 1
+  new_country = NewFixCountry (country, country_list);
+#else
   new_country = StringSave (country);
   FixCountryNames (&new_country);  	
   FindCountryName (&new_country, country_list);
   CountryColonToComma (&new_country);
   RemoveDoubleCommas (&new_country);
   FixForNamedRegions (&new_country);
+#endif
   return new_country;
 }
 
+
+extern ValNodePtr ListFeaturesInLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice)
+{
+  ValNodePtr        feat_list = NULL;
+  SeqMgrFeatContext fcontext;
+  SeqFeatPtr        sfp;
+  Int4              loc_left, loc_right, tmp;
+
+  if (bsp == NULL || slp == NULL) return NULL;
+
+  loc_left = SeqLocStart (slp);
+  loc_right = SeqLocStop (slp);
+  if (loc_left > loc_right) {
+    tmp = loc_left;
+    loc_left = loc_right;
+    loc_right = tmp;
+  }
+  for (sfp = SeqMgrGetNextFeature (bsp, NULL, seqfeatChoice, featdefChoice, &fcontext);
+       sfp != NULL && fcontext.left <= loc_right;
+       sfp = SeqMgrGetNextFeature (bsp, sfp, seqfeatChoice, featdefChoice, &fcontext))
+  {
+    if (fcontext.right < loc_left) continue;
+    if (SeqLocCompare (sfp->location, slp) == SLC_A_IN_B)
+    {
+      ValNodeAddPointer (&feat_list, OBJ_SEQFEAT, sfp);
+    }
+  }
+  return feat_list;
+}
+
+
+extern ValNodePtr ListFeaturesOverlappingLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice)
+{
+  ValNodePtr        feat_list = NULL;
+  SeqMgrFeatContext fcontext;
+  SeqFeatPtr        sfp;
+  Int4              loc_left, loc_right, tmp;
+  Int4              cmp;
+
+  if (bsp == NULL || slp == NULL) return NULL;
+
+  loc_left = SeqLocStart (slp);
+  loc_right = SeqLocStop (slp);
+  if (loc_left > loc_right) {
+    tmp = loc_left;
+    loc_left = loc_right;
+    loc_right = tmp;
+  }
+  for (sfp = SeqMgrGetNextFeature (bsp, NULL, seqfeatChoice, featdefChoice, &fcontext);
+       sfp != NULL && fcontext.left <= loc_right;
+       sfp = SeqMgrGetNextFeature (bsp, sfp, seqfeatChoice, featdefChoice, &fcontext))
+  {
+    cmp = SeqLocCompare (sfp->location, slp);
+    if (cmp != SLC_NO_MATCH)
+    {
+      ValNodeAddPointer (&feat_list, OBJ_SEQFEAT, sfp);
+    }
+  }
+  return feat_list;
+}
+
+
+static void CDSInSrcFeatCallback (BioseqPtr bsp, Pointer data)
+{
+  SeqMgrFeatContext fcontext;
+  SeqFeatPtr        sfp;
+
+  if (bsp == NULL || ISA_aa (bsp->mol) || data == NULL) return;
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_BIOSRC, &fcontext);
+  while (sfp != NULL)
+  {
+    ValNodeLink ((ValNodePtr PNTR) data, ListFeaturesInLocation (bsp, sfp->location, 0, FEATDEF_CDS));
+    sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_BIOSRC, &fcontext);
+  }
+}
+
+extern ValNodePtr ListCodingRegionsContainedInSourceFeatures (SeqEntryPtr sep)
+{
+  ValNodePtr feat_list = NULL;
+
+  VisitBioseqsInSep (sep, &feat_list, CDSInSrcFeatCallback);
+  return feat_list;
+}
+
+
diff --git a/api/sqnutil4.c b/api/sqnutil4.c
new file mode 100755
index 00000000..5e805abc
--- /dev/null
+++ b/api/sqnutil4.c
@@ -0,0 +1,10460 @@
+/*   sqnutil4.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  sqnutil4.c
+*
+* Author:  Colleen Bollin
+*
+* Version Creation Date:   12/27/2007
+*
+* $Revision: 1.9 $
+*
+* File Description: 
+* This file contains functions for automatically generating definition lines.
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* Date     Name        Description of modification
+* -------  ----------  -----------------------------------------------------
+*
+*
+* ==========================================================================
+*/
+#include <sqnutils.h>
+#include <ncbilang.h>
+#include <objfdef.h>
+#include <gather.h>
+#include <explore.h>
+#include <edutil.h>
+#include <salutil.h>
+#include <tofasta.h>
+#include <gbftdef.h>
+#include <gbfeat.h>
+#include <findrepl.h>
+
+/* This is a list of the modifiers that are of interest */
+/* Note that if you modify the DefLineModifiers array, */ 
+/* you should make the corresponding change to the DefLinePos enum. */
+
+ModifierItemGlobalData DefLineModifiers[] = {
+  { "Acronym"              , TRUE , ORGMOD_acronym              },
+  { "Anamorph"             , TRUE , ORGMOD_anamorph             },
+  { "Authority"            , TRUE , ORGMOD_authority            },
+  { "Bio-material"         , TRUE,  ORGMOD_bio_material         },
+  { "Biotype"              , TRUE , ORGMOD_biotype              },
+  { "Biovar"               , TRUE , ORGMOD_biovar               },
+  { "Breed"                , TRUE , ORGMOD_breed                },
+  { "Cell-line"            , FALSE, SUBSRC_cell_line            },
+  { "Cell-type"            , FALSE, SUBSRC_cell_type            },
+  { "Chemovar"             , TRUE , ORGMOD_chemovar             },
+  { "Chromosome"           , FALSE, SUBSRC_chromosome           },
+  { "Clone"                , FALSE, SUBSRC_clone                },
+  { "Clone-lib"            , FALSE, SUBSRC_clone_lib            },
+  { "Collected-by"         , FALSE, SUBSRC_collected_by         },
+  { "Collection-date"      , FALSE, SUBSRC_collection_date      },
+  { "Common"               , TRUE , ORGMOD_common               },
+  { "Country"              , FALSE, SUBSRC_country              },
+  { "Cultivar"             , TRUE , ORGMOD_cultivar             },
+  { "Culture-collection"   , TRUE , ORGMOD_culture_collection   },
+  { "Dev-stage"            , FALSE, SUBSRC_dev_stage            },
+  { "Ecotype"              , TRUE , ORGMOD_ecotype              },
+  { "Endogenous-virus-name", FALSE, SUBSRC_endogenous_virus_name},
+  { "Environmental-sample" , FALSE, SUBSRC_environmental_sample },
+  { "Forma"                , TRUE , ORGMOD_forma                },
+  { "Forma-specialis"      , TRUE , ORGMOD_forma_specialis      },
+  { "Frequency"            , FALSE, SUBSRC_frequency            },
+  { "Genotype"             , FALSE, SUBSRC_genotype             },
+  { "Germline"             , FALSE, SUBSRC_germline             },
+  { "Group"                , TRUE , ORGMOD_group                },
+  { "Haplotype"            , FALSE, SUBSRC_haplotype            },
+  { "Identified-by"        , FALSE, SUBSRC_identified_by        },
+  { "Isolate"              , TRUE , ORGMOD_isolate              },
+  { "Isolation-source"     , FALSE, SUBSRC_isolation_source     },
+  { "Lab-host"             , FALSE, SUBSRC_lab_host             },
+  { "Lat-lon"              , FALSE, SUBSRC_lat_lon              },
+  { "Map"                  , FALSE, SUBSRC_map                  },
+  { "Metagenomic"          , FALSE, SUBSRC_metagenomic          },
+  {	"Note-OrgMod"          , TRUE,  ORGMOD_other                },
+  {	"Note-SubSrc"          , FALSE, SUBSRC_other                },
+  { "Pathovar"             , TRUE , ORGMOD_pathovar             },
+  { "Plasmid-name"         , FALSE, SUBSRC_plasmid_name         },
+  { "Plastid-name"         , FALSE, SUBSRC_plastid_name         },
+  { "Pop-variant"          , FALSE, SUBSRC_pop_variant          },
+  { "Rearranged"           , FALSE, SUBSRC_rearranged           },
+  { "Segment"              , FALSE, SUBSRC_segment              },
+  { "Serogroup"            , TRUE , ORGMOD_serogroup            },
+  { "Serotype"             , TRUE , ORGMOD_serotype             },
+  { "Serovar"              , TRUE , ORGMOD_serovar              },
+  { "Sex"                  , FALSE, SUBSRC_sex                  },
+  { "Specific-host"        , TRUE , ORGMOD_nat_host             },
+  { "Specimen voucher"     , TRUE , ORGMOD_specimen_voucher     },
+  { "Strain"               , TRUE , ORGMOD_strain               },
+  { "Subclone"             , FALSE, SUBSRC_subclone             },
+  { "Subgroup"             , TRUE , ORGMOD_subgroup             },
+  { "Sub-species"          , TRUE , ORGMOD_sub_species          },
+  { "Substrain"            , TRUE , ORGMOD_substrain            },
+  { "Subtype"              , TRUE , ORGMOD_subtype              },
+  { "Synonym"              , TRUE , ORGMOD_synonym              },
+  { "Teleomorph"           , TRUE , ORGMOD_teleomorph           },
+  { "Tissue-lib"           , FALSE, SUBSRC_tissue_lib           },
+  { "Tissue-type"          , FALSE, SUBSRC_tissue_type          },
+  { "Transgenic"           , FALSE, SUBSRC_transgenic           },
+  { "Type"                 , TRUE , ORGMOD_type                 },
+  { "Variety"              , TRUE , ORGMOD_variety              }
+};
+
+#define numDefLineModifiers (sizeof (DefLineModifiers) / sizeof (ModifierItemGlobalData))
+
+NLM_EXTERN size_t NumDefLineModifiers (void)
+
+{
+  return numDefLineModifiers;
+}
+
+NLM_EXTERN CharPtr MergeValNodeStrings (ValNodePtr list, Boolean useReturn)
+
+{
+  size_t      len;
+  CharPtr     ptr;
+  CharPtr     str;
+  CharPtr     tmp;
+  ValNodePtr  vnp;
+
+
+  ptr = NULL;
+  if (list != NULL) {
+    vnp = list;
+    len = 0;
+    while (vnp != NULL) {
+      if (vnp->data.ptrvalue != NULL) {
+        len += StringLen ((CharPtr) vnp->data.ptrvalue) + 1;
+      }
+      vnp = vnp->next;
+    }
+    if (len > 0) {
+      ptr = MemNew (sizeof (Char) * (len + 2));
+      if (ptr != NULL) {
+        vnp = list;
+        tmp = NULL;
+        while (vnp != NULL) {
+          str = (CharPtr) vnp->data.ptrvalue;
+          if (str != NULL) {
+            if (tmp == NULL) {
+              tmp = ptr;
+            } else if (useReturn) {
+              tmp = StringMove (tmp, "\n");
+            } else if (IsJapanese () && (tmp - ptr > 2) &&
+            		IsMBLetter (tmp - 2) && IsMBLetter (str)) {
+              /* no space required between two Japanese letters. */
+              tmp = tmp;
+            } else if (str [0] != ',' && str [0] != ';' && str [0] != ':') {
+              tmp = StringMove (tmp, " ");
+            } else {
+              tmp = StringMove (tmp, " ");
+            }
+            tmp = StringMove (tmp, str);
+          }
+          vnp = vnp->next;
+        }
+      }
+    }
+  }
+  return ptr;
+}
+
+
+/* The matchFunction functions are used to identify features that meet
+ * specific requirements, usually that the feature is of a particular type.
+ * This function is used instead of simply using the subtype for the feature
+ * because some features are identified based on the contents or presence of
+ * certain modifiers.
+ * Functions of this type should always return FALSE if handed a NULL argument.
+ */
+typedef Boolean (LIBCALLBACK *matchFunction) (
+  SeqFeatPtr sfp
+);
+
+static void ListClauses (
+  ValNodePtr clauselist,
+  ValNodePtr PNTR strings,
+  Boolean    allow_semicolons,
+  Boolean    suppress_final_and
+);
+
+static void LabelClauses 
+( ValNodePtr clause_list,
+  Uint1      biomol,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp);
+
+static CharPtr GetProductName 
+( SeqFeatPtr cds,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp);
+
+#define DEFLINE_FEATLIST    1
+#define DEFLINE_CLAUSEPLUS  2
+#define DEFLINE_REMOVEFEAT  3
+
+typedef struct featurelabeldata {
+  Boolean pluralizable;
+  Boolean is_typeword_first;
+  CharPtr typeword;
+  CharPtr description;
+  CharPtr productname;
+} FeatureLabelData, PNTR FeatureLabelPtr;
+
+
+typedef struct featureclause {
+  ValNodePtr       featlist;
+  FeatureLabelData feature_label_data;
+  CharPtr          allelename;
+  CharPtr          interval;
+  Boolean          is_alt_spliced;
+  Boolean          has_mrna;
+  SeqLocPtr        slp;
+  GeneRefPtr       grp;
+  Boolean          clause_info_only;
+  Boolean          is_unknown;
+  Boolean          make_plural;
+  Boolean          delete_me;
+  /* this information used only for segments */
+  Int2             numivals;
+  Int4Ptr          ivals;
+} FeatureClauseData, PNTR FeatureClausePtr;
+
+FeatureClausePtr NewFeatureClause (
+  SeqFeatPtr sfp,
+  BioseqPtr bsp,
+  DeflineFeatureRequestListPtr rp);
+
+static void PluralizeConsolidatedClauseDescription (
+  FeatureClausePtr fcp
+);
+
+typedef Boolean (LIBCALLBACK *ShouldRemoveFunction) (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr        bsp,
+  Boolean          isLonely,
+  Boolean          isRequested,
+  Boolean          isSegment,
+  DeflineFeatureRequestListPtr rp
+);
+
+/* This section of the code contains some functions for dealing with
+ * linked lists of strings */
+
+/* This function finds the first occurrence of "search" in one of the
+ * strings in list "strings".
+ * "search" could be part of the string or could be the entire string.
+ */
+static ValNodePtr FindStringInStrings (
+  ValNodePtr strings,
+  CharPtr search
+)
+{
+  while (strings != NULL)
+  {
+    if (StringStr (strings->data.ptrvalue, search))
+    {
+      return strings;
+    }
+    strings = strings->next;
+  }
+  return NULL;
+}
+
+/* This function finds the first item in "strings" that is identical to
+ * "value".
+ */
+extern ValNodePtr FindExactStringInStrings (
+  ValNodePtr strings,
+  CharPtr    value
+)
+{
+  ValNodePtr    string_match;
+
+  for (string_match = FindStringInStrings (strings, value);
+       string_match != NULL
+         && StringCmp (string_match->data.ptrvalue, value) != 0;
+       string_match = FindStringInStrings (string_match->next, value))
+  {}
+  return string_match;
+}
+
+/* This function creates a new linked list of strings with copies of
+ * contents of orig.
+ */
+static ValNodePtr CopyStrings (
+  ValNodePtr orig
+)
+{
+  ValNodePtr new_string_start = NULL;
+
+  while (orig != NULL)
+  {
+    ValNodeAddStr (&new_string_start, 0,
+      StringSave (orig->data.ptrvalue));
+    orig = orig->next;
+  }
+  return new_string_start;
+}
+
+/*
+ * This section of the code contains functions and structures for obtaining a
+ * description of the organism in the record, including functions for finding
+ * the combination of modifiers that will make each organism description 
+ * unique.
+ * The method used for determining the best combination of modifiers involves
+ * creating a list of required modifiers, and then creating a list of
+ * combinations of modifiers by adding modifiers one at a time
+ * to see if the additional modifiers provide any more differentiation in
+ * the list.
+ * In order to do this, I start with a list of required modifiers, and 
+ * then create copies of this list.  For each copy I add one of the modifiers
+ * that are present in the bio sources and not already on the list.
+ * If adding the modifier increases the differentiation, I add that copy to
+ * the list of possible combinations, otherwise I discard it.
+ * I then make copies of all of the new items I added to the list and
+ * add another modifier to each list, keeping the combinations that increase
+ * the differentiation and discarding the rest.
+ * This process continues until I have a combination that produces completely
+ * differentiated bio sources, or I run out of possible combinations.
+ * If I run out of possible combinations, I select the best combination from
+ * the list.
+ * This search process occurs in FindBestCombo.  The majority of the functions
+ * in this section are here to support FindBestCombo, specifically to create,
+ * copy, and grow lists of combinations. 
+ */
+
+/* BioSrcDescData is used to calculate the best possible combination of
+ * source and organism modifiers for uniqueness.
+ * biop contains the BioSourcePtr from a sequence in the record.
+ * strings contains a list of string representations of the modifiers
+ * for this combination for this organism.
+ */
+typedef struct biosrcdescdata {
+  BioSourcePtr  biop;
+  ValNodePtr    strings;
+  Pointer       next;
+} BioSrcDescData, PNTR BioSrcDescPtr;
+
+/* OrgGroupData is used to calculate the best possible combination of
+ * source and organism modifiers for uniqueness.
+ * org_list is a list of all organisms that have identical descriptions
+ * using the current set of modifiers.
+ * num_organisms contains the number of organisms with identical descriptions.
+ */
+typedef struct orggroupdata {
+  BioSrcDescPtr org_list;
+  Int4          num_organisms;
+  Pointer       next;
+} OrgGroupData, PNTR OrgGroupPtr;
+
+/* ModifierCombinationData is used to calculate the best possible combination
+ * of source and organism modifiers for uniqueness.
+ * num_groups is the number of groups of organisms with identical descriptions
+ *           using the modifiers specified in modifier_indices.
+ * num_mods is the number of modifiers specified in modifier_indices.
+ * max_orgs_in_group is the maximum number of organisms in any one group.
+ * num_unique_orgs is the number of organisms that are alone in their groups
+ *           i.e., their description is unique.
+ * modifier_indices is the list of modifier indices for this combination.
+ * group_list is the list of groups of organisms with identical descriptions
+ *           using the modifiers specified in modifier_indices.
+ */
+typedef struct modifiercombination {
+  Int4         num_groups;
+  Int4         num_mods;
+  Int4         max_orgs_in_group;
+  Int4         num_unique_orgs;
+  ValNodePtr   modifier_indices;
+  OrgGroupPtr  group_list;
+  Pointer      next;
+} ModifierCombinationData, PNTR ModifierCombinationPtr;
+
+static Boolean IsDeflineModifierRequiredByDefault (Boolean is_orgmod, Int2 index)
+{
+  if (!is_orgmod
+      && (index == SUBSRC_endogenous_virus_name
+          || index == SUBSRC_plasmid_name
+          || index == SUBSRC_transgenic)) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+
+static void AddOneSubtypeField (ValNodePtr PNTR sq_list, SourceQualDescPtr orig, CharPtr str, Uint1 subfield)
+{
+  SourceQualDescPtr sqdp_cpy;
+
+  if (sq_list == NULL || orig == NULL) {
+    return;
+  }
+  sqdp_cpy = (SourceQualDescPtr) MemNew (sizeof (SourceQualDescData));
+  MemCpy (sqdp_cpy, orig, sizeof (SourceQualDescData));
+
+  sqdp_cpy->name = str;
+  sqdp_cpy->subfield = subfield;
+
+  ValNodeAddPointer (sq_list, 0, sqdp_cpy);  
+}
+
+
+static void AddSubtypeFields (ValNodePtr PNTR sq_list, SourceQualDescPtr orig)
+{
+  if (sq_list == NULL || orig == NULL) return;
+
+  if (orig->isOrgMod) {
+    switch (orig->subtype) {
+      case ORGMOD_specimen_voucher:
+        AddOneSubtypeField (sq_list, orig, "specimen-voucher INST", 1);
+        AddOneSubtypeField (sq_list, orig, "specimen-voucher COLL", 2);
+        AddOneSubtypeField (sq_list, orig, "specimen-voucher SpecID", 3);
+        break;  
+      case ORGMOD_culture_collection:
+        AddOneSubtypeField (sq_list, orig, "culture-collection INST", 1);
+        AddOneSubtypeField (sq_list, orig, "culture-collection COLL", 2);
+        AddOneSubtypeField (sq_list, orig, "culture-collection SpecID", 3);
+        break;  
+      case ORGMOD_bio_material:
+        AddOneSubtypeField (sq_list, orig, "bio-material INST", 1);
+        AddOneSubtypeField (sq_list, orig, "bio-material COLL", 2);
+        AddOneSubtypeField (sq_list, orig, "bio-material SpecID", 3);
+        break; 
+    }
+  } 
+}
+
+
+static void AddQualList (ValNodePtr PNTR list, Nlm_QualNameAssocPtr qual_list, Boolean is_orgmod, Boolean use_alternate_note_name)
+{
+  Int4              k;
+  SourceQualDescPtr sqdp;
+  
+  for (k = 0; qual_list[k].name != NULL; k++) {
+    if (StringHasNoText (qual_list[k].name)) {
+      continue;
+    } 
+    sqdp = (SourceQualDescPtr) MemNew (sizeof (SourceQualDescData));
+    if (sqdp != NULL)
+    {
+      if (use_alternate_note_name 
+          && ((is_orgmod && qual_list[k].value == ORGMOD_other)
+              || (!is_orgmod && qual_list[k].value == SUBSRC_other))) 
+      {
+        if (is_orgmod) {
+          sqdp->name = "Note -- OrgMod";
+        } else {
+          sqdp->name = "Note -- SubSource";
+        }
+      } else {
+        sqdp->name = qual_list[k].name;
+      }
+      sqdp->isOrgMod = is_orgmod;
+      sqdp->subtype = qual_list[k].value;
+      sqdp->subfield = 0;
+      ValNodeAddPointer (list, 0, sqdp);
+    }
+    AddSubtypeFields (list, sqdp);
+  }
+}
+
+
+static void AddNoteQual (ValNodePtr PNTR list, Boolean is_orgmod, Boolean use_alternate_note_name)
+{
+  SourceQualDescPtr sqdp;
+
+  if (list == NULL) return;
+
+  sqdp = (SourceQualDescPtr) MemNew (sizeof (SourceQualDescData));
+  if (sqdp != NULL)
+  {
+    if (use_alternate_note_name) 
+    {
+      if (is_orgmod) {
+        sqdp->name = "Note -- OrgMod";
+      } else {
+        sqdp->name = "Note -- SubSource";
+      }
+    } else {
+      sqdp->name = "Note";
+    }
+    sqdp->isOrgMod = is_orgmod;
+    if (is_orgmod) {
+      sqdp->subtype = ORGMOD_other;
+    } else {
+      sqdp->subtype = SUBSRC_other;
+    }
+    sqdp->subfield = 0;
+    ValNodeAddPointer (list, 0, sqdp);
+  }
+}
+
+
+static int LIBCALLBACK SortVnpBySourceQualDesc (VoidPtr ptr1, VoidPtr ptr2)
+
+{
+  SourceQualDescPtr     str1;
+  SourceQualDescPtr     str2;
+  ValNodePtr  vnp1;
+  ValNodePtr  vnp2;
+
+  if (ptr1 != NULL && ptr2 != NULL) {
+    vnp1 = *((ValNodePtr PNTR) ptr1);
+    vnp2 = *((ValNodePtr PNTR) ptr2);
+    if (vnp1 != NULL && vnp2 != NULL) {
+      str1 = (SourceQualDescPtr) vnp1->data.ptrvalue;
+      str2 = (SourceQualDescPtr) vnp2->data.ptrvalue;
+      if (str1 != NULL && str2 != NULL
+          && str1->name != NULL && str2->name != NULL) {
+        return StringICmp (str1->name, str2->name);
+      }
+    }
+  }
+  return 0;
+}
+
+
+extern ValNodePtr GetSourceQualDescList (Boolean get_subsrc, Boolean get_orgmod, Boolean get_discouraged, Boolean get_discontinued)
+{
+  ValNodePtr        source_qual_list = NULL;
+
+  if (get_orgmod) {
+    AddQualList (&source_qual_list, current_orgmod_subtype_alist, TRUE, get_subsrc);
+    if (get_discouraged) {
+      AddQualList (&source_qual_list, discouraged_orgmod_subtype_alist, TRUE, get_subsrc);
+    }
+    if (get_discontinued) {
+      AddQualList (&source_qual_list, discontinued_orgmod_subtype_alist, TRUE, get_subsrc);
+    }
+    AddNoteQual (&source_qual_list, TRUE, get_subsrc);
+  }
+  if (get_subsrc) {
+    AddQualList (&source_qual_list, current_subsource_subtype_alist, FALSE, get_orgmod);
+    if (get_discouraged) {
+      AddQualList (&source_qual_list, discouraged_subsource_subtype_alist, FALSE, get_orgmod);
+    }
+    if (get_discontinued) {
+      AddQualList (&source_qual_list, discontinued_subsource_subtype_alist, FALSE, get_orgmod);
+    }
+    AddNoteQual (&source_qual_list, FALSE, get_orgmod);
+  }
+
+  source_qual_list = ValNodeSort (source_qual_list, SortVnpBySourceQualDesc);
+  return source_qual_list;
+}
+
+/*
+ * The CountModifiersProc is used as the callback function for
+ * VisitBioSourcesInSep when we are getting a list of all the modifiers
+ * that appear in the sources.  We also obtain, for each modifier class,
+ * the first value seen, whether or not each value seen is unique for
+ * for the modifier, and whether or not the modifier is present for all
+ * sources.
+ */
+static void CountModifiersProc (
+  BioSourcePtr biop,
+  Pointer userdata
+)
+{
+  ModifierItemLocalPtr ItemList;
+  OrgModPtr     mod;
+  SubSourcePtr  ssp;
+  Int2 i;
+  Boolean       found_this_modifier;
+
+  if (biop == NULL) return;
+  ItemList = (ModifierItemLocalPtr) userdata;
+
+  for (i=0; i < numDefLineModifiers; i++)
+  {
+    found_this_modifier = FALSE;
+    if (DefLineModifiers[i].isOrgMod)
+    {
+      if ( biop->org != NULL && biop->org->orgname != NULL) 
+      {
+        mod = biop->org->orgname->mod;
+        while (mod != NULL
+          && mod->subtype != DefLineModifiers[i].subtype)
+        {
+          mod = mod->next;
+        }
+        if (mod != NULL && mod->subname != NULL)
+        {
+          found_this_modifier = TRUE;
+          if (ItemList[i].first_value_seen != NULL)
+          {
+            if (StringCmp (ItemList[i].first_value_seen, mod->subname) != 0)
+            {
+              ItemList[i].is_unique = FALSE;
+            }
+          }
+          else
+          {
+            ItemList[i].first_value_seen = mod->subname;
+          }
+          if ( FindExactStringInStrings (ItemList[i].values_seen, mod->subname)
+            == NULL)
+          {
+            ValNodeAddStr (&ItemList[i].values_seen, 0, mod->subname);
+          }
+          else
+          {
+            ItemList[i].all_unique = FALSE;
+          }
+        }
+      }
+    } else {
+      ssp = biop->subtype;
+      while (ssp != NULL && ssp->subtype != DefLineModifiers[i].subtype)
+      {
+        ssp = ssp->next;
+      }
+      if (ssp != NULL && ssp->name != NULL)
+      {
+        found_this_modifier = TRUE;
+        if (ItemList[i].first_value_seen != NULL)
+        {
+          if (StringCmp (ItemList[i].first_value_seen, ssp->name) != 0)
+          {
+            ItemList[i].is_unique = FALSE;
+          }
+        }
+        else
+        {
+          ItemList[i].first_value_seen = ssp->name;
+        }
+        if ( FindExactStringInStrings (ItemList[i].values_seen, ssp->name)
+          == NULL)
+        {
+          ValNodeAddStr (&ItemList[i].values_seen, 0, ssp->name);
+        }
+        else
+        {
+          ItemList[i].all_unique = FALSE;
+        }
+      }
+    }
+    if (found_this_modifier)
+    {
+      ItemList[i].any_present = TRUE;
+    } else {
+      ItemList[i].all_present = FALSE;
+    }
+  }
+} 
+
+/* The CountModifiers function visits all of the bio sources, determining
+ * which modifiers are present, which modifiers have only one value,
+ * which modifiers have all different values, and which modifiers are
+ * present in all sources.
+ * After this survey is complete, the function prepares a short summary
+ * of the above information for each modifier, which is used in the 
+ * definition line options dialog.
+ */ 
+NLM_EXTERN void CountModifiers (
+  ModifierItemLocalPtr ItemList,
+  SeqEntryPtr sep
+)
+{
+  Int2 i;
+
+  for (i=0; i < numDefLineModifiers; i++)
+  {
+    ItemList[i].all_present = TRUE;
+    ItemList[i].is_unique = TRUE;
+    ItemList[i].first_value_seen = NULL;
+    ItemList[i].values_seen = NULL;
+    ItemList[i].all_unique = TRUE;
+  }
+
+  VisitBioSourcesInSep (sep, ItemList, CountModifiersProc);
+ 
+  for (i=0; i < numDefLineModifiers; i++)
+  {
+    if (ItemList[i].all_present && ItemList[i].all_unique)
+    {
+      ItemList[i].status = "All present, all unique";
+    }
+    else if (ItemList[i].all_present && ItemList[i].is_unique)
+    {
+      ItemList[i].status = "All present, one unique";
+    }
+    else if (ItemList[i].all_present && ! ItemList[i].is_unique)
+    {
+      ItemList[i].status = "All present, mixed";
+    }
+    else if (! ItemList[i].all_present && ItemList[i].all_unique)
+    {
+      ItemList[i].status = "Some missing, all unique";
+    }
+    else if (! ItemList[i].all_present && ItemList[i].is_unique)
+    {
+      ItemList[i].status = "Some missing, one unique";
+    }
+    else if (! ItemList[i].all_present && ! ItemList[i].is_unique)
+    {
+      ItemList[i].status = "Some missing, mixed";
+    }
+  }
+}
+
+/* The BioSrcDescData structure is used to hold a BioSourcePtr, a list
+ * of strings used to describe the biosource, including the taxonomy name
+ * and the values of all of the modifiers selected so far for this bio
+ * source, and a pointer to the next BioSrcDescData structure in the list.
+ */
+
+/* The CopyBioSrcDescPtr function creates a copy of the linked list of
+ * BioSrcDescData structures.
+ */
+static BioSrcDescPtr CopyBioSrcDescPtr (
+  BioSrcDescPtr orig
+)
+{
+  BioSrcDescPtr new_bsdp_start;
+
+  if (orig == NULL) return NULL;
+
+  new_bsdp_start = (BioSrcDescPtr) MemNew (sizeof (BioSrcDescData));
+  if (new_bsdp_start == NULL) return NULL;
+
+  new_bsdp_start->biop = orig->biop;
+  new_bsdp_start->strings = CopyStrings (orig->strings);
+  new_bsdp_start->next = CopyBioSrcDescPtr (orig->next);
+  return new_bsdp_start;
+}
+
+/* The FreeBioSrcDescPtr function frees the memory associated with a
+ * linked list of BioSrcDescData structures.
+ */
+static void FreeBioSrcDescPtr (
+  BioSrcDescPtr bsdp
+)
+{
+  if (bsdp == NULL) return;
+  FreeBioSrcDescPtr (bsdp->next);
+  bsdp->biop = NULL;
+  ValNodeFreeData (bsdp->strings);
+  MemFree (bsdp);
+}
+
+/* The AddQualToBioSrcDescPtr function finds the qualifier at the
+ * feature_index position in the DefLineModifiers array in the
+ * BioSourcePtr and adds the value for that modifier to the array
+ * of strings describing the bio source.
+ */
+static void AddQualToBioSrcDescPtr (
+  BioSrcDescPtr bsdp,
+  ModifierItemLocalPtr qual,
+  Int2 feature_index
+)
+{
+  OrgModPtr          mod;
+  SubSourcePtr       ssp;
+  CharPtr            tmp;
+
+  if (bsdp == NULL) return;
+  if (bsdp->biop == NULL) return;
+
+  if (DefLineModifiers[feature_index].isOrgMod)
+  {
+    if (bsdp->biop->org == NULL || bsdp->biop->org->orgname == NULL) return;
+    mod = bsdp->biop->org->orgname->mod;
+    while (mod != NULL
+        && mod->subtype != DefLineModifiers[feature_index].subtype)
+    {
+      mod = mod->next;
+    }
+    if (mod != NULL && mod->subname != NULL)
+    {
+      if (mod->subtype == ORGMOD_specimen_voucher && StringNICmp (mod->subname, "personal:", 9) == 0)
+      {
+        tmp = mod->subname + 9;
+        while (isspace (*tmp)) 
+        {
+          tmp++;
+        }
+      }
+      else
+      {
+        tmp = mod->subname;
+      }
+      ValNodeCopyStr( &(bsdp->strings), 0, tmp);
+    } 
+  } else {
+    ssp = bsdp->biop->subtype;
+    while (ssp != NULL
+        && ssp->subtype != DefLineModifiers[feature_index].subtype)
+    {
+      ssp = ssp->next;
+    }
+    if (ssp != NULL)
+    {
+      if (ssp->subtype == SUBSRC_transgenic)
+      {
+        ValNodeCopyStr( &(bsdp->strings), 0, "transgenic");
+      }
+      else if (ssp->name != NULL)
+      {
+        ValNodeCopyStr( &(bsdp->strings), 0, ssp->name);
+      }
+    }
+  }
+}
+ 
+/* The CompareOrganismDescriptors function compares the contents of the
+ * lists of strings for each BioSrcDesc item.
+ * The function returns:
+ *     -1 if org1 < org2
+ *      0 if org1 = org2
+ *      1 if org1 > org2
+ */
+static int CompareOrganismDescriptors (
+  BioSrcDescPtr org1,
+  BioSrcDescPtr org2
+)
+{
+  ValNodePtr vnp1, vnp2;
+  int cmpval;
+
+  vnp1 = org1->strings;
+  vnp2 = org2->strings;
+
+  while (vnp1 != NULL && vnp2 != NULL)
+  {
+    cmpval = StringCmp (vnp1->data.ptrvalue, vnp2->data.ptrvalue);
+    if (cmpval != 0) return cmpval;
+
+    vnp1 = vnp1->next;
+    vnp2 = vnp2->next;
+  }
+  if (vnp1 == NULL && vnp2 == NULL)
+  {
+    return 0;
+  }
+  else if (vnp1 != NULL && vnp2 == NULL)
+  {
+    return 1;
+  }
+  else
+  {
+    return -1;
+  }
+}
+
+/* The OrgGroupData structure contains a list of BioSrcDescData items
+ * for which the contents of the descriptive strings list are identical,
+ * i.e., all the organisms in the group would have the same description
+ * if you used the modifiers used to generate this list of strings.
+ * The structure also contains the number of organisms in the list
+ * so that it will be easy to tell that the OrgGroup now contains a
+ * single organism with a unique description.
+ */
+
+/* The CopyOrgGroupList function creates a copy of the list of OrgGroups */
+static OrgGroupPtr CopyOrgGroupList (
+  OrgGroupPtr orig
+)
+{
+  OrgGroupPtr new_ogp_start;
+
+  if (orig == NULL) return NULL;
+
+  new_ogp_start = (OrgGroupPtr) MemNew (sizeof (OrgGroupData));
+  if (new_ogp_start == NULL) return NULL;
+
+  new_ogp_start->num_organisms = orig->num_organisms;
+  new_ogp_start->org_list = CopyBioSrcDescPtr (orig->org_list);
+  new_ogp_start->next = CopyOrgGroupList (orig->next);
+  return new_ogp_start;
+}
+
+/* The FreeOrgGroupPtr function frees the memory associated with a
+ * list of OrgGroups */
+static void FreeOrgGroupPtr (
+  OrgGroupPtr ogp
+)
+{
+  if (ogp == NULL) return;
+  FreeOrgGroupPtr (ogp->next);
+  FreeBioSrcDescPtr (ogp->org_list);
+  MemFree (ogp);
+  return;
+}
+
+/* The ReorderGroupOrgs function sorts the OrgGroup list based on the results
+ * of the CompareOrganismDescriptors function.
+ */
+static void ReorderGroupOrgs (
+  OrgGroupPtr this_group
+)
+{
+  BioSrcDescPtr bsdp;
+  BioSrcDescPtr nextBsdp;
+  BioSrcDescPtr prevBsdp;
+  Boolean swap_needed = TRUE;
+
+  if (this_group->org_list == NULL) return;
+  if (this_group->org_list->next == NULL) return;
+
+  while (swap_needed)
+  {
+    swap_needed = FALSE;
+    bsdp = this_group->org_list;
+    prevBsdp = NULL;
+    while (bsdp->next != NULL)
+    {
+      nextBsdp = bsdp->next;
+      if (CompareOrganismDescriptors (bsdp, nextBsdp) > 0)
+      {
+        swap_needed = TRUE;
+        bsdp->next = nextBsdp->next;
+        nextBsdp->next = bsdp;
+        if (prevBsdp == NULL)
+        {
+          this_group->org_list = nextBsdp;
+        }
+        else
+        {
+          prevBsdp->next = nextBsdp;
+        }
+        prevBsdp = nextBsdp;
+      }
+      else
+      {
+        prevBsdp = bsdp;
+        bsdp = bsdp->next;
+      }
+    }
+  }
+}
+
+/* The ReGroupOrgs function operates on a single OrgGroup item.
+ * If any of the BioSrcDesc items in the group now have different
+ * descriptions, the function breaks it up into smaller, homogenous OrgGroups.
+ */
+static void ReGroupOrgs (
+  OrgGroupPtr this_group
+)
+{
+  BioSrcDescPtr bsdp;
+  OrgGroupPtr new_group;
+  int num_organisms;
+
+  if (this_group == NULL) return;
+  bsdp = this_group->org_list;
+  if (bsdp == NULL) return;
+  num_organisms = 0;
+  while (bsdp->next != NULL)
+  {
+    num_organisms ++;
+    if (CompareOrganismDescriptors (bsdp, bsdp->next) != 0)
+    {
+      /* create new group to hold next set of organisms */
+      new_group = (OrgGroupPtr) MemNew (sizeof (OrgGroupData));
+      if (new_group == NULL) return;
+      new_group->org_list = bsdp->next;
+      new_group->num_organisms = this_group->num_organisms - num_organisms;
+      new_group->next = this_group->next;
+      this_group->next = new_group;
+      this_group->num_organisms = num_organisms;
+      bsdp->next = NULL;
+      ReGroupOrgs (new_group);
+    }
+    else
+    {
+      bsdp = bsdp->next;
+    }
+  }
+}
+
+/* The AddQualToGroup function operates on a single OrgGroup item.
+ * The function adds a qualifier to each BioSrcDesc item in the OrgGroup,
+ * breaks the group into multiple groups if the group is no longer
+ * homogenous, and sorts the new list.
+ */
+static void AddQualToGroup (
+  OrgGroupPtr this_group,
+  ModifierItemLocalPtr qual,
+  Int2 feature_index
+)
+{
+  BioSrcDescPtr bsdp;
+
+  if (this_group == NULL) return;
+
+  bsdp = this_group->org_list;
+  while (bsdp != NULL)
+  {
+    AddQualToBioSrcDescPtr (bsdp, qual, feature_index);
+    bsdp= bsdp->next;
+  }
+
+  /* now reorder organisms and break up group */
+  ReorderGroupOrgs (this_group);
+
+  ReGroupOrgs (this_group);
+}
+
+/* The AddQualToGroupList function operates on a list of OrgGroup items.
+ * It calls AddQualToGroup for each item in the list.
+ */
+static void AddQualToGroupList (
+  OrgGroupPtr group_list,
+  ModifierItemLocalPtr qual,
+  Int2 feature_index
+)
+{
+  OrgGroupPtr ogp;
+
+  ogp = group_list;
+  while (ogp != NULL)
+  {
+    AddQualToGroup (ogp, qual, feature_index);
+    ogp = ogp->next;
+  }
+}
+
+/* The CopyModifierIndices function creates a new ValNode list with the
+ * same data.intvalue values for each node as the original modifier_indices
+ * ValNode list.
+ */
+static ValNodePtr CopyModifierIndices (
+  ValNodePtr modifier_indices
+)
+{
+  ValNodePtr new_indices;
+
+  if (modifier_indices == NULL) return NULL;
+  new_indices = ValNodeNew (NULL);
+  if (new_indices == NULL) return NULL;
+  new_indices->choice = modifier_indices->choice;
+  new_indices->data.intvalue = modifier_indices->data.intvalue;
+  new_indices->next = CopyModifierIndices (modifier_indices->next);
+  return new_indices;
+}
+ 
+/* The CopyModifierCombo creates a copy of a ModificationCombination item.
+ * This includes creating a copy of the number and list of modifiers
+ * and a copy of the number and list of OrgGroups, as well as copying the
+ * maximum number of organisms in any one group and the number of unique
+ * organism descriptions produced by this combination of modifiers.
+ */
+static ModifierCombinationPtr CopyModifierCombo (
+  ModifierCombinationPtr m
+)
+{
+  ModifierCombinationPtr newm;
+  ValNodePtr  vnp;
+  ValNodePtr  newval;
+
+  newm = (ModifierCombinationPtr) MemNew (sizeof (ModifierCombinationData));
+  if (newm == NULL) return NULL;
+
+  newm->next = NULL;
+
+  /* copy list of modifier indices */
+  newm->num_mods = m->num_mods;
+  newm->modifier_indices = NULL;
+  vnp = m->modifier_indices;
+  if (vnp != NULL)
+  {
+    newm->modifier_indices = ValNodeNew (NULL);
+    if (newm->modifier_indices == NULL) return NULL;
+    newm->modifier_indices->data.intvalue = vnp->data.intvalue;
+    vnp = vnp->next;
+    while (vnp != NULL)
+    {
+      newval = ValNodeNew (newm->modifier_indices);
+      if (newval == NULL) return NULL;
+      newval->data.intvalue = vnp->data.intvalue;
+      vnp = vnp->next;
+    }
+  }
+  
+  /* copy groups */
+  newm->num_groups = m->num_groups;
+  newm->group_list = CopyOrgGroupList (m->group_list);
+ 
+  return newm; 
+}
+
+/* This function creates a new ModifierCombination item using the supplied
+ * OrgGroup list.  It calculates the number of groups, maximum number of 
+ * organisms in any one group, and number of unique organisms.
+ * Initially there are no modifiers.
+ */
+static ModifierCombinationPtr NewModifierCombo (
+  OrgGroupPtr group_list
+)
+{
+  ModifierCombinationPtr newm;
+  OrgGroupPtr  ogp;
+
+  newm = (ModifierCombinationPtr) MemNew (sizeof (ModifierCombinationData));
+  if (newm == NULL) return NULL;
+
+  newm->num_mods = 0;
+  newm->modifier_indices = NULL;
+  newm->num_unique_orgs = 0;
+  
+  /* copy groups */
+  newm->group_list = CopyOrgGroupList (group_list);
+ 
+  ogp = newm->group_list;
+  newm->max_orgs_in_group = 0;
+  newm->num_groups = 0;
+  while (ogp != NULL)
+  {
+    if (newm->max_orgs_in_group < ogp->num_organisms)
+      newm->max_orgs_in_group = ogp->num_organisms;
+    if (ogp->num_organisms == 1)
+      newm->num_unique_orgs ++;
+    newm->num_groups ++;
+    ogp = ogp->next;
+  }
+
+  newm->next = NULL;
+  return newm; 
+}
+
+/* This function frees the memory associated with a list of
+ * ModifierCombination items.
+ */
+static void FreeModifierCombo (
+  ModifierCombinationPtr m
+)
+{
+  if (m == NULL) return;
+  FreeModifierCombo (m->next);
+  ValNodeFree (m->modifier_indices);
+  FreeOrgGroupPtr (m->group_list);
+  MemFree (m);
+}
+
+/* This function adds the qualifier at the feature_index position in the
+ * DefLineModifiers array to each OrgGroup in the list and recalculates
+ * the maximum number of organisms in any one group and the number of
+ * unique organism descriptions generated by this new combination of 
+ * modifiers.
+ */
+static void AddQualToModifierCombo (
+  ModifierCombinationPtr m,
+  ModifierItemLocalPtr qual,
+  Int2 feature_index
+)
+{
+  OrgGroupPtr ogp;
+  ValNodePtr vnp;
+
+  if (m == NULL) return;
+
+  /* now try adding the modifier, see if the number of groups goes up */
+  /* if the number of organisms in each group is one, we can stop */
+  vnp = ValNodeNew (m->modifier_indices);
+  if (vnp == NULL) return;
+  if (m->modifier_indices == NULL)
+  {
+    m->modifier_indices = vnp;
+  }
+  vnp->data.intvalue = feature_index;
+  m->num_mods ++;
+  AddQualToGroupList (m->group_list, qual, feature_index);
+  ogp = m->group_list;
+  m->max_orgs_in_group = 0;
+  m->num_unique_orgs = 0;
+  m->num_groups = 0;
+  while (ogp != NULL)
+  {
+    if (m->max_orgs_in_group < ogp->num_organisms)
+      m->max_orgs_in_group = ogp->num_organisms;
+    if (ogp->num_organisms == 1)
+      m->num_unique_orgs ++;
+    m->num_groups ++;
+    ogp = ogp->next;
+  }
+}
+
+/* This function creates the initial OrgGroup list that is copied for every
+ * ModifierCombination item.
+ */
+static void BuildTaxOrgGroupList (
+  BioSourcePtr biop,
+  Pointer userdata
+)
+{
+  OrgGroupPtr   ogp;
+  OrgGroupPtr   prevOgp;
+  OrgGroupPtr PNTR pogp;
+  BioSrcDescPtr newBsdp;
+  OrgRefPtr     orp;
+  int cmpval;
+
+  pogp = (OrgGroupPtr PNTR) userdata;
+  ogp = *pogp;
+
+  newBsdp = (BioSrcDescPtr) MemNew (sizeof (BioSrcDescData));
+  if (newBsdp == NULL) return;
+  newBsdp->biop = biop;
+  newBsdp->next = NULL;
+  newBsdp->strings = NULL;
+
+  /* add tax name as first string */
+  /* later, move this into a separate function and add special handling */
+  orp = biop->org;
+  if (orp != NULL && orp->taxname != NULL)
+  {
+    ValNodeCopyStr (&(newBsdp->strings), 0, orp->taxname);
+  }
+
+  prevOgp = NULL;
+  cmpval = -1;
+  while (ogp != NULL && cmpval < 0)
+  {
+    if (ogp->org_list != NULL)
+    {
+      cmpval = CompareOrganismDescriptors (ogp->org_list, newBsdp);
+      if (cmpval == 0)
+      {
+        newBsdp->next = ogp->org_list;
+        ogp->org_list = newBsdp;
+        ogp->num_organisms ++;
+      }
+    }
+    if (cmpval < 0)
+    {
+      prevOgp = ogp;
+      ogp = ogp->next;
+    }
+  }
+  if (cmpval != 0)
+  {
+    /* create new group */
+    ogp = (OrgGroupPtr) MemNew (sizeof (OrgGroupData));
+    if (ogp == NULL) return;
+    ogp->org_list = newBsdp;
+    ogp->num_organisms = 1;
+    ogp->next = NULL;
+    if (prevOgp == NULL)
+    {
+      ogp->next = *pogp;
+      *pogp = ogp;
+    }
+    else
+    {
+      ogp->next = prevOgp->next;
+      prevOgp->next = ogp;
+    }
+  }
+}
+
+typedef struct bestsortdata {
+  Int4    feature_index;
+  Boolean all_unique;
+  Boolean all_present;
+  Boolean is_unique;
+} BestSortData, PNTR BestSortPtr;
+
+static Boolean Index1FoundBeforeIndex2 (
+  Int4 index1,
+  Int4 index2,
+  ValNodePtr list
+)
+{
+  ValNodePtr  vnp;
+  BestSortPtr bsp;
+  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  {
+    if ((bsp = vnp->data.ptrvalue) == NULL)
+    {
+      continue;
+    }
+    if (bsp->feature_index == index1) return TRUE;
+    if (bsp->feature_index == index2) return FALSE;
+  }
+  return FALSE;
+}
+
+/* This function determines whether or not we should try adding this modifier
+ * to our combination.  If we've already tried it and not added it to the list,
+ * there's no reason to try adding it again.
+ */
+static Boolean OkToTryAddingQual (
+  ModifierCombinationPtr m,
+  ModifierItemLocalPtr ItemList,
+  ValNodePtr           available_modifiers_list,
+  Int2 feature_index
+)
+{
+  ValNodePtr vnp;
+
+  /* if feature_index indicates a value we don't use for best combos, skip */
+  if (feature_index == DEFLINE_POS_Map)
+  {
+    return FALSE;
+  }
+
+  if (m == NULL) return TRUE;
+
+  /* if feature_index is lower than anything else on list (other than */
+  /* a required value, this is a repeat combination, so skip it */
+  vnp = m->modifier_indices;
+  while (vnp != NULL)
+  {
+    if (feature_index == m->modifier_indices->data.intvalue)
+      return FALSE;
+    if (! ItemList[m->modifier_indices->data.intvalue].required &&
+      Index1FoundBeforeIndex2 (feature_index,
+                               m->modifier_indices->data.intvalue, 
+                               available_modifiers_list))
+    {
+      return FALSE;
+    }
+    vnp = vnp->next;
+  }
+  return TRUE;
+}
+
+static ValNodePtr GetListOfAvailableModifiers ( ModifierItemLocalPtr ItemList)
+{
+  ValNodePtr  vnp, head;
+  Int2        feature_index;
+  BestSortPtr bsp;
+
+  head = NULL;
+  for (feature_index = 0; feature_index < numDefLineModifiers; feature_index++)
+  {
+    if ( ItemList[feature_index].any_present)
+    {
+      bsp = (BestSortPtr) MemNew (sizeof (BestSortData));
+      if (bsp == NULL) return NULL;
+      bsp->feature_index = feature_index;
+      bsp->all_unique = ItemList[feature_index].all_unique;
+      bsp->all_present = ItemList[feature_index].all_present;
+      bsp->is_unique = ItemList[feature_index].is_unique;
+      vnp = ValNodeNew (head);
+      if (vnp == NULL) return NULL;
+      vnp->data.ptrvalue = bsp;
+      if (head == NULL) head = vnp;
+    }
+  }
+  return head;
+}
+
+static Int4 DefLineQualSortOrder [] = {
+  DEFLINE_POS_Transgenic,
+  DEFLINE_POS_Plasmid_name,
+  DEFLINE_POS_Endogenous_virus_name,
+  DEFLINE_POS_Strain,
+  DEFLINE_POS_Clone,
+  DEFLINE_POS_Isolate,
+  DEFLINE_POS_Haplotype,
+  DEFLINE_POS_Cultivar,
+  DEFLINE_POS_Specimen_voucher,
+  DEFLINE_POS_Ecotype,
+  DEFLINE_POS_Type,
+  DEFLINE_POS_Serotype,
+  DEFLINE_POS_Authority,
+  DEFLINE_POS_Breed
+};
+
+static int LIBCALLBACK SortByImportanceAndPresence (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+{
+  ValNodePtr  vnp1;
+  ValNodePtr  vnp2;
+  BestSortPtr bsp1, bsp2; 
+  Int4       num_defline_qual_sort_order, index;
+
+  if (ptr1 == NULL && ptr2 == NULL) return 0;
+  
+  if (ptr1 == NULL && ptr2 != NULL) return -1;
+  if (ptr1 != NULL && ptr2 == NULL) return 1;
+ 
+  vnp1 = *((ValNodePtr PNTR) ptr1);
+  vnp2 = *((ValNodePtr PNTR) ptr2);
+  if (vnp1 == NULL || vnp2 == NULL) return 0;
+  if (vnp1->data.ptrvalue == NULL || vnp2->data.ptrvalue == NULL) return 0;
+
+  bsp1 = vnp1->data.ptrvalue;
+  bsp2 = vnp2->data.ptrvalue;
+  if (bsp1->feature_index == bsp2->feature_index) return 0;
+
+  if (bsp1->all_present && bsp1->all_unique
+    && (! bsp2->all_present || ! bsp2->all_unique))
+  {
+    return -1;
+  }
+  if (bsp2->all_present && bsp2->all_unique
+    && (! bsp1->all_present || ! bsp1->all_unique))
+  {
+    return 1;
+  }
+
+  if ( ! bsp1->is_unique && bsp2->is_unique) return -1;
+  if ( ! bsp2->is_unique && bsp1->is_unique) return 1;
+
+  num_defline_qual_sort_order = sizeof (DefLineQualSortOrder) / sizeof (Int4);
+  for (index = 0; index < num_defline_qual_sort_order; index++)
+  {
+    if (bsp1->feature_index == DefLineQualSortOrder [ index ]) return -1;
+    if (bsp2->feature_index == DefLineQualSortOrder [ index ]) return 1;
+  }
+
+  if (bsp1->feature_index > bsp2->feature_index) return 1;
+  if (bsp1->feature_index < bsp2->feature_index) return -1;
+  return 0;
+}
+
+
+/* The function FindBestCombo tries to find the best combination of modifiers
+ * to create unique organism descriptions.  This is accomplished by
+ * creating a list of required modifiers, and then creating a list of
+ * combinations of modifiers by adding modifiers one at a time
+ * to see if the additional modifiers provide any more differentiation in
+ * the list.
+ * In order to do this, I start with a list of required modifiers, and 
+ * then create copies of this list.  For each copy I add one of the modifiers
+ * that are present in the bio sources and not already on the list.
+ * If adding the modifier increases the differentiation, I add that copy to
+ * the list of possible combinations, otherwise I discard it.
+ * The function then makes copies of all of the new items added to the list,
+ * starting with the item pointed to by start_of_expand, and adds another
+ * modifier to each combination, keeping the combinations that increase
+ * the differentiation and discarding the rest.
+ * This process continues until I have a combination that produces completely
+ * differentiated bio sources, or I run out of possible combinations.
+ * If the list of possible combinations is exhausted before each organism
+ * has a unique description, the function selects the combination from the
+ * list with the largest number of unique organism descriptions.  If more 
+ * than one combination produces the largest number of unique organisms,
+ * the combination with the largest number of unique organisms and the
+ * largest number of groups will be selected.
+ */
+static ModifierCombinationPtr FindBestCombo(
+  SeqEntryPtr sep,
+  ModifierItemLocalPtr ItemList
+)
+{
+  OrgGroupPtr group_list;
+  ModifierCombinationPtr mc_list, start_of_expand, best_found, end_of_list;
+  ModifierCombinationPtr next_start_of_expand, m, newm;
+  Int4 num_to_expand, next_num_to_expand;
+  Int2 i;
+  ValNodePtr available_modifier_list, vnp;
+  BestSortPtr bsp;
+
+  best_found = NULL;
+
+  /* first, get list of organisms */
+  group_list = NULL;
+  VisitBioSourcesInSep (sep, &group_list, BuildTaxOrgGroupList);
+
+  /* create combo with just the org groups */
+  mc_list = NewModifierCombo (group_list);
+  if (mc_list == NULL) return NULL;
+
+  available_modifier_list = GetListOfAvailableModifiers (ItemList);
+
+  /* next, add in any required qualifiers */
+  for (vnp = available_modifier_list; vnp != NULL; vnp = vnp->next)
+  {
+    bsp = vnp->data.ptrvalue;
+    if (bsp == NULL) return NULL;
+    if (ItemList[bsp->feature_index].required)
+    {
+      AddQualToModifierCombo (mc_list, ItemList + bsp->feature_index,
+                                       bsp->feature_index);
+    }
+  }
+  if (mc_list->max_orgs_in_group == 1)
+  {
+    /* we're done - they're all unique */
+    best_found = mc_list;
+    return best_found;
+  }
+
+  available_modifier_list = ValNodeSort (available_modifier_list,
+                                         SortByImportanceAndPresence);
+  start_of_expand = mc_list;
+  end_of_list = mc_list;
+  num_to_expand = 1;
+  while (best_found == NULL && start_of_expand != NULL)
+  {
+    next_num_to_expand = 0;
+    next_start_of_expand = NULL;
+    for (i=0; i < num_to_expand && start_of_expand != NULL; i++)
+    {
+      /* try adding qualifiers */ 
+      for (vnp = available_modifier_list;
+           vnp != NULL && best_found == NULL;
+           vnp = vnp->next)
+      {
+        bsp = vnp->data.ptrvalue;
+        if (bsp == NULL) return NULL;
+        if (OkToTryAddingQual (start_of_expand, ItemList,
+                               available_modifier_list,
+                               bsp->feature_index))
+        {
+          newm = CopyModifierCombo (start_of_expand);
+          AddQualToModifierCombo (newm, ItemList + bsp->feature_index,
+                                  bsp->feature_index);
+          if (start_of_expand->num_groups >= newm->num_groups)
+          {
+            /* situation didn't get better, don't bother to add this one */
+            FreeModifierCombo (newm);
+            newm = NULL;
+          }
+          else if (newm->max_orgs_in_group == 1)
+          {
+            best_found = newm;
+          }
+          else
+          {
+            end_of_list->next = newm;
+            end_of_list = end_of_list->next;
+            if (next_start_of_expand == NULL)
+              next_start_of_expand = newm;
+            next_num_to_expand++;
+          }
+        }
+      }
+      if (start_of_expand != NULL)
+      {
+        start_of_expand = start_of_expand->next;
+      }
+    }
+    num_to_expand = next_num_to_expand;
+    if (start_of_expand != NULL)
+    {
+      start_of_expand = start_of_expand->next;
+    }
+  }
+
+  if (best_found != NULL)
+  {
+    FreeModifierCombo (mc_list);
+    return best_found;
+  }
+  
+  /* we want to find the one with the highest number of unique organisms */
+  best_found = mc_list;
+  m = mc_list->next;
+  while (m!= NULL)
+  {
+    if (m->num_unique_orgs > best_found->num_unique_orgs)
+    {
+      best_found = m;
+    }
+    else if (m->num_unique_orgs == best_found->num_unique_orgs
+           && m->num_groups > best_found->num_groups)
+    {
+      best_found = m;
+    }
+    else if (m->num_unique_orgs == best_found->num_unique_orgs
+           && m->num_groups == best_found->num_groups
+           && m->num_mods < best_found->num_mods)
+    {
+      best_found = m;
+    }
+    m = m->next;
+  }
+
+  m = mc_list;
+  while (m != NULL)
+  {
+    if (m != best_found)
+    {
+      newm = m->next;
+      m->next = NULL;
+      FreeModifierCombo (m);
+      m = newm;
+    }
+    else
+    {
+      FreeModifierCombo (m->next);
+      m->next = NULL;
+      m = NULL;
+    }
+  }
+  return best_found;
+}
+
+
+NLM_EXTERN ValNodePtr FindBestModifiers(
+  SeqEntryPtr sep,
+  ModifierItemLocalPtr ItemList
+)
+
+{
+  ModifierCombinationPtr m;
+  ValNodePtr modifier_indices;
+
+  m = FindBestCombo (sep, ItemList);
+  modifier_indices = CopyModifierIndices (m->modifier_indices);
+  FreeModifierCombo (m);
+  return modifier_indices;
+}
+
+
+/* create combo with the specified modifiers */
+NLM_EXTERN ValNodePtr GetModifierIndicesFromModList (
+  ModifierItemLocalPtr modList
+)
+{
+  Int4       feature_index;
+  ValNodePtr modifier_indices = NULL;
+
+  if (modList == NULL) return NULL;
+  for (feature_index = 0; feature_index < numDefLineModifiers; feature_index++)
+  {
+    if (modList[feature_index].any_present && modList [feature_index].required)
+    {
+      ValNodeAddInt (&modifier_indices, 0, feature_index);
+    }
+  }
+  return modifier_indices;
+}
+
+
+/* This is the callback function for sorting the modifier list.  It 
+ * implements an order specified by the indexers.
+ */
+static Int4 DefLineQualPresentationOrder [] = {
+  DEFLINE_POS_Transgenic,
+  DEFLINE_POS_Strain,
+  DEFLINE_POS_Isolate,
+  DEFLINE_POS_Cultivar,
+  DEFLINE_POS_Specimen_voucher,
+  DEFLINE_POS_Ecotype,
+  DEFLINE_POS_Type,
+  DEFLINE_POS_Serotype,
+  DEFLINE_POS_Authority,
+  DEFLINE_POS_Breed
+};
+
+static int LIBCALLBACK SortByImportance (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+{
+  ValNodePtr vnp1;
+  ValNodePtr vnp2;
+  Int4       num_defline_qual_sort_order, index;
+
+  if (ptr1 == NULL && ptr2 == NULL) return 0;
+  
+  if (ptr1 == NULL && ptr2 != NULL) return -1;
+  if (ptr1 != NULL && ptr2 == NULL) return 1;
+ 
+  vnp1 = *((ValNodePtr PNTR) ptr1);
+  vnp2 = *((ValNodePtr PNTR) ptr2);
+  if (vnp1 == NULL || vnp2 == NULL) return 0;
+  if (vnp1->data.intvalue == vnp2->data.intvalue) return 0;
+
+  num_defline_qual_sort_order = sizeof (DefLineQualPresentationOrder) / sizeof (Int4);
+  for (index = 0; index < num_defline_qual_sort_order; index++)
+  {
+    if (vnp1->data.intvalue == DefLineQualPresentationOrder [ index ]) return -1;
+    if (vnp2->data.intvalue == DefLineQualPresentationOrder [ index ]) return 1;
+  }
+
+  if ((vnp1->data.intvalue < 0 || vnp1->data.intvalue > numDefLineModifiers)
+    && (vnp2->data.intvalue < 0 || vnp2->data.intvalue > numDefLineModifiers))
+  {
+    return 0;
+  }
+  if (vnp1->data.intvalue < 0 || vnp1->data.intvalue > numDefLineModifiers)
+  {
+    return 1;
+  }
+  if (vnp2->data.intvalue < 0 || vnp2->data.intvalue > numDefLineModifiers)
+  {
+    return -1;
+  }
+
+  if (DefLineModifiers [ vnp1->data.intvalue].isOrgMod
+    && (! DefLineModifiers [ vnp2->data.intvalue].isOrgMod
+      || vnp2->data.intvalue == DEFLINE_POS_Plasmid_name
+      || vnp2->data.intvalue == DEFLINE_POS_Endogenous_virus_name))
+  {
+    return -1;
+  }
+  if (DefLineModifiers [ vnp2->data.intvalue].isOrgMod
+    && (! DefLineModifiers [ vnp1->data.intvalue].isOrgMod
+      || vnp1->data.intvalue == DEFLINE_POS_Plasmid_name
+      || vnp1->data.intvalue == DEFLINE_POS_Endogenous_virus_name))
+  {
+    return 1;
+  }
+  
+  if (vnp1->data.intvalue == DEFLINE_POS_Plasmid_name)
+  {
+    return -1;
+  }
+  if (vnp2->data.intvalue == DEFLINE_POS_Plasmid_name)
+  {
+    return 1;
+  }
+    
+  if (vnp1->data.intvalue == DEFLINE_POS_Endogenous_virus_name)
+  {
+    return -1;
+  }
+  if (vnp2->data.intvalue == DEFLINE_POS_Endogenous_virus_name)
+  {
+    return 1;
+  }
+
+  if (! DefLineModifiers [ vnp1->data.intvalue].isOrgMod
+     && vnp2->data.intvalue == DEFLINE_POS_Clone)
+  {
+    return 1;
+  }
+  if (! DefLineModifiers [ vnp2->data.intvalue].isOrgMod
+     && vnp1->data.intvalue == DEFLINE_POS_Clone)
+  {
+    return -1;
+  }
+
+  if (! DefLineModifiers [ vnp1->data.intvalue].isOrgMod
+     && vnp2->data.intvalue == DEFLINE_POS_Haplotype)
+  {
+    return 1;
+  }
+  if (! DefLineModifiers [ vnp2->data.intvalue].isOrgMod
+     && vnp1->data.intvalue == DEFLINE_POS_Haplotype)
+  {
+    return -1;
+  }
+
+  if (vnp1->data.intvalue > vnp2->data.intvalue) return 1;
+  if (vnp1->data.intvalue < vnp2->data.intvalue) return -1;
+  return 0;
+}
+
+static Boolean RecordHasModifier (
+  BioSourcePtr biop,
+  Int4         modifier_index
+)
+{
+  OrgModPtr     mod;
+  OrgNamePtr    onp;
+  SubSourcePtr  ssp;
+
+  if (biop == NULL
+    || modifier_index < 0
+    || modifier_index >= numDefLineModifiers)
+  {
+    return FALSE;
+  }
+  if (DefLineModifiers[modifier_index].isOrgMod)
+  {
+    if (biop->org == NULL || (onp = biop->org->orgname) == NULL)
+    {
+      return FALSE;
+    }
+    mod = onp->mod;
+    while (mod != NULL
+        && mod->subtype != DefLineModifiers[modifier_index].subtype)
+    {
+      mod = mod->next;
+    }
+    if (mod != NULL && mod->subname != NULL)
+    {
+      return TRUE;
+    }
+  } else {
+    ssp = biop->subtype;
+    while (ssp != NULL && ssp->subtype != DefLineModifiers[modifier_index].subtype)
+    {
+      ssp = ssp->next;
+    }
+    if (ssp != NULL && ssp->name != NULL)
+    {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+  
+/* This function adds in required modifiers for HIV sequences */
+static void AddHIVModifierIndices (
+  ValNodePtr PNTR modifier_indices,
+  BioSourcePtr biop,
+  ModifierItemLocalPtr modList,
+  CharPtr taxName,
+  Int4    clone_isolate_HIV_rule_num
+)
+{
+  ValNodePtr  vnp;
+  Boolean have_country_in_list;
+  Boolean have_isolate_in_list;
+  Boolean have_clone_in_list;
+  Boolean have_country_mod;
+  Boolean have_isolate_mod;
+  Boolean have_clone_mod;
+
+  /* special handling for HIV */
+  if (StringICmp (taxName, "HIV-1") != 0
+    && StringICmp (taxName, "HIV-2") != 0)
+  {
+    return;
+  }
+
+  have_country_in_list = FALSE;
+  have_isolate_in_list = FALSE;
+  have_clone_in_list = FALSE;
+  have_country_mod = RecordHasModifier (biop, DEFLINE_POS_Country);
+  have_isolate_mod = RecordHasModifier (biop, DEFLINE_POS_Isolate);
+  have_clone_mod = RecordHasModifier (biop, DEFLINE_POS_Clone);
+
+  if (modifier_indices != NULL)
+  {
+    for (vnp = *modifier_indices;
+         vnp != NULL
+           && (! have_country_in_list
+             || ! have_isolate_in_list
+             || ! have_clone_in_list);
+         vnp = vnp->next)
+    {
+      if (vnp->data.intvalue == DEFLINE_POS_Country)
+      {
+        have_country_in_list = TRUE;
+      }
+      else if (vnp->data.intvalue == DEFLINE_POS_Isolate)
+      {
+        have_isolate_in_list = TRUE;
+      }
+      else if (vnp->data.intvalue == DEFLINE_POS_Clone)
+      {
+        have_clone_in_list = TRUE;
+      }
+    }
+  }
+
+  if ( ! have_country_in_list && have_country_mod)
+  {
+    vnp = ValNodeNew (*modifier_indices);
+    vnp->data.intvalue = DEFLINE_POS_Country;
+    if (*modifier_indices == NULL) *modifier_indices = vnp;
+  }
+
+  if ((have_clone_in_list && have_clone_mod)
+      || (have_isolate_in_list && have_isolate_mod))
+  {
+    /* don't need HIV rule */
+  }
+  else
+  {
+    if ( ! have_isolate_in_list
+        && have_isolate_mod
+        && ( clone_isolate_HIV_rule_num == clone_isolate_HIV_rule_prefer_isolate
+          || clone_isolate_HIV_rule_num == clone_isolate_HIV_rule_want_both
+          || ! have_clone_mod))
+    {
+      vnp = ValNodeNew (*modifier_indices);
+      vnp->data.intvalue = DEFLINE_POS_Isolate;
+      if (*modifier_indices == NULL) *modifier_indices = vnp;
+    }
+    
+    if ( ! have_clone_in_list
+        && have_clone_mod
+        && ( clone_isolate_HIV_rule_num == clone_isolate_HIV_rule_prefer_clone
+          || clone_isolate_HIV_rule_num == clone_isolate_HIV_rule_want_both
+          || ! have_isolate_mod))
+    {
+      vnp = ValNodeNew (*modifier_indices);
+      vnp->data.intvalue = DEFLINE_POS_Clone;
+      if (*modifier_indices == NULL) *modifier_indices = vnp;
+    }
+  }
+}
+
+/* This function looks for an OrgMod note that contains the phrase
+ * "type strain of".  This function is used to determine whether
+ * strain is a required modifier for the defline for this source.
+ */
+static Boolean HasTypeStrainComment (BioSourcePtr biop)
+{
+  OrgModPtr mod;
+  
+  if (biop == NULL || biop->org == NULL || biop->org->orgname == NULL)
+  {
+    return FALSE;
+  }
+  
+  mod = biop->org->orgname->mod;
+  while (mod != NULL && mod->subtype != ORGMOD_strain)
+  {
+    mod = mod->next;
+  }
+  
+  if (mod == NULL)
+  {
+    return FALSE;
+  }
+  
+  if (!UseOrgModifier (mod, biop->org->taxname))
+  {
+    return FALSE;
+  }
+  
+  mod = biop->org->orgname->mod;
+  while (mod != NULL)
+  {
+    if (mod->subtype == 255
+        && StringISearch (mod->subname, "type strain of") != NULL)
+    {
+      return TRUE;
+    }
+    mod = mod->next;
+  }
+  return FALSE;
+}
+
+
+/* This function checks to see if there is a type strain comment on
+ * the bio source.  If there is one, it checks to see whether strain
+ * is already in the list of modifiers for the definition line.
+ * If strain is not already in the list, it is added.
+ */
+static void 
+AddTypeStrainModifierIndices 
+(ValNodePtr PNTR modifier_indices,
+ BioSourcePtr    biop)
+{
+  ValNodePtr vnp;
+  
+  if (modifier_indices == NULL || biop == NULL || ! HasTypeStrainComment (biop))
+  {
+    return;
+  }
+
+  for (vnp = *modifier_indices;
+       vnp != NULL && vnp->data.intvalue != DEFLINE_POS_Strain;
+       vnp = vnp->next)
+  {
+  }
+  
+  if (vnp == NULL)
+  {
+    ValNodeAddInt (modifier_indices, 0, DEFLINE_POS_Strain);
+  }
+}
+
+static Boolean SpecialHandlingForSpecialTechniques (
+  BioseqPtr bsp
+);
+
+/* This function checks to see if the Bioseq has a WGS technique.
+ * If so, and if the strain text is not present in the taxname,
+ * and strain is not already in the list of modifiers for the 
+ * definition line, add strain.
+ */
+static void 
+AddWGSModifierIndices 
+(ValNodePtr PNTR modifier_indices,
+ BioSourcePtr    biop,
+ BioseqPtr       bsp)
+{
+  ValNodePtr vnp;
+  OrgModPtr  omp;
+  
+  if (modifier_indices == NULL || biop == NULL 
+      || biop->org == NULL
+      || biop->org->orgname == NULL
+      || biop->org->orgname->mod == NULL
+      || ! SpecialHandlingForSpecialTechniques (bsp))
+  {
+    return;
+  }
+
+  for (vnp = *modifier_indices;
+       vnp != NULL && vnp->data.intvalue != DEFLINE_POS_Strain;
+       vnp = vnp->next)
+  {
+  }
+  
+  if (vnp == NULL)
+  {
+    omp = biop->org->orgname->mod;
+    while (omp != NULL && omp->subtype != ORGMOD_strain) 
+    {
+      omp = omp->next;
+    }
+    if (omp != NULL) 
+    {
+      if (StringStr (biop->org->taxname, omp->subname) != NULL) 
+      {
+        /* don't add, present already */
+      } else {
+        /* add strain modifier */
+        ValNodeAddInt (modifier_indices, 0, DEFLINE_POS_Strain);
+      }
+    }
+  }
+}
+
+/* This function provides a label to be used in the definition line for
+ * each modifier that requires one.  Most modifiers use a label that is 
+ * similar to the name of the modifier displayed in the definition line
+ * options dialog.
+ */
+NLM_EXTERN void AddModifierLabel (
+  Boolean use_labels,
+  Boolean is_orgmod,
+  Uint1   subtype,
+  CharPtr modifier_text
+)
+{
+  CharPtr cp;
+  if (!is_orgmod && subtype == SUBSRC_endogenous_virus_name)
+  {
+    StringCpy (modifier_text, "endogenous virus");
+  }
+  else if (is_orgmod && subtype == ORGMOD_specimen_voucher)
+  {
+    if (use_labels)
+    {
+      StringCpy (modifier_text, "voucher");
+    } 
+    else
+    {
+      modifier_text [0] = 0;
+    }
+  }
+  else if (use_labels 
+           || (!is_orgmod 
+               && (subtype == SUBSRC_transgenic
+                   || subtype == SUBSRC_plasmid_name)))
+  {
+    if (is_orgmod) 
+    {
+      StringCpy (modifier_text, GetOrgModQualName (subtype));
+    } else {
+      StringCpy (modifier_text, GetSubsourceQualName (subtype));
+    }
+    modifier_text[0] = tolower(modifier_text[0]);
+    cp = StringStr (modifier_text, "-name");
+    if (cp != NULL) *cp = 0;
+  }
+  else
+  {
+    modifier_text[0] = 0;
+  }
+}
+
+typedef struct orgmodabbrevdata {
+  Int2    subtype;
+  CharPtr abbrev;
+} OrgModAbbrevData, PNTR OrgModAbbrevPtr;
+
+static OrgModAbbrevData orgmod_abbrevs[] = {
+  { ORGMOD_variety, "var." },
+  { ORGMOD_forma, "f." },
+  { ORGMOD_forma_specialis, "f. sp." },
+  { ORGMOD_pathovar, "pv." }
+};
+
+/* The UseOrgModifier function looks for the values of certain kinds of 
+ * modifiers in the taxonomy name, so that they will not be added to the
+ * definition line as modifiers if they are already present in the
+ * taxonomy name.
+ */
+NLM_EXTERN Boolean UseOrgModifier (
+  OrgModPtr mod,
+  CharPtr   taxName
+)
+{
+  CharPtr value_found;
+  Int4    value_len;
+  Int4    num_abbrevs, i;
+  CharPtr abbrev_start;
+  Boolean other_abbrev_found;
+
+  if (mod == NULL || mod->subname == NULL) return FALSE;
+
+  num_abbrevs = sizeof (orgmod_abbrevs) / sizeof (OrgModAbbrevData);
+
+  /* If selected modifiers already appear in the tax Name, */
+  /* don't use them in the organism description again */
+  if (mod->subtype == ORGMOD_strain
+    || mod->subtype == ORGMOD_variety
+    || mod->subtype == ORGMOD_sub_species
+    || mod->subtype == ORGMOD_forma
+    || mod->subtype == ORGMOD_forma_specialis
+    || mod->subtype == ORGMOD_pathovar
+    || mod->subtype == ORGMOD_specimen_voucher)
+  {
+    value_found = StringStr (taxName, mod->subname);
+    value_len = StringLen (mod->subname);
+    while (value_found != NULL)
+    {
+      if (value_found == taxName)
+      {
+        value_found = StringStr (value_found + 1, mod->subname);
+        continue;
+      }
+      if (*(value_found - 1) != ' ' && *(value_found - 1) != '(')
+      {
+        value_found = StringStr (value_found + 1, mod->subname);
+        continue;
+      }
+      if (*(value_found - 1) == ')' && *(value_found + value_len) != ')')
+      {
+        value_found = StringStr (value_found + 1, mod->subname);
+        continue;
+      }
+      if (*(value_found + value_len) != ' ' && *(value_found + value_len) != 0)
+      {
+        value_found = StringStr (value_found + 1, mod->subname);
+        continue;
+      }
+      other_abbrev_found = FALSE;
+      for (i = 0; i < num_abbrevs; i++)
+      {
+        abbrev_start = value_found - StringLen (orgmod_abbrevs[i].abbrev) - 1;
+        if (abbrev_start > taxName
+          && StringNCmp (abbrev_start,
+                         orgmod_abbrevs[i].abbrev,
+                         StringLen (orgmod_abbrevs[i].abbrev)) == 0)
+        {
+          if (mod->subtype == orgmod_abbrevs[i].subtype)
+          {
+            return FALSE;
+          }
+          else
+          {
+            other_abbrev_found = TRUE;
+          }
+        }
+      }
+      if ( ! other_abbrev_found 
+        && ( mod->subtype == ORGMOD_strain
+          || mod->subtype == ORGMOD_sub_species
+          || mod->subtype == ORGMOD_specimen_voucher))
+      {
+        return FALSE;
+      }
+      value_found = StringStr (value_found + 1, mod->subname);
+    }
+  }
+  return TRUE;
+}
+
+/* The SetRequiredModifiers function copies the default required values from
+ * the global DefLineModifiers array into the local list of modifier
+ * information.
+ */
+NLM_EXTERN void SetRequiredModifiers (
+  ModifierItemLocalPtr modList
+)
+{
+  Int4  item_index;
+
+  for (item_index = 0; item_index < numDefLineModifiers; item_index++)
+  {
+    modList[item_index].required = IsDeflineModifierRequiredByDefault(DefLineModifiers[item_index].isOrgMod,
+                                                                      DefLineModifiers[item_index].subtype);
+  }
+  
+}
+
+/* This function fixes HIV abbreviations, removes items in parentheses,
+ * and trims spaces around the taxonomy name.
+ */
+NLM_EXTERN void CleanUpTaxName (
+  CharPtr taxName,
+  Boolean keep_in_paren
+)
+{
+  CharPtr ptr;
+
+  if (StringICmp (taxName, "Human immunodeficiency virus type 1") == 0
+    || StringICmp (taxName, "Human immunodeficiency virus 1") == 0)
+  {
+    StringCpy (taxName, "HIV-1");
+  }
+  else if (StringICmp (taxName, "Human immunodeficiency virus type 2") == 0
+    || StringICmp (taxName, "Human immunodeficiency virus 2") == 0)
+  {
+    StringCpy (taxName, "HIV-2");
+  }
+  else
+  {
+    if (! keep_in_paren)
+    {
+      ptr = StringStr (taxName, "(");
+      if (ptr != NULL)
+        *ptr = '\0';
+    }
+    TrimSpacesAroundString (taxName);
+  }
+}
+
+/* This function gets the BioSource descriptor for the BioSeq. */
+NLM_EXTERN BioSourcePtr GetBiopForBsp (
+  BioseqPtr bsp
+)
+{
+  SeqMgrDescContext  dcontext;
+  SeqDescrPtr    sdp;
+  BioSourcePtr    biop;
+
+  if (bsp == NULL) return NULL;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  if (sdp != NULL) {
+    biop = (BioSourcePtr) sdp->data.ptrvalue;
+    return biop;
+  }
+  
+  return NULL;
+}
+
+
+NLM_EXTERN Boolean IsSpName (CharPtr taxName)
+{
+  CharPtr cp;
+
+  cp = StringStr (taxName, " sp.");
+  /* check to make sure not "f. sp." */
+  if (cp != NULL && cp[4] == ' '
+      && (cp - taxName < 2 || *(cp - 2) != 'f' || *(cp - 1) != '.'))
+  {
+    return TRUE;
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+
+static ValNodePtr ValNodeIntCopy (ValNodePtr orig)
+{
+  ValNodePtr cpy = NULL, last = NULL, vnp;
+
+  while (orig != NULL) {
+    vnp = ValNodeNew (NULL);
+    vnp->choice = orig->choice;
+    vnp->data.intvalue = orig->data.intvalue;
+    if (last == NULL) {
+      cpy = vnp;
+    } else {
+      last->next = vnp;
+    }
+    last = vnp;
+    orig = orig->next;
+  }
+  return cpy;
+}
+
+
+/* This function generates a string describing the organism based on the
+ * modifiers selected and other organism description options.
+ */
+static CharPtr GetOrganismDescription (
+  BioseqPtr bsp, 
+  ModifierItemLocalPtr modList,
+  ValNodePtr   modifier_indices,
+  OrganismDescriptionModifiersPtr odmp
+)
+{
+  Char         taxName [196];
+  Char         modifier_text [256];
+  ValNodePtr   strings;
+  BioSourcePtr biop;
+  OrgModPtr    mod;
+  SubSourcePtr ssp;
+  ValNodePtr   vnp;
+  Int2         feature_index;
+  CharPtr      org_desc;
+  CharPtr      cp;
+  Uint4        no_semicolon_len, label_len;
+  CharPtr      tmp;
+
+  biop = NULL;
+  strings = NULL;
+  taxName [0] = '\0';
+
+  biop = GetBiopForBsp (bsp);
+  if (biop == NULL) return NULL;
+  if (biop->org == NULL) return NULL;
+  if (biop->org->taxname == NULL) return NULL;
+  StringNCpy (taxName, biop->org->taxname, sizeof (taxName) - 1);
+  taxName [ sizeof (taxName) - 1] = 0;
+
+  CleanUpTaxName (taxName, odmp->keep_paren);
+
+  if (odmp->exclude_sp && IsSpName(taxName))
+  {
+    return StringSave (taxName);
+  }
+
+  if (odmp->exclude_cf)
+  {
+    cp = StringStr (taxName, " cf.");
+    if (cp != NULL)
+    {
+      return StringSave (taxName);
+    }
+  }
+  
+  if (odmp->exclude_aff)
+  {
+    cp = StringStr (taxName, " aff.");
+    if (cp != NULL)
+    {
+      return StringSave (taxName);
+    }
+  }
+  if (odmp->exclude_nr)
+  {
+    cp = StringStr (taxName, " nr.");
+    if (cp != NULL)
+    {
+      return StringSave (taxName);
+    }
+  }
+  
+  if (biop->origin == ORG_MUT)
+  {
+    ValNodeAddStr (&strings, 0, StringSave ("Mutant"));
+  }
+
+  ValNodeAddStr (&strings, 0, StringSave (taxName));
+
+  if (HasTypeStrainComment (biop))
+  {
+    
+  } 
+
+  /* copy modifier indices list */
+  modifier_indices = ValNodeIntCopy (modifier_indices);
+  AddHIVModifierIndices (&modifier_indices, biop, modList, taxName,
+                         odmp->clone_isolate_HIV_rule_num);
+  AddTypeStrainModifierIndices (&modifier_indices, biop);
+  AddWGSModifierIndices (&modifier_indices, biop, bsp);
+  
+  modifier_indices = ValNodeSort (modifier_indices, SortByImportance);
+  for (vnp = modifier_indices;
+       vnp != NULL && (odmp->max_mods == -99 || odmp->max_mods > 0);
+       vnp = vnp->next)
+  {
+    feature_index = vnp->data.intvalue;
+    if (! odmp->use_modifiers && !IsDeflineModifierRequiredByDefault(DefLineModifiers[feature_index].isOrgMod,
+                                                                     DefLineModifiers[feature_index].subtype))
+    {
+      /* do nothing */
+    }
+    else if (DefLineModifiers[feature_index].isOrgMod)
+    {
+      if (biop->org == NULL || biop->org->orgname == NULL) continue;
+      mod = biop->org->orgname->mod;
+      while (mod != NULL
+        && mod->subtype != DefLineModifiers[feature_index].subtype)
+      {
+        mod = mod->next;
+      }
+      if ( UseOrgModifier (mod, taxName))
+      {
+        if (odmp->allow_semicolon_in_modifier) {
+          no_semicolon_len = StringLen (mod->subname);
+        } else {
+          no_semicolon_len = StringCSpn (mod->subname, ";");
+        }
+
+        if (mod->subtype == ORGMOD_nat_host)
+        {
+          sprintf (modifier_text, "from ");
+          if (no_semicolon_len > sizeof (modifier_text) - 6)
+          {
+            no_semicolon_len = sizeof (modifier_text) - 6;
+          }
+          StringNCpy (modifier_text + 5, mod->subname,
+                      no_semicolon_len);
+          modifier_text[no_semicolon_len + 5] = 0;
+        }
+        else
+        {
+          AddModifierLabel (odmp->use_labels, TRUE, mod->subtype, modifier_text);
+          if (modifier_text[0] != 0)
+            StringCat (modifier_text, " ");
+          label_len = StringLen (modifier_text);
+          if (no_semicolon_len > (Int4) sizeof (modifier_text) - label_len - 1)
+          {
+            no_semicolon_len = (Int4) sizeof (modifier_text) - label_len - 1;
+          } 
+          if (mod->subtype == ORGMOD_specimen_voucher && StringNICmp (mod->subname, "personal:", 9) == 0)
+          {
+            tmp = mod->subname + 9;
+            while (isspace (*tmp)) 
+            {
+              tmp++;
+            }
+            if (odmp->allow_semicolon_in_modifier) {
+              no_semicolon_len = StringLen (tmp);
+            } else {
+              no_semicolon_len = StringCSpn (tmp, ";");
+            }
+          }
+          else
+          {
+            tmp = mod->subname;
+          }
+
+          StringNCat (modifier_text, tmp,
+                      no_semicolon_len);
+          modifier_text [ no_semicolon_len + label_len] = 0;
+        }
+        ValNodeCopyStr( &strings, 0, modifier_text);
+        if (odmp->max_mods != -99)
+          odmp->max_mods --;
+      }
+    } else {
+      ssp = biop->subtype;
+      while (ssp != NULL
+          && ssp->subtype != DefLineModifiers[feature_index].subtype)
+      {
+        ssp = ssp->next;
+      }
+      if (ssp != NULL)
+      {
+        if (odmp->include_country_extra || odmp->allow_semicolon_in_modifier)
+        {
+          no_semicolon_len = StringLen (ssp->name);
+        }
+        else
+        {
+          no_semicolon_len = StringCSpn (ssp->name, ";");
+        }
+        AddModifierLabel (odmp->use_labels, FALSE, ssp->subtype, modifier_text);
+        if (ssp->subtype == SUBSRC_transgenic)
+        {
+          /* do nothing, transgenic already captured from label */
+        }
+        else if (ssp->subtype == SUBSRC_country)
+        {
+          sprintf (modifier_text, "from ");
+          if (no_semicolon_len > sizeof (modifier_text) - 6)
+          {
+            no_semicolon_len = sizeof (modifier_text) - 6;
+          }
+          StringNCpy (modifier_text + 5, ssp->name, no_semicolon_len);
+          modifier_text[5 + no_semicolon_len] = 0;
+          if (!odmp->include_country_extra)
+          {
+            cp = StringChr (modifier_text, ':');
+            if (cp != NULL) *cp = 0;
+          }
+        }
+        else if (ssp->name != NULL && ssp->name[0] != 0
+          && (ssp->subtype != SUBSRC_plasmid_name
+            || StringCmp (ssp->name, "unnamed") != 0))
+        {
+          if (modifier_text[0] != 0)
+            StringCat (modifier_text, " ");
+          label_len = StringLen (modifier_text);
+          if (no_semicolon_len > sizeof (modifier_text) - 1 - label_len)
+          {
+            no_semicolon_len = sizeof (modifier_text) - 1 - label_len;
+          }
+          StringNCat (modifier_text, ssp->name, no_semicolon_len);
+          modifier_text [ no_semicolon_len + label_len ] = 0;
+        }
+        ValNodeCopyStr( &strings, 0, modifier_text);
+        if (odmp->max_mods != -99)
+          odmp->max_mods --;
+      }
+    }
+  }
+  
+  org_desc = MergeValNodeStrings (strings, FALSE);
+  ValNodeFreeData (strings);
+  modifier_indices = ValNodeFree (modifier_indices);
+  return org_desc;
+
+}
+
+/* end of organism description section */
+
+/* This section of code contains functions which are useful for dealing
+ * with locations of features (SeqLocPtr objects).
+ */
+
+/* This function determines whether location A is on the same strand as
+ * location B
+ */
+static Boolean AreAAndBOnSameStrand (
+  SeqLocPtr slp1,
+  SeqLocPtr slp2
+)
+{
+  Uint1 strand1;
+  Uint2 strand2;
+
+  strand1 = SeqLocStrand (slp1);
+  strand2 = SeqLocStrand (slp2);
+  if (strand1 == Seq_strand_minus && strand2 != Seq_strand_minus)
+    return FALSE;
+  else if (strand1 != Seq_strand_minus && strand2 == Seq_strand_minus)
+    return FALSE;
+  else
+    return TRUE;
+}
+
+/* This function determines whether location A is contained in or equal to
+ * location B and on the same strand as location B.
+ */
+NLM_EXTERN Boolean IsLocAInBonSameStrand (
+  SeqLocPtr slp1,
+  SeqLocPtr slp2
+)
+{
+  if (! AreAAndBOnSameStrand ( slp1, slp2))
+  {
+    return FALSE;
+  }
+  else if ( SeqLocAinB (slp1, slp2) < 0)
+  {
+    return FALSE;
+  }
+  else
+  {
+    return TRUE;
+  }
+}
+
+/* This function calculates the intersection between two locations.
+ */
+static SeqLocPtr SeqLocIntersection (
+  SeqLocPtr slp1,
+  SeqLocPtr slp2,
+  BioseqPtr bsp
+)
+{
+  SeqLocPtr diff1, diff2, result;
+
+  diff1 = SeqLocMerge ( bsp, slp1, NULL, FALSE, TRUE, FALSE);
+  diff1 = SeqLocSubtract (diff1, slp2);
+  diff2 = SeqLocMerge ( bsp, slp2, NULL, FALSE, TRUE, FALSE);
+  diff2 = SeqLocSubtract (diff2, slp1);
+  result = SeqLocMerge ( bsp, slp1, slp2, FALSE, TRUE, FALSE);
+  
+  if (diff1 != NULL)
+  {
+    result = SeqLocSubtract (result, diff1);
+    SeqLocFree (diff1);
+    if (result == NULL) return NULL;
+  }
+  if (diff2 != NULL)
+  {
+    result = SeqLocSubtract (result, diff2);
+    SeqLocFree (diff2);
+    if (result == NULL) return NULL;
+  }
+  return result;
+}
+
+#define ADJACENT_TYPE_ANY        0
+#define ADJACENT_TYPE_UPSTREAM   1
+#define ADJACENT_TYPE_DOWNSTREAM 2
+
+/* This function determines whether A is "next to" B and upstream or downstream
+ * from B.  A cannot overlap B.  If allow_interval is TRUE, there can be
+ * space between A and B.
+ */
+static Boolean IsAAdjacentToB (
+  SeqLocPtr a,
+  SeqLocPtr b,
+  BioseqPtr bsp,
+  Int2      adjacent_type,
+  Boolean   allow_interval
+)
+{
+  Int4      a_end, b_end;
+  Uint2     strand;
+ 
+  if (adjacent_type != ADJACENT_TYPE_ANY
+    && adjacent_type != ADJACENT_TYPE_UPSTREAM
+    && adjacent_type != ADJACENT_TYPE_DOWNSTREAM)
+  {
+    return FALSE;
+  }
+  
+  if ( ! AreAAndBOnSameStrand (a, b))
+  {
+    return FALSE;
+  }
+
+  strand = SeqLocStrand (a);
+  if ( adjacent_type == ADJACENT_TYPE_ANY)
+  {
+    a_end = GetOffsetInBioseq (a, bsp, SEQLOC_RIGHT_END);
+    b_end = GetOffsetInBioseq (b, bsp, SEQLOC_LEFT_END);
+    if ((allow_interval && b_end < a_end)
+      || b_end == a_end + 1)
+    {
+      return TRUE;
+    }
+    a_end = GetOffsetInBioseq (a, bsp, SEQLOC_LEFT_END);
+    b_end = GetOffsetInBioseq (b, bsp, SEQLOC_RIGHT_END);
+    if ((allow_interval && b_end > a_end)
+      || a_end == b_end + 1)
+    {
+      return TRUE;
+    }
+    return FALSE;
+  }
+  else if ( (strand == Seq_strand_minus
+      && adjacent_type == ADJACENT_TYPE_UPSTREAM)
+    || (strand != Seq_strand_minus
+      && adjacent_type == ADJACENT_TYPE_DOWNSTREAM))
+  {
+    a_end = GetOffsetInBioseq (a, bsp, SEQLOC_RIGHT_END);
+    b_end = GetOffsetInBioseq (b, bsp, SEQLOC_LEFT_END);
+    if ((allow_interval && b_end < a_end)
+      || b_end == a_end + 1)
+    {
+      return TRUE;
+    }
+    else
+    {
+      return FALSE;
+    }
+  }
+  else
+  {
+    a_end = GetOffsetInBioseq (a, bsp, SEQLOC_LEFT_END);
+    b_end = GetOffsetInBioseq (b, bsp, SEQLOC_RIGHT_END);
+    if ((allow_interval && b_end > a_end)
+      || a_end == b_end + 1)
+    {
+      return TRUE;
+    }
+    else
+    {
+      return FALSE;
+    }
+  }
+}
+
+static Boolean IsAEmptyIntervalOfB (SeqLocPtr a, SeqLocPtr b, BioseqPtr bsp)
+{
+  Int4 a_right, a_left, b_right, b_left, prev_right, prev_left;
+  SeqLocPtr slp;
+  Uint1 a_strand, b_strand;
+  
+  if (a == NULL || b == NULL || bsp == NULL) return FALSE;
+  
+  a_strand = SeqLocStrand (a);
+  b_strand = SeqLocStrand (b);
+  if ((a_strand == Seq_strand_minus && b_strand != Seq_strand_minus)
+      || (a_strand != Seq_strand_minus && b_strand == Seq_strand_minus)) {
+      return FALSE;
+  }
+  
+  a_right = GetOffsetInBioseq (a, bsp, SEQLOC_RIGHT_END);
+  a_left = GetOffsetInBioseq (a, bsp, SEQLOC_LEFT_END);
+  
+  slp = SeqLocFindNext (b, NULL);
+  prev_right = GetOffsetInBioseq (slp, bsp, SEQLOC_RIGHT_END);
+  prev_left = GetOffsetInBioseq (slp, bsp, SEQLOC_LEFT_END);
+  slp = SeqLocFindNext (b, slp);
+  while (slp != NULL) {
+    b_right = GetOffsetInBioseq (slp, bsp, SEQLOC_RIGHT_END);
+    b_left = GetOffsetInBioseq (slp, bsp, SEQLOC_LEFT_END);
+    if (a_left == prev_right + 1 && a_right == b_left - 1) {
+      return TRUE;
+    } else if (a_left == b_right + 1 && a_right == prev_left - 1) {
+      return TRUE;
+    } else {
+      prev_right = b_right;
+      prev_left = b_left;
+      slp = SeqLocFindNext (b, slp);
+    }
+  }
+  return FALSE;
+}
+
+
+static Boolean LocAContainsIntervalOfB (SeqLocPtr a, SeqLocPtr b)
+{
+  SeqLocPtr interval;
+  Boolean   rval = FALSE;
+
+  if (a == NULL || b == NULL) return FALSE;
+
+  interval = SeqLocFindNext (b, NULL);
+  while (interval != NULL && !rval) {
+    if (IsLocAInBonSameStrand (interval, a)) {
+      rval = TRUE;
+    } else {
+      interval = SeqLocFindNext (b, interval);
+    }
+  }
+  return rval;
+}
+
+
+/* This section of code deals with identifying and labeling features
+ * for the definition line.
+ * The features currently handled are:
+ *     genes
+ *     exons
+ *     introns
+ *     LTRs
+ *     3' UTRs
+ *     5' UTRs
+ *     CDSs
+ *     rRNA
+ *     mRNA
+ *     misc RNA
+ *     snRNA
+ *     snoRNA
+ *     insertion sequences
+ *     integrons
+ *     D-loops
+ *     mRNA
+ *     tRNA
+ *     control regions
+ *     misc feature listed as intergenic spacer in comment
+ *     satellite sequences
+ *     promoter regions
+ *     endogenous virus source features
+ *     transposons
+ */
+
+static Boolean LIBCALLBACK IsGene (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_GENE) return FALSE;
+  return TRUE;
+}
+
+static CharPtr GetGeneName (GeneRefPtr grp, Boolean suppress_locus_tag)
+{
+  ValNodePtr syn;
+
+  if (grp == NULL) return NULL;
+  if (SeqMgrGeneIsSuppressed (grp)) return NULL;
+  if (StringDoesHaveText (grp->locus)) return grp->locus;
+  if (! suppress_locus_tag && StringDoesHaveText (grp->locus_tag)) 
+      return grp->locus_tag;
+  if (StringDoesHaveText (grp->desc)) return grp->desc;
+  for (syn = grp->syn; syn != NULL; syn = syn->next)
+  {
+    if (syn != NULL && syn->data.ptrvalue != NULL)
+      return syn->data.ptrvalue;
+  }
+  return NULL;
+}
+
+static CharPtr GetAlleleName (GeneRefPtr grp, Boolean suppress_locus_tag)
+{
+  size_t  lenallele;
+  size_t  lengenename;
+  CharPtr  gene_name;
+  CharPtr  buffer;
+
+  if (grp == NULL) return NULL;
+  if (StringHasNoText (grp->allele)) return NULL;
+  gene_name = GetGeneName (grp, suppress_locus_tag);
+  if (StringHasNoText (gene_name)) return NULL;
+  lenallele = StringLen (grp->allele);
+  lengenename = StringLen (gene_name);
+  
+  if (lenallele > lengenename
+    && StringNICmp (gene_name, grp->allele, lengenename) == 0)
+  {
+    return StringSave (grp->allele);
+  }
+  else if (grp->allele[0] == '-')
+  {
+    buffer = MemNew (lenallele + lengenename + 1);
+    if (buffer == NULL) return NULL;
+    StringCpy (buffer, gene_name);
+    StringCat (buffer, grp->allele);
+  }
+  else
+  {
+    buffer = MemNew (lenallele + lengenename + 2);
+    if (buffer == NULL) return NULL;
+    StringCpy (buffer, gene_name);
+    StringCat (buffer, "-");
+    StringCat (buffer, grp->allele);
+  }
+
+  return buffer;
+}
+
+/* This function compares the gene names and allele names of the gene
+ * to see if they match.
+ */
+static Boolean DoGenesMatch 
+(GeneRefPtr grp1,
+ GeneRefPtr grp2,
+ Boolean suppress_locus_tag)
+{
+  CharPtr name1;
+  CharPtr name2;
+
+  name1 = GetGeneName (grp1, suppress_locus_tag);
+  name2 = GetGeneName (grp2, suppress_locus_tag);
+  if (StringCmp (name1, name2) != 0) return FALSE;
+  
+  name1 = GetAlleleName (grp1, suppress_locus_tag);
+  name2 = GetAlleleName (grp2, suppress_locus_tag);
+  if ((name1 == NULL && name2 != NULL)
+    || (name1 != NULL && name2 == NULL))
+  {
+    if (name1 != NULL) MemFree (name1);
+    if (name2 != NULL) MemFree (name2);
+    return FALSE;
+  }
+
+  if ((name1 == NULL && name2 == NULL)
+           || (StringCmp (name1, name2) == 0))
+  {
+    if (name1 != NULL) MemFree (name1);
+    if (name2 != NULL) MemFree (name2);
+    return TRUE;
+  }
+  
+  if (name1 != NULL) MemFree (name1);
+  if (name2 != NULL) MemFree (name2);
+  return  FALSE;
+}
+
+/* This function looks at the pseudo flag on the object itself as well as
+ * the pseudo flag on the gene reference for the object (if one is present).
+ */
+static Boolean IsPseudo (
+  SeqFeatPtr sfp
+)
+{
+  GeneRefPtr grp;
+  SeqMgrFeatContext context;
+
+  if (sfp == NULL) return FALSE;
+  if (sfp->pseudo) return TRUE;
+  if (sfp->data.choice == SEQFEAT_GENE)
+  {
+    grp = sfp->data.value.ptrvalue;
+  }
+  else
+  { 
+    grp = SeqMgrGetGeneXref (sfp);
+  }
+  if (grp == NULL) 
+  {
+    if (sfp->data.choice != SEQFEAT_GENE) {
+      sfp = SeqMgrGetOverlappingGene(sfp->location, &context);
+      return IsPseudo(sfp);
+    } else {
+      return FALSE;
+    }
+  } else {
+    return grp->pseudo;
+  }
+}
+
+static Boolean LIBCALLBACK IsExon (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_exon) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsIntron (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_intron) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsExonOrIntron (SeqFeatPtr sfp)
+{
+  return IsExon(sfp) || IsIntron(sfp);
+}
+
+static Boolean LIBCALLBACK IsLTR (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_LTR) return FALSE;
+  return TRUE;
+}
+
+static CharPtr GetLTRDescription (
+  SeqFeatPtr sfp
+)
+{
+  CharPtr description;
+  size_t comment_len;
+  if (sfp == NULL) return NULL;
+  if (sfp->comment == NULL) return NULL;
+  comment_len = StringLen (sfp->comment);
+  if (comment_len > 3 && StringCmp (sfp->comment + comment_len - 3, "LTR") == 0)
+  {
+    description = (CharPtr) MemNew (comment_len - 3);
+    if (description == NULL) return NULL;
+    StringNCpy (description, sfp->comment, comment_len - 4);
+    description[comment_len - 4] = 0;
+  }
+  else
+  {
+    description = StringSave (sfp->comment);
+  }
+  return description;
+}
+
+static Boolean LIBCALLBACK Is3UTR (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_3UTR) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK Is5UTR (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_5UTR) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsCDS (SeqFeatPtr sfp)
+{
+  if (sfp == NULL) return FALSE;
+  if (sfp->data.choice == SEQFEAT_CDREGION)
+    return TRUE;
+  return FALSE;
+}
+
+static Boolean LIBCALLBACK IsrRNA (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_rRNA) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsMiscRNA (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL 
+    || (sfp->idx.subtype != FEATDEF_misc_RNA
+      && sfp->idx.subtype != FEATDEF_otherRNA)) 
+  {
+    return FALSE;
+  }
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsncRNA (
+  SeqFeatPtr sfp
+)
+{
+  RnaRefPtr rrp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return FALSE;
+  if (sfp->idx.subtype == FEATDEF_scRNA 
+      || sfp->idx.subtype == FEATDEF_snRNA 
+      || sfp->idx.subtype == FEATDEF_snoRNA
+      || sfp->idx.subtype == FEATDEF_ncRNA
+      || sfp->idx.subtype == FEATDEF_tmRNA)
+  {
+    return TRUE;
+  }
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (rrp == NULL || rrp->type != 255 || rrp->ext.choice != 1)
+  {
+    return FALSE;
+  }
+  else if (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
+      || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
+      || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0
+      || IsStringInNcRNAClassList (rrp->ext.value.ptrvalue))
+  {
+    return TRUE;
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+
+static CharPtr GetncRNAProduct (SeqFeatPtr sfp, Boolean use_ncrna_note)
+{
+  GBQualPtr gbq = NULL, q_class = NULL, q_product = NULL;
+  CharPtr product = NULL;
+
+  if (sfp == NULL)
+  {
+    return NULL;
+  }
+  
+  gbq = sfp->qual;
+  while (gbq != NULL && q_product == NULL) {
+    if (StringICmp (gbq->qual, "ncRNA_class") == 0
+        && !StringHasNoText (gbq->val)) {
+      q_class = gbq;
+    } else if (StringICmp (gbq->qual, "product") == 0
+        && !StringHasNoText (gbq->val)) {
+      q_product = gbq;
+    }
+    gbq = gbq->next;
+  }
+  if (q_product != NULL) {
+    product = StringSave (q_product->val);
+  } else if (q_class != NULL) {
+    if (use_ncrna_note && !StringHasNoText (sfp->comment)) {
+      product = StringSave (sfp->comment);
+    } else {
+      product = StringSave (q_class->val);
+    }
+  } else if (use_ncrna_note && !StringHasNoText (sfp->comment)) {
+    product = StringSave (sfp->comment);
+  }
+  return product;
+}
+
+
+static Boolean LIBCALLBACK IsPrecursorRNA (SeqFeatPtr sfp)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_preRNA) return FALSE;
+  return TRUE;
+}
+
+
+static CharPtr mobile_element_keywords [] = {
+  "insertion sequence",
+  "retrotransposon",
+  "non-LTR retrotransposon",
+  "transposon",
+  "integron",
+  "other",
+  "SINE",
+  "MITE",
+  "LINE"
+};
+
+enum mobile_element_keyword_nums 
+{
+  eMobileElementInsertionSequence = 0,
+  eMobileElementRetrotransposon,
+  eMobileElementNonLTRRetrotransposon,
+  eMobileElementTransposon,
+  eMobileElementIntegron,
+  eMobileElementOther,
+  eMobileElementSINE,
+  eMobileElementMITE,
+  eMobileElementLINE
+};
+
+static Int4 StartsWithMobileElementKeyword (CharPtr txt)
+{
+  Int4 i, keyword_len;
+    
+  for (i=0; i < sizeof (mobile_element_keywords) / sizeof (CharPtr); i++) {
+    keyword_len = StringLen (mobile_element_keywords[i]);
+    if (StringNCmp (txt, mobile_element_keywords[i], keyword_len) == 0
+        && (*(txt + keyword_len) == ':' || *(txt + keyword_len) == 0)) {      
+      return i;
+    }
+  }
+  return -1;
+}
+
+static Int4 IsMobileElementGBQual (GBQualPtr gbqual)
+{
+  Int4 keyword_idx;
+  if (gbqual == NULL || gbqual->qual == NULL || gbqual->val == NULL) return -1;
+  if (StringCmp (gbqual->qual, "mobile_element") != 0) return -1;
+  keyword_idx = StartsWithMobileElementKeyword (gbqual->val);
+  if (keyword_idx < 0) return -1;
+  if (keyword_idx == eMobileElementOther
+      && StringStr (gbqual->val, "transposable element") == NULL) {
+    return -1;
+  } else {
+    return keyword_idx;
+  }
+}
+
+
+static Boolean FeatureDoesNotGetPartialComplete (SeqFeatPtr sfp)
+{
+  GBQualPtr gbqual;
+  Int4 keyword_idx;
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_repeat_region) return FALSE;
+  
+  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
+  {
+    keyword_idx = IsMobileElementGBQual(gbqual);
+    if (keyword_idx == eMobileElementSINE
+        || keyword_idx == eMobileElementLINE) {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+
+NLM_EXTERN Boolean LIBCALLBACK IsMobileElement (SeqFeatPtr sfp)
+{
+  GBQualPtr gbqual;
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_repeat_region) return FALSE;
+  
+  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
+  {
+    if (IsMobileElementGBQual(gbqual) > -1) {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+static Boolean LIBCALLBACK IsRemovableMobileElement (SeqFeatPtr sfp)
+{
+  GBQualPtr gbqual;
+  Int4 keyword_idx;
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_repeat_region) return FALSE;
+  
+  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
+  {
+    keyword_idx = IsMobileElementGBQual(gbqual);
+    if (keyword_idx >= eMobileElementSINE
+        && keyword_idx <= eMobileElementLINE) {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+static CharPtr GetMobileElementTypeword (CharPtr desc_start, Int4 keyword_idx)
+{
+  if (keyword_idx < 0) return NULL;
+  if (StringHasNoText (desc_start)) {
+    return mobile_element_keywords[keyword_idx];
+  }
+  switch (keyword_idx) {
+    case eMobileElementTransposon:
+      if (StringStr (desc_start, "P-element") != NULL) {
+        return "P-element";
+      } else if (StringStr (desc_start, "MITE") != NULL) {
+        return "MITE";
+      } else {
+        return mobile_element_keywords[keyword_idx];
+      }
+      break;
+    case eMobileElementOther:
+      return "transposable element";
+      break;
+    case eMobileElementIntegron:
+      if (StringStr (desc_start, "superintegron") != NULL) {
+        return "superintegron";
+      } else {
+        return mobile_element_keywords[keyword_idx];
+      }
+      break;
+    default:
+      return mobile_element_keywords[keyword_idx];
+      break;
+  }      
+}
+
+
+static void LIBCALLBACK GetMobileElementFeatureLabel (
+  ValNodePtr      featlist,
+  BioseqPtr       bsp,
+  Uint1           biomol,
+  FeatureLabelPtr flp
+)
+{
+  GBQualPtr  gbqual;
+  Int4    keyword_idx = -1;
+  Int4    keyword_len;
+  Int4    val_len;
+  SeqFeatPtr      sfp;
+  CharPtr         desc_start = NULL, typeword, cp;
+
+  flp->pluralizable = TRUE;
+  flp->is_typeword_first = FALSE;
+  flp->typeword = NULL;
+  flp->description = NULL;
+
+  if (featlist == NULL) return;
+  sfp = featlist->data.ptrvalue;
+  if (sfp == NULL) return;
+
+  gbqual = sfp->qual;
+  while (gbqual != NULL 
+         && (keyword_idx = IsMobileElementGBQual(gbqual)) < 0)
+  {
+    gbqual = gbqual->next;
+  }
+  if (gbqual == NULL) return;
+    
+  keyword_len = StringLen (mobile_element_keywords[keyword_idx]);
+  desc_start = gbqual->val + keyword_len;
+  while (isspace (*desc_start) || *desc_start == ':') {
+    desc_start++;
+  }
+
+  /* find alternate typewords */
+  typeword = GetMobileElementTypeword(desc_start, keyword_idx);
+  if (typeword == NULL) return;
+  keyword_len = StringLen (typeword);
+
+  flp->typeword = StringSave (typeword);
+  val_len = StringLen (desc_start);
+  
+  if (StringHasNoText (desc_start))
+  {
+    flp->is_typeword_first = FALSE;
+    flp->description = NULL;
+  } else if (StringCmp (desc_start, typeword) == 0) {
+    /* just the keyword */
+    flp->is_typeword_first = FALSE;
+    flp->description = NULL;
+    return;
+  } else if (StringNCmp (desc_start, typeword, keyword_len) == 0) {
+    /* starts with keyword */
+    /* if keyword is hyphenated portion of name, no pluralization */
+    if (desc_start[keyword_len] == '-') {
+      flp->description = StringSave (desc_start);
+      flp->typeword = MemFree (flp->typeword);
+      flp->typeword = StringSave ("");
+      flp->pluralizable = FALSE;
+    } else {
+      flp->is_typeword_first = TRUE;
+      flp->description = StringSave (desc_start + keyword_len + 1);
+    }
+    return;
+  } else if (val_len > 8 && StringCmp (desc_start + val_len - keyword_len, typeword) == 0
+             && val_len - keyword_len - 1 >= 0
+             && isspace (*(desc_start + val_len - keyword_len - 1))) {
+    /* ends with keyword */
+    flp->is_typeword_first = FALSE;
+    flp->description = MemNew (val_len - keyword_len);
+    if (flp->description == NULL) return;
+    StringNCpy (flp->description, desc_start, val_len - keyword_len - 1);
+    flp->description[val_len - keyword_len -1] = 0;
+  } else if ((cp = StringStr (desc_start, typeword)) != NULL
+             && cp != desc_start
+             && isspace (*(cp -1))) {
+    /* keyword in the middle */
+    flp->description = StringSave (desc_start);
+    flp->typeword = MemFree (flp->typeword);
+    flp->typeword = StringSave ("");
+    flp->pluralizable = FALSE;
+  } else {
+    /* keyword not in description */
+    if (StringICmp (flp->typeword, "integron") == 0) {
+      flp->is_typeword_first = FALSE;
+    } else {
+      flp->is_typeword_first = TRUE;
+    }
+    flp->description = StringSave (desc_start);
+    if (StringCmp (flp->description, "") == 0) {
+      flp->is_typeword_first = FALSE;
+    }
+  }
+  if (StringCmp (flp->description, "unnamed") == 0) {
+    flp->description = MemFree (flp->description);
+  }
+}
+
+
+static Boolean LIBCALLBACK IsEndogenousVirusSequence (
+  SeqFeatPtr sfp
+)
+{
+  GBQualPtr gbqual;
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_repeat_region) return FALSE;
+  
+  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
+  {
+    if (StringCmp (gbqual->qual, "endogenous_virus") == 0)
+      return TRUE;
+  }
+  return FALSE;
+}
+
+static CharPtr GetEndogenousVirusSequenceDescription (
+  SeqFeatPtr sfp
+)
+{
+  GBQualPtr gbqual;
+
+  if (sfp == NULL) return NULL;
+  
+  gbqual = sfp->qual;
+  while (gbqual != NULL && StringCmp (gbqual->qual, "endogenous_virus") != 0)
+  {
+    gbqual = gbqual->next;
+  }
+  if (gbqual != NULL)
+  {
+    if (StringDoesHaveText (gbqual->val)
+      && StringCmp (gbqual->val, "unnamed") != 0)
+    {
+      return StringSave (gbqual->val);
+    }
+  }
+  return NULL;
+}
+
+static Boolean LIBCALLBACK IsDloop (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_D_loop) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsmRNA (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_mRNA) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IstRNA (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_tRNA) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsControlRegion (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL
+    || sfp->idx.subtype != FEATDEF_misc_feature
+    || sfp->comment == NULL
+    || StringNCmp (sfp->comment, "control region", StringLen ("control region")) != 0)
+  {
+    return FALSE;
+  }
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsGeneCluster (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL
+    || sfp->idx.subtype != FEATDEF_misc_feature
+    || sfp->comment == NULL
+    || (StringStr (sfp->comment, "gene cluster") == NULL
+        && StringStr (sfp->comment, "gene locus") == NULL))
+  {
+    return FALSE;
+  }
+  return TRUE;
+}
+
+
+static void LIBCALLBACK GetGeneClusterFeatureLabel (
+  ValNodePtr      featlist,
+  BioseqPtr       bsp,
+  Uint1           biomol,
+  FeatureLabelPtr flp
+)
+{
+  SeqFeatPtr main_feat;
+  CharPtr    cp;
+  Int4       datalen;
+
+  if (featlist == NULL || featlist->data.ptrvalue == NULL) return;
+  main_feat = featlist->data.ptrvalue;
+  if (StringHasNoText (main_feat->comment)) return;
+  cp = StringStr (main_feat->comment, "gene cluster");
+  if (cp == NULL)
+  {
+    cp = StringStr (main_feat->comment, "gene locus");
+    if (cp == NULL) return;
+    flp->typeword = StringSave ("gene locus");
+  }
+  else
+  {
+    flp->typeword = StringSave ("gene cluster");
+  }
+  flp->pluralizable = FALSE;
+  flp->is_typeword_first = FALSE;
+  datalen = cp - main_feat->comment;
+  if (datalen > 0)
+  {
+    flp->description = (CharPtr) MemNew ((datalen + 1) * sizeof (Char));
+    StringNCpy (flp->description, main_feat->comment, datalen);
+    flp->description [datalen] = 0;
+    TrimSpacesAroundString (flp->description);
+  }
+  else
+  {
+    flp->description = NULL;
+  }
+}
+
+
+static Boolean LIBCALLBACK IsIntergenicSpacer (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL
+    || sfp->idx.subtype != FEATDEF_misc_feature
+    || sfp->comment == NULL
+    || StringStr (sfp->comment, "intergenic spacer") == NULL)
+  {
+    return FALSE;
+  }
+  return TRUE;
+}
+
+/* This function produces the default definition line label for a misc_feature 
+ * that has the word "intergenic spacer" in the comment.  If the comment starts
+ * with the word "contains", "contains" is ignored.  If "intergenic spacer"
+ * appears first in the comment (or first after the word "contains", the text
+ * after the words "intergenic spacer" but before the first semicolon (if any)
+ * appear after the words "intergenic spacer" in the definition line.  If there
+ * are words after "contains" or at the beginning of the comment before the words
+ * "intergenic spacer", this text will appear in the definition line before the words
+ * "intergenic spacer".
+ */
+static void LIBCALLBACK GetIntergenicSpacerFeatureLabel (
+  ValNodePtr      featlist,
+  BioseqPtr       bsp,
+  Uint1           biomol,
+  FeatureLabelPtr flp
+)
+{
+  SeqFeatPtr main_feat;
+  CharPtr    cp, buffer;
+  Int4       datalen, offset;
+
+  if (featlist == NULL || featlist->data.ptrvalue == NULL) return;
+  main_feat = featlist->data.ptrvalue;
+  if (StringHasNoText (main_feat->comment)) return;
+  if (StringNCmp (main_feat->comment, "contains ", 9) == 0)
+  {
+    buffer = main_feat->comment + 9;
+  }
+  else
+  {
+    buffer = main_feat->comment;
+  }
+  cp = StringStr (buffer, "intergenic spacer");
+  if (cp == NULL) return;
+  flp->typeword = StringSave ("intergenic spacer");
+  flp->pluralizable = FALSE;
+  if (cp == buffer)
+  {
+    flp->is_typeword_first = TRUE;
+    offset = StringLen ("intergenic spacer") + 1;
+    if (StringNCmp (cp + offset, "and ", 4) == 0
+        || *(cp + StringLen("intergenic spacer")) == 0)
+    {
+      flp->description = NULL;
+    }
+    else
+    {
+      flp->description = StringSave (cp + StringLen ("intergenic spacer") + 1);
+      cp = StringChr (flp->description, ';');
+      if (cp != NULL)
+      {
+        *cp = 0;
+      }
+    }
+  }
+  else
+  {
+    flp->is_typeword_first = FALSE;
+    datalen = cp - buffer;
+    flp->description = MemNew ( datalen + 1);
+    if (flp->description == NULL) return;
+    StringNCpy (flp->description, buffer, datalen);
+    flp->description [datalen] = 0;
+    TrimSpacesAroundString (flp->description);
+  }
+}
+
+/* These structures are used for parsing tRNA and intergenic spacer information
+ * from misc_feature comments. 
+ */
+typedef struct commentfeat
+{
+  CharPtr product_name;
+  CharPtr gene_name;
+} CommentFeatData, PNTR CommentFeatPtr;
+
+
+static CommentFeatPtr CommentFeatFree (CommentFeatPtr cfp)
+{
+  if (cfp != NULL) {
+    cfp->product_name = MemFree (cfp->product_name);
+    cfp->gene_name = MemFree (cfp->gene_name);
+    cfp = MemFree (cfp);
+  }
+  return cfp;
+}
+
+
+typedef struct intergenicspacerdef
+{
+  CharPtr first_gene;
+  CharPtr second_gene;
+} IntergenicSpacerDefData, PNTR IntergenicSpacerDefPtr;
+
+static IntergenicSpacerDefPtr IntergenicSpacerDefFree (IntergenicSpacerDefPtr ip)
+{
+  if (ip != NULL) {
+    ip->first_gene = MemFree (ip->first_gene);
+    ip->second_gene = MemFree (ip->second_gene);
+    ip = MemFree (ip);
+  }
+  return ip;
+}
+
+
+static Boolean IsUpperCaseChar (Char ch)
+{
+  if (StringChr("ABCDEFGHIJKLMNOPQRSTUVWXYZ",ch) != NULL)
+    return TRUE;
+  else
+    return FALSE;
+}
+
+static Boolean IsLowerCaseChar (Char ch)
+{
+  if (StringChr("abcdefghijklmnopqrstuvwxyz",ch) != NULL)
+    return TRUE;
+  else
+    return FALSE;
+}
+
+static CommentFeatPtr ParseGeneFromNoteForDefLine (CharPtr PNTR comment)
+{
+  CommentFeatPtr tdp;
+  CharPtr    product_start, product_end, gene_start, gene_end, cp;
+  Int4       product_len, gene_len;
+  
+  if (comment == NULL || *comment == NULL)
+  {
+    return NULL;
+  }
+  
+  /* tRNA name must start with "tRNA-" and be followed by one uppercase letter and
+   * two lowercase letters.
+   */
+  product_start = *comment;
+  gene_start = product_start;
+  while (*gene_start != 0 && !isspace (*gene_start)) {
+    gene_start++;
+  }
+  if (gene_start == product_start) {
+    return NULL;
+  }
+  product_end = gene_start;
+  while (isspace (*gene_start)) {
+    gene_start++;
+  }
+  if (*gene_start != '(') {
+    return NULL;
+  }
+  gene_start++;
+  gene_end = gene_start;
+  while (*gene_end != 0 && *gene_end != ')') {
+    gene_end++;
+  }
+  if (*gene_end == 0) {
+    return NULL;
+  }
+  cp = gene_end + 1;
+  while (*cp != 0 && isspace (*cp)) {
+    cp++;
+  }
+
+  if (StringNCmp (cp, "gene", 4) != 0) {
+    return NULL;
+  }
+
+  tdp = (CommentFeatPtr) MemNew (sizeof (CommentFeatData));
+  if (tdp == NULL)
+  {
+    return NULL;
+  }
+  product_len = product_end - product_start;
+  tdp->product_name = (CharPtr) MemNew (sizeof (Char) * (1 + product_len));
+  StringNCpy (tdp->product_name, product_start, product_len);
+  tdp->product_name[product_len] = 0;
+  
+  gene_len = gene_end - gene_start;
+  tdp->gene_name = (CharPtr) MemNew (sizeof (Char) * (1 + gene_len));
+  StringNCpy (tdp->gene_name, gene_start, gene_len);
+  tdp->gene_name[gene_len] = 0;
+  
+  *comment = cp + 4;
+  return tdp;
+}
+
+
+static IntergenicSpacerDefPtr ParseIntergenicSpacerFromNoteForDef (CharPtr PNTR comment)
+{
+  IntergenicSpacerDefPtr idp;
+  CharPtr                first_gene_start, dash, second_gene_start, second_gene_end, cp;
+  Int4                   first_gene_len, second_gene_len;
+  
+  if (comment == NULL || *comment == NULL)
+  {
+    return NULL;
+  }
+  
+  /* description must start with "trn" and be followed by one uppercase letter, followed
+   * by a dash, followed by "trn", followed by one uppercase letter, followed by whitespace,
+   * followed by the phrase "intergenic spacer".
+   */
+  first_gene_start = *comment;
+  dash = first_gene_start;
+  while (*dash != 0 && isalpha (*dash)) {
+    dash++;
+  }
+  if (*dash != '-') {
+    return NULL;
+  }
+  second_gene_start = dash + 1;
+  second_gene_end = second_gene_start;
+  while (*second_gene_end != 0 && isalpha (*second_gene_end)) {
+    second_gene_end ++;
+  }
+  if (!isspace (*second_gene_end)) {
+    return NULL;
+  }
+  cp = second_gene_end;
+  while (isspace (*cp)) {
+    cp++;
+  }
+  if (StringNCmp (cp, "intergenic spacer", 17) != 0) {
+    return NULL;
+  }
+  
+  idp = (IntergenicSpacerDefPtr) MemNew (sizeof (IntergenicSpacerDefData));
+  if (idp == NULL)
+  {
+    return NULL;
+  }
+  
+  first_gene_len = dash - first_gene_start;
+  idp->first_gene = (CharPtr) MemNew (sizeof (Char) * (1 + first_gene_len));
+  StringNCpy (idp->first_gene, first_gene_start, first_gene_len);
+  idp->first_gene [first_gene_len] = 0;
+
+  second_gene_len = second_gene_end - second_gene_start;
+  idp->second_gene = (CharPtr) MemNew (sizeof (Char) * (1 + second_gene_len));
+  StringNCpy (idp->second_gene, second_gene_start, second_gene_len);
+  idp->second_gene [second_gene_len] = 0;
+
+  *comment = cp + 17;
+  return idp;
+}
+
+/* This creates a feature clause from a tRNADef structure. */
+static FeatureClausePtr 
+FeatureClauseFromParsedComment 
+(CommentFeatPtr tdp,
+ SeqFeatPtr misc_feat,
+ Boolean    is_partial,
+ BioseqPtr  bsp,
+ DeflineFeatureRequestListPtr rp)
+{
+  FeatureClausePtr fcp;
+  
+  if (tdp == NULL)
+  {
+    return NULL;
+  }
+  
+  fcp = NewFeatureClause ( misc_feat, bsp, rp);
+  if (fcp != NULL)
+  {
+    fcp->feature_label_data.is_typeword_first = FALSE;
+    fcp->feature_label_data.typeword = StringSave ("gene");
+    fcp->feature_label_data.description = (CharPtr) MemNew (16 * sizeof (Char));
+    if (fcp->feature_label_data.description != NULL)
+    {
+      sprintf (fcp->feature_label_data.description, "%s (%s)",
+               tdp->product_name, tdp->gene_name);
+    }
+    if (is_partial)
+    {
+      fcp->interval = StringSave ("partial sequence");
+    }
+    else
+    {
+      fcp->interval = StringSave ("complete sequence");
+    }
+  }
+  return fcp;
+}
+
+/* This function produces a feature clause list that should replace the original
+ * single clause for a misc_feat that contains a note with one or more tRNAs and
+ * an intergenic spacer.
+ */
+static ValNodePtr 
+ParsetRNAIntergenicSpacerElements 
+(SeqFeatPtr misc_feat,
+BioseqPtr   bsp,
+DeflineFeatureRequestListPtr rp)
+{
+  FeatureClausePtr fcp;
+  ValNodePtr head, vnp;
+  Boolean partial5, partial3;
+  CharPtr                cp;
+  IntergenicSpacerDefPtr spacer = NULL;
+  CommentFeatPtr         gene1 = NULL, gene2 = NULL;
+  Boolean                parse_list = TRUE;
+  
+
+  if (misc_feat == NULL 
+      || StringHasNoText (misc_feat->comment)) 
+  {
+    return NULL;
+  }
+  
+  /* for list, must start with the word "contains" */
+  if (StringNICmp (misc_feat->comment, "contains ", 9) == 0)
+  {
+    cp = misc_feat->comment + 9;
+  }
+  else
+  {
+    return NULL;
+  }
+  
+  while (isspace (*cp))
+  {
+    cp ++;
+  }
+  
+  gene1 = ParseGeneFromNoteForDefLine (&cp);
+  if (gene1 != NULL)
+  {
+    if (*cp == ',')
+    {
+      cp++;
+    }
+    if (StringNCmp (cp, " and", 4) == 0)
+    {
+      cp += 4;
+    }
+    while (isspace (*cp))
+    {
+      cp++;
+    }
+  }
+ 
+  spacer = ParseIntergenicSpacerFromNoteForDef (&cp);
+
+  if (spacer == NULL) {
+    gene1 = CommentFeatFree (gene1);
+    return NULL;
+  }
+  if (spacer != NULL)
+  {
+    if (*cp == ',')
+    {
+      cp++;
+    }
+    if (StringNCmp (cp, " and", 4) == 0)
+    {
+      cp += 4;
+    }
+    while (isspace (*cp))
+    {
+      cp++;
+    }
+  }
+  
+  gene2 = ParseGeneFromNoteForDefLine (&cp);
+  
+  while (isspace (*cp))
+  {
+    cp++;
+  }
+  
+  head = NULL;
+  CheckSeqLocForPartial (misc_feat->location, &partial5, &partial3);
+
+  if ((*cp != 0 && *cp != ';') /* this must be the complete note or be separated from 
+                                * the rest of the note by a semicolon
+                                */
+      || ! parse_list /* didn't start with "contains" */
+      || spacer == NULL /* no spacer */
+      /* don't parse if genes don't match up */
+      || (gene1 != NULL && StringCmp (gene1->gene_name, spacer->first_gene) != 0)
+      || (gene2 != NULL && StringCmp (gene2->gene_name, spacer->second_gene) != 0))
+  {
+    /* do nothing - special parse conditions not met */
+    gene1 = CommentFeatFree (gene1);
+    gene2 = CommentFeatFree (gene2);
+    spacer = IntergenicSpacerDefFree (spacer);
+    return NULL;
+  }
+  
+  /* add clause for tRNA before spacer (if any) */
+  fcp = FeatureClauseFromParsedComment (gene1, misc_feat, partial5, bsp, rp);
+  if (fcp != NULL)
+  {   
+    vnp = ValNodeNew (head);
+    if (head == NULL) head = vnp;
+    if (vnp == NULL) return NULL;
+    vnp->data.ptrvalue = fcp;
+    vnp->choice = DEFLINE_CLAUSEPLUS;
+  }
+  
+  /* spacer was already checked, so we know it is not NULL */
+  fcp = NewFeatureClause ( misc_feat, bsp, rp);
+  if (fcp != NULL)
+  {
+    fcp->feature_label_data.is_typeword_first = FALSE;
+    fcp->feature_label_data.typeword = StringSave ("intergenic spacer");
+    fcp->feature_label_data.description = (CharPtr) MemNew (10 * sizeof (Char));
+    if (fcp->feature_label_data.description != NULL)
+    {
+      sprintf (fcp->feature_label_data.description, "%s-%s",
+               spacer->first_gene, spacer->second_gene);
+    }
+    if ((gene1 == NULL && partial5) || (gene2 == NULL && partial3))
+    {
+      fcp->interval = StringSave ("partial sequence");
+    }
+    else
+    {
+      fcp->interval = StringSave ("complete sequence");
+    }
+      
+    vnp = ValNodeNew (head);
+    if (head == NULL) head = vnp;
+    if (vnp == NULL) return NULL;
+    vnp->data.ptrvalue = fcp;
+    vnp->choice = DEFLINE_CLAUSEPLUS;
+  }
+
+  /* add clause for tRNA after spacer (if any) */
+  fcp = FeatureClauseFromParsedComment (gene2, misc_feat, partial3, bsp, rp);
+  if (fcp != NULL)
+  {   
+    vnp = ValNodeNew (head);
+    if (head == NULL) head = vnp;
+    if (vnp == NULL) return NULL;
+    vnp->data.ptrvalue = fcp;
+    vnp->choice = DEFLINE_CLAUSEPLUS;
+  }
+  spacer = IntergenicSpacerDefFree (spacer);
+  gene1 = CommentFeatFree (gene1);
+  gene2 = CommentFeatFree (gene2);
+  
+  return head;
+}
+
+static Boolean LIBCALLBACK IsSatelliteSequence (
+  SeqFeatPtr sfp
+)
+{
+  GBQualPtr gbqual;
+  if (sfp == NULL
+    || sfp->idx.subtype != FEATDEF_repeat_region
+    || StringHasNoText (sfp->comment)
+    || (StringNCmp (sfp->comment, "microsatellite", 14) != 0
+      && StringNCmp (sfp->comment, "satellite", 9) != 0))
+  {
+    return FALSE;
+  }
+
+  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
+  {
+    if (StringCmp (gbqual->qual, "rpt_type") == 0
+      && StringCmp (gbqual->val, "tandem") == 0)
+    {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+static Boolean LIBCALLBACK IsPromoter (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_promoter) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsEndogenousVirusSourceFeature (
+  SeqFeatPtr sfp
+)
+{
+  BioSourcePtr biop;
+  SubSourcePtr  ssp;
+
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_BIOSRC) return FALSE;
+  if ((biop = sfp->data.value.ptrvalue) == NULL) return FALSE;
+  ssp = biop->subtype;
+  while (ssp != NULL && ssp->subtype != SUBSRC_endogenous_virus_name)
+  {
+    ssp = ssp->next;
+  }
+  if (ssp != NULL) return TRUE;
+  return FALSE;
+}
+
+static CharPtr GetEndogenousVirusSourceFeatureDescription (
+  SeqFeatPtr sfp
+)
+{
+  BioSourcePtr biop;
+  SubSourcePtr  ssp;
+
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_BIOSRC) return NULL;
+  if ((biop = sfp->data.value.ptrvalue) == NULL) return NULL;
+  ssp = biop->subtype;
+  while (ssp != NULL && ssp->subtype != SUBSRC_endogenous_virus_name)
+  {
+    ssp = ssp->next;
+  }
+  if (ssp != NULL && ssp->name != NULL)
+  {
+    return StringSave (ssp->name);
+  }
+  return NULL;
+}
+
+
+static CharPtr noncoding_feature_keywords[] = {
+  "similar to ",
+  "contains "
+};
+
+static CharPtr find_noncoding_feature_keyword (
+  CharPtr comment
+)
+{
+  Int4 i, num_noncoding_feature_keywords, keywordlen;
+  CharPtr cp, buffer;
+
+  if (comment == NULL) return NULL;
+  num_noncoding_feature_keywords = sizeof (noncoding_feature_keywords) / sizeof (CharPtr);
+  for (i=0; i < num_noncoding_feature_keywords; i++)
+  {
+    keywordlen = StringLen (noncoding_feature_keywords [i]);
+    buffer = comment;
+    while ((cp = StringStr (buffer, noncoding_feature_keywords [i])) != NULL)
+    {
+      if ( StringNCmp (cp + keywordlen,
+                       "GenBank Accession Number",
+                       StringLen ("GenBank Accession Number")) != 0)
+      {
+        return cp + keywordlen;
+      }
+      else
+      {
+        buffer = cp + 1;
+      }
+    }
+  }
+  return NULL;
+}
+
+static Boolean LIBCALLBACK IsNoncodingProductFeat (
+  SeqFeatPtr sfp
+)
+{
+  if ( sfp == NULL
+    || sfp->idx.subtype != FEATDEF_misc_feature
+    || sfp->comment == NULL
+    || StringStr (sfp->comment, "intergenic") != NULL
+    || (find_noncoding_feature_keyword (sfp->comment) == NULL
+      && (StringStr (sfp->comment, "nonfunctional ") == NULL
+        || StringStr (sfp->comment, " due to ") == NULL)))
+  {
+    return FALSE;
+  }
+
+  return TRUE;
+}
+
+static CharPtr GetNoncodingProductFeatProduct (
+  SeqFeatPtr sfp
+)
+{
+  CharPtr productname;
+  Int4    namelen, compare_len;
+  CharPtr name_start, sep;
+
+  if (sfp == NULL || sfp->comment == NULL) return NULL;
+
+  if ((name_start = StringStr (sfp->comment, "nonfunctional ")) != NULL
+    && (sep = StringStr (sfp->comment, " due to ")) != NULL
+    && sep > name_start)
+  {
+    productname = StringSave (name_start);
+    productname [ sep - name_start] = 0;
+    return productname;
+  }
+
+  name_start = find_noncoding_feature_keyword (sfp->comment);
+  if (name_start == NULL) return NULL;
+
+  sep = StringStr (name_start, ";");
+  if (sep == NULL)
+  {
+    namelen = StringLen (name_start);
+  }
+  else
+  {
+    namelen = sep - name_start;
+  }
+
+  productname = MemNew (namelen + 6);
+  if (productname == NULL) return NULL;
+
+  StringNCpy (productname, name_start, namelen);
+  productname [namelen] = 0;
+  
+  /* remove sequence from end of name if present */
+  compare_len = StringLen (" sequence");
+  if (StringCmp (productname + namelen - compare_len, " sequence") == 0)
+  {
+    productname [ namelen - compare_len] = 0;
+    namelen = StringLen (productname);
+  }
+  /* add "-like" if not present */
+  compare_len = StringLen ("-like");
+  if (StringCmp (productname + namelen - compare_len, "-like") != 0)
+  {
+    StringCat (productname, "-like");
+    namelen = StringLen (productname);
+  }
+  return productname;
+}
+
+static Boolean LIBCALLBACK IsMiscFeat (
+  SeqFeatPtr sfp
+)
+{
+  if ( sfp == NULL
+    || sfp->idx.subtype != FEATDEF_misc_feature
+    || sfp->comment == NULL)
+  {
+    return FALSE;
+  }
+
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK IsOperon (
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL 
+    || sfp->idx.subtype != FEATDEF_operon)
+  {
+    return FALSE;
+  }
+
+  return TRUE;
+}
+
+static Boolean IsRecognizedFeature (
+  SeqFeatPtr sfp
+)
+{
+  if (IsGene (sfp)
+    || IsCDS (sfp)
+    || IsExon (sfp)
+    || IsIntron (sfp)
+    || IsLTR (sfp)
+    || IsrRNA (sfp)
+    || IstRNA (sfp)
+    || IsmRNA (sfp)
+    || IsMiscRNA (sfp)
+    || IsncRNA (sfp)
+    || IsPrecursorRNA (sfp)
+    || Is3UTR (sfp)
+    || Is5UTR (sfp)
+    || IsMobileElement (sfp)
+    || IsEndogenousVirusSequence (sfp)
+    || IsEndogenousVirusSourceFeature (sfp)
+    || IsDloop (sfp)
+    || IsSatelliteSequence (sfp)
+    || IsControlRegion (sfp)
+    || IsIntergenicSpacer (sfp)
+    || IsGeneCluster (sfp)
+    || IsNoncodingProductFeat (sfp)
+    || IsPromoter (sfp)
+    || IsMiscFeat (sfp)
+    || IsOperon (sfp))
+  {
+    return TRUE;
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+/* The following section of code contains functions for dealing with lists of
+ * clauses.
+ */
+
+/* The functions for freeing the memory associated with lists of clauses 
+ * are recursive.
+ */
+static void FreeListElement (ValNodePtr element);
+
+/* This function simply frees the ValNodePtr, since there is no extra
+ * memory associated with a DEFLINE_FEATLIST item - the sfp that is
+ * pointed to by data.ptrvalue came from the sequence indexing functions
+ * and should under no circumstances be freed.
+ */
+static void FreeFeatlist (
+  ValNodePtr featlist
+)
+{
+
+  if (featlist == NULL) return;
+  ValNodeFree (featlist);
+}
+ 
+/* This function frees the memory associated with a FeatureClause, including
+ * the memory associated with any subclauses.
+ */
+static void FreeClausePlusData (
+  FeatureClausePtr fcp
+)
+{
+  if (fcp->interval != NULL)
+  {
+    MemFree (fcp->interval);
+    fcp->interval = NULL;
+  }
+  if (fcp->allelename != NULL)
+  {
+    MemFree (fcp->allelename);
+    fcp->allelename = NULL;
+  }
+  if (fcp->feature_label_data.typeword != NULL)
+  {
+    MemFree (fcp->feature_label_data.typeword);
+    fcp->feature_label_data.typeword = NULL;
+  }
+  if (fcp->feature_label_data.description != NULL)
+  {
+    MemFree (fcp->feature_label_data.description);
+    fcp->feature_label_data.description = NULL;
+  }
+  if (fcp->feature_label_data.productname != NULL)
+  {
+    MemFree (fcp->feature_label_data.productname);
+    fcp->feature_label_data.productname = NULL;
+  }
+  if (fcp->featlist != NULL)
+  {
+    FreeListElement (fcp->featlist);
+    fcp->featlist = NULL;
+  }
+  if (fcp->slp != NULL)
+  {
+    SeqLocFree (fcp->slp);
+  }
+}
+    
+/* This function frees the data associated with the FeatureClause
+ * and then frees the ValNode.
+ */
+static void FreeClausePlus (
+  ValNodePtr clauseplus
+)
+{
+  FeatureClausePtr data_struct;
+
+  if (clauseplus == NULL) return;
+  data_struct = (FeatureClausePtr) clauseplus->data.ptrvalue;
+  if (data_struct != NULL)
+  {
+    FreeClausePlusData (data_struct); 
+    MemFree (data_struct);
+    clauseplus->data.ptrvalue = NULL;
+  }
+  ValNodeFree (clauseplus);
+}
+ 
+/* This function frees a list of DEFLINE_FEATLIST, DEFLINE_REMOVEFEAT,
+ * and DEFLINE_CLAUSEPLUS items, starting with the last item in the list.
+ * It recursively frees memory associated with subclauses.
+ */ 
+static void FreeListElement (
+  ValNodePtr element
+)
+{
+  if (element == NULL) return;
+
+  FreeListElement (element->next);
+  element->next = NULL;
+  if (element->choice == DEFLINE_FEATLIST 
+    || element->choice == DEFLINE_REMOVEFEAT)
+  {
+    FreeFeatlist (element);
+  }
+  else if (element->choice == DEFLINE_CLAUSEPLUS)
+  {
+    FreeClausePlus (element);
+  }
+}
+
+/* This function excises from the list pointed to by head all of the clauses
+ * with the delete_me flag set to TRUE and all of the ValNodes with a choice
+ * of DEFLINE_REMOVEFEAT.
+ */
+static void DeleteFeatureClauses (
+  ValNodePtr PNTR head
+)
+{
+  ValNodePtr vnp, prev;
+  FeatureClausePtr fcp;
+  Boolean          delete_this_one;
+
+  if (head == NULL) return;
+
+  prev = NULL;
+  vnp = *head;
+  while (vnp != NULL)
+  {
+    delete_this_one = FALSE;
+
+    if (vnp->choice == DEFLINE_CLAUSEPLUS)
+    {
+      fcp = vnp->data.ptrvalue;
+      if (fcp == NULL || fcp->delete_me || fcp->featlist == NULL) 
+      {
+        delete_this_one = TRUE;
+      }
+      else
+      {
+        DeleteFeatureClauses (&fcp->featlist);
+        if (fcp->featlist == NULL) delete_this_one = TRUE;
+      }
+    }
+    else if (vnp->choice == DEFLINE_REMOVEFEAT)
+    {
+      delete_this_one = TRUE;
+    }
+
+    if (delete_this_one)
+    {
+      if (prev == NULL)
+      {
+        *head = vnp->next;
+        vnp->next = NULL;
+        FreeListElement (vnp);
+        if (*head == NULL) return;
+        vnp = *head;
+      }
+      else
+      {
+        prev->next = vnp->next;
+        vnp->next = NULL;
+        FreeListElement (vnp);
+        vnp = prev->next;
+      }
+    }
+    else
+    {
+      prev = vnp;
+      vnp = vnp->next;
+    }
+  }
+}
+
+/* This function counts the number of features in the feature list that
+ * satisfy the itemmatch function (or all of them, if itemmatch is NULL).
+ * If recurse_past_found_item, the function will not count features in
+ * subclauses of features that satisfy itemmatch.
+ */
+static Int4 CountFeatures (
+  ValNodePtr clause_list,
+  matchFunction  itemmatch,
+  Boolean    recurse_past_found_item
+)
+{
+  ValNodePtr       vnp;
+  Int4             num_features;
+  FeatureClausePtr fcp;
+
+  num_features = 0;
+  for (vnp = clause_list;
+       vnp != NULL;
+       vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_FEATLIST 
+      && (itemmatch == NULL || itemmatch (vnp->data.ptrvalue)))
+    {
+      num_features++;
+      if (! recurse_past_found_item)
+      {
+        return num_features;
+      }
+    }
+    else if (vnp->choice == DEFLINE_CLAUSEPLUS
+      && (fcp = vnp->data.ptrvalue) != NULL)
+    {
+      num_features += CountFeatures (fcp->featlist,
+                                     itemmatch,
+                                     recurse_past_found_item);   
+    }
+  }
+  return num_features;
+}
+
+/* The following section of code contains functions for grouping features. */
+
+typedef struct matchruledata {
+  matchFunction is_item;
+  Int4          num_match_rules;
+  matchFunction *match_rules;
+} MatchRuleData, PNTR MatchRulePtr;
+
+static void InitRuleForTopLevelClauses (MatchRulePtr mrp)
+{
+  if (mrp == NULL)
+  {
+    return;
+  }
+  mrp->num_match_rules = 4;
+  mrp->match_rules = MemNew (mrp->num_match_rules
+                                    * sizeof (matchFunction));
+  if (mrp->match_rules == NULL) return;
+  mrp->match_rules[0] = IsMobileElement;
+  mrp->match_rules[1] = IsEndogenousVirusSourceFeature;
+  mrp->match_rules[2] = IsOperon;
+  mrp->match_rules[3] = IsGeneCluster;
+}
+
+static void InitRuleForBottomLevelClauses (MatchRulePtr mrp)
+{
+  if (mrp == NULL)
+  {
+    return;
+  }
+  mrp->num_match_rules = 6;
+  mrp->match_rules = MemNew (mrp->num_match_rules
+                                    * sizeof (matchFunction));
+  if (mrp->match_rules == NULL) return;
+  mrp->match_rules[0] = IsCDS;
+  mrp->match_rules[1] = IsmRNA;
+  mrp->match_rules[2] = IsGene;
+  mrp->match_rules[3] = IsEndogenousVirusSourceFeature;
+  mrp->match_rules[4] = IsOperon;
+  mrp->match_rules[5] = IsGeneCluster;
+}
+
+/* NumGroupingRules is the number of features for which there is a list of
+ * features to group under.
+ * When grouping features, each feature in the list is examined sequentially.
+ * If there is a rule set that applies to that feature, the entire feature 
+ * list is searched for each feature type that this feature might group
+ * beneath.  This preserves the biological order that was generated by the
+ * original listing of features by sequence indexing.
+ */
+#define  NumGroupingRules 13
+static MatchRulePtr InitializeGroupingRules()
+{
+  MatchRulePtr grouping_rules;
+
+  grouping_rules = MemNew (NumGroupingRules * sizeof (MatchRuleData));
+  if (grouping_rules == NULL) return NULL;
+
+  grouping_rules[0].is_item = IsExon;
+  grouping_rules[0].num_match_rules = 8;
+  grouping_rules[0].match_rules = MemNew (grouping_rules[0].num_match_rules
+                                    * sizeof (matchFunction));
+  if (grouping_rules[0].match_rules == NULL) return NULL;
+  grouping_rules[0].match_rules[0] = IsCDS;
+  grouping_rules[0].match_rules[1] = IsNoncodingProductFeat;
+  grouping_rules[0].match_rules[2] = IsDloop;
+  grouping_rules[0].match_rules[3] = IsmRNA;
+  grouping_rules[0].match_rules[4] = IsGene;
+  grouping_rules[0].match_rules[5] = IsEndogenousVirusSourceFeature;
+  grouping_rules[0].match_rules[6] = IsOperon;
+  grouping_rules[0].match_rules[7] = IsGeneCluster;
+
+  grouping_rules[1].is_item = IsIntron;
+  grouping_rules[1].num_match_rules = 8;
+  grouping_rules[1].match_rules = MemNew (grouping_rules[1].num_match_rules
+                                    * sizeof (matchFunction));
+  if (grouping_rules[1].match_rules == NULL) return NULL;
+  grouping_rules[1].match_rules[0] = IsCDS;
+  grouping_rules[1].match_rules[1] = IsNoncodingProductFeat;
+  grouping_rules[1].match_rules[2] = IstRNA;
+  grouping_rules[1].match_rules[3] = IsDloop;
+  grouping_rules[1].match_rules[4] = IsGene;
+  grouping_rules[1].match_rules[5] = IsEndogenousVirusSourceFeature;
+  grouping_rules[1].match_rules[6] = IsOperon;
+  grouping_rules[1].match_rules[7] = IsGeneCluster;
+  
+  grouping_rules[2].is_item = IsPromoter;
+  InitRuleForBottomLevelClauses (grouping_rules + 2);
+ 
+  grouping_rules[3].is_item = IsCDS;
+  grouping_rules[3].num_match_rules = 5;
+  grouping_rules[3].match_rules = MemNew (grouping_rules[3].num_match_rules
+                                    * sizeof (matchFunction));
+  if (grouping_rules[3].match_rules == NULL) return NULL;
+  grouping_rules[3].match_rules[0] = IsmRNA;
+  grouping_rules[3].match_rules[1] = IsMobileElement;
+  grouping_rules[3].match_rules[2] = IsEndogenousVirusSourceFeature;
+  grouping_rules[3].match_rules[3] = IsOperon;
+  grouping_rules[3].match_rules[4] = IsGeneCluster;
+  
+  grouping_rules[4].is_item = IsMobileElement;
+  InitRuleForTopLevelClauses (grouping_rules + 4);
+ 
+  grouping_rules[5].is_item = Is3UTR;
+  InitRuleForBottomLevelClauses (grouping_rules + 5);
+ 
+  grouping_rules[6].is_item = Is5UTR;
+  InitRuleForBottomLevelClauses (grouping_rules + 6);
+ 
+  grouping_rules[7].is_item = IsLTR;
+  InitRuleForBottomLevelClauses (grouping_rules + 7);
+ 
+  grouping_rules[8].is_item = IsGene;
+  InitRuleForTopLevelClauses (grouping_rules + 8);
+  
+  grouping_rules[9].is_item = IsIntergenicSpacer;
+  InitRuleForTopLevelClauses (grouping_rules + 9);
+
+  grouping_rules[10].is_item = IsNoncodingProductFeat;
+  InitRuleForTopLevelClauses (grouping_rules + 10);
+ 
+  grouping_rules[11].is_item = IsOperon;
+  InitRuleForTopLevelClauses (grouping_rules + 11);
+ 
+  grouping_rules[12].is_item = IsGeneCluster;
+  InitRuleForTopLevelClauses (grouping_rules + 12);
+
+  return grouping_rules; 
+}
+
+static void FreeGroupingRules(
+  MatchRulePtr grouping_rules
+)
+{
+  Int4 i;
+
+  if (grouping_rules == NULL) return;
+
+  for (i = 0; i < NumGroupingRules; i++)
+  {
+    if (grouping_rules[i].match_rules != NULL)
+    MemFree (grouping_rules[i].match_rules);
+    grouping_rules[i].match_rules = NULL;
+  }
+  MemFree (grouping_rules);
+}
+
+static Boolean IsmRNASequence (BioseqPtr bsp)
+{
+  SeqDescrPtr sdp;
+  MolInfoPtr  mip;
+  
+  if (bsp == NULL || bsp->mol != Seq_mol_rna || bsp->descr == NULL)
+  {
+    return FALSE;
+  }
+  sdp = bsp->descr;
+  while (sdp != NULL && sdp->choice != Seq_descr_molinfo)
+  {
+    sdp = sdp->next;
+  }
+  if (sdp == NULL || sdp->data.ptrvalue == NULL)
+  {
+    return FALSE;
+  }
+  mip = (MolInfoPtr) sdp->data.ptrvalue;
+  
+  if (mip->biomol == 3)
+  {
+    return TRUE;
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+typedef struct matchcandidate 
+{
+  ValNodePtr matched_clause;
+  SeqLocPtr  slp;
+} MatchCandidateData, PNTR MatchCandidatePtr;
+
+/* This function searches the search_list for features that satisfy the
+ * match function and satisfy locational requirements relative to the
+ * clause.
+ * If more than one clause meets the match requirements, the smallest one
+ * is chosen.
+ */
+static void FindBestMatchCandidate 
+(FeatureClausePtr  clause,
+ ValNodePtr        search_list,
+ FeatureClausePtr  search_parent,
+ matchFunction     match,
+ Boolean           gene_cluster_opp_strand,
+ BioseqPtr         bsp,
+ MatchCandidatePtr current_candidate)
+{
+  ValNodePtr       search_clause;
+  SeqFeatPtr       addsfp, clause_sfp;
+  FeatureClausePtr searchfcp;
+  SeqLocPtr        slp;
+
+  if (clause == NULL || clause->slp == NULL || current_candidate == NULL) return;
+  
+  clause_sfp = (SeqFeatPtr) (clause->featlist->data.ptrvalue);
+
+  for (search_clause = search_list;
+       search_clause != NULL;
+       search_clause = search_clause->next)
+  {
+    if (search_clause->data.ptrvalue == clause)
+      continue;
+    if (search_clause->choice == DEFLINE_FEATLIST
+      && search_clause->data.ptrvalue != NULL)
+    {
+      addsfp = search_clause->data.ptrvalue;
+      /* slp is the location of the feature we are trying to
+       * group this feature with
+       */ 
+      if (search_parent != NULL)
+      {
+        slp = search_parent->slp;
+      }
+      else
+      {
+        slp = addsfp->location;
+      }
+      if (match (search_clause->data.ptrvalue))
+      { 
+        /* Transposons, insertion sequences, integrons, and endogenous virii
+         * take subfeatures regardless of whether the subfeature is
+         * on the same strand.
+         * Gene Clusters can optionally take subfeatures on either
+         * strand (gene_cluster_opp_strand is flag).
+         * Promoters will match up to features that are adjacent.
+         * Introns will match up to coding regions whose intervals
+         * are adjacent to the endpoints of the intron, or to other
+         * features if the intron location is inside the other feature.
+         * All other feature matches must be that the feature to
+         * go into the clause must fit inside the location of the
+         * other clause.
+         */
+        if (((match == IsMobileElement
+             || match == IsEndogenousVirusSourceFeature
+             || (match == IsGeneCluster && gene_cluster_opp_strand))
+            && SeqLocAinB (clause->slp, slp) > -1)
+          || IsLocAInBonSameStrand (clause->slp, slp)
+          || ( IsPromoter (clause_sfp)
+            && IsAAdjacentToB (clause->slp, search_parent->slp, bsp,
+                               ADJACENT_TYPE_UPSTREAM, TRUE))
+          || (IsmRNASequence (bsp) 
+              && match != IsMobileElement 
+              && match != IsEndogenousVirusSourceFeature
+              && match != IsGeneCluster)
+          || (match == IsCDS 
+              && IsIntron (clause_sfp)
+              && IsAEmptyIntervalOfB (clause->slp, slp, bsp))
+          || (match == IsCDS
+              && IsExon (clause_sfp)
+              && LocAContainsIntervalOfB (clause->slp, slp)))
+        {
+          /* if we don't already have a candidate, or if this
+           * candidate's location is inside the current candidate,
+           * take this candidate.
+           */
+          if (current_candidate->matched_clause == NULL
+              || SeqLocAinB (slp, current_candidate->slp) > 0)
+          {
+            current_candidate->matched_clause = search_clause;
+            current_candidate->slp = slp;
+          }
+        }
+      }
+    }
+    else if (search_clause->choice == DEFLINE_CLAUSEPLUS 
+      && search_clause->data.ptrvalue != NULL)
+    {
+      searchfcp = search_clause->data.ptrvalue;
+      FindBestMatchCandidate (clause, searchfcp->featlist, searchfcp,
+                              match, gene_cluster_opp_strand, bsp,
+                              current_candidate);
+    }
+  }
+}
+
+
+/* This function iterates through the matches in the specified grouping rule.
+ * If more than one match is found, the clause with the smallest location is
+ * used.
+ * If a match is found, the clause is added to the list of clauses for that
+ * feature's parent clause.
+ */
+static Boolean GroupClauseByRule (
+  FeatureClausePtr clause,
+  ValNodePtr       search_list,
+  MatchRulePtr     grouping_rule,
+  Boolean          gene_cluster_opp_strand,
+  BioseqPtr        bsp
+)
+{
+  Int4               rule_index;
+  MatchCandidateData mcd;  
+  Boolean            rval = FALSE;
+  ValNodePtr         newfeat;
+  
+  mcd.slp = NULL;
+  mcd.matched_clause = NULL;
+
+  for (rule_index = 0;
+       rule_index < grouping_rule->num_match_rules;
+       rule_index ++)
+  {
+  
+    FindBestMatchCandidate (clause, search_list, NULL, 
+                            grouping_rule->match_rules[rule_index],
+                            gene_cluster_opp_strand, bsp, &mcd);
+  }
+  if (mcd.matched_clause != NULL)
+  {
+    newfeat = ValNodeNew (mcd.matched_clause);
+    if (newfeat == NULL) return FALSE;
+    newfeat->choice = DEFLINE_CLAUSEPLUS;
+    newfeat->data.ptrvalue = clause;
+    rval = TRUE;
+  }
+  return rval;
+}
+
+
+/* This function determines whether a subclause contains just a 3' UTR feature
+ * and no other details.
+ */
+static Boolean Is3UTRClause (FeatureClausePtr clause)
+{  
+  if (clause == NULL
+      || clause->featlist == NULL 
+      || clause->featlist->choice != DEFLINE_FEATLIST
+      || clause->featlist->data.ptrvalue == NULL
+      || clause->featlist->next != NULL)
+  {
+    return FALSE;
+  }
+  return Is3UTR(clause->featlist->data.ptrvalue);
+}
+
+
+/* This function will move 3' UTRs to the end of any subfeat lists
+ * so that they can be listed after the partial/complete CDS.
+ */
+static void Move3UTRToEndOfSubFeatList (ValNodePtr clause_list)
+{
+  ValNodePtr vnp, prev, last_vnp;
+  FeatureClausePtr clause;
+  
+  if (clause_list == NULL || clause_list->next == NULL) 
+  {
+    return;
+  }
+  prev = clause_list;
+  for (vnp = clause_list->next; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->data.ptrvalue != NULL && vnp->choice == DEFLINE_CLAUSEPLUS)
+    {
+      clause = vnp->data.ptrvalue;
+      if (Is3UTRClause (clause))
+      {
+        if (vnp->next != NULL)
+        {
+          /* move to end of clause list */
+          last_vnp = vnp->next;
+          while (last_vnp->next != NULL)
+          {
+            last_vnp = last_vnp->next;
+          }
+          prev->next = vnp->next;
+          last_vnp->next = vnp;
+          vnp->next = NULL;
+        }
+      }
+      else
+      {
+        prev = vnp;
+        Move3UTRToEndOfSubFeatList (clause->featlist);
+      }
+    }
+    else
+    {
+      prev = vnp;
+    }
+  }  
+}
+
+/* This function iterates over the list of features, attempting to find and
+ * apply grouping rules for each feature.
+ */
+static void GroupAllClauses (
+  ValNodePtr PNTR clause_list,
+  Boolean         gene_cluster_opp_strand,
+  BioseqPtr       bsp
+)
+{
+  MatchRulePtr     grouping_rules;
+  ValNodePtr       vnp, prev;
+  FeatureClausePtr clause;
+  SeqFeatPtr       main_feat;
+  Int4             rule_index;
+
+  grouping_rules = InitializeGroupingRules();
+  if (grouping_rules == NULL) return;
+
+  for (vnp = *clause_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
+    {
+      clause = vnp->data.ptrvalue;
+      if (clause->featlist != NULL
+        && clause->featlist->choice == DEFLINE_FEATLIST
+        && clause->featlist->data.ptrvalue != NULL)
+      {
+        main_feat = clause->featlist->data.ptrvalue;
+        for (rule_index = 0;
+             rule_index < NumGroupingRules 
+               && ! grouping_rules[rule_index].is_item (main_feat);
+             rule_index++)
+        {
+        }
+        if (rule_index < NumGroupingRules)
+        {
+          if ( GroupClauseByRule (clause, *clause_list,
+                                  grouping_rules + rule_index, 
+                                  gene_cluster_opp_strand,
+                                  bsp))
+          {
+            vnp->data.ptrvalue = NULL;
+          }
+        }
+      }
+    }
+  }
+  FreeGroupingRules(grouping_rules);
+
+  vnp = *clause_list;
+  prev = NULL;
+  while (vnp != NULL)
+  {
+    if (vnp->data.ptrvalue == NULL)
+    {
+      if (prev == NULL)
+      {
+        *clause_list = vnp->next;
+        vnp->next = NULL;
+        ValNodeFree (vnp);
+        vnp = *clause_list;
+      }
+      else
+      {
+        prev->next = vnp->next;
+        vnp->next = NULL;
+        ValNodeFree (vnp);
+        vnp = prev->next;
+      }
+    }
+    else
+    {
+      prev = vnp;
+      vnp = vnp->next;
+    }
+  }
+  
+  Move3UTRToEndOfSubFeatList (*clause_list);
+}
+
+/* This function exists to handle the special case where two or more exons
+ * are alternatively spliced, but there are no CDSs to represent some of the
+ * alternatively spliced forms.  In order to make sure that all of the exons
+ * that are alternatively spliced together appear with the CDS, they are
+ * temporarily consolidated into a single clause with a location that
+ * is the intersection of the exons' locations.  The clause will be
+ * re-expanded after grouping by the ExpandAltSplicedExons function.
+ */
+static void GroupAltSplicedExons (
+  ValNodePtr PNTR clause_list,
+  BioseqPtr       bsp,
+  Boolean         delete_now
+)
+{
+  ValNodePtr       clause, search_clause, vnp;
+  FeatureClausePtr fcp, search_fcp;
+  SeqFeatPtr       sfp, search_sfp;
+  SeqLocPtr        new_slp;
+
+  if (clause_list == NULL) return;
+ 
+  for (clause = *clause_list; clause != NULL; clause = clause->next)
+  {
+    if (clause->choice != DEFLINE_CLAUSEPLUS
+      || clause->data.ptrvalue == NULL)
+    {
+      continue;
+    }
+    fcp = clause->data.ptrvalue;
+    if ( ! fcp->is_alt_spliced
+      || fcp->delete_me
+      || fcp->featlist == NULL
+      || fcp->featlist->choice != DEFLINE_FEATLIST)
+    {
+      continue;
+    }
+    sfp = fcp->featlist->data.ptrvalue;
+    if ( ! IsExon (sfp))
+    {
+      continue;
+    }
+
+    for ( search_clause = clause->next; 
+          search_clause != NULL
+            && search_clause->choice == DEFLINE_CLAUSEPLUS
+            && search_clause->data.ptrvalue != NULL
+            && (search_fcp = search_clause->data.ptrvalue) != NULL
+            && ! search_fcp->delete_me
+            && search_fcp->is_alt_spliced
+            && search_fcp->featlist != NULL
+            && search_fcp->featlist->choice == DEFLINE_FEATLIST
+            && (search_sfp = search_fcp->featlist->data.ptrvalue) != NULL
+            && IsExon (search_sfp)
+            && TestFeatOverlap (sfp, search_sfp, SIMPLE_OVERLAP) != -1;
+          search_clause = search_clause->next)
+    {
+      vnp = ValNodeNew (fcp->featlist);
+      if (vnp == NULL) return;
+      vnp->choice = DEFLINE_FEATLIST;
+      vnp->data.ptrvalue = search_sfp;
+      search_fcp->delete_me = TRUE;
+      new_slp = SeqLocIntersection (fcp->slp, search_fcp->slp, bsp);
+      SeqLocFree (fcp->slp);
+      fcp->slp = new_slp;
+    }
+  }
+  if (delete_now)
+  {
+    DeleteFeatureClauses (clause_list);
+  }
+}
+
+/* This function expands a clause filled with alternatively-spliced exons
+ * that was created in the GroupAltSplicedExons function.
+ */
+static void ExpandAltSplicedExons (
+  ValNodePtr clause_list,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  ValNodePtr clause, rest_of_list, featlist, new_clause;
+  FeatureClausePtr fcp, new_fcp;
+  SeqFeatPtr sfp;
+
+  for (clause = clause_list;
+       clause != NULL;
+       clause = clause->next)
+  {
+    if (clause->choice != DEFLINE_CLAUSEPLUS
+      || (fcp = clause->data.ptrvalue) == NULL
+      || fcp->featlist == NULL)
+    {
+      continue;
+    }
+    if ( fcp->featlist->choice == DEFLINE_FEATLIST
+      && (sfp = fcp->featlist->data.ptrvalue) != NULL
+      && IsExon (sfp)
+      && fcp->featlist->next != NULL
+      && fcp->featlist->next->choice == DEFLINE_FEATLIST
+      && IsExon (fcp->featlist->next->data.ptrvalue))
+    {
+      rest_of_list = clause->next;
+      clause->next = NULL;
+      for (featlist = fcp->featlist->next;
+           featlist != NULL
+             && featlist->choice == DEFLINE_FEATLIST
+             && IsExon (featlist->data.ptrvalue);
+           featlist = featlist->next)
+      {
+        new_clause = ValNodeNew (clause);
+        if (new_clause == NULL) return;
+        new_fcp = NewFeatureClause (featlist->data.ptrvalue, bsp, rp);
+        if (new_fcp == NULL) return;
+        new_fcp->grp = fcp->grp;
+        new_fcp->is_alt_spliced = fcp->is_alt_spliced;
+        new_fcp->make_plural = fcp->make_plural;
+        new_clause->choice = DEFLINE_CLAUSEPLUS;
+        new_clause->data.ptrvalue = new_fcp;
+      }
+      ValNodeFree (fcp->featlist->next);
+      fcp->featlist->next = NULL;
+      new_clause->next = rest_of_list;
+
+      /* put back location for first exon - was reduced to union of 
+       * all exon intervals in GroupAltSplicedExons
+       */
+      SeqLocFree (fcp->slp);
+      sfp = fcp->featlist->data.ptrvalue;
+      fcp->slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, TRUE, FALSE);
+    }
+    else
+    {
+      ExpandAltSplicedExons (fcp->featlist, bsp, rp);
+    }
+  }
+}
+
+
+
+static Boolean DoFeaturesShareGene (SeqFeatPtr sfp1, SeqFeatPtr sfp2)
+{
+  Boolean share_gene = FALSE;
+  SeqFeatPtr found_gene1, found_gene2;
+  
+  if (sfp1 != NULL && sfp2 != NULL
+      && !SeqMgrGeneIsSuppressed (SeqMgrGetGeneXref(sfp1))
+      && !SeqMgrGeneIsSuppressed (SeqMgrGetGeneXref(sfp2)))
+  {
+    found_gene1 = SeqMgrGetOverlappingGene (sfp1->location, NULL);
+    found_gene2 = SeqMgrGetOverlappingGene (sfp2->location, NULL);
+    if (found_gene1 == found_gene2 && found_gene1 != NULL)
+    {
+      share_gene = TRUE;
+    }
+  }
+  return share_gene;
+}
+
+/* This function determines whether two features share the same product name */
+static Boolean 
+DoProductNamesMatch 
+(SeqFeatPtr sfp1,
+ SeqFeatPtr sfp2, 
+ BioseqPtr  bsp,
+ DeflineFeatureRequestListPtr rp)
+{
+  CharPtr productname1;
+  CharPtr productname2;
+  Boolean names_match = FALSE;
+   
+  productname1 = GetProductName (sfp1, bsp, rp);
+  productname2 = GetProductName (sfp2, bsp, rp);
+  if (StringHasNoText (productname1) && StringHasNoText (productname2))
+  {
+    names_match = TRUE;
+  }
+  else if (StringCmp (productname1, productname2) == 0)
+  {
+    names_match = TRUE;
+  }
+  
+  productname1 = MemFree (productname1);
+  productname2 = MemFree (productname2);
+  
+  return names_match;  
+}
+
+/* This function should combine CDSs that do not have a joined location
+ * but are part of the same gene and have the same protein name.
+ */
+static void GroupSegmentedCDSs (
+  ValNodePtr PNTR clause_list,
+  BioseqPtr       bsp,
+  Boolean         delete_now,
+  DeflineFeatureRequestListPtr rp
+)
+{
+  ValNodePtr       clause, search_clause, vnp;
+  FeatureClausePtr fcp, search_fcp;
+  SeqFeatPtr       sfp, search_sfp;
+  SeqLocPtr        new_slp;
+
+  if (clause_list == NULL) return;
+ 
+  for (clause = *clause_list; clause != NULL; clause = clause->next)
+  {
+    if (clause->choice != DEFLINE_CLAUSEPLUS
+      || clause->data.ptrvalue == NULL)
+    {
+      continue;
+    }
+    fcp = clause->data.ptrvalue;
+    if (fcp->delete_me
+      || fcp->featlist == NULL
+      || fcp->featlist->choice != DEFLINE_FEATLIST)
+    {
+      continue;
+    }
+    sfp = fcp->featlist->data.ptrvalue;
+    if ( ! IsCDS (sfp))
+    {
+      continue;
+    }
+
+    for ( search_clause = clause->next; 
+          search_clause != NULL;
+          search_clause = search_clause->next)
+    {
+      if (search_clause->choice != DEFLINE_CLAUSEPLUS
+          || search_clause->data.ptrvalue == NULL
+          || (search_fcp = search_clause->data.ptrvalue) == NULL
+          || search_fcp->delete_me
+          || search_fcp->featlist == NULL
+          || search_fcp->featlist->choice != DEFLINE_FEATLIST
+          || (search_sfp = search_fcp->featlist->data.ptrvalue) == NULL
+          || ! IsCDS (search_sfp)
+          || ! DoFeaturesShareGene (sfp, search_sfp)
+          || ! DoProductNamesMatch (sfp, search_sfp, bsp, rp))
+      {
+        continue;
+      }
+      vnp = ValNodeNew (fcp->featlist);
+      if (vnp == NULL) return;
+      vnp->choice = DEFLINE_FEATLIST;
+      vnp->data.ptrvalue = search_sfp;
+      search_fcp->delete_me = TRUE;
+      new_slp = SeqLocMerge (bsp, fcp->slp, search_fcp->slp,
+                             FALSE, TRUE, FALSE);
+
+      SeqLocFree (fcp->slp);
+      fcp->slp = new_slp;
+    }
+  }
+  if (delete_now)
+  {
+    DeleteFeatureClauses (clause_list);
+  }
+}
+
+
+/* This function searches this list for clauses to which this gene should
+ * apply.  This is not taken care of by the GroupAllClauses function
+ * because genes are added to clauses as a GeneRefPtr instead of as an
+ * additional feature in the list, and because a gene can apply to more
+ * than one clause, while other features should really only belong to
+ * one clause.
+ */
+static Boolean AddGeneToClauses 
+( SeqFeatPtr gene,
+  CharPtr    gene_productname,
+  ValNodePtr clause_list,
+  Boolean    suppress_locus_tag)
+{
+  ValNodePtr    clause;
+  FeatureClausePtr fcp;
+  SeqFeatPtr    sfp, found_gene;
+  GeneRefPtr    grp;
+  Boolean    used_gene;
+  
+  if (gene == NULL || gene->data.value.ptrvalue == NULL) return FALSE;
+  if (clause_list == NULL) return FALSE;
+
+  used_gene = FALSE;
+  grp = gene->data.value.ptrvalue;
+  for (clause = clause_list; clause != NULL; clause = clause->next)
+  {
+    fcp = clause->data.ptrvalue;
+    if (fcp == NULL || fcp->featlist == NULL) return FALSE;
+    sfp = fcp->featlist->data.ptrvalue;
+    if (sfp != NULL && !SeqMgrGeneIsSuppressed (SeqMgrGetGeneXref(sfp))
+        && (IsCDS (sfp)
+            || IsrRNA (sfp)
+            || IstRNA (sfp)
+            || IsmRNA (sfp)
+            || IsMiscRNA (sfp)
+            || IsncRNA (sfp)
+            || IsPrecursorRNA (sfp)
+            || IsNoncodingProductFeat (sfp)))
+    {
+      if (fcp->grp == NULL)
+      {
+        found_gene = SeqMgrGetOverlappingGene (sfp->location, NULL);
+        if (found_gene != NULL)
+        {
+          fcp->grp = (GeneRefPtr) found_gene->data.value.ptrvalue;
+        }
+      }
+
+      if (fcp->grp != NULL && DoGenesMatch (fcp->grp, grp, suppress_locus_tag))
+      {
+        used_gene = TRUE;
+        if (gene_productname != NULL
+          && fcp->feature_label_data.productname == NULL
+          && IsCDS (sfp))
+        {
+          fcp->feature_label_data.productname =
+              StringSave (gene_productname);
+        }
+      }
+      else if (fcp->grp == NULL
+        && IsLocAInBonSameStrand (sfp->location, gene->location))
+      {
+        fcp->grp = grp;
+        used_gene = TRUE;
+        if (gene_productname != NULL
+          && fcp->feature_label_data.productname == NULL
+          && IsCDS (sfp))
+        {
+          fcp->feature_label_data.productname =
+              StringSave (gene_productname);
+        }
+      }
+    }
+  }
+  return used_gene;
+}
+
+/* This function iterates through the list of features and calls
+ * AddGeneToClauses for each gene feature it finds.
+ */
+static void GroupGenes (ValNodePtr PNTR clause_list, Boolean suppress_locus_tag)
+{
+  ValNodePtr  vnp;
+  ValNodePtr  featlist;
+  FeatureClausePtr fcp;
+
+  for (vnp = *clause_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice != DEFLINE_CLAUSEPLUS) return;
+    fcp = (FeatureClausePtr) vnp->data.ptrvalue;
+    if (fcp == NULL) return;
+
+    featlist = fcp->featlist;
+    if (featlist != NULL
+      && featlist->choice == DEFLINE_FEATLIST
+      && IsGene (featlist->data.ptrvalue))
+    {
+      AddGeneToClauses (featlist->data.ptrvalue,
+                        fcp->feature_label_data.productname,
+                        vnp->next, suppress_locus_tag);
+    }
+  } 
+}
+
+/* This function searches this list for clauses to which this mRNA should
+ * apply.  This is not taken care of by the GroupAllClauses function
+ * because when an mRNA is added to a CDS, the product for the clause is
+ * replaced and the location for the clause is expanded, rather than simply
+ * adding the mRNA as an additional feature in the list, and because an 
+ * mRNA can apply to more than one clause, while other features should 
+ * really only belong to one clause.
+ */
+static Boolean AddmRNAToClauses 
+( SeqFeatPtr mRNA,
+  ValNodePtr clause_list,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  ValNodePtr    clause;
+  FeatureClausePtr fcp;
+  SeqFeatPtr    sfp;
+  Boolean    used_mRNA;
+  CharPtr       productname;
+  SeqLocPtr     new_slp;
+  
+  if (mRNA == NULL || mRNA->data.value.ptrvalue == NULL) return FALSE;
+  if (clause_list == NULL) return FALSE;
+
+  used_mRNA = FALSE;
+  productname = GetProductName (mRNA, bsp, rp);
+  if (productname == NULL) return TRUE;
+
+  for (clause = clause_list; clause != NULL; clause = clause->next)
+  {
+    fcp = clause->data.ptrvalue;
+    if (fcp == NULL || fcp->featlist == NULL) return FALSE;
+    sfp = fcp->featlist->data.ptrvalue;
+    if (sfp == NULL)
+    {
+    }
+    else if (IsCDS (sfp)
+      && fcp->feature_label_data.productname != NULL
+      && StringCmp (fcp->feature_label_data.productname, productname) == 0)
+    {
+      used_mRNA = TRUE;
+      fcp->has_mrna = TRUE;
+      if (IsLocAInBonSameStrand (sfp->location, mRNA->location))
+      {
+        new_slp = SeqLocMerge (bsp, fcp->slp, mRNA->location,
+                                 FALSE, TRUE, FALSE);
+        if (new_slp == NULL) return FALSE;
+        if (fcp->slp != NULL)
+        {
+          SeqLocFree (fcp->slp);
+        }
+        fcp->slp = new_slp;
+      }
+    }
+    else if (fcp->feature_label_data.productname == NULL
+      && (IsCDS (sfp) || IsGene (sfp))
+      && (IsLocAInBonSameStrand (sfp->location, mRNA->location)
+        || IsLocAInBonSameStrand (mRNA->location, sfp->location)))
+    {
+      fcp->feature_label_data.productname = StringSave (productname);
+      used_mRNA = TRUE;
+      fcp->has_mrna = TRUE;
+      new_slp = SeqLocMerge (bsp, fcp->slp, mRNA->location,
+                                 FALSE, TRUE, FALSE);
+      if (new_slp == NULL) return FALSE;
+      if (fcp->slp != NULL)
+      {
+        SeqLocFree (fcp->slp);
+      }
+      fcp->slp = new_slp;
+    }
+  }
+  return used_mRNA;
+}
+
+/* This function iterates through the list of features and calls
+ * AddmRNAToClauses for each mRNA feature it finds.
+ */
+static void GroupmRNAs (
+  ValNodePtr PNTR clause_list,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp
+)
+{
+  ValNodePtr  vnp;
+  ValNodePtr  featlist;
+  FeatureClausePtr fcp;
+
+  for (vnp = *clause_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice != DEFLINE_CLAUSEPLUS) return;
+    fcp = (FeatureClausePtr) vnp->data.ptrvalue;
+    if (fcp == NULL) return;
+
+    featlist = fcp->featlist;
+    if (featlist != NULL
+      && featlist->choice == DEFLINE_FEATLIST
+      && IsmRNA (featlist->data.ptrvalue))
+    {
+      if (AddmRNAToClauses (featlist->data.ptrvalue, *clause_list, bsp, rp))
+      {
+        fcp->delete_me = TRUE;
+      }
+    }
+  } 
+  DeleteFeatureClauses (clause_list);
+}
+
+/* This section of code contains functions for generating labels for
+ * clauses for the definition lines.
+ */
+
+/* This function examines the specified typeword and determines whether it
+ * should appear before or after the description of the feature in the
+ * definition line.
+ */
+static Boolean IsTypeWordFirst (
+  CharPtr typeword
+)
+{
+  Int4 i;
+  if (typeword == NULL) return FALSE;
+  if (StringCmp (typeword, "exon") == 0
+    || StringCmp (typeword, "intron") == 0
+    || StringCmp (typeword, "endogenous virus") == 0)
+  {
+    return TRUE;
+  }
+  else
+  {
+    i = StartsWithMobileElementKeyword (typeword);
+    if (i >= 0 && i != eMobileElementIntegron) {
+      return TRUE;
+    }
+    return FALSE;
+  }
+}
+
+/* This function determines the word to use to indicate what type of feature
+ * is being described in the definition line.  For certain feature types,
+ * the word to use in the definition line varies based on the type of
+ * molecule in the record.
+ */
+static CharPtr GetFeatureTypeWord (
+  Uint1 biomol,
+  SeqFeatPtr sfp
+)
+{
+  if (sfp == NULL) return NULL;
+  if ( IsExon (sfp))
+  {
+    return StringSave ("exon");
+  } 
+  else if(IsIntron (sfp))
+  {
+    return StringSave ("intron");
+  }
+  else if (IsEndogenousVirusSequence (sfp))
+  {
+    return StringSave ("endogenous virus");
+  }
+  else if (IsControlRegion (sfp))
+  {
+    return StringSave ("control region");
+  }
+  else if (IsEndogenousVirusSourceFeature (sfp))
+  {
+    return StringSave ("endogenous virus");
+  }
+  else if (IsDloop (sfp))
+  {
+    return StringSave ("D-loop");
+  }
+  else if (IsLTR (sfp))
+  {
+    return StringSave ("LTR");
+  }
+  else if (Is3UTR (sfp))
+  {
+    return StringSave ("3' UTR");
+  }
+  else if (Is5UTR (sfp))
+  {
+    return StringSave ("5' UTR");
+  }
+  else if (IsOperon (sfp))
+  {
+    return StringSave ("operon");
+  }
+  else if (biomol == MOLECULE_TYPE_GENOMIC || biomol == MOLECULE_TYPE_CRNA)
+  {
+    if (IsPseudo (sfp))
+    {
+      return StringSave ("pseudogene");
+    }
+    else
+    {
+      return StringSave ("gene");
+    }
+  }
+  else if ( IsrRNA (sfp) || IsncRNA (sfp))
+  {
+    return NULL;
+  }
+  else if (IsPrecursorRNA (sfp))
+  {
+    return StringSave ("precursor RNA");
+  }
+  else if (biomol == MOLECULE_TYPE_MRNA)
+  {
+    if (IsPseudo (sfp))
+    {
+      return StringSave ("pseudogene mRNA");
+    }
+    else
+    {
+      return StringSave ("mRNA");
+    }
+  }
+  else if (biomol == MOLECULE_TYPE_PRE_MRNA)
+  {
+    if (IsPseudo (sfp))
+    {
+      return StringSave ("pseudogene precursor RNA");
+    }
+    else
+    {
+      return StringSave ("precursor RNA");
+    }
+  }
+  else if (biomol == MOLECULE_TYPE_OTHER_GENETIC_MATERIAL)
+  {
+    return StringSave ("gene");
+  }
+  return StringSave ("");
+}
+
+/* Frequently the product associated with a feature is listed as part of the
+ * description of the feature in the definition line.  This function determines
+ * the name of the product associated with this specific feature.  Some
+ * features will be listed with the product of a feature that is associated
+ * with the feature being described - this function does not look at other
+ * features to determine a product name.
+ * If the feature is a misc_feat with particular keywords in the comment,
+ * the product will be determined based on the contents of the comment.
+ * If the feature is a CDS and is marked as pseudo, the product will be
+ * determined based on the contents of the comment.
+ * If the feature is a gene and has different strings in the description than
+ * in the locus or locus tag, the description will be used as the product for
+ * the gene.
+ * If none of the above conditions apply, the sequence indexing context label
+ * will be used to obtain the product name for the feature.
+ */
+static CharPtr GetProductName 
+( SeqFeatPtr cds,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  CharPtr protein_name;
+  CharPtr semicolon;
+  size_t len_to_copy;
+  SeqMgrFeatContext  context;
+  GeneRefPtr  grp;
+  CharPtr gene_name;
+  RnaRefPtr rrp;
+  Boolean suppress_locus_tag = FALSE;
+
+  if (cds == NULL) return NULL;
+  protein_name = NULL;
+  if (rp != NULL)
+  {
+    suppress_locus_tag = rp->suppress_locus_tags;
+  }
+  if (IsNoncodingProductFeat (cds))
+  {
+    return GetNoncodingProductFeatProduct (cds);
+  }
+  else if (cds->data.choice == SEQFEAT_CDREGION && cds->pseudo)
+  {
+    if (cds->comment != NULL)
+    {
+      semicolon = StringChr (cds->comment, ';');
+      if (semicolon != NULL)
+      {
+        len_to_copy = semicolon - cds->comment;
+      }
+      else
+      {
+        len_to_copy = StringLen (cds->comment);
+      }
+      protein_name = MemNew (len_to_copy + 1);
+      if (protein_name == NULL) return NULL;
+      StringNCpy (protein_name, cds->comment, len_to_copy);
+      protein_name[len_to_copy] = 0;
+    }
+    return protein_name;
+  }
+  else if (cds->data.choice == SEQFEAT_GENE)
+  {
+    grp = (GeneRefPtr) cds->data.value.ptrvalue;
+    if (grp == NULL) return NULL;
+    gene_name = GetGeneName (grp, suppress_locus_tag);
+    if (grp->desc != NULL
+      && StringCmp (grp->desc, gene_name) != 0)
+    {
+      return StringSave (grp->desc);
+    }
+#if 0
+    /* removed by request from Linda Yankie */    
+    if (grp->locus_tag != NULL && ! suppress_locus_tag
+      && StringCmp (grp->locus_tag, gene_name) != 0)
+    {
+      return StringSave (grp->locus_tag);
+    }
+#endif    
+  }
+  else if (IsncRNA (cds))
+  {
+    return GetncRNAProduct(cds, rp == NULL ? FALSE : rp->use_ncrna_note);
+  }
+  else if (IstRNA (cds) 
+           && SeqMgrGetDesiredFeature (0, bsp, 0, 0, cds, &context) == cds
+           && context.label != NULL)
+  {
+    if (StringCmp (context.label, "Xxx") == 0) {
+      protein_name = StringSave ("tRNA-OTHER");
+    } else {
+      protein_name = MemNew ( StringLen (context.label) + 6);
+      if ( protein_name == NULL) return NULL;
+      sprintf (protein_name, "tRNA-%s", context.label);
+    }
+    return protein_name;
+  }
+  else if (cds->data.choice == SEQFEAT_RNA)
+  {
+    
+    rrp = (RnaRefPtr) cds->data.value.ptrvalue;
+    if (rrp != NULL && rrp->ext.choice == 1 && !StringHasNoText (rrp->ext.value.ptrvalue))
+    {
+      return StringSave (rrp->ext.value.ptrvalue);
+    }
+  }
+  else if (SeqMgrGetDesiredFeature (0, bsp, 0, 0, cds, &context) == cds
+           && context.label != NULL)
+  {
+    if ((IsCDS(cds) && StringCmp (context.label, "CDS") != 0)
+        || (IsmRNA(cds) && StringCmp (context.label, "mRNA") != 0)
+        || (! IsCDS(cds) && ! IsmRNA(cds)))
+    {
+      protein_name = StringSave (context.label);
+      return protein_name;
+    }
+  }
+  return NULL;
+}
+
+/* This function searches a list of features recursively for a
+ * feature that satisfies the itemmatch condition and is associated with
+ * the same gene as the fcp clause passed to the function.
+ * This is used to obtain a product for a feature that may share a gene with
+ * a product-producing feature but may not be contained in the interval of
+ * the product-producing feature.
+ */
+static FeatureClausePtr FindProductInFeatureList (
+  FeatureClausePtr fcp,
+  ValNodePtr       clause_list,
+  matchFunction    itemmatch,
+  Boolean          suppress_locus_tag)
+{
+  ValNodePtr       vnp;
+  FeatureClausePtr vnp_fcp;
+  
+  for (vnp = clause_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
+    {
+      vnp_fcp = vnp->data.ptrvalue;
+      if (DoGenesMatch (vnp_fcp->grp, fcp->grp, suppress_locus_tag)
+        && vnp_fcp->featlist != NULL
+        && vnp_fcp->featlist->choice == DEFLINE_FEATLIST
+        && itemmatch (vnp_fcp->featlist->data.ptrvalue))
+      {
+        return vnp_fcp;
+      }
+      else
+      {
+        vnp_fcp = FindProductInFeatureList (fcp, vnp_fcp->featlist,
+                                            itemmatch, suppress_locus_tag);
+        if (vnp_fcp != NULL) return vnp_fcp;
+      }
+    }
+  }
+  return NULL;
+}
+
+/* This function uses the available information in the clause to generate
+ * a description from the name of the gene (if any) and the name of the
+ * product for the feature (if any).
+ * If there is only a gene, the description will be the name of the gene.
+ * If there is only a product, the description will be the name of the product.
+ * If there is a gene and a product, the description will be the name of
+ * the product followed by the name of the gene in parentheses.
+ */
+static CharPtr GetGeneProtDescription 
+( FeatureClausePtr fcp,
+  BioseqPtr        bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  SeqFeatPtr    sfp;
+  CharPtr    protein_name;
+  CharPtr    gene_name;
+  size_t    description_length;
+  CharPtr    description;
+
+  if (fcp == NULL
+    || fcp->featlist == NULL
+    || fcp->featlist->data.ptrvalue == NULL)
+  {
+    return NULL;
+  }
+  sfp = fcp->featlist->data.ptrvalue;
+
+  description_length = 0;
+
+  if (fcp->feature_label_data.productname != NULL)
+  {
+    protein_name = StringSave (fcp->feature_label_data.productname);
+  }
+  else
+  {
+    protein_name = GetProductName (sfp, bsp, rp);
+    if (protein_name == NULL && IsGene (sfp))
+    {
+      
+    }
+  }
+  if (protein_name != NULL)
+  {
+    description_length += StringLen (protein_name);
+  }
+     
+  gene_name = GetGeneName (fcp->grp, rp == NULL ? FALSE : rp->suppress_locus_tags);
+  if (gene_name != NULL)
+  {
+    description_length += StringLen (gene_name);
+    if (protein_name != NULL)
+    {
+      description_length += 3;
+    }
+  }
+  description = (CharPtr) MemNew (description_length + 1);
+  if (description == NULL) return NULL;
+  if (protein_name != NULL)
+  {
+    if (gene_name != NULL)
+    {
+      sprintf (description, "%s (%s)", protein_name, gene_name);
+    }
+    else
+    {
+      sprintf (description, "%s", protein_name);
+    }
+  }
+  else
+  {
+    if (gene_name != NULL)
+      sprintf (description, gene_name);
+  }
+  if (protein_name != NULL) MemFree (protein_name);
+  return description;
+}
+
+/* This array of match functions is used to identify, in order of preference,
+ * the features that might be used to generate a product for a gene-protein
+ * description if the feature has not already been grouped with a product
+ * feature.
+ */
+static matchFunction productfeatures[] = {
+  IsCDS, IsmRNA, IstRNA
+}; 
+
+/* This function finds gene features without products and looks for 
+ * features that might provide products for them.
+ */
+static void FindGeneProducts 
+( ValNodePtr clause_list,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  ValNodePtr       vnp;
+  FeatureClausePtr fcp, productfcp;
+  Int4             i, NumProductFeatureTypes;
+  Boolean          suppress_locus_tag = (rp == NULL ? FALSE : rp->suppress_locus_tags);
+
+  NumProductFeatureTypes = sizeof (productfeatures) / sizeof (matchFunction);
+
+  for (vnp = clause_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_CLAUSEPLUS
+      && (fcp = vnp->data.ptrvalue) != NULL
+      && fcp->featlist != NULL)
+    {
+      if (fcp->featlist->choice == DEFLINE_FEATLIST
+        && IsGene (fcp->featlist->data.ptrvalue)
+        && fcp->feature_label_data.productname == NULL)
+      {
+        productfcp = NULL;
+        for (i=0; i < NumProductFeatureTypes && productfcp == NULL; i++)
+        {
+          productfcp = FindProductInFeatureList (fcp, clause_list,
+                                                 productfeatures[i],
+                                                 suppress_locus_tag);
+        }
+        if (productfcp != NULL)
+        {
+          fcp->is_alt_spliced = productfcp->is_alt_spliced;
+          if (productfcp->feature_label_data.productname != NULL)
+          {
+            fcp->feature_label_data.productname =
+                  StringSave (productfcp->feature_label_data.productname);
+          }
+          else
+          {
+            fcp->feature_label_data.productname
+                  = GetProductName (productfcp->featlist->data.ptrvalue, 
+                                    bsp, rp);
+          }
+          if (fcp->feature_label_data.description != NULL)
+          {
+            MemFree (fcp->feature_label_data.description);
+            fcp->feature_label_data.description = NULL;
+          }
+          fcp->feature_label_data.description =
+            GetGeneProtDescription (fcp, bsp, rp);
+        }
+      }
+      else
+      {
+        FindGeneProducts (fcp->featlist, bsp, rp);
+      }
+    }
+  }
+}
+
+static Boolean ShowInterval (
+  SeqFeatPtr sfp
+)
+{
+  if (IsSatelliteSequence (sfp) || IsExon (sfp) || IsIntron (sfp)
+    || IsPromoter (sfp) || Is3UTR (sfp) || Is5UTR (sfp))
+    return FALSE;
+  return TRUE;
+}
+
+static CharPtr GetExonDescription (
+  BioseqPtr bsp,
+  SeqFeatPtr sfp
+)
+{
+  SeqMgrFeatContext  context;
+  SeqFeatPtr new_sfp;
+  CharPtr    label;
+
+  if ((new_sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, bsp, 0, 0, sfp, &context)) != sfp
+      || context.label == NULL)
+  {
+    if ((new_sfp = SeqMgrGetDesiredFeature (0, bsp, 0, 0, sfp, &context)) != sfp
+      || context.label == NULL)
+    {
+      return NULL;
+    }
+  }
+  if ((IsExon (sfp) && StringCmp (context.label, "exon") == 0)
+    || (IsIntron (sfp) && StringCmp (context.label, "intron") == 0))
+  {
+    return NULL;
+  }
+  
+  label = StringSave (context.label);
+  return label;
+}
+
+static CharPtr GetFeatureDescription 
+( FeatureClausePtr fcp,
+  BioseqPtr        bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  SeqFeatPtr    sfp;
+
+  if ( fcp == NULL
+    || fcp->featlist == NULL
+    || fcp->featlist->data.ptrvalue == NULL)
+  {
+    return NULL;
+  }
+  sfp = fcp->featlist->data.ptrvalue;
+  if (sfp == NULL) return NULL;
+
+  if (IsExon (sfp) || IsIntron (sfp))
+  {
+    return GetExonDescription (bsp, sfp);
+  }
+  else if (IsEndogenousVirusSequence (sfp))
+  {
+    return GetEndogenousVirusSequenceDescription (sfp);
+  }
+  else if (IsEndogenousVirusSourceFeature (sfp))
+  {
+    return GetEndogenousVirusSourceFeatureDescription (sfp);
+  }
+  else if (IsControlRegion (sfp))
+  {
+    return NULL;
+  }
+  else if (IsDloop (sfp))
+  {
+    return NULL;
+  }
+  else if (Is3UTR (sfp))
+  {
+    return NULL;
+  }
+  else if (Is5UTR (sfp))
+  {
+    return NULL;
+  }
+  else if (IsLTR (sfp))
+  {
+    return GetLTRDescription (sfp);
+  }
+  else
+  {
+    return GetGeneProtDescription (fcp, bsp, rp);
+  }
+}
+
+static void LIBCALLBACK GetSatelliteFeatureLabel (
+  ValNodePtr      featlist,
+  BioseqPtr       bsp,
+  Uint1           biomol,
+  FeatureLabelPtr flp
+)
+{
+  SeqFeatPtr main_feat;
+  CharPtr    semicolon;
+
+  flp->description = NULL; 
+  flp->typeword = StringSave ("sequence");
+  flp->pluralizable = FALSE;
+  flp->is_typeword_first = FALSE;
+ 
+  if (featlist == NULL) return;
+  main_feat = featlist->data.ptrvalue;
+  if (main_feat == NULL) return;
+  if (StringHasNoText (main_feat->comment)) return;
+
+  flp->description = StringSave (main_feat->comment);
+  if ((semicolon = StringStr (flp->description, ";")) != NULL)
+  {
+    *semicolon = 0;
+  }
+}
+
+static void LIBCALLBACK GetPromoterFeatureLabel (
+  ValNodePtr      featlist,
+  BioseqPtr       bsp,
+  Uint1           biomol,
+  FeatureLabelPtr flp
+)
+{
+  SeqFeatPtr main_feat;
+  
+  flp->description = NULL;
+  flp->typeword = StringSave ("promoter region");
+
+  if (featlist == NULL) return;
+  main_feat = featlist->data.ptrvalue;
+  if (main_feat == NULL) return;
+
+  flp->description =  NULL;
+  flp->pluralizable = FALSE;
+  flp->is_typeword_first = FALSE;
+
+}
+
+/* This function temporarily removes a 3' UTR clause from the end of
+ * a clause list so that it will not be included in the list of subfeatures
+ * before a CDS in the definition line.
+ * The 3' UTR clause should be put back if it was not the only clause in the
+ * list.
+ */
+static ValNodePtr Remove3UTRFromEndOfFeatList (ValNodePtr PNTR featlist)
+{
+  ValNodePtr vnp, prev = NULL;
+  
+  if (featlist == NULL || *featlist == NULL) return NULL;
+  
+  for (vnp = *featlist; vnp != NULL && vnp->next != NULL; vnp = vnp->next)
+  {
+    prev = vnp;
+  }
+  if (vnp->choice == DEFLINE_CLAUSEPLUS && Is3UTRClause (vnp->data.ptrvalue))
+  {
+    if (prev == NULL)
+    {
+      *featlist = NULL;
+    }
+    else
+    {
+      prev->next = NULL;        
+    }
+  }
+  else
+  {
+    vnp = NULL;
+  }
+  return vnp;
+}
+
+static Uint1 GetMoleculeType (BioseqPtr bsp, Uint2     entityID);
+static void ConsolidateClauses (
+  ValNodePtr PNTR list,
+  BioseqPtr  bsp,
+  Uint1      biomol,
+  Boolean    delete_now,
+  DeflineFeatureRequestListPtr rp);
+
+
+/* This function calculates the "interval" for a clause in the definition
+ * line.  The interval could be an empty string, it could indicate whether
+ * the location of the feature is partial or complete and whether or not
+ * the feature is a CDS, the interval could be a description of the
+ * subfeatures of the clause, or the interval could be a combination of the
+ * last two items if the feature is a CDS.
+ */
+static CharPtr GetGenericInterval 
+( FeatureClausePtr fcp,
+  Uint1            biomol,
+  BioseqPtr        bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  CharPtr    interval;
+  Boolean    partial5, partial3;
+  SeqFeatPtr sfp;
+  ValNodePtr featlist, strings, prev_feat;
+  CharPtr    subfeatlist;
+  Int4       len;
+  Boolean    suppress_final_and;
+  ValNodePtr utr3vnp = NULL;
+  ValNodePtr last_feat;
+  Uint1      molecule_type;
+
+  if ( fcp == NULL || fcp->featlist == NULL) return NULL;
+  if (fcp->is_unknown) return NULL;
+  featlist = fcp->featlist;
+  sfp = featlist->data.ptrvalue;
+  if (sfp == NULL) return NULL;
+  if ( IsExon (sfp) && fcp->is_alt_spliced)
+  {
+    return StringSave ("alternatively spliced");
+  }
+  if ( ! ShowInterval (sfp)) return NULL;
+
+  subfeatlist = NULL;
+  len = 50;
+  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+
+  strings = NULL;
+  prev_feat = NULL;
+  while (featlist != NULL && featlist->choice != DEFLINE_CLAUSEPLUS)
+  {
+    prev_feat = featlist;
+    featlist = featlist->next;
+  }
+  if (IsCDS (sfp))
+  {
+    utr3vnp = Remove3UTRFromEndOfFeatList (&featlist);
+  }
+  if (featlist != NULL)
+  {
+    suppress_final_and = FALSE;
+    if (( IsCDS (sfp) && ! fcp->clause_info_only)
+        || utr3vnp != NULL)
+    {
+      suppress_final_and = TRUE;
+    }
+    LabelClauses (featlist, biomol, bsp, rp);
+    
+    molecule_type = GetMoleculeType (bsp, bsp->idx.entityID);
+    /* consolidate genes/proteins with the same names (usually hypothetical proteins) */
+    ConsolidateClauses (&featlist, bsp, molecule_type, TRUE,
+                        rp);
+
+    /* make sure featlist is still intact - may have consolidated it */
+    if (prev_feat == NULL)
+    {
+      fcp->featlist = featlist;
+    }
+    else
+    {
+      prev_feat->next = featlist;
+    }
+
+    ListClauses (featlist, &strings, FALSE, suppress_final_and);
+    subfeatlist = MergeValNodeStrings (strings, FALSE);
+	  ValNodeFreeData (strings);
+    len += StringLen (subfeatlist) + 7;
+    
+    if (utr3vnp != NULL)
+    {
+      len += 14;
+    }
+  }
+
+  interval = (CharPtr) MemNew (len * sizeof (Char));
+  if (interval == NULL) return NULL;
+  interval[0] = 0;
+
+  if (StringDoesHaveText (subfeatlist))
+  {
+    StringCat (interval, subfeatlist);
+    if ( ! IsCDS (sfp) || fcp->clause_info_only)
+    {
+      if (utr3vnp != NULL)
+      {
+        if (featlist->next != NULL)
+        {
+          StringCat (interval, ",");
+        }
+        StringCat (interval, " and 3' UTR");
+        /* put 3' UTR back at end of featlist */
+        if (featlist != NULL)
+        {
+          last_feat = featlist;
+          while (last_feat != NULL && last_feat->next != NULL)
+          {
+            last_feat = last_feat->next;
+          }
+          last_feat->next = utr3vnp;
+        }
+      }
+      if (subfeatlist != NULL) MemFree (subfeatlist);
+      return interval;
+    }
+    if (utr3vnp == NULL)
+    {
+      StringCat (interval, " and ");
+    }
+    else
+    {
+      StringCat (interval, ", ");
+    }
+  }
+
+  if (FeatureDoesNotGetPartialComplete (sfp)) 
+  {
+    /* don't add partial or complete */
+  } 
+  else if (partial5 || partial3)
+  {
+    StringCat (interval, "partial ");
+  }
+  else
+  {
+    StringCat (interval, "complete ");
+  }
+  if (IsCDS (sfp) && ! IsPseudo (sfp))
+  {
+    StringCat (interval, "cds");
+    if (fcp->is_alt_spliced)
+      StringCat (interval, ", alternatively spliced");
+  }
+  else
+  {
+    StringCat (interval, "sequence");
+    if (IsNoncodingProductFeat (sfp) && fcp->is_alt_spliced)
+    {
+      StringCat (interval, ", alternatively spliced");
+    }
+  }
+  
+  if (utr3vnp != NULL)
+  {
+    /* tack UTR3 on at end of clause */
+    if (StringDoesHaveText (subfeatlist))
+    {
+      StringCat (interval, ",");
+    }
+    StringCat (interval, " and 3' UTR");
+    
+    /* put 3' UTR back at end of featlist */
+    if (featlist != NULL)
+    {
+      last_feat = featlist;
+      while (last_feat != NULL && last_feat->next != NULL)
+      {
+        last_feat = last_feat->next;
+      }
+      last_feat->next = utr3vnp;
+    }
+  }
+  
+  if (subfeatlist != NULL) MemFree (subfeatlist);    
+  
+  return interval;
+} 
+
+
+/* This function is used to generate feature label information for
+ * a feature clause.  It is called by the LabelFeature function if
+ * a "GetFeatureLabel" function is not found for the specific feature
+ * type.
+ * In the future it may be advisable to create "GetFeatureLabel" functions
+ * for more of the specific feature types, to reduce the number of times
+ * that the feature must be identified as being a certain type.
+ */ 
+static void LIBCALLBACK GetGenericFeatureLabel 
+( FeatureClausePtr fcp,
+  BioseqPtr        bsp,
+  Uint1            biomol,
+  FeatureLabelPtr  flp,
+  DeflineFeatureRequestListPtr rp)
+{
+  SeqFeatPtr main_feat;
+  
+  if (fcp == NULL
+    || fcp->featlist == NULL
+    || fcp->featlist->data.ptrvalue == NULL)
+  {
+    return;
+  }
+  main_feat = fcp->featlist->data.ptrvalue;
+  if (main_feat == NULL) return;
+
+  if (flp->typeword == NULL)
+  {
+    flp->typeword = GetFeatureTypeWord (biomol, main_feat);
+    flp->is_typeword_first = IsTypeWordFirst (flp->typeword);
+    flp->pluralizable = TRUE;
+  }
+  if (flp->productname == NULL)
+  {
+    flp->productname = GetProductName (main_feat, bsp, rp);
+  }
+  if (flp->description == NULL
+    && (! IsMiscRNA (main_feat)
+      || StringStr (flp->productname, "spacer") == NULL ))
+  {
+    flp->description = GetFeatureDescription (fcp, bsp, rp);
+  }
+
+}
+
+typedef void (LIBCALLBACK *GetFeatureLabelFunction) (
+  ValNodePtr      featlist,
+  BioseqPtr       bsp,
+  Uint1           biomol,
+  FeatureLabelPtr flp
+);
+
+typedef struct matchlabelfunction {
+  matchFunction           itemmatch;
+  GetFeatureLabelFunction labelfunction;
+} MatchLabelFunctionData, PNTR MatchLabelFunctionPtr;
+
+static MatchLabelFunctionData label_functions[] = {
+ { IsSatelliteSequence, GetSatelliteFeatureLabel         },
+ { IsMobileElement,     GetMobileElementFeatureLabel        },
+ { IsPromoter,          GetPromoterFeatureLabel          },
+ { IsIntergenicSpacer,  GetIntergenicSpacerFeatureLabel  },
+ { IsGeneCluster,       GetGeneClusterFeatureLabel       }
+};
+
+typedef enum {
+ DEFLINE_FEATLABEL_Satellite = 0,
+ DEFLINE_FEATLABEL_Transposon,
+ DEFLINE_FEATLABEL_Promoter,
+ DEFLINE_FEATLABEL_IntergenicSpacer,
+ DEFLINE_FEATLABEL_GeneCluster,
+ NumDefLineFeatLabels
+} DefLineFeatLabel;
+
+static void LabelFeature 
+( BioseqPtr        bsp,
+  Uint1            biomol,
+  FeatureClausePtr new_clauseplus,
+  DeflineFeatureRequestListPtr rp)
+{
+  Int4             i;
+  SeqFeatPtr       main_feat;
+
+  if (new_clauseplus == NULL || new_clauseplus->featlist == NULL) return;
+
+  if (new_clauseplus->featlist->choice == DEFLINE_FEATLIST)
+  {
+    main_feat = (SeqFeatPtr) new_clauseplus->featlist->data.ptrvalue;
+    
+    new_clauseplus->allelename = GetAlleleName (new_clauseplus->grp,
+                                                rp == NULL ? FALSE : rp->suppress_locus_tags);
+    if (new_clauseplus->interval == NULL)
+    {
+      new_clauseplus->interval =
+                  GetGenericInterval (new_clauseplus, biomol, bsp, rp);
+    }
+
+    for (i=0; i < NumDefLineFeatLabels; i++)
+    {
+      if (label_functions [i].itemmatch (main_feat))
+      {
+        label_functions [i].labelfunction ( new_clauseplus->featlist,
+                                          bsp, biomol,
+                                          &new_clauseplus->feature_label_data);
+        return;
+      }
+    }
+
+    GetGenericFeatureLabel ( new_clauseplus, bsp, biomol, 
+                           &new_clauseplus->feature_label_data, rp);
+    return;
+  }
+}
+
+/* This function is used to calculate the parts of a product name that
+ * are "the same" for use as the name of an alternatively spliced product.
+ * The common portion of the string must end at a recognized separator,
+ * such as a space, comma, or dash instead of in the middle of a word.
+ * The matching portions of the string could occur at the beginning or end
+ * of the string, or even occasionally at the beginning and end of a
+ * string, but not as the center of the string with a different beginning
+ * and ending.
+ */
+static CharPtr FindStringIntersection (
+  CharPtr str1,
+  CharPtr str2,
+  Boolean str1_previously_stripped
+)
+{
+  Int4 matchleftlen = 0;
+  Int4 matchlefttoken = 0;
+  Int4 matchrightidx1 = 0;
+  Int4 matchrightidx2 = 0;
+  Int4 matchrighttoken = 0;
+  CharPtr match_string;
+  Int4 len1;
+  Int4 len2;
+  Int4 match_len;
+
+  if (str1 == NULL || str2 == NULL) return NULL;
+  if (StringCmp (str1, str2) == 0) return StringSave (str1);
+  len1 = StringLen (str1);
+  len2 = StringLen (str2);
+
+  while (str1[matchleftlen] != 0 && str2[matchleftlen] != 0
+         && str1[matchleftlen] == str2[matchleftlen])
+  {
+    if (str1 [matchleftlen] == ','
+      || str1 [matchleftlen] == '-')
+    {
+      matchlefttoken = matchleftlen;
+    }
+    else if (str1 [matchleftlen] == ' '
+      && matchlefttoken != matchleftlen - 1)
+    {
+      matchlefttoken = matchleftlen;
+    }
+    matchleftlen++;
+  }
+  if (matchleftlen == len1 && str1_previously_stripped) 
+  {
+    matchlefttoken = matchleftlen;
+  }
+  else
+  {
+    matchleftlen = matchlefttoken;
+  }
+
+  matchrightidx1 = len1;
+  matchrightidx2 = len2;
+
+  while (matchrightidx1 > -1 && matchrightidx2 > -1
+         && str1[matchrightidx1] == str2[matchrightidx2])
+  {
+    if (str1 [matchrightidx1] == ' '
+      || str1[matchrightidx1] == ','
+      || str1[matchrightidx1] == '-')
+    {
+      matchrighttoken = matchrightidx1;
+    }
+    matchrightidx1--;
+    matchrightidx2--;
+  }
+  if (matchrightidx1 == -1)
+  {
+    matchrighttoken = matchrightidx1;
+  }
+  else if (matchrighttoken > 0) 
+  {
+    matchrightidx1 = matchrighttoken;
+  } 
+  else if (str1_previously_stripped && matchrightidx1 < len1 - 1)
+  {
+    /* matchrightidx1 = matchrighttoken; */
+    /* do nothing, leave right index where it is */
+  }
+  else
+  {
+    matchrightidx1 = len1;
+  }
+
+  match_len = matchleftlen;
+  if (matchrightidx1 < len1 - 1)
+  {
+    match_len += len1 - matchrightidx1 - 1;
+  }
+
+  if (match_len <= 0) return NULL;
+
+  match_string = MemNew (match_len + 2);
+  if (match_string == NULL) return NULL;
+  if (matchleftlen != 0)
+  {
+    StringNCpy (match_string, str1, matchleftlen);
+    match_string[matchleftlen] = 0;
+  }
+  else
+  {
+    match_string[0] = 0;
+  }
+  if (matchrightidx1 < len1)
+  {
+    if (match_string[0] != 0) StringCat (match_string, " ");
+    StringCat (match_string, str1 + matchrightidx1 + 1);
+  }
+  return match_string;
+}
+
+/* These are the words that are used to introduced the part of the protein
+ * name that differs in alt-spliced products - they should not be part of
+ * the alt-spliced product name.
+ * Note that splice variant is listed before "variant" so that it will be
+ * found first and "variant" will not be removed from "splice variant", leaving
+ * splice as an orphan.
+ */
+
+static CharPtr UnwantedWords [] = {
+ "splice variant",
+ "splice product",
+ "variant",
+ "isoform"
+};
+
+static void TrimUnwantedWordsFromAltSpliceProductName (
+  CharPtr productname
+)
+{
+  Int4    num_unwanted_words, i;
+  size_t  unwanted_word_len;
+  CharPtr cp, tmp;
+  
+  num_unwanted_words = sizeof (UnwantedWords) / sizeof (CharPtr);
+  for (i = 0; i < num_unwanted_words; i++)
+  {
+    unwanted_word_len = StringLen (UnwantedWords [i]);
+    cp = StringStr (productname, UnwantedWords [i]);
+    if (cp != NULL)
+    {
+      if (cp == productname)
+      {
+        /* word occurs in beginning of phrase */
+        tmp = StringSave (productname + unwanted_word_len);
+        StringCpy (productname, tmp);
+        MemFree (tmp);
+      }
+      else if (cp - productname < StringLen (productname) - unwanted_word_len)
+      {
+        /* word occurs in middle of phrase */
+        tmp = StringSave (cp + unwanted_word_len);
+        StringCpy (cp - 1, tmp);
+        MemFree (tmp);
+      }
+      else
+      {
+        /* word occurs at end of phrase */
+        *cp = 0;
+      }
+    }
+  }
+}
+
+
+static Boolean PreviouslyStripped (SeqFeatPtr cds, BioseqPtr bsp, CharPtr productname)
+{
+  CharPtr expected_product_name;
+  Boolean rval = FALSE;
+  
+  if (cds == NULL || StringHasNoText (productname)) return FALSE;
+  expected_product_name = GetProductName (cds, bsp, FALSE);
+  if (StringCmp (productname, expected_product_name) != 0) {
+    rval = TRUE;
+  }
+  expected_product_name = MemFree (expected_product_name);
+  return rval;
+}
+
+/* This function determines whether two CDSs meet the conditions for
+ * alternative splicing, and if so, it returns the name of the alternatively
+ * spliced product.  In order to be alternatively spliced, the two CDSs 
+ * must have the same gene, must share a complete interval, and must have
+ * similarly named products.
+ */
+static CharPtr MeetAltSpliceRules 
+( FeatureClausePtr cdsfcp1,
+  FeatureClausePtr cdsfcp2,
+  BioseqPtr        bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  SeqFeatPtr cds1, cds2;
+  CharPtr match_string;
+  Int4    res;
+  
+  if (cdsfcp1 == NULL || cdsfcp2 == NULL
+    || cdsfcp1->featlist == NULL || cdsfcp2->featlist == NULL)
+  {
+    return NULL;
+  }
+
+  cds1 = cdsfcp1->featlist->data.ptrvalue;
+  cds2 = cdsfcp2->featlist->data.ptrvalue;
+  if (! DoGenesMatch (cdsfcp1->grp, cdsfcp2->grp, rp == NULL ? FALSE : rp->suppress_locus_tags))
+    return NULL;
+
+  if ( (res = TestFeatOverlap (cds1, cds2, COMMON_INTERVAL)) != -1)
+  {
+    match_string = FindStringIntersection (
+                     cdsfcp1->feature_label_data.productname,
+                     cdsfcp2->feature_label_data.productname,
+                     PreviouslyStripped(cds1, bsp, cdsfcp1->feature_label_data.productname));
+    return match_string;
+  }
+  return NULL;
+}
+
+/* This function is used by the FindAltSplices function to locate the
+ * next CDS in a list of feature clauses.
+ */
+static ValNodePtr FindNextCDSClause (ValNodePtr vnp)
+{
+  FeatureClausePtr fcp;
+
+  while (vnp != NULL)
+  {
+    if (vnp->choice == DEFLINE_CLAUSEPLUS)
+    {
+      fcp = vnp->data.ptrvalue;
+      if (fcp != NULL && !fcp->delete_me && fcp->featlist != NULL
+        && IsCDS (fcp->featlist->data.ptrvalue))
+      {
+        return vnp;
+      }
+    }
+    vnp = vnp->next;
+  }
+  return NULL;
+}
+
+/* This function is used by the FindAltSplices function to move the features
+ * and subclauses from the second CDS in an alternatively spliced pair of 
+ * CDSs to the feature clause for the first CDS, so that the subfeatures
+ * can be properly listed.
+ */
+static void MoveSubclauses (
+  FeatureClausePtr dstfcp,
+  FeatureClausePtr srcfcp
+)
+{
+  ValNodePtr dst_last_feat, dst_first_clause, dst_last_clause;
+  ValNodePtr src_last_feat, src_first_clause;
+
+  if (dstfcp == NULL || srcfcp == NULL || srcfcp->featlist == NULL) return;
+
+  dst_first_clause = NULL;
+  dst_last_clause = NULL;
+  src_first_clause = NULL;
+
+  dst_last_feat = dstfcp->featlist;
+  while (dst_last_feat != NULL 
+      && dst_last_feat->next != NULL
+      && dst_last_feat->next->choice == DEFLINE_FEATLIST)
+  {
+    dst_last_feat = dst_last_feat->next;
+  }
+  if (dst_last_feat != NULL)
+  {
+    dst_first_clause = dst_last_feat->next;
+  }
+  dst_last_clause = dst_first_clause;
+  while (dst_last_clause != NULL && dst_last_clause->next != NULL)
+  {
+    dst_last_clause = dst_last_clause->next;
+  }
+
+  src_last_feat = srcfcp->featlist;
+  while (src_last_feat != NULL 
+      && src_last_feat->next != NULL
+      && src_last_feat->next->choice == DEFLINE_FEATLIST)
+  {
+    src_last_feat = src_last_feat->next;
+  }
+  if (src_last_feat != NULL)
+  {
+    src_first_clause = src_last_feat->next;
+  }
+
+  /* insert features before clauses */
+  if (dst_last_feat == NULL)
+  {
+    dstfcp->featlist = srcfcp->featlist;
+    dst_last_feat = src_last_feat;
+  }
+  else
+  {
+    dst_last_feat->next = srcfcp->featlist;
+  }
+  /* insert clauses after feats */
+  if (dst_first_clause != NULL)
+  {
+    src_last_feat->next = dst_first_clause;
+    dst_last_clause->next = src_first_clause;
+  }
+  srcfcp->featlist = NULL;
+}
+ 
+/* we want to look through the list for CDS features */
+/* if we find two CDSs that are alternatively spliced, */
+/* we replace the first alternatively spliced CDS feature */
+/* with a new CDS feature that has the new protein name as */
+/* a comment and a data.choice value that indicates alt splicing */
+/* we remove the second alternatively spliced CDS feature from the list */
+
+static void FindAltSplices 
+( ValNodePtr clause_list,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  FeatureClausePtr  fcp1, fcp2;
+  ValNodePtr cdsclause1, cdsclause2;
+  ValNodePtr searchclause;
+  CharPtr  combined_protein_name;
+  Boolean    partial3_1, partial5_1, partial3_2, partial5_2;
+  Int4       left1, left2, right1, right2;
+
+  if (clause_list == NULL) return;
+  
+  cdsclause1 = FindNextCDSClause (clause_list);
+  while (cdsclause1 != NULL)
+  {
+    fcp1 = (FeatureClausePtr) cdsclause1->data.ptrvalue;
+    if (fcp1->feature_label_data.productname == NULL)
+    {
+      fcp1->feature_label_data.productname = 
+           GetProductName (fcp1->featlist->data.ptrvalue, bsp, rp);
+    }
+    searchclause = cdsclause1->next;
+    cdsclause2 = FindNextCDSClause (searchclause);
+    while (cdsclause2 != NULL) 
+    {
+      fcp2 = (FeatureClausePtr) cdsclause2->data.ptrvalue;
+      if (fcp2->feature_label_data.productname == NULL)
+      {
+        fcp2->feature_label_data.productname =
+           GetProductName (fcp2->featlist->data.ptrvalue, bsp, rp);
+      }
+      combined_protein_name = MeetAltSpliceRules (fcp1, fcp2, bsp, rp);
+      if (combined_protein_name != NULL)
+      {
+        /* get rid of variant, splice variant, splice product, isoform, etc.*/
+        TrimUnwantedWordsFromAltSpliceProductName (combined_protein_name);
+
+        /* get rid of trailing spaces in protein name */
+        TrimSpacesAroundString (combined_protein_name);
+
+        /* copy new protein name into first clause */
+        MemFree (fcp1->feature_label_data.productname);
+        fcp1->feature_label_data.productname = combined_protein_name;
+        CheckSeqLocForPartial (fcp1->slp, &partial5_1, &partial3_1);
+        left1 = GetOffsetInBioseq (fcp1->slp, bsp, SEQLOC_LEFT_END);
+        right1 = GetOffsetInBioseq (fcp1->slp, bsp, SEQLOC_RIGHT_END);
+        CheckSeqLocForPartial (fcp2->slp, &partial5_2, &partial3_2);
+        left2 = GetOffsetInBioseq (fcp2->slp, bsp, SEQLOC_LEFT_END);
+        right2 = GetOffsetInBioseq (fcp2->slp, bsp, SEQLOC_RIGHT_END);
+        fcp1->slp = SeqLocMerge (bsp, fcp1->slp, fcp2->slp,
+                                 FALSE, TRUE, FALSE);
+        if (left1 == left2)
+        {
+          partial5_1 |= partial5_2;
+        }
+        else
+        {
+          partial5_1 = left1 < left2 ? partial5_1 : partial5_2;
+        }
+        if (right1 == right2)
+        {
+          partial3_1 |= partial3_2;
+        }
+        else
+        {
+          partial3_1 = right1 > right2 ? partial3_1 : partial3_2;
+        }
+        SetSeqLocPartial (fcp1->slp, partial5_1, partial3_1);
+        fcp1->is_alt_spliced = TRUE;
+
+        /* copy over fcp2 subclauses */
+        MoveSubclauses (fcp1, fcp2);
+
+        /* remove second clause */
+        fcp2->delete_me = TRUE;
+      }
+      searchclause = cdsclause2->next;
+      cdsclause2 = FindNextCDSClause (searchclause);
+    }
+    cdsclause1 = FindNextCDSClause (cdsclause1->next);
+  } 
+  DeleteFeatureClauses (&clause_list);
+}
+
+static void LabelClauses 
+( ValNodePtr clause_list,
+  Uint1      biomol,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  ValNodePtr clause;
+ 
+  clause = clause_list;
+  while (clause != NULL)
+  { 
+    LabelFeature ( bsp, biomol, clause->data.ptrvalue, rp);
+    clause = clause->next;
+  }
+}
+
+static CharPtr misc_words [] = {
+  "internal transcribed spacer",
+  "external transcribed spacer",
+  "ribosomal RNA intergenic spacer",
+  "ribosomal RNA",
+  "intergenic spacer"
+};
+
+typedef enum {
+  MISC_RNA_WORD_INTERNAL_SPACER = 0,
+  MISC_RNA_WORD_EXTERNAL_SPACER,
+  MISC_RNA_WORD_RNA_INTERGENIC_SPACER,
+  MISC_RNA_WORD_RNA,
+  MISC_RNA_WORD_INTERGENIC_SPACER,
+  NUM_MISC_RNA_WORDS
+} MiscWord;
+
+static CharPtr separators [] = {
+  ", and ",
+  " and ",
+  ", ",
+  "; "
+};
+
+#define num_separators 3
+
+static ValNodePtr GetMiscRNAelements 
+( SeqFeatPtr misc_rna,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  CharPtr buffer;
+  Int4    i, best_i;
+  CharPtr cansep [num_separators];
+  CharPtr dataval;
+  Int4    datalen;
+  FeatureClausePtr fcp;
+  FeatureClausePtr lastfcp;
+  Int4    num_clauses;
+  ValNodePtr head, vnp;
+  Boolean partial5, partial3;
+  Int4    word_i;
+  CharPtr to_free;
+  CharPtr word_loc;
+
+  to_free = NULL;
+
+  if (misc_rna == NULL) return NULL;
+  buffer = GetProductName (misc_rna, bsp, rp);
+  to_free = buffer;
+  if (buffer == NULL) 
+  {
+    buffer = misc_rna->comment;
+  }
+  else if (StringNCmp (buffer, misc_rna->comment, StringLen (buffer) -1) == 0
+    && buffer [ StringLen (buffer) - 1] == '>')
+  {
+    MemFree (buffer);
+    to_free = NULL;
+    buffer = misc_rna->comment;
+  }
+
+  if ( StringStr (buffer, "spacer") == NULL)
+  {
+    if (to_free != NULL)
+    {
+      MemFree (to_free);
+    }
+    return NULL;
+  }
+  
+  if (StringNCmp (buffer, "contains ", 9) == 0)
+  {
+    buffer = buffer + 9;
+  }
+
+  head = NULL;
+  CheckSeqLocForPartial (misc_rna->location, &partial5, &partial3);
+  num_clauses = 0;
+
+  while (buffer != NULL 
+         && buffer[0] != 0)
+  {
+    best_i = -1;
+    for (i=0; i < num_separators; i++)
+    {
+      cansep [i] = StringStr (buffer, separators [i]);
+      if (cansep [i] != NULL 
+        && (best_i == -1 
+          || cansep [i] < cansep [best_i]))
+      {
+        best_i = i;
+      }
+    }
+
+    if (best_i == -1)
+    {
+      datalen = StringLen (buffer);
+    }
+    else
+    {
+      datalen = cansep [best_i] - buffer;
+    }
+
+    dataval = MemNew (datalen + 1);
+    if (dataval == NULL) return NULL;
+    StringNCpy (dataval, buffer, datalen);
+    dataval [datalen] = 0;
+
+    for (word_i=0;
+         word_i < NUM_MISC_RNA_WORDS
+           && (word_loc = StringStr (dataval, misc_words [word_i])) == NULL;
+         word_i++) {}
+    if (word_i < NUM_MISC_RNA_WORDS)
+    {
+      fcp = NewFeatureClause ( misc_rna, bsp, rp);
+      if (fcp == NULL) return NULL;
+      if (word_i == MISC_RNA_WORD_INTERNAL_SPACER
+        || word_i == MISC_RNA_WORD_EXTERNAL_SPACER
+        || word_i == MISC_RNA_WORD_RNA_INTERGENIC_SPACER
+        || word_i == MISC_RNA_WORD_INTERGENIC_SPACER)
+      {
+        if (word_loc == dataval)
+        {
+          fcp->feature_label_data.is_typeword_first = TRUE;
+          fcp->feature_label_data.typeword = StringSave (misc_words [word_i]);
+          if (StringLen (misc_words [word_i]) + 1 < StringLen (dataval))
+          {
+            fcp->feature_label_data.description =
+                  StringSave ( dataval + StringLen (misc_words [word_i]) + 1);
+          }
+        }
+        else
+        {
+          fcp->feature_label_data.is_typeword_first = FALSE;
+          fcp->feature_label_data.typeword = StringSave (misc_words [word_i]);
+          if (StringLen (misc_words [word_i]) + 1 < StringLen (dataval))
+          {
+            fcp->feature_label_data.description =
+                  StringSave ( dataval);
+            fcp->feature_label_data.description [word_loc - dataval - 1] = 0;
+          }
+        }
+        MemFree (dataval);
+      }
+      else if (word_i == MISC_RNA_WORD_RNA)
+      {
+        fcp->feature_label_data.description = dataval;
+      }
+      if (num_clauses == 0 && partial5)
+      {
+        fcp->interval = StringSave ("partial sequence");
+      }
+      else
+      {
+        fcp->interval = StringSave ("complete sequence");
+      }
+   
+      num_clauses ++;
+      lastfcp = fcp;
+      
+      vnp = ValNodeNew (head);
+      if (head == NULL) head = vnp;
+      if (vnp == NULL) return NULL;
+      vnp->data.ptrvalue = fcp;
+      vnp->choice = DEFLINE_CLAUSEPLUS;
+    }
+    else
+    {
+      MemFree (dataval);
+    }
+    buffer += datalen;
+    if (best_i != -1)
+    {
+      buffer += StringLen ( separators [best_i]);
+    }
+  }
+
+  if ((num_clauses == 1 && partial3 && ! partial5)
+    || (num_clauses > 1 && partial3))
+  {
+    MemFree (lastfcp->interval);
+    lastfcp->interval = StringSave ("partial sequence");
+  }
+  if (to_free != NULL) MemFree (to_free);
+  return head;
+}
+
+/* Some misc_RNA clauses have a comment that actually lists multiple
+ * features.  This function creates a clause for each element in the
+ * comment and inserts the list of new clauses into the feature list
+ * at the point where the single previous clause was.
+ */
+static void ReplaceRNAClauses (
+  ValNodePtr PNTR clause_list,
+  BioseqPtr       bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  FeatureClausePtr fcp;
+  SeqFeatPtr main_feat;
+  ValNodePtr clause, replacement_clauses, nextclause, vnp;
+
+  if (clause_list == NULL || *clause_list == NULL) return;
+  clause = *clause_list;
+  while (clause != NULL)
+  {
+    nextclause = clause->next;
+    fcp = (clause->data.ptrvalue);
+    if (fcp == NULL
+      || fcp->featlist == NULL
+      || fcp->featlist->choice != DEFLINE_FEATLIST)
+    {
+      return;
+    }
+    main_feat = (SeqFeatPtr) fcp->featlist->data.ptrvalue;
+  
+    if (IsrRNA (main_feat) || IsMiscRNA (main_feat))
+    {
+      replacement_clauses = GetMiscRNAelements ( main_feat, bsp, rp );
+      if (replacement_clauses != NULL)
+      {
+        for (vnp = replacement_clauses; vnp->next != NULL; vnp = vnp->next) {}
+        vnp->next = clause->next;
+        clause->next = replacement_clauses;
+        fcp->delete_me = TRUE;
+      }
+    }
+    clause = nextclause;
+  }
+  DeleteFeatureClauses (clause_list);
+}
+
+/* Some misc_feat clauses have a comment that lists one or more tRNAs and
+ * an intergenic spacer.  This function creates a clause for each element 
+ * in the comment and inserts the list of new clauses into the feature list
+ * at the point where the single previous clause was.
+ */
+static void ReplaceIntergenicSpacerClauses (
+  ValNodePtr PNTR clause_list,
+  BioseqPtr       bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  FeatureClausePtr fcp;
+  SeqFeatPtr main_feat;
+  ValNodePtr clause, replacement_clauses, nextclause, vnp;
+
+  if (clause_list == NULL || *clause_list == NULL) return;
+  clause = *clause_list;
+  while (clause != NULL)
+  {
+    nextclause = clause->next;
+    fcp = (clause->data.ptrvalue);
+    if (fcp == NULL
+      || fcp->featlist == NULL
+      || fcp->featlist->choice != DEFLINE_FEATLIST)
+    {
+      return;
+    }
+    main_feat = (SeqFeatPtr) fcp->featlist->data.ptrvalue;
+  
+    if (IsIntergenicSpacer (main_feat) 
+        && (replacement_clauses = ParsetRNAIntergenicSpacerElements ( main_feat, bsp, rp)) != NULL)
+    {
+      for (vnp = replacement_clauses; vnp->next != NULL; vnp = vnp->next) {}
+      vnp->next = clause->next;
+      clause->next = replacement_clauses;
+      fcp->delete_me = TRUE;
+    }
+    clause = nextclause;
+  }
+  DeleteFeatureClauses (clause_list);
+}
+
+/* If we are applying a different rule for misc_feats, we need to recalculate
+ * their descriptions.
+ */
+static void RenameMiscFeats (ValNodePtr clause_list, Uint1 biomol)
+{
+  ValNodePtr       vnp, featlist;
+  FeatureClausePtr fcp, featlistclause;
+  SeqFeatPtr       sfp;
+  Int4             name_len;
+
+  for (vnp = clause_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice != DEFLINE_CLAUSEPLUS || vnp->data.ptrvalue == NULL)
+    {
+      continue;
+    }
+    fcp = vnp->data.ptrvalue;
+    for (featlist = fcp->featlist; featlist != NULL; featlist = featlist->next)
+    {
+      if ( featlist->data.ptrvalue == NULL)
+      {
+        continue;
+      }
+      if (featlist->choice == DEFLINE_CLAUSEPLUS)
+      {
+        featlistclause = featlist->data.ptrvalue;
+        RenameMiscFeats (featlistclause->featlist, biomol);
+        continue;
+      }
+      if (featlist->choice != DEFLINE_FEATLIST)
+      {
+        continue;
+      }
+      sfp = featlist->data.ptrvalue;
+      if (sfp->idx.subtype != FEATDEF_misc_feature
+        || sfp->comment == NULL
+        || IsIntergenicSpacer (sfp)
+        || IsGeneCluster (sfp)
+        || IsControlRegion (sfp)) 
+      {
+        continue;
+      }
+      if (fcp->feature_label_data.description != NULL) 
+      {
+        fcp->feature_label_data.description
+                   = MemFree (fcp->feature_label_data.description);
+      }
+      name_len = StringCSpn (sfp->comment, ";");
+	  /* make sure we have space for terminating NULL */
+      fcp->feature_label_data.description = MemNew ((name_len + 1) * sizeof (Char));
+      if (fcp->feature_label_data.description == NULL) return;
+      StringNCpy (fcp->feature_label_data.description, sfp->comment, name_len);
+      fcp->feature_label_data.description [ name_len ] = 0;
+      fcp->feature_label_data.typeword =
+            MemFree (fcp->feature_label_data.typeword);
+      if (biomol == MOLECULE_TYPE_GENOMIC)
+      {
+        fcp->feature_label_data.typeword = StringSave ("genomic sequence");
+      }
+      else if (biomol == MOLECULE_TYPE_MRNA)
+      {
+        fcp->feature_label_data.typeword = StringSave ("mRNA sequence");
+      }
+      else
+      {
+        fcp->feature_label_data.typeword = StringSave ("sequence");
+      }
+     
+      fcp->interval = MemFree (fcp->interval);
+      fcp->interval = StringSave ("");
+    }
+  }
+}
+
+static void RemoveUnwantedMiscFeats (
+  ValNodePtr PNTR clause_list,
+  Boolean delete_now
+)
+{
+  ValNodePtr       vnp, featlist;
+  FeatureClausePtr fcp, featlistclause;
+  SeqFeatPtr       sfp;
+
+  for (vnp = *clause_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice != DEFLINE_CLAUSEPLUS || vnp->data.ptrvalue == NULL)
+    {
+      continue;
+    }
+    fcp = vnp->data.ptrvalue;
+    for (featlist = fcp->featlist; featlist != NULL; featlist = featlist->next)
+    {
+      if ( featlist->data.ptrvalue == NULL)
+      {
+        continue;
+      }
+      if (featlist->choice == DEFLINE_CLAUSEPLUS)
+      {
+        featlistclause = featlist->data.ptrvalue;
+        RemoveUnwantedMiscFeats (&(featlistclause->featlist), FALSE);
+        continue;
+      }
+      if (featlist->choice != DEFLINE_FEATLIST)
+      {
+        continue;
+      }
+      sfp = featlist->data.ptrvalue;
+      if ( sfp->idx.subtype == FEATDEF_misc_feature
+        && ! IsNoncodingProductFeat (sfp)
+        && ! IsControlRegion (sfp)
+        && ! IsIntergenicSpacer (sfp)
+        && ! IsGeneCluster (sfp))
+      {
+        fcp->delete_me = TRUE;
+      }
+    }
+  }
+  DeleteFeatureClauses (clause_list);
+}
+
+/* When a feature is on the minus strand, the clauses are listed by 
+ * sequence indexing in reverse biological order - we reverse the subclauses
+ * for the feature in order to have them listed in the definition line
+ * in biological order.
+ * This is most noticeable when the main feature is a CDS with multiple
+ * exons numbered sequentially.  If the exons are on the minus strand and
+ * appear as 9, 8, 7, 6, we want to display them in the definition line as
+ * 6, 7, 8, 9.
+ */
+static void ReverseClauses (
+  ValNodePtr PNTR clause_list,
+  matchFunction   itemmatch
+)
+{
+  ValNodePtr vnp, last_feat, first_feat, next_item, new_list;
+  FeatureClausePtr fcp;
+
+  if (clause_list == NULL || *clause_list == NULL) return;
+
+  last_feat = NULL;
+  first_feat = NULL;
+  new_list = NULL;
+  vnp = *clause_list;
+  while (vnp != NULL)
+  {
+    next_item = vnp->next;
+    fcp = NULL;
+    if (vnp->choice == DEFLINE_CLAUSEPLUS
+      && (fcp = vnp->data.ptrvalue) != NULL
+      && fcp->slp != NULL
+      && SeqLocStrand (fcp->slp) == Seq_strand_minus
+      && fcp->featlist != NULL
+      && fcp->featlist->choice == DEFLINE_FEATLIST
+      && itemmatch (fcp->featlist->data.ptrvalue))
+    {
+      vnp->next = new_list;
+      new_list = vnp;
+    }
+    else
+    {
+      if (first_feat == NULL)
+      {
+        first_feat = vnp;
+        last_feat = vnp;
+      }
+      else
+      {
+        last_feat->next = vnp;
+        last_feat = vnp;
+        last_feat->next = NULL;
+      }
+    }
+    if (fcp != NULL)
+    {
+      ReverseClauses (&(fcp->featlist), itemmatch);
+    }
+    vnp = next_item;
+  }
+  if (first_feat == NULL)
+  {
+    *clause_list = new_list;
+  }
+  else
+  {
+    last_feat->next = new_list;
+    *clause_list = first_feat;
+  }
+}
+
+/* This function is used to determine whether two features are both exons
+ * and whether they are numerically sequential - i.e., exon 7 and exon 8
+ * are a pair of consecutive exons, exon 7 and exon 9 are not, and exon 7
+ * and intron 9 are not.
+ */
+static Boolean ClausePairIsTwoConsecutiveExons (
+  ValNodePtr vnp1,
+  ValNodePtr vnp2,
+  BioseqPtr  bsp
+)
+{
+  FeatureClausePtr fcp1, fcp2;
+  SeqFeatPtr       exon1, exon2;
+  Int4 num1, num2;
+  CharPtr          exdesc1, exdesc2;
+
+  if (vnp1 == NULL || vnp2 == NULL 
+    || vnp1->choice != DEFLINE_CLAUSEPLUS
+    || vnp2->choice != DEFLINE_CLAUSEPLUS
+    || vnp1->data.ptrvalue == NULL
+    || vnp2->data.ptrvalue == NULL)
+  {
+    return FALSE;
+  }
+  fcp1 = vnp1->data.ptrvalue;
+  fcp2 = vnp2->data.ptrvalue;
+  if ( fcp1->featlist == NULL
+    || fcp1->featlist->data.ptrvalue == NULL
+    || fcp2->featlist == NULL
+    || fcp2->featlist->data.ptrvalue == NULL
+    || fcp1->featlist->choice != DEFLINE_FEATLIST
+    || fcp2->featlist->choice != DEFLINE_FEATLIST
+    || ! IsExon (fcp1->featlist->data.ptrvalue)
+    || ! IsExon (fcp2->featlist->data.ptrvalue)
+    || (fcp1->is_alt_spliced && ! fcp2->is_alt_spliced)
+    || (! fcp1->is_alt_spliced && fcp2->is_alt_spliced))
+  {
+    return FALSE;
+  }
+
+  exon1 = (SeqFeatPtr)(fcp1->featlist->data.ptrvalue);
+  exon2 = (SeqFeatPtr)(fcp2->featlist->data.ptrvalue);
+
+  exdesc1 = GetExonDescription (bsp, exon1);
+  exdesc2 = GetExonDescription (bsp, exon2);
+  if (exdesc1 == NULL || exdesc2 == NULL)
+  {
+    if (exdesc1 != NULL) MemFree (exdesc1);
+    if (exdesc2 != NULL) MemFree (exdesc2);
+    return FALSE;
+  }
+  
+  num1 = atoi (exdesc1);
+  num2 = atoi (exdesc2);
+  MemFree (exdesc1);
+  MemFree (exdesc2);
+
+  if (abs (num1 - num2) == 1)
+  {
+    return TRUE;
+  }
+
+  return FALSE; 
+}
+
+/* This function counts the number of consecutive exons in a list.
+ */
+static Int4 GetNumberOfConsecutiveExons (
+  ValNodePtr list,
+  BioseqPtr  bsp
+)
+{
+  ValNodePtr check;
+  Int4       num_exons;
+ 
+  num_exons = 0;
+  check = list->next;
+  if ( ! ClausePairIsTwoConsecutiveExons (list, check, bsp)) return 0;
+  
+  num_exons = 2;
+  while ( check != NULL
+    && ClausePairIsTwoConsecutiveExons (check, check->next, bsp))
+  {
+    num_exons++;
+    check = check->next;
+  }
+  return num_exons;
+}
+
+/* This function replaces a list of three or more consecutive exon clauses
+ * with a single "summary" clause that gives the range of exons present -
+ * i.e., if you have exons 1, 2, 3, and 4, a clause will be created that
+ * contains all four of those features and has a description of "1 through 4".
+ */
+static void ReplaceExonClauseList (
+  FeatureClausePtr fcp,
+  ValNodePtr       clause,
+  Int4             num_exons,
+  BioseqPtr        bsp
+)
+{
+  ValNodePtr       lastfeat, tmpclause;
+  FeatureClausePtr tmpfcp;
+  Int4             i;
+  CharPtr          new_description;
+  Int4             new_description_len;
+  CharPtr          exdesc1, exdesc2;
+
+  if (fcp == NULL || clause == NULL) return;
+
+  lastfeat = fcp->featlist;
+  while (lastfeat != NULL && lastfeat->next != NULL)
+  {
+    lastfeat = lastfeat->next;
+  }
+  tmpclause = clause->next;
+  for (i=0; i < num_exons - 1 && tmpclause != NULL; i++)
+  {
+    tmpfcp = tmpclause->data.ptrvalue;
+    tmpfcp->delete_me = TRUE;
+    if (lastfeat == NULL)
+    {
+      fcp->featlist = tmpfcp->featlist;
+    }
+    else
+    {
+      lastfeat->next = tmpfcp->featlist;
+    }
+    tmpfcp->featlist = NULL;
+    while (lastfeat != NULL && lastfeat->next != NULL)
+    {
+      lastfeat = lastfeat->next;
+    }
+          
+    tmpclause = tmpclause->next;
+  }
+
+  exdesc1 = GetExonDescription (bsp, fcp->featlist->data.ptrvalue);
+  exdesc2 = GetExonDescription (bsp, lastfeat->data.ptrvalue);
+  if (exdesc1 == NULL || exdesc2 == NULL)
+  {
+    if (exdesc1 != NULL) MemFree (exdesc1);
+    if (exdesc2 != NULL) MemFree (exdesc2);
+    return;
+  }
+  new_description_len =
+        StringLen (exdesc1)
+      + StringLen (exdesc2)
+      + StringLen (" through ")
+      + 1;
+  new_description = MemNew (new_description_len * sizeof (Char));
+  if (new_description == NULL) return;
+  sprintf (new_description, "%s through %s", exdesc1, exdesc2);
+  MemFree (exdesc1);
+  MemFree (exdesc2);
+  if (fcp->feature_label_data.description != NULL)
+  {
+    MemFree (fcp->feature_label_data.description);
+  }
+  fcp->feature_label_data.description = new_description;
+}
+
+/* This function recursively searches for lists of consecutive exons
+ * and calls ReplaceExonClauseList to consolidate the exons into a list
+ * clause.
+ */
+static void RenameExonSequences (
+  ValNodePtr PNTR list,
+  BioseqPtr       bsp,
+  Boolean         delete_now
+)
+{
+  ValNodePtr       clause;
+  Int4             num_exons;
+  FeatureClausePtr fcp;
+ 
+  if (list == NULL) return; 
+  clause = *list;
+  while (clause != NULL)
+  {
+    if (clause->choice == DEFLINE_CLAUSEPLUS
+      && clause->data.ptrvalue != NULL)
+    {
+      fcp = clause->data.ptrvalue;
+      if ( ! fcp->delete_me)
+      {
+        num_exons = GetNumberOfConsecutiveExons (clause, bsp);
+        if (num_exons > 2)
+        {
+          ReplaceExonClauseList (fcp, clause, num_exons, bsp);
+        }
+        else
+        {
+          RenameExonSequences (&fcp->featlist, bsp, FALSE);
+        }
+      }
+    }
+    clause = clause->next;
+  }
+  if (delete_now) DeleteFeatureClauses (list);
+}
+
+static CharPtr organelleByGenome [] = {
+  NULL,
+  NULL,
+  "chloroplast",
+  "chromoplast",
+  "kinetoplast",
+  "mitochondrial",
+  "plastid",
+  "",
+  "",
+  "",
+  "",
+  "",
+  "cyanelle",
+  "",
+  "",
+  "",
+  "apicoplast",
+  "leucoplast",
+  "proplastid",
+  "",
+  "hydrogenosome",
+  NULL,
+};
+
+static CharPtr organelleByPopup [] = {
+  NULL,
+  "mitochondrial",
+  "chloroplast",
+  "kinetoplast",
+  "plastid",
+  "chromoplast",
+  "cyanelle",
+  "apicoplast",
+  "leucoplast",
+  "proplastid",
+  NULL
+};
+
+static void 
+AddProductEnding 
+(CharPtr    str, 
+ BioseqPtr  bsp,
+ Int2       mitochloroflag,
+ ValNodePtr strings)
+{
+  Char orgnelle [80];
+  BioSourcePtr  biop;
+  ValNodePtr last_string;
+  Int4 num_genes;
+  SubSourcePtr  ssp;
+
+  num_genes = 0;
+  biop = GetBiopForBsp (bsp);
+
+  if (biop != NULL) {
+    if (FindStringInStrings (strings, "genes"))
+    {
+      num_genes = 2;
+    }
+    else if ((last_string = FindStringInStrings (strings, "gene")) != NULL
+      && last_string->next != NULL
+      && (last_string = FindStringInStrings (last_string->next, "gene")) != NULL)
+    {
+      num_genes = 2;
+    }
+    else
+    {
+      num_genes = 1;
+    }
+
+    orgnelle [0] = '\0';
+  
+    switch (biop->genome) {
+    case GENOME_macronuclear :
+      StringCat (str, "; macronuclear");
+      break;
+    case GENOME_nucleomorph :
+      StringCat (str, "; nucleomorph");
+      break;
+    case GENOME_apicoplast :
+    case GENOME_chloroplast :
+    case GENOME_chromoplast :
+    case GENOME_kinetoplast :
+    case GENOME_mitochondrion :
+    case GENOME_plastid :
+    case GENOME_cyanelle :
+    case GENOME_leucoplast :
+    case GENOME_proplastid :
+    case GENOME_hydrogenosome :
+      sprintf (orgnelle, "; %s", organelleByGenome [biop->genome]);
+      StringCat (str, orgnelle);
+      break;
+    default :
+      ssp = biop->subtype;
+      while (ssp != NULL && ssp->subtype != 255)
+      {
+        ssp = ssp->next;
+      }
+      if (ssp != NULL
+        && ssp->name != NULL
+        && StringStr (ssp->name, "micronuclear"))
+      {
+        StringCat (str, "; micronuclear");
+      }
+      else if (mitochloroflag > 0) {
+        if (mitochloroflag > 9) {
+          /* beyond list */
+        }
+        else {
+          if (num_genes > 1)
+          {
+            sprintf (orgnelle, "; nuclear genes for %s products",
+                     organelleByPopup [mitochloroflag]);
+          }
+          else 
+          {
+            sprintf (orgnelle, "; nuclear gene for %s product",
+                     organelleByPopup [mitochloroflag]);
+          }
+          StringCat (str, orgnelle);
+        }
+      }
+      break;
+    }
+  }  
+}
+
+/*---------------------------------------------------------------------*/
+/*                                                                     */
+/* AutoDef_AddEnding () -- Add an ending on to the definition line     */
+/*                         after the last feature.                     */
+/*                                                                     */
+/*---------------------------------------------------------------------*/
+
+static void AutoDef_AddEnding (
+  ValNodePtr   clause_list,
+  ValNodePtr PNTR strings,
+  BioseqPtr    bsp,
+  Int2         mitochloroflag,
+  Boolean      alternate_splice_flag
+)
+{
+  Char str [200];
+  ValNodePtr last_string;
+  Int4 new_data_len;
+  CharPtr new_data;
+
+  str[0] = 0;
+  AddProductEnding (str, bsp, mitochloroflag, *strings);
+  if (alternate_splice_flag) {
+    StringCat (str, ", alternatively spliced");
+  }
+
+  StringCat (str, ".");
+
+  last_string = *strings;
+  if (last_string == NULL)
+  {
+    ValNodeAddStr (strings, 0, StringSave ( str));
+  }
+  else
+  {
+    while (last_string->next != NULL) last_string = last_string->next;
+    new_data_len = StringLen (last_string->data.ptrvalue) + StringLen (str) + 1;
+    new_data = (CharPtr) MemNew (new_data_len);
+    if (new_data == NULL) return;
+    StringCpy (new_data, last_string->data.ptrvalue);
+    StringCat (new_data, str);
+    MemFree (last_string->data.ptrvalue);
+    last_string->data.ptrvalue = new_data;
+  }
+}
+
+static Boolean LastIntervalChangeBeforeEnd (
+  FeatureClausePtr onebefore,
+  FeatureClausePtr thisclause,
+  ValNodePtr rest_of_list
+)
+{
+  ValNodePtr       vnp;
+  FeatureClausePtr fcp;
+
+  if (onebefore == NULL || rest_of_list == NULL) return FALSE;
+ 
+  if (StringCmp (onebefore->interval, thisclause->interval) == 0) return FALSE;
+  
+  for (vnp = rest_of_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
+    {
+      fcp = vnp->data.ptrvalue;
+      if (StringCmp (thisclause->interval, fcp->interval) != 0) return FALSE;
+    }
+  }
+  return TRUE;
+    
+}
+
+static void PluralizeClauseIntervals (
+  FeatureClausePtr fcp
+)
+{
+  CharPtr new_interval, cp;
+
+  if (fcp->interval != NULL
+    && (cp = StringStr (fcp->interval, "gene, ")) != NULL)
+  {
+    new_interval = MemNew (StringLen (fcp->interval) + 2);
+    if (new_interval == NULL) return;
+    StringCpy (new_interval, fcp->interval);
+    new_interval [ cp - fcp->interval + 4] = 's';
+    StringCpy (new_interval + (cp - fcp->interval) + 5,
+               cp + 4);
+    MemFree (fcp->interval);
+    fcp->interval = new_interval;
+  }
+}  
+
+static Boolean DisplayAlleleName (FeatureClausePtr thisclause)
+{
+  if (thisclause == NULL) return FALSE;
+  if (StringCmp (thisclause->feature_label_data.typeword, "gene") == 0
+    || StringCmp (thisclause->feature_label_data.typeword, "pseudogene") == 0
+    || StringCmp (thisclause->feature_label_data.typeword, "mRNA") == 0
+    || StringCmp (thisclause->feature_label_data.typeword, "pseudogene mRNA") == 0
+    || StringCmp (thisclause->feature_label_data.typeword, "precursor RNA") == 0
+    || StringCmp (thisclause->feature_label_data.typeword, "pseudogene precursor RNA") == 0)
+  {
+    return TRUE;
+  }
+  return FALSE;
+}
+
+static void ListClauses (
+  ValNodePtr clauselist,
+  ValNodePtr PNTR strings,
+  Boolean    allow_semicolons,
+  Boolean    suppress_final_and
+)
+{
+  FeatureClausePtr thisclause, onebefore, twobefore, oneafter, twoafter;
+  Boolean print_typeword;
+  Boolean print_and;
+  Boolean print_comma;
+  Boolean print_semicolon;
+  Boolean print_comma_between_description_and_typeword;
+  Boolean typeword_is_plural;
+  size_t clause_len;
+  CharPtr clause_string;
+  Boolean oneafter_has_detail_change;
+  Boolean oneafter_has_interval_change;
+  Boolean oneafter_has_typeword_change;
+  Boolean onebefore_has_detail_change;
+  Boolean onebefore_has_interval_change;
+  Boolean onebefore_has_typeword_change;
+  SeqFeatPtr main_feat;
+  CharPtr new_interval;
+  ValNodePtr voneafter, vtwoafter;
+
+  while (clauselist != NULL && clauselist->choice != DEFLINE_CLAUSEPLUS)
+  {
+    clauselist = clauselist->next;
+  }
+  if (clauselist == NULL) return;
+
+  thisclause = clauselist->data.ptrvalue;
+  onebefore = NULL;
+  twobefore = NULL;
+  
+  while (thisclause != NULL)
+  {
+    oneafter_has_detail_change = FALSE;
+    oneafter_has_interval_change = FALSE;
+    oneafter_has_typeword_change = FALSE;
+    onebefore_has_detail_change = FALSE;
+    onebefore_has_interval_change = FALSE;
+    onebefore_has_typeword_change = FALSE;
+    if (onebefore != NULL)
+    {
+      if (StringCmp (onebefore->interval, thisclause->interval) != 0)
+        onebefore_has_interval_change = TRUE;
+      if (StringCmp (onebefore->feature_label_data.typeword,
+                     thisclause->feature_label_data.typeword) != 0)
+      {
+        onebefore_has_typeword_change = TRUE;
+      }
+      if (onebefore_has_typeword_change || onebefore_has_interval_change
+          || (DisplayAlleleName (onebefore) && StringLen (onebefore->allelename) != 0)
+          || (DisplayAlleleName (thisclause) && StringLen (thisclause->allelename) != 0))
+     {
+        onebefore_has_detail_change = TRUE;  
+      }
+    }
+    voneafter = clauselist->next;
+    while (voneafter != NULL && voneafter->choice != DEFLINE_CLAUSEPLUS)
+    {
+      voneafter = voneafter->next;
+    }
+    if (voneafter == NULL)
+    {
+      vtwoafter = NULL;
+    }
+    else
+    {
+      vtwoafter = voneafter->next;
+      while (vtwoafter != NULL && vtwoafter->choice != DEFLINE_CLAUSEPLUS)
+      {
+        vtwoafter = vtwoafter->next;
+      }
+    }
+
+    if (voneafter != NULL)
+    {
+      oneafter = voneafter->data.ptrvalue;
+      if (StringCmp (oneafter->interval, thisclause->interval) != 0)
+        oneafter_has_interval_change = TRUE;
+      if (StringCmp (oneafter->feature_label_data.typeword,
+                     thisclause->feature_label_data.typeword) != 0)
+      {
+        oneafter_has_typeword_change = TRUE;
+      }
+      if (oneafter_has_typeword_change  || oneafter_has_interval_change
+          || (DisplayAlleleName (thisclause) && StringLen (thisclause->allelename) != 0)
+          || (DisplayAlleleName (oneafter) && StringLen (oneafter->allelename) != 0))
+      {
+        oneafter_has_detail_change = TRUE;
+      }
+      if (vtwoafter != NULL)
+      {
+        twoafter = vtwoafter->data.ptrvalue;
+      }
+      else
+      {
+        twoafter = NULL;
+      }
+    }
+    else
+    {
+      oneafter = NULL;
+      twoafter = NULL;
+    }
+    print_typeword = FALSE;
+    typeword_is_plural = FALSE;
+    print_and = FALSE;
+    print_comma = FALSE;
+    print_semicolon = FALSE;
+
+    if (thisclause->feature_label_data.is_typeword_first)
+    {
+      if (onebefore == NULL || onebefore_has_detail_change)
+      {
+        print_typeword = TRUE;
+        if (oneafter != NULL && ! oneafter_has_detail_change)
+        {
+          typeword_is_plural = TRUE;
+        }
+        else if (StringStr (thisclause->feature_label_data.description, " through ") != NULL
+          && StringCmp (thisclause->feature_label_data.typeword, "exon") == 0)
+        {
+          typeword_is_plural = TRUE;
+        }
+      }
+    }
+    else
+    {
+      if (oneafter == NULL || oneafter_has_detail_change)
+      {
+        print_typeword = TRUE;
+        if (onebefore != NULL && ! onebefore_has_detail_change)
+        {
+          typeword_is_plural = TRUE;
+        }
+      }
+    }
+
+    /* when to print and before this section */
+    if ( onebefore != NULL
+         && ! onebefore_has_detail_change
+         && (oneafter == NULL || oneafter_has_detail_change))
+    {
+      print_and = TRUE;
+    }
+    else if (oneafter == NULL && onebefore != NULL)
+    {
+      print_and = TRUE;
+    }
+    else if (onebefore != NULL
+         && ! onebefore_has_interval_change
+         && oneafter_has_interval_change)
+    {
+      print_and = TRUE;
+    }
+    else if ( LastIntervalChangeBeforeEnd ( onebefore, 
+                                            thisclause,
+                                            clauselist->next))
+    {
+      print_and = TRUE;
+    }
+
+    if (suppress_final_and && oneafter == NULL)
+    {
+      print_and = FALSE;
+    }
+    if (suppress_final_and && oneafter != NULL && twoafter == NULL)
+    {
+      print_comma = TRUE;
+    }
+    
+    /* when to print semicolon after this section */
+    /* after every interval change except when exons change "interval" */
+    /* exons changing interval are going from alt-spliced to not */
+    /* or vice versa, in either case we don't want a semicolon or comma */
+    if (oneafter != NULL && oneafter_has_interval_change
+      && (StringCmp (thisclause->feature_label_data.typeword, "exon") != 0
+         || StringCmp (oneafter->feature_label_data.typeword, "exon") != 0))
+    {
+      print_semicolon = TRUE;
+    }
+
+    /* when to print comma after this section */
+    if (onebefore != NULL && oneafter != NULL
+      && ! onebefore_has_detail_change
+      && ! oneafter_has_detail_change )
+    {
+      print_comma = TRUE;
+    }
+    else if (oneafter != NULL && onebefore != NULL
+      && ! onebefore_has_interval_change && ! oneafter_has_interval_change
+      &&  onebefore_has_typeword_change &&  oneafter_has_typeword_change)
+    {
+      print_comma = TRUE;
+    }
+    else if (oneafter != NULL && twoafter != NULL
+      && ! oneafter_has_detail_change
+      && StringCmp (twoafter->feature_label_data.typeword,
+                    thisclause->feature_label_data.typeword) == 0
+      && StringCmp (twoafter->interval,
+                    thisclause->interval) == 0)
+    {
+      print_comma = TRUE;
+    }
+    else if (oneafter != NULL  && twoafter != NULL
+      && oneafter_has_typeword_change
+      && StringCmp (twoafter->feature_label_data.typeword,
+                    oneafter->feature_label_data.typeword) == 0
+      && StringCmp (twoafter->interval,
+                    oneafter->interval) == 0
+      && ! print_and)
+    {
+      print_comma = TRUE;
+    }
+    else if (((oneafter_has_interval_change || oneafter == NULL)
+      && StringDoesHaveText (thisclause->interval))
+      || (oneafter_has_interval_change && oneafter != NULL && ! print_semicolon))
+    {
+      print_comma = TRUE;
+    }
+    else if (oneafter != NULL && twoafter != NULL
+      && !oneafter_has_interval_change
+      && StringCmp (thisclause->interval, twoafter->interval) == 0
+      && oneafter_has_typeword_change
+      && StringCmp (thisclause->feature_label_data.typeword,
+                    twoafter->feature_label_data.typeword) != 0)
+    {
+      print_comma = TRUE;
+    }
+    else if (oneafter != NULL && onebefore != NULL && twoafter != NULL
+      && ! oneafter_has_interval_change && ! onebefore_has_interval_change
+      && StringCmp (thisclause->interval, twoafter->interval) == 0
+      && oneafter_has_typeword_change)
+    {
+      print_comma = TRUE;
+    }
+    else if (oneafter != NULL && twoafter != NULL
+      && oneafter_has_typeword_change
+      && StringCmp (oneafter->feature_label_data.typeword,
+                    twoafter->feature_label_data.typeword) != 0
+      && ! oneafter_has_interval_change
+      && StringCmp (oneafter->interval, twoafter->interval) == 0)
+    {
+      /* spacer 1, foo RNA gene, and spacer2, complete sequence */
+      /*         ^ */
+      print_comma = TRUE;
+    }
+    else if (oneafter != NULL && twoafter != NULL 
+      && ! oneafter_has_interval_change && StringCmp (thisclause->interval, twoafter->interval) == 0
+      && ((DisplayAlleleName (oneafter) && StringLen (oneafter->allelename) > 0)
+        || (DisplayAlleleName (thisclause) && StringLen (thisclause->allelename) > 0)))
+    {
+      print_comma = TRUE;  	
+    }
+    else if (oneafter != NULL && onebefore != NULL
+      && ! oneafter_has_interval_change && ! onebefore_has_interval_change
+      && ((DisplayAlleleName (oneafter) && StringLen (oneafter->allelename) > 0)
+        || (DisplayAlleleName (thisclause) && StringLen (thisclause->allelename) > 0)))
+    {
+      print_comma = TRUE;  	
+    }
+
+    if (thisclause->featlist != NULL
+      && thisclause->featlist->data.ptrvalue != NULL
+      && StringDoesHaveText (thisclause->interval)
+      && StringNCmp (thisclause->interval, "partial", 7) != 0
+      && StringNCmp (thisclause->interval, "complete", 8) != 0)
+    {
+      main_feat = thisclause->featlist->data.ptrvalue;
+      if (IsMobileElement (main_feat)
+        || IsEndogenousVirusSourceFeature (main_feat) )
+      {
+        print_comma = FALSE;
+      }
+    }
+
+    if (onebefore != NULL
+      && ! onebefore_has_interval_change
+      && (oneafter_has_interval_change || oneafter == NULL))
+    {
+      PluralizeClauseIntervals (thisclause);
+    }
+
+    if ( thisclause->make_plural )
+    {
+      if ((onebefore != NULL && ! onebefore_has_detail_change)
+        || (oneafter != NULL && !oneafter_has_detail_change))
+      {
+        PluralizeConsolidatedClauseDescription (thisclause);
+      }
+      else
+      {
+        typeword_is_plural = TRUE;
+      }
+    }
+
+    clause_len = StringLen (thisclause->feature_label_data.description) + 1;
+    
+    /* add one in case we need to add the semicolon to this clause (when
+     * the interval has changed because this clause has no interval and
+     * the next one does).
+     */
+    clause_len++;
+
+    /* we need to place a comma between the description and the type word 
+     * when the description ends with "precursor" or when the type word
+     * starts with "precursor"
+     */
+    if ( thisclause->feature_label_data.description != NULL
+      && ! thisclause->feature_label_data.is_typeword_first
+      && print_typeword
+      && ! StringHasNoText (thisclause->feature_label_data.typeword)
+      && ((StringNCmp (thisclause->feature_label_data.typeword, "precursor", 9) == 0
+            && thisclause->feature_label_data.description [StringLen (thisclause->feature_label_data.description) - 1] != ')')
+          || (clause_len > StringLen ("precursor")
+              && StringCmp ( thisclause->feature_label_data.description
+                     + clause_len - StringLen ("precursor") - 2,
+                     "precursor") == 0)))
+    {
+      print_comma_between_description_and_typeword = TRUE;
+      clause_len += 1;
+    }
+    else
+    {
+      print_comma_between_description_and_typeword = FALSE;
+    }
+
+    if (print_typeword)
+      clause_len += StringLen (thisclause->feature_label_data.typeword) + 1;
+    if (typeword_is_plural)
+      clause_len += 1;
+    if (print_and)
+      clause_len += 4;
+    if (print_comma)
+      clause_len += 2;
+    if (DisplayAlleleName (thisclause))
+    {
+      clause_len += StringLen (thisclause->allelename) + 10;
+      if (StringLen (thisclause->allelename) > 0) 
+      {
+        clause_len += StringLen (thisclause->allelename) + StringLen ("allele ");
+      }
+    }
+    
+    clause_string = (CharPtr) MemNew (clause_len);
+    if (clause_string == NULL)
+      return;
+    clause_string[0] = 0;
+    if (print_and)
+      StringCat (clause_string, "and ");
+    if (thisclause->feature_label_data.is_typeword_first && print_typeword
+      && thisclause->feature_label_data.typeword != NULL
+      && ! StringHasNoText (thisclause->feature_label_data.typeword))
+    {
+      StringCat (clause_string, thisclause->feature_label_data.typeword);
+      if (typeword_is_plural)
+        StringCat (clause_string, "s");
+      if (thisclause->feature_label_data.description != NULL)
+        StringCat (clause_string, " ");
+    }
+    if (thisclause->feature_label_data.description != NULL)
+    {
+      StringCat (clause_string, thisclause->feature_label_data.description);
+      if (print_comma_between_description_and_typeword)
+      {
+        StringCat (clause_string, ",");
+      }
+    }
+    if (! thisclause->feature_label_data.is_typeword_first && print_typeword
+      && thisclause->feature_label_data.typeword != NULL
+      && ! StringHasNoText (thisclause->feature_label_data.typeword))
+    {
+      if (thisclause->feature_label_data.description != NULL)
+        StringCat (clause_string, " ");
+      StringCat (clause_string, thisclause->feature_label_data.typeword);
+      if (typeword_is_plural)
+        StringCat (clause_string, "s");
+      if (DisplayAlleleName (thisclause)
+        && thisclause->allelename != NULL)
+      {
+        StringCat (clause_string, ", ");
+        StringCat (clause_string, thisclause->allelename);
+        StringCat (clause_string, " allele");
+      }
+    }
+    if (StringLen (clause_string) > 0 ) 
+    {
+      if (print_comma)
+        StringCat (clause_string, ",");
+      ValNodeAddStr (strings, 0, clause_string);
+    }
+    else 
+    {
+    	MemFree (clause_string);
+    	clause_string = NULL;
+    }
+ 
+    if (oneafter == NULL || oneafter_has_interval_change)
+    {
+      if (print_semicolon) {
+        if (thisclause->interval == NULL
+          || StringHasNoText(thisclause->interval)) {
+          if (clause_string != NULL) {
+            StringCat (clause_string, ";");
+          }
+        } else if (thisclause->interval[StringLen (thisclause->interval)] != ';') {
+          new_interval = MemNew (StringLen (thisclause->interval) + 2);
+          if (new_interval == NULL) return;
+          StringCpy (new_interval, thisclause->interval);
+          if (allow_semicolons) 
+          {
+            StringCat (new_interval, ";");
+          }
+          else
+          {
+            StringCat (new_interval, ",");
+          }
+          MemFree (thisclause->interval);
+          thisclause->interval = new_interval;
+        }
+      }
+      if (thisclause->interval != NULL
+        && !StringHasNoText (thisclause->interval))
+      {
+        ValNodeAddStr (strings, 0, StringSave (thisclause->interval));
+      }
+    }
+    twobefore = onebefore;
+    onebefore = thisclause;   
+    thisclause = oneafter;
+    clauselist = voneafter;
+  }
+}
+
+static Uint1 GetMoleculeType 
+(BioseqPtr bsp,
+ Uint2     entityID)
+{
+  SeqDescPtr         sdp;
+  MolInfoPtr         mip;
+  SeqMgrDescContext  dcontext;
+
+  if (bsp == NULL) return MOLECULE_TYPE_GENOMIC;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp == NULL) return MOLECULE_TYPE_GENOMIC;
+  mip = (MolInfoPtr) sdp->data.ptrvalue;
+  if (mip == NULL) return MOLECULE_TYPE_GENOMIC;
+  return mip->biomol;
+}
+
+static Boolean SpecialHandlingForSpecialTechniques (
+  BioseqPtr bsp
+)
+{
+  SeqDescPtr sdp;
+  MolInfoPtr mip;
+  ValNodePtr vnp;
+
+  if (bsp == NULL) return MOLECULE_TYPE_GENOMIC;
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, NULL);
+  if (sdp == NULL)
+  {
+    for (sdp = bsp->descr;
+         sdp != NULL && sdp->choice != Seq_descr_molinfo;
+         sdp = sdp->next)
+    {}
+  }
+  if (sdp == NULL) return FALSE;
+  mip = (MolInfoPtr) sdp->data.ptrvalue;
+  if (mip == NULL) return FALSE;
+  if (mip->tech == MI_TECH_htgs_0 ||
+      mip->tech == MI_TECH_htgs_1 ||
+      mip->tech == MI_TECH_htgs_2 ||
+      mip->tech == MI_TECH_est ||
+      mip->tech == MI_TECH_sts ||
+      mip->tech == MI_TECH_survey ||
+      mip->tech == MI_TECH_wgs) {
+    vnp = ValNodeExtract (&(bsp->descr), Seq_descr_title);
+    if (vnp != NULL)
+      vnp = ValNodeFreeData (vnp);
+    return TRUE;
+  }
+
+  return FALSE;
+}
+
+static Boolean LIBCALLBACK ShouldRemoveExon (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp,
+  Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp
+)
+{
+  Boolean partial3, partial5;
+  SeqFeatPtr main_feat;
+
+  if (isSegment || isLonely || isRequested) return FALSE;
+  if (parent_fcp == NULL
+    || parent_fcp->featlist == NULL
+    || parent_fcp->featlist->data.ptrvalue == NULL)
+  {
+    return TRUE;
+  }
+  
+  main_feat = parent_fcp->featlist->data.ptrvalue;
+  if ( IsCDS (main_feat))
+  {
+    CheckSeqLocForPartial (main_feat->location, &partial5, &partial3);
+    if (partial5 || partial3) return FALSE;
+  }
+  else if (IsmRNA (main_feat) || parent_fcp->has_mrna)
+  {
+    return FALSE;
+  }
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK ShouldRemoveCDS (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp,
+  Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp)
+{
+  CharPtr description;
+  Boolean retval = FALSE;
+
+  description = GetGeneProtDescription (this_fcp, bsp, rp);
+  if (StringHasNoText (description))
+  {
+    retval = TRUE;
+  }
+  if (description != NULL) MemFree (description);
+  return retval;
+}
+
+static Boolean LIBCALLBACK ShouldRemoveNoncodingProductFeat (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp, Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp
+)
+{
+  if (isRequested) return FALSE;
+  return TRUE;
+}
+
+static Boolean LIBCALLBACK ShouldRemovePromoter (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp, Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp
+)
+{
+  /* remove a promoter if it is in an mRNA or gene clause */
+  if (isRequested)
+  {
+    return FALSE;
+  }
+  else if (parent_fcp != NULL 
+      && (parent_fcp->has_mrna 
+        || (parent_fcp->featlist != NULL
+           && parent_fcp->featlist->choice == DEFLINE_FEATLIST
+           && parent_fcp->featlist->data.ptrvalue != NULL
+           && IsmRNA (parent_fcp->featlist->data.ptrvalue))))
+  {
+    return TRUE;
+  }
+  else if (isLonely)
+  {
+    return FALSE;
+  }
+  else
+  {
+    return TRUE;
+  }
+}
+
+static Boolean LIBCALLBACK ShouldRemoveLTR (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp,
+  Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp
+)
+{
+  if (isRequested)
+  {
+    return FALSE;
+  }
+  else if (parent_fcp != NULL)
+  {
+    return TRUE;
+  }
+  else if (isLonely)
+    return FALSE;
+  else
+    return TRUE;
+}
+
+static Boolean LIBCALLBACK ShouldRemove3UTR (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp,
+  Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp
+)
+{ 
+  if (isLonely || isRequested)
+    return FALSE;
+  else
+    return TRUE;
+}
+
+static Boolean LIBCALLBACK ShouldRemove5UTR (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp,
+  Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp
+)
+{
+  if (isLonely || isRequested)
+    return FALSE;
+  else
+    return TRUE;
+}
+
+static Boolean LIBCALLBACK ShouldRemoveIntron (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp, Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp
+)
+{
+  if (isRequested)
+  {
+    return FALSE;
+  }
+  else if (parent_fcp != NULL 
+      && (parent_fcp->has_mrna 
+        || (parent_fcp->featlist != NULL
+           && parent_fcp->featlist->choice == DEFLINE_FEATLIST
+           && parent_fcp->featlist->data.ptrvalue != NULL
+           && IsmRNA (parent_fcp->featlist->data.ptrvalue))))
+  {
+    return TRUE;
+  }
+  else if (isLonely)
+  {
+    return FALSE;
+  }
+  else
+  {
+    return TRUE;
+  }
+}
+
+static Boolean LIBCALLBACK ShouldRemoveMobileElement
+( SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp,
+  Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp)
+{
+  return (!isLonely && !isRequested);
+}
+
+static Boolean LIBCALLBACK ShouldRemoveGeneric 
+( SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp,
+  Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp)
+{
+  CharPtr productname;
+  Boolean rval;
+
+  rval = FALSE;
+  if (IsMiscRNA (sfp) && ( productname = GetProductName (sfp, bsp, rp)) != NULL)
+  {
+    if (StringStr (productname, "trans-spliced leader") != NULL)
+    {
+      rval = TRUE;
+    }
+    MemFree (productname);
+  }
+    
+  return rval;
+}
+
+
+static Boolean IsBioseqPrecursorRNA (BioseqPtr bsp)
+{
+  SeqDescrPtr       sdp;
+  SeqMgrDescContext context;
+  MolInfoPtr        mol;
+  
+  if (bsp == NULL) return FALSE;
+  
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &context);
+  if (sdp != NULL && sdp->data.ptrvalue != NULL)
+  {
+		mol = (MolInfoPtr) sdp->data.ptrvalue;
+    if (mol->biomol == 2)
+    {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+static Boolean LIBCALLBACK ShouldRemovePrecursorRNA
+( SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp,
+  Boolean isLonely,
+  Boolean isRequested,
+  Boolean isSegment,
+  DeflineFeatureRequestListPtr rp)
+{
+  if (!isLonely && IsBioseqPrecursorRNA(bsp))
+  {
+    return TRUE;
+  }
+  else
+  {
+    return ShouldRemoveGeneric (sfp, parent_fcp, this_fcp, bsp, isLonely, 
+                                isRequested, isSegment, rp);
+  }
+}
+
+
+typedef struct removableitemglobal {
+  matchFunction  itemmatch;
+  ShouldRemoveFunction ShouldRemove;
+  CharPtr  group_name;
+} RemovableItemGlobalData, PNTR RemovableItemGlobalPtr;
+
+typedef struct removableitemlocal {
+/*  ButtoN  keep_request; */
+  Boolean  keep;
+} RemovableItemLocalData, PNTR RemovableItemLocalPtr;
+
+static RemovableItemGlobalData remove_items[] = {
+  { IsExon, ShouldRemoveExon, "Exons" },
+  { IsIntron, ShouldRemoveIntron, "Introns" },
+  { Is5UTR, ShouldRemove5UTR, "5' UTRs" },
+  { Is3UTR, ShouldRemove3UTR, "3' UTRs" },
+  { IsCDS,  ShouldRemoveCDS, "CDSs" },
+  { IsPromoter, ShouldRemovePromoter, "Promoters:" },
+  { IsLTR, ShouldRemoveLTR, "LTRs" },
+  { IsNoncodingProductFeat,  ShouldRemoveNoncodingProductFeat, "Misc feats with comments:" },
+  { IsRemovableMobileElement, ShouldRemoveMobileElement, "Optional Mobile Element" },
+  { IsPrecursorRNA, ShouldRemovePrecursorRNA, "Precursor RNAs" }
+};
+
+
+NLM_EXTERN CharPtr GetRemovableItemName (Int4 i)
+{
+  if (i < 0 || i >= NumRemovableItems) {
+    return NULL;
+  } else {
+    return remove_items[i].group_name;
+  }
+}
+
+NLM_EXTERN void InitFeatureRequests (
+  DeflineFeatureRequestListPtr feature_requests
+)
+{
+  Int4 i;
+  for (i=0; i < NumRemovableItems; i++)
+  {
+    feature_requests->keep_items[i] = FALSE;
+  }
+  feature_requests->add_fake_promoters = TRUE;
+  feature_requests->suppress_alt_splice_phrase = FALSE;
+  feature_requests->remove_subfeatures = FALSE;
+  feature_requests->feature_list_type = DEFLINE_USE_FEATURES;
+  feature_requests->misc_feat_parse_rule = 2;
+  feature_requests->suppress_locus_tags = FALSE;
+  feature_requests->suppressed_feature_list = NULL;
+  feature_requests->use_ncrna_note = FALSE;
+}
+
+static Boolean RemoveCondition (
+  SeqFeatPtr sfp,
+  FeatureClausePtr parent_fcp,
+  FeatureClausePtr this_fcp,
+  BioseqPtr bsp,
+  Boolean isLonely,
+  Boolean isSegment,
+  DeflineFeatureRequestList *feature_requests
+)
+{
+  Int4 i;
+  if (sfp == NULL) return TRUE;
+  for (i=0; i < NumRemovableItems; i++)
+  {
+    if (remove_items[i].itemmatch (sfp))
+      return remove_items[i].ShouldRemove (sfp, parent_fcp, this_fcp, bsp,
+                                           isLonely, feature_requests->keep_items[i],
+                                           isSegment,
+                                           feature_requests);
+  }
+  return ShouldRemoveGeneric(sfp, parent_fcp, this_fcp, bsp, isLonely, FALSE,
+                             isSegment, feature_requests);
+}
+
+static Boolean FindOtherGeneClause 
+( ValNodePtr feature_list,
+  ValNodePtr me,
+  GeneRefPtr grp,
+  Boolean    suppress_locus_tag)
+{
+  ValNodePtr vnp;
+  FeatureClausePtr fcp;
+
+  if (grp == NULL) return FALSE;
+
+  for (vnp = feature_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp == me) continue;
+    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
+    {
+      fcp = vnp->data.ptrvalue;
+      if (fcp->delete_me) continue;
+      if ( fcp->grp == grp
+        || (fcp->grp != NULL && DoGenesMatch (fcp->grp, grp, suppress_locus_tag)))
+      {
+        return TRUE;
+      }
+      if ( FindOtherGeneClause (fcp->featlist, me, grp, suppress_locus_tag))
+      {
+        return TRUE;
+      }
+    }
+  }
+  return FALSE;
+}
+ 
+static void RemoveGenesMentionedElsewhere 
+( ValNodePtr PNTR feature_list,
+  ValNodePtr      search_list,
+  Boolean         delete_now,
+  Boolean         suppress_locus_tag)
+{
+  ValNodePtr vnp;
+  FeatureClausePtr fcp;
+
+  for (vnp = *feature_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
+    {
+      fcp = vnp->data.ptrvalue;
+      if (fcp->featlist == NULL)
+      {
+        continue;
+      }
+      if ( IsGene (fcp->featlist->data.ptrvalue)
+        && fcp->featlist->next == NULL
+        && FindOtherGeneClause ( search_list, vnp, fcp->grp, suppress_locus_tag))
+      {
+        fcp->delete_me = TRUE;
+      }
+      else
+      {
+        RemoveGenesMentionedElsewhere ( &(fcp->featlist), search_list, FALSE, suppress_locus_tag);
+      }
+    }
+  }
+  if (delete_now)
+  {
+    DeleteFeatureClauses (feature_list);
+  }
+}
+
+static void MarkUnwantedFeatureClauseForRemoval (
+  ValNodePtr clause,
+  BioseqPtr  bsp,
+  Boolean    isLonely,
+  FeatureClausePtr parent_fcp,
+  Boolean    isSegment,
+  DeflineFeatureRequestList PNTR feature_requests
+)
+{
+  FeatureClausePtr fcp;
+  ValNodePtr       featlist;
+  ValNodePtr       firstfeat;
+  Int4             clause_count;
+  SeqFeatPtr       sfp;
+
+  if (clause == NULL
+    || clause->choice != DEFLINE_CLAUSEPLUS
+    || clause->data.ptrvalue == NULL)
+  {
+    return;
+  }
+
+  fcp = clause->data.ptrvalue;
+  firstfeat = fcp->featlist;
+  clause_count = 0;
+  for (featlist = firstfeat;
+       featlist != NULL && isLonely;
+       featlist = featlist->next)
+  {
+    if (featlist->choice == DEFLINE_CLAUSEPLUS)
+    {
+      clause_count ++;
+      if (clause_count > 1)
+      {
+        isLonely = FALSE;
+      }
+    }
+  }
+    
+  featlist = firstfeat;
+  while (featlist != NULL)
+  {  
+    if (featlist->choice == DEFLINE_FEATLIST
+      && featlist->data.ptrvalue != NULL)
+    {
+      sfp = (SeqFeatPtr) featlist->data.ptrvalue;
+      if (RemoveCondition (featlist->data.ptrvalue, parent_fcp, fcp, bsp, 
+                          isLonely, isSegment, feature_requests))
+      {
+        fcp->delete_me = TRUE;
+      }
+      else if (! IsGene (sfp) && ! IsmRNA (sfp))
+      {
+        isLonely = FALSE;
+      }
+    }
+    else if (featlist->choice == DEFLINE_CLAUSEPLUS 
+      && featlist->data.ptrvalue != NULL)
+    {
+      MarkUnwantedFeatureClauseForRemoval (featlist, bsp, isLonely, fcp,
+                                           isSegment,
+                                           feature_requests);
+    }
+    featlist = featlist->next;
+  }
+}
+  
+static void RemoveUnwantedFeatures (
+  ValNodePtr PNTR list,
+  BioseqPtr bsp,
+  Boolean   isSegment,
+  DeflineFeatureRequestList PNTR feature_requests
+)
+{
+  ValNodePtr       vnp;
+  Boolean          isLonely;
+
+  if (list == NULL) return;
+
+  isLonely = TRUE;
+
+  for (vnp = *list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->next != NULL) isLonely = FALSE;
+    if (vnp->choice == DEFLINE_CLAUSEPLUS)
+    {
+      MarkUnwantedFeatureClauseForRemoval (vnp, bsp, isLonely, NULL,
+                                           isSegment, feature_requests);
+    }
+  }
+  DeleteFeatureClauses (list);
+}
+
+static Boolean IsFeatureInSelectionList (SeqFeatPtr sfp, ValNodePtr feat_list)
+{
+  ValNodePtr       vnp;
+
+  if (sfp == NULL || feat_list == NULL)
+  {
+    return FALSE;
+  }
+  
+  for (vnp = feat_list; vnp != NULL && sfp->idx.subtype != vnp->choice; vnp = vnp->next)
+  {
+  }
+  if (vnp == NULL)
+  {
+    return FALSE;
+  }
+  else
+  {
+    return TRUE;
+  }
+}
+
+static void MarkSuppressedFeatureClauseForRemoval (
+  ValNodePtr clause,
+  ValNodePtr suppressed_feature_list
+)
+{
+  FeatureClausePtr fcp;
+  ValNodePtr       featlist;
+  ValNodePtr       firstfeat;
+  SeqFeatPtr       sfp;
+
+  if (clause == NULL
+    || clause->choice != DEFLINE_CLAUSEPLUS
+    || clause->data.ptrvalue == NULL)
+  {
+    return;
+  }
+
+  fcp = clause->data.ptrvalue;
+  firstfeat = fcp->featlist;
+    
+  featlist = firstfeat;
+  while (featlist != NULL)
+  {  
+    if (featlist->choice == DEFLINE_FEATLIST
+      && featlist->data.ptrvalue != NULL)
+    {
+      sfp = (SeqFeatPtr) featlist->data.ptrvalue;
+      if (IsFeatureInSelectionList (sfp, suppressed_feature_list))
+      {
+        fcp->delete_me = TRUE;
+      }
+    }
+    else if (featlist->choice == DEFLINE_CLAUSEPLUS 
+      && featlist->data.ptrvalue != NULL)
+    {
+      MarkSuppressedFeatureClauseForRemoval (featlist, suppressed_feature_list);
+    }
+    featlist = featlist->next;
+  }
+}
+  
+static void RemoveSuppressedFeatures (ValNodePtr PNTR list,
+                                      ValNodePtr suppressed_feature_list)
+{
+  ValNodePtr vnp;
+  
+  if (list == NULL || *list == NULL || suppressed_feature_list == NULL)
+  {
+    return;
+  }
+  
+  for (vnp = *list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_CLAUSEPLUS)
+    {
+      MarkSuppressedFeatureClauseForRemoval (vnp, suppressed_feature_list);
+    }
+  }
+  DeleteFeatureClauses (list);  
+}
+
+static Boolean LIBCALLBACK IsMasterClause (
+  SeqFeatPtr sfp
+)
+{
+  if ( IsMobileElement (sfp)) return TRUE;
+  return FALSE;
+}
+
+static void DeleteSubfeatures (
+  ValNodePtr PNTR feature_list,
+  Boolean         delete_now
+)
+{
+  ValNodePtr       clause, featlist;
+  FeatureClausePtr clause_fcp, fcp;
+
+  if (feature_list == NULL) return;
+  for (clause = *feature_list; clause != NULL; clause = clause->next)
+  {
+    if (clause->choice != DEFLINE_CLAUSEPLUS
+      || (clause_fcp = clause->data.ptrvalue) == NULL
+      || clause_fcp->featlist == NULL)
+    {
+      continue;
+    }
+    if (clause_fcp->featlist->choice == DEFLINE_FEATLIST
+      && IsMasterClause (clause_fcp->featlist->data.ptrvalue))
+    {
+      for (featlist = clause_fcp->featlist->next;
+           featlist != NULL;
+           featlist = featlist->next)
+      {
+        if (featlist->choice == DEFLINE_CLAUSEPLUS
+          && (fcp = featlist->data.ptrvalue) != NULL)
+        {
+          fcp->delete_me = TRUE;
+        }
+      }
+    }
+    else
+    {
+      DeleteSubfeatures ( &(clause_fcp->featlist), FALSE);
+    }
+  }
+  if (delete_now) 
+  {
+    DeleteFeatureClauses (feature_list);
+  }
+}
+
+static void DeleteOperonAndGeneClusterSubfeatures (
+  ValNodePtr PNTR feature_list,
+  Boolean         delete_now
+)
+{
+  ValNodePtr       clause, featlist;
+  FeatureClausePtr clause_fcp, fcp;
+
+  if (feature_list == NULL) return;
+  for (clause = *feature_list; clause != NULL; clause = clause->next)
+  {
+    if (clause->choice != DEFLINE_CLAUSEPLUS
+      || (clause_fcp = clause->data.ptrvalue) == NULL
+      || clause_fcp->featlist == NULL)
+    {
+      continue;
+    }
+    if (clause_fcp->featlist->choice == DEFLINE_FEATLIST
+      && (IsOperon (clause_fcp->featlist->data.ptrvalue) 
+          || IsGeneCluster (clause_fcp->featlist->data.ptrvalue)))
+    {
+      for (featlist = clause_fcp->featlist->next;
+           featlist != NULL;
+           featlist = featlist->next)
+      {
+        if (featlist->choice == DEFLINE_CLAUSEPLUS
+          && (fcp = featlist->data.ptrvalue) != NULL)
+        {
+          fcp->delete_me = TRUE;
+        }
+      }
+    }
+    else
+    {
+      DeleteOperonAndGeneClusterSubfeatures ( &(clause_fcp->featlist), FALSE);
+    }
+  }
+  if (delete_now) 
+  {
+    DeleteFeatureClauses (feature_list);
+  }
+}
+
+static void RemoveFeats (
+  ValNodePtr    list,
+  matchFunction itemmatch
+)
+{
+  ValNodePtr vnp;
+  FeatureClausePtr fcp;
+  
+  if (list == NULL) return;
+
+  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_FEATLIST
+      && itemmatch (vnp->data.ptrvalue))
+    {
+      vnp->choice = DEFLINE_REMOVEFEAT;
+    }
+    else if (vnp->choice == DEFLINE_CLAUSEPLUS
+      && (fcp = vnp->data.ptrvalue) != NULL)
+    {
+      RemoveFeats (fcp->featlist, itemmatch);
+    }
+  }
+}
+
+/* A clause is "tall" if it has only one clause at any level */
+static Boolean IsClauseTall (
+  FeatureClausePtr fcp
+)
+{
+  ValNodePtr featlist;
+  Int4       num_clauses;
+  FeatureClausePtr subclause;
+
+  num_clauses = 0;
+  if (fcp == NULL) return FALSE;
+  subclause = NULL;
+  if (fcp->featlist == NULL) return FALSE;
+  for (featlist = fcp->featlist;
+       featlist != NULL;
+       featlist = featlist->next)
+  {
+    if (featlist->choice == DEFLINE_CLAUSEPLUS)
+    {
+      subclause = featlist->data.ptrvalue;
+      if (subclause == NULL || ! IsClauseTall (subclause))
+      {
+        return FALSE;
+      }
+      num_clauses ++;
+      if (num_clauses > 1) return FALSE;
+    }
+  }
+  if (subclause == NULL || ! subclause->feature_label_data.is_typeword_first)
+  {
+    return TRUE;
+  }
+  return FALSE;
+}
+
+static void SmashOneTallClause (
+  FeatureClausePtr fcp
+)
+{
+  FeatureClausePtr subclause;
+  ValNodePtr       featlist;
+  ValNodePtr       subclause_featlist;
+  ValNodePtr       subclause_firstclause;
+  CharPtr          new_description;
+  Int4             new_description_len;
+  SeqFeatPtr       main_feat;
+
+  if (fcp == NULL || fcp->featlist == NULL) return;
+
+  /* move features up */
+  featlist = fcp->featlist;
+  if (featlist->choice == DEFLINE_FEATLIST)
+  {
+    main_feat = fcp->featlist->data.ptrvalue;
+  }
+  else
+  {
+    main_feat = NULL;
+  }
+  
+  while (featlist != NULL && featlist->choice != DEFLINE_CLAUSEPLUS)
+  {
+    featlist = featlist->next;
+  }
+  if (featlist == NULL) return;
+  subclause = featlist->data.ptrvalue;
+  if (subclause == NULL) return;
+ 
+  /* move subclause feats to top of list */
+  if (subclause->featlist != NULL
+    && subclause->featlist->choice == DEFLINE_FEATLIST)
+  {
+    subclause_featlist = subclause->featlist;
+    while (subclause->featlist != NULL
+           && subclause->featlist->next != NULL
+           && subclause->featlist->next->choice == DEFLINE_FEATLIST)
+    {
+      subclause->featlist = subclause->featlist->next;
+    }
+    if (subclause->featlist != NULL)
+    {
+      subclause_firstclause = subclause->featlist->next;
+      subclause->featlist->next = fcp->featlist;
+      fcp->featlist = subclause->featlist;
+      subclause->featlist = subclause_firstclause;
+    }
+  }
+
+  /* create new description */
+  new_description_len = StringLen (subclause->feature_label_data.description)
+                   + StringLen (fcp->feature_label_data.description)
+                   + StringLen (fcp->feature_label_data.typeword)
+                   + 4;
+  new_description = (CharPtr) MemNew (new_description_len);
+  if (new_description == NULL) return;
+  new_description [0] = 0;
+  if ( fcp->feature_label_data.is_typeword_first)
+  {
+    StringCat (new_description, fcp->feature_label_data.typeword);
+    StringCat (new_description, " ");
+  }
+  StringCat (new_description, fcp->feature_label_data.description);
+  if ( ! fcp->feature_label_data.is_typeword_first)
+  {
+    StringCat (new_description, fcp->feature_label_data.typeword);
+  }
+
+  if ( ! IsMobileElement (main_feat)
+    && ! IsEndogenousVirusSourceFeature (main_feat))
+  {
+    StringCat (new_description, ",");
+  }
+  StringCat (new_description, " ");
+  StringCat (new_description, subclause->feature_label_data.description);
+
+  if (fcp->feature_label_data.description != NULL)
+  {
+    MemFree (fcp->feature_label_data.description);
+  }
+  fcp->feature_label_data.description = new_description;
+ 
+  /* move interval up */
+  if (fcp->interval != NULL)
+  {
+    MemFree (fcp->interval);
+  }
+  fcp->interval = subclause->interval;
+  subclause->interval = NULL;
+
+  /* move typeword up */
+  fcp->feature_label_data.typeword = subclause->feature_label_data.typeword;
+  fcp->feature_label_data.is_typeword_first = 
+               subclause->feature_label_data.is_typeword_first;
+  subclause->feature_label_data.typeword = NULL;
+  subclause->delete_me = TRUE;
+
+}
+
+
+static void SmashTallClauses (
+  ValNodePtr PNTR clause_list,
+  Boolean         delete_now
+)
+{
+  ValNodePtr clause;
+  FeatureClausePtr fcp;
+
+  if (clause_list == NULL) return;
+  for (clause = *clause_list; clause != NULL; clause = clause->next)
+  {
+    if (clause->choice != DEFLINE_CLAUSEPLUS || clause->data.ptrvalue == NULL)
+    {
+      continue;
+    }
+    fcp = clause->data.ptrvalue;
+    if ( IsClauseTall (fcp))
+    {
+      SmashOneTallClause (fcp);
+    }
+    else
+    {
+      SmashTallClauses (& (fcp->featlist), FALSE);
+    }
+  }
+  if (delete_now) 
+  {
+    DeleteFeatureClauses (clause_list);
+  }
+}
+
+static ValNodePtr RemoveAllButLastCDS (
+  ValNodePtr list,
+  ValNodePtr last_cds
+)
+{
+  ValNodePtr vnp;
+  FeatureClausePtr fcp;
+
+  /* now remove all CDSs except the last one */
+  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_FEATLIST
+      && IsCDS (vnp->data.ptrvalue))
+    {
+      if (last_cds != NULL)
+      {
+        last_cds->choice = DEFLINE_REMOVEFEAT;
+      }
+      last_cds = vnp;
+    }
+    else if (vnp->choice == DEFLINE_CLAUSEPLUS
+      && (fcp = vnp->data.ptrvalue) != NULL)
+    {
+      last_cds = RemoveAllButLastCDS (fcp->featlist, last_cds);
+    }
+  }
+  return last_cds;
+}
+
+static Boolean OkToConsolidate (
+  CharPtr last_desc,
+  CharPtr new_desc,
+  Boolean last_partial,
+  Boolean new_partial,
+  FeatureClausePtr last_fcp,
+  FeatureClausePtr fcp
+)
+{
+  if (StringCmp (last_desc, new_desc) != 0) return FALSE;
+  if (new_partial != last_partial) return FALSE;
+  if ( ( fcp->is_alt_spliced && ! last_fcp->is_alt_spliced)
+      || (! fcp->is_alt_spliced && last_fcp->is_alt_spliced))
+  {
+    return FALSE;
+  }
+  if (fcp->featlist == NULL || last_fcp->featlist == NULL) return FALSE;
+  if ( fcp->featlist->choice != DEFLINE_FEATLIST) return FALSE;
+  if ( last_fcp->featlist->choice != DEFLINE_FEATLIST) return FALSE;
+  if ( (IsCDS (fcp->featlist->data.ptrvalue)
+        && ! IsCDS (last_fcp->featlist->data.ptrvalue)
+        && ! IsGene (last_fcp->featlist->data.ptrvalue))
+      || (! IsCDS (fcp->featlist->data.ptrvalue)
+        && ! IsGene (fcp->featlist->data.ptrvalue)
+        && IsCDS (last_fcp->featlist->data.ptrvalue)))
+  {
+    return FALSE;
+  }
+  if ((IsExon (fcp->featlist->data.ptrvalue) && !IsExon(last_fcp->featlist->data.ptrvalue))
+      || (IsExon (last_fcp->featlist->data.ptrvalue) && !IsExon(fcp->featlist->data.ptrvalue))
+      || (IsIntron (fcp->featlist->data.ptrvalue) && !IsIntron(last_fcp->featlist->data.ptrvalue))
+      || (IsIntron (last_fcp->featlist->data.ptrvalue) && !IsIntron(fcp->featlist->data.ptrvalue)))
+  {
+    return FALSE;
+  }
+  return TRUE;
+}
+
+static void RemoveRedundantGeneFeatureFromConsolidatedClause (
+  FeatureClausePtr fcp
+)
+{
+  ValNodePtr featlist, prevfeat, tmpfeat;
+  SeqFeatPtr feat1, feat2;
+
+  prevfeat = NULL;
+  featlist = fcp->featlist;
+  while ( featlist != NULL
+         && featlist->choice == DEFLINE_FEATLIST
+         && featlist->next != NULL
+         && featlist->next->choice == DEFLINE_FEATLIST)
+  {
+    feat1 = featlist->data.ptrvalue;
+    feat2 = featlist->next->data.ptrvalue;
+    if (feat1 == NULL || feat2 == NULL) return;
+    if (IsGene (feat1) && ! IsGene (feat2))
+    {
+      if (prevfeat == NULL)
+      {
+        fcp->featlist = featlist->next;
+        featlist->next = NULL;
+        FreeListElement (featlist);
+        featlist = fcp->featlist->next;
+      }
+      else
+      {
+        prevfeat->next = featlist->next;
+        featlist->next = NULL;
+        FreeListElement (featlist);
+        featlist = prevfeat->next;
+      }
+    }
+    else if ( !IsGene (feat1) && IsGene (feat2))
+    {
+      tmpfeat = featlist->next;
+      featlist->next = tmpfeat->next;
+      tmpfeat->next = NULL;
+      FreeListElement (tmpfeat);
+    }
+    else
+    {
+      featlist = featlist->next;
+    }
+  }
+}
+
+static void PluralizeConsolidatedClauseDescription (
+  FeatureClausePtr fcp
+)
+{
+  CharPtr new_desc;
+
+  /* prevent crash */
+  if (fcp == NULL || fcp->feature_label_data.description == NULL) return;
+
+  /* don't pluralize tRNA names */
+  if (StringNCmp (fcp->feature_label_data.description, "tRNA-", 5) ==0) return;
+
+  new_desc = MemNew (StringLen (fcp->feature_label_data.description) + 2);
+  if (new_desc == NULL) return;
+
+  StringCpy (new_desc, fcp->feature_label_data.description);
+  StringCat (new_desc, "s");
+  MemFree (fcp->feature_label_data.description);
+  fcp->feature_label_data.description = new_desc;
+}
+
+static void ConsolidateClauses (
+  ValNodePtr PNTR list,
+  BioseqPtr  bsp,
+  Uint1      biomol,
+  Boolean    delete_now,
+  DeflineFeatureRequestListPtr rp)
+{
+  ValNodePtr       vnp;
+  FeatureClausePtr fcp;
+  FeatureClausePtr last_cds_fcp;
+  CharPtr          last_desc, new_desc;
+  Boolean          last_partial, new_partial, partial3, partial5;
+
+  if (list == NULL || *list == NULL) return;
+  last_cds_fcp = NULL;
+  last_desc = NULL;
+  for (vnp = *list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice != DEFLINE_CLAUSEPLUS
+      || (fcp = vnp->data.ptrvalue) == NULL
+      || fcp->featlist == NULL
+      || fcp->featlist->choice != DEFLINE_FEATLIST)
+    {
+      continue;
+    }
+
+    ConsolidateClauses (&(fcp->featlist), bsp, biomol, FALSE, rp);
+
+    if (last_cds_fcp == NULL)
+    {
+      last_cds_fcp = fcp;
+      if (fcp->feature_label_data.description == NULL)
+      {
+        last_desc = GetGeneProtDescription (fcp, bsp, rp);
+      }
+      else
+      {
+        last_desc = StringSave (fcp->feature_label_data.description);
+      }
+      CheckSeqLocForPartial (fcp->slp, &partial5, &partial3);
+      if (partial5 || partial3) 
+      {
+        last_partial = TRUE;
+      }
+      else
+      {
+        last_partial = FALSE;
+      }
+    }
+    else 
+    {
+      if (fcp->feature_label_data.description == NULL)
+      {
+        new_desc = GetGeneProtDescription (fcp, bsp, rp);
+      }
+      else
+      {
+        new_desc = StringSave (fcp->feature_label_data.description);
+      }
+      CheckSeqLocForPartial (fcp->slp, &partial5, &partial3);
+      if (partial5 || partial3) 
+      {
+        new_partial = TRUE;
+      }
+      else
+      {
+        new_partial = FALSE;
+      }
+      if ( OkToConsolidate (last_desc, new_desc,
+                            last_partial, new_partial,
+                            last_cds_fcp, fcp))
+      {
+        /* two clauses have identical descriptions - combine them */
+        MoveSubclauses (last_cds_fcp, fcp);
+        RemoveRedundantGeneFeatureFromConsolidatedClause (last_cds_fcp);
+        fcp->featlist = NULL;
+        fcp->delete_me = TRUE;
+        last_cds_fcp->slp = SeqLocMerge (bsp, last_cds_fcp->slp, fcp->slp,
+                                         FALSE, TRUE, FALSE);
+        /* if we have two clauses that are really identical instead of
+         * just sharing a "prefix", make the description plural
+         */
+        if (StringCmp (last_cds_fcp->interval, fcp->interval) == 0)
+        {
+          last_cds_fcp->make_plural = TRUE;
+/*          PluralizeConsolidatedClauseDescription (last_cds_fcp); */
+        }
+
+        /* Recalculate the interval */
+        if (last_cds_fcp->interval != NULL)
+        {
+          MemFree (last_cds_fcp->interval);
+        }
+        last_cds_fcp->interval =
+                  GetGenericInterval (last_cds_fcp, biomol, bsp, rp);
+        MemFree (new_desc);
+      }
+      else
+      {
+        MemFree (last_desc);
+        last_desc = new_desc;
+        last_cds_fcp = fcp;
+        last_partial = new_partial;
+      }
+    }  
+  }   
+  if (delete_now) 
+  {
+    DeleteFeatureClauses (list);
+  }
+} 
+
+static void CountUnknownGenes (
+  ValNodePtr PNTR clause_list,
+  BioseqPtr       bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  FeatureClausePtr fcp, new_fcp;
+  ValNodePtr vnp, new_vnp;
+  CharPtr gene_name;
+  Int4 num_unknown_genes;
+  
+  num_unknown_genes = 0;
+  vnp = *clause_list;
+  new_vnp = NULL;
+  new_fcp = NULL;
+  while (vnp != NULL)
+  {
+    if (vnp->choice == DEFLINE_CLAUSEPLUS
+      && (fcp = vnp->data.ptrvalue) != NULL
+      && ! fcp->is_unknown) 
+    {
+      CountUnknownGenes (&(fcp->featlist), bsp, rp);
+      gene_name = GetGeneProtDescription (fcp, bsp, rp);
+      if (StringCmp (gene_name, "unknown") == 0
+        && fcp->featlist != NULL
+        && fcp->featlist->choice == DEFLINE_FEATLIST)
+      {
+        if (new_fcp == NULL)
+        {
+          new_vnp = ValNodeNew (*clause_list);
+          if (new_vnp == NULL) return;
+          new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue, 
+                                      bsp, rp);
+          new_fcp->is_unknown = TRUE;
+          new_vnp->choice = DEFLINE_CLAUSEPLUS;
+          new_vnp->data.ptrvalue = new_fcp;
+        }
+        else
+        {
+          new_vnp = ValNodeNew (new_fcp->featlist);
+          if (new_vnp == NULL) return;
+          new_vnp->choice = DEFLINE_FEATLIST;
+          new_vnp->data.ptrvalue = fcp->featlist->data.ptrvalue;
+        }  
+        num_unknown_genes ++;
+        fcp->delete_me = TRUE;
+      }
+    }
+    vnp = vnp->next;
+  }
+   
+  if (num_unknown_genes > 0)
+  {
+    DeleteFeatureClauses (clause_list);
+    if (num_unknown_genes > 1)
+    {
+      new_fcp->feature_label_data.typeword = StringSave ("genes");
+    }
+  }
+}
+
+static void ReplaceDefinitionLine (
+  SeqEntryPtr sep,
+  CharPtr defline
+)
+{
+  ValNodePtr ttl;
+  if (sep == NULL || defline == NULL) return;
+
+  ttl = SeqEntryGetSeqDescr (sep, Seq_descr_title, NULL);
+  if (ttl == NULL)
+    ttl = CreateNewDescriptor (sep, Seq_descr_title);
+  if (ttl != NULL) {
+    MemFree (ttl->data.ptrvalue);
+    ttl->data.ptrvalue = defline;
+    defline = NULL;
+  }
+  MemFree (defline);
+}
+
+FeatureClausePtr NewFeatureClause 
+( SeqFeatPtr sfp,
+  BioseqPtr  bsp,
+  DeflineFeatureRequestListPtr rp)
+{
+  FeatureClausePtr fcp;
+  Boolean          partial5, partial3;
+
+  fcp = (FeatureClausePtr) MemNew (sizeof (FeatureClauseData));
+  if (fcp == NULL) return NULL;
+
+  fcp->feature_label_data.typeword = NULL;
+  fcp->feature_label_data.description = NULL;
+  fcp->feature_label_data.productname = NULL;
+  fcp->feature_label_data.pluralizable = FALSE;
+  fcp->feature_label_data.is_typeword_first = FALSE;
+  fcp->allelename = NULL;
+  fcp->interval = NULL;
+  fcp->featlist = NULL;
+  fcp->delete_me = FALSE;
+  fcp->clause_info_only = FALSE;
+  fcp->make_plural = FALSE;
+  fcp->is_unknown = FALSE;
+  fcp->grp = NULL;
+  if (sfp == NULL) return fcp;
+  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+  fcp->slp = SeqLocMerge (bsp, sfp->location, NULL,
+                                 FALSE, TRUE, FALSE);
+  SetSeqLocPartial (fcp->slp, partial5, partial3);
+  
+  if (sfp->data.choice == SEQFEAT_GENE)
+  {
+    fcp->grp = sfp->data.value.ptrvalue;
+  }
+  else
+  { 
+    fcp->grp = SeqMgrGetGeneXref (sfp);
+  }
+  if (( IsCDS (sfp) || IsExon (sfp) || IsNoncodingProductFeat (sfp))
+    && StringStr (sfp->comment, "alternatively spliced") != NULL) 
+  {
+    fcp->is_alt_spliced = TRUE;
+  }
+  else
+  {
+    fcp->is_alt_spliced = FALSE;
+  }
+  if (IsCDS (sfp))
+  {
+    fcp->feature_label_data.productname = GetProductName (sfp, bsp, rp);
+  }
+  fcp->featlist = ValNodeNew (NULL);
+  if (fcp->featlist == NULL)
+  {
+    MemFree (fcp);
+    return NULL;
+  }
+
+  fcp->featlist->data.ptrvalue = sfp;
+  fcp->featlist->choice = DEFLINE_FEATLIST;
+  
+  return fcp;
+}
+
+static ValNodePtr GetFeatureList (BioseqPtr bsp, DeflineFeatureRequestListPtr rp)
+{
+  ValNodePtr        head, vnp;
+  SeqFeatPtr        sfp;
+  FeatureClausePtr  fcp;
+  SeqMgrFeatContext fcontext;
+
+  if (bsp == NULL) return NULL;
+
+  /* get list of all recognized features */
+  head = NULL;
+  sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
+  while (sfp != NULL)
+  {
+    if (IsRecognizedFeature (sfp))
+    {
+      fcp = NewFeatureClause (sfp, bsp, rp);
+      if (fcp == NULL) return NULL;
+      fcp->numivals = fcontext.numivals;
+      fcp->ivals = fcontext.ivals;
+      vnp = ValNodeNew (head);
+      if (head == NULL) head = vnp;
+      if (vnp == NULL) return NULL;
+      vnp->data.ptrvalue = fcp;
+      vnp->choice = DEFLINE_CLAUSEPLUS;
+    }
+    sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
+  }
+  return head;
+}
+
+static void ExtractSegmentClauses (
+  ValNodePtr segment_features,
+  ValNodePtr parent_features,
+  ValNodePtr PNTR segment_clauses
+);
+
+static Boolean FeatureIsOnSegment (
+  SeqFeatPtr sfp, 
+  ValNodePtr segment_features
+)
+{
+  ValNodePtr vnp, featclause;
+  FeatureClausePtr fcp;
+
+  for (vnp = segment_features; vnp != NULL; vnp = vnp->next)
+  {
+    fcp = vnp->data.ptrvalue;
+    if (fcp != NULL)
+    {
+      for (featclause = fcp->featlist;
+           featclause != NULL;
+           featclause = featclause->next)
+      {
+        if (featclause->data.ptrvalue == sfp) return TRUE;
+      }
+    }
+  }
+  return FALSE;
+}
+
+static Boolean FeatureClauseIsOnSegment (
+  FeatureClausePtr fcp,
+  ValNodePtr segment_features
+)
+{
+  ValNodePtr vnp;
+
+  if (fcp == NULL || fcp->featlist == NULL) return FALSE;
+  for (vnp = fcp->featlist; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_FEATLIST 
+      && FeatureIsOnSegment (vnp->data.ptrvalue, segment_features))
+    {
+      return TRUE;
+    }
+    else if (vnp->choice == DEFLINE_CLAUSEPLUS)
+    {
+      if (FeatureClauseIsOnSegment (vnp->data.ptrvalue, segment_features))
+      {
+        return TRUE;
+      }     
+    }
+  }
+  return FALSE;
+}
+
+static FeatureClausePtr CopyMatchingClauses (
+  FeatureClausePtr fcp,
+  ValNodePtr segment_features
+)
+{
+  FeatureClausePtr new_fcp, copy_clause;
+  ValNodePtr       featlist, new_feat;
+  Boolean          found_feat_on_segment;
+  Boolean          partial5, partial3;
+
+  new_fcp = (FeatureClausePtr) MemNew (sizeof (FeatureClauseData));
+  if (new_fcp == NULL) return NULL;
+  new_fcp->feature_label_data.pluralizable = 
+    fcp->feature_label_data.pluralizable;
+  new_fcp->feature_label_data.is_typeword_first = 
+    fcp->feature_label_data.is_typeword_first;
+  new_fcp->feature_label_data.typeword =
+    StringSave (fcp->feature_label_data.typeword);
+  new_fcp->feature_label_data.description = 
+    StringSave (fcp->feature_label_data.description);
+  new_fcp->feature_label_data.productname =
+    StringSave (fcp->feature_label_data.productname);
+  new_fcp->allelename = StringSave (fcp->allelename);
+  new_fcp->interval = StringSave (fcp->interval);
+  new_fcp->is_alt_spliced = fcp->is_alt_spliced;
+  CheckSeqLocForPartial (fcp->slp, &partial5, &partial3);
+  new_fcp->slp = (SeqLocPtr) AsnIoMemCopy (fcp->slp, (AsnReadFunc) SeqLocAsnRead,
+                                           (AsnWriteFunc) SeqLocAsnWrite);
+  SetSeqLocPartial (new_fcp->slp, partial5, partial3);
+  new_fcp->grp = fcp->grp;
+  new_fcp->has_mrna = fcp->has_mrna;
+  new_fcp->delete_me = FALSE;
+  new_fcp->clause_info_only = fcp->clause_info_only;
+  new_fcp->featlist = NULL;
+  found_feat_on_segment = FALSE;
+  for (featlist = fcp->featlist; featlist != NULL; featlist = featlist->next)
+  {
+    new_feat = NULL;
+    if (featlist->choice == DEFLINE_FEATLIST)
+    {
+      new_feat = ValNodeNew (new_fcp->featlist);
+      if (new_feat == NULL) return NULL;
+      new_feat->data.ptrvalue = featlist->data.ptrvalue;
+      new_feat->choice = DEFLINE_FEATLIST;
+
+      /* some portions of the clause are present for product and gene info */
+      /* if they aren't actually on the segment */
+      if ( segment_features == NULL
+        || FeatureIsOnSegment (new_feat->data.ptrvalue, segment_features))
+      {
+        found_feat_on_segment = TRUE;
+      }
+    }
+    else if (featlist->choice == DEFLINE_CLAUSEPLUS)
+    {
+      copy_clause = featlist->data.ptrvalue;
+      if ( segment_features == NULL
+        || FeatureClauseIsOnSegment ( copy_clause, segment_features))
+      {
+        new_feat = ValNodeNew (new_fcp->featlist);
+        if (new_feat == NULL) return NULL;
+        new_feat->data.ptrvalue = CopyMatchingClauses ( copy_clause,
+                                                        segment_features);
+        new_feat->choice = DEFLINE_CLAUSEPLUS;
+      }
+    }
+    if (new_feat != NULL && new_fcp->featlist == NULL) 
+    {
+      new_fcp->featlist = new_feat;
+    }
+  }
+  if (found_feat_on_segment)
+  {
+    new_fcp->clause_info_only = FALSE;
+  }
+  else
+  {
+    new_fcp->clause_info_only = TRUE;
+  }
+  return new_fcp; 
+}
+
+static void CopyFeatureList (
+  ValNodePtr match_features,
+  ValNodePtr parent_features,
+  ValNodePtr PNTR new_list
+)
+{
+  ValNodePtr vnp, addvnp;
+
+  for (vnp = parent_features;
+       vnp != NULL;
+       vnp = vnp->next)
+  {
+    if (vnp->choice == DEFLINE_FEATLIST 
+      && (match_features == NULL
+        || FeatureIsOnSegment ( vnp->data.ptrvalue, match_features)))
+    {
+      addvnp = ValNodeNew (*new_list);
+      if (addvnp == NULL) return;
+      addvnp->data.ptrvalue = vnp->data.ptrvalue;
+      addvnp->choice = DEFLINE_FEATLIST;
+      if (*new_list == NULL) *new_list = addvnp;
+    }
+    else if (vnp->choice == DEFLINE_CLAUSEPLUS
+      && (match_features == NULL
+        || FeatureClauseIsOnSegment ( vnp->data.ptrvalue, match_features)))
+    {
+      addvnp = ValNodeNew (*new_list);
+      if (addvnp == NULL) return;
+      addvnp->data.ptrvalue = CopyMatchingClauses ( vnp->data.ptrvalue,
+                                                    match_features);
+      addvnp->choice = DEFLINE_CLAUSEPLUS;
+      if (*new_list == NULL) *new_list = addvnp;
+    }
+  }
+    
+}
+
+static void ExtractSegmentClauses (
+  ValNodePtr segment_features,
+  ValNodePtr parent_features,
+  ValNodePtr PNTR segment_clauses
+)
+{
+  CopyFeatureList (segment_features, parent_features, segment_clauses);
+}
+
+typedef struct segmentdeflinedata {
+  BioseqPtr  parent_bsp;
+  ValNodePtr parent_feature_list;
+  Uint1      molecule_type;
+  DeflineFeatureRequestList PNTR feature_requests;
+  ModifierCombinationPtr m;
+  ModifierItemLocalPtr modList;
+  OrganismDescriptionModifiersPtr odmp;
+  Int2 product_flag;
+} SegmentDefLineData, PNTR SegmentDefLinePtr;
+
+typedef struct segmentdeflinefeatureclausedata {
+  BioseqPtr  parent_bsp;
+  ValNodePtr parent_feature_list;
+  Uint1      molecule_type;
+  DeflineFeatureRequestList PNTR feature_requests;
+  Int2            product_flag;
+  Boolean         alternate_splice_flag;
+  Boolean         gene_cluster_opp_strand;
+  ValNodePtr PNTR list;
+} SegmentDefLineFeatureClauseData, PNTR SegmentDefLineFeatureClausePtr;
+
+typedef struct deflinefeatclause {
+  SeqEntryPtr sep;
+  BioseqPtr   bsp;
+  CharPtr     clauselist;
+} DefLineFeatClauseData, PNTR DefLineFeatClausePtr;
+
+NLM_EXTERN void DefLineFeatClauseListFree (ValNodePtr vnp)
+{
+  DefLineFeatClausePtr deflist;
+
+  if (vnp == NULL) return;
+  DefLineFeatClauseListFree (vnp->next);
+  vnp->next = NULL;
+  deflist = vnp->data.ptrvalue;
+  if (deflist != NULL)
+  {
+    MemFree (deflist->clauselist);
+    MemFree (deflist);
+  }
+  ValNodeFree (vnp);
+}
+
+
+static Boolean IntervalIntersectsIvals 
+(Int2    numivals,
+ Int4Ptr ivals,
+ SeqMgrSegmentContextPtr context)
+{
+  Int2 idx;
+  Int4 start, stop;
+
+  if (numivals == 0 || ivals == NULL || context == NULL) return FALSE;
+
+  for (idx = 0; idx < numivals; idx ++) {
+    start = ivals [idx * 2];
+    stop = ivals [idx * 2 + 1];
+    if ( start <= context->cumOffset + context->to - context->from
+         && stop >= context->cumOffset)
+    {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+
+
+/* if there are no features at all on this segment, select the genes that 
+ * traverse the segment.
+ */
+static ValNodePtr GrabTraversingGenes 
+(ValNodePtr              parent_feature_list,
+ SeqMgrSegmentContextPtr context,
+ BioseqPtr               parent_bsp,
+ DeflineFeatureRequestListPtr rp)
+{
+  FeatureClausePtr  fcp, new_fcp;
+  ValNodePtr        clause;
+  SeqFeatPtr        sfp;
+  ValNodePtr        segment_feature_list;
+  ValNodePtr        vnp;
+
+  segment_feature_list = NULL;
+  for (clause = parent_feature_list;
+       clause != NULL;
+       clause = clause->next)
+  {
+    fcp = clause->data.ptrvalue;
+
+    if (fcp != NULL  &&  fcp->featlist != NULL
+        &&  (sfp = fcp->featlist->data.ptrvalue) != NULL
+        &&  sfp->idx.subtype == FEATDEF_GENE
+        &&  fcp->ivals != NULL && fcp->numivals > 0)
+    {
+      if (IntervalIntersectsIvals (fcp->numivals, fcp->ivals, context)) {
+        new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue, parent_bsp,
+                                    rp);
+        if (new_fcp == NULL) return FALSE;
+        vnp = ValNodeNew (segment_feature_list);
+        if (vnp == NULL) return FALSE;
+        vnp->data.ptrvalue = new_fcp;
+        vnp->choice = DEFLINE_CLAUSEPLUS;
+        if (segment_feature_list == NULL) segment_feature_list = vnp;
+      }
+    } 
+  }
+  return segment_feature_list;
+}
+
+
+static CharPtr BuildFeatureClauses (
+  BioseqPtr   bsp,
+  Uint1       molecule_type,
+  SeqEntryPtr sep,
+  ValNodePtr  PNTR feature_list,
+  Boolean     isSegment,
+  ValNodePtr  PNTR seg_feature_list,
+  Int2        product_flag,
+  Boolean     alternate_splice_flag,
+  Boolean     gene_cluster_opp_strand,
+  DeflineFeatureRequestList PNTR feature_requests
+);
+
+static Boolean LIBCALLBACK GetFeatureClauseForSeg (
+  SeqLocPtr slp,
+  SeqMgrSegmentContextPtr context)
+{
+  SegmentDefLineFeatureClausePtr sdlp;
+  ValNodePtr        clause, tmp_parent_list;
+  FeatureClausePtr  fcp, new_fcp;
+  Int2              idx;
+  Int4              start, stop;
+  ValNodePtr        segment_feature_list, vnp;
+  SeqIdPtr          sip;
+  BioseqPtr         bsp;
+  Uint2             entityID;
+  SeqLocPtr         loc;
+  DefLineFeatClausePtr deflist;
+
+  if (slp == NULL || context == NULL) return FALSE;
+  sdlp = (SegmentDefLineFeatureClausePtr) context->userdata;
+
+  sip = SeqLocId (slp);
+  
+  if (sip == NULL) {
+    loc = SeqLocFindNext (slp, NULL);
+    if (loc != NULL) {
+      sip = SeqLocId (loc);
+    }
+  }
+  if (sip == NULL) return TRUE;
+
+  bsp = BioseqFind (sip);
+
+  if (bsp == NULL) return TRUE;
+
+
+  segment_feature_list = NULL;
+  for (clause = sdlp->parent_feature_list;
+       clause != NULL;
+       clause = clause->next)
+  {
+    fcp = clause->data.ptrvalue;
+
+    if (fcp != NULL && fcp->ivals != NULL && fcp->numivals > 0)
+    {
+      idx = (fcp->numivals - 1) * 2;
+      start = fcp->ivals [idx];
+      stop = fcp->ivals [idx + 1];
+      if ( stop <= context->cumOffset + context->to - context->from
+           && stop >= context->cumOffset)
+      {
+        new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue,
+                                    sdlp->parent_bsp, 
+                                    sdlp->feature_requests);
+        if (new_fcp == NULL) return FALSE;
+        vnp = ValNodeNew (segment_feature_list);
+        if (vnp == NULL) return FALSE;
+        vnp->data.ptrvalue = new_fcp;
+        vnp->choice = DEFLINE_CLAUSEPLUS;
+        if (segment_feature_list == NULL) segment_feature_list = vnp;
+      }
+    } 
+  }
+
+  if (segment_feature_list == NULL) {
+    segment_feature_list = GrabTraversingGenes (sdlp->parent_feature_list,
+                                                context, sdlp->parent_bsp,
+                                                sdlp->feature_requests);
+  }
+
+  entityID = ObjMgrGetEntityIDForPointer (bsp);
+
+  tmp_parent_list = NULL;
+  CopyFeatureList (NULL, sdlp->parent_feature_list, &tmp_parent_list);
+
+  deflist = (DefLineFeatClausePtr) MemNew (sizeof (DefLineFeatClauseData));
+  if (deflist == NULL) return TRUE;
+  deflist->sep = SeqMgrGetSeqEntryForData (bsp);
+  deflist->bsp = bsp;
+  deflist->clauselist = BuildFeatureClauses (sdlp->parent_bsp,
+                            sdlp->molecule_type,
+                            SeqMgrGetSeqEntryForData (bsp),
+                            &tmp_parent_list,
+                            TRUE,
+                            &segment_feature_list,
+                            sdlp->product_flag,
+							              sdlp->alternate_splice_flag,
+							              sdlp->gene_cluster_opp_strand,
+                            sdlp->feature_requests);
+  vnp = ValNodeNew (*(sdlp->list));
+  if (vnp == NULL) return TRUE;
+  if (*(sdlp->list) == NULL) *(sdlp->list) = vnp;
+  vnp->data.ptrvalue = deflist;
+
+  FreeListElement (tmp_parent_list);
+  FreeListElement (segment_feature_list);
+  DeleteMarkedObjects (entityID, 0, NULL);
+  return TRUE;
+}
+
+static Boolean HasAnyPromoters (BioseqPtr bsp)
+{
+  SeqFeatPtr sfp;
+  SeqMgrFeatContext fcontext;
+  
+  sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_promoter, &fcontext);
+  if (sfp == NULL) {
+    return FALSE;
+  } else {
+    return TRUE;
+  }
+}
+
+static void AddFakePromoterClause (ValNodePtr PNTR feature_list, BioseqPtr bsp, DeflineFeatureRequestListPtr rp)
+{
+  FeatureClausePtr fcp;
+  SeqFeatPtr       sfp = NULL;
+  
+  /* create fake promoter */
+  sfp = CreateNewFeature (SeqMgrGetSeqEntryForData (bsp), NULL,
+                          SEQFEAT_IMP, NULL);
+
+  sfp->location = SeqLocIntNew (0, bsp->length - 1, Seq_strand_plus, SeqIdDup (bsp->id));
+  sfp->data.choice = SEQFEAT_IMP;
+  sfp->idx.subtype = FEATDEF_promoter;
+  /* mark promoter for deletion */
+  sfp->idx.deleteme = TRUE;
+  
+  fcp = NewFeatureClause (sfp, bsp, rp);
+  if (fcp == NULL) return;
+  fcp->numivals = 1;
+  fcp->ivals = (Int4Ptr) MemNew (sizeof (Int4) * 2);
+  fcp->ivals[0] = 0;
+  fcp->ivals[1] = bsp->length - 1;
+  ValNodeAddPointer (feature_list, DEFLINE_CLAUSEPLUS, fcp);
+  
+}
+
+static Boolean IsInGenProdSet (BioseqPtr bsp)
+{
+  BioseqSetPtr bssp;
+  if (bsp == NULL || bsp->idx.parentptr == NULL || bsp->idx.parenttype != OBJ_BIOSEQSET) {
+    return FALSE;
+  }
+  bssp = (BioseqSetPtr) bsp->idx.parentptr;
+  if (bssp->_class != BioseqseqSet_class_nuc_prot || bssp->idx.parentptr == NULL || bsp->idx.parenttype != OBJ_BIOSEQSET) {
+    return FALSE;
+  }
+  bssp = bssp->idx.parentptr;
+  if (bssp->_class == BioseqseqSet_class_gen_prod_set) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+/* NOTE: under some circumstances this function will create features that
+ * are marked for deletion, so DeleteMarkedObjects should always be called
+ * at some later point.
+ */
+static CharPtr BuildFeatureClauses (
+  BioseqPtr   bsp,
+  Uint1       molecule_type,
+  SeqEntryPtr sep,
+  ValNodePtr  PNTR feature_list,
+  Boolean     isSegment,
+  ValNodePtr  PNTR seg_feature_list,
+  Int2        product_flag,
+  Boolean     alternate_splice_flag,
+  Boolean     gene_cluster_opp_strand,
+  DeflineFeatureRequestList PNTR feature_requests
+)
+{
+  ValNodePtr   strings = NULL;
+  ValNodePtr   clause;
+  CharPtr      str = NULL;
+  Char         ending_str [200];
+  ValNodePtr   tmp_feat_list;
+  BioSourcePtr biop;
+
+  if ((feature_requests->feature_list_type == DEFLINE_USE_FEATURES
+       || (IsmRNASequence(bsp) && IsInGenProdSet(bsp)))
+      && (! isSegment || (seg_feature_list != NULL && *seg_feature_list != NULL)))
+  {
+    /* remove features that indexer has chosen to suppress before they are grouped
+     * with other features or used to determine loneliness etc.
+     */
+    RemoveSuppressedFeatures (feature_list, feature_requests->suppressed_feature_list);
+  
+    GroupmRNAs (feature_list, bsp, feature_requests);
+
+    /* genes are added to other clauses */
+    GroupGenes (feature_list, feature_requests->suppress_locus_tags);
+
+    if (! feature_requests->suppress_alt_splice_phrase)
+    {
+      /* find alt-spliced CDSs */
+      FindAltSplices (*feature_list, bsp, feature_requests);
+    }
+
+    GroupAltSplicedExons (feature_list, bsp, TRUE);
+    
+    if (!isSegment)
+    {
+       /* group CDSs that have the same name and are under the same gene together */
+      GroupSegmentedCDSs (feature_list, bsp, TRUE, feature_requests);
+    }
+
+    /* per Susan's request, if promoters are requested and no promoters are found, add a promoter */
+    if (feature_requests->keep_items[RemovablePromoter] 
+        && feature_requests->add_fake_promoters
+        && !HasAnyPromoters (bsp)) {
+      AddFakePromoterClause (feature_list, bsp, feature_requests);
+    }
+
+    /* now group clauses */
+    GroupAllClauses ( feature_list, gene_cluster_opp_strand, bsp );
+
+    ExpandAltSplicedExons (*feature_list, bsp, feature_requests);
+
+    FindGeneProducts (*feature_list, bsp, feature_requests);
+
+    if (seg_feature_list != NULL && *seg_feature_list != NULL)
+    {
+      tmp_feat_list = NULL; 
+      ExtractSegmentClauses ( *seg_feature_list, *feature_list, &tmp_feat_list);
+      FreeListElement (*feature_list);
+      DeleteMarkedObjects (bsp->idx.entityID, 0, NULL);
+      *feature_list = tmp_feat_list;
+    }
+   
+    /* remove exons and other unwanted features */
+    RemoveUnwantedFeatures (feature_list, bsp, isSegment, feature_requests);
+
+    RemoveGenesMentionedElsewhere (feature_list, *feature_list, TRUE,
+                                   feature_requests->suppress_locus_tags);
+
+    if (feature_requests->remove_subfeatures)
+    {
+      DeleteSubfeatures (feature_list, TRUE);
+    }
+
+    DeleteOperonAndGeneClusterSubfeatures (feature_list, TRUE);
+
+    CountUnknownGenes (feature_list, bsp, feature_requests);
+
+    if (feature_requests->misc_feat_parse_rule == 1)
+    {
+      RenameMiscFeats (*feature_list, molecule_type);
+    }
+    else
+    {
+      RemoveUnwantedMiscFeats (feature_list, TRUE);
+    }
+
+    ReplaceRNAClauses (feature_list, bsp, feature_requests);
+
+    /* take any exons on the minus strand */
+    /* and reverse their order within the clause */
+    ReverseClauses (feature_list, IsExonOrIntron);
+
+    RenameExonSequences ( feature_list, bsp, TRUE);
+
+    LabelClauses (*feature_list, molecule_type, bsp, 
+                  feature_requests);
+
+    /* parse lists of tRNA and intergenic spacer clauses in misc_feat notes */
+    /* need to do this after LabelClauses, since LabelClauses labels intergenic
+     * spacers with more relaxed restrictions.  The labels from LabelClauses
+     * for intergenic spacers are the default values.
+     */
+    ReplaceIntergenicSpacerClauses (feature_list, bsp, feature_requests);
+
+    ConsolidateClauses (feature_list, bsp, molecule_type, TRUE,
+                        feature_requests);
+
+    /* this allows genes to be listed together even if they are from */
+    /* separate sequences */
+/*    SmashTallClauses (feature_list, TRUE); */
+
+    clause = *feature_list;
+    ListClauses (clause, &strings, TRUE, FALSE);
+
+    AutoDef_AddEnding (clause, &strings, bsp, 
+                       product_flag, alternate_splice_flag);
+    str = MergeValNodeStrings (strings, FALSE);
+	  ValNodeFreeData (strings);
+  }
+  else if (feature_requests->feature_list_type == DEFLINE_COMPLETE_SEQUENCE)
+  {
+    str = StringSave (", complete sequence.");
+  }
+  else if (feature_requests->feature_list_type == DEFLINE_COMPLETE_GENOME)
+  {
+    ending_str [0] = 0;
+    biop = GetBiopForBsp (bsp);
+    if (biop != NULL)
+    {
+      switch (biop->genome) {
+        case GENOME_macronuclear :
+          sprintf (ending_str, "macronuclear");
+          break;
+        case GENOME_nucleomorph :
+          sprintf (ending_str, "nucleomorph");
+          break;
+        case GENOME_mitochondrion :
+          sprintf (ending_str, "mitochondrion");
+          break;
+        case GENOME_apicoplast :
+        case GENOME_chloroplast :
+        case GENOME_chromoplast :
+        case GENOME_kinetoplast :
+        case GENOME_plastid :
+        case GENOME_cyanelle :
+        case GENOME_leucoplast :
+        case GENOME_proplastid :
+        case GENOME_hydrogenosome :
+          sprintf (ending_str, "%s", organelleByGenome [biop->genome]);
+          break;
+      }
+    }
+    StringCat (ending_str, ", complete genome.");
+    str = StringSave (ending_str);
+  }
+  else
+  {
+    str = StringSave ("");
+  }
+  
+  return str;
+}
+
+/* This function looks at the product names for the CDSs on the Bioseq,
+ * and sets the flag for the "nuclear genes for X products" ending
+ * based on the contents of the CDS products. */
+static Int2 GetProductFlagFromCDSProductNames (BioseqPtr bsp)
+{
+  SeqMgrFeatContext context;
+  SeqFeatPtr        cds = NULL;
+  Int2              product_flag;
+  Int2              i;
+  CharPtr           found;
+  Char              ch_before, ch_after;
+
+  product_flag = 0;
+  for (cds = SeqMgrGetNextFeature (bsp, cds, SEQFEAT_CDREGION, 0, &context);
+       cds != NULL && product_flag == 0;
+       cds = cds->next)
+  {
+    for (i = 1; organelleByPopup[i] != NULL && product_flag == 0; i++)
+    {
+      found = StringStr (context.label, organelleByPopup[i]);
+      if (found != NULL)
+      {
+        if (found == context.label) {
+          ch_before = ' ';
+        } else {
+          ch_before = *(found - 1);
+        }
+        ch_after = *(found + StringLen (organelleByPopup[i]));
+        if (ch_before == ' ' && (ch_after == 0 || ch_after == ' '))
+        {
+          product_flag = i;
+        }
+      }
+    }
+  }
+
+  return product_flag;
+}
+
+NLM_EXTERN void BuildDefLineFeatClauseList (
+  SeqEntryPtr sep,
+  Uint2 entityID,
+  DeflineFeatureRequestList PNTR feature_requests,
+  Int2 product_flag,
+  Boolean alternate_splice_flag,
+  Boolean gene_cluster_opp_strand,
+  ValNodePtr PNTR list
+)
+{
+  BioseqSetPtr    bssp;
+  BioseqPtr    bsp;
+  ValNodePtr    head;
+  Uint1      molecule_type;
+  SeqEntryPtr   nsep;
+  SegmentDefLineFeatureClauseData sdld;
+  DefLineFeatClausePtr deflist;
+  ValNodePtr    vnp;
+
+  if (sep == NULL || list == NULL) return;
+
+  if ( IS_Bioseq_set (sep))
+  {
+    bssp = (BioseqSetPtr) sep->data.ptrvalue;
+    if (bssp == NULL) return;
+    if ( bssp->_class == 7 || IsPopPhyEtcSet (bssp->_class)
+        || bssp->_class == BioseqseqSet_class_gen_prod_set
+        || bssp->_class == BioseqseqSet_class_not_set)
+    {
+      for (sep = bssp->seq_set; sep != NULL; sep = sep->next)
+      {
+        BuildDefLineFeatClauseList (sep, entityID, feature_requests,
+                                    product_flag, alternate_splice_flag,
+                                    gene_cluster_opp_strand, list);
+      }
+      return;
+    }
+  }
+    
+  nsep = FindNucSeqEntry (sep);
+  if (nsep != NULL)
+  {
+    bsp = (BioseqPtr) nsep->data.ptrvalue;
+    if ( SpecialHandlingForSpecialTechniques (bsp)) 
+    {
+      return;
+    }
+    if (bsp != NULL && bsp->repr == Seq_repr_seg &&
+      bsp->seq_ext != NULL && bsp->seq_ext_type == 1) 
+    {
+      /* get default product flag if necessary */
+	  if (product_flag == -1 || product_flag == DEFAULT_ORGANELLE_CLAUSE) {
+	    product_flag = GetProductFlagFromCDSProductNames (bsp);
+	  }
+
+      sdld.parent_bsp = bsp;
+      sdld.molecule_type = GetMoleculeType (bsp, entityID);
+      sdld.parent_feature_list = GetFeatureList (bsp, 
+                                                 feature_requests);
+
+      sdld.feature_requests =  feature_requests;
+      sdld.product_flag = product_flag;
+      sdld.alternate_splice_flag = alternate_splice_flag;
+      sdld.gene_cluster_opp_strand = gene_cluster_opp_strand;
+      sdld.list = list;
+      SeqMgrExploreSegments (bsp, (Pointer) &sdld, GetFeatureClauseForSeg);
+      deflist = (DefLineFeatClausePtr) MemNew (sizeof (DefLineFeatClauseData));
+      if (deflist == NULL) return;
+      deflist->sep = SeqMgrGetSeqEntryForData (bsp),
+      deflist->bsp = bsp;
+
+      deflist->clauselist = BuildFeatureClauses (bsp,
+                            sdld.molecule_type,
+                            SeqMgrGetSeqEntryForData (bsp),
+                            &sdld.parent_feature_list,
+                            FALSE,
+                            NULL,
+                            product_flag,
+                            alternate_splice_flag,
+                            gene_cluster_opp_strand,
+                            feature_requests);
+      vnp = ValNodeNew (*list);
+      if (vnp == NULL) return;
+      if (*list == NULL) *list = vnp;
+      vnp->data.ptrvalue = deflist;
+      FreeListElement (sdld.parent_feature_list);
+      DeleteMarkedObjects (entityID, 0, NULL);
+      return;
+    }
+  }
+
+  if (nsep != NULL && nsep != sep)
+    sep = nsep;
+
+
+  if (! IS_Bioseq (sep)) return;
+
+  /* get list of all recognized features */
+  bsp = (BioseqPtr) sep->data.ptrvalue;
+  if (bsp == NULL) return;
+  if ( SpecialHandlingForSpecialTechniques (bsp)) 
+  {
+    return;
+  }
+  molecule_type = GetMoleculeType (bsp, entityID);
+  head = GetFeatureList (bsp, feature_requests);
+
+  /* get default product flag if necessary */
+  if (product_flag == -1 || product_flag == DEFAULT_ORGANELLE_CLAUSE) {
+    product_flag = GetProductFlagFromCDSProductNames (bsp);
+  }
+
+  deflist = (DefLineFeatClausePtr) MemNew (sizeof (DefLineFeatClauseData));
+  if (deflist == NULL) return;
+  deflist->sep = SeqMgrGetSeqEntryForData (bsp),
+  deflist->bsp = bsp;
+  deflist->clauselist = BuildFeatureClauses (bsp,
+                                             molecule_type,
+                                             SeqMgrGetSeqEntryForData (bsp),
+                                             &head,
+                                             FALSE,
+                                             NULL,
+                                             product_flag,
+                                             alternate_splice_flag,
+                                             gene_cluster_opp_strand,
+                                             feature_requests);
+  vnp = ValNodeNew (*list);
+  if (vnp == NULL) return;
+  if (*list == NULL) *list = vnp;
+  vnp->data.ptrvalue = deflist;
+  FreeListElement (head);
+  DeleteMarkedObjects (entityID, 0, NULL);
+}
+
+static Boolean IdenticalExceptForPartialComplete (CharPtr str1, CharPtr str2)
+{
+    CharPtr cp, word_in_first, word_in_second;
+    Int4    first_len, second_len, compare_len;
+    
+    if (StringHasNoText (str1) && StringHasNoText (str2)) {
+        return TRUE;
+    } else if (StringHasNoText (str1) || StringHasNoText (str2)) {
+        return FALSE;
+    }
+    
+    word_in_first = StringISearch (str1, "partial");
+    cp = StringISearch (str1, "complete");
+    if (word_in_first == NULL || (cp != NULL && word_in_first > cp)) {
+        word_in_first = cp;
+        first_len = 8;
+    } else {
+        first_len = 7;
+    }
+    
+    word_in_second = StringISearch (str2, "partial");
+    cp = StringISearch (str2, "complete");
+    if (word_in_second == NULL || (cp != NULL && word_in_second > cp)) {
+        word_in_second = cp;
+        second_len = 8;
+    } else {
+        second_len = 7;
+    }
+    
+    if (word_in_first == NULL && word_in_second == NULL) {
+        if (StringCmp (str1, str2) == 0) {
+            return TRUE;
+        } else {
+            return FALSE;
+        }
+    } else if (word_in_first == NULL || word_in_second == NULL) {
+        return FALSE;
+    } else if ((compare_len = word_in_first - str1) != word_in_second - str2) {
+        return FALSE;
+    } else if (StringNCmp (str1, str2, compare_len) != 0) {
+        return FALSE;
+    } else {
+        return IdenticalExceptForPartialComplete (word_in_first + first_len, word_in_second + second_len);
+    }    
+}
+
+
+NLM_EXTERN Boolean AreFeatureClausesUnique (ValNodePtr list)
+{
+  ValNodePtr vnp1, vnp2;
+  DefLineFeatClausePtr deflist1, deflist2;
+
+  for (vnp1 = list; vnp1 != NULL && vnp1->next != NULL; vnp1 = vnp1->next)
+  {
+    deflist1 = vnp1->data.ptrvalue;
+    if (deflist1 == NULL || deflist1->clauselist == NULL) return FALSE;
+    
+    for (vnp2 = vnp1->next; vnp2 != NULL; vnp2 = vnp2->next)
+    {
+      deflist2 = vnp2->data.ptrvalue;
+      if (deflist2 == NULL || deflist2->clauselist == NULL
+        || IdenticalExceptForPartialComplete (deflist1->clauselist, deflist2->clauselist))
+      {
+        return FALSE;
+      }
+    }
+  }
+  return TRUE;
+}
+
+
+static CharPtr GetKeywordPrefix (SeqEntryPtr sep)
+{
+  ValNodePtr vnp;
+  GBBlockPtr gbp;
+  
+  vnp = SeqEntryGetSeqDescr (sep, Seq_descr_genbank, NULL);
+	if (vnp != NULL) {
+	  gbp = (GBBlockPtr) vnp->data.ptrvalue;
+	  if (gbp != NULL)
+	  {
+	    for (vnp = gbp->keywords; vnp != NULL; vnp = vnp->next)
+	    {
+	      if (StringICmp((CharPtr)vnp->data.ptrvalue, "TPA:inferential") == 0)
+	      {
+	        return "TPA_inf: ";
+	      }
+	      else if (StringICmp((CharPtr)vnp->data.ptrvalue, "TPA:experimental") == 0)
+	      {
+	        return "TPA_exp: ";
+	      }
+	    }
+	  }
+	}
+	return "";
+}
+
+NLM_EXTERN void BuildDefinitionLinesFromFeatureClauseLists (
+  ValNodePtr list,
+  ModifierItemLocalPtr modList,
+  ValNodePtr modifier_indices,
+  OrganismDescriptionModifiersPtr odmp
+)
+{
+  ValNodePtr vnp;
+  DefLineFeatClausePtr defline_featclause;
+  CharPtr    org_desc, tmp_str, keyword_prefix;
+
+  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->data.ptrvalue != NULL)
+    {
+      defline_featclause = vnp->data.ptrvalue;
+      
+      keyword_prefix = GetKeywordPrefix (defline_featclause->sep);
+      
+      org_desc = GetOrganismDescription (defline_featclause->bsp,
+                                         modList, modifier_indices, odmp);
+      tmp_str = (CharPtr) MemNew (StringLen (keyword_prefix) 
+                                  + StringLen (org_desc) 
+                                  + StringLen (defline_featclause->clauselist) + 2);
+      if (tmp_str == NULL) return;
+      tmp_str [0] = 0;
+      if (keyword_prefix != NULL)
+      {
+        StringCat (tmp_str, keyword_prefix);
+      }
+      StringCat (tmp_str, org_desc);
+      if (defline_featclause->clauselist != NULL
+        && defline_featclause->clauselist [0] != ','
+        && defline_featclause->clauselist [0] != '.'
+        && defline_featclause->clauselist [0] != 0)
+      {
+        StringCat (tmp_str, " ");
+      }
+      StringCat (tmp_str, defline_featclause->clauselist);
+      tmp_str [0] = toupper (tmp_str [0]);
+      ReplaceDefinitionLine (defline_featclause->sep, tmp_str);
+      MemFree (org_desc);
+    }
+  }
+}
+
+
+/* This removes redundant titles on nuc-prot sets, which will not be
+ * visible in the flat file if all sequences in the nuc-prot set have
+ * their own title.
+ */
+NLM_EXTERN void RemoveNucProtSetTitles (SeqEntryPtr sep)
+{
+  BioseqSetPtr bssp;
+  SeqEntryPtr  this_sep;
+  SeqDescrPtr  sdp, prev = NULL, sdp_next;
+  
+  if (sep == NULL || ! IS_Bioseq_set (sep))
+  {
+    return;
+  }
+  bssp = (BioseqSetPtr) sep->data.ptrvalue;
+  if (bssp == NULL) return;
+  for (this_sep = bssp->seq_set; this_sep != NULL; this_sep = this_sep->next)
+  {
+    RemoveNucProtSetTitles (this_sep);
+  }
+  
+  if (bssp->_class != BioseqseqSet_class_nuc_prot) 
+  {
+    return;
+  }
+  for (sdp = bssp->descr; sdp != NULL; sdp = sdp_next)
+  {
+    sdp_next = sdp->next;
+    if (sdp->choice == Seq_descr_title)
+    {
+      if (prev == NULL)
+      {
+        bssp->descr = sdp->next;
+      }
+      else
+      {
+        prev->next = sdp->next;
+      }
+      sdp->next = NULL;
+      SeqDescrFree (sdp);
+    }
+    else
+    {
+      prev = sdp;
+    }
+  }
+}
+
+
+NLM_EXTERN void 
+AutoDefForSeqEntry 
+(SeqEntryPtr sep,
+ Uint2 entityID,
+ OrganismDescriptionModifiersPtr odmp,
+ ModifierItemLocalPtr modList,
+ ValNodePtr modifier_indices,
+ DeflineFeatureRequestListPtr feature_requests,
+ Int2 product_flag,
+ Boolean alternate_splice_flag,
+ Boolean gene_cluster_opp_strand)
+{
+  ValNodePtr defline_clauses = NULL;
+
+  if (sep == NULL) return;
+
+  RemoveNucProtSetTitles (sep);
+  
+  SeqEntrySetScope (sep);
+
+  BuildDefLineFeatClauseList (sep, entityID,
+                              feature_requests,
+                              product_flag, alternate_splice_flag,
+                              gene_cluster_opp_strand,
+                              &defline_clauses);
+                              
+/*  dlfp->feature_requests.suppressed_feature_list = ValNodeFree (dlfp->feature_requests.suppressed_feature_list);                               */
+
+  BuildDefinitionLinesFromFeatureClauseLists (defline_clauses, modList,
+                                              modifier_indices, odmp);
+  DefLineFeatClauseListFree (defline_clauses);
+  ClearProteinTitlesInNucProts (entityID, NULL);
+  InstantiateProteinTitles (entityID, NULL);
+}
+
+
+/* functions for editing seq-locs */
+NLM_EXTERN Int4 ExtendSeqLocToEnd (SeqLocPtr slp, BioseqPtr bsp, Boolean end5)
+{
+  Uint1          strand;
+  SeqLocPtr      slp_to_change, slp_index;
+  Int4           extent_to_change;
+  Int4           start, stop;
+  SeqIdPtr       sip;
+  Int4           start_diff = 0;
+  
+  if (slp == NULL || bsp == NULL) return 0;
+
+  slp_to_change = NULL;
+  strand = SeqLocStrand (slp);
+  switch (slp->choice)
+  {
+    case SEQLOC_INT:
+      slp_to_change = slp;
+      break;
+    case SEQLOC_MIX:
+  	case SEQLOC_PACKED_INT:
+      sip = SeqLocId (slp);
+      if (sip == NULL) return 0; /* can only process if all on one bioseq */
+      slp_to_change = NULL;
+      if ((strand == Seq_strand_minus && end5)
+        || (strand != Seq_strand_minus && !end5))
+      {
+        extent_to_change = 0;
+        for (slp_index = (SeqLocPtr)slp->data.ptrvalue; slp_index != NULL; slp_index = slp_index->next)
+        {
+          stop = GetOffsetInBioseq (slp_index, bsp, SEQLOC_STOP);
+          if (stop > extent_to_change)
+          {
+            slp_to_change = slp_index;
+            extent_to_change = stop;
+          }
+        }
+      }
+      else
+      {
+        extent_to_change = bsp->length;
+        for (slp_index = (SeqLocPtr)slp->data.ptrvalue; slp_index != NULL; slp_index = slp_index->next)
+        {
+          start = GetOffsetInBioseq (slp_index, bsp, SEQLOC_START);
+          if (start < extent_to_change)
+          {
+            slp_to_change = slp_index;
+            extent_to_change = start;
+          }
+        }
+      }
+      break;
+  }
+
+  if (slp_to_change != NULL)
+  {
+    if ((strand == Seq_strand_minus && end5)
+      || (strand != Seq_strand_minus && !end5))
+    {
+      start = GetOffsetInBioseq (slp_to_change, bsp, SEQLOC_START);
+      stop = bsp->length - 1;
+    }
+    else
+    {
+      start = 0;
+      stop = GetOffsetInBioseq (slp_to_change, bsp, SEQLOC_STOP);
+    }
+    if (end5) {
+        if (strand == Seq_strand_minus) {
+            start_diff = bsp->length - 1 - GetOffsetInBioseq(slp_to_change, bsp, SEQLOC_START);
+        } else {
+            start_diff = GetOffsetInBioseq(slp_to_change, bsp, SEQLOC_START);
+        }
+    }
+    
+    expand_seq_loc (start, stop, strand, slp_to_change);
+  }
+  return start_diff;
+}
+
+
+
+
+
diff --git a/api/sqnutils.h b/api/sqnutils.h
index 37e977ba..e2a0dc53 100644
--- a/api/sqnutils.h
+++ b/api/sqnutils.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.186 $
+* $Revision: 6.224 $
 *
 * File Description: 
 *
@@ -50,6 +50,7 @@
 #include <objpubme.h>
 #include <objentgene.h>
 #include <util/creaders/alnread.h>
+#include <subutil.h>
 
 #undef NLM_EXTERN
 #ifdef NLM_IMPORT
@@ -547,6 +548,12 @@ NLM_EXTERN void AddQualifierToFeature (SeqFeatPtr sfp, CharPtr qual, CharPtr val
 NLM_EXTERN CharPtr TrimSpacesAndSemicolons (CharPtr str);
 NLM_EXTERN CharPtr TrimSpacesAndJunkFromEnds (CharPtr str, Boolean allowEllipsis);
 
+/* specialized cleanup for subsource and orgmod lists */
+NLM_EXTERN void CleanSubSourceList (SubSourcePtr PNTR sspp, Uint1 location);
+NLM_EXTERN void CleanOrgModList (OrgModPtr PNTR ompp);
+
+NLM_EXTERN Boolean PubIsEffectivelyEmpty (PubdescPtr pdp);
+
 /* BasicSeqEntryCleanup cleans up strings, moves gbquals to the appropriate field, and
 does several other conversions, all without changing the itemID structure (which would
 require reindexing) */
@@ -807,9 +814,10 @@ NewClickableItem
  CharPtr         description_fmt,
  ValNodePtr      item_list);
  
+extern ClickableItemPtr ClickableItemFree (ClickableItemPtr cip);
 extern ValNodePtr FreeClickableList (ValNodePtr list);
 
-
+extern int LIBCALLBACK SortVnpByClickableItemDescription (VoidPtr ptr1, VoidPtr ptr2);
 
 /* To add a new type of test, do ALL Of the following:
  * 1. add an item to the DiscrepancyType enum (this will fill the clickable_item_type value)
@@ -861,6 +869,11 @@ typedef enum {
   DISC_TRANSL_TOO_LONG,
   DISC_CDS_OVERLAP_TRNA,
   DISC_COUNT_PROTEINS,
+  DISC_FEAT_OVERLAP_SRCFEAT,
+  DISC_MISSING_GENPRODSET_PROTEIN,
+  DISC_DUP_GENPRODSET_PROTEIN,
+  DISC_MISSING_GENPRODSET_TRANSCRIPT_ID,
+  DISC_DUP_GENPRODSET_TRANSCRIPT_ID,
   MAX_DISC_TYPE
 } DiscrepancyType;
 
@@ -879,16 +892,96 @@ extern DiscrepancyConfigPtr DiscrepancyConfigNew (void);
 extern DiscrepancyConfigPtr ReadDiscrepancyConfig (void);
 extern void SaveDiscrepancyConfig (DiscrepancyConfigPtr dcp);
 extern void DisableTRNATests (DiscrepancyConfigPtr dcp);
+extern CharPtr SetDiscrepancyReportTestsFromString (CharPtr list, Boolean enable, DiscrepancyConfigPtr dcp);
 
 typedef void (*PerformDiscrepancyTest) PROTO ((ValNodePtr PNTR, ValNodePtr));
 
 extern ValNodePtr CollectDiscrepancies (DiscrepancyConfigPtr dcp, ValNodePtr sep_list, PerformDiscrepancyTest taxlookup);
 extern CharPtr GetDiscrepancyItemText (ValNodePtr vnp);
+extern void VisitGenProdSetFeatures (SeqEntryPtr sep, Pointer userdata, VisitFeaturesFunc callback);
+extern ValNodePtr ReplaceDiscrepancyItemWithFeatureTableStrings (ValNodePtr feat_list);
+extern CharPtr GetParentLabelForDiscrepancyItem (ValNodePtr vnp);
 extern void WriteDiscrepancy (FILE *fp, ClickableItemPtr dip, Boolean use_feature_table_fmt);
 extern void WriteDiscrepancyEx (FILE *fp, ClickableItemPtr dip, Boolean use_feature_table_fmt, ValNodePtr filename_list, CharPtr descr_prefix);
 
+/* structure shared by tbl2asn and discrepancy report functions */
+typedef struct genprodsetdiscrepancylists {
+  ValNodePtr cds_product_list;
+  ValNodePtr mrna_product_list;
+  ValNodePtr missing_mrna_product;
+  ValNodePtr missing_protein_id;
+} GenProdSetDiscrepancyListsData, PNTR GenProdSetDiscrepancyListsPtr;
+
+extern void CheckGenProdSetsInSeqEntry (SeqEntryPtr sep, GenProdSetDiscrepancyListsPtr lists);  
+
+
+typedef struct protidlists {
+  ValNodePtr missing_gnl_list;
+  ValNodePtr gnl_list;
+} ProtIdListsData, PNTR ProtIdListsPtr;
+
+/* structure shared by tbl2asn and discrepancy report functions */
+typedef struct globaldiscrepancy {
+  CharPtr str;
+  Uint1   data_choice;
+  Pointer data;
+} GlobalDiscrepancyData, PNTR GlobalDiscrepancyPtr;
+
+extern GlobalDiscrepancyPtr GlobalDiscrepancyNew (CharPtr str, Uint1 data_choice, Pointer data);
+extern GlobalDiscrepancyPtr GlobalDiscrepancyFree (GlobalDiscrepancyPtr g);
+extern ValNodePtr FreeGlobalDiscrepancyList (ValNodePtr vnp);
+extern void ConvertGlobalDiscrepancyToText (GlobalDiscrepancyPtr g, Boolean use_feature_fmt);
+extern void ConvertGlobalDiscrepancyListToText (ValNodePtr vnp, Boolean use_feature_fmt);
+extern ValNodePtr GetGlobalDiscrepancyItem (GlobalDiscrepancyPtr g);
+extern CharPtr GetGlobalDiscrepancyStr (GlobalDiscrepancyPtr g);
+NLM_EXTERN int LIBCALLBACK SortVnpByGlobalDiscrepancyString (VoidPtr ptr1, VoidPtr ptr2);
+extern ClickableItemPtr
+ReportNonUniqueGlobalDiscrepancy 
+(ValNodePtr vnp, 
+ CharPtr    label_fmt,
+ CharPtr    ind_cat_fmt,
+ Uint4      clickable_item_type,
+ Boolean    keep_top_category);
+extern ValNodePtr ReportInconsistentGlobalDiscrepancyPrefixes
+(ValNodePtr vnp, 
+ CharPtr    label_fmt,
+ Uint4      clickable_item_type);
+extern ValNodePtr ReportInconsistentGlobalDiscrepancyStrings
+(ValNodePtr vnp, 
+ CharPtr    label_fmt,
+ Uint4      clickable_item_type);
+extern ClickableItemPtr ReportMissingFields (ValNodePtr list, CharPtr label_fmt, Uint4 clickable_item_type);
+extern ClickableItemPtr ReportBadLocusTagFormat (ValNodePtr list);
+extern ClickableItemPtr FindAdjacentDuplicateLocusTagGenes (ValNodePtr locus_tag_list);
+extern void FindProteinIDCallback (BioseqPtr bsp, Pointer userdata);
+
+
+/* formats for global discrepancies also used by tbl2asn */
+extern CharPtr discReportDuplicateLocusTagFmt;
+extern CharPtr discReportOneDuplicateLocusTagFmt;
+extern CharPtr discReportDuplicateProteinIDFmt;
+extern CharPtr discReportOneDuplicateProteinIDFmt;
+extern CharPtr discReportDuplicateTranscriptIdFmt;
+extern CharPtr discReportOneDuplicateTranscriptIdFmt;
+extern CharPtr discReportInconsistentLocusTagPrefixFmt;
+extern CharPtr discReportMissingLocusTags;
+extern CharPtr discReportInconsistentProteinIDPrefixFmt;
+extern CharPtr discReportBadProteinIdFmt;
+extern CharPtr discReportMissingTranscriptIDFmt;
+
 extern CharPtr GetBioseqSetLabel (BioseqSetPtr bssp);
 
+NLM_EXTERN ValNodePtr ValNodeDupStringList (ValNodePtr vnp);
+
+
+typedef enum {
+  eLocusTagErrorBadFormat,
+  eLocusTagErrorDuplicate,
+  eLocusTagErrorInconsistentPrefix
+} ELocusTagError;
+
+NLM_EXTERN ValNodePtr FindBadLocusTagsInList (ValNodePtr list);
+
 /* for the Barcode Discrepancy Test */
 typedef enum {
   eBarcodeTest_Length = 0,
@@ -935,6 +1028,8 @@ extern ValNodePtr GetBarcodeDiscrepancies (ValNodePtr sep_list, BarcodeTestConfi
 /* This one lists accessions that fail */
 extern ValNodePtr GetBarcodeFailedAccessionList (SeqEntryPtr sep, BarcodeTestConfigPtr cfg);
 extern ValNodePtr GetBarcodePassFail (SeqEntryPtr sep, BarcodeTestConfigPtr cfg);
+/* This one lists passes and failures, with reasons for failures */
+extern void WriteBarcodeTestComprehensive (FILE *fp, ValNodePtr results_list);
 extern void WriteBarcodeDiscrepancies (FILE *fp, ValNodePtr results_list);
 extern void WriteBarcodeTestCompliance (FILE *fp, ValNodePtr results_list);
 extern void WriteBarcodeTagTable (FILE *fp, ValNodePtr results_list);
@@ -947,6 +1042,20 @@ extern Boolean PassBarcodeTests (BarcodeTestResultsPtr res);
 #define FILENAME_LIST_ENTITY_ID_ITEM 1
 #define FILENAME_LIST_FILENAME_ITEM  2
 
+extern ValNodePtr FreeFilenameList (ValNodePtr filename_list);
+
+typedef struct discreportoutputconfig {
+  Boolean use_feature_table_format;
+  Boolean expand_report_categories[MAX_DISC_TYPE];
+  Boolean summary_report;
+  ValNodePtr filename_list;
+} DiscReportOutputConfigData, PNTR DiscReportOutputConfigPtr;
+
+extern CharPtr ExpandDiscrepancyReportTestsFromString (CharPtr list, Boolean expand, DiscReportOutputConfigPtr dcp);
+extern void CollateDiscrepancyReports (ValNodePtr PNTR discrepancy_reports);
+extern void WriteAsnDiscReport (ValNodePtr discrepancy_list, FILE *ofp, DiscReportOutputConfigPtr oc, Boolean use_flag);
+
+
 /* extern to allow access to subsource_subtype_alist */
 typedef struct Nlm_qual_name_assoc {
    Nlm_CharPtr name; 
@@ -976,10 +1085,335 @@ extern Boolean GeneRefMatch (GeneRefPtr grp1, GeneRefPtr grp2);
 
 extern void IsCorrectLatLonFormat (CharPtr lat_lon, BoolPtr format_correct, BoolPtr lat_in_range, BoolPtr lon_in_range);
 extern CharPtr FixLatLonFormat (CharPtr orig_lat_lon);
+extern Boolean ParseLatLon (CharPtr lat_lon, FloatHi PNTR latP, FloatHi PNTR lonP);
 extern void ApplyBarcodeDbxrefsToBioseq (BioseqPtr bsp, Pointer data);
 
 extern CharPtr GetCountryFix (CharPtr country, CharPtr PNTR country_list);
 
+extern CharPtr ncrnaClassList[];
+extern Int4 NcrnaOTHER;
+extern Boolean IsStringInNcRNAClassList (CharPtr str);
+extern ValNodePtr ListFeaturesInLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice);
+extern ValNodePtr ListCodingRegionsContainedInSourceFeatures (SeqEntryPtr sep);
+extern ValNodePtr ListFeaturesOverlappingLocation (BioseqPtr bsp, SeqLocPtr slp, Uint1 seqfeatChoice, Uint1 featdefChoice);
+
+extern void ConvertSourceFeatDescProc (SeqFeatPtr sfp, Pointer userdata);
+
+/* for correcting capitalization */
+NLM_EXTERN void 
+FixCapitalizationInElement 
+(CharPtr PNTR pEl,
+ Boolean      bAbbrev, 
+ Boolean      bShortWords,
+ Boolean      bApostrophes);
+
+NLM_EXTERN void FixAbbreviationsInElement (CharPtr PNTR pEl);
+NLM_EXTERN void FixOrgNamesInString (CharPtr str, ValNodePtr org_names);
+NLM_EXTERN void ResetCapitalization (Boolean first_is_upper, CharPtr pString);
+
+NLM_EXTERN SeqIdPtr CreateSeqIdFromText (CharPtr id_str, SeqEntryPtr sep);
+NLM_EXTERN SeqLocPtr SeqLocWholeNew (BioseqPtr bsp);
+NLM_EXTERN Int4 GetDeltaSeqLen (DeltaSeqPtr dsp);
+
+typedef SeqAlignPtr (*GlobalAlignFunc) PROTO ((BioseqPtr, BioseqPtr, BoolPtr));
+
+typedef struct adjustfeatforgap {
+  ValNodePtr feature_list;
+  Boolean    unknown_gaps;
+  Boolean    known_gaps;
+  Boolean    make_partial;
+  Boolean    partial_for_pseudo;
+  Boolean    trim_ends;
+  Boolean    split_internal;
+  GlobalAlignFunc align_func;
+  ValNodePtr features_in_gap;
+} AdjustFeatForGapData, PNTR AdjustFeatForGapPtr;
+
+NLM_EXTERN AdjustFeatForGapPtr AdjustFeatForGapFree (AdjustFeatForGapPtr agp);
+NLM_EXTERN Boolean FeatureOkForFeatureList (SeqFeatPtr sfp, ValNodePtr feature_list);
+NLM_EXTERN void
+LocationContainsGaps
+(SeqLocPtr slp,
+ BioseqPtr bsp,
+ Boolean   unknown_gaps,
+ Boolean   known_gaps,
+ BoolPtr   terminal_gaps,
+ BoolPtr   internal_gaps,
+ BoolPtr   entirely_in_gap);
+
+NLM_EXTERN void AdjustFeatureForGapsCallback (SeqFeatPtr sfp, Pointer data);
+NLM_EXTERN void MarkFeaturesInGapsForDeletion (AdjustFeatForGapPtr afgp);
+NLM_EXTERN void AdjustCDSLocationsForUnknownGapsCallback (SeqFeatPtr sfp, Pointer data);
+NLM_EXTERN Boolean GapInLocation (Int4 seq_offset, Int4 length, SeqLocPtr loc);
+NLM_EXTERN BioseqPtr 
+AddProteinSequenceCopy 
+(BioseqPtr  protbsp, 
+ BioseqPtr  featbsp,
+ SeqFeatPtr new_sfp,
+ Uint2      entityID);
+NLM_EXTERN void AdjustFrame (SeqFeatPtr sfp, BioseqPtr oldprot);
+NLM_EXTERN void SetProductSequencePartials (BioseqPtr protbsp, Boolean partial5, Boolean partial3);
+NLM_EXTERN void AddCDSGapComment (SeqFeatPtr sfp);
+
+
+NLM_EXTERN Boolean SeqEdFixProteinFeatures (BioseqPtr oldbsp, BioseqPtr newbsp, Boolean force_fix, GlobalAlignFunc align_func);
+NLM_EXTERN void SeqEdTranslateOneCDS (SeqFeatPtr sfp, BioseqPtr featbsp, Uint2 entityID, GlobalAlignFunc align_func);
+
+NLM_EXTERN CharPtr GetStateAbbreviation (CharPtr state);
+
+extern const CharPtr TSA_assembly_from;
+extern const CharPtr TSA_assembly_to;
+extern const CharPtr TSA_primary_id;
+extern const CharPtr TSA_primary_from;
+extern const CharPtr TSA_primary_to;
+
+NLM_EXTERN UserFieldPtr AddLineToTranscriptomeTable (Int4 assembly_from, Int4 assembly_to, CharPtr primary_id, Int4 primary_from, Int4 primary_to);
+NLM_EXTERN Boolean AddTranscriptomeTable (BioseqPtr bsp, FILE *fp);
+NLM_EXTERN SeqFeatPtr GetGeneForFeature (SeqFeatPtr sfp);
+
+NLM_EXTERN Boolean IsStringInSpanInList (CharPtr str, CharPtr list);
+
+NLM_EXTERN void ParseGoTermsFromFields (SeqEntryPtr sep);
+
+/* for autodef */
+typedef enum {
+  RemovableExon = 0,
+  RemovableIntron,
+  Removable5UTR,
+  Removable3UTR,
+  RemovableCDS,
+  RemovablePromoter,
+  RemovableLTR,
+  RemovableNoncodingProductFeat,
+  RemovableMobileElement,
+  RemovablePrecursorRNA,
+  NumRemovableItems
+} RemovableList;
+NLM_EXTERN CharPtr GetRemovableItemName (Int4 i);
+
+typedef enum {
+  DEFLINE_USE_FEATURES = 1,
+  DEFLINE_COMPLETE_SEQUENCE,
+  DEFLINE_COMPLETE_GENOME
+} DefLineType;
+
+typedef struct deflinefeaturerequestlist {
+  Boolean      keep_items[NumRemovableItems];
+  Boolean      add_fake_promoters;
+  Boolean      suppress_alt_splice_phrase;
+  Boolean      remove_subfeatures;
+  DefLineType  feature_list_type;
+  Int4         misc_feat_parse_rule;
+  Boolean      suppress_locus_tags;
+  ValNodePtr   suppressed_feature_list;
+  Boolean      use_ncrna_note;
+} DeflineFeatureRequestList, PNTR DeflineFeatureRequestListPtr;
+
+NLM_EXTERN void InitFeatureRequests (DeflineFeatureRequestListPtr feature_requests);
+
+
+/* ModifierItemLocalData is used to store information about the results of
+ * a search of the set of organisms in a record and the results of user
+ * input to a dialog for deciding which modifiers should be used in the
+ * organism description.
+ */
+typedef struct modifieritemlocal {
+/*  ButtoN        button; */
+  Boolean       any_present;
+  Boolean       all_present;
+  Boolean       is_unique;
+  CharPtr       first_value_seen;
+  ValNodePtr    values_seen;
+  Boolean       all_unique;
+  CharPtr       status;
+  Boolean       required;
+} ModifierItemLocalData, PNTR ModifierItemLocalPtr;
+
+typedef enum {
+  DEFLINE_POS_Acronym = 0,
+  DEFLINE_POS_Anamorph,
+  DEFLINE_POS_Authority,
+  DEFLINE_POS_Bio_material,
+  DEFLINE_POS_Biotype,
+  DEFLINE_POS_Biovar,
+  DEFLINE_POS_Breed,
+  DEFLINE_POS_Cell_line,
+  DEFLINE_POS_Cell_type,
+  DEFLINE_POS_Chemovar,
+  DEFLINE_POS_Chromosome,
+  DEFLINE_POS_Clone,
+  DEFLINE_POS_Clone_lib,
+  DEFLINE_POS_Collected_by,
+  DEFLINE_POS_Collection_date,
+  DEFLINE_POS_Common,
+  DEFLINE_POS_Country,
+  DEFLINE_POS_Cultivar,
+  DEFLINE_POS_Culture_collection,
+  DEFLINE_POS_Dev_stage,
+  DEFLINE_POS_Ecotype,
+  DEFLINE_POS_Endogenous_virus_name,
+  DEFLINE_POS_Environmental_sample,
+  DEFLINE_POS_Forma,
+  DEFLINE_POS_Forma_specialis,
+  DEFLINE_POS_Frequency,
+  DEFLINE_POS_Genotype,
+  DEFLINE_POS_Germline,
+  DEFLINE_POS_Group,
+  DEFLINE_POS_Haplotype,
+  DEFLINE_POS_Identified_by,
+  DEFLINE_POS_Isolate,
+  DEFLINE_POS_Isolation_source,
+  DEFLINE_POS_Lab_host,
+  DEFLINE_POS_Lat_lon,
+  DEFLINE_POS_Map,
+  DEFLINE_POS_Metagenomic,
+  DEFLINE_POS_Note_orgmod,
+  DEFLINE_POS_Note_subsrc,
+  DEFLINE_POS_Pathovar,
+  DEFLINE_POS_Plasmid_name,
+  DEFLINE_POS_Plastid_name,
+  DEFLINE_POS_Pop_variant,
+  DEFLINE_POS_Rearranged,
+  DEFLINE_POS_Segment,
+  DEFLINE_POS_Serogroup,
+  DEFLINE_POS_Serotype,
+  DEFLINE_POS_Serovar,
+  DEFLINE_POS_Sex,
+  DEFLINE_POS_Specific_host,
+  DEFLINE_POS_Specimen_voucher,
+  DEFLINE_POS_Strain,
+  DEFLINE_POS_Subclone,
+  DEFLINE_POS_Subgroup,
+  DEFLINE_POS_Sub_species,
+  DEFLINE_POS_Substrain,
+  DEFLINE_POS_Subtype,
+  DEFLINE_POS_Synonym,
+  DEFLINE_POS_Teleomorph,
+  DEFLINE_POS_Tissue_lib,
+  DEFLINE_POS_Tissue_type,
+  DEFLINE_POS_Transgenic,
+  DEFLINE_POS_Type,
+  DEFLINE_POS_Variety
+} DefLinePos;
+
+/* ModifierItemGlobalData is used to store information about the available
+ * modifiers - the name to use when displaying a list of checkboxes, whether
+ * the modifier is an Organism modifier or a Source modifier, the subtype
+ * to use when looking for the modifier in the organism qualifier list,
+ * and whether this modifier is required by default.
+ */
+typedef struct modifieritemglobal {
+  CharPtr       name;
+  Boolean       isOrgMod;
+  Uint1         subtype;
+} ModifierItemGlobalData, PNTR ModifierItemGlobalPtr;
+
+extern ModifierItemGlobalData DefLineModifiers[];
+NLM_EXTERN size_t NumDefLineModifiers (void);
+
+/* OrganismDescriptionModifiers is used to apply specific user preferences
+ * for how to construct the organism descriptions - whether or not to use
+ * labels for the modifiers, whether and how to limit the number of modifiers
+ * used in any one organism description, whether to keep or remove modifier
+ * information in parentheses in the organism taxonomy name, and whether or
+ * not to apply modifiers to organisms with "sp." in the middle of the
+ * taxonomy name.
+ */
+typedef struct organismdescriptionmodifiers {
+  Boolean  use_labels;
+  Int2     max_mods;
+  Boolean  keep_paren;
+  Boolean  exclude_sp;
+  Boolean  exclude_cf;
+  Boolean  exclude_aff;
+  Boolean  exclude_nr;
+  Boolean  include_country_extra;
+  Int4     clone_isolate_HIV_rule_num;
+  Boolean  use_modifiers;
+  Boolean  allow_semicolon_in_modifier;
+} OrganismDescriptionModifiers, PNTR OrganismDescriptionModifiersPtr;
+
+/* These values are used for the clone_isolate_HIV_rule_num value in OrganismDescriptionModifiers */
+typedef enum {
+  clone_isolate_HIV_rule_prefer_clone = 1,
+  clone_isolate_HIV_rule_prefer_isolate,
+  clone_isolate_HIV_rule_want_both
+} clone_isolate_HIV_rule_values;
+  
+
+typedef struct sourcequaldesc
+{
+  CharPtr       name;
+  Boolean       isOrgMod;
+  Uint1         subtype;
+  Uint1         subfield;
+} SourceQualDescData, PNTR SourceQualDescPtr;
+
+NLM_EXTERN void SetRequiredModifiers (ModifierItemLocalPtr modList);
+NLM_EXTERN void CountModifiers (ModifierItemLocalPtr ItemList, SeqEntryPtr sep);
+NLM_EXTERN ValNodePtr FindBestModifiers(SeqEntryPtr sep, ModifierItemLocalPtr ItemList);
+NLM_EXTERN ValNodePtr GetModifierIndicesFromModList (ModifierItemLocalPtr modList);
+
+
+
+NLM_EXTERN CharPtr MergeValNodeStrings (ValNodePtr list, Boolean useReturn);
+
+NLM_EXTERN void BuildDefLineFeatClauseList 
+( SeqEntryPtr sep,
+  Uint2 entityID,
+  DeflineFeatureRequestList PNTR feature_requests,
+  Int2 product_flag,
+  Boolean alternate_splice_flag,
+  Boolean gene_cluster_opp_strand,
+  ValNodePtr PNTR list);
+
+NLM_EXTERN Boolean AreFeatureClausesUnique (ValNodePtr list);
+NLM_EXTERN void DefLineFeatClauseListFree (ValNodePtr vnp);
+
+NLM_EXTERN void 
+BuildDefinitionLinesFromFeatureClauseLists 
+(ValNodePtr list,
+ ModifierItemLocalPtr modList,
+ ValNodePtr modifier_indices,
+ OrganismDescriptionModifiersPtr odmp);
+
+NLM_EXTERN void 
+AutoDefForSeqEntry 
+(SeqEntryPtr sep,
+ Uint2 entityID,
+ OrganismDescriptionModifiersPtr odmp,
+ ModifierItemLocalPtr modList,
+ ValNodePtr modifier_indices,
+ DeflineFeatureRequestListPtr feature_requests,
+ Int2 product_flag,
+ Boolean alternate_splice_flag,
+ Boolean gene_cluster_opp_strand);
+
+NLM_EXTERN Boolean IsSpName (CharPtr taxName);
+
+#define DEFAULT_ORGANELLE_CLAUSE 10
+NLM_EXTERN BioSourcePtr GetBiopForBsp (BioseqPtr bsp);
+NLM_EXTERN Boolean IsLocAInBonSameStrand (SeqLocPtr slp1, SeqLocPtr slp2);
+NLM_EXTERN void CleanUpTaxName (CharPtr taxName, Boolean keep_in_paren);
+NLM_EXTERN Boolean UseOrgModifier (OrgModPtr mod, CharPtr   taxName);
+NLM_EXTERN void AddModifierLabel 
+( Boolean use_labels,
+  Boolean is_orgmod,
+  Uint1   subtype,
+  CharPtr modifier_text);
+NLM_EXTERN Boolean LIBCALLBACK IsMobileElement (SeqFeatPtr sfp);
+NLM_EXTERN void RemoveNucProtSetTitles (SeqEntryPtr sep);
+
+
+NLM_EXTERN ValNodePtr ReadTabTableFromFile (FILE *fp);
+NLM_EXTERN ValNodePtr FreeTabTable (ValNodePtr row_list);
+NLM_EXTERN ValNodePtr CountTabTableBlanks (ValNodePtr row_list);
+NLM_EXTERN ValNodePtr ScanTabTableForSpecialCharacters (ValNodePtr row_list);
+
+NLM_EXTERN void SpecialCharFindWithContext (CharPtr PNTR strp, Pointer userdata, BoolPtr did_find, BoolPtr did_change);
+NLM_EXTERN ValNodePtr FreeContextList (ValNodePtr context_list);
+
+NLM_EXTERN Int4 ExtendSeqLocToEnd (SeqLocPtr slp, BioseqPtr bsp, Boolean end5);
 
 #ifdef __cplusplus
 }
diff --git a/api/subutil.c b/api/subutil.c
index d962350e..416c2521 100644
--- a/api/subutil.c
+++ b/api/subutil.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 11/3/93
 *
-* $Revision: 6.71 $
+* $Revision: 6.72 $
 *
 * File Description: Utilities for creating ASN.1 submissions
 *
@@ -39,339 +39,6 @@
 * -------  ----------  -----------------------------------------------------
 *
 *
-* $Log: subutil.c,v $
-* Revision 6.71  2007/06/26 15:50:57  kans
-* cleanup GO: and GO_REF: prefixes on go id or go ref
-*
-* Revision 6.70  2007/06/08 14:48:46  kans
-* AddToGeneOntologyUserObject adds goref argument
-*
-* Revision 6.69  2007/05/07 13:28:35  kans
-* added casts for Seq-data.gap (SeqDataPtr, SeqGapPtr, ByteStorePtr)
-*
-* Revision 6.68  2007/04/05 19:14:13  bollin
-* Added function for adding a Pnt location to another location without creating
-* an intermediate SeqFeat.
-*
-* Revision 6.67  2006/09/22 15:00:56  kans
-* removed NCBI from StructuredCommentPrefix/Suffix
-*
-* Revision 6.66  2006/09/18 18:40:30  kans
-* special symbols for structured comment prefix, suffix, for parsing flatfile
-*
-* Revision 6.65  2006/07/13 17:06:39  bollin
-* use Uint4 instead of Uint2 for itemID values
-* removed unused variables
-* resolved compiler warnings
-*
-* Revision 6.64  2006/05/05 19:49:40  kans
-* added StructuredComment user object creation functions
-*
-* Revision 6.63  2006/03/23 19:35:55  kans
-* expand keywords with semicolons in AddGenBankBlockToEntry, not BSEC - already done in ParseTitleIntoGenBank
-*
-* Revision 6.62  2006/02/06 19:00:15  kans
-* added CreateFeatureFetchPolicyUserObject
-*
-* Revision 6.61  2006/01/23 20:57:04  kans
-* cosmetic change
-*
-* Revision 6.60  2006/01/23 16:39:57  kans
-* added CreateAnnotDescCommentPolicyUserObject
-*
-* Revision 6.59  2006/01/17 20:47:05  kans
-* fixed AddIDsToGenomeProjectsDBUserObject
-*
-* Revision 6.58  2006/01/17 18:25:06  kans
-* support for genomeprojectsdb user object
-*
-* Revision 6.57  2005/10/26 21:30:46  kans
-* bug fix in AddSecondaryAccnToEntry provided by Joe Carlson
-*
-* Revision 6.56  2005/03/30 21:13:49  bollin
-* added function AddIntToSeqLoc
-*
-* Revision 6.55  2003/10/16 17:16:33  mjohnson
-*
-* Added ORG_* and IS_ORG_* defines for origins. Use these constants
-* and macros instead of small integers.
-*
-* Revision 6.54  2003/10/08 16:46:44  kans
-* fix in AddCompleteness (KT)
-*
-* Revision 6.53  2003/07/11 18:22:45  kans
-* AddSourceToRefGeneTrackUserObject
-*
-* Revision 6.52  2002/11/05 17:01:55  kans
-* refgene tracking user object uses comment as name if accession is empty
-*
-* Revision 6.51  2002/09/30 16:31:36  kans
-* support for new BioseqseqSet_class_wgs_set
-*
-* Revision 6.50  2002/07/10 14:36:29  kans
-* fixed TpaAssembly user object - from and to were being placed at wrong level
-*
-* Revision 6.49  2002/07/09 16:25:45  kans
-* if from and to are 0, do not add those fields to TPA user object
-*
-* Revision 6.48  2002/07/09 16:17:35  kans
-* AddAccessionToTpaAssemblyUserObject takes from and to parameters
-*
-* Revision 6.47  2002/06/04 14:40:29  kans
-* added AddPntToSeqFeat
-*
-* Revision 6.46  2002/03/27 19:26:31  kans
-* AddToGeneOntologyUserObject takes string for GO id to keep leading zeroes
-*
-* Revision 6.45  2001/12/11 16:50:41  kans
-* added TpaAssembly user object creation functions
-*
-* Revision 6.44  2001/11/09 19:51:42  kans
-* fix in FindModelEvidenceField
-*
-* Revision 6.43  2001/11/09 15:12:21  kans
-* moved collaborator to separate function per user object
-*
-* Revision 6.42  2001/11/09 13:21:08  kans
-* added collaborator field to reftrack user object
-*
-* Revision 6.41  2001/11/09 12:54:47  kans
-* added model evidence user object functions
-*
-* Revision 6.40  2001/10/12 21:55:20  kans
-* convert nucleotide X to N
-*
-* Revision 6.39  2001/07/30 19:54:14  kans
-* forgot to set dbt->db to taxon
-*
-* Revision 6.38  2001/07/29 16:23:58  kans
-* added AddOrganismToEntryEx to allow entry of taxonID
-*
-* Revision 6.37  2001/02/14 23:58:42  kans
-* handle BioseqseqSet_class_eco_set
-*
-* Revision 6.36  2001/01/25 19:55:13  kans
-* added AddGenBankSetToSubmission for patents and other bulk submissions of unrelated sequences
-*
-* Revision 6.35  2000/11/15 23:17:59  kans
-* gene ontology user object functions
-*
-* Revision 6.34  2000/09/25 23:19:52  kans
-* mrna prot link user object now uses fasta long on the single best id, preferring refseq
-*
-* Revision 6.33  2000/09/20 12:32:53  kans
-* removed AddMethodToRefGeneTrackUserObject and AddSupportToRefGeneTrackUserObject
-*
-* Revision 6.32  2000/08/29 22:27:01  kans
-* reftrack support now has organism field
-*
-* Revision 6.31  2000/07/21 11:08:00  kans
-* place method after status and above accession or support user object fields
-*
-* Revision 6.30  2000/07/21 10:54:13  kans
-* added functions for adding Method and Support to RefGeneTrack user object
-*
-* Revision 6.29  2000/03/14 13:33:32  kans
-* NCBISubValidate sets indexing, adds AppProperty to shut off specific messages to be decided later
-*
-* Revision 6.28  2000/03/10 18:35:45  kans
-* added CreateContigCloneUserObject for genome contig RefSeq records
-*
-* Revision 6.27  2000/02/28 19:02:57  kans
-* AddSecondaryAccnToEntry does not need submission parameter set
-*
-* Revision 6.26  2000/02/28 18:46:12  kans
-* fixes for add phrap to seqlit
-*
-* Revision 6.25  2000/02/26 23:55:33  kans
-* added AddPhrapGraphToSeqLit, using internal extended SeqLit to track, readjust graphs to current position of seqlit in delta seq - may need to move fields to public SeqLit if problems arise
-*
-* Revision 6.24  2000/02/24 23:15:00  kans
-* added AddSecondaryAccnToEntry
-*
-* Revision 6.23  2000/02/23 19:25:53  kans
-* AddFakeGapToDeltaSeq returns SeqLitPtr so program can set fuzz after SpreadGapsInDeltaSeq is no longer being called
-*
-* Revision 6.22  2000/02/23 18:28:38  kans
-* added AddFakeGapToDeltaSeq to set fuzz even if nonzero length is passed in
-*
-* Revision 6.21  2000/02/07 16:48:07  ostell
-* added AddDeltaSeqToNucProtEntry()
-*
-* Revision 6.20  1999/12/23 17:26:29  kans
-* free old reftrack status string if replacing
-*
-* Revision 6.19  1999/12/20 20:35:12  kans
-* fixed problem with add refseq status field
-*
-* Revision 6.18  1999/12/20 19:57:44  kans
-* added AddStatusToRefGeneTrackUserObject
-*
-* Revision 6.17  1999/12/08 20:00:14  kans
-* AddOrgModToEntry calls OrgNameNew if necessary
-*
-* Revision 6.16  1999/10/05 17:24:54  kans
-* SeqDescrNew and SeqDescrAdd for new descriptors
-*
-* Revision 6.15  1999/08/05 20:43:44  kans
-* added CreateSubmissionUserObject (JP)
-*
-* Revision 6.14  1998/12/09 20:38:25  kans
-* changed compl to compr to avoid new c++ symbol collision
-*
-* Revision 6.13  1998/10/02 17:48:11  kans
-* new parameters to AddAccessionToRefGeneTrackUserObject, and added CreateMrnaProteinLinkUserObject
-*
-* Revision 6.12  1998/09/23 16:41:48  kans
-* removed from and to from AddAccessionToRefGeneTrackUserObject
-*
-* Revision 6.11  1998/08/20 20:36:58  kans
-* add comment parameter to reftrack user object function
-*
-* Revision 6.10  1998/08/11 22:27:25  kans
-* added CreateRefGeneTrackUserObject and AddAccessionToRefGeneTrackUserObject
-*
-* Revision 6.9  1998/05/27 20:42:05  kans
-* default hup is one year from the end of current month
-*
-* Revision 6.8  1998/03/02 17:19:15  kans
-* changed SixMonthsFromToday to DateAdvance
-*
-* Revision 6.7  1998/03/02 17:13:46  shavirin
-* ... and in the case when hold_until_publish == TRUE
-*
-* Revision 6.6  1998/03/02 17:08:39  shavirin
-* Added SixMonthsFromToday(NULL); in NCBISubCreate()
-*
-* Revision 6.5  1998/02/05 19:19:25  kans
-* added AddPhrapGraph
-*
-* Revision 6.4  1998/01/09 20:16:47  shavirin
-* Removed creation of Imprint in CitArtBuild () and CitSubUpdateBuild()
-*
-* Revision 6.3  1998/01/06 03:29:46  ostell
-* added AddGeneticCodetoEntry()
-*
-* Revision 6.2  1997/12/15 17:31:43  kans
-* backed out accidental checkin
-*
-* Revision 6.0  1997/08/25 18:07:35  madden
-* Revision changed to 6.0
-*
-* Revision 5.19  1997/08/19 17:15:11  kans
-* included utilpars.h
-*
-* Revision 5.18  1997/08/19 16:51:52  tatiana
-* added ValidAminoAcid() to MakeRNAFeature
-*
-* Revision 5.17  1997/07/11 18:23:24  kans
-* added Add[Pop/Phy/Mut]SetToSubmission
-*
-* Revision 5.16  1997/06/19 18:39:09  vakatov
-* [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
-*
-* Revision 5.15  1997/05/16 19:13:57  ostell
-* moved prototype of NewDescrOnSeqEntry from subutil.c to subutil.h to make
-* it external.
-*
- * Revision 5.14  1996/09/05  20:20:28  ostell
- * added CitSubUpdateBuild()
- *
- * Revision 5.13  1996/09/04  22:33:06  ostell
- * added MakeCommentFeature()
- *
- * Revision 5.12  1996/08/30  13:17:01  ostell
- * made accession check allow 2+6 form
- *
- * Revision 5.11  1996/08/20  15:32:10  tatiana
- * static removed from AddBasesToByteStore and AddAAsToByteStore
- *
- * Revision 5.10  1996/08/15  20:29:19  ostell
- * in MaketRNAFeature() added support for 'U' in codon and for 'R'and 'Y' as
- * wobble bases
- *
- * Revision 5.9  1996/07/19  22:13:13  ostell
- * added SpreadGapsInDeltaSeq()
- *
- * Revision 5.8  1996/06/18  01:21:56  ostell
- * removed the step of adding exp-ev qualifier as well as etting flag in feat
- *
- * Revision 5.7  1996/06/14  19:01:54  ostell
- * minor fixes
- *
- * Revision 5.6  1996/06/14  19:00:06  ostell
- * fixed line wraps
- *
- * Revision 5.5  1996/06/14  18:07:38  ostell
- * added AddOrgModToEntry() and AddSubSourceToEntry()
- *
- * Revision 5.4  1996/06/14  17:14:55  ostell
- * fixed make of Dbtag
- *
- * Revision 5.3  1996/06/14  14:11:46  kans
- * fixed proper uninitialized seqlit variable (JO)
- *
- * Revision 5.2  1996/06/14  00:13:35  ostell
- * fixed unitnitialized variable
- *
- * Revision 5.1  1996/06/13  03:34:53  ostell
- * added support for delta seqs and submittor_key
- * fixed memory leak in AddAminoAcidsToBioseq()
- *
- * Revision 5.0  1996/05/28  13:23:23  ostell
- * Set to revision 5.0
- *
- * Revision 4.9  1996/03/12  13:48:41  ostell
- * added a cast
- *
- * Revision 4.8  1996/03/05  17:05:25  tatiana
- * change in NCBISubNewBioseq, moltype goes to MolInfo
- * ,
- *
- * Revision 4.7  1996/02/01  18:12:42  ostell
- * added curley braces to make gcc happy
- *
- * Revision 4.6  1996/01/31  02:35:00  ostell
- * added AddCodeBreakToCdRegion() and AddAntiCodonTotRNA()
- *
- * Revision 4.5  1995/10/05  14:48:29  tatiana
- * error msg added "Illegal character in Bioseq"
- *
- * Revision 4.4  1995/09/28  17:30:41  kans
- * added static to GetDNAConv and GetProteinConv
- *
- * Revision 4.3  1995/09/28  16:28:54  tatiana
- * a bug fixed in AddBasesToBioseq()
- *
- * Revision 4.2  1995/09/27  19:50:39  tatiana
- * check for illegal residues added
- *
- * Revision 4.1  1995/08/31  20:49:57  tatiana
- * strain length is set to 70 not to exeed the buffer length
- *
- * Revision 4.0  1995/07/26  13:49:01  ostell
- * force revision to 4.0
- *
- * Revision 1.20  1995/07/25  14:47:09  tatiana
- * remove static
- *
- * Revision 1.19  1995/07/20  19:37:31  tatiana
- * change SeqIdprint to SeqIdWrite
- *
- * Revision 1.18  1995/07/20  17:48:27  kans
- * removed static on AddModifierToEntry and AddPubToEntry
- *
- * Revision 1.17  1995/07/14  18:33:34  kans
- * added statics to functions, removed unused variables
- *
- * Revision 1.16  1995/07/14  18:08:43  tatiana
- * BioSource added
- *
- * Revision 1.11  1995/05/15  21:46:05  ostell
- * added Log line
- *
-*
-*
 * ==========================================================================
 */
 
@@ -4551,6 +4218,43 @@ NLM_EXTERN void AddStatusToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr st
   curr->data.ptrvalue = (Pointer) StringSave (status);
 }
 
+NLM_EXTERN void AddGeneratedToRefGeneTrackUserObject (UserObjectPtr uop, Boolean generated)
+
+{
+  UserFieldPtr  curr;
+  ObjectIdPtr   oip;
+  UserFieldPtr  prev = NULL;
+
+  if (uop == NULL) return;
+  oip = uop->type;
+  if (oip == NULL || StringICmp (oip->str, "RefGeneTracking") != 0) return;
+
+  for (curr = uop->data; curr != NULL; curr = curr->next) {
+    oip = curr->label;
+    if (oip != NULL && StringICmp (oip->str, "Generated") == 0) {
+      break;
+    }
+    prev = curr;
+  }
+
+  if (curr == NULL) {
+    curr = UserFieldNew ();
+    oip = ObjectIdNew ();
+    oip->str = StringSave ("Generated");
+    curr->label = oip;
+    curr->choice = 4; /* boolean */
+    curr->data.boolvalue = generated;
+
+    /* link source at end of list */
+
+    if (prev != NULL) {
+      prev->next = curr;
+    } else {
+      uop->data = curr;
+    }
+  }
+}
+
 NLM_EXTERN void AddCuratorToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr collaborator)
 
 {
@@ -4640,10 +4344,8 @@ NLM_EXTERN void AddSourceToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr ge
 }
 
 NLM_EXTERN void AddAccessionToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr field,
-                                                      CharPtr accn, Int4 gi,
-                                                      Boolean sequenceChange,
-                                                      Boolean annotationChange,
-                                                      CharPtr comment)
+                                                      CharPtr accn, Int4 gi, Int4 from,
+                                                      Int4 to, CharPtr comment)
 
 {
   UserFieldPtr  curr;
@@ -4731,28 +4433,6 @@ NLM_EXTERN void AddAccessionToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr
     last = ufp;
   }
 
-  if (sequenceChange) {
-    ufp = UserFieldNew ();
-    oip = ObjectIdNew ();
-    oip->str = StringSave ("sequenceChange");
-    ufp->label = oip;
-    ufp->choice = 4; /* Boolean */
-    ufp->data.boolvalue = sequenceChange;
-    last->next = ufp;
-    last = ufp;
-  }
-
-  if (annotationChange) {
-    ufp = UserFieldNew ();
-    oip = ObjectIdNew ();
-    oip->str = StringSave ("annotationChange");
-    ufp->label = oip;
-    ufp->choice = 4; /* Boolean */
-    ufp->data.boolvalue = annotationChange;
-    last->next = ufp;
-    last = ufp;
-  }
-
   if (comment != NULL && *comment != '\0') {
     ufp = UserFieldNew ();
     oip = ObjectIdNew ();
@@ -4763,6 +4443,27 @@ NLM_EXTERN void AddAccessionToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr
     last->next = ufp;
     last = ufp;
   }
+
+  if (from == 0 && to == 0) return;
+  oip = curr->label;
+  if (oip == NULL || StringICmp (oip->str, "Assembly") != 0) return;
+
+  ufp = UserFieldNew ();
+  oip = ObjectIdNew ();
+  oip->str = StringSave ("from");
+  ufp->label = oip;
+  ufp->choice = 2; /* integer */
+  ufp->data.intvalue = from;
+  last->next = ufp;
+  last = ufp;
+
+  ufp = UserFieldNew ();
+  oip = ObjectIdNew ();
+  oip->str = StringSave ("to");
+  ufp->label = oip;
+  ufp->choice = 2; /* integer */
+  ufp->data.intvalue = to;
+  last->next = ufp;
 }
 
 NLM_EXTERN UserObjectPtr CreateMrnaProteinLinkUserObject (BioseqPtr bsp)
diff --git a/api/subutil.h b/api/subutil.h
index e593ef95..cfc2debc 100644
--- a/api/subutil.h
+++ b/api/subutil.h
@@ -31,7 +31,7 @@
 *   
 * Version Creation Date: 11/3/93
 *
-* $Revision: 6.61 $
+* $Revision: 6.64 $
 *
 * File Description: Utilities for creating ASN.1 submissions
 *
@@ -42,6 +42,15 @@
 *
 *
 * $Log: subutil.h,v $
+* Revision 6.64  2007/11/28 21:47:58  kans
+* added defines for mip->biomol ncRNA and tmRNA
+*
+* Revision 6.63  2007/11/08 16:43:18  kans
+* added chromosome and chromatophore to BioSource.genome defines
+*
+* Revision 6.62  2007/10/11 21:57:44  kans
+* added AddGeneratedToRefGeneTrackUserObject, changed AddAccessionToRefGeneTrackUserObject
+*
 * Revision 6.61  2007/07/17 14:46:42  kans
 * added support for metagenome_source orgmod
 *
@@ -703,6 +712,8 @@ NLM_EXTERN SeqLitPtr AddLiteralToDeltaSeq (
 #define MOLECULE_TYPE_CRNA 11
 #define MOLECULE_TYPE_SNORNA 12
 #define MOLECULE_TYPE_TRANSCRIBED_RNA 13
+#define MOLECULE_TYPE_NCRNA 14
+#define MOLECULE_TYPE_TMRNA 15
 
 #define TOPOLOGY_LINEAR 1
 #define TOPOLOGY_CIRCULAR 2
@@ -876,6 +887,8 @@ NLM_EXTERN Boolean AddGenBankBlockToEntry (
 #define GENOME_proplastid 18
 #define GENOME_endogenous_virus 19
 #define GENOME_hydrogenosome 20
+#define GENOME_chromosome 21
+#define GENOME_chromatophore 22
 
 /********************************************
 *  Genome describes the type of genome from which the DNA or gene for
@@ -1664,13 +1677,12 @@ NLM_EXTERN Boolean AddPhrapGraphToSeqLit (
 /* internal functions for reference gene project */
 NLM_EXTERN UserObjectPtr CreateRefGeneTrackUserObject (void);
 NLM_EXTERN void AddStatusToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr status);
+NLM_EXTERN void AddGeneratedToRefGeneTrackUserObject (UserObjectPtr uop, Boolean generated);
 NLM_EXTERN void AddCuratorToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr collaborator);
 NLM_EXTERN void AddSourceToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr genomicSource);
 NLM_EXTERN void AddAccessionToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr field,
-                                                      CharPtr accn, Int4 gi,
-                                                      Boolean sequenceChange,
-                                                      Boolean annotationChange,
-                                                      CharPtr comment);
+                                                      CharPtr accn, Int4 gi, Int4 from,
+                                                      Int4 to, CharPtr comment);
 
 /* experimental function to associate mRNA with protein product in cases of alt splicing */
 NLM_EXTERN UserObjectPtr CreateMrnaProteinLinkUserObject (BioseqPtr protbsp);
diff --git a/api/tofasta.c b/api/tofasta.c
index ac5dcfeb..8eb545d0 100644
--- a/api/tofasta.c
+++ b/api/tofasta.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/12/91
 *
-* $Revision: 6.159 $
+* $Revision: 6.165 $
 *
 * File Description:  various sequence objects to fasta output
 *
@@ -38,703 +38,6 @@
 * Date	   Name        Description of modification
 * -------  ----------  -----------------------------------------------------
 *
-* $Log: tofasta.c,v $
-* Revision 6.159  2007/08/14 13:08:17  bollin
-* Corrected bug - not allocating enough memory for plasmid phrase in
-* auto-generated definition line.
-*
-* Revision 6.158  2007/06/12 15:23:36  kans
-* UseOrgMods takes tech argument, adds plasmid if wgs
-*
-* Revision 6.157  2007/05/07 13:28:35  kans
-* added casts for Seq-data.gap (SeqDataPtr, SeqGapPtr, ByteStorePtr)
-*
-* Revision 6.156  2007/04/12 21:23:49  kans
-* BioseqFastaStreamInternalEx removes > characters from FASTA defline - should only occur at start of line before seq-id
-*
-* Revision 6.155  2007/01/29 17:20:46  bollin
-* Added Ex methods to allow substitution of nucleotide sequence ID when exporting
-* protein FASTA.
-*
-* Revision 6.154  2006/11/16 22:05:34  kans
-* StrainNotAtEndOfTaxname now checks for strain in single quotes at end of orgname
-*
-* Revision 6.153  2006/07/13 17:06:39  bollin
-* use Uint4 instead of Uint2 for itemID values
-* removed unused variables
-* resolved compiler warnings
-*
-* Revision 6.152  2006/03/29 16:04:47  kans
-* in AddNcTitles, do not clear mip->completeness - cannot determine why this was done in the past
-*
-* Revision 6.151  2006/03/08 21:29:47  kans
-* FindNMDefLine calls ReplaceFlyDashPwithDashR if Drosophila melanogaster curated RefSeq
-*
-* Revision 6.150  2006/01/10 22:19:29  kans
-* CreateDefLine calls DoTpaPrefix to handle TPA_exp and TPA_inf
-*
-* Revision 6.149  2005/12/07 19:49:46  kans
-* in BioseqFastaStreamInternal, bail if virtual Bioseq
-*
-* Revision 6.148  2005/09/12 17:44:21  kans
-* in complete chromosome title, use virus instead of virion
-*
-* Revision 6.147  2005/07/15 19:01:37  kans
-* minor fixes for Xcode warnings
-*
-* Revision 6.146  2005/07/13 20:58:27  kans
-* FindNMDefLine looks for isoform in refseq record, changes to transcript variant for mrna title
-*
-* Revision 6.145  2005/06/15 20:26:13  dondosha
-* In FastaReadSequenceChunk, check for lines starting with comment characters # or !
-*
-* Revision 6.144  2005/06/01 18:03:27  camacho
-* Augmented FASTA_BUFFER_LEN by a factor of 4
-*
-* Revision 6.143  2005/05/23 15:44:37  dondosha
-* Skip empty lines in FastaReadSequenceChunk, also fixing a bug when one line is exactly 4096 characters long
-*
-* Revision 6.142  2005/04/27 14:30:33  kans
-* gpipe was making TPA defline, moved to its own case
-*
-* Revision 6.141  2005/04/26 21:33:52  kans
-* added SEQID_GPIPE
-*
-* Revision 6.140  2005/03/21 22:15:09  kans
-* added SeqLocFastaStream
-*
-* Revision 6.139  2004/10/22 19:56:45  kans
-* UseOrgMods has strain before chromosome and other qualifiers
-*
-* Revision 6.138  2004/10/14 19:36:34  kans
-* CreateDefLineExEx has extProtTitle argument, normally only use first protein name in defline
-*
-* Revision 6.137  2004/09/29 17:29:49  kans
-* FastaReadSequenceChunk checks return result of fgets, nulls out sequence [1] if failed
-*
-* Revision 6.136  2004/09/24 20:09:40  bollin
-* use best SeqID instead of first SeqID when exporting FASTA
-*
-* Revision 6.135  2004/07/23 20:55:52  kans
-* added BioseqFastaMemStream that takes byte store instead of file pointer
-*
-* Revision 6.134  2004/07/16 19:37:37  kans
-* SeqPortStream and FastaStream functions return Int4, negative count if any fetch failures
-*
-* Revision 6.133  2004/06/02 20:11:14  kans
-* In SeqEntryToFasta, if defline is >?unk100, make special local ID, recognized by tbl2asn
-*
-* Revision 6.132  2004/05/07 20:55:54  kans
-* MakeCompleteChromTitle handles organelles with multiple chromosomes, e.g., Guillardia theta nucleomorph
-*
-* Revision 6.131  2004/05/03 15:32:07  kans
-* BioseqFastaStream uses larger buffer for seqid because some RefSeqs use more than 41 characters for FASTA_LONG
-*
-* Revision 6.130  2004/04/21 14:42:36  kans
-* added blocklen and grouplen parameters to BioseqFastaStream and SeqEntryFastaStream, former also has do_defline parameter
-*
-* Revision 6.129  2004/04/20 20:38:03  kans
-* SimpleSegSeqTitle puts strain, clone, or isolate after organism name if no cds product present
-*
-* Revision 6.128  2004/04/06 14:03:32  bollin
-* use "extrachromosomal" instead of "extrachrom" in NC titles generated by
-* Special->Defline->NC_Cleanup
-*
-* Revision 6.127  2004/03/16 17:28:09  kans
-*  BioseqFastaStream indexes features if no title to speed up creation
-*
-* Revision 6.126  2004/03/15 19:56:09  kans
-* BioseqFastaStream takes StreamFlgType flags parameter, added SeqEntryFastaStream for exploration
-*
-* Revision 6.125  2004/01/21 19:22:14  kans
-* UseOrgMods capitalizes first letter of created defline
-*
-* Revision 6.124  2003/12/23 20:58:51  kans
-* ProtDefLine takes prp->activity if prp->name and prp->desc are not set
-*
-* Revision 6.123  2003/11/18 19:04:29  kans
-* added BioseqFastaStream, rapid generator based on SeqPortStream
-*
-* Revision 6.122  2003/11/05 19:24:55  kans
-* BioseqToFastaX checks for virtual with do_virtual not set, prints a single dash as the sequence
-*
-* Revision 6.121  2003/08/04 19:51:02  kans
-* for complete chromosome title, if > 3 clones (by counting semicolons) then just display count, not full text of clones
-*
-* Revision 6.120  2003/07/25 16:15:25  kans
-* FindProtDefLine of hypothetical protein only needs to look for locus_tag
-*
-* Revision 6.119  2003/07/25 15:34:07  kans
-* protect FindProtDefLine against no parent CDS (e.g., SWISS-PROT segmented record P33072)
-*
-* Revision 6.118  2003/07/24 21:51:04  kans
-* if hypothetical protein, find gene and add to name
-*
-* Revision 6.117  2003/07/23 20:37:02  kans
-* if making htgs title, do not set iip values
-*
-* Revision 6.116  2003/07/22 18:31:44  kans
-* Added support for EMBLBlockPtr keywords in addition to GBBlockPtr keywords in suppressing sequencing in progress message
-*
-* Revision 6.115  2003/05/02 16:22:24  kans
-* added FindNRDefLine to make NR_ deflines on the fly
-*
-* Revision 6.114  2003/03/25 17:00:53  kans
-* CreateDefLine htgs suffix only shows if delta seq with more than 0 gaps
-*
-* Revision 6.113  2003/01/17 21:26:28  kans
-* because getc fails in OS_UNIX_DARWIN, NLM_GETC used to choose between fgetc or getc
-*
-* Revision 6.112  2002/11/27 18:58:46  kans
-* FindProtDefLine, called from CreateDefLineEx, adds unnamed protein product as last resort
-*
-* Revision 6.111  2002/11/14 16:20:26  kans
-* added FindNMDefLine for default NM_ defline if no title instantiated
-*
-* Revision 6.110  2002/08/22 17:33:39  madden
-* Print range on FASTA output if only partial sequence written
-*
-* Revision 6.109  2002/07/18 19:28:35  kans
-*  working implementation of BioseqRawToFastaExtraEx, always zero out all of MyFsa struct, no need for fake seqloc
-*
-* Revision 6.107  2002/07/15 21:18:49  camacho
-* Fixed problem with revision 6.105
-*
-* Revision 6.105  2002/07/14 21:04:32  camacho
-* Added option to print a subsequence of a raw bioseq to fasta format
-*
-* Revision 6.104  2002/07/02 20:57:38  kimelman
-* GatherDescrOnBioseq: added parameter if only the first one required
-*
-* Revision 6.103  2002/06/19 13:56:25  kans
-* htgs_cancelled keyword suppresses sequencing in progress phrase in defline
-*
-* Revision 6.102  2002/05/28 19:02:53  dondosha
-* Correction to change in MakeTrustedID in revision 6.96
-*
-* Revision 6.101  2002/05/13 17:32:40  kans
-* restored complete sequence on phase 3
-*
-* Revision 6.100  2002/04/26 13:58:25  kans
-* phase 3 should not say complete sequence
-*
-* Revision 6.99  2002/04/25 20:34:08  kans
-* segments or pieces = CountGapsInDeltaSeq numgaps + 1, not numsegs - numgaps
-*
-* Revision 6.98  2002/04/24 18:47:21  kans
-* if >? construct, set is_gap variable, do not call FastaReadSequenceInternalEx, which overrides bsp->length
-*
-* Revision 6.97  2002/04/01 15:34:47  kans
-* changes for WGS master, individual deflines
-*
-* Revision 6.96  2002/03/11 21:21:35  dondosha
-* Change in MakeTrustedID: make use of the prefix argument
-*
-* Revision 6.95  2002/02/26 21:35:02  kans
-* UseOrgMods calls StrainNotAtEndOfTaxname
-*
-* Revision 6.94  2002/02/21 17:06:47  kans
-* CreateDefLineEx handles MI_TECH_wgs
-*
-* Revision 6.93  2002/01/16 17:02:04  camacho
-* Changed buflen and seqlen in MyFsa struct. to use Uint4, as well as some function prototypes
-*
-* Revision 6.92  2001/12/05 18:18:32  kans
-* for protein defline organism, check stop list before looking for overlapping source feature of parent CDS
-*
-* Revision 6.91  2001/10/12 21:55:21  kans
-* convert nucleotide X to N
-*
-* Revision 6.90  2001/10/09 15:28:04  kans
-* CreateDefLine adds TPA: prefix if third-party annotation record
-*
-* Revision 6.89  2001/08/31 15:29:53  kans
-* added CreateDefLineEx to ignore existing title descriptor, force generation of protein title computationally
-*
-* Revision 6.88  2001/08/17 13:56:18  kans
-* clear proteins only in NPS
-*
-* Revision 6.87  2001/08/17 13:27:26  kans
-* ClearProteinTitlesInNucProts, do not do it for outside protein databases
-*
-* Revision 6.86  2001/08/16 18:38:09  kans
-* ClearProtTitlesProc checks for ISA_aa (bsp->mol)
-*
-* Revision 6.85  2001/08/07 17:22:52  kans
-* added support for third party annotation SeqIDs
-*
-* Revision 6.84  2001/08/06 22:13:12  kans
-* using NUM_SEQID, added TPA ids to arrays
-*
-* Revision 6.83  2001/07/29 16:57:16  kans
-* MakeCompleteChromTitle adds the word segment unless it or DNA or RNA is in the ssp->name - additional logic may be desired later
-*
-* Revision 6.82  2001/06/25 23:47:47  kans
-* added InstantiateProteinTitles and ClearProteinTitles
-*
-* Revision 6.81  2001/06/08 14:41:35  kans
-* FindProtDefLine sees if features are indexed, and if so never calls the old gather-based functions if the indexed function returns NULL
-*
-* Revision 6.80  2001/04/18 22:07:41  kans
-* initialized mfa.printid_general in SeqEntrysToDefline
-*
-* Revision 6.79  2001/04/18 21:17:21  madden
-* set printid_general to fix umr in BioseqRawToFastaExtra
-*
-* Revision 6.78  2001/02/27 21:52:37  madden
-* Added BioseqToFastaDump and FastaDumpFileFunc for dumping BLAST db in FASTA
-*
-* Revision 6.77  2001/01/31 23:08:08  dondosha
-* Allow tab as well as space to be a separator between id and description
-*
-* Revision 6.76  2000/12/01 00:17:04  kans
-* MakeCompleteChromTitle uses completeness flag to say complete or partial sequence, complete genome or just genome
-*
-* Revision 6.75  2000/10/27 20:15:04  shavirin
-* Changed creation of Protein SeqIds to MT-safe function.
-*
-* Revision 6.74  2000/10/12 16:03:57  kans
-* added SeqEntryToFastaEx, printid_general field to MyFsa structure, to support processing software that requires gnl ID in FASTA defline even in the presence of higher-priority ref ID
-*
-* Revision 6.73  2000/07/20 17:48:58  dondosha
-* Added function FastaToSeqBuffForDb analogous to FastaToSeqEntryForDb
-*
-* Revision 6.72  2000/07/12 16:22:43  madden
-* Fixed problem with reading FASTA definition lines
-*
-* Revision 6.71  2000/06/23 13:25:18  madden
-* Fix for comment lines
-*
-* Revision 6.70  2000/06/19 21:22:52  kans
-* FastaReadSequenceChunk looks for null byte to limit length, otherwise can be fooled by text pasted in from web with no newline at end
-*
-* Revision 6.69  2000/06/14 19:07:48  kans
-* chrom defline generator now handles the new SUBSRC_segment
-*
-* Revision 6.68  2000/06/14 14:50:11  madden
-* Fix for multiple line returns between sequences
-*
-* Revision 6.67  2000/05/31 20:13:23  madden
-* More replacement of getc with fgets
-*
-* Revision 6.66  2000/05/30 19:44:44  ostell
-* added FastaSeqLineEx() with another parameter, do_virtual
-*
-* Revision 6.65  2000/05/25 16:53:31  kans
-* FastaToSeqEntryInternalExEx and MakeTrustedID called by FastaToSeqEntryForDb to delay seqid indexing
-*
-* Revision 6.64  2000/05/23 21:11:13  madden
-* use fgets in place of getc
-*
-* Revision 6.63  2000/05/19 15:18:04  kans
-* parsing of >? now skips white space before scanning size, so can handle >?# and >? #
-*
-* Revision 6.62  2000/05/16 15:12:50  kans
-* moved SeqMgrAddToBioseqIndex call after assignment of bsp->id
-*
-* Revision 6.61  2000/04/28 20:10:44  kans
-* if organism has virus in name, and /virion or /proviral, do not add organelle to NC_ defline
-*
-* Revision 6.60  2000/04/27 15:30:26  kans
-* changed proviral to provirus if NC_ and not plasmid
-*
-* Revision 6.59  2000/04/26 21:27:30  kans
-* more changes to genome defline, cleanup of its code
-*
-* Revision 6.58  2000/04/22 00:13:48  kans
-* nc_ genome titles handles genomic or other_genetic (usually plasmids), and lower cases any Plasmid or Element text in the defline (JK and TW)
-*
-* Revision 6.57  2000/04/04 17:02:44  kans
-* cleanup keywords is now also part of NC_Cleanup
-*
-* Revision 6.56  2000/04/03 22:09:26  kans
-* added ClearGenBankKeywords for RefSeq processing
-*
-* Revision 6.55  2000/03/29 22:00:23  kans
-* added NC_Cleanup function used internally for genome RefSeq processing
-*
-* Revision 6.54  2000/03/22 13:08:27  madden
-* Enlarged buffer for definition lines
-*
-* Revision 6.53  2000/03/10 17:07:41  kans
-* do not read dash into sequence (SW)
-*
-* Revision 6.52  2000/03/02 18:13:48  kans
-* improvements to complete chromosome defline
-*
-* Revision 6.51  2000/03/01 19:09:33  shavirin
-* Added parameter SeqIdPtr into function FastaReadSequenceInternalEx().
-*
-* Revision 6.50  2000/02/28 16:04:05  kans
-* After CreateDefLine calls FindProtDefLine, if the organism parameter is NULL it does an indexed search for BioSource, using the results to set organism - this will simplify production of BLAST deflines
-*
-* Revision 6.49  2000/02/17 17:20:57  sicotte
-* Add Reading of Lowercase Characters as SeqLoc for inputting masking informatioin. Use FastaToSeqEntryForDb or FastaToSeqEntryInternalEx
-*
-* Revision 6.48  2000/02/04 16:38:28  kans
-* added FastaToSeqEntryForDb and FastaToSeqEntryInternalEx, giving control over generation of unique SeqID
-*
-* Revision 6.47  2000/02/01 23:22:48  kans
-* indexed get descr now copies values to iip if not NULL
-*
-* Revision 6.46  2000/02/01 19:43:39  kans
-* FindProtDefLine calls indexed explore functions first to avoid multiple targeted gathers
-*
-* Revision 6.45  2000/01/16 19:08:55  kans
-* MakeCompleteChromTitle handles plasmids, does not need completedness flag set, does not override existing title descriptor in CreateDefLine
-*
-* Revision 6.44  1999/12/15 19:15:33  kans
-* FindProtDefLine now handles gene xrefs, initializes diff_lowest to INT4_MAX so SeqLocAinB test works
-*
-* Revision 6.43  1999/12/14 21:47:02  kans
-* FindProtDefLine already did gene product with grp->locus, now cascades down to first synonym, then description
-*
-* Revision 6.42  1999/11/30 20:58:56  kans
-* fasta read functions also report error for question mark in input data
-*
-* Revision 6.41  1999/10/30 00:38:53  kans
-* CreateDefLine says complete chromosome only for NC_ reference sequence, and say SEQUENCING IN PROGRESS unless HTGS_DRAFT keyword, in which case say WORKING DRAFT SEQUENCE
-*
-* Revision 6.40  1999/10/06 20:29:55  bazhin
-* Removed memory leak.
-*
-* Revision 6.39  1999/10/05 21:44:06  kans
-* CreateDefLine calls SimpleSegSeqTitle for bsp->repr == Seq_repr_seg if no title descriptor - more work to be done later
-*
-* Revision 6.38  1999/09/30 21:38:19  kans
-* create title valnode with SeqDescrNew
-*
-* Revision 6.37  1999/09/29 18:34:29  kans
-* fix to CreateDefLine to return title IDs unless actually using MolInfo
-*
-* Revision 6.36  1999/09/22 23:03:05  kans
-* changed wording of complete mitochondrial chromosome
-*
-* Revision 6.35  1999/09/22 22:36:11  kans
-* added MakeCompleteChromTitle so CreateDefLine generates standard title for complete chromosome
-*
-* Revision 6.34  1999/09/20 18:36:30  shavirin
-* Added function Int4 GetOrderBySeqId().
-*
-* Revision 6.33  1999/08/05 11:37:04  kans
-* allow # or ! as comment symbols
-*
-* Revision 6.32  1999/08/04 22:59:00  kans
-* FastaToSeqEntry ignores lines beginning with ! if read from file
-*
-* Revision 6.31  1999/04/07 12:49:06  ostell
-* made changes to rank RefSeq ids higher for BLAST deflines
-*
-* Revision 6.30  1999/03/22 19:15:02  ostell
-* forced generation of unfinished HTG deflines
-*
-* Revision 6.29  1999/03/16 13:42:27  ostell
-* corrected oversight in CreateDefLine so sometimes [organism] would be
-* dropped from protein deflines.
-*
-* Revision 6.28  1999/03/12 18:38:40  kans
-* fixed ErrPostEx cast
-*
-* Revision 6.27  1999/03/12 15:52:21  kans
-* changes to CreateDefLine for HTGS phrases (JO)
-*
-* Revision 6.26  1999/03/11 23:32:08  kans
-* sprintf casts
-*
-* Revision 6.25  1998/11/03 21:43:57  kans
-* call SeqMapTableConvert to map asterisk to appropriate alphabet - BLAST is using ncbistdaa, not ncbieaa or iupacaa
-*
-* Revision 6.24  1998/10/26 22:35:53  kans
-* filter out terminal asterisk in protein sequence
-*
-* Revision 6.23  1998/10/06 21:04:43  tatiana
-* a bug fixed in CreateDefline()
-*
-* Revision 6.22  1998/09/04 13:09:22  volodya
-* fix the memory bug and the memory leaks in CreateDefLine()
-*
-* Revision 6.21  1998/07/10 12:47:56  egorov
-* Sequence code bug fixed
-*
-* Revision 6.20  1998/07/07 18:43:06  egorov
-* Revert the BioseqToFastaX() to use FASTA_ID as it was before
-*
-* Revision 6.19  1998/03/19 21:14:29  kans
-* defline says map instead of from for map source qualifier
-*
-* Revision 6.18  1998/03/12 17:40:52  kans
-* added GSS to defline handling
-*
-* Revision 6.17  1998/02/25 20:06:30  kans
-* default deflines for est, sts records
-*
-* Revision 6.16  1998/02/23 16:51:24  egorov
-* Changes to make the tofasta.c independent on readdb.h
-*
-* Revision 6.15  1998/02/12 21:44:57  madden
-* Set code before callto BioseqToFastaX
-*
-* Revision 6.14  1998/02/11 20:36:40  tatiana
-* ABW error fixed
-*
-* Revision 6.13  1998/02/11 19:05:35  madden
-* Changes to allow formatdb to take ASN.1 as input
-*
-* Revision 6.12  1998/02/09 18:54:07  kans
-* MakeSeqID only in sqnutils, makes oid->id if numeric
-*
-* Revision 6.11  1998/01/27 20:28:08  madden
-* Added BioseqRawToFastaExtra with line_length arg
-*
-* Revision 6.10  1997/12/08 18:15:19  ostell
-* Hsiu-chuan sets tech value back to zero for repeated loading in HSP
-*
-* Revision 6.9  1997/12/02 19:04:45  shavirin
-* Fixed typecast warnings and removed unused functions
-*
-* Revision 6.8  1997/11/28 15:55:47  shavirin
-* Fixed some warnings. Removed redundant "*" and added function return type
-*
-* Revision 6.7  1997/11/14 15:49:47  tatiana
-* added pdbip protection in CreateDefline()
-*
-* Revision 6.6  1997/11/13 19:39:59  tatiana
-* *** empty log message ***
-*
-* Revision 6.5  1997/11/12 21:24:07  tatiana
-* PDB special case in CreateDefline
-*
-* Revision 6.4  1997/11/05 19:25:23  kans
-* special_symbol returned for &{}[]
-*
-* Revision 6.3  1997/11/03 20:46:54  shavirin
-* Removed memory leak
-*
-* Revision 6.2  1997/10/22 16:43:06  shavirin
-* Added new external functions FastaReadSequence() and FastaReadSequenceMem()
-*
-* Revision 6.1  1997/08/27 14:35:02  kans
-* fixed memory leak in FastaReadSequenceInternal where an error message buffer was allocated but no bad characters were found
-*
-* Revision 6.0  1997/08/25 18:07:44  madden
-* Revision changed to 6.0
-*
-* Revision 5.46  1997/06/20 19:13:34  kans
-* treat - as illegal character for errmsg
-*
-* Revision 5.45  1997/06/19 18:39:17  vakatov
-* [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
-*
-* Revision 5.44  1997/05/28 18:38:17  tatiana
-* a typo fixed in CreateDefLine
-*
-* Revision 5.43  1997/05/21 17:42:09  tatiana
-* fixed uninitialized iip in UseOrgMods
-*
-* Revision 5.42  1997/05/21 17:22:00  tatiana
-* CreateDefLine changed to take info from BioSource.mod
-*
-* Revision 5.41  1997/04/17 17:19:06  shavirin
-* Removed truncation of one character in sequence without '>' in
-* the beginning.
-* FastaToSeqEntry()
-*
- * Revision 5.40  1997/04/10  20:03:47  shavirin
- * Fixed bug in function FastaToSeqBuff()
- *
- *
- * Revision 5.39  1997/04/01  21:36:49  shavirin
- * Function FastaToSeqEntryInternal() was disintegrated into 2
- * functions: new function FastaReadSequenceInternal() was added
- * for this reason. This function may use used to create sequence
- * reding functions without creation SeqEntryPtr.
- *
- * Revision 5.38  1997/03/28  21:41:40  tatiana
- * turn off HTG phase 3 in CreateDefLine()
- *
- * Revision 5.37  1997/03/13  15:21:05  tatiana
- * CreateFeLine change to protect from 'HTG phase' duplication
- *
- * Revision 5.36  1997/02/20  15:07:54  kans
- * added call to SeqMgrAddToBioseqIndex, removed obsolete FastaIntSec
- * and GetLineFromBuff functions, added kludge to convert U to T for
- * nucleotides prior to SeqMapTableConvert lookup
- *
- * Revision 5.35  1997/02/11  01:14:10  kans
- * CountGapsInDeltaSeq takes 0, not NULL, as last parameter
- *
- * Revision 5.34  1997/02/10  22:08:20  tatiana
- * a bug fixed in CreateDefLine()
- *
- * Revision 5.32  1997/01/21  17:03:47  tatiana
- * added a check for SEQUENCING IN PROGRESS already existing in title
- * in CreateDefLine()
- *
- * Revision 5.31  1997/01/15  17:35:06  tatiana
- * a bug fixed in CreateDefLine()
- *
- * Revision 5.30  1997/01/13  23:20:54  tatiana
- * added SEQUENCING IN PROGRESS for htg phase 1 and 2 in CreateDefLine()
- *
- * Revision 5.28  1997/01/08  22:49:50  tatiana
- * buf and buflen arguments added to CountGapsInDeltaSeq()
- *
- * Revision 5.27  1996/11/25  18:59:52  shavirin
- * Reading from file in FastaToSeqEntryInternal() changed from FileRead
- * to getc back (from revision 5.16 due to Windows specific problems
- *
- * Revision 5.26  1996/11/19  22:45:09  tatiana
- * CreateDefLine changed for HTG
- *
- * Revision 5.25  1996/11/18  20:36:39  shavirin
- * Default coding for protein is set to ncbieaa in
- * FastaToSeqEntryInternal()
- *
- * Revision 5.24  1996/11/15  17:44:51  shavirin
- * Removed difference in upper and lower bad characters
- *
- * Revision 5.23  1996/11/04  17:59:33  tatiana
- * memory leaks cleaning in CreateDefline
- *
- * Revision 5.22  1996/10/30  16:52:07  kans
- * SeqIdDup now calls SeqIdFindBest first.  Also, removed unused variable.
- *
- * Revision 5.21  1996/10/28  21:51:47  tatiana
- * a bug fixed in FastaToSeqEntryInternal()
- *
- * Revision 5.20  1996/10/25  21:48:14  shavirin
- * Windows NT specific change - in FastaToSeqEntryInternal()
- * changed \n \r check to opposite id defline processing.
- *
- * Revision 5.19  1996/10/22  16:01:25  shavirin
- * Added support to disable sequence printing with new
- * parameter no_sequence and removed unused variables and functions
- *
- * Revision 5.18  1996/10/21  21:36:28  shavirin
- * Added new functions : SeqEntrysToDefline() and static DeflineFunc()
- *
- * Revision 5.17  1996/10/18  18:54:30  shavirin
- * Changed getc() macros to FileRead() function,
- * exit(1) to return NULL end ErrLogPrintf to ErrPostEx()
- *
- * Revision 5.16  1996/10/16  17:41:26  zjing
- * replace ch in getc from Char to Int1
- *
- * Revision 5.15  1996/10/11  20:30:09  shavirin
- * *** empty log message ***
- *
- * Revision 5.14  1996/10/11  18:47:01  shavirin
- * In FastaToSeqEntryInternal removed bad characters processing if
- * we do not require it
- *
- * Revision 5.13  1996/10/09  00:06:39  shavirin
- * Removed few unused variables and function definitions
- *
- * Revision 5.12  1996/10/08  22:25:52  shavirin
- * Rewritten engine for FastaToSeqEntry functions set.
- * Removed hardcoded limit of 255 characters for defline.
- *
- * Revision 5.11  1996/09/27  20:00:32  ostell
- * made FastaToSeqEntry call BioseqPack instead of BioseqConvert(ncbi4na)
- *
- * Revision 5.10  1996/08/30  14:57:11  tatiana
- * memory leak cleaned up in GatherDescrOnBioseq()
- *
- * Revision 5.9  1996/08/26  20:45:43  kans
- * FindProtDefLine length was uninitialized, also now protects against
- * prp->name with NULL ->data.ptrvalue.  (The latter is fixed in cdrgn.c.)
- *
- * Revision 5.8  1996/08/19  18:02:27  tatiana
- * a bug fixed in FindProtDefLine
- *
- * Revision 5.6  1996/08/15  18:15:52  tatiana
- * CreateDefLine() added
- *
- * Revision 5.5  1996/07/29  15:20:12  kans
- * converted errpost to errpostex
- *
- * Revision 5.4  1996/07/25  02:32:26  ostell
- * changed fastadefline() for elta seqs
- *
- * Revision 5.3  1996/07/11  16:25:31  kans
- * FastaToSeqEntry now calls MakeNewProteinSeqId to make unique ID
- *
- * Revision 5.2  1996/07/05  15:57:07  shavirin
- * Added support to parce buffers with multiple fasta entries in FastaToSeqBuff()
- *
- * Revision 5.1  1996/06/15  17:29:44  ostell
- * changed MyFsa structure by adding do_virtual and tech fields
- * added value of 3 for group_segs
- * addes support of tech to FastaDefLine()
- *
- * Revision 5.0  1996/05/28  13:23:23  ostell
- * Set to revision 5.0
- *
- * Revision 4.14  1996/05/07  21:25:17  madden
- * GetLineFromBuff has new check for length of buffer.
- *
- * Revision 4.13  1996/05/01  21:41:47  vakatov
- * GetLineFromBuff() function rewritten so that it can process DOS end-of-line
- * sequence
- *
- * Revision 4.12  1996/04/30  21:23:41  shavirin
- * Fixed bug for Macintosh in FastaToSeqBuff() function
- *
- * Revision 4.10  1996/04/03  15:15:06  kans
- * added parseSeqId to "Ex" functions
- *
- * Revision 4.9  1996/03/27  04:10:18  shavirin
- * Fixed problem with one-line sequence in
- * the function FastaToSeqBuff()
- *
- * Revision 4.8  1996/03/13  19:42:50  shavirin
- * Added new functions FastaToSeqBuff() and FastaToSeqBuffEx() that allow to transfer
- * FASTA entries into SeqEntry structure.
- * Redefined functions FastaToSeqEntry() and FastaToSeqEntryEx() using common engine -
- * internal function FastaIntSeq.
- * Added auxiliary function CharPtr GetLineFromBuff()
- *
- * Revision 4.7  1996/02/23  15:44:51  kans
- * FastaToSeqEntry now allows selenocysteine (U)
- *
- * Revision 4.6  1996/02/19  20:29:08  kans
- * FastaToSeqEntryEx now reports counts of individual illegal characters
- *
- * Revision 4.5  1996/02/17  00:51:54  kans
- * new FastaToSeqEntryEx hidden function
- *
- * Revision 4.4  1996/01/17  18:32:34  kans
- * added TrimSpacesAroundString, called by FastaToSeqEntry for each line
- *
- * Revision 4.3  1995/10/13  21:36:59  madden
- * ID's that contain a "|", but are not legal, are put in a local
- * ID in MakeSeqID.
- *
- * Revision 4.2  1995/09/29  15:03:06  ostell
- * changed FastaToSeqentry() so that if seqid fails to parse, makes a type local
- *
- * Revision 4.1  1995/09/26  12:52:57  ostell
- * removed extra newline from PATENT def line
- *
- * Revision 4.0  1995/07/26  13:49:01  ostell
- * force revision to 4.0
- *
- * Revision 2.26  1995/07/20  19:42:53  tatiana
- * change SeqIdPrint to SeqIdWrite
- *
- * Revision 2.25  1995/06/07  18:52:39  kans
- * kludge to allow - in nucleotide sequence, convert to Seq_code_ncbi4na)
- *
- * Revision 2.24  1995/06/07  16:59:41  kans
- * allow - and * in proteins, use Seq_code_ncbieaa
- *
- * Revision 2.23  1995/05/26  20:34:57  kans
- * gap of unknown length now makes virtual sequence of length -1
- *
- * Revision 2.22  1995/05/09  18:43:09  ostell
- * added support for (accession) on GenPept deflines and [organism] on
- * GenPept and PRF deflines
- *
 *
 * ==========================================================================
 */
@@ -799,7 +102,7 @@ static Uint1 aa_order[NUM_SEQID] = {   /* order of nucleic acid deflines */
         60   /* 18 = tpd */
     };
 
-#define FASTA_BUFFER_LEN 262144
+#define FASTA_BUFFER_LEN 524288
 #define PATENT_ORDER 110         /* order for any patent */
 
 /*****************************************************************************
@@ -3320,14 +2623,34 @@ static ValNodePtr IndexedGatherDescrOnBioseq (ItemInfoPtr iip, BioseqPtr bsp, Ui
 
 static ValNodePtr GatherDescrOnBioseq(ItemInfoPtr iip, BioseqPtr bsp, Uint1 choice, Boolean get_first)
 {
-	ValNodePtr   vnp;
-
-	GatherScope  gsc;
-	SeqLocPtr    slp = NULL;
-	Uint2        bspID;
-	DescrInfoPtr dsp;
-	Uint2 entityID;
+	ValNodePtr    vnp = NULL;
+	/*
+	GatherScope   gsc;
+	SeqLocPtr     slp;
+	Uint2         bspID;
+	DescrInfoPtr  dsp;
+	Uint2         entityID;
+	*/
+	ObjValNodePtr ovp;
+
+  if (ISA_aa(bsp->mol) && !is_pdb(bsp)) {
+    vnp = BioseqGetSeqDescr (bsp, choice, NULL);
+  } else {
+    vnp = GetNextDescriptorUnindexed (bsp, choice, NULL);
+  }
+  if (vnp != NULL) {
+    if (iip != NULL) {
+      if (vnp->extended != 0) {
+        ovp = (ObjValNodePtr) vnp;
+        iip->entityID = ovp->idx.entityID;
+        iip->itemtype = ovp->idx.itemtype;
+        iip->itemID = ovp->idx.itemID;
+      }
+    }
+  }
+  return vnp;
 
+#if 0
 	entityID = ObjMgrGetEntityIDForPointer (bsp);
 	if (SeqMgrFeaturesAreIndexed (entityID)) {
 		return IndexedGatherDescrOnBioseq (iip, bsp, choice);
@@ -3375,8 +2698,210 @@ static ValNodePtr GatherDescrOnBioseq(ItemInfoPtr iip, BioseqPtr bsp, Uint1 choi
 	MemFree(dsp->iip);
 	MemFree(dsp);
 	return NULL;
+#endif
+}
+
+/* more efficient versions of feature gather functions for protein defline */
+
+typedef struct unidxfeatdata {
+  SeqIdPtr    bspid;
+  SeqLocPtr   loc;
+  Int4        longest;
+  Int4        shortest;
+  SeqFeatPtr  sfp;
+} UndxFeatData, PNTR UndxFeatPtr;
+
+static void GetLongestProtFeat (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  Int4         len;
+  SeqIdPtr     sip;
+  UndxFeatPtr  ufp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT) return;
+  ufp = (UndxFeatPtr) userdata;
+  if (ufp == NULL) return;
+
+  sip = SeqLocId (sfp->location);
+  if (sip == NULL) return;
+  if (! SeqIdIn (sip, ufp->bspid)) return;
+
+  len = SeqLocLen (sfp->location);
+  if (len == -1) return;
+
+  if (len > ufp->longest) {
+    ufp->sfp = sfp;
+    ufp->longest = len;
+  }
 }
 
+static SeqFeatPtr GetLongestProteinUnindexed (
+  BioseqPtr bsp
+)
+
+{
+  BioseqSetPtr  bssp = NULL;
+  UndxFeatData  ufd;
+
+  if (bsp == NULL) return NULL;
+
+  MemSet ((Pointer) &ufd, 0, sizeof (UndxFeatData));
+  ufd.bspid = bsp->id;
+  ufd.longest = 0;
+  ufd.sfp = NULL;
+
+  VisitFeaturesOnBsp (bsp, (Pointer) &ufd, GetLongestProtFeat);
+
+  if (bsp->idx.parenttype == OBJ_BIOSEQSET) {
+    bssp = (BioseqSetPtr) bsp->idx.parentptr;
+  }
+
+  if (bssp != NULL && bssp->_class == BioseqseqSet_class_parts) {
+    VisitFeaturesOnSet (bssp, (Pointer) &ufd, GetLongestProtFeat);
+    if (bssp->idx.parenttype == OBJ_BIOSEQSET) {
+      bssp = (BioseqSetPtr) bssp->idx.parentptr;
+    }
+  }
+
+  if (bssp != NULL && bssp->_class == BioseqseqSet_class_segset) {
+    VisitFeaturesOnSet (bssp, (Pointer) &ufd, GetLongestProtFeat);
+  }
+
+  return ufd.sfp;
+}
+
+static void GetCDSProtFeat (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  SeqIdPtr     sip;
+  UndxFeatPtr  ufp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return;
+  ufp = (UndxFeatPtr) userdata;
+  if (ufp == NULL) return;
+
+  sip = SeqLocId (sfp->product);
+  if (sip == NULL) return;
+  if (! SeqIdIn (sip, ufp->bspid)) return;
+
+  ufp->sfp = sfp;
+}
+
+static SeqFeatPtr GetCDSProtUnindexed (
+  BioseqPtr bsp
+)
+
+{
+  Uint2         entityID;
+  SeqEntryPtr   sep;
+  UndxFeatData  ufd;
+
+  if (bsp == NULL) return NULL;
+
+  entityID = ObjMgrGetEntityIDForPointer (bsp);
+  sep = GetTopSeqEntryForEntityID (entityID);
+  if (sep == NULL) return NULL;
+
+  MemSet ((Pointer) &ufd, 0, sizeof (UndxFeatData));
+  ufd.bspid = bsp->id;
+  ufd.sfp = NULL;
+
+  VisitFeaturesInSep (sep, (Pointer) &ufd, GetCDSProtFeat);
+
+  return ufd.sfp;
+}
+
+static void GetBestGeneFeat (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  Int4         diff;
+  SeqIdPtr     sip;
+  UndxFeatPtr  ufp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_GENE) return;
+  ufp = (UndxFeatPtr) userdata;
+  if (ufp == NULL) return;
+
+  sip = SeqLocId (sfp->location);
+  if (sip == NULL) return;
+  if (! SeqIdIn (sip, ufp->bspid)) return;
+
+  diff = SeqLocAinB (ufp->loc, sfp->location);
+  if (diff >= 0) {
+    if (diff < ufp->shortest)
+    ufp->sfp = sfp;
+    ufp->shortest = diff;
+  }
+}
+
+static SeqFeatPtr GetBestGeneUnindexed (
+  SeqLocPtr slp,
+  Uint2 entityID
+)
+
+{
+  BioseqPtr     bsp;
+  SeqEntryPtr   sep;
+  SeqIdPtr      sip;
+  UndxFeatData  ufd;
+
+  if (slp == NULL) return NULL;
+  sip = SeqLocId (slp);
+  if (sip == NULL) return NULL;
+  bsp = BioseqFindCore (sip);
+  if (bsp == NULL) return NULL;
+
+  sep = GetTopSeqEntryForEntityID (entityID);
+  if (sep == NULL) return NULL;
+
+  MemSet ((Pointer) &ufd, 0, sizeof (UndxFeatData));
+  ufd.bspid = bsp->id;
+  ufd.loc = slp;
+  ufd.shortest = INT4_MAX;
+  ufd.sfp = NULL;
+
+  VisitFeaturesInSep (sep, (Pointer) &ufd, GetBestGeneFeat);
+
+  return ufd.sfp;
+}
+
+/* GatherProtCDS is still faster than GetCDSProtUnindexed for some reason */
+
+static SeqFeatPtr GatherProtCDS(BioseqPtr bsp)
+{
+	GatherScope gsc;
+	SeqLocPtr slp = NULL;
+	Uint2 bspID;
+	SeqFeatPtr sfp;
+
+  	MemSet ((Pointer) (&gsc), 0, sizeof (GatherScope));
+	MemSet ((Pointer) (gsc.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof(Boolean)));
+	gsc.ignore[OBJ_SEQFEAT] = FALSE;
+	gsc.ignore[OBJ_SEQANNOT] = FALSE;
+	gsc.get_feats_product = TRUE;
+	bspID = ObjMgrGetEntityIDForPointer(bsp);
+	slp = ValNodeNew(NULL);
+	slp->choice = SEQLOC_WHOLE;
+	slp->data.ptrvalue = (SeqIdPtr) SeqIdDup (SeqIdFindBest (bsp->id, 0));
+	gsc.target = slp;
+	sfp = NULL;
+	GatherEntity(bspID, &sfp, GetFeatCDS, &gsc); 
+	SeqLocFree(slp);
+	
+	return sfp;
+}
+
+/* obsolete functions, replaced by Unindexed versions */
+
 static SeqFeatPtr GatherSeqFeatProt(BioseqPtr bsp)
 {
 	GatherScope gsc;
@@ -3388,6 +2913,9 @@ static SeqFeatPtr GatherSeqFeatProt(BioseqPtr bsp)
 	Int4 length, longest_length=0;
 
   	MemSet ((Pointer) (&gsc), 0, sizeof (GatherScope));
+	MemSet ((Pointer) (gsc.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof(Boolean)));
+	gsc.ignore[OBJ_SEQFEAT] = FALSE;
+	gsc.ignore[OBJ_SEQANNOT] = FALSE;
 	gsc.get_feats_location = TRUE;
 	bspID = ObjMgrGetEntityIDForPointer(bsp);
 	slp = ValNodeNew(NULL);
@@ -3411,26 +2939,6 @@ static SeqFeatPtr GatherSeqFeatProt(BioseqPtr bsp)
 	return sfp;
 }
 
-static SeqFeatPtr GatherProtCDS(BioseqPtr bsp)
-{
-	GatherScope gsc;
-	SeqLocPtr slp = NULL;
-	Uint2 bspID;
-	SeqFeatPtr sfp;
-
-  	MemSet ((Pointer) (&gsc), 0, sizeof (GatherScope));
-	gsc.get_feats_product = TRUE;
-	bspID = ObjMgrGetEntityIDForPointer(bsp);
-	slp = ValNodeNew(NULL);
-	slp->choice = SEQLOC_WHOLE;
-	slp->data.ptrvalue = (SeqIdPtr) SeqIdDup (SeqIdFindBest (bsp->id, 0));
-	gsc.target = slp;
-	sfp = NULL;
-	GatherEntity(bspID, &sfp, GetFeatCDS, &gsc); 
-	SeqLocFree(slp);
-	
-	return sfp;
-}
 static ValNodePtr GatherGenesForCDS(SeqLocPtr slp)
 {
 	GatherScope gsc;
@@ -3443,6 +2951,9 @@ static ValNodePtr GatherGenesForCDS(SeqLocPtr slp)
 		return NULL;
 	bspID = ObjMgrGetEntityIDForPointer(bsp);
   	MemSet ((Pointer) (&gsc), 0, sizeof (GatherScope));
+	MemSet ((Pointer) (gsc.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof(Boolean)));
+	gsc.ignore[OBJ_SEQFEAT] = FALSE;
+	gsc.ignore[OBJ_SEQANNOT] = FALSE;
 	gsc.get_feats_location = TRUE;
 	gsc.target = slp;
 	vnp = NULL;
@@ -3690,6 +3201,12 @@ static CharPtr FindNRDefLine (BioseqPtr bsp)
         case MOLECULE_TYPE_TRANSCRIBED_RNA :
           rna = "miscRNA";
           break;
+        case MOLECULE_TYPE_NCRNA :
+          rna = "ncRNA";
+          break;
+        case MOLECULE_TYPE_TMRNA :
+          rna = "tmRNA";
+          break;
         default :
           break;
       }
@@ -3711,14 +3228,16 @@ static CharPtr FindNRDefLine (BioseqPtr bsp)
 
 static CharPtr FindProtDefLine(BioseqPtr bsp, Boolean extProtTitle)
 {
-	SeqFeatPtr sfp = NULL, f;
+	SeqFeatPtr sfp = NULL /* , f */;
 	ProtRefPtr prp;
 	SeqFeatXrefPtr xref;
 	GeneRefPtr grp=NULL;
-	ValNodePtr vnp, v, syn;
+	ValNodePtr vnp, /* v, */ syn;
 	SeqLocPtr loc;
 	CharPtr title = NULL, s, geneprod;
-	Int4 diff_lowest = /* 0 */ INT4_MAX, diff_current;
+	/*
+	Int4 diff_lowest = INT4_MAX, diff_current;
+	*/
 	Int2 length = 0;
 	SeqFeatPtr best_gene = NULL;
 	Uint2 entityID;
@@ -3734,7 +3253,12 @@ static CharPtr FindProtDefLine(BioseqPtr bsp, Boolean extProtTitle)
 	if (indexed) {
 		sfp = SeqMgrGetBestProteinFeature (bsp, NULL);
 	} else {
-		sfp = GatherSeqFeatProt(bsp);
+	    sfp = GetLongestProteinUnindexed (bsp);
+	    /*
+	    if (sfp == NULL) {
+		    sfp = GatherSeqFeatProt(bsp);
+	    }
+	    */
 	}
 	if (sfp != NULL) {
 		prp = (ProtRefPtr) sfp->data.value.ptrvalue;
@@ -3761,6 +3285,9 @@ static CharPtr FindProtDefLine(BioseqPtr bsp, Boolean extProtTitle)
 				if (indexed) {
 					sfp = SeqMgrGetCDSgivenProduct (bsp, NULL);
 				} else {
+				    /*
+				    sfp = GetCDSProtUnindexed (bsp);
+					*/
 					sfp = GatherProtCDS(bsp);
 				}
 				if (sfp != NULL) {
@@ -3771,6 +3298,8 @@ static CharPtr FindProtDefLine(BioseqPtr bsp, Boolean extProtTitle)
 						if (indexed) {
 							best_gene = SeqMgrGetOverlappingGene (loc, NULL);
 						} else {
+						    best_gene = GetBestGeneUnindexed (loc, entityID);
+							/*
 							vnp = GatherGenesForCDS(loc);
 							for (v=vnp; v; v=v->next) {
 								f = (SeqFeatPtr) v->data.ptrvalue;
@@ -3786,6 +3315,7 @@ static CharPtr FindProtDefLine(BioseqPtr bsp, Boolean extProtTitle)
 								}
 							}
 							ValNodeFree(vnp);
+							*/
 						}
 						if (best_gene != NULL) {
 							grp = (GeneRefPtr) best_gene->data.value.ptrvalue;
@@ -3820,6 +3350,9 @@ static CharPtr FindProtDefLine(BioseqPtr bsp, Boolean extProtTitle)
 		if (indexed) {
 			sfp = SeqMgrGetCDSgivenProduct (bsp, NULL);
 		} else {
+			/*
+			sfp = GetCDSProtUnindexed (bsp);
+			*/
 			sfp = GatherProtCDS(bsp);
 		}
 		if (sfp != NULL) {
@@ -3850,6 +3383,8 @@ static CharPtr FindProtDefLine(BioseqPtr bsp, Boolean extProtTitle)
 				if (indexed) {
 					best_gene = SeqMgrGetOverlappingGene (loc, NULL);
 				} else {
+				    best_gene = GetBestGeneUnindexed (loc, entityID);
+					/*
 					vnp = GatherGenesForCDS(loc);
 					for (v=vnp; v; v=v->next) {
 						f = (SeqFeatPtr) v->data.ptrvalue;
@@ -3865,6 +3400,7 @@ static CharPtr FindProtDefLine(BioseqPtr bsp, Boolean extProtTitle)
 						}
 					}
 					ValNodeFree(vnp);
+					*/
 				}
 				if (best_gene != NULL) {
 					grp = (GeneRefPtr) best_gene->data.value.ptrvalue;
@@ -4335,8 +3871,8 @@ static CharPtr MakeCompleteChromTitle (BioseqPtr bsp, Uint1 biomol, Uint1 comple
 		} else {
 			orgnl = organelleByItself [genome];
 		}
-		if (StringISearch (name, "virus") != NULL) {
-			if (genome == 13 || genome == 14) {
+		if (StringISearch (name, "virus") != NULL || StringISearch (name, "phage") != NULL) {
+			if (genome == GENOME_proviral || genome == GENOME_virion) {
 				orgnl = NULL;
 			}
 		}
@@ -4550,9 +4086,19 @@ NLM_EXTERN Boolean CreateDefLineExEx (ItemInfoPtr iip, BioseqPtr bsp, CharPtr bu
 	SeqMgrDescContext dcontext;
 	SeqMgrFeatContext fcontext;
 	SeqFeatPtr sfp, src;
+	Uint2 entityID;
 
 	if ((bsp == NULL) || (buf == NULL) || buflen == 0) return FALSE;
 
+    /* now using GetNextDescriptorUnindexed, so need to have called AssignIDsInEntityEx */
+
+    if (bsp->idx.entityID == 0) {
+      entityID = ObjMgrGetEntityIDForPointer (bsp);
+      if (entityID != 0) {
+        AssignIDsInEntityEx (entityID, 0, NULL, NULL);
+      }
+    }
+
 	for (sip = bsp->id; sip != NULL; sip = sip->next) {
 		switch (sip->choice) {
 			case SEQID_OTHER :
diff --git a/api/txalign.c b/api/txalign.c
index 80e7de41..5877f9c4 100644
--- a/api/txalign.c
+++ b/api/txalign.c
@@ -1,4 +1,4 @@
-/* $Id: txalign.c,v 6.94 2007/05/07 13:28:35 kans Exp $
+/* $Id: txalign.c,v 6.95 2008/01/07 23:20:06 bealer Exp $
 ***************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -27,13 +27,17 @@
 *
 * File Name:  txalign.c
 *
-* $Revision: 6.94 $
+* $Revision: 6.95 $
 * 
 * File Description:  Formating of text alignment for the BLAST output
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * $Log: txalign.c,v $
+* Revision 6.95  2008/01/07 23:20:06  bealer
+* - Fix condition found by valgrind - conditional statement on
+*   unassigned location.
+*
 * Revision 6.94  2007/05/07 13:28:35  kans
 * added casts for Seq-data.gap (SeqDataPtr, SeqGapPtr, ByteStorePtr)
 *
@@ -3760,6 +3764,8 @@ static Boolean ShowAlignNodeText2Ex(ValNodePtr anp_list, Int2 num_node, Int4 lin
                             as.target_sip = anp->sip;
                             as.is_aa = (m_bsp->mol == Seq_mol_aa);
                             as.ooframe = FALSE; /* Not supported */
+                            as.m_frame_set = FALSE;
+                            as.t_frame_set = FALSE;
                             asp = &as;
                         } else
                             asp = NULL;
diff --git a/api/utilpub.c b/api/utilpub.c
index c58d4897..3d3dd5ad 100644
--- a/api/utilpub.c
+++ b/api/utilpub.c
@@ -1442,7 +1442,7 @@ NLM_EXTERN void cleanup_pub(ValNodePtr pub)
 	}
 }
 
-static Boolean empty_citgen(CitGenPtr  cit)
+NLM_EXTERN Boolean empty_citgen(CitGenPtr  cit)
 {
 	if (cit == NULL)
 		return TRUE;
diff --git a/api/utilpub.h b/api/utilpub.h
index d7a6fe9f..a712195d 100644
--- a/api/utilpub.h
+++ b/api/utilpub.h
@@ -60,6 +60,8 @@ NLM_EXTERN ValNodePtr OrganizePubList PROTO((ValNodePtr vnp));
 
 NLM_EXTERN void cleanup_pub PROTO((ValNodePtr pub));
 
+NLM_EXTERN Boolean empty_citgen PROTO((CitGenPtr  cit));
+
 NLM_EXTERN void EntryStripSerialNumber PROTO((SeqEntryPtr sep));
 
 NLM_EXTERN void VnpHeapSort PROTO ((ValNodePtr PNTR vnp, int (LIBCALLBACK *compar )PROTO ((Nlm_VoidPtr, Nlm_VoidPtr ))));	
diff --git a/api/valid.c b/api/valid.c
index 79590e93..4ae1a41a 100644
--- a/api/valid.c
+++ b/api/valid.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 1/1/94
 *
-* $Revision: 6.970 $
+* $Revision: 6.1032 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -101,7 +101,7 @@ NLM_EXTERN void SpliceCheck (ValidStructPtr vsp, SeqFeatPtr sfp);
 static void     CdConflictCheck (ValidStructPtr vsp, SeqFeatPtr sfp);
 static void     SpliceCheckEx (ValidStructPtr vsp, SeqFeatPtr sfp, Boolean checkAll);
 static void     CdsProductIdCheck (ValidStructPtr vsp, SeqFeatPtr sfp);
-static void     ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSourcePtr biop, SeqFeatPtr sfp);
+static void     ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSourcePtr biop, SeqFeatPtr sfp, ValNodePtr sdp);
 static void     ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, PubdescPtr pdp);
 static void     LookForMultiplePubs (ValidStructPtr vsp, GatherContextPtr gcp, SeqDescrPtr sdp);
 static void     ValidateSfpCit (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPtr sfp);
@@ -573,7 +573,9 @@ static CharPtr err2Label [] = {
   "LatLonRange",
   "LatLonValue",
   "LatLonCountry",
-  "LatLonState"
+  "LatLonState",
+  "BadSpecificHost",
+  "RefGeneTrackingIllegalStatus"
 };
 
 static CharPtr err3Label [] = {
@@ -760,7 +762,11 @@ static CharPtr err5Label [] = {
   "BadAuthorSuffix",
   "BadAnticodonAA",
   "BadAnticodonCodon",
-  "BadAnticodonStrand"
+  "BadAnticodonStrand",
+  "UndesiredGeneSynonym",
+  "UndesiredProteinName",
+  "FeatureBeginsOrEndsInGap",
+  "GeneOntologyTermMissingGOID"
 };
 
 static CharPtr err6Label [] = {
@@ -1471,7 +1477,7 @@ static Boolean Valid1GatherProc (GatherContextPtr gcp)
         if (sfp != NULL) {
           if (sfp->data.choice == SEQFEAT_BIOSRC) {
             biop = (BioSourcePtr) sfp->data.value.ptrvalue;
-            ValidateBioSource (vsp, gcp, biop, sfp);
+            ValidateBioSource (vsp, gcp, biop, sfp, NULL);
           }
           if (sfp->data.choice == SEQFEAT_PUB) {
             pdp = (PubdescPtr) sfp->data.value.ptrvalue;
@@ -1545,7 +1551,7 @@ static Boolean Valid1GatherProc (GatherContextPtr gcp)
       if (sdp != NULL) {
         if (sdp->choice == Seq_descr_source) {
           biop = (BioSourcePtr) sdp->data.ptrvalue;
-          ValidateBioSource (vsp, gcp, biop, NULL);
+          ValidateBioSource (vsp, gcp, biop, NULL, sdp);
         }
         if (sdp->choice == Seq_descr_pub) {
           pdp = (PubdescPtr) sdp->data.ptrvalue;
@@ -2256,6 +2262,21 @@ typedef struct vsicdata {
   ValNodePtr      tailid;
 } VsicData, PNTR VsicDataPtr;
 
+static Boolean IsNCBIFileID (SeqIdPtr sip)
+{
+  DbtagPtr dbt;
+
+  if (sip == NULL || sip->choice != SEQID_GENERAL) return FALSE;
+  dbt = (DbtagPtr) sip->data.ptrvalue;
+  if (dbt == NULL) return FALSE;
+  if (StringCmp (dbt->db, "NCBIFILE") == 0) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+
 static void CaptureTextSeqIDs (BioseqPtr bsp, Pointer userdata)
 
 {
@@ -2269,6 +2290,7 @@ static void CaptureTextSeqIDs (BioseqPtr bsp, Pointer userdata)
 
   for (sip = bsp->id; sip != NULL; sip = sip->next) {
     if (sip->choice == SEQID_GI || sip->choice == SEQID_GIBBSQ || sip->choice == SEQID_GIBBMT) continue;
+    if (IsNCBIFileID (sip)) continue;
     SeqIdWrite (sip, buf, PRINTID_FASTA_SHORT, sizeof (buf) - 1);
     vnp = ValNodeCopyStr (&(vdp->tailid), 0, buf);
     if (vdp->headid == NULL) {
@@ -2593,6 +2615,7 @@ typedef struct vvmdata {
   Boolean     accounted_for;
   Boolean     products_unique;
   Boolean     featid_matched;
+  Boolean     feat_touches_gap;
   SeqFeatPtr  nearbygene;
   SeqFeatPtr  nearbycds;
   SeqFeatPtr  nearbymrna;
@@ -3575,6 +3598,94 @@ static Boolean CheckForInconsistentBiosources (SeqEntryPtr sep, ValidStructPtr v
   return TRUE;
 }
 
+static Boolean CheckForInconsistentMolInfos (SeqEntryPtr sep, ValidStructPtr vsp, MolInfoPtr PNTR mipp, BioseqSetPtr top)
+
+{
+  BioseqPtr          bsp;
+  BioseqSetPtr       bssp;
+  SeqMgrDescContext  dcontext;
+  Uint2              entityID = 0, oldEntityID;
+  MolInfoPtr         firstmip;
+  GatherContextPtr   gcp;
+  Uint4              itemID = 0, oldItemID;
+  Uint2              itemtype = 0, oldItemtype;
+  MolInfoPtr         mip;
+  ValNodePtr         sdp;
+  SeqEntryPtr        tmp;
+
+  if (sep == NULL || vsp == NULL || mipp == NULL)
+    return FALSE;
+  gcp = vsp->gcp;
+
+  if (IS_Bioseq_set (sep)) {
+    bssp = (BioseqSetPtr) sep->data.ptrvalue;
+    if (bssp == NULL)
+      return FALSE;
+    for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) {
+      if (CheckForInconsistentMolInfos (tmp, vsp, mipp, top))
+        return TRUE;
+    }
+    return FALSE;
+  }
+
+  if (!IS_Bioseq (sep))
+    return FALSE;
+  bsp = (BioseqPtr) sep->data.ptrvalue;
+  if (bsp == NULL)
+    return FALSE;
+
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
+  if (sdp == NULL) return FALSE;
+  mip = (MolInfoPtr) sdp->data.ptrvalue;
+  if (mip == NULL || mip->biomol == MOLECULE_TYPE_PEPTIDE) return FALSE;
+
+  firstmip = *mipp;
+  if (firstmip == NULL) {
+    *mipp = mip;
+    return FALSE;
+  }
+
+  if (mip->biomol == firstmip->biomol) return FALSE;
+
+  oldEntityID = gcp->entityID;
+  oldItemID = gcp->itemID;
+  oldItemtype = gcp->thistype;
+
+  gcp->entityID = entityID;
+  gcp->itemID = itemID;
+  gcp->thistype = itemtype;
+
+  if (top != NULL) {
+    gcp->entityID = top->idx.entityID;
+    gcp->itemID = top->idx.itemID;
+    gcp->thistype = OBJ_BIOSEQSET;
+  }
+
+  /* only report the first one that doesn't match */
+
+  ValidErr (vsp, SEV_WARNING, ERR_SEQ_PKG_InconsistentMolInfoBiomols, "Pop/phy/mut/eco set contains inconsistent MolInfo biomols");
+
+  gcp->entityID = oldEntityID;
+  gcp->itemID = oldItemID;
+  gcp->thistype = oldItemtype;
+
+  return TRUE;
+}
+
+static void LookForMolInfoInconsistency (BioseqSetPtr bssp, ValidStructPtr vsp)
+
+{
+  MolInfoPtr    mip = NULL;
+  SeqEntryPtr   sep;
+
+  if (bssp == NULL) return;
+
+  for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
+    if (CheckForInconsistentMolInfos (sep, vsp, &mip, bssp))
+      return;
+  }
+}
+
 static void ValidatePopSet (BioseqSetPtr bssp, ValidStructPtr vsp)
 
 {
@@ -3596,6 +3707,8 @@ static void ValidatePopSet (BioseqSetPtr bssp, ValidStructPtr vsp)
     }
   }
 
+  LookForMolInfoInconsistency (bssp, vsp);
+
   for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
     if (CheckForInconsistentBiosources (sep, vsp, &orp, bssp))
       return;
@@ -3636,6 +3749,8 @@ static void ValidatePhyMutEcoWgsSet (BioseqSetPtr bssp, ValidStructPtr vsp)
                 "Bioseq-set contains internal GenBank Bioseq-set");
     }
   }
+
+  LookForMolInfoInconsistency (bssp, vsp);
 }
 
 static void ValidateGenProdSet (BioseqSetPtr bssp, ValidStructPtr vsp)
@@ -4405,6 +4520,18 @@ static void CheckDeltaForReuse (ValidStructPtr vsp, GatherContextPtr gcp, Bioseq
   ValNodeFreeData (head);
 }
 
+static CharPtr legal_refgene_status_strings [] = {
+  "Inferred",
+  "Provisional",
+  "Predicted",
+  "Validated",
+  "Reviewed",
+  "Model",
+  "WGS",
+  "Pipeline",
+  NULL
+};
+
 static void ValidateBioseqInst (GatherContextPtr gcp)
 {
   Boolean         retval = TRUE;
@@ -4459,14 +4586,17 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
   Boolean         in_N;
   Boolean         isActiveFin = FALSE;
   Boolean         isDraft = FALSE;
+  Boolean         isFullTop = FALSE;
   Boolean         isGB = FALSE;
   Boolean         isPatent = FALSE;
   Boolean         isPDB = FALSE;
+  Boolean         isPreFin = FALSE;
   Boolean         isNC = FALSE;
   Boolean         isNTorNC = FALSE;
   Boolean         isNZ;
   Boolean         is_gps = FALSE;
   Boolean         isRefSeq = FALSE;
+  Boolean         isSwissProt = FALSE;
   Boolean         last_is_gap;
   Boolean         non_interspersed_gaps;
   Int2            num_adjacent_gaps;
@@ -4497,6 +4627,7 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
   ObjectIdPtr     oip;
   Boolean         hasRefGeneTracking = FALSE;
   Boolean         hasRefTrackStatus;
+  Boolean         hasLegalStatus;
   Int2            accn_count = 0;
   Int2            gi_count = 0;
   Int4            runsofn;
@@ -4548,6 +4679,8 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
       hasGi = TRUE;
     } else if (sip1->choice == SEQID_GENBANK) {
       isGB = TRUE;
+    } else if (sip1->choice == SEQID_SWISSPROT) {
+      isSwissProt = TRUE;
     }
 
     for (sip2 = sip1->next; sip2 != NULL; sip2 = sip2->next) {
@@ -4774,10 +4907,30 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
         } else if (oip != NULL && StringICmp (oip->str, "RefGeneTracking") == 0) {
           hasRefGeneTracking = TRUE;
           hasRefTrackStatus = FALSE;
+          hasLegalStatus = FALSE;
           for (ufp = uop->data; ufp != NULL; ufp = ufp->next) {
             oip = ufp->label;
             if (oip != NULL && StringCmp (oip->str, "Status") == 0) {
               hasRefTrackStatus = TRUE;
+              str = (CharPtr) ufp->data.ptrvalue;
+              if (StringHasNoText (str)) {
+                str = "?";
+              }
+              for (i = 0; legal_refgene_status_strings [i] != NULL; i++) {
+                if (StringICmp (str, legal_refgene_status_strings [i]) == 0) {
+                  hasLegalStatus = TRUE;
+                  break;
+                }
+              }
+              if (! hasLegalStatus) {
+                olditemid = gcp->itemID;
+                olditemtype = gcp->thistype;
+                gcp->itemID = context.itemID;
+                gcp->thistype = OBJ_SEQDESC;
+                ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_RefGeneTrackingIllegalStatus, "RefGeneTracking object has illegal Status '%s'", str);
+                gcp->itemID = olditemid;
+                gcp->thistype = olditemtype;
+              }
             }
           }
           if (! hasRefTrackStatus) {
@@ -5346,6 +5499,10 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
             isActiveFin = TRUE;
           } else if (StringICmp (str, "HTGS_DRAFT") == 0) {
             isDraft = TRUE;
+          } else if (StringICmp (str, "HTGS_FULLTOP") == 0) {
+            isFullTop = TRUE;
+          } else if (StringICmp (str, "HTGS_PREFIN") == 0) {
+            isPreFin = TRUE;
           }
         }
       }
@@ -5473,11 +5630,16 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
               }
             }
           } else if (slitp->length == 0) {
+            if (isSwissProt) {
+              sev = SEV_WARNING;
+            } else {
+              sev = SEV_ERROR;
+            }
             ifp = slitp->fuzz;
             if (ifp == NULL || ifp->choice != 4 || ifp->a != 0) {
-              ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_SeqLitGapLength0, "Gap of length 0 in delta chain");
+              ValidErr (vsp, sev, ERR_SEQ_INST_SeqLitGapLength0, "Gap of length 0 in delta chain");
             } else {
-              ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_SeqLitGapLength0, "Gap of length 0 with unknown fuzz in delta chain");
+              ValidErr (vsp, sev, ERR_SEQ_INST_SeqLitGapLength0, "Gap of length 0 with unknown fuzz in delta chain");
             }
           }
           len += slitp->length;
@@ -5628,9 +5790,18 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
     }
   }
 
-  if (mip != NULL) {
-    if (isDraft && mip->tech == MI_TECH_htgs_3) {
-      ValidErr (vsp, SEV_WARNING, ERR_SEQ_INST_BadHTGSeq, "HTGS 3 sequence should not have HTGS_DRAFT keyword");
+  if (mip != NULL && mip->tech == MI_TECH_htgs_3) {
+    if (isDraft) {
+      ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadHTGSeq, "HTGS 3 sequence should not have HTGS_DRAFT keyword");
+    }
+    if (isPreFin) {
+      ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadHTGSeq, "HTGS 3 sequence should not have HTGS_PREFIN keyword");
+    }
+    if (isActiveFin) {
+      ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadHTGSeq, "HTGS 3 sequence should not have HTGS_ACTIVEFIN keyword");
+    }
+    if (isFullTop) {
+      ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadHTGSeq, "HTGS 3 sequence should not have HTGS_FULLTOP keyword");
     }
   }
 
@@ -5783,6 +5954,14 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
           /* check generated protein defline with first prp->name - new convention */
           if (buf != NULL && CreateDefLineExEx (&ii, bsp, buf, buflen, tech, NULL, NULL, TRUE, FALSE)) {
             if (StringICmp (buf, title) != 0) {
+              /* okay if instantiated title has single trailing period */
+              len2 = StringLen (buf);
+              len3 = StringLen (title);
+              if (len3 == len2 + 1 && title [len3 - 1] == '.' && len3 > 3 && title [len3 - 2] != '.') {
+                StringCat (buf, ".");
+              }
+            }
+            if (StringICmp (buf, title) != 0) {
               /* also check generated protein defline with all prp->names - old convention */
               if (CreateDefLineExEx (&ii, bsp, buf, buflen, tech, NULL, NULL, TRUE, TRUE)) {
                 if (StringICmp (buf, title) != 0) {
@@ -6561,6 +6740,9 @@ static void ValidatePubdesc (ValidStructPtr vsp, GatherContextPtr gcp, PubdescPt
             if (imp->pubstatus == PUBSTATUS_aheadofprint && imp->prepub != 2) {
               ValidErr (vsp, SEV_WARNING, ERR_GENERIC_PublicationInconsistency, "Ahead-of-print without in-press");
             }
+            if (imp->pubstatus == PUBSTATUS_epublish && imp->prepub == 2) {
+              ValidErr (vsp, SEV_WARNING, ERR_GENERIC_PublicationInconsistency, "Electronic-only publication should not also be in-press");
+            }
           }
         }
         break;
@@ -7270,7 +7452,6 @@ static CharPtr  Nlm_valid_country_codes [] = {
   "Saudi Arabia",
   "Senegal",
   "Serbia",
-  "Serbia and Montenegro",
   "Seychelles",
   "Sierra Leone",
   "Singapore",
@@ -7321,19 +7502,31 @@ static CharPtr  Nlm_valid_country_codes [] = {
   "West Bank",
   "Western Sahara",
   "Yemen",
-  "Yugoslavia",
   "Zambia",
   "Zimbabwe",
   NULL
 };
 
+static CharPtr  Nlm_formerly_valid_country_codes [] = {
+  "British Guiana",
+  "Burma",
+  "Czechoslovakia",
+  "Ivory Coast",
+  "Serbia and Montenegro",
+  "Siam",
+  "USSR",
+  "Yugoslavia",
+  "Zaire",
+  NULL
+};
+
 NLM_EXTERN CharPtr PNTR GetValidCountryList (void)
 
 {
   return (CharPtr PNTR) Nlm_valid_country_codes;
 }
 
-static Boolean CountryIsValid (CharPtr name)
+NLM_EXTERN Boolean CountryIsValid (CharPtr name, BoolPtr old_countryP)
 {
   Int2            L, R, mid;
   CharPtr         ptr;
@@ -7363,6 +7556,25 @@ static Boolean CountryIsValid (CharPtr name)
     return TRUE;
   }
 
+  L = 0;
+  R = sizeof (Nlm_formerly_valid_country_codes) / sizeof (Nlm_formerly_valid_country_codes[0]) - 1; /* -1 because now NULL terminated */
+
+  while (L < R) {
+    mid = (L + R) / 2;
+    if (StringICmp (Nlm_formerly_valid_country_codes[mid], str) < 0) {
+      L = mid + 1;
+    } else {
+      R = mid;
+    }
+  }
+
+  if (StringICmp (Nlm_formerly_valid_country_codes[R], str) == 0) {
+    if (old_countryP != NULL) {
+      *old_countryP = TRUE;
+    }
+    return FALSE;
+  }
+
   return FALSE;
 }
 
@@ -7439,7 +7651,8 @@ static CharPtr ctry_lat_lon [] = {
   "Central African Republic\tCT\t14.4\t2.2\t27.5\t11.0",
   "Chad\tCD\t13.4\t7.4\t24.0\t23.5",
   "Chile\tCI\t-75.8\t-56.0\t-66.4\t-17.5",
-  "China\tCH\t73.5\t20.2\t134.8\t53.6",
+  "China\tCH\t73.5\t20.2\t134.8\t53.6\t108.6\t18.1\t111.1\t20.2",
+  "China: Hainan\tXX\t108.6\t18.1\t111.1\t20.2",
   "Christmas Island\tKT\t105.5\t-10.6\t105.7\t-10.4",
   "Clipperton Island\tIP\t-109.3\t10.2\t-109.2\t10.3",
   "Cocos Islands\tCK\t96.8\t-12.2\t96.9\t-11.8",
@@ -7609,7 +7822,6 @@ static CharPtr ctry_lat_lon [] = {
   "Saudi Arabia\tSA\t34.4\t15.6\t55.7\t32.2",
   "Senegal\tSG\t-17.6\t12.3\t-11.4\t16.7",
   "Serbia\tRB\t18.8\t41.8\t23.1\t46.2",
-  "Serbia and Montenegro\tYI\t",
   "Seychelles\tSE\t50.7\t-9.6\t51.1\t-9.2\t52.7\t-7.2\t52.8\t-7.0\t53.0\t-6.3\t53.7\t-5.1\t55.2\t-5.9\t56.0\t-3.7\t56.2\t-7.2\t56.3\t-7.1",
   "Sierra Leone\tSL\t-13.4\t6.9\t-10.3\t10.0",
   "Singapore\tSN\t103.6\t1.1\t104.1\t1.5",
@@ -7712,40 +7924,57 @@ static CharPtr ctry_lat_lon [] = {
   "West Bank\tWE\t34.8\t31.3\t35.6\t32.6",
   "Western Sahara\tWI\t-17.2\t20.7\t-8.7\t27.7",
   "Yemen\tYM\t41.8\t11.7\t54.5\t19.0",
-  "Yugoslavia\tXX\t13.3\t40.8\t23.0\t46.9",
   "Zambia\tZA\t21.9\t-18.1\t33.7\t-8.2",
   "Zimbabwe\tZI\t25.2\t-22.5\t33.1\t-15.6",
   NULL
 };
 
-typedef struct ctdata {
-  CharPtr  country;
+
+/* one CtBlock for each discontiguous area per country */
+
+typedef struct ctblock {
+  CharPtr  country;       /* points to instance in countries list */
   FloatHi  minx;
   FloatHi  miny;
   FloatHi  maxx;
   FloatHi  maxy;
-} CtData, PNTR CtDataPtr;
-
-typedef struct ctlist {
-  ValNodePtr      countries;
-  ValNodePtr      boundaries;
-  CtDataPtr PNTR  ctarray;
-  CtDataPtr PNTR  bdarray;
-  Int2            num;
-} CtList, PNTR CtListPtr;
-
-static int LIBCALLBACK SortCdpByCountry (VoidPtr ptr1, VoidPtr ptr2)
+} CtBlock, PNTR CtBlockPtr;
+
+/* one CtGrid for each 10-degree-by-10-degree area touched by a CtBlock */
+
+typedef struct ctgrid {
+  CtBlockPtr  cbp;
+  Int2        xindex;
+  Int2        yindex;
+} CtGrid, PNTR CtGridPtr;
+
+/* main structure for country/lat-lon lookup */
+
+typedef struct ctset {
+  ValNodePtr       countries;
+  ValNodePtr       blocks;
+  ValNodePtr       grids;
+  CtBlockPtr PNTR  bkarray;     /* sorted by country name */
+  CtGridPtr PNTR   gdarray;     /* sorted by geographic index */
+  Int4             num_blocks;
+  Int4             num_grids;
+} CtSet, PNTR CtSetPtr;
+
+static int LIBCALLBACK SortCbpByCountry (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
 
 {
-  int        compare;
-  CtDataPtr  cdp1, cdp2;
+  int         compare;
+  CtBlockPtr  cbp1, cbp2;
 
   if (ptr1 == NULL || ptr2 == NULL) return 0;
-  cdp1 = *((CtDataPtr PNTR) ptr1);
-  cdp2 = *((CtDataPtr PNTR) ptr2);
-  if (cdp1 == NULL || cdp2 == NULL) return 0;
+  cbp1 = *((CtBlockPtr PNTR) ptr1);
+  cbp2 = *((CtBlockPtr PNTR) ptr2);
+  if (cbp1 == NULL || cbp2 == NULL) return 0;
 
-  compare = StringICmp (cdp1->country, cdp2->country);
+  compare = StringICmp (cbp1->country, cbp2->country);
   if (compare > 0) {
     return 1;
   } else if (compare < 0) {
@@ -7755,98 +7984,172 @@ static int LIBCALLBACK SortCdpByCountry (VoidPtr ptr1, VoidPtr ptr2)
   return 0;
 }
 
-static int LIBCALLBACK SortCdpByBounds (VoidPtr ptr1, VoidPtr ptr2)
+static int CgpGridComp (
+  CtGridPtr cgp1,
+  Int2 xindex,
+  Int2 yindex
+)
 
 {
-  CtDataPtr  cdp1, cdp2;
+  if (cgp1 == NULL) return 0;
+
+  if (cgp1->xindex > xindex) {
+    return 1;
+  } else if (cgp1->xindex < xindex) {
+    return -1;
+  }
+
+  if (cgp1->yindex > yindex) {
+    return 1;
+  } else if (cgp1->yindex < yindex) {
+    return -1;
+  }
+
+  return 0;
+}
+
+static int LIBCALLBACK SortCgpByGrid (
+  VoidPtr ptr1,
+  VoidPtr ptr2
+)
+
+{
+  CtBlockPtr  cbp1, cbp2;
+  CtGridPtr   cgp1, cgp2;
+  int         compare;
 
   if (ptr1 == NULL || ptr2 == NULL) return 0;
-  cdp1 = *((CtDataPtr PNTR) ptr1);
-  cdp2 = *((CtDataPtr PNTR) ptr2);
-  if (cdp1 == NULL || cdp2 == NULL) return 0;
+  cgp1 = *((CtGridPtr PNTR) ptr1);
+  cgp2 = *((CtGridPtr PNTR) ptr2);
+  if (cgp1 == NULL || cgp2 == NULL) return 0;
 
-  if (cdp1->minx > cdp2->minx) {
+  compare = CgpGridComp (cgp1, cgp2->xindex, cgp2->yindex);
+  if (compare > 0) {
     return 1;
-  } else if (cdp1->minx < cdp2->minx) {
+  } else if (compare < 0) {
     return -1;
   }
 
-  if (cdp1->maxx > cdp2->maxx) {
+  cbp1 = cgp1->cbp;
+  cbp2 = cgp2->cbp;
+  if (cbp1 == NULL || cbp2 == NULL) return 0;
+
+  if (cbp1->minx > cbp2->minx) {
+    return 1;
+  } else if (cbp1->minx < cbp2->minx) {
     return -1;
-  } else if (cdp1->maxx < cdp2->maxx) {
+  }
+
+  if (cbp1->maxx > cbp2->maxx) {
+    return -1;
+  } else if (cbp1->maxx < cbp2->maxx) {
     return 1;
   }
 
-  if (cdp1->miny > cdp2->miny) {
+  if (cbp1->miny > cbp2->miny) {
     return 1;
-  } else if (cdp1->miny < cdp2->miny) {
+  } else if (cbp1->miny < cbp2->miny) {
     return -1;
   }
 
-  if (cdp1->maxy > cdp2->maxy) {
+  if (cbp1->maxy > cbp2->maxy) {
     return -1;
-  } else if (cdp1->maxy < cdp2->maxy) {
+  } else if (cbp1->maxy < cbp2->maxy) {
     return 1;
   }
 
+  compare = StringICmp (cbp1->country, cbp2->country);
+  if (compare > 0) {
+    return 1;
+  } else if (compare < 0) {
+    return -1;
+  }
+
   return 0;
 }
 
-static CtListPtr CtLatLonDataFree (
-  CtListPtr clp
+static Int2 LatLonDegreeToIndex (
+  FloatHi coord
 )
 
 {
-  if (clp == NULL) return NULL;
+  double  fval;
+  long    ival;
 
-  ValNodeFreeData (clp->countries);
-  ValNodeFreeData (clp->boundaries);
+  fval = coord;
+  fval += 200.0;
+  fval /= 10.0;
+  ival = (long) fval;
+  ival -= 20;
 
-  MemFree (clp->ctarray);
-  MemFree (clp->bdarray);
+  return ival;
+}
+
+static CtSetPtr CtSetDataFree (
+  CtSetPtr csp
+)
+
+{
+  if (csp == NULL) return NULL;
+
+  ValNodeFreeData (csp->countries);
+  ValNodeFreeData (csp->blocks);
+  ValNodeFreeData (csp->grids);
 
-  MemFree (clp);
+  MemFree (csp->bkarray);
+  MemFree (csp->gdarray);
+
+  MemFree (csp);
 
   return NULL;
 }
 
-static Boolean ct_list_not_found = FALSE;
+static Boolean ct_set_not_found = FALSE;
 
-static CtListPtr GetCtLatLonDataInt (
+static CtSetPtr GetCtSetLatLonDataInt (
   CharPtr prop,
   CharPtr file,
   CharPtr PNTR local
 )
 
 {
-  ValNodePtr      boundaries = NULL;
-  FloatHi         bounds [4];
-  CtDataPtr       cdp;
-  CtDataPtr PNTR  ctarray;
-  CtDataPtr PNTR  bdarray;
-  CtListPtr       clp;
-  ValNodePtr      countries = NULL;
-  CharPtr         country;
-  FileCache       fc;
-  FILE            *fp = NULL;
-  Int2            i;
-  Int2            j = 0;
-  ValNodePtr      lastbdry = NULL;
-  ValNodePtr      lastctry = NULL;
-  Char            line [1024];
-  Int4            num;
-  Char            path [PATH_MAX];
-  CharPtr         ptr;
-  ErrSev          sev;
-  CharPtr         str = NULL;
-  double          val;
-  ValNodePtr      vnp;
-  CharPtr         wrk;
-
-  clp = (CtListPtr) GetAppProperty (prop);
-  if (clp != NULL) return clp;
-
-  if (ct_list_not_found) return NULL;
+  CtBlockPtr PNTR  bkarray;
+  ValNodePtr       blocks = NULL;
+  FloatHi          bounds [4];
+  CtBlockPtr       cbp;
+  CtGridPtr        cgp;
+  ValNodePtr       countries = NULL;
+  CharPtr          country;
+  CtSetPtr         csp;
+  FileCache        fc;
+  FILE             *fp = NULL;
+  CtGridPtr PNTR   gdarray;
+  ValNodePtr       grids = NULL;
+  Int2             hix;
+  Int2             hiy;
+  Int2             i;
+  Int2             j = 0;
+  ValNodePtr       lastblk = NULL;
+  ValNodePtr       lastctry = NULL;
+  ValNodePtr       lastgrd = NULL;
+  Char             line [1024];
+  Int2             lox;
+  Int2             loy;
+  Int4             num;
+  Char             path [PATH_MAX];
+  CharPtr          ptr;
+  ErrSev           sev;
+  CharPtr          str = NULL;
+  double           val;
+  ValNodePtr       vnp;
+  CharPtr          wrk;
+  Int2             x;
+  Int2             y;
+
+  csp = (CtSetPtr) GetAppProperty (prop);
+  if (csp != NULL) return csp;
+
+  if (ct_set_not_found) return NULL;
 
   if (FindPath ("ncbi", "ncbi", "data", path, sizeof (path))) {
     FileBuildPath (path, NULL, file);
@@ -7888,42 +8191,69 @@ static CtListPtr GetCtLatLonDataInt (
             wrk = StringSave (ptr);
             str = wrk;
             i = 0;
+
             while (StringDoesHaveText (str)) {
               ptr = StringChr (str, '\t');
               if (ptr != NULL) {
                 *ptr = '\0';
                 ptr++;
               }
+
               if (sscanf (str, "%lf", &val) == 1) {
                 bounds [i] = (FloatHi) val;
                 i++;
                 if (i > 3) {
 
-                  cdp = (CtDataPtr) MemNew (sizeof (CtData));
-                  if (cdp != NULL) {
-                    cdp->country = country;
-                    cdp->minx = bounds [0];
-                    cdp->miny = bounds [1];
-                    cdp->maxx = bounds [2];
-                    cdp->maxy = bounds [3];
-
-                    vnp = ValNodeAddPointer (&lastbdry, 0, (Pointer) cdp);
-                    if (boundaries == NULL) {
-                      boundaries = vnp;
+                  cbp = (CtBlockPtr) MemNew (sizeof (CtBlock));
+                  if (cbp != NULL) {
+                    cbp->country = country;
+                    cbp->minx = bounds [0];
+                    cbp->miny = bounds [1];
+                    cbp->maxx = bounds [2];
+                    cbp->maxy = bounds [3];
+
+                    vnp = ValNodeAddPointer (&lastblk, 0, (Pointer) cbp);
+                    if (blocks == NULL) {
+                      blocks = vnp;
+                    }
+                    lastblk = vnp;
+
+                    lox = LatLonDegreeToIndex (cbp->minx);
+                    loy = LatLonDegreeToIndex (cbp->miny);
+                    hix = LatLonDegreeToIndex (cbp->maxx);
+                    hiy = LatLonDegreeToIndex (cbp->maxy);
+
+                    for (x = lox; x <= hix; x++) {
+                      for (y = loy; y <= hiy; y++) {
+                        cgp = (CtGridPtr) MemNew (sizeof (CtGrid));
+                        if (cgp != NULL) {
+                          cgp->cbp = cbp;
+                          cgp->xindex = x;
+                          cgp->yindex = y;
+
+                          vnp = ValNodeAddPointer (&lastgrd, 0, (Pointer) cgp);
+                          if (grids == NULL) {
+                            grids = vnp;
+                          }
+                          lastgrd = vnp;
+                        }
+                      }
                     }
-                    lastbdry = vnp;
                   }
 
                   i = 0;
                 }
               }
+
               str = ptr;
             }
+
             MemFree (wrk);
           }
         }
       }
     }
+
     if (fp != NULL) {
       str = FileCacheReadLine (&fc, line, sizeof (line), NULL);
     } else {
@@ -7940,55 +8270,59 @@ static CtListPtr GetCtLatLonDataInt (
     FileClose (fp);
   }
 
-  if (countries == NULL || boundaries == NULL) {
-    ct_list_not_found = TRUE;
+  if (countries == NULL || blocks == NULL || grids == NULL) {
+    ct_set_not_found = TRUE;
     return NULL;
   }
 
-  clp = (CtListPtr) MemNew (sizeof (CtList));
-  if (clp == NULL) return NULL;
+  csp = (CtSetPtr) MemNew (sizeof (CtSet));
+  if (csp == NULL) return NULL;
 
   /* now populate, heap sort arrays */
 
-  num = ValNodeLen (boundaries);
+  num = ValNodeLen (blocks);
 
-  clp->countries = countries;
-  clp->boundaries = boundaries;
-  clp->num = (Int2) num;
+  csp->countries = countries;
+  csp->blocks = blocks;
+  csp->num_blocks = (Int2) num;
 
-  ctarray = (CtDataPtr PNTR) MemNew (sizeof (CtDataPtr) * (num + 1));
-  if (ctarray != NULL) {
-    for (vnp = boundaries, i = 0; vnp != NULL; vnp = vnp->next, i++) {
-      cdp = (CtDataPtr) vnp->data.ptrvalue;
-      ctarray [i] = cdp;
+  bkarray = (CtBlockPtr PNTR) MemNew (sizeof (CtBlockPtr) * (num + 1));
+  if (bkarray != NULL) {
+    for (vnp = blocks, i = 0; vnp != NULL; vnp = vnp->next, i++) {
+      cbp = (CtBlockPtr) vnp->data.ptrvalue;
+      bkarray [i] = cbp;
     }
 
-    HeapSort (ctarray, (size_t) num, sizeof (CtDataPtr), SortCdpByCountry);
-    clp->ctarray = ctarray;
+    HeapSort (bkarray, (size_t) num, sizeof (CtBlockPtr), SortCbpByCountry);
+    csp->bkarray = bkarray;
   }
 
-  bdarray = (CtDataPtr PNTR) MemNew (sizeof (CtDataPtr) * (num + 1));
-  if (bdarray != NULL) {
-    for (vnp = boundaries, i = 0; vnp != NULL; vnp = vnp->next, i++) {
-      cdp = (CtDataPtr) vnp->data.ptrvalue;
-      bdarray [i] = cdp;
+  num = ValNodeLen (grids);
+
+  csp->num_grids = (Int2) num;
+
+  gdarray = (CtGridPtr PNTR) MemNew (sizeof (CtGridPtr) * (num + 1));
+  if (gdarray != NULL) {
+    for (vnp = grids, i = 0; vnp != NULL; vnp = vnp->next, i++) {
+      cgp = (CtGridPtr) vnp->data.ptrvalue;
+      gdarray [i] = cgp;
     }
 
-    HeapSort (bdarray, (size_t) num, sizeof (CtDataPtr), SortCdpByBounds);
-    clp->bdarray = bdarray;
+    HeapSort (gdarray, (size_t) num, sizeof (CtGridPtr), SortCgpByGrid);
+    csp->gdarray = gdarray;
   }
 
-  SetAppProperty (prop, (Pointer) clp);
+  SetAppProperty (prop, (Pointer) csp);
 
-  return clp;
+  return csp;
 }
 
-static CtListPtr GetCtLatLonData (
+static CtSetPtr GetCtSetLatLonData (
   void
 )
 
 {
-  return GetCtLatLonDataInt ("CountryLatLonList", "country_lat_lon.txt", ctry_lat_lon);
+  return GetCtSetLatLonDataInt ("CountryLatLonList", "country_lat_lon.txt", ctry_lat_lon);
 }
 
 NLM_EXTERN Boolean IsCountryInLatLonList (
@@ -7996,34 +8330,34 @@ NLM_EXTERN Boolean IsCountryInLatLonList (
 )
 
 {
-  CtDataPtr       cdp;
-  CtDataPtr PNTR  ctarray;
-  CtListPtr       clp;
-  Int2            L, R, mid;
+  CtBlockPtr       cbp;
+  CtBlockPtr PNTR  bkarray;
+  CtSetPtr         csp;
+  Int2             L, R, mid;
 
   if (StringHasNoText (country)) return FALSE;
 
-  clp = GetCtLatLonData ();
-  if (clp == NULL) return FALSE;
+  csp = GetCtSetLatLonData ();
+  if (csp == NULL) return FALSE;
 
-  ctarray = clp->ctarray;
-  if (ctarray == NULL) return FALSE;
+  bkarray = csp->bkarray;
+  if (bkarray == NULL) return FALSE;
 
   L = 0;
-  R = clp->num - 1;
+  R = csp->num_blocks - 1;
 
   while (L < R) {
     mid = (L + R) / 2;
-    cdp = ctarray [mid];
-    if (cdp != NULL && StringICmp (cdp->country, country) < 0) {
+    cbp = bkarray [mid];
+    if (cbp != NULL && StringICmp (cbp->country, country) < 0) {
       L = mid + 1;
     } else {
       R = mid;
     }
   }
 
-  cdp = ctarray [R];
-  if (cdp != NULL && StringICmp (cdp->country, country) == 0) return TRUE;
+  cbp = bkarray [R];
+  if (cbp != NULL && StringICmp (cbp->country, country) == 0) return TRUE;
 
   return FALSE;
 }
@@ -8035,37 +8369,37 @@ NLM_EXTERN Boolean TestLatLonForCountry (
 )
 
 {
-  CtDataPtr       cdp;
-  CtDataPtr PNTR  ctarray;
-  CtListPtr       clp;
-  Int2            L, R, mid;
+  CtBlockPtr       cbp;
+  CtBlockPtr PNTR  bkarray;
+  CtSetPtr         csp;
+  Int2             L, R, mid;
 
   if (StringHasNoText (country)) return FALSE;
 
-  clp = GetCtLatLonData ();
-  if (clp == NULL) return FALSE;
+  csp = GetCtSetLatLonData ();
+  if (csp == NULL) return FALSE;
 
-  ctarray = clp->ctarray;
-  if (ctarray == NULL) return FALSE;
+  bkarray = csp->bkarray;
+  if (bkarray == NULL) return FALSE;
 
   L = 0;
-  R = clp->num - 1;
+  R = csp->num_blocks - 1;
 
   while (L < R) {
     mid = (L + R) / 2;
-    cdp = ctarray [mid];
-    if (cdp != NULL && StringICmp (cdp->country, country) < 0) {
+    cbp = bkarray [mid];
+    if (cbp != NULL && StringICmp (cbp->country, country) < 0) {
       L = mid + 1;
     } else {
       R = mid;
     }
   }
 
-  while (R < clp->num) {
-    cdp = ctarray [R];
-    if (cdp == NULL) return FALSE;
-    if (StringICmp (cdp->country, country) != 0) return FALSE;
-    if (lon >= cdp->minx && lat >= cdp->miny && lon <= cdp->maxx && lat <= cdp->maxy) return TRUE;
+  while (R < csp->num_blocks) {
+    cbp = bkarray [R];
+    if (cbp == NULL) return FALSE;
+    if (StringICmp (cbp->country, country) != 0) return FALSE;
+    if (lon >= cbp->minx && lat >= cbp->miny && lon <= cbp->maxx && lat <= cbp->maxy) return TRUE;
     R++;
   }
 
@@ -8078,44 +8412,53 @@ NLM_EXTERN CharPtr GuessCountryForLatLon (
 )
 
 {
-  CtDataPtr PNTR  bdarray;
-  CtDataPtr       cdp;
-  CtListPtr       clp;
+  CtBlockPtr      cbp;
+  CtGridPtr       cgp;
   CharPtr         country = NULL;
+  CtSetPtr        csp;
+  CtGridPtr PNTR  gdarray;
   Int2            L, R, mid;
+  Int2            x;
+  Int2            y;
 
-  clp = GetCtLatLonData ();
-  if (clp == NULL) return NULL;
+  csp = GetCtSetLatLonData ();
+  if (csp == NULL) return NULL;
 
-  bdarray = clp->bdarray;
-  if (bdarray == NULL) return NULL;
+  gdarray = csp->gdarray;
+  if (gdarray == NULL) return NULL;
 
   L = 0;
-  R = clp->num - 1;
+  R = csp->num_grids - 1;
+
+  x = LatLonDegreeToIndex (lon);
+  y = LatLonDegreeToIndex (lat);
 
   while (L < R) {
     mid = (L + R) / 2;
-    cdp = bdarray [mid];
-    if (cdp != NULL && cdp->maxx < lon) {
+    cgp = gdarray [mid];
+    if (cgp != NULL && CgpGridComp (cgp, x, y) < 0) {
       L = mid + 1;
     } else {
       R = mid;
     }
   }
 
-  while (mid < clp->num) {
-    cdp = bdarray [mid];
-    if (cdp == NULL) return country;
-    if (cdp->minx > lon) return country;
-    if (lon >= cdp->minx && lat >= cdp->miny && lon <= cdp->maxx && lat <= cdp->maxy) {
-      country = cdp->country;
+  while (R < csp->num_grids) {
+    cgp = gdarray [R];
+    if (cgp == NULL) return country;
+    if (cgp->xindex != x || cgp->yindex != y) return country;
+    cbp = cgp->cbp;
+    if (cbp == NULL) return country;
+    if (lon >= cbp->minx && lat >= cbp->miny && lon <= cbp->maxx && lat <= cbp->maxy) {
+      country = cbp->country;
     }
-    mid++;
+    R++;
   }
 
   return country;
 }
 
+
 static CharPtr bodiesOfWater [] = {
   "Bay",
   "Canal",
@@ -8166,7 +8509,7 @@ static TextFsaPtr GetBodiesOfWaterFSA (void)
   return fsa;
 }
 
-static Boolean StringContainsBodyOfWater (CharPtr str)
+NLM_EXTERN Boolean StringContainsBodyOfWater (CharPtr str)
 
 {
   Char        ch;
@@ -8200,61 +8543,6 @@ static Boolean StringContainsBodyOfWater (CharPtr str)
 
 
 
-NLM_EXTERN Boolean ParseLatLon (
-  CharPtr lat_lon,
-  FloatHi PNTR latP,
-  FloatHi PNTR lonP
-)
-
-{
-  char    ew;
-  double  lat;
-  double  lon;
-  char    ns;
-
-  if (latP != NULL) {
-    *latP = 0.0;
-  }
-  if (lonP != NULL) {
-    *lonP = 0.0;
-  }
-
-  if (StringHasNoText (lat_lon)) return FALSE;
-
-  if (sscanf (lat_lon, "%lf %c %lf %c", &lat, &ns, &lon, &ew) == 4) {
-    if (lon < -180.0) {
-      lon = -180.0;
-    }
-    if (lat < -90.0) {
-      lat = -90.0;
-    }
-    if (lon > 180.0) {
-      lon = 180.0;
-    }
-    if (lat > 90.0) {
-      lat = 90.0;
-    }
-    if (ew == 'W') {
-      lon = -lon;
-    }
-    if (ns == 'S') {
-      lat = -lat;
-    }
-
-    if (latP != NULL) {
-      *latP = (FloatHi) lat;
-    }
-    if (lonP != NULL) {
-      *lonP = (FloatHi) lon;
-    }
-
-    return TRUE;
-  }
-
-  return FALSE;
-}
-
-
 
 static CharPtr GetDash (CharPtr str)
 
@@ -9049,12 +9337,13 @@ static void ValidateLatLon (ValidStructPtr vsp, CharPtr lat_lon)
 *      Gather callback helper function for validating context on a Bioseq
 *
 *****************************************************************************/
-static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSourcePtr biop, SeqFeatPtr sfp)
+static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSourcePtr biop, SeqFeatPtr sfp, ValNodePtr sdp)
 {
   Char            badch;
   Boolean         bad_frequency;
+  BioseqPtr       bsp;
+  BioseqSetPtr    bssp;
   Char            buf [256];
-  CharPtr         casecounts;
   Char            ch;
   Boolean         chromconf = FALSE;
   Int2            chromcount = 0;
@@ -9063,38 +9352,46 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
   ValNodePtr      db;
   DbtagPtr        dbt;
   Boolean         format_ok;
+  CharPtr         gb_synonym = NULL;
   Boolean         germline = FALSE;
   CharPtr         guess = NULL;
   Boolean         has_strain = FALSE;
   Boolean         has_fwd_pcr_seq = FALSE;
   Boolean         has_rev_pcr_seq = FALSE;
   Boolean         has_pcr_name = FALSE;
-  Int2            i;
+  Boolean         has_metagenome_source = FALSE;
   Int4            id;
   Boolean         is_env_sample = FALSE;
   Boolean         is_iso_source = FALSE;
   Boolean         is_metagenomic = FALSE;
   Boolean         is_specific_host = FALSE;
   Boolean         is_transgenic = FALSE;
+  Boolean         isViral = FALSE;
   CharPtr         last_db = NULL;
   FloatHi         lat = 0.0;
   FloatHi         lon = 0.0;
   CharPtr         lat_lon = NULL;
   Boolean         lat_in_range;
   Boolean         lon_in_range;
+  Boolean         old_country = FALSE;
   OrgNamePtr      onp;
   OrgModPtr       omp;
   OrgRefPtr       orp;
+  ObjValNodePtr   ovp;
   Int4            primer_len_before;
   Int4            primer_len_after;
   ValNodePtr      pset;
   CharPtr         ptr;
   Boolean         rearranged = FALSE;
+  SeqEntryPtr     sep;
   ErrSev          sev;
   SubSourcePtr    ssp;
   CharPtr         str;
   Boolean         strict = TRUE;
+  CharPtr         synonym = NULL;
   Char            tmp [128];
+  Int4            dbvalid;
+  CharPtr         dbxerr;
 
   if (vsp->sourceQualTags == NULL) {
     InitializeSourceQualTags (vsp);
@@ -9105,6 +9402,17 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
     ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_ObsoleteSourceLocation,
               "Transposon and insertion sequence are no longer legal locations");
   }
+
+  orp = biop->org;
+  if (orp != NULL) {
+    onp = orp->orgname;
+    if (onp != NULL) {
+      if (StringNICmp (onp->lineage, "Viruses; ", 9) == 0) {
+        isViral = TRUE;
+      }
+    }
+  }
+
   ssp = biop->subtype;
   while (ssp != NULL) {
     if (ssp->subtype == SUBSRC_country) {
@@ -9112,11 +9420,15 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadCountryCode, "Multiple country names on BioSource");
       }
       countryname = ssp->name;
-      if (! CountryIsValid (countryname)) {
+      if (! CountryIsValid (countryname, &old_country)) {
         if (StringHasNoText (countryname)) {
           countryname = "?";
         }
-        ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_BadCountryCode, "Bad country name [%s]", countryname);
+        if (old_country) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadCountryCode, "Replaced country name [%s]", countryname);
+        } else {
+          ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_BadCountryCode, "Bad country name [%s]", countryname);
+        }
       }
     } else if (ssp->subtype == SUBSRC_chromosome) {
       chromcount++;
@@ -9166,10 +9478,42 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
       }
     } else if (ssp->subtype == SUBSRC_isolation_source) {
       is_iso_source = TRUE;
-     } else if (ssp->subtype == SUBSRC_plasmid_name) {
+    } else if (ssp->subtype == SUBSRC_plasmid_name) {
       if (biop->genome != GENOME_plasmid) {
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Plasmid subsource but not plasmid location");
       }
+    } else if (ssp->subtype == SUBSRC_plastid_name) {
+      if (StringCmp (ssp->name, "chloroplast") == 0) {
+        if (biop->genome != GENOME_chloroplast) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Plastid name subsource chloroplast but not chloroplast location");
+        }
+      } else if (StringCmp (ssp->name, "chromoplast") == 0) {
+        if (biop->genome != GENOME_chromoplast) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Plastid name subsource chromoplast but not chromoplast location");
+        }
+      } else if (StringCmp (ssp->name, "kinetoplast") == 0) {
+        if (biop->genome != GENOME_kinetoplast) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Plastid name subsource kinetoplast but not kinetoplast location");
+        }
+      } else if (StringCmp (ssp->name, "plastid") == 0) {    
+        if (biop->genome != GENOME_plastid) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Plastid name subsource plastid but not plastid location");
+        }
+      } else if (StringCmp (ssp->name, "apicoplast") == 0) {  
+        if (biop->genome != GENOME_apicoplast) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Plastid name subsource apicoplast but not apicoplast location");
+        }
+      } else if (StringCmp (ssp->name, "leucoplast") == 0) {  
+        if (biop->genome != GENOME_leucoplast) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Plastid name subsource leucoplast but not leucoplast location");
+        }
+      } else if (StringCmp (ssp->name, "proplastid") == 0) {  
+        if (biop->genome != GENOME_proplastid) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Plastid name subsource proplastid but not proplastid location");
+        }
+      } else {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Plastid name subsource contains unrecognized value");
+      }  
     } else if (ssp->subtype == SUBSRC_collection_date) {
       if (! CollectionDateIsValid (ssp->name)) {
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadCollectionDate, "Collection_date format is not in DD-Mmm-YYYY format");
@@ -9258,6 +9602,14 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
           ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "bad frequency qualifier value %s", ssp->name);
         }
       }
+    } else if (ssp->subtype == SUBSRC_sex && isViral) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Virus has unexpected sex qualifier");
+    } else if (ssp->subtype == SUBSRC_cell_line && isViral) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Virus has unexpected cell_line qualifier");
+    } else if (ssp->subtype == SUBSRC_cell_type && isViral) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Virus has unexpected cell_type qualifier");
+    } else if (ssp->subtype == SUBSRC_tissue_type && isViral) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Virus has unexpected tissue_type qualifier");
     }
     ssp = ssp->next;
   }
@@ -9330,9 +9682,10 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
         */
         } else if (TestLatLonForCountry (buf, lon, lat)) {
           ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_LatLonValue, "Latitude and longitude values appear to be exchanged");
+        /*
         } else if (strict) {
-          /* single unqualified country name, report at info level for now */
           ValidErr (vsp, SEV_INFO, ERR_SEQ_DESCR_LatLonCountry, "Lat_lon '%s' does not map to '%s'", lat_lon, buf);
+        */
         } else {
           if (vsp->strictLatLonCountry || (! StringContainsBodyOfWater (countryname))) {
             guess = GuessCountryForLatLon (lat, lon);
@@ -9398,6 +9751,35 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
       if (biop->genome != GENOME_proviral && biop->genome != GENOME_virion) {
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "HIV should be proviral or virion");
       }
+    } else if (StringICmp (orp->taxname, "uncultured bacterium") == 0) {
+      bsp = NULL;
+      if (sfp != NULL) {
+        bsp = BioseqFindFromSeqLoc (sfp->location);
+      } else if (sdp != NULL && sdp->extended != 0) {
+        ovp = (ObjValNodePtr) sdp;
+        if (ovp->idx.parenttype == OBJ_BIOSEQ) {
+          bsp = (BioseqPtr) ovp->idx.parentptr;
+        } else if (ovp->idx.parenttype == OBJ_BIOSEQSET) {
+          bssp = (BioseqSetPtr) ovp->idx.parentptr;
+          if (bssp != NULL) {
+            sep = bssp->seqentry;
+            if (sep != NULL) {
+              sep = FindNthBioseq (sep, 1);
+              if (sep != NULL && IS_Bioseq (sep)) {
+                bsp = (BioseqPtr) sep->data.ptrvalue;
+              }
+            }
+          }
+        }
+      }
+      if (bsp != NULL && bsp->length >= 10000) {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Uncultured bacterium sequence length is suspiciously high");
+      }
+    }
+    if (StringNICmp (orp->taxname, "uncultured ", 11) == 0) {
+      if (! is_env_sample) {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Uncultured should also have /environmental_sample");
+      }
     }
   }
   if (orp == NULL || (StringHasNoText (orp->taxname) && StringHasNoText (orp->common))) {
@@ -9435,6 +9817,14 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadOrganelle, "Only Chlorarachniophyceae and Cryptophyta have nucleomorphs");
       }
     }
+
+    /* warn if bacteria has organelle location */
+    if (StringCmp (onp->div, "BCT") == 0 
+        && biop->genome != GENOME_unknown 
+        && biop->genome != GENOME_genomic
+        && biop->genome != GENOME_plasmid) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Bacterial source should not have organelle location");
+    }
   }
   for (db = orp->db; db != NULL; db = db->next) {
     dbt = (DbtagPtr) db->data.ptrvalue;
@@ -9458,12 +9848,15 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
         }
         has_strain = TRUE;
       } else if (omp->subtype == ORGMOD_variety) {
-        if ((! StringHasNoText (onp->div)) && StringICmp (onp->div, "PLN") != 0) {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadOrgMod, "Orgmod variety should only be in plants or fungi");
+        if ((! StringHasNoText (onp->div)) && StringICmp (onp->div, "PLN") != 0 && StringStr (onp->lineage, "Cyanobacteria") == 0) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadOrgMod, "Orgmod variety should only be in plants, fungi, or cyanobacteria");
         }
         ValidateOrgModInTaxName (vsp, omp, orp->taxname);
       } else if (omp->subtype == ORGMOD_nat_host) {
         is_specific_host = TRUE;
+        if (StringICmp (omp->subname, orp->taxname) == 0) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadOrgMod, "Specific host is identical to taxname");
+        }
       } else if (omp->subtype == ORGMOD_other) {
         ValidateSourceQualTags (vsp, gcp, biop, omp->subname);
       } else if (omp->subtype == ORGMOD_biovar
@@ -9472,6 +9865,16 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
                  || omp->subtype == ORGMOD_sub_species
                  || omp->subtype == ORGMOD_pathovar) {         
         ValidateOrgModInTaxName (vsp, omp, orp->taxname);
+      } else if (omp->subtype == ORGMOD_metagenome_source) {
+        has_metagenome_source = TRUE;
+      } else if (omp->subtype == ORGMOD_common) {
+        if (StringICmp (omp->subname, orp->common) == 0) {
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadOrgMod, "OrgMod common is identical to Org-ref common");
+        }
+      } else if (omp->subtype == ORGMOD_synonym) {
+        synonym = omp->subname;
+      } else if (omp->subtype == ORGMOD_gb_synonym) {
+        gb_synonym = omp->subname;
       }
       omp = omp->next;
     }
@@ -9482,38 +9885,25 @@ static void ValidateBioSource (ValidStructPtr vsp, GatherContextPtr gcp, BioSour
   if (is_env_sample && (! is_iso_source) && (! is_specific_host)) {
     ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Environmental sample should also have isolation source or specific host annotated");
   }
+  if (has_metagenome_source && (! is_metagenomic)) {
+    ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_BioSourceInconsistency, "Metagenome source should also have metagenomic qualifier");
+  }
+  if (StringDoesHaveText (synonym) && StringDoesHaveText (gb_synonym)) {
+    if (StringICmp (synonym, gb_synonym) == 0) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "OrgMod synonym is identical to OrgMod gb_synonym");
+    }
+  }
 
   for (db = orp->db; db != NULL; db = db->next) {
     id = -1;
     dbt = (DbtagPtr) db->data.ptrvalue;
     if (dbt != NULL && dbt->db != NULL) {
-      casecounts = NULL;
-      for (i = 0; legalDbXrefs [i] != NULL; i++) {
-        if (StringCmp (dbt->db, legalDbXrefs [i]) == 0) {
-          id = i;
-          break;
-        } else if (StringICmp (dbt->db, legalDbXrefs [i]) == 0) {
-          casecounts = legalDbXrefs [i];
-        }
-      }
-      if (id == -1 || id < 4) {
-        if (StringDoesHaveText (casecounts)) {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_IllegalDbXref, "Illegal db_xref type %s, legal capitalization is %s", dbt->db, casecounts);
-        } else {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_IllegalDbXref, "Illegal db_xref type %s", dbt->db);
-        }
-      }
-    }
-  }
-
-  if (sfp != NULL) {
-    for (db = sfp->dbxref; db != NULL; db = db->next) {
-      dbt = (DbtagPtr) db->data.ptrvalue;
-      if (dbt != NULL) {
-        if (StringICmp (dbt->db, "taxon") == 0) {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_TaxonDbxrefOnFeature, "BioSource feature has taxon xref in common feature db_xref list");
-        }
-      }
+      dbxerr = NULL;
+      dbvalid = IsDbxrefValid (dbt->db, NULL, orp, FALSE, &dbxerr);
+      if (dbxerr != NULL) {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_IllegalDbXref, dbxerr);
+        dbxerr = MemFree (dbxerr);
+      } 
     }
   }
 
@@ -9861,7 +10251,7 @@ static Boolean ValidateSeqDescrCommon (ValNodePtr sdp, BioseqValidStrPtr bvsp, V
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_InvalidForType, "Molinfo-biomol other should be used if Biosource-location is synthetic");
       }
     }
-    /* ValidateBioSource (vsp, gcp, biop, NULL); */
+    /* ValidateBioSource (vsp, gcp, biop, NULL, vnp); */
     this_org = biop->org;
     /* fall into Seq_descr_org */
   case Seq_descr_org:
@@ -10205,6 +10595,20 @@ static Boolean IsGenBankAccn (SeqEntryPtr sep, SeqLocPtr location)
   return FALSE;
 }
 
+static Boolean IsEMBLAccn (SeqEntryPtr sep, SeqLocPtr location)
+{
+  BioseqPtr  bsp;
+  SeqIdPtr   sip;
+
+  bsp = BioseqFindFromSeqLoc (location);
+  if (bsp != NULL) {
+    for (sip = bsp->id; sip != NULL; sip = sip->next) {
+      if (sip->choice == SEQID_EMBL) return TRUE;
+    }
+  }
+  return FALSE;
+}
+
 static Boolean IsGeneralAccn (SeqEntryPtr sep, SeqLocPtr location)
 {
   BioseqPtr  bsp;
@@ -10836,6 +11240,8 @@ static void ValidateCDSmRNAmatch (
 
 {
   BioSourcePtr       biop;
+  ValNodePtr         cdshead = NULL;
+  ValNodePtr         cdstail = NULL;
   SeqMgrDescContext  dcontext;
   SeqMgrFeatContext  fcontext, rcontext;
   GatherContextPtr   gcp;
@@ -10846,6 +11252,7 @@ static void ValidateCDSmRNAmatch (
   Int2               i, j, k, numfeats, tmpnumcds, tmpnummrna, count;
   Boolean            is_genbank = FALSE;
   LpData             ld;
+  Int2               num_no_mrna = 0;
   Int4               num_repeat_regions;
   Uint2              olditemtype = 0;
   Uint4              olditemid = 0;
@@ -10859,6 +11266,7 @@ static void ValidateCDSmRNAmatch (
   SeqFeatPtr         sfp;
   SeqIdPtr           sip;
   VvmDataPtr         vdp;
+  ValNodePtr         vnp;
 
   if (vsp == NULL || bsp == NULL) return;
   if (! ISA_na (bsp->mol)) return;
@@ -11078,6 +11486,7 @@ static void ValidateCDSmRNAmatch (
           rpt_region = SeqMgrGetOverlappingFeature (sfp->location, 0, repeat_region_array, num_repeat_regions,
                                                     NULL, CONTAINED_WITHIN, &rcontext);
           if (rpt_region == NULL) {
+            /*
             if (gcp != NULL) {
               gcp->itemID = sfp->idx.itemID;
               gcp->thistype = OBJ_SEQFEAT;
@@ -11085,6 +11494,13 @@ static void ValidateCDSmRNAmatch (
             vsp->descr = NULL;
             vsp->sfp = sfp;
             ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_CDSwithNoMRNAOverlap, "CDS overlapped by 0 mRNAs");
+            */
+            vnp = ValNodeAddPointer (&cdstail, 0, (Pointer) sfp);
+            if (cdshead == NULL) {
+              cdshead = vnp;
+            }
+            cdstail = vnp;
+            num_no_mrna++;
           }
         }
       }
@@ -11094,6 +11510,34 @@ static void ValidateCDSmRNAmatch (
 
   MemFree (repeat_region_array);
 
+  if (num_no_mrna > 0) {
+    if (num_no_mrna >= 10) {
+      if (gcp != NULL) {
+        gcp->itemID = olditemid;
+        gcp->thistype = olditemtype;
+      }
+      vsp->descr = NULL;
+      vsp->sfp = NULL;
+      vsp->bsp = bsp;
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_CDSwithNoMRNAOverlap,
+                "%d out of %d CDSs overlapped by 0 mRNAs", (int) num_no_mrna, (int) numcds);
+    } else {
+      for (vnp = cdshead; vnp != NULL; vnp = vnp->next) {
+        sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+        if (sfp == NULL) continue;
+        if (gcp != NULL) {
+          gcp->itemID = sfp->idx.itemID;
+          gcp->thistype = OBJ_SEQFEAT;
+        }
+        vsp->descr = NULL;
+        vsp->sfp = sfp;
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_CDSwithNoMRNAOverlap, "CDS overlapped by 0 mRNAs");
+      }
+    }
+  }
+
+  ValNodeFree (cdshead);
+
   if (gcp != NULL) {
     gcp->itemID = olditemid;
     gcp->thistype = olditemtype;
@@ -11138,6 +11582,7 @@ static Boolean HaveUniqueFeatIDXrefs (SeqFeatXrefPtr xref1, SeqFeatXrefPtr xref2
 static Int2 WhichRNA (SeqFeatPtr sfp)
 
 {
+  GBQualPtr  gbq;
   RnaRefPtr  rrp;
   CharPtr    str;
 
@@ -11168,6 +11613,13 @@ static Int2 WhichRNA (SeqFeatPtr sfp)
     if (StringNICmp (str, "23 ", 3) == 0) return RIGHT_RIBOSOMAL_SUBUNIT;
   }
   if (rrp->type == 255) {
+    if (StringICmp (str, "misc_RNA") == 0) {
+      for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
+        if (StringICmp (gbq->qual, "product") != 0) continue;
+        if (StringHasNoText (gbq->val)) continue;
+        str = gbq->val;
+      }
+    }
     if (StringICmp (str, "internal transcribed spacer 1") == 0) return INTERNAL_SPACER_1;
     if (StringICmp (str, "internal transcribed spacer 2") == 0) return INTERNAL_SPACER_2;
     /* variant spellings */
@@ -11285,17 +11737,24 @@ static Boolean LIBCALLBACK GetFeatsInGaps (
 )
 
 {
+  BioseqPtr         bsp;
   Int4              dashes;
   Int2              first = 0;
   GatherContextPtr  gcp;
   Int2              last = 0;
+  Int4              len;
+  SeqLocPtr         loc;
+  Boolean           needToStream = TRUE;
   Int4              Ns;
   Uint2             olditemtype = 0;
   Uint4             olditemid = 0;
   Int4              plusses;
+  Int2              prefix = 0;
+  Int2              suffix = 0;
   Int4              realBases;
   Int2              res;
   StreamCache       sc;
+  SeqIntPtr         sintp;
   ValidStructPtr    vsp;
 
   if (sfp == NULL || fcontext == NULL) return FALSE;
@@ -11305,6 +11764,8 @@ static Boolean LIBCALLBACK GetFeatsInGaps (
   if (gcp == NULL) return FALSE;
 
   if (sfp->idx.subtype == FEATDEF_gap) return TRUE;
+  loc = sfp->location;
+  if (loc == NULL) return TRUE;
 
   olditemid = gcp->itemID;
   olditemtype = gcp->thistype;
@@ -11319,7 +11780,43 @@ static Boolean LIBCALLBACK GetFeatsInGaps (
   Ns = 0;
   realBases = 0;
 
-  if (StreamCacheSetup (NULL, sfp->location, EXPAND_GAPS_TO_DASHES | KNOWN_GAP_AS_PLUS, &sc)) {
+  /* special check for single interval misc_features that may exactly cover a gap */
+  if (loc->choice == SEQLOC_INT && sfp->idx.subtype == FEATDEF_misc_feature) {
+    sintp = (SeqIntPtr) loc->data.ptrvalue;
+    if (sintp != NULL) {
+      bsp = BioseqFind (sintp->id);
+      if (bsp != NULL && sintp->from > 0 && sintp->to < bsp->length - 1) {
+        len = SeqLocLen (loc);
+        if (StreamCacheSetup (bsp, NULL, EXPAND_GAPS_TO_DASHES | KNOWN_GAP_AS_PLUS, &sc)) {
+          StreamCacheSetPosition (&sc, sintp->from - 1);
+          prefix = StreamCacheGetResidue (&sc);
+          while ((res = StreamCacheGetResidue (&sc)) != '\0' && len > 0) {
+            if (IS_LOWER (res)) {
+              res = TO_UPPER (res);
+            }
+            if (first == 0) {
+              first = res;
+            }
+            last = res;
+            if (res == '-') {
+              dashes++;
+            } else if (res == '+') {
+              plusses++;
+            } else if (res == 'N') {
+              Ns++;
+            } else if (res != 0) {
+              realBases++;
+            }
+            len--;
+          }
+          suffix = StreamCacheGetResidue (&sc);
+          needToStream = FALSE;
+        }
+      }
+    }
+  }
+
+  if (needToStream && StreamCacheSetup (NULL, loc, EXPAND_GAPS_TO_DASHES | KNOWN_GAP_AS_PLUS, &sc)) {
     while ((res = StreamCacheGetResidue (&sc)) != '\0') {
       if (IS_LOWER (res)) {
         res = TO_UPPER (res);
@@ -11334,7 +11831,7 @@ static Boolean LIBCALLBACK GetFeatsInGaps (
         plusses++;
       } else if (res == 'N') {
         Ns++;
-      } else {
+      } else if (res != 0) {
         realBases++;
       }
     }
@@ -11344,7 +11841,9 @@ static Boolean LIBCALLBACK GetFeatsInGaps (
     /* ignore features that do not cover any gap characters */
   } else if (first == '-' || first == '+' || last == '-' || last == '+') {
     if (realBases > 0) {
-      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_FeatureCrossesGap, "Feature crosses sequence gap");
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_FeatureBeginsOrEndsInGap, "Feature begins or ends in gap");
+    } else if (IS_ALPHA (prefix) && IS_ALPHA (suffix)) {
+      /* ignore (misc_) features that exactly cover the gap */
     } else {
       ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_FeatureInsideGap, "Feature inside sequence gap");
     }
@@ -11352,17 +11851,19 @@ static Boolean LIBCALLBACK GetFeatsInGaps (
     /* ignore genes, unless they start or stop in a gap */
   } else if (dashes == 0 && plusses == 0 && Ns > 0) {
     if (realBases > 0) {
+      /*
       ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_FeatureCrossesGap, "Feature crosses gap of Ns");
+      */
     } else {
       ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_FeatureInsideGap, "Feature inside gap of Ns");
     }
   } else if (dashes > 0) {
     if (realBases > 0) {
       if (sfp->idx.subtype == FEATDEF_CDS || sfp->idx.subtype == FEATDEF_mRNA) {
-        ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_FeatureCrossesGap, "Feature crosses sequence gap");
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_FeatureCrossesGap, "Feature crosses gap of unknown length");
       }
     } else {
-      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_FeatureInsideGap, "Feature inside sequence gap");
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_FeatureInsideGap, "Feature inside gap of unknown length");
     }
   } else if (plusses > 0) {
     if (realBases > 0) {
@@ -11381,19 +11882,39 @@ static Boolean LIBCALLBACK GetFeatsInGaps (
   return TRUE;
 }
 
+static Boolean LIBCALLBACK MarkFeatsInGaps (
+  SeqFeatPtr sfp,
+  SeqMgrFeatContextPtr fcontext
+)
+
+{
+  VvmDataPtr         vdp;
+
+  if (sfp == NULL) return TRUE;
+  vdp = (VvmDataPtr) sfp->idx.scratch;
+  if (vdp == NULL) return TRUE;
+
+  vdp->feat_touches_gap = TRUE;
+
+  return TRUE;
+}
+
 static void CheckBioseqForFeatsInGap (
   BioseqPtr bsp,
   ValidStructPtr vsp
 )
 
 {
-  Int4         currpos = 0;
-  SeqLitPtr    litp;
-  SeqInt       si;
-  SeqIdPtr     sip;
-  SeqLoc       sl;
-  SeqLocPtr    slp;
-  ValNodePtr   vnp;
+  Int4               currpos = 0;
+  SeqMgrFeatContext  fcontext;
+  SeqLitPtr          litp;
+  SeqFeatPtr         sfp;
+  SeqInt             si;
+  SeqIdPtr           sip;
+  SeqLoc             sl;
+  SeqLocPtr          slp;
+  VvmDataPtr         vdp;
+  ValNodePtr         vnp;
 
   if (bsp == NULL || bsp->repr != Seq_repr_delta || ISA_aa (bsp->mol)) return;
   sip = SeqIdFindBest (bsp->id, 0);
@@ -11417,11 +11938,22 @@ static void CheckBioseqForFeatsInGap (
         si.id = sip;
         sl.choice = SEQLOC_INT;
         sl.data.ptrvalue = (Pointer) &si;
-        SeqMgrExploreFeatures (bsp, (Pointer) vsp, GetFeatsInGaps, &sl, NULL, NULL);
+        SeqMgrExploreFeatures (bsp, (Pointer) vsp, MarkFeatsInGaps, &sl, NULL, NULL);
+        /* SeqMgrExploreFeatures (bsp, (Pointer) vsp, GetFeatsInGaps, &sl, NULL, NULL); */
       }
       currpos += litp->length;
     }
   }
+
+  sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
+  while (sfp != NULL) {
+    vdp = (VvmDataPtr) sfp->idx.scratch;
+    if (vdp != NULL && vdp->feat_touches_gap) {
+      fcontext.userdata = (Pointer) vsp;
+      GetFeatsInGaps (sfp, &fcontext);
+    }
+    sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
+  }
 }
 
 static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bvsp)
@@ -11872,7 +12404,7 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
                 if (suppress_duplicate_messages && (featdeftype == FEATDEF_CDS || featdeftype == FEATDEF_mRNA) && HaveUniqueFeatIDXrefs (xref, sfp->xref)) {
                   /* do not report CDS or mRNA if every one has a unique product and unique featID xrefs */
                 } else {
-                  ValidErr (vsp, severity, ERR_SEQ_FEAT_DuplicateFeat, "Features have identical intervals, but labels differ (packaged in different feature table)");
+                  ValidErr (vsp, /* severity */ SEV_WARNING, ERR_SEQ_FEAT_DuplicateFeat, "Features have identical intervals, but labels differ (packaged in different feature table)");
                 }
               }
             }
@@ -12642,6 +13174,7 @@ static void ValidateBioseqContext (GatherContextPtr gcp)
   Boolean         is_neg_strand_virus = FALSE;
   Boolean         is_ambisense_virus = FALSE;
   Boolean         is_transgenic = FALSE;
+  Boolean         has_cds = FALSE;
   ErrSev          sev;
   SubSourcePtr    ssp;
   CharPtr         str;
@@ -12804,6 +13337,7 @@ static void ValidateBioseqContext (GatherContextPtr gcp)
 
     sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &fcontext);
     while (sfp != NULL) {
+      has_cds = TRUE;
       if (SeqLocStrand (sfp->location) == Seq_strand_minus) {
         if (mip->biomol != MOLECULE_TYPE_GENOMIC) {
           ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Negative-strand virus with minus strand CDS should be genomic");
@@ -12815,6 +13349,23 @@ static void ValidateBioseqContext (GatherContextPtr gcp)
       }
       sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_CDREGION, 0, &fcontext);
     }
+    if (! has_cds) {
+      sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_misc_feature, &fcontext);
+      while (sfp != NULL) {
+        if (StringISearch (sfp->comment, "nonfunctional") != NULL) {
+          if (SeqLocStrand (sfp->location) == Seq_strand_minus) {
+            if (mip->biomol != MOLECULE_TYPE_GENOMIC) {
+              ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Negative-strand virus with nonfunctional minus strand misc_feature should be mRNA or cRNA");
+            }
+          } else {
+            if (mip->biomol != MOLECULE_TYPE_MRNA && mip->biomol != MOLECULE_TYPE_CRNA && (! is_ambisense_virus)) {
+              ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BioSourceInconsistency, "Negative-strand virus with nonfunctional plus strand misc_feature should be mRNA or cRNA");
+            }
+          }
+        }
+        sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_misc_feature, &fcontext);
+      }
+    }
 
     gcp->entityID = oldEntityID;
     gcp->itemID = oldItemID;
@@ -14120,7 +14671,7 @@ static Boolean ValidateECnumber (CharPtr str)
 NLM_EXTERN void ECNumberFSAFreeAll (void)
 
 {
-  CtListPtr   clp;
+  CtSetPtr    csp;
   TextFsaPtr  fsa;
 
   fsa = (TextFsaPtr) GetAppProperty ("SpecificECNumberFSA");
@@ -14153,10 +14704,10 @@ NLM_EXTERN void ECNumberFSAFreeAll (void)
     TextFsaFree (fsa);
   }
 
-  clp = (CtListPtr) GetAppProperty ("CountryLatLonList");
-  if (clp != NULL) {
+  csp = (CtSetPtr) GetAppProperty ("CountryLatLonList");
+  if (csp != NULL) {
     SetAppProperty ("CountryLatLonList", NULL);
-    CtLatLonDataFree (clp);
+    CtSetDataFree (csp);
   }
 }
 
@@ -14723,6 +15274,10 @@ static void ValidateImpFeat (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPt
           if (!found) {
             ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_InvalidQualifierValue, "%s is not a legal value for qualifier %s", gbqual->val, gbqual->qual);
           }
+        } else if (val == GBQUAL_frequency) {
+          if (StringCmp (gbqual->val, "1") == 0 || StringCmp (gbqual->val, "1.0") == 0 || StringCmp (gbqual->val, "1.00") == 0) {
+            ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_InvalidQualifierValue, "%s is a suspicious value for qualifier %s", gbqual->val, gbqual->qual);
+          }
         } else if (val == GBQUAL_compare) {
           multi_compare = FALSE;
           ptr = gbqual->val;
@@ -15157,6 +15712,85 @@ static Boolean PartialAtSpliceSiteOrGap (ValidStructPtr vsp, SeqLocPtr head, Uin
   return rsult;
 }
 
+
+static void 
+ValidateIntronEndsAtSpliceSiteOrGap 
+(ValidStructPtr vsp, 
+ SeqLocPtr slp)
+{
+  BioseqPtr       bsp;
+  SeqIdPtr        sip;
+  Uint1           strand;
+  Int4            strt, stop, pos;
+  Boolean         partial5, partial3;
+  Char            buf[3];
+  Char            id_buf[150];
+
+  if (slp == NULL) return;
+  CheckSeqLocForPartial (slp, &partial5, &partial3);
+  if (partial5 && partial3) return;
+
+  sip = SeqLocId (slp);
+  if (sip == NULL)
+    return;
+  
+  bsp = NULL;
+  if (sip != NULL && (sip->choice != SEQID_GI || sip->data.intvalue > 0)) {
+    bsp = BioseqLockById (sip);
+  }
+  if (bsp == NULL)
+    return;
+
+  BioseqLabel (bsp, id_buf, sizeof (id_buf) - 1, OM_LABEL_CONTENT);
+
+  strt = SeqLocStart (slp);
+  stop = SeqLocStop (slp);
+
+  strand = SeqLocStrand (slp);
+
+  if (!partial5) {
+    if (strand == Seq_strand_minus) {
+      SeqPortStreamInt (bsp, stop - 1, stop, Seq_strand_minus, EXPAND_GAPS_TO_DASHES, (Pointer) buf, NULL);
+      pos = stop;
+    } else {
+      SeqPortStreamInt (bsp, strt, strt + 1, Seq_strand_plus, EXPAND_GAPS_TO_DASHES, (Pointer) buf, NULL);
+      pos = strt;
+    }
+    if ((buf[0] == '-' && buf[1] == '-')
+        || (buf[0] == 'G' && buf[1] == 'T')
+        || (buf[0] == 'G' && buf[1] == 'C')) {
+      /* location is ok */
+    } else if (pos == 0 || pos == bsp->length - 1) {
+      ValidErr (vsp, SEV_INFO, ERR_SEQ_FEAT_NotSpliceConsensusDonor,
+                "Splice donor consensus (GT) not found at start of terminal intron, position %ld of %s", (long) (pos + 1), id_buf);
+    } else {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_NotSpliceConsensusDonor,
+                "Splice donor consensus (GT) not found at start of intron, position %ld of %s", (long) (pos + 1), id_buf);
+    }
+  }
+  if (!partial3) {
+    if (strand == Seq_strand_minus) {
+      SeqPortStreamInt (bsp, strt, strt + 1, Seq_strand_minus, EXPAND_GAPS_TO_DASHES, (Pointer) buf, NULL);
+      pos = strt;
+    } else {
+      SeqPortStreamInt (bsp, stop - 1, stop, Seq_strand_plus, EXPAND_GAPS_TO_DASHES, (Pointer) buf, NULL);
+      pos = stop;
+    }
+    if ((buf[0] == '-' && buf[1] == '-')
+        || (buf[0] == 'A' && buf[1] == 'G')) {
+      /* location is ok */
+    } else if (pos == 0 || pos == bsp->length - 1) {
+      ValidErr (vsp, SEV_INFO, ERR_SEQ_FEAT_NotSpliceConsensusAcceptor,
+                "Splice acceptor consensus (AG) not found at end of terminal intron, position %ld of %s, but at end of sequence", (long) (pos + 1), id_buf);
+    } else {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_NotSpliceConsensusAcceptor,
+                "Splice acceptor consensus (AG) not found at end of intron, position %ld of %s", (long) (pos + 1), id_buf);
+    }
+  }
+  BioseqUnlock (bsp);  
+}
+
+
 #if 0
 static void CheckTrnaCodons (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPtr sfp, tRNAPtr trp)
 {
@@ -16129,67 +16763,27 @@ static Boolean OverlappingGeneIsPseudo (SeqFeatPtr sfp)
   return FALSE;
 }
 
-static CharPtr legalDbXrefOnRefSeq [] = {
-  "GenBank",
-  "EMBL",
-  "DDBJ",
-  NULL
-};
-
-static CharPtr badDbXref [] = {
-  "PIDe",
-  "PIDd",
-  "PIDg",
-  "PID",
-  "NID",
-  "GI",
-  NULL
-};
-
 static void CheckForIllegalDbxref (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPtr sfp, ValNodePtr dbxref)
 
 {
-  CharPtr     casecounts;            
+  CharPtr     dbxerr;          
   DbtagPtr    db;
-  Int2        i;
   Int4        id;
   ValNodePtr  vnp;
+  Boolean     valid;
 
   for (vnp = dbxref; vnp != NULL; vnp = vnp->next) {
     id = -1;
     db = (DbtagPtr) vnp->data.ptrvalue;
     if (db != NULL && db->db != NULL) {
-      casecounts = NULL;
-      for (i = 0; legalDbXrefs [i] != NULL; i++) {
-        if (StringCmp (db->db, legalDbXrefs [i]) == 0) {
-          id = i;
-          break;
-        } else if (StringICmp (db->db, legalDbXrefs [i]) == 0) {
-          casecounts = legalDbXrefs [i];
-        }
-      }
-      if (id == -1 && GPSorRefSeq (vsp->sep, sfp->location)) {
-        for (i = 0; legalDbXrefOnRefSeq [i] != NULL; i++) {
-          if (StringCmp (db->db, legalDbXrefOnRefSeq [i]) == 0) return;
-        }
-        for (i = 0; legalRefSeqDbXrefs [i] != NULL; i++) {
-          if (StringCmp (db->db, legalRefSeqDbXrefs [i]) == 0) return;
-        }
-      }
-      if (id == -1 || (sfp->data.choice != SEQFEAT_CDREGION && id < 4)) {
-        if (StringDoesHaveText (casecounts)) {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_IllegalDbXref, "Illegal db_xref type %s, legal capitalization is %s", db->db, casecounts);
-        } else {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_IllegalDbXref, "Illegal db_xref type %s", db->db);
-        }
-      } else {
-        for (i = 0; badDbXref [i] != NULL; i++) {
-          if (StringICmp (db->db, badDbXref [i]) == 0) {
-            ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_IllegalDbXref,
-                      "db_xref type %s is only created by the flatfile generator, and should not be in the record as a separate xref", db->db);
-          }
-        }
-      }
+      dbxerr = NULL;
+      valid = IsDbxrefValid (db->db, sfp, NULL,
+                             GPSorRefSeq (vsp->sep, sfp->location),
+                             &dbxerr);
+      if (dbxerr != NULL) {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_IllegalDbXref, dbxerr);
+        dbxerr = MemFree (dbxerr);
+      }                 
     }
   }
 }
@@ -17133,6 +17727,9 @@ static void ValidateGoTerms (
   for (vnp = head; vnp != NULL; vnp = vnp->next) {
     gsp = (GovStrucPtr) vnp->data.ptrvalue;
     if (gsp == NULL) continue;
+    if (StringHasNoText (gsp->goid)) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_GeneOntologyTermMissingGOID, "GO term does not have GO identifier");
+    }
     if (lastgsp != NULL) {
       if (StringICmp (gsp->term, lastgsp->term) == 0 || StringICmp (gsp->goid, lastgsp->goid) == 0) {
         if (gsp->pmid == lastgsp->pmid && StringICmp (gsp->evidence, lastgsp->evidence) == 0) {
@@ -17333,6 +17930,227 @@ static Boolean ValStrandsMatch (Uint1 featstrand, Uint1 locstrand)
   return FALSE;
 }
 
+static CharPtr badGeneSyn [] = {
+  "alpha",
+  "alternative",
+  "beta",
+  "cellular",
+  "cytokine",
+  "drosophila",
+  "gamma",
+  "HLA",
+  "homolog",
+  "mouse",
+  "orf",
+  "partial",
+  "plasma",
+  "precursor",
+  "pseudogene",
+  "putative",
+  "rearranged",
+  "small",
+  "trna",
+  "unknown function",
+  "unknown protein",
+  "unknown",
+  "unnamed",
+  NULL
+};
+
+static CharPtr badProtName [] = {
+  "'hypothetical protein",
+  "alpha",
+  "alternative",
+  "alternatively spliced",
+  "bacteriophage hypothetical protein",
+  "beta",
+  "cellular",
+  "cnserved hypothetical protein",
+  "conesrved hypothetical protein",
+  "conserevd hypothetical protein",
+  "conserved archaeal protein",
+  "conserved domain protein",
+  "conserved hypohetical protein",
+  "conserved hypotehtical protein",
+  "conserved hypotheical protein",
+  "conserved hypothertical protein",
+  "conserved hypothetcial protein",
+  "conserved hypothetical exported protein",
+  "conserved hypothetical integral membrane protein",
+  "conserved hypothetical membrane protein",
+  "conserved hypothetical phage protein",
+  "conserved hypothetical prophage protein",
+  "conserved hypothetical protein - phage associated",
+  "conserved hypothetical protein fragment 3",
+  "conserved hypothetical protein, fragment",
+  "conserved hypothetical protein, putative",
+  "conserved hypothetical protein, truncated",
+  "conserved hypothetical protein, truncation",
+  "conserved hypothetical protein; possible membrane protein",
+  "conserved hypothetical protein; putative membrane protein",
+  "conserved hypothetical protein.",
+  "conserved hypothetical protein",
+  "conserved hypothetical proteins",
+  "conserved hypothetical protien",
+  "conserved hypothetical transmembrane protein",
+  "conserved hypothetical",
+  "conserved hypotheticcal protein",
+  "conserved hypthetical protein",
+  "conserved in bacteria",
+  "conserved membrane protein",
+  "conserved protein of unknown function ; putative membrane protein",
+  "conserved protein of unknown function",
+  "conserved protein",
+  "conserved unknown protein",
+  "conservedhypothetical protein",
+  "conserverd hypothetical protein",
+  "conservered hypothetical protein",
+  "consrved hypothetical protein",
+  "converved hypothetical protein",
+  "cytokine",
+  "drosophila",
+  "duplicated hypothetical protein",
+  "gamma",
+  "HLA",
+  "homeodomain protein",
+  "homeodomain",
+  "homolog",
+  "hyopthetical protein",
+  "hypotethical",
+  "hypotheical protein",
+  "hypothertical protein",
+  "hypothetcical protein",
+  "hypothetical  protein",
+  "hypothetical conserved protein",
+  "hypothetical exported protein",
+  "hypothetical novel protein",
+  "hypothetical orf",
+  "hypothetical phage protein",
+  "hypothetical prophage protein",
+  "hypothetical protein - phage associated",
+  "hypothetical protein (fragment)",
+  "hypothetical protein (multi-domain)",
+  "hypothetical protein (phage associated)",
+  "hypothetical protein fragment ",
+  "hypothetical protein fragment 1",
+  "hypothetical protein predicted by genemark",
+  "hypothetical protein predicted by glimmer",
+  "hypothetical protein predicted by glimmer/critica",
+  "hypothetical protein-putative conserved hypothetical protein",
+  "hypothetical protein, conserved",
+  "hypothetical protein, phage associated",
+  "hypothetical protein, truncated",
+  "hypothetical protein.",
+  "hypothetical protein",
+  "hypothetical proteins",
+  "hypothetical protien",
+  "hypothetical transmembrane protein",
+  "hypothetical",
+  "hypothetoical protein",
+  "hypothteical protein",
+  "identified by sequence similarity; putative; ORF located\nusing Blastx/FrameD",
+  "identified by sequence similarity; putative; ORF located\nusing Blastx/Glimmer/Genemark",
+  "ion channel",
+  "membrane protein, putative",
+  "mouse",
+  "narrowly conserved hypothetical protein ",
+  "novel protein",
+  "orf, conserved hypothetical protein",
+  "orf, hypothetical protein",
+  "orf, hypothetical, fragment",
+  "orf, hypothetical",
+  "orf, partial conserved hypothetical protein",
+  "orf; hypothetical protein",
+  "orf; unknown function",
+  "orf",
+  "partial cds, hypothetical",
+  "partial",
+  "partially conserved hypothetical protein",
+  "phage hypothetical protein",
+  "phage-related conserved hypothetical protein",
+  "phage-related protein",
+  "plasma",
+  "possible hypothetical protein",
+  "precursor",
+  "predicted coding region",
+  "predicted protein (pseudogene)",
+  "predicted protein family",
+  "predicted protein",
+  "product uncharacterised protein family",
+  "protein family",
+  "protein of unknown function",
+  "pseudogene",
+  "putative conserved protein",
+  "putative exported protein",
+  "putative hypothetical protein",
+  "putative membrane protein",
+  "putative orf; unknown function",
+  "putative phage protein",
+  "putative protein",
+  "putative",
+  "putative",
+  "rearranged",
+  "repeats containing protein",
+  "reserved",
+  "ribosomal protein",
+  "similar to",
+  "small hypothetical protein",
+  "small",
+  "transmembrane protein",
+  "trna",
+  "trp repeat",
+  "trp-repeat protein",
+  "truncated conserved hypothetical protein",
+  "truncated hypothetical protein",
+  "uncharacterized conserved membrane protein",
+  "uncharacterized conserved protein",
+  "uncharacterized conserved secreted protein",
+  "uncharacterized protein conserved in archaea",
+  "uncharacterized protein conserved in bacteria",
+  "uncharacterized protein",
+  "unique hypothetical protein",
+  "unique hypothetical",
+  "unknown CDS",
+  "unknown function",
+  "unknown gene",
+  "unknown protein",
+  "unknown protein",
+  "unknown-related protein",
+  "unknown, conserved protein",
+  "unknown, hypothetical",
+  "unknown; predicted coding region",
+  "unknown",
+  "unknown",
+  "unnamed protein product",
+  "unnamed",
+  "very hypothetical protein",
+  NULL
+};
+
+static Boolean NameInList (CharPtr name, CharPtr PNTR list, size_t numelements)
+
+{
+  Int2  L, R, mid;
+
+  if (StringHasNoText (name) || list == NULL || numelements < 1) return FALSE;
+
+  L = 0;
+  R = numelements - 1; /* -1 because now NULL terminated */
+
+  while (L < R) {
+    mid = (L + R) / 2;
+    if (StringICmp (list [mid], name) < 0) {
+      L = mid + 1;
+    } else {
+      R = mid;
+    }
+  }
+
+  if (StringICmp (list [R], name) == 0) return TRUE;
+
+  return FALSE;
+}
+
 NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
 {
   Int2            type, i, j;
@@ -17403,6 +18221,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
   Boolean         isgap;
   Boolean         badseq;
   Boolean         is_seqloc_bond;
+  SeqBondPtr      sbp;
   SeqFeatXrefPtr  xref, matchxref;
   SeqFeatPtr      matchsfp, origsfp;
   Boolean         hasxref;
@@ -17420,6 +18239,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
   Boolean         farFetchProd;
   Boolean         skip;
   Boolean         is_nc = FALSE;
+  Boolean         no_nonconsensus_except = TRUE;
 
 
   vsp = (ValidStructPtr) (gcp->userdata);
@@ -17458,6 +18278,16 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
   partials[0] = SeqLocPartialCheckEx (sfp->product, farFetchProd);
   partials[1] = SeqLocPartialCheck (sfp->location);
 
+  if (sfp->excpt) {
+    if (StringISearch (sfp->except_text, "nonconsensus splice site") != NULL) {
+      no_nonconsensus_except = FALSE;
+    }
+  }
+
+  if (sfp->idx.subtype == FEATDEF_intron && no_nonconsensus_except) {
+    ValidateIntronEndsAtSpliceSiteOrGap (vsp, sfp->location);
+  }
+
   if ((partials[0] != SLP_COMPLETE) || (partials[1] != SLP_COMPLETE) || (sfp->partial)) {       /* partialness */
     /* a feature on a partial sequence should be partial -- if often isn't */
     if ((!sfp->partial) && (partials[1] != SLP_COMPLETE) && (sfp->location->choice == SEQLOC_WHOLE)) {
@@ -17588,13 +18418,17 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
           } else if (sfp->data.choice == SEQFEAT_CDREGION && sfp->excpt &&
                      StringStr (sfp->except_text, "rearrangement required for product") != NULL) {
           } else if (sfp->data.choice == SEQFEAT_CDREGION && j == 0) {
-            ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_PartialProblem,
-              "%s: %s", parterr[i], "5' partial is not at start AND"
-              " is not at consensus splice site");
+            if (no_nonconsensus_except) {
+              ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_PartialProblem,
+                "%s: %s", parterr[i], "5' partial is not at start AND"
+                " is not at consensus splice site");
+            }
           } else if (sfp->data.choice == SEQFEAT_CDREGION && j == 1) {
-            ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_PartialProblem,
-              "%s: %s", parterr[i], "3' partial is not at stop AND"
-              " is not at consensus splice site");
+            if (no_nonconsensus_except) {
+              ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_PartialProblem,
+                "%s: %s", parterr[i], "3' partial is not at stop AND"
+                " is not at consensus splice site");
+            }
           } else {
             ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_PartialProblem,
               "%s: %s", parterr[i], parterrs[j]);
@@ -17700,6 +18534,21 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
           }
         }
       }
+      if (grp->syn != NULL && vsp->is_refseq_in_sep) {
+        for (vnp = grp->syn; vnp != NULL; vnp = vnp->next) {
+          str = (CharPtr) vnp->data.ptrvalue;
+          if (StringHasNoText (str)) continue;
+          if (NameInList (str, badGeneSyn, sizeof (badGeneSyn) / sizeof (badGeneSyn [0]))) {
+            ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_UndesiredGeneSynonym, "Uninformative gene synonym '%s", str);
+          }
+          if (StringDoesHaveText (grp->locus) && StringCmp (grp->locus, str) == 0) {
+            ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_UndesiredGeneSynonym, "gene synonym has same value as gene locus");
+          }
+        }
+      }
+      if (StringDoesHaveText (grp->locus) && StringDoesHaveText (grp->desc) && StringCmp (grp->locus, grp->desc) == 0) {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_UndesiredGeneSynonym, "gene description has same value as gene locus");
+      }
       /* - need to ignore if curated drosophila - add to vsp internal flags for efficiency?
       if (StringDoesHaveText (grp->locus)) {
         for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
@@ -17802,7 +18651,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
         }
       }
       if (pseudo && SeqMgrGetProtXref (sfp) != NULL) {
-        if (NGorNT (vsp->sep, sfp->location, &is_nc)) {
+        if (NGorNT (vsp->sep, sfp->location, &is_nc) || IsEMBLAccn (vsp->sep, sfp->location)) {
           sev = SEV_WARNING;
         } else {
           sev = SEV_ERROR;
@@ -17992,7 +18841,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
             if (ECnumberWasDeleted (str)) {
               ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_BadEcNumberValue, "EC_number %s was deleted", str);
             } else if (ECnumberWasReplaced (str)) {
-              ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_BadEcNumberValue, "EC_number %s was replaced", str);
+              ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_BadEcNumberValue, "EC_number %s was transferred and is no longer valid", str);
             } else {
               ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_BadEcNumberValue, "%s is not a legal value for qualifier EC_number", str);
             }
@@ -18002,6 +18851,15 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
         }
       }
     }
+    if (prp->name != NULL && vsp->is_refseq_in_sep) {
+      for (vnp = prp->name; vnp != NULL; vnp = vnp->next) {
+        str = (CharPtr) vnp->data.ptrvalue;
+        if (StringHasNoText (str)) continue;
+          if (NameInList (str, badProtName, sizeof (badProtName) / sizeof (badProtName [0]))) {
+            ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_UndesiredProteinName, "Uninformative protein name '%s'", str);
+          }
+        }
+      }
     break;
   case 5:                      /* RNA-ref */
     rrp = (RnaRefPtr) (sfp->data.value.ptrvalue);
@@ -18101,6 +18959,17 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
         }
       }
     }
+    if (rrp->type == 255 && rrp->ext.choice == 1) {
+      str = (CharPtr) rrp->ext.value.ptrvalue;
+      if (StringICmp (str, "ncRNA") == 0) {
+        for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
+          if (StringICmp (gbq->qual, "ncRNA_class") != 0) continue;
+          if (StringHasNoText (gbq->val)) continue;
+          if (IsStringInNcRNAClassList (gbq->val)) continue;
+          ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_InvalidQualifierValue, "Illegal ncRNA_class value '%s'", gbq->val);
+        }
+      }
+    }
     if (sfp->product != NULL) {
       CheckRnaProductType (vsp, gcp, sfp, rrp);
     }
@@ -18197,14 +19066,32 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
       }
     }
     /*
-       ValidateBioSource (vsp, gcp, biop, sfp);
+       ValidateBioSource (vsp, gcp, biop, sfp, NULL);
      */
     break;
   default:
     ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_InvalidType, "Invalid SeqFeat type [%d]", (int) (type));
     break;
   }
-  if (type != SEQFEAT_BOND) {
+  if (type == SEQFEAT_HET) {
+    /* heterogen can have mix of bonds with just "a" point specified */
+    is_seqloc_bond = FALSE;
+    slp = SeqLocFindNext (sfp->location, NULL);
+    while (slp != NULL) {
+      if (slp->choice == SEQLOC_BOND) {
+        sbp = (SeqBondPtr) slp->data.ptrvalue;
+        if (sbp != NULL) {
+          if (sbp->a == NULL || sbp->b != NULL) {
+            is_seqloc_bond = TRUE;
+          }
+        }
+      }
+      slp = SeqLocFindNext (sfp->location, slp);
+    }
+    if (is_seqloc_bond) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_ImproperBondLocation, "Bond location should only be on bond features");
+    }
+  } else if (type != SEQFEAT_BOND) {
     is_seqloc_bond = FALSE;
     slp = SeqLocFindNext (sfp->location, NULL);
     while (slp != NULL) {
@@ -19882,7 +20769,8 @@ static void SpliceCheckEx (ValidStructPtr vsp, SeqFeatPtr sfp, Boolean checkAll)
       residue2 = SeqPortGetResidue (spp);
       */
       if (residue1 == '-' && residue2 == '-') {
-        /* ignore gap */
+        /* ignore gap, and suppress UnnecessaryException message */
+        has_errors = TRUE;
       } else if (IS_residue (residue1) && IS_residue (residue2)) {
         if (residue1 != 'G' || residue2 != 'T') {        /* not T */
           if (residue1 == 'G' && residue2 == 'C') {       /* GC minor splice site */
@@ -19947,7 +20835,8 @@ static void SpliceCheckEx (ValidStructPtr vsp, SeqFeatPtr sfp, Boolean checkAll)
       residue2 = SeqPortGetResidue (spp);
       */
       if (residue1 == '-' && residue2 == '-') {
-        /* ignore gap */
+        /* ignore gap, and suppress UnnecessaryException message */
+        has_errors = TRUE;
       } else if (IS_residue (residue1) && IS_residue (residue2)) {
         if (residue1 != 'A' || residue2 != 'G') {
           if (gpsOrRefSeq) {
diff --git a/api/valid.h b/api/valid.h
index e56c7cfe..ae0c486a 100644
--- a/api/valid.h
+++ b/api/valid.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 1/1/94
 *
-* $Revision: 6.36 $
+* $Revision: 6.39 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -178,13 +178,13 @@ NLM_EXTERN CharPtr GetValidErrorName (int errcode, int subcode);
 NLM_EXTERN CharPtr GetValidExplanation (int errcode, int subcode);
 
 NLM_EXTERN CharPtr PNTR GetValidCountryList (void);
+NLM_EXTERN Boolean CountryIsValid (CharPtr name, BoolPtr old_countryP);
 NLM_EXTERN Boolean LookForECnumberPattern (CharPtr str);
 
 NLM_EXTERN Boolean IsCountryInLatLonList (CharPtr country);
 NLM_EXTERN Boolean TestLatLonForCountry (CharPtr country, FloatHi lat, FloatHi lon);
 NLM_EXTERN CharPtr GuessCountryForLatLon (FloatHi lat, FloatHi lon);
-
-NLM_EXTERN Boolean ParseLatLon (CharPtr lat_lon, FloatHi PNTR latP, FloatHi PNTR lonP);
+NLM_EXTERN Boolean StringContainsBodyOfWater (CharPtr str);
 
 /* EC_number finite state machine persists to avoid expensive reload, should free on program exit */
 NLM_EXTERN void ECNumberFSAFreeAll (void);
diff --git a/api/valid.msg b/api/valid.msg
index ea171b43..c17a4f2b 100644
--- a/api/valid.msg
+++ b/api/valid.msg
@@ -404,6 +404,14 @@ The lat_lon coordinate does not map to the indicated country.
 $^   LatLonState, 49
 The lat_lon coordinate does not map to the indicated state or province.
 
+$^   BadSpecificHost, 50
+A BioSource descriptor or feature has a specific host value that may
+require a taxonomy consult.
+
+$^   RefGeneTrackingIllegalStatus, 51
+The RefGeneTracking user object has an illegal Status value.
+
+
 $$ GENERIC, 3
 
 $^   NonAsciiAsn, 1
@@ -490,7 +498,7 @@ Bioseq packaged in the set, perhaps within a nuc-prot set.  RefSeq records may
 however be referenced remotely.
 
 $^   InconsistentMolInfoBiomols, 12
-Mol-info.biomol is inconsistent within a segset or parts set.
+Mol-info.biomol is inconsistent within a segset, parts set, or pop/phy/mut/eco set.
 
 $^   ArchaicFeatureLocation, 13
 A feature location should refer to the accession or gi number, not a local or general ID.
@@ -1080,6 +1088,18 @@ and wobble expansion of the anticodon sequence.
 $^   BadAnticodonStrand, 147
 The tRNA feature location and anticodon location are not on the same strand.
 
+$^   UndesiredGeneSynonym, 148
+The gene synonym is uninformative.
+
+$^   UndesiredProteinName, 149
+The protein name is uninformative.
+
+$^ FeatureBeginsOrEndsInGap, 150
+The feature starts or stops within a sequence gap.
+
+$^ GeneOntologyTermMissingGOID, 151
+A Gene Ontology (GO) term is missing the GO Identifier.
+
 $$ SEQ_ALIGN, 6
 
 $^   SeqIdProblem, 1
diff --git a/api/validerr.h b/api/validerr.h
index 482a04ed..7478931d 100644
--- a/api/validerr.h
+++ b/api/validerr.h
@@ -114,6 +114,8 @@
 #define ERR_SEQ_DESCR_LatLonValue  2,47
 #define ERR_SEQ_DESCR_LatLonCountry  2,48
 #define ERR_SEQ_DESCR_LatLonState  2,49
+#define ERR_SEQ_DESCR_BadSpecificHost  2,50
+#define ERR_SEQ_DESCR_RefGeneTrackingIllegalStatus  2,51
 #define ERR_GENERIC  3,0
 #define ERR_GENERIC_NonAsciiAsn  3,1
 #define ERR_GENERIC_Spell  3,2
@@ -292,6 +294,10 @@
 #define ERR_SEQ_FEAT_BadAnticodonAA  5,145
 #define ERR_SEQ_FEAT_BadAnticodonCodon  5,146
 #define ERR_SEQ_FEAT_BadAnticodonStrand  5,147
+#define ERR_SEQ_FEAT_UndesiredGeneSynonym  5,148
+#define ERR_SEQ_FEAT_UndesiredProteinName  5,149
+#define ERR_SEQ_FEAT_FeatureBeginsOrEndsInGap  5,150
+#define ERR_SEQ_FEAT_GeneOntologyTermMissingGOID  5,151
 #define ERR_SEQ_ALIGN  6,0
 #define ERR_SEQ_ALIGN_SeqIdProblem  6,1
 #define ERR_SEQ_ALIGN_StrandRev  6,2
diff --git a/asn/all.bat b/asn/all.bat
index d3aab846..f196a4c0 100644
--- a/asn/all.bat
+++ b/asn/all.bat
@@ -5,6 +5,6 @@ copy head.all+general.asn+biblio.asn+medline.asn+pubmed.asn+medlars.asn 1.tmp
 copy 1.tmp+pub.asn+seqloc.asn+seq.asn+seqset.asn+seqcode.asn+seqblock.asn 2.tmp
 copy 2.tmp+seqfeat.asn+seqalign.asn+seqres.asn+submit.asn+..\biostruc\cn3d\cn3d.asn 3.tmp
 copy 3.tmp+proj.asn+access.asn+featdef.asn+ncbimime.asn+objprt.asn 4.tmp
-copy 4.tmp+gbseq.asn+insdseq.asn+tinyseq.asn asn.all
+copy 4.tmp+gbseq.asn+insdseq.asn+tinyseq.asn+seqtable.asn+..\sequin\macro.asn asn.all
 
 del 1.tmp 2.tmp 3.tmp 4.tmp
diff --git a/asn/all.mac b/asn/all.mac
index 3aaf3592..3627508c 100644
--- a/asn/all.mac
+++ b/asn/all.mac
@@ -1,4 +1,4 @@
 #
 
-mpwsh 'Directory "::asn:"; Delete -i asn.all; Catenate head.all general.asn biblio.asn medline.asn pubmed.asn medlars.asn pub.asn seqloc.asn seq.asn seqset.asn seqcode.asn seqblock.asn seqfeat.asn seqalign.asn seqres.asn submit.asn ::biostruc:cn3d:cn3d.asn proj.asn access.asn featdef.asn ncbimime.asn objprt.asn > asn.all; Exit {Status}'
+mpwsh 'Directory "::asn:"; Delete -i asn.all; Catenate head.all general.asn biblio.asn medline.asn pubmed.asn medlars.asn pub.asn seqloc.asn seq.asn seqset.asn seqcode.asn seqblock.asn seqfeat.asn seqtable.asn seqalign.asn seqres.asn submit.asn ::biostruc:cn3d:cn3d.asn proj.asn access.asn featdef.asn ncbimime.asn objprt.asn ::sequin:macro.asn > asn.all; Exit {Status}'
 echo "all.mac: Done."
diff --git a/asn/all.unx b/asn/all.unx
index 673c9963..aaf3e2e5 100755
--- a/asn/all.unx
+++ b/asn/all.unx
@@ -3,9 +3,9 @@
 rm -f asn.all
 FILES="\
 head.all general.asn biblio.asn medline.asn pubmed.asn medlars.asn pub.asn \
-seqloc.asn seq.asn seqset.asn seqcode.asn seqblock.asn \
-seqfeat.asn seqalign.asn seqres.asn submit.asn ../biostruc/cn3d/cn3d.asn \
+seqloc.asn seq.asn seqset.asn seqcode.asn seqblock.asn seqfeat.asn \
+seqtable.asn seqalign.asn seqres.asn submit.asn ../biostruc/cn3d/cn3d.asn \
 proj.asn access.asn featdef.asn ncbimime.asn objprt.asn gbseq.asn insdseq.asn \
-tinyseq.asn scoremat.asn "
+tinyseq.asn scoremat.asn ../sequin/macro.asn "
 cat $FILES > asn.all
 exit $?
diff --git a/asn/asn.all b/asn/asn.all
index ffea182e..7286a595 100644
--- a/asn/asn.all
+++ b/asn/asn.all
@@ -740,7 +740,7 @@ Seq-loc-equiv ::= SET OF Seq-loc      -- for a set of equivalent locations
 END
     
 
---$Revision: 6.16 $
+--$Revision: 6.19 $
 --**********************************************************************
 --
 --  NCBI Sequence elements
@@ -769,7 +769,8 @@ IMPORTS Date, Int-fuzz, Dbtag, Object-id, User-object FROM NCBI-General
         EMBL-block FROM EMBL-General
         SP-block FROM SP-General
         PRF-block FROM PRF-General
-        PDB-block FROM PDB-General;
+        PDB-block FROM PDB-General
+        Seq-table FROM NCBI-SeqTable;
 
 --*** Sequence ********************************
 --*
@@ -844,6 +845,8 @@ MolInfo ::= SEQUENCE {
         cRNA (11) ,              -- viral RNA genome copy intermediate
         snoRNA (12) ,            -- small nucleolar RNA
         transcribed-RNA (13) ,   -- transcribed RNA other than existing classes
+        ncRNA (14) ,
+        tmRNA (15) ,
         other (255) } DEFAULT unknown ,
     tech INTEGER {
         unknown (0) ,
@@ -869,6 +872,7 @@ MolInfo ::= SEQUENCE {
         wgs (20) ,              -- whole genome shotgun sequencing
         barcode (21) ,          -- barcode of life project
         composite-wgs-htgs (22) , -- composite of WGS and HTGS
+        tsa (23) ,              -- transcriptome shotgun assembly
         other (255) }           -- use Source.techexp
                DEFAULT unknown ,
     techexp VisibleString OPTIONAL ,   -- explanation if tech not enough
@@ -887,7 +891,8 @@ MolInfo ::= SEQUENCE {
       no-ends (5) ,                    -- missing both ends
       has-left (6) ,                   -- 5' or NH3 end present
       has-right (7) ,                  -- 3' or COOH end present
-      other (255) } DEFAULT unknown }
+      other (255) } DEFAULT unknown ,
+    gbmoltype VisibleString OPTIONAL } -- identifies particular ncRNA
 
 
 GIBB-mol ::= ENUMERATED {       -- type of molecule represented
@@ -981,12 +986,12 @@ Pubdesc ::= SEQUENCE {              -- how sequence presented in pub
     seq-raw StringStore OPTIONAL ,  -- original sequence from paper
     align-group INTEGER OPTIONAL ,  -- this seq aligned with others in paper
     comment VisibleString OPTIONAL, -- any comment on this pub in context
-	reftype INTEGER {           -- type of reference in a GenBank record
-		seq (0) ,               -- refers to sequence
-		sites (1) ,             -- refers to unspecified features
-		feats (2) ,             -- refers to specified features
-		no-target (3) }         -- nothing specified (EMBL)
-		DEFAULT seq }
+    reftype INTEGER {           -- type of reference in a GenBank record
+        seq (0) ,               -- refers to sequence
+        sites (1) ,             -- refers to unspecified features
+        feats (2) ,             -- refers to specified features
+        no-target (3) }         -- nothing specified (EMBL)
+        DEFAULT seq }
 
 Heterogen ::= VisibleString       -- cofactor, prosthetic group, inhibitor, etc
 
@@ -1175,8 +1180,9 @@ Seq-annot ::= SEQUENCE {
         ftable SET OF Seq-feat ,
         align SET OF Seq-align ,
         graph SET OF Seq-graph ,
-        ids SET OF Seq-id ,        -- used for communication between tools
-        locs SET OF Seq-loc } }    -- used for communication between tools
+        ids SET OF Seq-id ,      -- used for communication between tools
+        locs SET OF Seq-loc ,    -- used for communication between tools
+        seq-table Seq-table } }  -- features in table form
 
 END
 
@@ -1537,7 +1543,7 @@ PDB-replace ::= SEQUENCE {
 
 END
 
---$Revision: 6.18 $
+--$Revision: 6.19 $
 --**********************************************************************
 --
 --  NCBI Sequence Feature elements
@@ -1983,7 +1989,8 @@ BioSource ::= SEQUENCE {
         proplastid (18) ,
         endogenous-virus (19) ,
         hydrogenosome (20) ,
-        chromosome (21)
+        chromosome (21) ,
+        chromatophore (22)
       } DEFAULT unknown ,
     origin INTEGER {
       unknown (0) ,
@@ -2159,6 +2166,232 @@ Tx-evidence ::= SEQUENCE {
     
 END
 
+--$Revision: 1.5 $
+--  ----------------------------------------------------------------------------
+--
+--                            PUBLIC DOMAIN NOTICE
+--                National Center for Biotechnology Information
+--
+--  This software/database is a "United States Government Work" under the terms
+--  of the United States Copyright Act.  It was written as part of the author's
+--  official duties as a United States Government employee and thus cannot be
+--  copyrighted.  This software/database is freely available to the public for
+--  use.  The National Library of Medicine and the U.S. Government have not
+--  placed any restriction on its use or reproduction.
+--
+--  Although all reasonable efforts have been taken to ensure the accuracy and
+--  reliability of the software and data, the NLM and the U.S. Government do not
+--  and cannot warrant the performance or results that may be obtained by using
+--  this software or data.  The NLM and the U.S. Government disclaim all
+--  warranties, express or implied, including warranties of performance,
+--  merchantability or fitness for any particular purpose.
+--
+--  Please cite the authors in any work or product based on this material.
+--
+--  ----------------------------------------------------------------------------
+--
+--  Authors: Mike DiCuccio, Eugene Vasilchenko
+--
+--  ASN.1 interface to table readers
+--
+--  ----------------------------------------------------------------------------
+
+NCBI-SeqTable DEFINITIONS ::=
+
+BEGIN
+
+EXPORTS
+    SeqTable-column-info, SeqTable-column, Seq-table;
+    
+IMPORTS
+    Seq-id, Seq-loc, Seq-interval   FROM NCBI-Seqloc;
+
+
+SeqTable-column-info ::= SEQUENCE {
+    -- user friendly column name, can be skipped
+    title VisibleString OPTIONAL,
+
+    -- identification of the column data in the objects described by the table
+    field-id INTEGER { -- known column data types
+        -- position types
+        location        (0), -- location as Seq-loc
+        location-id     (1), -- location Seq-id
+        location-gi     (2), -- gi
+        location-from   (3), -- interval from
+        location-to     (4), -- interval to
+        location-strand (5), -- location strand
+        location-fuzz-from-lim (6),
+        location-fuzz-to-lim   (7),
+
+        product         (10), -- product as Seq-loc
+        product-id      (11), -- product Seq-id
+        product-gi      (12), -- product gi
+        product-from    (13), -- product interval from
+        product-to      (14), -- product interval to
+        product-strand  (15), -- product strand
+        product-fuzz-from-lim (16),
+        product-fuzz-to-lim   (17),
+        
+        -- main feature fields
+        id-local        (20), -- id.local.id
+        xref-id-local   (21), -- xref.id.local.id
+        partial         (22),
+        comment         (23),
+        title           (24),
+        ext             (25), -- field-name must be "E.xxx", see below
+        qual            (26), -- field-name must be "Q.xxx", see below
+        dbxref          (27), -- field-name must be "D.xxx", see below
+
+        -- various data fields
+        data-imp-key        (30),
+        data-region         (31),
+        data-cdregion-frame (32),
+
+        -- extra fields, see also special values for str below
+        ext-type        (40),
+        qual-qual       (41),
+        qual-val        (42),
+        dbxref-db       (43),
+        dbxref-tag      (44)
+    } OPTIONAL,
+
+    -- any column can be identified by ASN.1 text locator string
+    -- with omitted object type.
+    -- examples:
+    --   "data.gene.locus" for Seq-feat.data.gene.locus
+    --   "data.imp.key" for Seq-feat.data.imp.key
+    --   "qual.qual"
+    --    - Seq-feat.qual is SEQUENCE so several columns are allowed
+    --      see also "Q.xxx" special value for shorter qual representation
+    --   "ext.type.str"
+    --   "ext.data.label.str"
+    --   "ext.data.data.int"
+    --      see also "E.xxx" special value for shorter ext representation
+    -- special values start with capital letter:
+    --   "E.xxx" - ext.data.label.str = xxx, ext.data.data = data
+    --    - Seq-feat.ext.data is SEQUENCE so several columns are allowed
+    --   "Q.xxx" - qual.qual = xxx, qual.val = data
+    --    - Seq-feat.qual is SEQUENCE so several columns are allowed
+    --   "D.xxx" - dbxref.id = xxx, dbxref.tag = data
+    --    - Seq-feat.dbxref is SET so several columns are allowed
+    field-name  VisibleString OPTIONAL
+}
+
+
+CommonString-table ::= SEQUENCE {
+    -- set of possible values
+    strings     SEQUENCE OF VisibleString,
+
+    -- indexes of values
+    indexes     SEQUENCE OF INTEGER
+}
+
+
+CommonBytes-table ::= SEQUENCE {
+    -- set of possible values
+    bytes       SEQUENCE OF OCTET STRING,
+
+    -- indexes of values
+    indexes     SEQUENCE OF INTEGER
+}
+
+
+SeqTable-multi-data ::= CHOICE {
+    -- a set of integers, one per row
+    int         SEQUENCE OF INTEGER,
+    
+    -- a set of reals, one per row
+    real        SEQUENCE OF REAL,
+
+    -- a set of strings, one per row
+    string      SEQUENCE OF VisibleString,
+
+    -- a set of byte arrays, one per row
+    bytes       SEQUENCE OF OCTET STRING,
+
+    -- a set of string with small set of possible values
+    common-string   CommonString-table,
+
+    -- a set of byte arrays with small set of possible values
+    common-bytes    CommonBytes-table,
+
+    -- a set of bits, one per row
+    -- this uses bm::bvector<> as its storage mechanism
+    bit         OCTET STRING,
+
+    -- a set of locations, one per row
+    loc         SEQUENCE OF Seq-loc,
+    id          SEQUENCE OF Seq-id,
+    interval    SEQUENCE OF Seq-interval
+}
+
+
+SeqTable-single-data ::= CHOICE {
+    -- integer
+    int         INTEGER,
+    
+    -- real
+    real        REAL,
+
+    -- string
+    string      VisibleString,
+
+    -- byte array
+    bytes       OCTET STRING,
+
+    -- bit
+    bit         BOOLEAN,
+
+    -- location
+    loc         Seq-loc,
+    id          Seq-id,
+    interval    Seq-interval
+}
+
+
+SeqTable-sparse-index ::= CHOICE {
+    -- indexed of rows with values
+    indexes SEQUENCE OF INTEGER,
+
+    -- bitset of rows with values
+    bit-set OCTET STRING
+}
+
+
+SeqTable-column ::= SEQUENCE {
+    -- column description or reference to previously defined info
+    header      SeqTable-column-info,   -- information about data
+
+    -- row data
+    data        SeqTable-multi-data OPTIONAL,
+
+    -- in case not all rows contain data this field will contain sparse info
+    sparse      SeqTable-sparse-index OPTIONAL,
+
+    -- default value for sparse table, or if row data is too short
+    default     SeqTable-single-data OPTIONAL,
+
+    -- single value for indexes not listed in sparse table
+    sparse-other SeqTable-single-data OPTIONAL
+}
+
+
+Seq-table ::= SEQUENCE {
+    -- type of features in this table, equal to Seq-feat.data variant index
+    feat-type   INTEGER,
+
+    -- subtype of features in this table, defined in header SeqFeatData.hpp
+    feat-subtype INTEGER OPTIONAL,
+
+    -- number of rows
+    num-rows    INTEGER,
+
+    -- data in columns
+    columns     SEQUENCE OF SeqTable-column
+}
+
+
+END
 --$Revision: 6.3 $
 --**********************************************************************
 --
@@ -3854,3 +4087,817 @@ PssmWithParameters ::= SEQUENCE {
 }
 
 END
+--$Revision: 1.13 $
+--**********************************************************************
+--
+--  NCBI ASN.1 macro editing language specifications
+--
+--  by Colleen Bollin, 2007
+--
+--**********************************************************************
+
+NCBI-Macro DEFINITIONS ::=
+BEGIN
+
+EXPORTS AECR-action, Parse-action, Macro-action-list;
+
+-- simple constraints --
+
+String-location ::= ENUMERATED {
+    contains (1) ,
+    equals (2) ,
+    starts (3) ,
+    ends (4) ,
+    inlist (5) }
+
+String-constraint ::= SEQUENCE {
+    match-text VisibleString ,
+    match-location String-location DEFAULT contains ,
+    case-sensitive BOOLEAN DEFAULT FALSE ,
+    whole-word BOOLEAN DEFAULT FALSE ,
+    not-present BOOLEAN DEFAULT FALSE }
+
+Strand-constraint ::= ENUMERATED {
+    any (0) ,
+    plus (1) ,
+    minus (2) }
+
+Seqtype-constraint ::= ENUMERATED {
+    any (0) ,
+    nuc (1) ,
+    prot (2) }
+
+Location-constraint ::= SEQUENCE {
+    strand Strand-constraint DEFAULT any ,
+    seq-type Seqtype-constraint DEFAULT any }
+
+Object-type-constraint ::= ENUMERATED {
+    any (0) ,
+    feature (1) ,
+    descriptor (2) }
+
+
+-- feature values --
+
+Feature-type ::= ENUMERATED {
+    any (0) ,
+    gene (1) ,
+    org (2) ,
+    cds (3) ,
+    prot (4) ,
+    preRNA (5) ,
+    mRNA (6) ,
+    tRNA (7) ,
+    rRNA (8) ,
+    snRNA (9) ,
+    scRNA (10) ,
+    otherRNA (11) ,
+    pub (12) ,
+    seq (13) ,
+    imp (14) ,
+    allele (15) ,
+    attenuator (16) ,
+    c-region (17) ,
+    caat-signal (18) ,
+    imp-CDS (19) ,
+    conflict (20) ,
+    d-loop (21) ,
+    d-segment (22) ,
+    enhancer (23) ,
+    exon (24) ,
+    gC-signal (25) ,
+    iDNA (26) ,
+    intron (27) ,
+    j-segment (28) ,
+    ltr (29) ,
+    mat-peptide (30) ,
+    misc-binding (31) ,
+    misc-difference (32) ,
+    misc-feature (33) ,
+    misc-recomb (34) ,
+    misc-RNA (35) ,
+    misc-signal (36) ,
+    misc-structure (37) ,
+    modified-base (38) ,
+    mutation (39) ,
+    n-region (40) ,
+    old-sequence (41) ,
+    polyA-signal (42) ,
+    polyA-site (43) ,
+    precursor-RNA (44) ,
+    prim-transcript (45) ,
+    primer-bind (46) ,
+    promoter (47) ,
+    protein-bind (48) ,
+    rbs (49) ,
+    repeat-region (50) ,
+    repeat-unit (51) ,
+    rep-origin (52) ,
+    s-region (53) ,
+    satellite (54) ,
+    sig-peptide (55) ,
+    source (56) ,
+    stem-loop (57) ,
+    sts (58) ,
+    tata-signal (59) ,
+    terminator (60) ,
+    transit-peptide (61) ,
+    unsure (62) ,
+    v-region (63) ,
+    v-segment (64) ,
+    variation (65) ,
+    virion (66) ,
+    n3clip (67) ,
+    n3UTR (68) ,
+    n5clip (69) ,
+    n5UTR (70) ,
+    n10-signal (71) ,
+    n35-signal (72) ,
+    site-ref (73) ,
+    region (74) ,
+    comment (75) ,
+    bond (76) ,
+    site (77) ,
+    rsite (78) ,
+    user (79) ,
+    txinit (80) ,
+    num (81) ,
+    psec-str (82) ,
+    non-std-residue (83) ,
+    het (84) ,
+    biosrc (85) ,
+    preprotein (86) ,
+    mat-peptide-aa (87) ,
+    sig-peptide-aa (88) ,
+    transit-peptide-aa (89) ,
+    snoRNA (90) ,
+    gap (91) ,
+    operon (92) ,
+    oriT (93) ,
+    ncRNA (94) ,
+    tmRNA (95) }
+
+Feat-qual-legal ::= ENUMERATED {
+    allele (1) ,
+    activity (2) ,
+    anticodon (3) ,
+    bound-moiety (4) ,
+    chromosome (5),
+    citation (6),
+    codon (7) ,
+    codon-start (8) ,
+    codons-recognized (9) ,
+    compare (10) ,
+    cons-splice (11) ,
+    db-xref (12) ,
+    description (13) ,
+    direction (14) ,
+    ec-number (15) ,
+    environmental-sample (16) ,
+    evidence (17) ,
+    exception (18) ,
+    experiment (19) ,
+    focus (20) ,
+    frequency (21) ,
+    function (22) ,
+    gene (23) ,
+    gene-description (24) ,
+    inference (25) ,
+    label (26) ,
+    locus-tag (27) ,
+    map (28) ,
+    mobile-element (29) ,
+    mod-base (30) ,
+    mol-type (31) ,
+    ncRNA-class (32) ,
+    note (33) ,
+    number (34) ,
+    old-locus-tag (35) ,
+    operon (36) ,
+    organism (37) ,
+    organelle (38) ,
+    partial (39) ,
+    phenotype (40) ,
+    plasmid (41) ,
+    product (42) ,
+    protein-id (43) ,
+    pseudo (44) ,
+    rearranged (45) ,
+    replace (46) ,
+    rpt-family (47) ,
+    rpt-type (48) ,
+    rpt-unit (49) ,
+    rpt-unit-seq (50) ,
+    rpt-unit-range (51) ,
+    segment (52) ,
+    sequenced-mol (53) ,
+    standard-name (54) ,
+    synonym (55) ,
+    transcript-id (56) ,
+    transgenic (57) ,
+    translation (58) ,
+    transl-except (59) ,
+    transl-table (60) ,
+    usedin (61) }
+
+Feat-qual-legal-val ::= SEQUENCE {
+    qual Feat-qual-legal ,
+    val  VisibleString }
+
+Feat-qual-legal-val-choice ::= CHOICE {
+    qual Feat-qual-legal-val }
+
+Feat-qual-legal-set ::= SET OF Feat-qual-legal-val-choice
+
+Feat-qual-choice ::= CHOICE {
+    legal-qual Feat-qual-legal ,
+    illegal-qual String-constraint }
+
+Feature-field ::= SEQUENCE {
+    type Feature-type ,
+    field Feat-qual-choice }
+
+Feature-field-legal ::= SEQUENCE {
+    type Feature-type ,
+    field Feat-qual-legal }
+
+Feature-field-pair ::= SEQUENCE {
+    type Feature-type ,
+    field-from Feat-qual-choice ,
+    field-to Feat-qual-choice }
+
+Source-qual ::= ENUMERATED {
+    acronym (1) ,
+    anamorph (2) ,
+    authority (3) ,
+    bio-material (4) ,
+    biotype (5) ,
+    biovar (6) ,
+    breed (7) ,
+    cell-line (8) ,
+    cell-type (9) ,
+    chemovar (10) ,
+    chromosome (11) ,
+    clone (12) ,
+    clone-lib (13) ,
+    collected-by (14) ,
+    collection-date (15) ,
+    common (16) ,
+    common-name (17) ,
+    country (18) ,
+    cultivar (19) ,
+    culture-collection (20) ,
+    dev-stage (21) ,
+    division (22) ,
+    dosage (23) ,
+    ecotype (24) ,
+    endogenous-virus-name (25) ,
+    environmental-sample (26) ,
+    forma (27) ,
+    forma-specialis (28) ,
+    frequency (29) ,
+    fwd-primer-name (30) ,
+    fwd-primer-seq (31) ,
+    gb-acronym (32) ,
+    gb-anamorph (33) ,
+    gb-synonym (34) ,
+    genotype (35) ,
+    germline (36) ,
+    group (37) ,
+    haplotype (38) ,
+    identified-by (39) ,
+    insertion-seq-name (40) ,
+    isolate (41) ,
+    isolation-source (42) ,
+    lab-host (43) ,
+    lat-lon (44) ,
+    lineage (45) ,
+    map (46) ,
+    metagenome-source (47) ,
+    metagenomic (48) ,
+    old-lineage (49) ,
+    old-name (50) ,
+    orgmod-note (51) ,
+    nat-host (52) ,
+    pathovar (53) ,
+    plasmid-name (54) ,
+    plastid-name (55) ,
+    pop-variant (56) ,
+    rearranged (57) ,
+    rev-primer-name (58) ,
+    rev-primer-seq (59) ,
+    segment (60) ,
+    serogroup (61) ,
+    serotype (62) ,
+    serovar (63) ,
+    sex (64) ,
+    specimen-voucher (65) ,
+    strain (66) ,
+    subclone (67) ,
+    subgroup (68) ,
+    subsource-note (69),
+    sub-species (70) ,
+    substrain (71) ,
+    subtype (72) ,
+    synonym (73) ,
+    taxname (74) ,
+    teleomorph (75) ,
+    tissue-lib (76) ,
+    tissue-type (77) ,
+    transgenic (78) ,
+    transposon-name (79) ,
+    type (80) ,
+    variety (81) }
+
+Source-qual-pair ::= SEQUENCE {
+    field-from Source-qual ,
+    field-to Source-qual }
+
+Source-location ::= ENUMERATED {
+    unknown (0) ,
+    genomic (1) ,
+    chloroplast (2) ,
+    chromoplast (3) ,
+    kinetoplast (4) ,
+    mitochondrion (5) ,
+    plastid (6) ,
+    macronuclear (7) ,
+    extrachrom (8) ,
+    plasmid (9) ,
+    transposon (10) ,
+    insertion-seq (11) ,
+    cyanelle (12) ,
+    proviral (13) ,
+    virion (14) ,
+    nucleomorph (15) ,
+    apicoplast (16) ,
+    leucoplast (17) ,
+    proplastid (18) ,
+    endogenous-virus (19) ,
+    hydrogenosome (20) ,
+    chromosome (21) ,
+    chromatophore (22) }
+
+Source-origin ::= ENUMERATED {
+    unknown (0) ,
+    natural (1) ,
+    natmut (2) ,
+    mut (3) ,
+    artificial (4) ,
+    synthetic (5) ,
+    other (255) }
+
+Source-qual-choice ::= CHOICE {
+    textqual Source-qual ,
+    location Source-location,
+    origin Source-origin }
+    
+
+CDSGeneProt-field ::= ENUMERATED {
+    cds-comment (1) ,
+    gene-locus (2) ,
+    gene-description (3) ,
+    gene-comment (4) ,
+    gene-allele (5) ,
+    gene-maploc (6) ,
+    gene-locus-tag (7) ,
+    gene-synonym (8) ,
+    gene-old-locus-tag (9) ,
+    mrna-product (10) ,
+    mrna-comment (11) ,
+    prot-name (12) ,
+    prot-description (13) ,
+    prot-ec-number (14) ,
+    prot-activity (15) ,
+    prot-comment (16) ,
+    mat-peptide-name (17) ,
+    mat-peptide-description (18) ,
+    mat-peptide-ec-number (19) ,
+    mat-peptide-activity (20) ,
+    mat-peptide-comment (21) }
+
+CDSGeneProt-field-pair ::= SEQUENCE {
+    field-from CDSGeneProt-field ,
+    field-to CDSGeneProt-field }
+
+Molecule-type ::= ENUMERATED {
+  unknown (0) ,
+  genomic (1) ,
+  precursor-RNA (2) ,
+  mRNA (3) ,
+  rRNA (4) ,
+  tRNA (5) ,
+  snRNA (6) ,
+  scRNA (7) ,
+  genomic-mRNA (8) ,
+  cRNA (9) ,
+  snoRNA (10) ,
+  transcribed-RNA (11) ,
+  ncRNA (12) ,
+  transfer-messenger-RNA (13) ,
+  other (14) }
+
+Technique-type ::= ENUMERATED {
+  unknown (0) , 
+  standard (1) ,
+  est (2) ,
+  sts (3) ,
+  survey (4) ,
+  genetic-map (5) ,
+  physical-map (6) ,
+  derived (7) ,
+  concept-trans (8) ,
+  seq-pept (9) ,
+  both (10) ,
+  seq-pept-overlap (11) ,
+  seq-pept-homol (12) , 
+  concept-trans-a (13) ,
+  htgs-1 (14) ,
+  htgs-2 (15) ,
+  htgs-3 (16) ,
+  fli-cDNA (17) ,
+  htgs-0 (18) ,
+  htc (19) ,
+  wgs (20) ,
+  barcode (21) ,
+  composite-wgs-htgs (22) ,
+  tsa (23) ,
+  other (24) }
+
+Completedness-type ::= ENUMERATED {
+  unknown (0) ,
+  complete (1) ,
+  partial (2) ,
+  no-left (3) ,
+  no-right (4) ,
+  no-ends (5) ,
+  has-left (6) ,
+  has-right (7) ,
+  other (6) }
+
+Molecule-class-type ::= ENUMERATED {
+  unknown (0) ,
+  dna (1) ,
+  rna (2) ,
+  protein (3) ,
+  nucleotide (4),
+  other (5) }
+
+Topology-type ::= ENUMERATED {
+  unknown (0) ,
+  linear (1) ,
+  circular (2) ,
+  tandem (3) ,
+  other (4) }
+
+Strand-type ::= ENUMERATED {
+  unknown (0) ,
+  single (1) ,
+  double (2) ,
+  mixed (3) ,
+  mixed-rev (4) ,
+  other (5) }
+
+Molinfo-field ::= CHOICE {
+    molecule Molecule-type ,
+    technique Technique-type ,
+    completedness Completedness-type ,
+    mol-class Molecule-class-type ,
+    topology Topology-type ,
+    strand Strand-type }
+
+Molinfo-molecule-pair ::= SEQUENCE {
+    from Molecule-type ,
+    to Molecule-type }
+
+Molinfo-technique-pair ::= SEQUENCE {
+    from Technique-type ,
+    to Technique-type }
+
+Molinfo-completedness-pair ::= SEQUENCE {
+    from Completedness-type ,
+    to Completedness-type }
+
+Molinfo-mol-class-pair ::= SEQUENCE {
+    from Molecule-class-type ,
+    to Molecule-class-type }
+
+Molinfo-topology-pair ::= SEQUENCE {
+    from Topology-type ,
+    to Topology-type }
+
+Molinfo-strand-pair ::= SEQUENCE {
+    from Strand-type ,
+    to Strand-type }
+
+Molinfo-field-pair ::= CHOICE {
+    molecule Molinfo-molecule-pair ,
+    technique Molinfo-technique-pair ,
+    completedness Molinfo-completedness-pair ,
+    mol-class Molinfo-mol-class-pair ,
+    topology Molinfo-topology-pair ,
+    strand Molinfo-strand-pair }
+   
+    
+-- complex constraints --
+
+Source-constraint ::= SEQUENCE {
+  field1 Source-qual-choice OPTIONAL ,
+  field2 Source-qual-choice OPTIONAL ,
+  constraint String-constraint OPTIONAL ,
+  type-constraint Object-type-constraint OPTIONAL }
+
+CDSGeneProt-feature-type-constraint ::= ENUMERATED {
+    gene (1) ,
+    mRNA (2) ,
+    cds (3) ,
+    prot (4) ,
+    exon (5) ,
+    mat-peptide (6) }
+
+CDSGeneProt-pseudo-constraint ::= SEQUENCE {
+    feature CDSGeneProt-feature-type-constraint ,
+    is-pseudo BOOLEAN DEFAULT TRUE }
+
+CDSGeneProt-constraint-field ::= CHOICE {
+  field CDSGeneProt-field }
+
+CDSGeneProt-qual-constraint ::= SEQUENCE {
+  field1 CDSGeneProt-constraint-field OPTIONAL ,
+  field2 CDSGeneProt-constraint-field OPTIONAL ,
+  constraint String-constraint OPTIONAL }
+  
+Sequence-constraint-rnamol ::= ENUMERATED {
+  any (0) ,
+  genomic (1) ,
+  precursor-RNA (2) ,
+  mRNA (3) ,
+  rRNA (4) ,
+  tRNA (5) ,
+  snRNA (6) ,
+  scRNA (7) ,
+  genomic-mRNA (8) ,
+  cRNA (9) ,
+  snoRNA (10) ,
+  transcribed-RNA (11) ,
+  ncRNA (12) ,
+  transfer-messenger-RNA (13) }
+
+Sequence-constraint-mol-type-constraint ::= CHOICE {
+  any NULL ,
+  nucleotide NULL ,
+  dna NULL ,
+  rna Sequence-constraint-rnamol ,
+  protein NULL }
+
+Sequence-constraint ::= SEQUENCE {
+    seqtype Sequence-constraint-mol-type-constraint OPTIONAL ,
+    id String-constraint OPTIONAL ,
+    feature Feature-type }
+
+Constraint-choice ::= CHOICE {
+    string String-constraint ,
+    location Location-constraint ,
+    source Source-constraint,
+    cdsgeneprot-qual CDSGeneProt-qual-constraint ,
+    cdsgeneprot-pseudo CDSGeneProt-pseudo-constraint ,
+    sequence Sequence-constraint }
+
+Constraint-choice-set ::= SET OF Constraint-choice
+
+Text-portion ::= SEQUENCE {
+    left-text VisibleString OPTIONAL ,
+    include-left BOOLEAN ,
+    right-text VisibleString OPTIONAL ,
+    include-right BOOLEAN ,
+    inside BOOLEAN ,
+    case-sensitive BOOLEAN DEFAULT FALSE ,
+    whole-word BOOLEAN DEFAULT FALSE }
+
+Field-edit-location ::= ENUMERATED {
+    anywhere (0) ,
+    beginning (1) ,
+    end (2) }
+
+Field-edit ::= SEQUENCE {
+    find-txt VisibleString ,
+    repl-txt VisibleString OPTIONAL ,
+    location Field-edit-location DEFAULT anywhere }
+
+Field-type ::= CHOICE {
+    source-qual Source-qual-choice ,
+    feature-field Feature-field ,
+    cds-gene-prot CDSGeneProt-field ,
+    molinfo-field Molinfo-field }
+
+Field-pair-type ::= CHOICE {
+    source-qual Source-qual-pair ,
+    feature-field Feature-field-pair ,
+    cds-gene-prot CDSGeneProt-field-pair ,
+    molinfo-field Molinfo-field-pair } 
+
+ExistingTextOption ::= ENUMERATED {
+  replace-old (1) ,
+  append-semi (2) ,
+  append-space (3) ,
+  append-colon (4) ,
+  append-none (5) ,
+  prefix-semi (6) ,
+  prefix-space (7) ,
+  prefix-colon (8) ,
+  prefix-none (9) ,
+  leave-old (10) }
+
+
+Apply-action ::= SEQUENCE {
+    field Field-type ,
+    value VisibleString ,
+    existing-text ExistingTextOption }
+
+Edit-action ::= SEQUENCE {
+    edit Field-edit ,
+    field Field-type }
+
+Convert-action ::= SEQUENCE {
+    fields Field-pair-type ,
+    existing-text ExistingTextOption }
+
+Copy-action ::= SEQUENCE {
+    fields Field-pair-type ,
+    existing-text ExistingTextOption }
+
+Swap-action ::= SEQUENCE {
+    fields Field-pair-type ,
+    field-to Field-type }
+
+AECRParse-action ::= SEQUENCE {
+    portion Text-portion ,
+    fields Field-pair-type ,
+    remove-from-parsed BOOLEAN DEFAULT FALSE ,
+    existing-text ExistingTextOption }
+
+Remove-action ::= SEQUENCE {
+    field Field-type }
+
+Action-choice ::= CHOICE {
+    apply Apply-action ,
+    edit Edit-action ,
+    convert Convert-action ,
+    copy Copy-action ,
+    swap Swap-action ,
+    remove Remove-action ,
+    parse AECRParse-action }
+
+AECR-action ::= SEQUENCE {
+    action Action-choice ,
+    constraint Constraint-choice-set OPTIONAL }
+
+Cap-change ::= ENUMERATED {
+    none (0) ,
+    tolower (1) ,
+    toupper (2) ,
+    firstcap (3) }
+
+Parse-src-org-choice ::= CHOICE {
+    source-qual Source-qual ,
+    taxname-after-binomial NULL }
+
+Parse-src-org ::= SEQUENCE {
+    field Parse-src-org-choice ,
+    type Object-type-constraint DEFAULT any }
+
+Parse-src ::= CHOICE {
+    defline NULL ,
+    flatfile NULL ,
+    local-id NULL ,
+    org Parse-src-org ,
+    comment NULL ,
+    bankit-comment NULL ,
+    structured-comment VisibleString ,
+    file-id NULL }
+
+Parse-dst-org ::= SEQUENCE {
+    field Source-qual-choice ,
+    type Object-type-constraint DEFAULT any }
+
+Parse-dest ::= CHOICE {
+    defline NULL ,
+    org Parse-dst-org ,
+    featqual Feature-field-legal ,
+    dbxref VisibleString }
+
+Parse-action ::= SEQUENCE {
+    portion Text-portion ,
+    src Parse-src ,
+    dest Parse-dest ,
+    capitalization Cap-change DEFAULT none ,
+    remove-from-parsed BOOLEAN DEFAULT FALSE ,
+    existing-text ExistingTextOption }
+
+
+Location-interval ::= SEQUENCE {
+    from INTEGER ,
+    to INTEGER  }
+
+Location-choice ::= CHOICE {
+    interval Location-interval ,
+    whole-sequence NULL }
+
+Sequence-list ::= SET OF VisibleString
+Sequence-list-choice ::= CHOICE {
+    list Sequence-list ,
+    all NULL }
+    
+Apply-feature-action ::= SEQUENCE {
+    type Feature-type ,
+    partial5 BOOLEAN DEFAULT FALSE ,
+    partial3 BOOLEAN DEFAULT FALSE ,
+    plus-strand BOOLEAN DEFAULT TRUE ,
+    location Location-choice ,
+    seq-list Sequence-list-choice ,
+    add-redundant BOOLEAN DEFAULT TRUE ,
+    add-mrna BOOLEAN DEFAULT FALSE ,
+    apply-to-parts BOOLEAN DEFAULT FALSE ,
+    only-seg-num INTEGER DEFAULT -1 ,
+    fields Feat-qual-legal-set OPTIONAL }
+
+Remove-feature-action ::= SEQUENCE {
+    type Feature-type ,
+    constraint Constraint-choice-set OPTIONAL }
+
+Feature-location-strand-from ::= ENUMERATED {
+  any (0) ,
+  plus (1) ,
+  minus (2) ,
+  unknown (3) ,
+  both (4) }
+
+Feature-location-strand-to ::= ENUMERATED {
+  plus (1) ,
+  minus (2) ,
+  unknown (3) ,
+  both (4) ,
+  reverse (5) }
+
+Edit-location-strand ::= SEQUENCE {
+  strand-from Feature-location-strand-from ,
+  strand-to   Feature-location-strand-to } 
+
+Partial-5-set-constraint ::= ENUMERATED {
+  all (0) ,
+  at-end (1) ,
+  bad-start (2) ,
+  frame-not-one (3) }
+
+Partial-5-set-action ::= SEQUENCE {
+  constraint Partial-5-set-constraint ,
+  extend BOOLEAN }
+
+Partial-5-clear-constraint ::= ENUMERATED {
+  all (0) ,
+  not-at-end (1) ,
+  good-start (2) }
+
+Partial-3-set-constraint ::= ENUMERATED {
+  all (0) ,
+  at-end (1) ,
+  bad-end (2) }
+
+Partial-3-set-action ::= SEQUENCE {
+  constraint Partial-3-set-constraint ,
+  extend BOOLEAN }
+
+Partial-3-clear-constraint ::= ENUMERATED {
+  all (0) ,
+  not-at-end (1) ,
+  good-end (2) }
+
+Convert-location-type ::= ENUMERATED {
+  join (1) ,
+  order (2) ,
+  merge (3) }
+
+Location-edit-type ::= CHOICE {
+  strand Edit-location-strand ,
+  set-5-partial Partial-5-set-action ,
+  clear-5-partial Partial-5-clear-constraint ,
+  set-3-partial Partial-3-set-action ,
+  clear-3-partial Partial-3-clear-constraint ,
+  convert Convert-location-type }
+
+Edit-feature-location-action ::= SEQUENCE {
+  type Feature-type ,
+  action Location-edit-type ,
+  constraint Constraint-choice-set OPTIONAL }
+
+Macro-action-choice ::= CHOICE {
+  aecr AECR-action ,
+  parse Parse-action ,
+  add-feature Apply-feature-action ,
+  remove-feature Remove-feature-action ,
+  edit-location Edit-feature-location-action }
+
+
+Macro-action-list ::= SET OF Macro-action-choice
+
+END
diff --git a/asn/makeload.bat b/asn/makeload.bat
index b8bd01b2..2e521ee6 100644
--- a/asn/makeload.bat
+++ b/asn/makeload.bat
@@ -1,6 +1,7 @@
 asntool -m ..\asn\general.asn -l asngen.h
 asntool -m ..\asn\seqset.asn -l asnsset.h
 asntool -m ..\asn\seqfeat.asn -l asnfeat.h
+asntool -m ..\asn\seqtable.asn -l asntable.h
 asntool -m ..\asn\seqalign.asn -l asnalign.h
 asntool -m ..\asn\seqloc.asn -l asnloc.h
 asntool -m ..\asn\seqres.asn -l asnres.h
diff --git a/asn/makeload.unx b/asn/makeload.unx
index 66f39535..55e44ba0 100755
--- a/asn/makeload.unx
+++ b/asn/makeload.unx
@@ -1,6 +1,7 @@
 asntool -m ../asn/general.asn -l asngen.h
 asntool -m ../asn/seqset.asn -l asnsset.h
 asntool -m ../asn/seqfeat.asn -l asnfeat.h
+asntool -m ../asn/seqtable.asn -l asntable.h
 asntool -m ../asn/seqalign.asn -l asnalign.h
 asntool -m ../asn/seqloc.asn -l asnloc.h
 asntool -m ../asn/seqres.asn -l asnres.h
diff --git a/asn/makestat.bat b/asn/makestat.bat
index 8f33674d..899af2db 100644
--- a/asn/makestat.bat
+++ b/asn/makestat.bat
@@ -1,6 +1,7 @@
 asntool -m ..\asn\general.asn -o asngen.h
 asntool -m ..\asn\seqset.asn -o asnsset.h
 asntool -m ..\asn\seqfeat.asn -o asnfeat.h
+asntool -m ..\asn\seqtable.asn -o asntable.h
 asntool -m ..\asn\seqalign.asn -o asnalign.h
 asntool -m ..\asn\seqloc.asn -o asnloc.h
 asntool -m ..\asn\seqres.asn -o asnres.h
@@ -42,3 +43,4 @@ asntool -m ..\access\mla2.asn -o asnmla2.h
 asntool -m ..\asn\gbseq.asn -o asngbseq.h
 asntool -m ..\asn\insdseq.asn -o asninsdseq.h
 asntool -m ..\asn\tinyseq.asn -o asntseq.h
+asntool -m ..\sequin\macro.asn -o asnmacro.h
diff --git a/asn/makestat.unx b/asn/makestat.unx
index 8eb52e0e..c82fefa6 100755
--- a/asn/makestat.unx
+++ b/asn/makestat.unx
@@ -1,6 +1,7 @@
 asntool -m ../asn/general.asn -o asngen.h
 asntool -m ../asn/seqset.asn -o asnsset.h
 asntool -m ../asn/seqfeat.asn -o asnfeat.h
+asntool -m ../asn/seqtable.asn -o asntable.h
 asntool -m ../asn/seqalign.asn -o asnalign.h
 asntool -m ../asn/seqloc.asn -o asnloc.h
 asntool -m ../asn/seqres.asn -o asnres.h
@@ -42,3 +43,4 @@ asntool -m ../access/mla2.asn -o asnmla2.h
 asntool -m ../asn/gbseq.asn -o asngbseq.h
 asntool -m ../asn/insdseq.asn -o asninsdseq.h
 asntool -m ../asn/tinyseq.asn -o asntseq.h
+asntool -m ../sequin/macro.asn -o asnmacro.h
diff --git a/asn/seq.asn b/asn/seq.asn
index 9696a68b..6b5ffce2 100644
--- a/asn/seq.asn
+++ b/asn/seq.asn
@@ -1,4 +1,4 @@
---$Revision: 6.16 $
+--$Revision: 6.19 $
 --**********************************************************************
 --
 --  NCBI Sequence elements
@@ -27,7 +27,8 @@ IMPORTS Date, Int-fuzz, Dbtag, Object-id, User-object FROM NCBI-General
         EMBL-block FROM EMBL-General
         SP-block FROM SP-General
         PRF-block FROM PRF-General
-        PDB-block FROM PDB-General;
+        PDB-block FROM PDB-General
+        Seq-table FROM NCBI-SeqTable;
 
 --*** Sequence ********************************
 --*
@@ -102,6 +103,8 @@ MolInfo ::= SEQUENCE {
         cRNA (11) ,              -- viral RNA genome copy intermediate
         snoRNA (12) ,            -- small nucleolar RNA
         transcribed-RNA (13) ,   -- transcribed RNA other than existing classes
+        ncRNA (14) ,
+        tmRNA (15) ,
         other (255) } DEFAULT unknown ,
     tech INTEGER {
         unknown (0) ,
@@ -127,6 +130,7 @@ MolInfo ::= SEQUENCE {
         wgs (20) ,              -- whole genome shotgun sequencing
         barcode (21) ,          -- barcode of life project
         composite-wgs-htgs (22) , -- composite of WGS and HTGS
+        tsa (23) ,              -- transcriptome shotgun assembly
         other (255) }           -- use Source.techexp
                DEFAULT unknown ,
     techexp VisibleString OPTIONAL ,   -- explanation if tech not enough
@@ -145,7 +149,8 @@ MolInfo ::= SEQUENCE {
       no-ends (5) ,                    -- missing both ends
       has-left (6) ,                   -- 5' or NH3 end present
       has-right (7) ,                  -- 3' or COOH end present
-      other (255) } DEFAULT unknown }
+      other (255) } DEFAULT unknown ,
+    gbmoltype VisibleString OPTIONAL } -- identifies particular ncRNA
 
 
 GIBB-mol ::= ENUMERATED {       -- type of molecule represented
@@ -239,12 +244,12 @@ Pubdesc ::= SEQUENCE {              -- how sequence presented in pub
     seq-raw StringStore OPTIONAL ,  -- original sequence from paper
     align-group INTEGER OPTIONAL ,  -- this seq aligned with others in paper
     comment VisibleString OPTIONAL, -- any comment on this pub in context
-	reftype INTEGER {           -- type of reference in a GenBank record
-		seq (0) ,               -- refers to sequence
-		sites (1) ,             -- refers to unspecified features
-		feats (2) ,             -- refers to specified features
-		no-target (3) }         -- nothing specified (EMBL)
-		DEFAULT seq }
+    reftype INTEGER {           -- type of reference in a GenBank record
+        seq (0) ,               -- refers to sequence
+        sites (1) ,             -- refers to unspecified features
+        feats (2) ,             -- refers to specified features
+        no-target (3) }         -- nothing specified (EMBL)
+        DEFAULT seq }
 
 Heterogen ::= VisibleString       -- cofactor, prosthetic group, inhibitor, etc
 
@@ -433,8 +438,9 @@ Seq-annot ::= SEQUENCE {
         ftable SET OF Seq-feat ,
         align SET OF Seq-align ,
         graph SET OF Seq-graph ,
-        ids SET OF Seq-id ,        -- used for communication between tools
-        locs SET OF Seq-loc } }    -- used for communication between tools
+        ids SET OF Seq-id ,      -- used for communication between tools
+        locs SET OF Seq-loc ,    -- used for communication between tools
+        seq-table Seq-table } }  -- features in table form
 
 END
 
diff --git a/asn/seqfeat.asn b/asn/seqfeat.asn
index 1752344a..f9b636ae 100644
--- a/asn/seqfeat.asn
+++ b/asn/seqfeat.asn
@@ -1,4 +1,4 @@
---$Revision: 6.18 $
+--$Revision: 6.19 $
 --**********************************************************************
 --
 --  NCBI Sequence Feature elements
@@ -444,7 +444,8 @@ BioSource ::= SEQUENCE {
         proplastid (18) ,
         endogenous-virus (19) ,
         hydrogenosome (20) ,
-        chromosome (21)
+        chromosome (21) ,
+        chromatophore (22)
       } DEFAULT unknown ,
     origin INTEGER {
       unknown (0) ,
diff --git a/asn/seqtable.asn b/asn/seqtable.asn
new file mode 100644
index 00000000..0cfd7957
--- /dev/null
+++ b/asn/seqtable.asn
@@ -0,0 +1,226 @@
+--$Revision: 1.5 $
+--  ----------------------------------------------------------------------------
+--
+--                            PUBLIC DOMAIN NOTICE
+--                National Center for Biotechnology Information
+--
+--  This software/database is a "United States Government Work" under the terms
+--  of the United States Copyright Act.  It was written as part of the author's
+--  official duties as a United States Government employee and thus cannot be
+--  copyrighted.  This software/database is freely available to the public for
+--  use.  The National Library of Medicine and the U.S. Government have not
+--  placed any restriction on its use or reproduction.
+--
+--  Although all reasonable efforts have been taken to ensure the accuracy and
+--  reliability of the software and data, the NLM and the U.S. Government do not
+--  and cannot warrant the performance or results that may be obtained by using
+--  this software or data.  The NLM and the U.S. Government disclaim all
+--  warranties, express or implied, including warranties of performance,
+--  merchantability or fitness for any particular purpose.
+--
+--  Please cite the authors in any work or product based on this material.
+--
+--  ----------------------------------------------------------------------------
+--
+--  Authors: Mike DiCuccio, Eugene Vasilchenko
+--
+--  ASN.1 interface to table readers
+--
+--  ----------------------------------------------------------------------------
+
+NCBI-SeqTable DEFINITIONS ::=
+
+BEGIN
+
+EXPORTS
+    SeqTable-column-info, SeqTable-column, Seq-table;
+    
+IMPORTS
+    Seq-id, Seq-loc, Seq-interval   FROM NCBI-Seqloc;
+
+
+SeqTable-column-info ::= SEQUENCE {
+    -- user friendly column name, can be skipped
+    title VisibleString OPTIONAL,
+
+    -- identification of the column data in the objects described by the table
+    field-id INTEGER { -- known column data types
+        -- position types
+        location        (0), -- location as Seq-loc
+        location-id     (1), -- location Seq-id
+        location-gi     (2), -- gi
+        location-from   (3), -- interval from
+        location-to     (4), -- interval to
+        location-strand (5), -- location strand
+        location-fuzz-from-lim (6),
+        location-fuzz-to-lim   (7),
+
+        product         (10), -- product as Seq-loc
+        product-id      (11), -- product Seq-id
+        product-gi      (12), -- product gi
+        product-from    (13), -- product interval from
+        product-to      (14), -- product interval to
+        product-strand  (15), -- product strand
+        product-fuzz-from-lim (16),
+        product-fuzz-to-lim   (17),
+        
+        -- main feature fields
+        id-local        (20), -- id.local.id
+        xref-id-local   (21), -- xref.id.local.id
+        partial         (22),
+        comment         (23),
+        title           (24),
+        ext             (25), -- field-name must be "E.xxx", see below
+        qual            (26), -- field-name must be "Q.xxx", see below
+        dbxref          (27), -- field-name must be "D.xxx", see below
+
+        -- various data fields
+        data-imp-key        (30),
+        data-region         (31),
+        data-cdregion-frame (32),
+
+        -- extra fields, see also special values for str below
+        ext-type        (40),
+        qual-qual       (41),
+        qual-val        (42),
+        dbxref-db       (43),
+        dbxref-tag      (44)
+    } OPTIONAL,
+
+    -- any column can be identified by ASN.1 text locator string
+    -- with omitted object type.
+    -- examples:
+    --   "data.gene.locus" for Seq-feat.data.gene.locus
+    --   "data.imp.key" for Seq-feat.data.imp.key
+    --   "qual.qual"
+    --    - Seq-feat.qual is SEQUENCE so several columns are allowed
+    --      see also "Q.xxx" special value for shorter qual representation
+    --   "ext.type.str"
+    --   "ext.data.label.str"
+    --   "ext.data.data.int"
+    --      see also "E.xxx" special value for shorter ext representation
+    -- special values start with capital letter:
+    --   "E.xxx" - ext.data.label.str = xxx, ext.data.data = data
+    --    - Seq-feat.ext.data is SEQUENCE so several columns are allowed
+    --   "Q.xxx" - qual.qual = xxx, qual.val = data
+    --    - Seq-feat.qual is SEQUENCE so several columns are allowed
+    --   "D.xxx" - dbxref.id = xxx, dbxref.tag = data
+    --    - Seq-feat.dbxref is SET so several columns are allowed
+    field-name  VisibleString OPTIONAL
+}
+
+
+CommonString-table ::= SEQUENCE {
+    -- set of possible values
+    strings     SEQUENCE OF VisibleString,
+
+    -- indexes of values
+    indexes     SEQUENCE OF INTEGER
+}
+
+
+CommonBytes-table ::= SEQUENCE {
+    -- set of possible values
+    bytes       SEQUENCE OF OCTET STRING,
+
+    -- indexes of values
+    indexes     SEQUENCE OF INTEGER
+}
+
+
+SeqTable-multi-data ::= CHOICE {
+    -- a set of integers, one per row
+    int         SEQUENCE OF INTEGER,
+    
+    -- a set of reals, one per row
+    real        SEQUENCE OF REAL,
+
+    -- a set of strings, one per row
+    string      SEQUENCE OF VisibleString,
+
+    -- a set of byte arrays, one per row
+    bytes       SEQUENCE OF OCTET STRING,
+
+    -- a set of string with small set of possible values
+    common-string   CommonString-table,
+
+    -- a set of byte arrays with small set of possible values
+    common-bytes    CommonBytes-table,
+
+    -- a set of bits, one per row
+    -- this uses bm::bvector<> as its storage mechanism
+    bit         OCTET STRING,
+
+    -- a set of locations, one per row
+    loc         SEQUENCE OF Seq-loc,
+    id          SEQUENCE OF Seq-id,
+    interval    SEQUENCE OF Seq-interval
+}
+
+
+SeqTable-single-data ::= CHOICE {
+    -- integer
+    int         INTEGER,
+    
+    -- real
+    real        REAL,
+
+    -- string
+    string      VisibleString,
+
+    -- byte array
+    bytes       OCTET STRING,
+
+    -- bit
+    bit         BOOLEAN,
+
+    -- location
+    loc         Seq-loc,
+    id          Seq-id,
+    interval    Seq-interval
+}
+
+
+SeqTable-sparse-index ::= CHOICE {
+    -- indexed of rows with values
+    indexes SEQUENCE OF INTEGER,
+
+    -- bitset of rows with values
+    bit-set OCTET STRING
+}
+
+
+SeqTable-column ::= SEQUENCE {
+    -- column description or reference to previously defined info
+    header      SeqTable-column-info,   -- information about data
+
+    -- row data
+    data        SeqTable-multi-data OPTIONAL,
+
+    -- in case not all rows contain data this field will contain sparse info
+    sparse      SeqTable-sparse-index OPTIONAL,
+
+    -- default value for sparse table, or if row data is too short
+    default     SeqTable-single-data OPTIONAL,
+
+    -- single value for indexes not listed in sparse table
+    sparse-other SeqTable-single-data OPTIONAL
+}
+
+
+Seq-table ::= SEQUENCE {
+    -- type of features in this table, equal to Seq-feat.data variant index
+    feat-type   INTEGER,
+
+    -- subtype of features in this table, defined in header SeqFeatData.hpp
+    feat-subtype INTEGER OPTIONAL,
+
+    -- number of rows
+    num-rows    INTEGER,
+
+    -- data in columns
+    columns     SEQUENCE OF SeqTable-column
+}
+
+
+END
diff --git a/asnlib/asnprint.c b/asnlib/asnprint.c
index da2d8840..ee10504f 100644
--- a/asnlib/asnprint.c
+++ b/asnlib/asnprint.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date: 3/4/91
 *
-* $Revision: 6.22 $
+* $Revision: 6.23 $
 *
 * File Description:
 *   Routines for printing ASN.1 value notation (text) messages and
@@ -42,6 +42,9 @@
 * 3/4/91   Kans        Stricter typecasting for GNU C and C++
 *
 * $Log: asnprint.c,v $
+* Revision 6.23  2007/12/03 18:15:31  gouriano
+* Corrected line length in AsnPrintString
+*
 * Revision 6.22  2004/12/08 04:39:38  beloslyu
 * c++ comment changed to c-style one. Anrdrei, please be careful
 *
@@ -1650,7 +1653,7 @@ NLM_EXTERN Boolean AsnPrintString (CharPtr the_string, AsnIoPtr aip)
             *current = *(str+1);
             *(current+1) = 0;
             pos = AsnPrintGetWordBreak(str_begin, 
-                                       aip->linelength - linepos_start);
+                                       aip->linepos - linepos_start);
 
             /* Save rest of string */
 
diff --git a/asnstat/all.h b/asnstat/all.h
index 4b709a29..e793b3de 100644
--- a/asnstat/all.h
+++ b/asnstat/all.h
@@ -10,7 +10,7 @@
 #endif
 
 static char * asnfilename = "all.h60";
-static AsnValxNode avnx[617] = {
+static AsnValxNode avnx[1107] = {
     {20,"unk" ,0,0.0,&avnx[1] } ,
     {20,"gt" ,1,0.0,&avnx[2] } ,
     {20,"lt" ,2,0.0,&avnx[3] } ,
@@ -273,363 +273,853 @@ static AsnValxNode avnx[617] = {
     {20,"proplastid" ,18,0.0,&avnx[260] } ,
     {20,"endogenous-virus" ,19,0.0,&avnx[261] } ,
     {20,"hydrogenosome" ,20,0.0,&avnx[262] } ,
-    {20,"chromosome" ,21,0.0,NULL } ,
+    {20,"chromosome" ,21,0.0,&avnx[263] } ,
+    {20,"chromatophore" ,22,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[265] } ,
-    {20,"natural" ,1,0.0,&avnx[266] } ,
-    {20,"natmut" ,2,0.0,&avnx[267] } ,
-    {20,"mut" ,3,0.0,&avnx[268] } ,
-    {20,"artificial" ,4,0.0,&avnx[269] } ,
-    {20,"synthetic" ,5,0.0,&avnx[270] } ,
+    {20,"unknown" ,0,0.0,&avnx[266] } ,
+    {20,"natural" ,1,0.0,&avnx[267] } ,
+    {20,"natmut" ,2,0.0,&avnx[268] } ,
+    {20,"mut" ,3,0.0,&avnx[269] } ,
+    {20,"artificial" ,4,0.0,&avnx[270] } ,
+    {20,"synthetic" ,5,0.0,&avnx[271] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"chromosome" ,1,0.0,&avnx[273] } ,
-    {20,"map" ,2,0.0,&avnx[274] } ,
-    {20,"clone" ,3,0.0,&avnx[275] } ,
-    {20,"subclone" ,4,0.0,&avnx[276] } ,
-    {20,"haplotype" ,5,0.0,&avnx[277] } ,
-    {20,"genotype" ,6,0.0,&avnx[278] } ,
-    {20,"sex" ,7,0.0,&avnx[279] } ,
-    {20,"cell-line" ,8,0.0,&avnx[280] } ,
-    {20,"cell-type" ,9,0.0,&avnx[281] } ,
-    {20,"tissue-type" ,10,0.0,&avnx[282] } ,
-    {20,"clone-lib" ,11,0.0,&avnx[283] } ,
-    {20,"dev-stage" ,12,0.0,&avnx[284] } ,
-    {20,"frequency" ,13,0.0,&avnx[285] } ,
-    {20,"germline" ,14,0.0,&avnx[286] } ,
-    {20,"rearranged" ,15,0.0,&avnx[287] } ,
-    {20,"lab-host" ,16,0.0,&avnx[288] } ,
-    {20,"pop-variant" ,17,0.0,&avnx[289] } ,
-    {20,"tissue-lib" ,18,0.0,&avnx[290] } ,
-    {20,"plasmid-name" ,19,0.0,&avnx[291] } ,
-    {20,"transposon-name" ,20,0.0,&avnx[292] } ,
-    {20,"insertion-seq-name" ,21,0.0,&avnx[293] } ,
-    {20,"plastid-name" ,22,0.0,&avnx[294] } ,
-    {20,"country" ,23,0.0,&avnx[295] } ,
-    {20,"segment" ,24,0.0,&avnx[296] } ,
-    {20,"endogenous-virus-name" ,25,0.0,&avnx[297] } ,
-    {20,"transgenic" ,26,0.0,&avnx[298] } ,
-    {20,"environmental-sample" ,27,0.0,&avnx[299] } ,
-    {20,"isolation-source" ,28,0.0,&avnx[300] } ,
-    {20,"lat-lon" ,29,0.0,&avnx[301] } ,
-    {20,"collection-date" ,30,0.0,&avnx[302] } ,
-    {20,"collected-by" ,31,0.0,&avnx[303] } ,
-    {20,"identified-by" ,32,0.0,&avnx[304] } ,
-    {20,"fwd-primer-seq" ,33,0.0,&avnx[305] } ,
-    {20,"rev-primer-seq" ,34,0.0,&avnx[306] } ,
-    {20,"fwd-primer-name" ,35,0.0,&avnx[307] } ,
-    {20,"rev-primer-name" ,36,0.0,&avnx[308] } ,
-    {20,"metagenomic" ,37,0.0,&avnx[309] } ,
+    {20,"chromosome" ,1,0.0,&avnx[274] } ,
+    {20,"map" ,2,0.0,&avnx[275] } ,
+    {20,"clone" ,3,0.0,&avnx[276] } ,
+    {20,"subclone" ,4,0.0,&avnx[277] } ,
+    {20,"haplotype" ,5,0.0,&avnx[278] } ,
+    {20,"genotype" ,6,0.0,&avnx[279] } ,
+    {20,"sex" ,7,0.0,&avnx[280] } ,
+    {20,"cell-line" ,8,0.0,&avnx[281] } ,
+    {20,"cell-type" ,9,0.0,&avnx[282] } ,
+    {20,"tissue-type" ,10,0.0,&avnx[283] } ,
+    {20,"clone-lib" ,11,0.0,&avnx[284] } ,
+    {20,"dev-stage" ,12,0.0,&avnx[285] } ,
+    {20,"frequency" ,13,0.0,&avnx[286] } ,
+    {20,"germline" ,14,0.0,&avnx[287] } ,
+    {20,"rearranged" ,15,0.0,&avnx[288] } ,
+    {20,"lab-host" ,16,0.0,&avnx[289] } ,
+    {20,"pop-variant" ,17,0.0,&avnx[290] } ,
+    {20,"tissue-lib" ,18,0.0,&avnx[291] } ,
+    {20,"plasmid-name" ,19,0.0,&avnx[292] } ,
+    {20,"transposon-name" ,20,0.0,&avnx[293] } ,
+    {20,"insertion-seq-name" ,21,0.0,&avnx[294] } ,
+    {20,"plastid-name" ,22,0.0,&avnx[295] } ,
+    {20,"country" ,23,0.0,&avnx[296] } ,
+    {20,"segment" ,24,0.0,&avnx[297] } ,
+    {20,"endogenous-virus-name" ,25,0.0,&avnx[298] } ,
+    {20,"transgenic" ,26,0.0,&avnx[299] } ,
+    {20,"environmental-sample" ,27,0.0,&avnx[300] } ,
+    {20,"isolation-source" ,28,0.0,&avnx[301] } ,
+    {20,"lat-lon" ,29,0.0,&avnx[302] } ,
+    {20,"collection-date" ,30,0.0,&avnx[303] } ,
+    {20,"collected-by" ,31,0.0,&avnx[304] } ,
+    {20,"identified-by" ,32,0.0,&avnx[305] } ,
+    {20,"fwd-primer-seq" ,33,0.0,&avnx[306] } ,
+    {20,"rev-primer-seq" ,34,0.0,&avnx[307] } ,
+    {20,"fwd-primer-name" ,35,0.0,&avnx[308] } ,
+    {20,"rev-primer-name" ,36,0.0,&avnx[309] } ,
+    {20,"metagenomic" ,37,0.0,&avnx[310] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[311] } ,
-    {20,"genomic" ,1,0.0,&avnx[312] } ,
-    {20,"pre-RNA" ,2,0.0,&avnx[313] } ,
-    {20,"mRNA" ,3,0.0,&avnx[314] } ,
-    {20,"rRNA" ,4,0.0,&avnx[315] } ,
-    {20,"tRNA" ,5,0.0,&avnx[316] } ,
-    {20,"snRNA" ,6,0.0,&avnx[317] } ,
-    {20,"scRNA" ,7,0.0,&avnx[318] } ,
-    {20,"peptide" ,8,0.0,&avnx[319] } ,
-    {20,"other-genetic" ,9,0.0,&avnx[320] } ,
-    {20,"genomic-mRNA" ,10,0.0,&avnx[321] } ,
-    {20,"cRNA" ,11,0.0,&avnx[322] } ,
-    {20,"snoRNA" ,12,0.0,&avnx[323] } ,
-    {20,"transcribed-RNA" ,13,0.0,&avnx[324] } ,
+    {20,"unknown" ,0,0.0,&avnx[312] } ,
+    {20,"genomic" ,1,0.0,&avnx[313] } ,
+    {20,"pre-RNA" ,2,0.0,&avnx[314] } ,
+    {20,"mRNA" ,3,0.0,&avnx[315] } ,
+    {20,"rRNA" ,4,0.0,&avnx[316] } ,
+    {20,"tRNA" ,5,0.0,&avnx[317] } ,
+    {20,"snRNA" ,6,0.0,&avnx[318] } ,
+    {20,"scRNA" ,7,0.0,&avnx[319] } ,
+    {20,"peptide" ,8,0.0,&avnx[320] } ,
+    {20,"other-genetic" ,9,0.0,&avnx[321] } ,
+    {20,"genomic-mRNA" ,10,0.0,&avnx[322] } ,
+    {20,"cRNA" ,11,0.0,&avnx[323] } ,
+    {20,"snoRNA" ,12,0.0,&avnx[324] } ,
+    {20,"transcribed-RNA" ,13,0.0,&avnx[325] } ,
+    {20,"ncRNA" ,14,0.0,&avnx[326] } ,
+    {20,"tmRNA" ,15,0.0,&avnx[327] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[327] } ,
-    {20,"standard" ,1,0.0,&avnx[328] } ,
-    {20,"est" ,2,0.0,&avnx[329] } ,
-    {20,"sts" ,3,0.0,&avnx[330] } ,
-    {20,"survey" ,4,0.0,&avnx[331] } ,
-    {20,"genemap" ,5,0.0,&avnx[332] } ,
-    {20,"physmap" ,6,0.0,&avnx[333] } ,
-    {20,"derived" ,7,0.0,&avnx[334] } ,
-    {20,"concept-trans" ,8,0.0,&avnx[335] } ,
-    {20,"seq-pept" ,9,0.0,&avnx[336] } ,
-    {20,"both" ,10,0.0,&avnx[337] } ,
-    {20,"seq-pept-overlap" ,11,0.0,&avnx[338] } ,
-    {20,"seq-pept-homol" ,12,0.0,&avnx[339] } ,
-    {20,"concept-trans-a" ,13,0.0,&avnx[340] } ,
-    {20,"htgs-1" ,14,0.0,&avnx[341] } ,
-    {20,"htgs-2" ,15,0.0,&avnx[342] } ,
-    {20,"htgs-3" ,16,0.0,&avnx[343] } ,
-    {20,"fli-cdna" ,17,0.0,&avnx[344] } ,
-    {20,"htgs-0" ,18,0.0,&avnx[345] } ,
-    {20,"htc" ,19,0.0,&avnx[346] } ,
-    {20,"wgs" ,20,0.0,&avnx[347] } ,
-    {20,"barcode" ,21,0.0,&avnx[348] } ,
-    {20,"composite-wgs-htgs" ,22,0.0,&avnx[349] } ,
+    {20,"unknown" ,0,0.0,&avnx[330] } ,
+    {20,"standard" ,1,0.0,&avnx[331] } ,
+    {20,"est" ,2,0.0,&avnx[332] } ,
+    {20,"sts" ,3,0.0,&avnx[333] } ,
+    {20,"survey" ,4,0.0,&avnx[334] } ,
+    {20,"genemap" ,5,0.0,&avnx[335] } ,
+    {20,"physmap" ,6,0.0,&avnx[336] } ,
+    {20,"derived" ,7,0.0,&avnx[337] } ,
+    {20,"concept-trans" ,8,0.0,&avnx[338] } ,
+    {20,"seq-pept" ,9,0.0,&avnx[339] } ,
+    {20,"both" ,10,0.0,&avnx[340] } ,
+    {20,"seq-pept-overlap" ,11,0.0,&avnx[341] } ,
+    {20,"seq-pept-homol" ,12,0.0,&avnx[342] } ,
+    {20,"concept-trans-a" ,13,0.0,&avnx[343] } ,
+    {20,"htgs-1" ,14,0.0,&avnx[344] } ,
+    {20,"htgs-2" ,15,0.0,&avnx[345] } ,
+    {20,"htgs-3" ,16,0.0,&avnx[346] } ,
+    {20,"fli-cdna" ,17,0.0,&avnx[347] } ,
+    {20,"htgs-0" ,18,0.0,&avnx[348] } ,
+    {20,"htc" ,19,0.0,&avnx[349] } ,
+    {20,"wgs" ,20,0.0,&avnx[350] } ,
+    {20,"barcode" ,21,0.0,&avnx[351] } ,
+    {20,"composite-wgs-htgs" ,22,0.0,&avnx[352] } ,
+    {20,"tsa" ,23,0.0,&avnx[353] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[352] } ,
-    {20,"complete" ,1,0.0,&avnx[353] } ,
-    {20,"partial" ,2,0.0,&avnx[354] } ,
-    {20,"no-left" ,3,0.0,&avnx[355] } ,
-    {20,"no-right" ,4,0.0,&avnx[356] } ,
-    {20,"no-ends" ,5,0.0,&avnx[357] } ,
-    {20,"has-left" ,6,0.0,&avnx[358] } ,
-    {20,"has-right" ,7,0.0,&avnx[359] } ,
+    {20,"unknown" ,0,0.0,&avnx[356] } ,
+    {20,"complete" ,1,0.0,&avnx[357] } ,
+    {20,"partial" ,2,0.0,&avnx[358] } ,
+    {20,"no-left" ,3,0.0,&avnx[359] } ,
+    {20,"no-right" ,4,0.0,&avnx[360] } ,
+    {20,"no-ends" ,5,0.0,&avnx[361] } ,
+    {20,"has-left" ,6,0.0,&avnx[362] } ,
+    {20,"has-right" ,7,0.0,&avnx[363] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[362] } ,
-    {20,"virtual" ,1,0.0,&avnx[363] } ,
-    {20,"raw" ,2,0.0,&avnx[364] } ,
-    {20,"seg" ,3,0.0,&avnx[365] } ,
-    {20,"const" ,4,0.0,&avnx[366] } ,
-    {20,"ref" ,5,0.0,&avnx[367] } ,
-    {20,"consen" ,6,0.0,&avnx[368] } ,
-    {20,"map" ,7,0.0,&avnx[369] } ,
-    {20,"delta" ,8,0.0,&avnx[370] } ,
+    {20,"not-set" ,0,0.0,&avnx[366] } ,
+    {20,"virtual" ,1,0.0,&avnx[367] } ,
+    {20,"raw" ,2,0.0,&avnx[368] } ,
+    {20,"seg" ,3,0.0,&avnx[369] } ,
+    {20,"const" ,4,0.0,&avnx[370] } ,
+    {20,"ref" ,5,0.0,&avnx[371] } ,
+    {20,"consen" ,6,0.0,&avnx[372] } ,
+    {20,"map" ,7,0.0,&avnx[373] } ,
+    {20,"delta" ,8,0.0,&avnx[374] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[372] } ,
-    {20,"dna" ,1,0.0,&avnx[373] } ,
-    {20,"rna" ,2,0.0,&avnx[374] } ,
-    {20,"aa" ,3,0.0,&avnx[375] } ,
-    {20,"na" ,4,0.0,&avnx[376] } ,
+    {20,"not-set" ,0,0.0,&avnx[376] } ,
+    {20,"dna" ,1,0.0,&avnx[377] } ,
+    {20,"rna" ,2,0.0,&avnx[378] } ,
+    {20,"aa" ,3,0.0,&avnx[379] } ,
+    {20,"na" ,4,0.0,&avnx[380] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[378] } ,
-    {20,"linear" ,1,0.0,&avnx[379] } ,
-    {20,"circular" ,2,0.0,&avnx[380] } ,
-    {20,"tandem" ,3,0.0,&avnx[381] } ,
+    {20,"not-set" ,0,0.0,&avnx[382] } ,
+    {20,"linear" ,1,0.0,&avnx[383] } ,
+    {20,"circular" ,2,0.0,&avnx[384] } ,
+    {20,"tandem" ,3,0.0,&avnx[385] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,1,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[384] } ,
-    {20,"ss" ,1,0.0,&avnx[385] } ,
-    {20,"ds" ,2,0.0,&avnx[386] } ,
-    {20,"mixed" ,3,0.0,&avnx[387] } ,
+    {20,"not-set" ,0,0.0,&avnx[388] } ,
+    {20,"ss" ,1,0.0,&avnx[389] } ,
+    {20,"ds" ,2,0.0,&avnx[390] } ,
+    {20,"mixed" ,3,0.0,&avnx[391] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[389] } ,
-    {20,"fragment" ,1,0.0,&avnx[390] } ,
-    {20,"clone" ,2,0.0,&avnx[391] } ,
-    {20,"short-arm" ,3,0.0,&avnx[392] } ,
-    {20,"heterochromatin" ,4,0.0,&avnx[393] } ,
-    {20,"centromere" ,5,0.0,&avnx[394] } ,
-    {20,"telomere" ,6,0.0,&avnx[395] } ,
-    {20,"repeat" ,7,0.0,&avnx[396] } ,
-    {20,"contig" ,8,0.0,&avnx[397] } ,
+    {20,"unknown" ,0,0.0,&avnx[393] } ,
+    {20,"fragment" ,1,0.0,&avnx[394] } ,
+    {20,"clone" ,2,0.0,&avnx[395] } ,
+    {20,"short-arm" ,3,0.0,&avnx[396] } ,
+    {20,"heterochromatin" ,4,0.0,&avnx[397] } ,
+    {20,"centromere" ,5,0.0,&avnx[398] } ,
+    {20,"telomere" ,6,0.0,&avnx[399] } ,
+    {20,"repeat" ,7,0.0,&avnx[400] } ,
+    {20,"contig" ,8,0.0,&avnx[401] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unlinked" ,0,0.0,&avnx[399] } ,
-    {20,"linked" ,1,0.0,&avnx[400] } ,
+    {20,"unlinked" ,0,0.0,&avnx[403] } ,
+    {20,"linked" ,1,0.0,&avnx[404] } ,
     {20,"other" ,255,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[403] } ,
-    {20,"one" ,1,0.0,&avnx[404] } ,
-    {20,"two" ,2,0.0,&avnx[405] } ,
+    {20,"not-set" ,0,0.0,&avnx[407] } ,
+    {20,"one" ,1,0.0,&avnx[408] } ,
+    {20,"two" ,2,0.0,&avnx[409] } ,
     {20,"three" ,3,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[408] } ,
-    {20,"preprotein" ,1,0.0,&avnx[409] } ,
-    {20,"mature" ,2,0.0,&avnx[410] } ,
-    {20,"signal-peptide" ,3,0.0,&avnx[411] } ,
+    {20,"not-set" ,0,0.0,&avnx[412] } ,
+    {20,"preprotein" ,1,0.0,&avnx[413] } ,
+    {20,"mature" ,2,0.0,&avnx[414] } ,
+    {20,"signal-peptide" ,3,0.0,&avnx[415] } ,
     {20,"transit-peptide" ,4,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[414] } ,
-    {20,"premsg" ,1,0.0,&avnx[415] } ,
-    {20,"mRNA" ,2,0.0,&avnx[416] } ,
-    {20,"tRNA" ,3,0.0,&avnx[417] } ,
-    {20,"rRNA" ,4,0.0,&avnx[418] } ,
-    {20,"snRNA" ,5,0.0,&avnx[419] } ,
-    {20,"scRNA" ,6,0.0,&avnx[420] } ,
-    {20,"snoRNA" ,7,0.0,&avnx[421] } ,
+    {20,"unknown" ,0,0.0,&avnx[418] } ,
+    {20,"premsg" ,1,0.0,&avnx[419] } ,
+    {20,"mRNA" ,2,0.0,&avnx[420] } ,
+    {20,"tRNA" ,3,0.0,&avnx[421] } ,
+    {20,"rRNA" ,4,0.0,&avnx[422] } ,
+    {20,"snRNA" ,5,0.0,&avnx[423] } ,
+    {20,"scRNA" ,6,0.0,&avnx[424] } ,
+    {20,"snoRNA" ,7,0.0,&avnx[425] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"disulfide" ,1,0.0,&avnx[423] } ,
-    {20,"thiolester" ,2,0.0,&avnx[424] } ,
-    {20,"xlink" ,3,0.0,&avnx[425] } ,
-    {20,"thioether" ,4,0.0,&avnx[426] } ,
+    {20,"disulfide" ,1,0.0,&avnx[427] } ,
+    {20,"thiolester" ,2,0.0,&avnx[428] } ,
+    {20,"xlink" ,3,0.0,&avnx[429] } ,
+    {20,"thioether" ,4,0.0,&avnx[430] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"active" ,1,0.0,&avnx[428] } ,
-    {20,"binding" ,2,0.0,&avnx[429] } ,
-    {20,"cleavage" ,3,0.0,&avnx[430] } ,
-    {20,"inhibit" ,4,0.0,&avnx[431] } ,
-    {20,"modified" ,5,0.0,&avnx[432] } ,
-    {20,"glycosylation" ,6,0.0,&avnx[433] } ,
-    {20,"myristoylation" ,7,0.0,&avnx[434] } ,
-    {20,"mutagenized" ,8,0.0,&avnx[435] } ,
-    {20,"metal-binding" ,9,0.0,&avnx[436] } ,
-    {20,"phosphorylation" ,10,0.0,&avnx[437] } ,
-    {20,"acetylation" ,11,0.0,&avnx[438] } ,
-    {20,"amidation" ,12,0.0,&avnx[439] } ,
-    {20,"methylation" ,13,0.0,&avnx[440] } ,
-    {20,"hydroxylation" ,14,0.0,&avnx[441] } ,
-    {20,"sulfatation" ,15,0.0,&avnx[442] } ,
-    {20,"oxidative-deamination" ,16,0.0,&avnx[443] } ,
-    {20,"pyrrolidone-carboxylic-acid" ,17,0.0,&avnx[444] } ,
-    {20,"gamma-carboxyglutamic-acid" ,18,0.0,&avnx[445] } ,
-    {20,"blocked" ,19,0.0,&avnx[446] } ,
-    {20,"lipid-binding" ,20,0.0,&avnx[447] } ,
-    {20,"np-binding" ,21,0.0,&avnx[448] } ,
-    {20,"dna-binding" ,22,0.0,&avnx[449] } ,
-    {20,"signal-peptide" ,23,0.0,&avnx[450] } ,
-    {20,"transit-peptide" ,24,0.0,&avnx[451] } ,
-    {20,"transmembrane-region" ,25,0.0,&avnx[452] } ,
-    {20,"nitrosylation" ,26,0.0,&avnx[453] } ,
+    {20,"active" ,1,0.0,&avnx[432] } ,
+    {20,"binding" ,2,0.0,&avnx[433] } ,
+    {20,"cleavage" ,3,0.0,&avnx[434] } ,
+    {20,"inhibit" ,4,0.0,&avnx[435] } ,
+    {20,"modified" ,5,0.0,&avnx[436] } ,
+    {20,"glycosylation" ,6,0.0,&avnx[437] } ,
+    {20,"myristoylation" ,7,0.0,&avnx[438] } ,
+    {20,"mutagenized" ,8,0.0,&avnx[439] } ,
+    {20,"metal-binding" ,9,0.0,&avnx[440] } ,
+    {20,"phosphorylation" ,10,0.0,&avnx[441] } ,
+    {20,"acetylation" ,11,0.0,&avnx[442] } ,
+    {20,"amidation" ,12,0.0,&avnx[443] } ,
+    {20,"methylation" ,13,0.0,&avnx[444] } ,
+    {20,"hydroxylation" ,14,0.0,&avnx[445] } ,
+    {20,"sulfatation" ,15,0.0,&avnx[446] } ,
+    {20,"oxidative-deamination" ,16,0.0,&avnx[447] } ,
+    {20,"pyrrolidone-carboxylic-acid" ,17,0.0,&avnx[448] } ,
+    {20,"gamma-carboxyglutamic-acid" ,18,0.0,&avnx[449] } ,
+    {20,"blocked" ,19,0.0,&avnx[450] } ,
+    {20,"lipid-binding" ,20,0.0,&avnx[451] } ,
+    {20,"np-binding" ,21,0.0,&avnx[452] } ,
+    {20,"dna-binding" ,22,0.0,&avnx[453] } ,
+    {20,"signal-peptide" ,23,0.0,&avnx[454] } ,
+    {20,"transit-peptide" ,24,0.0,&avnx[455] } ,
+    {20,"transmembrane-region" ,25,0.0,&avnx[456] } ,
+    {20,"nitrosylation" ,26,0.0,&avnx[457] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[455] } ,
-    {20,"pol1" ,1,0.0,&avnx[456] } ,
-    {20,"pol2" ,2,0.0,&avnx[457] } ,
-    {20,"pol3" ,3,0.0,&avnx[458] } ,
-    {20,"bacterial" ,4,0.0,&avnx[459] } ,
-    {20,"viral" ,5,0.0,&avnx[460] } ,
-    {20,"rna" ,6,0.0,&avnx[461] } ,
-    {20,"organelle" ,7,0.0,&avnx[462] } ,
+    {20,"unknown" ,0,0.0,&avnx[459] } ,
+    {20,"pol1" ,1,0.0,&avnx[460] } ,
+    {20,"pol2" ,2,0.0,&avnx[461] } ,
+    {20,"pol3" ,3,0.0,&avnx[462] } ,
+    {20,"bacterial" ,4,0.0,&avnx[463] } ,
+    {20,"viral" ,5,0.0,&avnx[464] } ,
+    {20,"rna" ,6,0.0,&avnx[465] } ,
+    {20,"organelle" ,7,0.0,&avnx[466] } ,
     {20,"other" ,255,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[466] } ,
-    {20,"single" ,1,0.0,&avnx[467] } ,
-    {20,"multiple" ,2,0.0,&avnx[468] } ,
-    {20,"region" ,3,0.0,NULL } ,
     {20,"unknown" ,0,0.0,&avnx[470] } ,
-    {20,"rna-seq" ,1,0.0,&avnx[471] } ,
-    {20,"rna-size" ,2,0.0,&avnx[472] } ,
-    {20,"np-map" ,3,0.0,&avnx[473] } ,
-    {20,"np-size" ,4,0.0,&avnx[474] } ,
-    {20,"pe-seq" ,5,0.0,&avnx[475] } ,
-    {20,"cDNA-seq" ,6,0.0,&avnx[476] } ,
-    {20,"pe-map" ,7,0.0,&avnx[477] } ,
-    {20,"pe-size" ,8,0.0,&avnx[478] } ,
-    {20,"pseudo-seq" ,9,0.0,&avnx[479] } ,
-    {20,"rev-pe-map" ,10,0.0,&avnx[480] } ,
+    {20,"single" ,1,0.0,&avnx[471] } ,
+    {20,"multiple" ,2,0.0,&avnx[472] } ,
+    {20,"region" ,3,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[474] } ,
+    {20,"rna-seq" ,1,0.0,&avnx[475] } ,
+    {20,"rna-size" ,2,0.0,&avnx[476] } ,
+    {20,"np-map" ,3,0.0,&avnx[477] } ,
+    {20,"np-size" ,4,0.0,&avnx[478] } ,
+    {20,"pe-seq" ,5,0.0,&avnx[479] } ,
+    {20,"cDNA-seq" ,6,0.0,&avnx[480] } ,
+    {20,"pe-map" ,7,0.0,&avnx[481] } ,
+    {20,"pe-size" ,8,0.0,&avnx[482] } ,
+    {20,"pseudo-seq" ,9,0.0,&avnx[483] } ,
+    {20,"rev-pe-map" ,10,0.0,&avnx[484] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[482] } ,
-    {20,"physiological" ,1,0.0,&avnx[483] } ,
-    {20,"in-vitro" ,2,0.0,&avnx[484] } ,
-    {20,"oocyte" ,3,0.0,&avnx[485] } ,
-    {20,"transfection" ,4,0.0,&avnx[486] } ,
-    {20,"transgenic" ,5,0.0,&avnx[487] } ,
+    {20,"unknown" ,0,0.0,&avnx[486] } ,
+    {20,"physiological" ,1,0.0,&avnx[487] } ,
+    {20,"in-vitro" ,2,0.0,&avnx[488] } ,
+    {20,"oocyte" ,3,0.0,&avnx[489] } ,
+    {20,"transfection" ,4,0.0,&avnx[490] } ,
+    {20,"transgenic" ,5,0.0,&avnx[491] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,1,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
-    {20,"helix" ,1,0.0,&avnx[492] } ,
-    {20,"sheet" ,2,0.0,&avnx[493] } ,
+    {20,"helix" ,1,0.0,&avnx[496] } ,
+    {20,"sheet" ,2,0.0,&avnx[497] } ,
     {20,"turn" ,3,0.0,NULL } ,
-    {20,"experimental" ,1,0.0,&avnx[495] } ,
+    {20,"experimental" ,1,0.0,&avnx[499] } ,
     {20,"not-experimental" ,2,0.0,NULL } ,
-    {20,"genbank" ,1,0.0,&avnx[497] } ,
-    {20,"embl" ,2,0.0,&avnx[498] } ,
-    {20,"ddbj" ,3,0.0,&avnx[499] } ,
-    {20,"pir" ,4,0.0,&avnx[500] } ,
-    {20,"sp" ,5,0.0,&avnx[501] } ,
-    {20,"bbone" ,6,0.0,&avnx[502] } ,
-    {20,"pdb" ,7,0.0,&avnx[503] } ,
+    {20,"genbank" ,1,0.0,&avnx[501] } ,
+    {20,"embl" ,2,0.0,&avnx[502] } ,
+    {20,"ddbj" ,3,0.0,&avnx[503] } ,
+    {20,"pir" ,4,0.0,&avnx[504] } ,
+    {20,"sp" ,5,0.0,&avnx[505] } ,
+    {20,"bbone" ,6,0.0,&avnx[506] } ,
+    {20,"pdb" ,7,0.0,&avnx[507] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[505] } ,
-    {20,"nuc-prot" ,1,0.0,&avnx[506] } ,
-    {20,"segset" ,2,0.0,&avnx[507] } ,
-    {20,"conset" ,3,0.0,&avnx[508] } ,
-    {20,"parts" ,4,0.0,&avnx[509] } ,
-    {20,"gibb" ,5,0.0,&avnx[510] } ,
-    {20,"gi" ,6,0.0,&avnx[511] } ,
-    {20,"genbank" ,7,0.0,&avnx[512] } ,
-    {20,"pir" ,8,0.0,&avnx[513] } ,
-    {20,"pub-set" ,9,0.0,&avnx[514] } ,
-    {20,"equiv" ,10,0.0,&avnx[515] } ,
-    {20,"swissprot" ,11,0.0,&avnx[516] } ,
-    {20,"pdb-entry" ,12,0.0,&avnx[517] } ,
-    {20,"mut-set" ,13,0.0,&avnx[518] } ,
-    {20,"pop-set" ,14,0.0,&avnx[519] } ,
-    {20,"phy-set" ,15,0.0,&avnx[520] } ,
-    {20,"eco-set" ,16,0.0,&avnx[521] } ,
-    {20,"gen-prod-set" ,17,0.0,&avnx[522] } ,
-    {20,"wgs-set" ,18,0.0,&avnx[523] } ,
+    {20,"location" ,0,0.0,&avnx[509] } ,
+    {20,"location-id" ,1,0.0,&avnx[510] } ,
+    {20,"location-gi" ,2,0.0,&avnx[511] } ,
+    {20,"location-from" ,3,0.0,&avnx[512] } ,
+    {20,"location-to" ,4,0.0,&avnx[513] } ,
+    {20,"location-strand" ,5,0.0,&avnx[514] } ,
+    {20,"location-fuzz-from-lim" ,6,0.0,&avnx[515] } ,
+    {20,"location-fuzz-to-lim" ,7,0.0,&avnx[516] } ,
+    {20,"product" ,10,0.0,&avnx[517] } ,
+    {20,"product-id" ,11,0.0,&avnx[518] } ,
+    {20,"product-gi" ,12,0.0,&avnx[519] } ,
+    {20,"product-from" ,13,0.0,&avnx[520] } ,
+    {20,"product-to" ,14,0.0,&avnx[521] } ,
+    {20,"product-strand" ,15,0.0,&avnx[522] } ,
+    {20,"product-fuzz-from-lim" ,16,0.0,&avnx[523] } ,
+    {20,"product-fuzz-to-lim" ,17,0.0,&avnx[524] } ,
+    {20,"id-local" ,20,0.0,&avnx[525] } ,
+    {20,"xref-id-local" ,21,0.0,&avnx[526] } ,
+    {20,"partial" ,22,0.0,&avnx[527] } ,
+    {20,"comment" ,23,0.0,&avnx[528] } ,
+    {20,"title" ,24,0.0,&avnx[529] } ,
+    {20,"ext" ,25,0.0,&avnx[530] } ,
+    {20,"qual" ,26,0.0,&avnx[531] } ,
+    {20,"dbxref" ,27,0.0,&avnx[532] } ,
+    {20,"data-imp-key" ,30,0.0,&avnx[533] } ,
+    {20,"data-region" ,31,0.0,&avnx[534] } ,
+    {20,"data-cdregion-frame" ,32,0.0,&avnx[535] } ,
+    {20,"ext-type" ,40,0.0,&avnx[536] } ,
+    {20,"qual-qual" ,41,0.0,&avnx[537] } ,
+    {20,"qual-val" ,42,0.0,&avnx[538] } ,
+    {20,"dbxref-db" ,43,0.0,&avnx[539] } ,
+    {20,"dbxref-tag" ,44,0.0,NULL } ,
+    {20,"not-set" ,0,0.0,&avnx[541] } ,
+    {20,"nuc-prot" ,1,0.0,&avnx[542] } ,
+    {20,"segset" ,2,0.0,&avnx[543] } ,
+    {20,"conset" ,3,0.0,&avnx[544] } ,
+    {20,"parts" ,4,0.0,&avnx[545] } ,
+    {20,"gibb" ,5,0.0,&avnx[546] } ,
+    {20,"gi" ,6,0.0,&avnx[547] } ,
+    {20,"genbank" ,7,0.0,&avnx[548] } ,
+    {20,"pir" ,8,0.0,&avnx[549] } ,
+    {20,"pub-set" ,9,0.0,&avnx[550] } ,
+    {20,"equiv" ,10,0.0,&avnx[551] } ,
+    {20,"swissprot" ,11,0.0,&avnx[552] } ,
+    {20,"pdb-entry" ,12,0.0,&avnx[553] } ,
+    {20,"mut-set" ,13,0.0,&avnx[554] } ,
+    {20,"pop-set" ,14,0.0,&avnx[555] } ,
+    {20,"phy-set" ,15,0.0,&avnx[556] } ,
+    {20,"eco-set" ,16,0.0,&avnx[557] } ,
+    {20,"gen-prod-set" ,17,0.0,&avnx[558] } ,
+    {20,"wgs-set" ,18,0.0,&avnx[559] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"iupacna" ,1,0.0,&avnx[526] } ,
-    {20,"iupacaa" ,2,0.0,&avnx[527] } ,
-    {20,"ncbi2na" ,3,0.0,&avnx[528] } ,
-    {20,"ncbi4na" ,4,0.0,&avnx[529] } ,
-    {20,"ncbi8na" ,5,0.0,&avnx[530] } ,
-    {20,"ncbipna" ,6,0.0,&avnx[531] } ,
-    {20,"ncbi8aa" ,7,0.0,&avnx[532] } ,
-    {20,"ncbieaa" ,8,0.0,&avnx[533] } ,
-    {20,"ncbipaa" ,9,0.0,&avnx[534] } ,
-    {20,"iupacaa3" ,10,0.0,&avnx[535] } ,
+    {20,"iupacna" ,1,0.0,&avnx[562] } ,
+    {20,"iupacaa" ,2,0.0,&avnx[563] } ,
+    {20,"ncbi2na" ,3,0.0,&avnx[564] } ,
+    {20,"ncbi4na" ,4,0.0,&avnx[565] } ,
+    {20,"ncbi8na" ,5,0.0,&avnx[566] } ,
+    {20,"ncbipna" ,6,0.0,&avnx[567] } ,
+    {20,"ncbi8aa" ,7,0.0,&avnx[568] } ,
+    {20,"ncbieaa" ,8,0.0,&avnx[569] } ,
+    {20,"ncbipaa" ,9,0.0,&avnx[570] } ,
+    {20,"iupacaa3" ,10,0.0,&avnx[571] } ,
     {20,"ncbistdaa" ,11,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
-    {20,"new" ,1,0.0,&avnx[540] } ,
-    {20,"update" ,2,0.0,&avnx[541] } ,
-    {20,"revision" ,3,0.0,&avnx[542] } ,
+    {20,"new" ,1,0.0,&avnx[576] } ,
+    {20,"update" ,2,0.0,&avnx[577] } ,
+    {20,"revision" ,3,0.0,&avnx[578] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"off" ,1,0.0,&avnx[544] } ,
-    {20,"trace" ,2,0.0,&avnx[545] } ,
-    {20,"partial" ,3,0.0,&avnx[546] } ,
+    {20,"off" ,1,0.0,&avnx[580] } ,
+    {20,"trace" ,2,0.0,&avnx[581] } ,
+    {20,"partial" ,3,0.0,&avnx[582] } ,
     {20,"complete" ,4,0.0,NULL } ,
-    {20,"wire" ,1,0.0,&avnx[548] } ,
-    {20,"tubes" ,2,0.0,&avnx[549] } ,
-    {20,"ball-and-stick" ,3,0.0,&avnx[550] } ,
-    {20,"space-fill" ,4,0.0,&avnx[551] } ,
-    {20,"wire-worm" ,5,0.0,&avnx[552] } ,
-    {20,"tube-worm" ,6,0.0,&avnx[553] } ,
-    {20,"with-arrows" ,7,0.0,&avnx[554] } ,
+    {20,"wire" ,1,0.0,&avnx[584] } ,
+    {20,"tubes" ,2,0.0,&avnx[585] } ,
+    {20,"ball-and-stick" ,3,0.0,&avnx[586] } ,
+    {20,"space-fill" ,4,0.0,&avnx[587] } ,
+    {20,"wire-worm" ,5,0.0,&avnx[588] } ,
+    {20,"tube-worm" ,6,0.0,&avnx[589] } ,
+    {20,"with-arrows" ,7,0.0,&avnx[590] } ,
     {20,"without-arrows" ,8,0.0,NULL } ,
-    {20,"element" ,1,0.0,&avnx[556] } ,
-    {20,"object" ,2,0.0,&avnx[557] } ,
-    {20,"molecule" ,3,0.0,&avnx[558] } ,
-    {20,"domain" ,4,0.0,&avnx[559] } ,
-    {20,"residue" ,20,0.0,&avnx[560] } ,
-    {20,"secondary-structure" ,5,0.0,&avnx[561] } ,
-    {20,"user-select" ,6,0.0,&avnx[562] } ,
-    {20,"aligned" ,7,0.0,&avnx[563] } ,
-    {20,"identity" ,8,0.0,&avnx[564] } ,
-    {20,"variety" ,9,0.0,&avnx[565] } ,
-    {20,"weighted-variety" ,10,0.0,&avnx[566] } ,
-    {20,"information-content" ,11,0.0,&avnx[567] } ,
-    {20,"fit" ,12,0.0,&avnx[568] } ,
-    {20,"block-fit" ,17,0.0,&avnx[569] } ,
-    {20,"block-z-fit" ,18,0.0,&avnx[570] } ,
-    {20,"block-row-fit" ,19,0.0,&avnx[571] } ,
-    {20,"temperature" ,13,0.0,&avnx[572] } ,
-    {20,"hydrophobicity" ,14,0.0,&avnx[573] } ,
-    {20,"charge" ,15,0.0,&avnx[574] } ,
+    {20,"element" ,1,0.0,&avnx[592] } ,
+    {20,"object" ,2,0.0,&avnx[593] } ,
+    {20,"molecule" ,3,0.0,&avnx[594] } ,
+    {20,"domain" ,4,0.0,&avnx[595] } ,
+    {20,"residue" ,20,0.0,&avnx[596] } ,
+    {20,"secondary-structure" ,5,0.0,&avnx[597] } ,
+    {20,"user-select" ,6,0.0,&avnx[598] } ,
+    {20,"aligned" ,7,0.0,&avnx[599] } ,
+    {20,"identity" ,8,0.0,&avnx[600] } ,
+    {20,"variety" ,9,0.0,&avnx[601] } ,
+    {20,"weighted-variety" ,10,0.0,&avnx[602] } ,
+    {20,"information-content" ,11,0.0,&avnx[603] } ,
+    {20,"fit" ,12,0.0,&avnx[604] } ,
+    {20,"block-fit" ,17,0.0,&avnx[605] } ,
+    {20,"block-z-fit" ,18,0.0,&avnx[606] } ,
+    {20,"block-row-fit" ,19,0.0,&avnx[607] } ,
+    {20,"temperature" ,13,0.0,&avnx[608] } ,
+    {20,"hydrophobicity" ,14,0.0,&avnx[609] } ,
+    {20,"charge" ,15,0.0,&avnx[610] } ,
     {20,"rainbow" ,16,0.0,NULL } ,
     {3,NULL,255,0.0,NULL } ,
     {3,NULL,255,0.0,NULL } ,
-    {20,"one-letter" ,1,0.0,&avnx[578] } ,
+    {20,"one-letter" ,1,0.0,&avnx[614] } ,
     {20,"three-letter" ,2,0.0,NULL } ,
-    {20,"none" ,0,0.0,&avnx[580] } ,
-    {20,"sequential" ,1,0.0,&avnx[581] } ,
+    {20,"none" ,0,0.0,&avnx[616] } ,
+    {20,"sequential" ,1,0.0,&avnx[617] } ,
     {20,"pdb" ,2,0.0,NULL } ,
-    {20,"aa" ,1,0.0,&avnx[583] } ,
-    {20,"na" ,2,0.0,&avnx[584] } ,
+    {20,"aa" ,1,0.0,&avnx[619] } ,
+    {20,"na" ,2,0.0,&avnx[620] } ,
     {20,"both" ,3,0.0,NULL } ,
-    {20,"docsum" ,1,0.0,&avnx[586] } ,
-    {20,"genbank" ,2,0.0,&avnx[587] } ,
-    {20,"genpept" ,3,0.0,&avnx[588] } ,
-    {20,"fasta" ,4,0.0,&avnx[589] } ,
-    {20,"asn1" ,5,0.0,&avnx[590] } ,
-    {20,"graphic" ,6,0.0,&avnx[591] } ,
-    {20,"alignment" ,7,0.0,&avnx[592] } ,
-    {20,"globalview" ,8,0.0,&avnx[593] } ,
-    {20,"report" ,9,0.0,&avnx[594] } ,
-    {20,"medlars" ,10,0.0,&avnx[595] } ,
-    {20,"embl" ,11,0.0,&avnx[596] } ,
-    {20,"pdb" ,12,0.0,&avnx[597] } ,
+    {20,"docsum" ,1,0.0,&avnx[622] } ,
+    {20,"genbank" ,2,0.0,&avnx[623] } ,
+    {20,"genpept" ,3,0.0,&avnx[624] } ,
+    {20,"fasta" ,4,0.0,&avnx[625] } ,
+    {20,"asn1" ,5,0.0,&avnx[626] } ,
+    {20,"graphic" ,6,0.0,&avnx[627] } ,
+    {20,"alignment" ,7,0.0,&avnx[628] } ,
+    {20,"globalview" ,8,0.0,&avnx[629] } ,
+    {20,"report" ,9,0.0,&avnx[630] } ,
+    {20,"medlars" ,10,0.0,&avnx[631] } ,
+    {20,"embl" ,11,0.0,&avnx[632] } ,
+    {20,"pdb" ,12,0.0,&avnx[633] } ,
     {20,"kinemage" ,13,0.0,NULL } ,
-    {20,"ncbi-backbone" ,2,0.0,&avnx[599] } ,
-    {20,"ncbi-all-atom" ,3,0.0,&avnx[600] } ,
+    {20,"ncbi-backbone" ,2,0.0,&avnx[635] } ,
+    {20,"ncbi-all-atom" ,3,0.0,&avnx[636] } ,
     {20,"pdb-model" ,4,0.0,NULL } ,
-    {20,"nucleotide" ,1,0.0,&avnx[602] } ,
+    {20,"nucleotide" ,1,0.0,&avnx[638] } ,
     {20,"protein" ,2,0.0,NULL } ,
     {2,NULL,1,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
     {3,NULL,1,0.0,NULL } ,
-    {20,"unassigned" ,0,0.0,&avnx[607] } ,
-    {20,"threshold" ,1,0.0,&avnx[608] } ,
-    {20,"minscore" ,2,0.0,&avnx[609] } ,
-    {20,"maxscore" ,3,0.0,&avnx[610] } ,
-    {20,"meanscore" ,4,0.0,&avnx[611] } ,
-    {20,"variance" ,5,0.0,&avnx[612] } ,
-    {20,"name" ,10,0.0,&avnx[613] } ,
-    {20,"is-optional" ,20,0.0,&avnx[614] } ,
+    {20,"unassigned" ,0,0.0,&avnx[643] } ,
+    {20,"threshold" ,1,0.0,&avnx[644] } ,
+    {20,"minscore" ,2,0.0,&avnx[645] } ,
+    {20,"maxscore" ,3,0.0,&avnx[646] } ,
+    {20,"meanscore" ,4,0.0,&avnx[647] } ,
+    {20,"variance" ,5,0.0,&avnx[648] } ,
+    {20,"name" ,10,0.0,&avnx[649] } ,
+    {20,"is-optional" ,20,0.0,&avnx[650] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {3,NULL,100000,0.0,NULL } };
-
-static AsnType atx[1758] = {
+    {3,NULL,100000,0.0,NULL } ,
+    {20,"acronym" ,1,0.0,&avnx[654] } ,
+    {20,"anamorph" ,2,0.0,&avnx[655] } ,
+    {20,"authority" ,3,0.0,&avnx[656] } ,
+    {20,"bio-material" ,4,0.0,&avnx[657] } ,
+    {20,"biotype" ,5,0.0,&avnx[658] } ,
+    {20,"biovar" ,6,0.0,&avnx[659] } ,
+    {20,"breed" ,7,0.0,&avnx[660] } ,
+    {20,"cell-line" ,8,0.0,&avnx[661] } ,
+    {20,"cell-type" ,9,0.0,&avnx[662] } ,
+    {20,"chemovar" ,10,0.0,&avnx[663] } ,
+    {20,"chromosome" ,11,0.0,&avnx[664] } ,
+    {20,"clone" ,12,0.0,&avnx[665] } ,
+    {20,"clone-lib" ,13,0.0,&avnx[666] } ,
+    {20,"collected-by" ,14,0.0,&avnx[667] } ,
+    {20,"collection-date" ,15,0.0,&avnx[668] } ,
+    {20,"common" ,16,0.0,&avnx[669] } ,
+    {20,"common-name" ,17,0.0,&avnx[670] } ,
+    {20,"country" ,18,0.0,&avnx[671] } ,
+    {20,"cultivar" ,19,0.0,&avnx[672] } ,
+    {20,"culture-collection" ,20,0.0,&avnx[673] } ,
+    {20,"dev-stage" ,21,0.0,&avnx[674] } ,
+    {20,"division" ,22,0.0,&avnx[675] } ,
+    {20,"dosage" ,23,0.0,&avnx[676] } ,
+    {20,"ecotype" ,24,0.0,&avnx[677] } ,
+    {20,"endogenous-virus-name" ,25,0.0,&avnx[678] } ,
+    {20,"environmental-sample" ,26,0.0,&avnx[679] } ,
+    {20,"forma" ,27,0.0,&avnx[680] } ,
+    {20,"forma-specialis" ,28,0.0,&avnx[681] } ,
+    {20,"frequency" ,29,0.0,&avnx[682] } ,
+    {20,"fwd-primer-name" ,30,0.0,&avnx[683] } ,
+    {20,"fwd-primer-seq" ,31,0.0,&avnx[684] } ,
+    {20,"gb-acronym" ,32,0.0,&avnx[685] } ,
+    {20,"gb-anamorph" ,33,0.0,&avnx[686] } ,
+    {20,"gb-synonym" ,34,0.0,&avnx[687] } ,
+    {20,"genotype" ,35,0.0,&avnx[688] } ,
+    {20,"germline" ,36,0.0,&avnx[689] } ,
+    {20,"group" ,37,0.0,&avnx[690] } ,
+    {20,"haplotype" ,38,0.0,&avnx[691] } ,
+    {20,"identified-by" ,39,0.0,&avnx[692] } ,
+    {20,"insertion-seq-name" ,40,0.0,&avnx[693] } ,
+    {20,"isolate" ,41,0.0,&avnx[694] } ,
+    {20,"isolation-source" ,42,0.0,&avnx[695] } ,
+    {20,"lab-host" ,43,0.0,&avnx[696] } ,
+    {20,"lat-lon" ,44,0.0,&avnx[697] } ,
+    {20,"lineage" ,45,0.0,&avnx[698] } ,
+    {20,"map" ,46,0.0,&avnx[699] } ,
+    {20,"metagenome-source" ,47,0.0,&avnx[700] } ,
+    {20,"metagenomic" ,48,0.0,&avnx[701] } ,
+    {20,"old-lineage" ,49,0.0,&avnx[702] } ,
+    {20,"old-name" ,50,0.0,&avnx[703] } ,
+    {20,"orgmod-note" ,51,0.0,&avnx[704] } ,
+    {20,"nat-host" ,52,0.0,&avnx[705] } ,
+    {20,"pathovar" ,53,0.0,&avnx[706] } ,
+    {20,"plasmid-name" ,54,0.0,&avnx[707] } ,
+    {20,"plastid-name" ,55,0.0,&avnx[708] } ,
+    {20,"pop-variant" ,56,0.0,&avnx[709] } ,
+    {20,"rearranged" ,57,0.0,&avnx[710] } ,
+    {20,"rev-primer-name" ,58,0.0,&avnx[711] } ,
+    {20,"rev-primer-seq" ,59,0.0,&avnx[712] } ,
+    {20,"segment" ,60,0.0,&avnx[713] } ,
+    {20,"serogroup" ,61,0.0,&avnx[714] } ,
+    {20,"serotype" ,62,0.0,&avnx[715] } ,
+    {20,"serovar" ,63,0.0,&avnx[716] } ,
+    {20,"sex" ,64,0.0,&avnx[717] } ,
+    {20,"specimen-voucher" ,65,0.0,&avnx[718] } ,
+    {20,"strain" ,66,0.0,&avnx[719] } ,
+    {20,"subclone" ,67,0.0,&avnx[720] } ,
+    {20,"subgroup" ,68,0.0,&avnx[721] } ,
+    {20,"subsource-note" ,69,0.0,&avnx[722] } ,
+    {20,"sub-species" ,70,0.0,&avnx[723] } ,
+    {20,"substrain" ,71,0.0,&avnx[724] } ,
+    {20,"subtype" ,72,0.0,&avnx[725] } ,
+    {20,"synonym" ,73,0.0,&avnx[726] } ,
+    {20,"taxname" ,74,0.0,&avnx[727] } ,
+    {20,"teleomorph" ,75,0.0,&avnx[728] } ,
+    {20,"tissue-lib" ,76,0.0,&avnx[729] } ,
+    {20,"tissue-type" ,77,0.0,&avnx[730] } ,
+    {20,"transgenic" ,78,0.0,&avnx[731] } ,
+    {20,"transposon-name" ,79,0.0,&avnx[732] } ,
+    {20,"type" ,80,0.0,&avnx[733] } ,
+    {20,"variety" ,81,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[735] } ,
+    {20,"genomic" ,1,0.0,&avnx[736] } ,
+    {20,"chloroplast" ,2,0.0,&avnx[737] } ,
+    {20,"chromoplast" ,3,0.0,&avnx[738] } ,
+    {20,"kinetoplast" ,4,0.0,&avnx[739] } ,
+    {20,"mitochondrion" ,5,0.0,&avnx[740] } ,
+    {20,"plastid" ,6,0.0,&avnx[741] } ,
+    {20,"macronuclear" ,7,0.0,&avnx[742] } ,
+    {20,"extrachrom" ,8,0.0,&avnx[743] } ,
+    {20,"plasmid" ,9,0.0,&avnx[744] } ,
+    {20,"transposon" ,10,0.0,&avnx[745] } ,
+    {20,"insertion-seq" ,11,0.0,&avnx[746] } ,
+    {20,"cyanelle" ,12,0.0,&avnx[747] } ,
+    {20,"proviral" ,13,0.0,&avnx[748] } ,
+    {20,"virion" ,14,0.0,&avnx[749] } ,
+    {20,"nucleomorph" ,15,0.0,&avnx[750] } ,
+    {20,"apicoplast" ,16,0.0,&avnx[751] } ,
+    {20,"leucoplast" ,17,0.0,&avnx[752] } ,
+    {20,"proplastid" ,18,0.0,&avnx[753] } ,
+    {20,"endogenous-virus" ,19,0.0,&avnx[754] } ,
+    {20,"hydrogenosome" ,20,0.0,&avnx[755] } ,
+    {20,"chromosome" ,21,0.0,&avnx[756] } ,
+    {20,"chromatophore" ,22,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[758] } ,
+    {20,"natural" ,1,0.0,&avnx[759] } ,
+    {20,"natmut" ,2,0.0,&avnx[760] } ,
+    {20,"mut" ,3,0.0,&avnx[761] } ,
+    {20,"artificial" ,4,0.0,&avnx[762] } ,
+    {20,"synthetic" ,5,0.0,&avnx[763] } ,
+    {20,"other" ,255,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[765] } ,
+    {20,"gene" ,1,0.0,&avnx[766] } ,
+    {20,"org" ,2,0.0,&avnx[767] } ,
+    {20,"cds" ,3,0.0,&avnx[768] } ,
+    {20,"prot" ,4,0.0,&avnx[769] } ,
+    {20,"preRNA" ,5,0.0,&avnx[770] } ,
+    {20,"mRNA" ,6,0.0,&avnx[771] } ,
+    {20,"tRNA" ,7,0.0,&avnx[772] } ,
+    {20,"rRNA" ,8,0.0,&avnx[773] } ,
+    {20,"snRNA" ,9,0.0,&avnx[774] } ,
+    {20,"scRNA" ,10,0.0,&avnx[775] } ,
+    {20,"otherRNA" ,11,0.0,&avnx[776] } ,
+    {20,"pub" ,12,0.0,&avnx[777] } ,
+    {20,"seq" ,13,0.0,&avnx[778] } ,
+    {20,"imp" ,14,0.0,&avnx[779] } ,
+    {20,"allele" ,15,0.0,&avnx[780] } ,
+    {20,"attenuator" ,16,0.0,&avnx[781] } ,
+    {20,"c-region" ,17,0.0,&avnx[782] } ,
+    {20,"caat-signal" ,18,0.0,&avnx[783] } ,
+    {20,"imp-CDS" ,19,0.0,&avnx[784] } ,
+    {20,"conflict" ,20,0.0,&avnx[785] } ,
+    {20,"d-loop" ,21,0.0,&avnx[786] } ,
+    {20,"d-segment" ,22,0.0,&avnx[787] } ,
+    {20,"enhancer" ,23,0.0,&avnx[788] } ,
+    {20,"exon" ,24,0.0,&avnx[789] } ,
+    {20,"gC-signal" ,25,0.0,&avnx[790] } ,
+    {20,"iDNA" ,26,0.0,&avnx[791] } ,
+    {20,"intron" ,27,0.0,&avnx[792] } ,
+    {20,"j-segment" ,28,0.0,&avnx[793] } ,
+    {20,"ltr" ,29,0.0,&avnx[794] } ,
+    {20,"mat-peptide" ,30,0.0,&avnx[795] } ,
+    {20,"misc-binding" ,31,0.0,&avnx[796] } ,
+    {20,"misc-difference" ,32,0.0,&avnx[797] } ,
+    {20,"misc-feature" ,33,0.0,&avnx[798] } ,
+    {20,"misc-recomb" ,34,0.0,&avnx[799] } ,
+    {20,"misc-RNA" ,35,0.0,&avnx[800] } ,
+    {20,"misc-signal" ,36,0.0,&avnx[801] } ,
+    {20,"misc-structure" ,37,0.0,&avnx[802] } ,
+    {20,"modified-base" ,38,0.0,&avnx[803] } ,
+    {20,"mutation" ,39,0.0,&avnx[804] } ,
+    {20,"n-region" ,40,0.0,&avnx[805] } ,
+    {20,"old-sequence" ,41,0.0,&avnx[806] } ,
+    {20,"polyA-signal" ,42,0.0,&avnx[807] } ,
+    {20,"polyA-site" ,43,0.0,&avnx[808] } ,
+    {20,"precursor-RNA" ,44,0.0,&avnx[809] } ,
+    {20,"prim-transcript" ,45,0.0,&avnx[810] } ,
+    {20,"primer-bind" ,46,0.0,&avnx[811] } ,
+    {20,"promoter" ,47,0.0,&avnx[812] } ,
+    {20,"protein-bind" ,48,0.0,&avnx[813] } ,
+    {20,"rbs" ,49,0.0,&avnx[814] } ,
+    {20,"repeat-region" ,50,0.0,&avnx[815] } ,
+    {20,"repeat-unit" ,51,0.0,&avnx[816] } ,
+    {20,"rep-origin" ,52,0.0,&avnx[817] } ,
+    {20,"s-region" ,53,0.0,&avnx[818] } ,
+    {20,"satellite" ,54,0.0,&avnx[819] } ,
+    {20,"sig-peptide" ,55,0.0,&avnx[820] } ,
+    {20,"source" ,56,0.0,&avnx[821] } ,
+    {20,"stem-loop" ,57,0.0,&avnx[822] } ,
+    {20,"sts" ,58,0.0,&avnx[823] } ,
+    {20,"tata-signal" ,59,0.0,&avnx[824] } ,
+    {20,"terminator" ,60,0.0,&avnx[825] } ,
+    {20,"transit-peptide" ,61,0.0,&avnx[826] } ,
+    {20,"unsure" ,62,0.0,&avnx[827] } ,
+    {20,"v-region" ,63,0.0,&avnx[828] } ,
+    {20,"v-segment" ,64,0.0,&avnx[829] } ,
+    {20,"variation" ,65,0.0,&avnx[830] } ,
+    {20,"virion" ,66,0.0,&avnx[831] } ,
+    {20,"n3clip" ,67,0.0,&avnx[832] } ,
+    {20,"n3UTR" ,68,0.0,&avnx[833] } ,
+    {20,"n5clip" ,69,0.0,&avnx[834] } ,
+    {20,"n5UTR" ,70,0.0,&avnx[835] } ,
+    {20,"n10-signal" ,71,0.0,&avnx[836] } ,
+    {20,"n35-signal" ,72,0.0,&avnx[837] } ,
+    {20,"site-ref" ,73,0.0,&avnx[838] } ,
+    {20,"region" ,74,0.0,&avnx[839] } ,
+    {20,"comment" ,75,0.0,&avnx[840] } ,
+    {20,"bond" ,76,0.0,&avnx[841] } ,
+    {20,"site" ,77,0.0,&avnx[842] } ,
+    {20,"rsite" ,78,0.0,&avnx[843] } ,
+    {20,"user" ,79,0.0,&avnx[844] } ,
+    {20,"txinit" ,80,0.0,&avnx[845] } ,
+    {20,"num" ,81,0.0,&avnx[846] } ,
+    {20,"psec-str" ,82,0.0,&avnx[847] } ,
+    {20,"non-std-residue" ,83,0.0,&avnx[848] } ,
+    {20,"het" ,84,0.0,&avnx[849] } ,
+    {20,"biosrc" ,85,0.0,&avnx[850] } ,
+    {20,"preprotein" ,86,0.0,&avnx[851] } ,
+    {20,"mat-peptide-aa" ,87,0.0,&avnx[852] } ,
+    {20,"sig-peptide-aa" ,88,0.0,&avnx[853] } ,
+    {20,"transit-peptide-aa" ,89,0.0,&avnx[854] } ,
+    {20,"snoRNA" ,90,0.0,&avnx[855] } ,
+    {20,"gap" ,91,0.0,&avnx[856] } ,
+    {20,"operon" ,92,0.0,&avnx[857] } ,
+    {20,"oriT" ,93,0.0,&avnx[858] } ,
+    {20,"ncRNA" ,94,0.0,&avnx[859] } ,
+    {20,"tmRNA" ,95,0.0,NULL } ,
+    {20,"allele" ,1,0.0,&avnx[861] } ,
+    {20,"activity" ,2,0.0,&avnx[862] } ,
+    {20,"anticodon" ,3,0.0,&avnx[863] } ,
+    {20,"bound-moiety" ,4,0.0,&avnx[864] } ,
+    {20,"chromosome" ,5,0.0,&avnx[865] } ,
+    {20,"citation" ,6,0.0,&avnx[866] } ,
+    {20,"codon" ,7,0.0,&avnx[867] } ,
+    {20,"codon-start" ,8,0.0,&avnx[868] } ,
+    {20,"codons-recognized" ,9,0.0,&avnx[869] } ,
+    {20,"compare" ,10,0.0,&avnx[870] } ,
+    {20,"cons-splice" ,11,0.0,&avnx[871] } ,
+    {20,"db-xref" ,12,0.0,&avnx[872] } ,
+    {20,"description" ,13,0.0,&avnx[873] } ,
+    {20,"direction" ,14,0.0,&avnx[874] } ,
+    {20,"ec-number" ,15,0.0,&avnx[875] } ,
+    {20,"environmental-sample" ,16,0.0,&avnx[876] } ,
+    {20,"evidence" ,17,0.0,&avnx[877] } ,
+    {20,"exception" ,18,0.0,&avnx[878] } ,
+    {20,"experiment" ,19,0.0,&avnx[879] } ,
+    {20,"focus" ,20,0.0,&avnx[880] } ,
+    {20,"frequency" ,21,0.0,&avnx[881] } ,
+    {20,"function" ,22,0.0,&avnx[882] } ,
+    {20,"gene" ,23,0.0,&avnx[883] } ,
+    {20,"gene-description" ,24,0.0,&avnx[884] } ,
+    {20,"inference" ,25,0.0,&avnx[885] } ,
+    {20,"label" ,26,0.0,&avnx[886] } ,
+    {20,"locus-tag" ,27,0.0,&avnx[887] } ,
+    {20,"map" ,28,0.0,&avnx[888] } ,
+    {20,"mobile-element" ,29,0.0,&avnx[889] } ,
+    {20,"mod-base" ,30,0.0,&avnx[890] } ,
+    {20,"mol-type" ,31,0.0,&avnx[891] } ,
+    {20,"ncRNA-class" ,32,0.0,&avnx[892] } ,
+    {20,"note" ,33,0.0,&avnx[893] } ,
+    {20,"number" ,34,0.0,&avnx[894] } ,
+    {20,"old-locus-tag" ,35,0.0,&avnx[895] } ,
+    {20,"operon" ,36,0.0,&avnx[896] } ,
+    {20,"organism" ,37,0.0,&avnx[897] } ,
+    {20,"organelle" ,38,0.0,&avnx[898] } ,
+    {20,"partial" ,39,0.0,&avnx[899] } ,
+    {20,"phenotype" ,40,0.0,&avnx[900] } ,
+    {20,"plasmid" ,41,0.0,&avnx[901] } ,
+    {20,"product" ,42,0.0,&avnx[902] } ,
+    {20,"protein-id" ,43,0.0,&avnx[903] } ,
+    {20,"pseudo" ,44,0.0,&avnx[904] } ,
+    {20,"rearranged" ,45,0.0,&avnx[905] } ,
+    {20,"replace" ,46,0.0,&avnx[906] } ,
+    {20,"rpt-family" ,47,0.0,&avnx[907] } ,
+    {20,"rpt-type" ,48,0.0,&avnx[908] } ,
+    {20,"rpt-unit" ,49,0.0,&avnx[909] } ,
+    {20,"rpt-unit-seq" ,50,0.0,&avnx[910] } ,
+    {20,"rpt-unit-range" ,51,0.0,&avnx[911] } ,
+    {20,"segment" ,52,0.0,&avnx[912] } ,
+    {20,"sequenced-mol" ,53,0.0,&avnx[913] } ,
+    {20,"standard-name" ,54,0.0,&avnx[914] } ,
+    {20,"synonym" ,55,0.0,&avnx[915] } ,
+    {20,"transcript-id" ,56,0.0,&avnx[916] } ,
+    {20,"transgenic" ,57,0.0,&avnx[917] } ,
+    {20,"translation" ,58,0.0,&avnx[918] } ,
+    {20,"transl-except" ,59,0.0,&avnx[919] } ,
+    {20,"transl-table" ,60,0.0,&avnx[920] } ,
+    {20,"usedin" ,61,0.0,NULL } ,
+    {3,NULL,1,0.0,NULL } ,
+    {20,"contains" ,1,0.0,&avnx[923] } ,
+    {20,"equals" ,2,0.0,&avnx[924] } ,
+    {20,"starts" ,3,0.0,&avnx[925] } ,
+    {20,"ends" ,4,0.0,&avnx[926] } ,
+    {20,"inlist" ,5,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {20,"cds-comment" ,1,0.0,&avnx[931] } ,
+    {20,"gene-locus" ,2,0.0,&avnx[932] } ,
+    {20,"gene-description" ,3,0.0,&avnx[933] } ,
+    {20,"gene-comment" ,4,0.0,&avnx[934] } ,
+    {20,"gene-allele" ,5,0.0,&avnx[935] } ,
+    {20,"gene-maploc" ,6,0.0,&avnx[936] } ,
+    {20,"gene-locus-tag" ,7,0.0,&avnx[937] } ,
+    {20,"gene-synonym" ,8,0.0,&avnx[938] } ,
+    {20,"gene-old-locus-tag" ,9,0.0,&avnx[939] } ,
+    {20,"mrna-product" ,10,0.0,&avnx[940] } ,
+    {20,"mrna-comment" ,11,0.0,&avnx[941] } ,
+    {20,"prot-name" ,12,0.0,&avnx[942] } ,
+    {20,"prot-description" ,13,0.0,&avnx[943] } ,
+    {20,"prot-ec-number" ,14,0.0,&avnx[944] } ,
+    {20,"prot-activity" ,15,0.0,&avnx[945] } ,
+    {20,"prot-comment" ,16,0.0,&avnx[946] } ,
+    {20,"mat-peptide-name" ,17,0.0,&avnx[947] } ,
+    {20,"mat-peptide-description" ,18,0.0,&avnx[948] } ,
+    {20,"mat-peptide-ec-number" ,19,0.0,&avnx[949] } ,
+    {20,"mat-peptide-activity" ,20,0.0,&avnx[950] } ,
+    {20,"mat-peptide-comment" ,21,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[952] } ,
+    {20,"genomic" ,1,0.0,&avnx[953] } ,
+    {20,"precursor-RNA" ,2,0.0,&avnx[954] } ,
+    {20,"mRNA" ,3,0.0,&avnx[955] } ,
+    {20,"rRNA" ,4,0.0,&avnx[956] } ,
+    {20,"tRNA" ,5,0.0,&avnx[957] } ,
+    {20,"snRNA" ,6,0.0,&avnx[958] } ,
+    {20,"scRNA" ,7,0.0,&avnx[959] } ,
+    {20,"genomic-mRNA" ,8,0.0,&avnx[960] } ,
+    {20,"cRNA" ,9,0.0,&avnx[961] } ,
+    {20,"snoRNA" ,10,0.0,&avnx[962] } ,
+    {20,"transcribed-RNA" ,11,0.0,&avnx[963] } ,
+    {20,"ncRNA" ,12,0.0,&avnx[964] } ,
+    {20,"transfer-messenger-RNA" ,13,0.0,&avnx[965] } ,
+    {20,"other" ,14,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[967] } ,
+    {20,"standard" ,1,0.0,&avnx[968] } ,
+    {20,"est" ,2,0.0,&avnx[969] } ,
+    {20,"sts" ,3,0.0,&avnx[970] } ,
+    {20,"survey" ,4,0.0,&avnx[971] } ,
+    {20,"genetic-map" ,5,0.0,&avnx[972] } ,
+    {20,"physical-map" ,6,0.0,&avnx[973] } ,
+    {20,"derived" ,7,0.0,&avnx[974] } ,
+    {20,"concept-trans" ,8,0.0,&avnx[975] } ,
+    {20,"seq-pept" ,9,0.0,&avnx[976] } ,
+    {20,"both" ,10,0.0,&avnx[977] } ,
+    {20,"seq-pept-overlap" ,11,0.0,&avnx[978] } ,
+    {20,"seq-pept-homol" ,12,0.0,&avnx[979] } ,
+    {20,"concept-trans-a" ,13,0.0,&avnx[980] } ,
+    {20,"htgs-1" ,14,0.0,&avnx[981] } ,
+    {20,"htgs-2" ,15,0.0,&avnx[982] } ,
+    {20,"htgs-3" ,16,0.0,&avnx[983] } ,
+    {20,"fli-cDNA" ,17,0.0,&avnx[984] } ,
+    {20,"htgs-0" ,18,0.0,&avnx[985] } ,
+    {20,"htc" ,19,0.0,&avnx[986] } ,
+    {20,"wgs" ,20,0.0,&avnx[987] } ,
+    {20,"barcode" ,21,0.0,&avnx[988] } ,
+    {20,"composite-wgs-htgs" ,22,0.0,&avnx[989] } ,
+    {20,"tsa" ,23,0.0,&avnx[990] } ,
+    {20,"other" ,24,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[992] } ,
+    {20,"complete" ,1,0.0,&avnx[993] } ,
+    {20,"partial" ,2,0.0,&avnx[994] } ,
+    {20,"no-left" ,3,0.0,&avnx[995] } ,
+    {20,"no-right" ,4,0.0,&avnx[996] } ,
+    {20,"no-ends" ,5,0.0,&avnx[997] } ,
+    {20,"has-left" ,6,0.0,&avnx[998] } ,
+    {20,"has-right" ,7,0.0,&avnx[999] } ,
+    {20,"other" ,6,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[1001] } ,
+    {20,"dna" ,1,0.0,&avnx[1002] } ,
+    {20,"rna" ,2,0.0,&avnx[1003] } ,
+    {20,"protein" ,3,0.0,&avnx[1004] } ,
+    {20,"nucleotide" ,4,0.0,&avnx[1005] } ,
+    {20,"other" ,5,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[1007] } ,
+    {20,"linear" ,1,0.0,&avnx[1008] } ,
+    {20,"circular" ,2,0.0,&avnx[1009] } ,
+    {20,"tandem" ,3,0.0,&avnx[1010] } ,
+    {20,"other" ,4,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[1012] } ,
+    {20,"single" ,1,0.0,&avnx[1013] } ,
+    {20,"double" ,2,0.0,&avnx[1014] } ,
+    {20,"mixed" ,3,0.0,&avnx[1015] } ,
+    {20,"mixed-rev" ,4,0.0,&avnx[1016] } ,
+    {20,"other" ,5,0.0,NULL } ,
+    {20,"replace-old" ,1,0.0,&avnx[1018] } ,
+    {20,"append-semi" ,2,0.0,&avnx[1019] } ,
+    {20,"append-space" ,3,0.0,&avnx[1020] } ,
+    {20,"append-colon" ,4,0.0,&avnx[1021] } ,
+    {20,"append-none" ,5,0.0,&avnx[1022] } ,
+    {20,"prefix-semi" ,6,0.0,&avnx[1023] } ,
+    {20,"prefix-space" ,7,0.0,&avnx[1024] } ,
+    {20,"prefix-colon" ,8,0.0,&avnx[1025] } ,
+    {20,"prefix-none" ,9,0.0,&avnx[1026] } ,
+    {20,"leave-old" ,10,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"anywhere" ,0,0.0,&avnx[1029] } ,
+    {20,"beginning" ,1,0.0,&avnx[1030] } ,
+    {20,"end" ,2,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[1036] } ,
+    {20,"plus" ,1,0.0,&avnx[1037] } ,
+    {20,"minus" ,2,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[1040] } ,
+    {20,"nuc" ,1,0.0,&avnx[1041] } ,
+    {20,"prot" ,2,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[1043] } ,
+    {20,"feature" ,1,0.0,&avnx[1044] } ,
+    {20,"descriptor" ,2,0.0,NULL } ,
+    {20,"gene" ,1,0.0,&avnx[1046] } ,
+    {20,"mRNA" ,2,0.0,&avnx[1047] } ,
+    {20,"cds" ,3,0.0,&avnx[1048] } ,
+    {20,"prot" ,4,0.0,&avnx[1049] } ,
+    {20,"exon" ,5,0.0,&avnx[1050] } ,
+    {20,"mat-peptide" ,6,0.0,NULL } ,
+    {2,NULL,1,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[1053] } ,
+    {20,"genomic" ,1,0.0,&avnx[1054] } ,
+    {20,"precursor-RNA" ,2,0.0,&avnx[1055] } ,
+    {20,"mRNA" ,3,0.0,&avnx[1056] } ,
+    {20,"rRNA" ,4,0.0,&avnx[1057] } ,
+    {20,"tRNA" ,5,0.0,&avnx[1058] } ,
+    {20,"snRNA" ,6,0.0,&avnx[1059] } ,
+    {20,"scRNA" ,7,0.0,&avnx[1060] } ,
+    {20,"genomic-mRNA" ,8,0.0,&avnx[1061] } ,
+    {20,"cRNA" ,9,0.0,&avnx[1062] } ,
+    {20,"snoRNA" ,10,0.0,&avnx[1063] } ,
+    {20,"transcribed-RNA" ,11,0.0,&avnx[1064] } ,
+    {20,"ncRNA" ,12,0.0,&avnx[1065] } ,
+    {20,"transfer-messenger-RNA" ,13,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"none" ,0,0.0,&avnx[1070] } ,
+    {20,"tolower" ,1,0.0,&avnx[1071] } ,
+    {20,"toupper" ,2,0.0,&avnx[1072] } ,
+    {20,"firstcap" ,3,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,1,0.0,NULL } ,
+    {2,NULL,1,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {3,NULL,-1,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[1082] } ,
+    {20,"plus" ,1,0.0,&avnx[1083] } ,
+    {20,"minus" ,2,0.0,&avnx[1084] } ,
+    {20,"unknown" ,3,0.0,&avnx[1085] } ,
+    {20,"both" ,4,0.0,NULL } ,
+    {20,"plus" ,1,0.0,&avnx[1087] } ,
+    {20,"minus" ,2,0.0,&avnx[1088] } ,
+    {20,"unknown" ,3,0.0,&avnx[1089] } ,
+    {20,"both" ,4,0.0,&avnx[1090] } ,
+    {20,"reverse" ,5,0.0,NULL } ,
+    {20,"all" ,0,0.0,&avnx[1092] } ,
+    {20,"at-end" ,1,0.0,&avnx[1093] } ,
+    {20,"bad-start" ,2,0.0,&avnx[1094] } ,
+    {20,"frame-not-one" ,3,0.0,NULL } ,
+    {20,"all" ,0,0.0,&avnx[1096] } ,
+    {20,"not-at-end" ,1,0.0,&avnx[1097] } ,
+    {20,"good-start" ,2,0.0,NULL } ,
+    {20,"all" ,0,0.0,&avnx[1099] } ,
+    {20,"at-end" ,1,0.0,&avnx[1100] } ,
+    {20,"bad-end" ,2,0.0,NULL } ,
+    {20,"all" ,0,0.0,&avnx[1102] } ,
+    {20,"not-at-end" ,1,0.0,&avnx[1103] } ,
+    {20,"good-end" ,2,0.0,NULL } ,
+    {20,"join" ,1,0.0,&avnx[1105] } ,
+    {20,"order" ,2,0.0,&avnx[1106] } ,
+    {20,"merge" ,3,0.0,NULL } };
+
+static AsnType atx[2093] = {
   {401, "Date" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[1],0,&atx[15]} ,
   {0, "str" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[3]} ,
   {323, "VisibleString" ,0,26,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
@@ -1058,20 +1548,20 @@ static AsnType atx[1758] = {
   {0, "b" ,128,1,0,1,0,0,0,0,NULL,&atx[404],NULL,0,NULL} ,
   {0, "feat" ,128,10,0,0,0,0,0,0,NULL,&atx[427],NULL,0,NULL} ,
   {414, "Feat-id" ,1,0,0,0,0,0,1,0,NULL,&atx[428],NULL,0,&atx[355]} ,
-  {402, "Feat-id" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[429],0,&atx[912]} ,
+  {402, "Feat-id" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[429],0,&atx[913]} ,
   {0, "gibb" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[430]} ,
   {0, "giim" ,128,1,0,0,0,0,0,0,NULL,&atx[431],NULL,0,&atx[432]} ,
-  {410, "Giimport-id" ,1,0,0,0,0,0,1,0,NULL,&atx[350],NULL,0,&atx[965]} ,
+  {410, "Giimport-id" ,1,0,0,0,0,0,1,0,NULL,&atx[350],NULL,0,&atx[966]} ,
   {0, "local" ,128,2,0,0,0,0,0,0,NULL,&atx[433],NULL,0,&atx[434]} ,
   {417, "Object-id" ,1,0,0,0,0,0,1,0,NULL,&atx[20],NULL,0,&atx[435]} ,
   {0, "general" ,128,3,0,0,0,0,0,0,NULL,&atx[435],NULL,0,NULL} ,
-  {418, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,&atx[17],NULL,0,&atx[983]} ,
+  {418, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,&atx[17],NULL,0,&atx[984]} ,
   {401, "Annotdesc" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[437],0,&atx[641]} ,
   {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[438]} ,
   {0, "title" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[439]} ,
   {0, "comment" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[440]} ,
   {0, "pub" ,128,3,0,0,0,0,0,0,NULL,&atx[441],NULL,0,&atx[627]} ,
-  {408, "Pubdesc" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[442],0,&atx[1074]} ,
+  {408, "Pubdesc" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[442],0,&atx[1075]} ,
   {0, "pub" ,128,0,0,0,0,0,0,0,NULL,&atx[443],NULL,0,&atx[444]} ,
   {426, "Pub-equiv" ,1,0,0,0,0,0,1,0,NULL,&atx[325],NULL,0,&atx[660]} ,
   {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[445]} ,
@@ -1079,20 +1569,20 @@ static AsnType atx[1758] = {
   {0, "num" ,128,3,0,1,0,0,0,0,NULL,&atx[447],NULL,0,&atx[619]} ,
   {407, "Numbering" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[448],0,&atx[441]} ,
   {0, "cont" ,128,0,0,0,0,0,0,0,NULL,&atx[449],NULL,0,&atx[453]} ,
-  {439, "Num-cont" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[450],0,&atx[454]} ,
+  {440, "Num-cont" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[450],0,&atx[454]} ,
   {0, "refnum" ,128,0,0,0,1,0,0,0,&avnx[78],&atx[6],NULL,0,&atx[451]} ,
   {0, "has-zero" ,128,1,0,0,1,0,0,0,&avnx[79],&atx[60],NULL,0,&atx[452]} ,
   {0, "ascending" ,128,2,0,0,1,0,0,0,&avnx[80],&atx[60],NULL,0,NULL} ,
   {0, "enum" ,128,1,0,0,0,0,0,0,NULL,&atx[454],NULL,0,&atx[458]} ,
-  {440, "Num-enum" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[455],0,&atx[459]} ,
+  {441, "Num-enum" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[455],0,&atx[459]} ,
   {0, "num" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[456]} ,
   {0, "names" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[457],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {0, "ref" ,128,2,0,0,0,0,0,0,NULL,&atx[459],NULL,0,&atx[614]} ,
-  {441, "Num-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[460],0,&atx[615]} ,
+  {442, "Num-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[460],0,&atx[615]} ,
   {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[81],0,&atx[461]} ,
   {0, "aligns" ,128,1,0,1,0,0,0,0,NULL,&atx[462],NULL,0,NULL} ,
-  {423, "Seq-align" ,1,0,0,0,0,0,1,0,NULL,&atx[463],NULL,0,&atx[883]} ,
+  {423, "Seq-align" ,1,0,0,0,0,0,1,0,NULL,&atx[463],NULL,0,&atx[884]} ,
   {401, "Seq-align" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[464],0,&atx[468]} ,
   {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[84],0,&atx[465]} ,
   {0, "dim" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[466]} ,
@@ -1245,7 +1735,7 @@ static AsnType atx[1758] = {
   {0, "ext" ,128,6,0,1,0,0,0,0,NULL,&atx[66],&atx[613],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[575],NULL,0,NULL} ,
   {0, "real" ,128,3,0,0,0,0,0,0,NULL,&atx[615],NULL,0,NULL} ,
-  {442, "Num-real" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[616],0,&atx[876]} ,
+  {443, "Num-real" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[616],0,&atx[877]} ,
   {0, "a" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[617]} ,
   {0, "b" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[618]} ,
   {0, "units" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
@@ -1260,12 +1750,12 @@ static AsnType atx[1758] = {
   {0, "user" ,128,4,0,0,0,0,0,0,NULL,&atx[628],NULL,0,&atx[629]} ,
   {422, "User-object" ,1,0,0,0,0,0,1,0,NULL,&atx[46],NULL,0,&atx[462]} ,
   {0, "create-date" ,128,5,0,0,0,0,0,0,NULL,&atx[630],NULL,0,&atx[631]} ,
-  {418, "Date" ,1,0,0,0,0,0,1,0,NULL,&atx[0],NULL,0,&atx[844]} ,
+  {418, "Date" ,1,0,0,0,0,0,1,0,NULL,&atx[0],NULL,0,&atx[845]} ,
   {0, "update-date" ,128,6,0,0,0,0,0,0,NULL,&atx[630],NULL,0,&atx[632]} ,
   {0, "src" ,128,7,0,0,0,0,0,0,NULL,&atx[633],NULL,0,&atx[634]} ,
   {429, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,&atx[344],NULL,0,&atx[640]} ,
   {0, "align" ,128,8,0,0,0,0,0,0,NULL,&atx[635],NULL,0,&atx[639]} ,
-  {460, "Align-def" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[636],0,NULL} ,
+  {461, "Align-def" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[636],0,NULL} ,
   {0, "align-type" ,128,0,0,0,0,0,0,0,NULL,&atx[6],&avnx[102],0,&atx[637]} ,
   {0, "ids" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[638],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[633],NULL,0,NULL} ,
@@ -1276,17 +1766,17 @@ static AsnType atx[1758] = {
   {403, "Bioseq" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[644],0,&atx[651]} ,
   {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[645],0,&atx[646]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[633],NULL,0,NULL} ,
-  {0, "descr" ,128,1,0,1,0,0,0,0,NULL,&atx[647],NULL,0,&atx[838]} ,
-  {412, "Seq-descr" ,1,0,0,0,0,1,0,0,NULL,&atx[45],&atx[648],0,&atx[874]} ,
+  {0, "descr" ,128,1,0,1,0,0,0,0,NULL,&atx[647],NULL,0,&atx[839]} ,
+  {412, "Seq-descr" ,1,0,0,0,0,1,0,0,NULL,&atx[45],&atx[648],0,&atx[875]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[649],NULL,0,NULL} ,
   {411, "Seqdesc" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[650],0,&atx[647]} ,
   {0, "mol-type" ,128,0,0,0,0,0,0,0,NULL,&atx[651],NULL,0,&atx[652]} ,
   {404, "GIBB-mol" ,1,0,0,0,0,1,0,0,NULL,&atx[42],&avnx[106],0,&atx[817]} ,
   {0, "modif" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[653],0,&atx[655]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[654],NULL,0,NULL} ,
-  {437, "GIBB-mod" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[118],0,&atx[656]} ,
+  {438, "GIBB-mod" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[118],0,&atx[656]} ,
   {0, "method" ,128,2,0,0,0,0,0,0,NULL,&atx[656],NULL,0,&atx[657]} ,
-  {438, "GIBB-method" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[146],0,&atx[449]} ,
+  {439, "GIBB-method" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[146],0,&atx[449]} ,
   {0, "name" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[658]} ,
   {0, "title" ,128,4,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[659]} ,
   {0, "org" ,128,5,0,0,0,0,0,0,NULL,&atx[660],NULL,0,&atx[702]} ,
@@ -1335,7 +1825,7 @@ static AsnType atx[1758] = {
   {0, "comment" ,128,6,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[703]} ,
   {0, "num" ,128,7,0,0,0,0,0,0,NULL,&atx[447],NULL,0,&atx[704]} ,
   {0, "maploc" ,128,8,0,0,0,0,0,0,NULL,&atx[705],NULL,0,&atx[706]} ,
-  {420, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,&atx[17],NULL,0,&atx[1079]} ,
+  {420, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,&atx[17],NULL,0,&atx[1080]} ,
   {0, "pir" ,128,9,0,0,0,0,0,0,NULL,&atx[707],NULL,0,&atx[725]} ,
   {432, "PIR-block" ,1,0,0,0,0,0,1,0,NULL,&atx[708],NULL,0,&atx[765]} ,
   {401, "PIR-block" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[709],0,&atx[724]} ,
@@ -1431,7 +1921,7 @@ static AsnType atx[1758] = {
   {0, "keywords" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[799],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {0, "pdb" ,128,20,0,0,0,0,0,0,NULL,&atx[801],NULL,0,&atx[816]} ,
-  {436, "PDB-block" ,1,0,0,0,0,0,1,0,NULL,&atx[802],NULL,0,&atx[654]} ,
+  {436, "PDB-block" ,1,0,0,0,0,0,1,0,NULL,&atx[802],NULL,0,&atx[1131]} ,
   {401, "PDB-block" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[803],0,&atx[804]} ,
   {0, "deposition" ,128,0,0,0,0,0,0,0,NULL,&atx[804],NULL,0,&atx[805]} ,
   {402, "Date" ,1,0,0,0,0,0,1,0,NULL,&atx[0],NULL,0,&atx[812]} ,
@@ -1451,945 +1941,1280 @@ static AsnType atx[1758] = {
   {0, "source" ,128,22,0,0,0,0,0,0,NULL,&atx[819],NULL,0,&atx[832]} ,
   {428, "BioSource" ,1,0,0,0,0,0,1,0,NULL,&atx[820],NULL,0,&atx[633]} ,
   {401, "BioSource" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[821],0,&atx[824]} ,
-  {0, "genome" ,128,0,0,0,1,0,0,0,&avnx[263],&atx[6],&avnx[241],0,&atx[822]} ,
-  {0, "origin" ,128,1,0,0,1,0,0,0,&avnx[271],&atx[6],&avnx[264],0,&atx[823]} ,
+  {0, "genome" ,128,0,0,0,1,0,0,0,&avnx[264],&atx[6],&avnx[241],0,&atx[822]} ,
+  {0, "origin" ,128,1,0,0,1,0,0,0,&avnx[272],&atx[6],&avnx[265],0,&atx[823]} ,
   {0, "org" ,128,2,0,0,0,0,0,0,NULL,&atx[824],NULL,0,&atx[825]} ,
   {402, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[661],NULL,0,&atx[827]} ,
   {0, "subtype" ,128,3,0,1,0,0,0,0,NULL,&atx[66],&atx[826],0,&atx[831]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[827],NULL,0,NULL} ,
   {403, "SubSource" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[828],0,NULL} ,
-  {0, "subtype" ,128,0,0,0,0,0,0,0,NULL,&atx[6],&avnx[272],0,&atx[829]} ,
+  {0, "subtype" ,128,0,0,0,0,0,0,0,NULL,&atx[6],&avnx[273],0,&atx[829]} ,
   {0, "name" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[830]} ,
   {0, "attrib" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {0, "is-focus" ,128,4,0,1,0,0,0,0,NULL,&atx[387],NULL,0,NULL} ,
   {0, "molinfo" ,128,23,0,0,0,0,0,0,NULL,&atx[833],NULL,0,NULL} ,
   {406, "MolInfo" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[834],0,&atx[447]} ,
-  {0, "biomol" ,128,0,0,0,1,0,0,0,&avnx[325],&atx[6],&avnx[310],0,&atx[835]} ,
-  {0, "tech" ,128,1,0,0,1,0,0,0,&avnx[350],&atx[6],&avnx[326],0,&atx[836]} ,
+  {0, "biomol" ,128,0,0,0,1,0,0,0,&avnx[328],&atx[6],&avnx[311],0,&atx[835]} ,
+  {0, "tech" ,128,1,0,0,1,0,0,0,&avnx[354],&atx[6],&avnx[329],0,&atx[836]} ,
   {0, "techexp" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[837]} ,
-  {0, "completeness" ,128,3,0,0,1,0,0,0,&avnx[360],&atx[6],&avnx[351],0,NULL} ,
-  {0, "inst" ,128,2,0,0,0,0,0,0,NULL,&atx[839],NULL,0,&atx[1072]} ,
-  {415, "Seq-inst" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[840],0,&atx[1055]} ,
-  {0, "repr" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[361],0,&atx[841]} ,
-  {0, "mol" ,128,1,0,0,0,0,0,0,NULL,&atx[42],&avnx[371],0,&atx[842]} ,
-  {0, "length" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[843]} ,
-  {0, "fuzz" ,128,3,0,1,0,0,0,0,NULL,&atx[844],NULL,0,&atx[845]} ,
+  {0, "completeness" ,128,3,0,0,1,0,0,0,&avnx[364],&atx[6],&avnx[355],0,&atx[838]} ,
+  {0, "gbmoltype" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "inst" ,128,2,0,0,0,0,0,0,NULL,&atx[840],NULL,0,&atx[1073]} ,
+  {415, "Seq-inst" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[841],0,&atx[1056]} ,
+  {0, "repr" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[365],0,&atx[842]} ,
+  {0, "mol" ,128,1,0,0,0,0,0,0,NULL,&atx[42],&avnx[375],0,&atx[843]} ,
+  {0, "length" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[844]} ,
+  {0, "fuzz" ,128,3,0,1,0,0,0,0,NULL,&atx[845],NULL,0,&atx[846]} ,
   {419, "Int-fuzz" ,1,0,0,0,0,0,1,0,NULL,&atx[35],NULL,0,&atx[705]} ,
-  {0, "topology" ,128,4,0,0,1,0,0,0,&avnx[382],&atx[42],&avnx[377],0,&atx[846]} ,
-  {0, "strand" ,128,5,0,1,0,0,0,0,NULL,&atx[42],&avnx[383],0,&atx[847]} ,
-  {0, "seq-data" ,128,6,0,1,0,0,0,0,NULL,&atx[848],NULL,0,&atx[873]} ,
-  {410, "Seq-data" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[849],0,&atx[649]} ,
-  {0, "iupacna" ,128,0,0,0,0,0,0,0,NULL,&atx[850],NULL,0,&atx[851]} ,
-  {448, "IUPACna" ,1,0,0,0,0,0,0,0,NULL,&atx[623],NULL,0,&atx[852]} ,
-  {0, "iupacaa" ,128,1,0,0,0,0,0,0,NULL,&atx[852],NULL,0,&atx[853]} ,
-  {449, "IUPACaa" ,1,0,0,0,0,0,0,0,NULL,&atx[623],NULL,0,&atx[854]} ,
-  {0, "ncbi2na" ,128,2,0,0,0,0,0,0,NULL,&atx[854],NULL,0,&atx[855]} ,
-  {450, "NCBI2na" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[856]} ,
-  {0, "ncbi4na" ,128,3,0,0,0,0,0,0,NULL,&atx[856],NULL,0,&atx[857]} ,
-  {451, "NCBI4na" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[858]} ,
-  {0, "ncbi8na" ,128,4,0,0,0,0,0,0,NULL,&atx[858],NULL,0,&atx[859]} ,
-  {452, "NCBI8na" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[860]} ,
-  {0, "ncbipna" ,128,5,0,0,0,0,0,0,NULL,&atx[860],NULL,0,&atx[861]} ,
-  {453, "NCBIpna" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[862]} ,
-  {0, "ncbi8aa" ,128,6,0,0,0,0,0,0,NULL,&atx[862],NULL,0,&atx[863]} ,
-  {454, "NCBI8aa" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[864]} ,
-  {0, "ncbieaa" ,128,7,0,0,0,0,0,0,NULL,&atx[864],NULL,0,&atx[865]} ,
-  {455, "NCBIeaa" ,1,0,0,0,0,0,0,0,NULL,&atx[623],NULL,0,&atx[866]} ,
-  {0, "ncbipaa" ,128,8,0,0,0,0,0,0,NULL,&atx[866],NULL,0,&atx[867]} ,
-  {456, "NCBIpaa" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[868]} ,
-  {0, "ncbistdaa" ,128,9,0,0,0,0,0,0,NULL,&atx[868],NULL,0,&atx[869]} ,
-  {457, "NCBIstdaa" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[870]} ,
-  {0, "gap" ,128,10,0,0,0,0,0,0,NULL,&atx[870],NULL,0,NULL} ,
-  {458, "Seq-gap" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[871],0,&atx[1077]} ,
-  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[6],&avnx[388],0,&atx[872]} ,
-  {0, "linkage" ,128,1,0,1,0,0,0,0,NULL,&atx[6],&avnx[398],0,NULL} ,
-  {0, "ext" ,128,7,0,1,0,0,0,0,NULL,&atx[874],NULL,0,&atx[1059]} ,
-  {413, "Seq-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[875],0,&atx[1060]} ,
-  {0, "seg" ,128,0,0,0,0,0,0,0,NULL,&atx[876],NULL,0,&atx[878]} ,
-  {443, "Seg-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[877],0,&atx[879]} ,
+  {0, "topology" ,128,4,0,0,1,0,0,0,&avnx[386],&atx[42],&avnx[381],0,&atx[847]} ,
+  {0, "strand" ,128,5,0,1,0,0,0,0,NULL,&atx[42],&avnx[387],0,&atx[848]} ,
+  {0, "seq-data" ,128,6,0,1,0,0,0,0,NULL,&atx[849],NULL,0,&atx[874]} ,
+  {410, "Seq-data" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[850],0,&atx[649]} ,
+  {0, "iupacna" ,128,0,0,0,0,0,0,0,NULL,&atx[851],NULL,0,&atx[852]} ,
+  {449, "IUPACna" ,1,0,0,0,0,0,0,0,NULL,&atx[623],NULL,0,&atx[853]} ,
+  {0, "iupacaa" ,128,1,0,0,0,0,0,0,NULL,&atx[853],NULL,0,&atx[854]} ,
+  {450, "IUPACaa" ,1,0,0,0,0,0,0,0,NULL,&atx[623],NULL,0,&atx[855]} ,
+  {0, "ncbi2na" ,128,2,0,0,0,0,0,0,NULL,&atx[855],NULL,0,&atx[856]} ,
+  {451, "NCBI2na" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[857]} ,
+  {0, "ncbi4na" ,128,3,0,0,0,0,0,0,NULL,&atx[857],NULL,0,&atx[858]} ,
+  {452, "NCBI4na" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[859]} ,
+  {0, "ncbi8na" ,128,4,0,0,0,0,0,0,NULL,&atx[859],NULL,0,&atx[860]} ,
+  {453, "NCBI8na" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[861]} ,
+  {0, "ncbipna" ,128,5,0,0,0,0,0,0,NULL,&atx[861],NULL,0,&atx[862]} ,
+  {454, "NCBIpna" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[863]} ,
+  {0, "ncbi8aa" ,128,6,0,0,0,0,0,0,NULL,&atx[863],NULL,0,&atx[864]} ,
+  {455, "NCBI8aa" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[865]} ,
+  {0, "ncbieaa" ,128,7,0,0,0,0,0,0,NULL,&atx[865],NULL,0,&atx[866]} ,
+  {456, "NCBIeaa" ,1,0,0,0,0,0,0,0,NULL,&atx[623],NULL,0,&atx[867]} ,
+  {0, "ncbipaa" ,128,8,0,0,0,0,0,0,NULL,&atx[867],NULL,0,&atx[868]} ,
+  {457, "NCBIpaa" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[869]} ,
+  {0, "ncbistdaa" ,128,9,0,0,0,0,0,0,NULL,&atx[869],NULL,0,&atx[870]} ,
+  {458, "NCBIstdaa" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[871]} ,
+  {0, "gap" ,128,10,0,0,0,0,0,0,NULL,&atx[871],NULL,0,NULL} ,
+  {459, "Seq-gap" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[872],0,&atx[1078]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[6],&avnx[392],0,&atx[873]} ,
+  {0, "linkage" ,128,1,0,1,0,0,0,0,NULL,&atx[6],&avnx[402],0,NULL} ,
+  {0, "ext" ,128,7,0,1,0,0,0,0,NULL,&atx[875],NULL,0,&atx[1060]} ,
+  {413, "Seq-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[876],0,&atx[1061]} ,
+  {0, "seg" ,128,0,0,0,0,0,0,0,NULL,&atx[877],NULL,0,&atx[879]} ,
+  {444, "Seg-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[878],0,&atx[880]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[640],NULL,0,NULL} ,
-  {0, "ref" ,128,1,0,0,0,0,0,0,NULL,&atx[879],NULL,0,&atx[880]} ,
-  {444, "Ref-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[640],NULL,0,&atx[881]} ,
-  {0, "map" ,128,2,0,0,0,0,0,0,NULL,&atx[881],NULL,0,&atx[1049]} ,
-  {445, "Map-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[882],0,&atx[1052]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[883],NULL,0,NULL} ,
-  {424, "Seq-feat" ,1,0,0,0,0,0,1,0,NULL,&atx[884],NULL,0,&atx[1092]} ,
-  {401, "Seq-feat" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[885],0,&atx[428]} ,
-  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[428],NULL,0,&atx[886]} ,
-  {0, "data" ,128,1,0,0,0,0,0,0,NULL,&atx[887],NULL,0,&atx[1021]} ,
-  {420, "SeqFeatData" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[888],0,&atx[1028]} ,
-  {0, "gene" ,128,0,0,0,0,0,0,0,NULL,&atx[889],NULL,0,&atx[902]} ,
-  {404, "Gene-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[890],NULL,0,&atx[933]} ,
-  {401, "Gene-ref" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[891],0,&atx[898]} ,
-  {0, "locus" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[892]} ,
-  {0, "allele" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[893]} ,
-  {0, "desc" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[894]} ,
-  {0, "maploc" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[895]} ,
-  {0, "pseudo" ,128,4,0,0,1,0,0,0,&avnx[401],&atx[60],NULL,0,&atx[896]} ,
-  {0, "db" ,128,5,0,1,0,0,0,0,NULL,&atx[45],&atx[897],0,&atx[899]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[898],NULL,0,NULL} ,
+  {0, "ref" ,128,1,0,0,0,0,0,0,NULL,&atx[880],NULL,0,&atx[881]} ,
+  {445, "Ref-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[640],NULL,0,&atx[882]} ,
+  {0, "map" ,128,2,0,0,0,0,0,0,NULL,&atx[882],NULL,0,&atx[1050]} ,
+  {446, "Map-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[883],0,&atx[1053]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[884],NULL,0,NULL} ,
+  {424, "Seq-feat" ,1,0,0,0,0,0,1,0,NULL,&atx[885],NULL,0,&atx[1093]} ,
+  {401, "Seq-feat" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[886],0,&atx[428]} ,
+  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[428],NULL,0,&atx[887]} ,
+  {0, "data" ,128,1,0,0,0,0,0,0,NULL,&atx[888],NULL,0,&atx[1022]} ,
+  {420, "SeqFeatData" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[889],0,&atx[1029]} ,
+  {0, "gene" ,128,0,0,0,0,0,0,0,NULL,&atx[890],NULL,0,&atx[903]} ,
+  {404, "Gene-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[891],NULL,0,&atx[934]} ,
+  {401, "Gene-ref" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[892],0,&atx[899]} ,
+  {0, "locus" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[893]} ,
+  {0, "allele" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[894]} ,
+  {0, "desc" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[895]} ,
+  {0, "maploc" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[896]} ,
+  {0, "pseudo" ,128,4,0,0,1,0,0,0,&avnx[405],&atx[60],NULL,0,&atx[897]} ,
+  {0, "db" ,128,5,0,1,0,0,0,0,NULL,&atx[45],&atx[898],0,&atx[900]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[899],NULL,0,NULL} ,
   {402, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,&atx[17],NULL,0,NULL} ,
-  {0, "syn" ,128,6,0,1,0,0,0,0,NULL,&atx[45],&atx[900],0,&atx[901]} ,
+  {0, "syn" ,128,6,0,1,0,0,0,0,NULL,&atx[45],&atx[901],0,&atx[902]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {0, "locus-tag" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "org" ,128,1,0,0,0,0,0,0,NULL,&atx[903],NULL,0,&atx[904]} ,
-  {406, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[661],NULL,0,&atx[1020]} ,
-  {0, "cdregion" ,128,2,0,0,0,0,0,0,NULL,&atx[905],NULL,0,&atx[932]} ,
-  {423, "Cdregion" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[906],0,&atx[968]} ,
-  {0, "orf" ,128,0,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[907]} ,
-  {0, "frame" ,128,1,0,0,1,0,0,0,&avnx[406],&atx[42],&avnx[402],0,&atx[908]} ,
-  {0, "conflict" ,128,2,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[909]} ,
-  {0, "gaps" ,128,3,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[910]} ,
-  {0, "mismatch" ,128,4,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[911]} ,
-  {0, "code" ,128,5,0,1,0,0,0,0,NULL,&atx[912],NULL,0,&atx[922]} ,
-  {403, "Genetic-code" ,1,0,0,0,0,1,0,0,NULL,&atx[45],&atx[913],0,&atx[889]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[14],&atx[914],0,NULL} ,
-  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[915]} ,
-  {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[916]} ,
-  {0, "ncbieaa" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[917]} ,
-  {0, "ncbi8aa" ,128,3,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[918]} ,
-  {0, "ncbistdaa" ,128,4,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[919]} ,
-  {0, "sncbieaa" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[920]} ,
-  {0, "sncbi8aa" ,128,6,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[921]} ,
+  {0, "org" ,128,1,0,0,0,0,0,0,NULL,&atx[904],NULL,0,&atx[905]} ,
+  {406, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[661],NULL,0,&atx[1021]} ,
+  {0, "cdregion" ,128,2,0,0,0,0,0,0,NULL,&atx[906],NULL,0,&atx[933]} ,
+  {423, "Cdregion" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[907],0,&atx[969]} ,
+  {0, "orf" ,128,0,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[908]} ,
+  {0, "frame" ,128,1,0,0,1,0,0,0,&avnx[410],&atx[42],&avnx[406],0,&atx[909]} ,
+  {0, "conflict" ,128,2,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[910]} ,
+  {0, "gaps" ,128,3,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[911]} ,
+  {0, "mismatch" ,128,4,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[912]} ,
+  {0, "code" ,128,5,0,1,0,0,0,0,NULL,&atx[913],NULL,0,&atx[923]} ,
+  {403, "Genetic-code" ,1,0,0,0,0,1,0,0,NULL,&atx[45],&atx[914],0,&atx[890]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[14],&atx[915],0,NULL} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[916]} ,
+  {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[917]} ,
+  {0, "ncbieaa" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[918]} ,
+  {0, "ncbi8aa" ,128,3,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[919]} ,
+  {0, "ncbistdaa" ,128,4,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[920]} ,
+  {0, "sncbieaa" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[921]} ,
+  {0, "sncbi8aa" ,128,6,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[922]} ,
   {0, "sncbistdaa" ,128,7,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} ,
-  {0, "code-break" ,128,6,0,1,0,0,0,0,NULL,&atx[66],&atx[923],0,&atx[931]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[924],NULL,0,NULL} ,
-  {425, "Code-break" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[925],0,&atx[1174]} ,
-  {0, "loc" ,128,0,0,0,0,0,0,0,NULL,&atx[926],NULL,0,&atx[927]} ,
+  {0, "code-break" ,128,6,0,1,0,0,0,0,NULL,&atx[66],&atx[924],0,&atx[932]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[925],NULL,0,NULL} ,
+  {425, "Code-break" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[926],0,&atx[1237]} ,
+  {0, "loc" ,128,0,0,0,0,0,0,0,NULL,&atx[927],NULL,0,&atx[928]} ,
   {409, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,&atx[385],NULL,0,&atx[431]} ,
-  {0, "aa" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[928],0,NULL} ,
-  {0, "ncbieaa" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[929]} ,
-  {0, "ncbi8aa" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[930]} ,
+  {0, "aa" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[929],0,NULL} ,
+  {0, "ncbieaa" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[930]} ,
+  {0, "ncbi8aa" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[931]} ,
   {0, "ncbistdaa" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
   {0, "stops" ,128,7,0,1,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "prot" ,128,3,0,0,0,0,0,0,NULL,&atx[933],NULL,0,&atx[946]} ,
-  {405, "Prot-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[934],NULL,0,&atx[903]} ,
-  {401, "Prot-ref" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[935],0,&atx[944]} ,
-  {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[936],0,&atx[937]} ,
+  {0, "prot" ,128,3,0,0,0,0,0,0,NULL,&atx[934],NULL,0,&atx[947]} ,
+  {405, "Prot-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[935],NULL,0,&atx[904]} ,
+  {401, "Prot-ref" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[936],0,&atx[945]} ,
+  {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[937],0,&atx[938]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "desc" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[938]} ,
-  {0, "ec" ,128,2,0,1,0,0,0,0,NULL,&atx[45],&atx[939],0,&atx[940]} ,
+  {0, "desc" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[939]} ,
+  {0, "ec" ,128,2,0,1,0,0,0,0,NULL,&atx[45],&atx[940],0,&atx[941]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "activity" ,128,3,0,1,0,0,0,0,NULL,&atx[45],&atx[941],0,&atx[942]} ,
+  {0, "activity" ,128,3,0,1,0,0,0,0,NULL,&atx[45],&atx[942],0,&atx[943]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "db" ,128,4,0,1,0,0,0,0,NULL,&atx[45],&atx[943],0,&atx[945]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[944],NULL,0,NULL} ,
+  {0, "db" ,128,4,0,1,0,0,0,0,NULL,&atx[45],&atx[944],0,&atx[946]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[945],NULL,0,NULL} ,
   {402, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,&atx[17],NULL,0,NULL} ,
-  {0, "processed" ,128,5,0,0,1,0,0,0,&avnx[412],&atx[42],&avnx[407],0,NULL} ,
-  {0, "rna" ,128,4,0,0,0,0,0,0,NULL,&atx[947],NULL,0,&atx[964]} ,
-  {408, "RNA-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[948],NULL,0,&atx[926]} ,
-  {401, "RNA-ref" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[949],0,&atx[954]} ,
-  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[413],0,&atx[950]} ,
-  {0, "pseudo" ,128,1,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[951]} ,
-  {0, "ext" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[952],0,NULL} ,
-  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[953]} ,
-  {0, "tRNA" ,128,1,0,0,0,0,0,0,NULL,&atx[954],NULL,0,NULL} ,
-  {402, "Trna-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[955],0,&atx[963]} ,
-  {0, "aa" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[956],0,&atx[960]} ,
-  {0, "iupacaa" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[957]} ,
-  {0, "ncbieaa" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[958]} ,
-  {0, "ncbi8aa" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[959]} ,
+  {0, "processed" ,128,5,0,0,1,0,0,0,&avnx[416],&atx[42],&avnx[411],0,NULL} ,
+  {0, "rna" ,128,4,0,0,0,0,0,0,NULL,&atx[948],NULL,0,&atx[965]} ,
+  {408, "RNA-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[949],NULL,0,&atx[927]} ,
+  {401, "RNA-ref" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[950],0,&atx[955]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[417],0,&atx[951]} ,
+  {0, "pseudo" ,128,1,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[952]} ,
+  {0, "ext" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[953],0,NULL} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[954]} ,
+  {0, "tRNA" ,128,1,0,0,0,0,0,0,NULL,&atx[955],NULL,0,NULL} ,
+  {402, "Trna-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[956],0,&atx[964]} ,
+  {0, "aa" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[957],0,&atx[961]} ,
+  {0, "iupacaa" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[958]} ,
+  {0, "ncbieaa" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[959]} ,
+  {0, "ncbi8aa" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[960]} ,
   {0, "ncbistdaa" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "codon" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[961],0,&atx[962]} ,
+  {0, "codon" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[962],0,&atx[963]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "anticodon" ,128,2,0,1,0,0,0,0,NULL,&atx[963],NULL,0,NULL} ,
+  {0, "anticodon" ,128,2,0,1,0,0,0,0,NULL,&atx[964],NULL,0,NULL} ,
   {403, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,&atx[385],NULL,0,NULL} ,
-  {0, "pub" ,128,5,0,0,0,0,0,0,NULL,&atx[965],NULL,0,&atx[966]} ,
-  {411, "Pubdesc" ,1,0,0,0,0,0,1,0,NULL,&atx[441],NULL,0,&atx[1014]} ,
-  {0, "seq" ,128,6,0,0,0,0,0,0,NULL,&atx[926],NULL,0,&atx[967]} ,
-  {0, "imp" ,128,7,0,0,0,0,0,0,NULL,&atx[968],NULL,0,&atx[972]} ,
-  {424, "Imp-feat" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[969],0,&atx[924]} ,
-  {0, "key" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[970]} ,
-  {0, "loc" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[971]} ,
+  {0, "pub" ,128,5,0,0,0,0,0,0,NULL,&atx[966],NULL,0,&atx[967]} ,
+  {411, "Pubdesc" ,1,0,0,0,0,0,1,0,NULL,&atx[441],NULL,0,&atx[1015]} ,
+  {0, "seq" ,128,6,0,0,0,0,0,0,NULL,&atx[927],NULL,0,&atx[968]} ,
+  {0, "imp" ,128,7,0,0,0,0,0,0,NULL,&atx[969],NULL,0,&atx[973]} ,
+  {424, "Imp-feat" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[970],0,&atx[925]} ,
+  {0, "key" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[971]} ,
+  {0, "loc" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[972]} ,
   {0, "descr" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "region" ,128,8,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[973]} ,
-  {0, "comment" ,128,9,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[974]} ,
-  {0, "bond" ,128,10,0,0,0,0,0,0,NULL,&atx[42],&avnx[422],0,&atx[975]} ,
-  {0, "site" ,128,11,0,0,0,0,0,0,NULL,&atx[42],&avnx[427],0,&atx[976]} ,
-  {0, "rsite" ,128,12,0,0,0,0,0,0,NULL,&atx[977],NULL,0,&atx[982]} ,
-  {414, "Rsite-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[978],NULL,0,&atx[985]} ,
-  {401, "Rsite-ref" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[979],0,&atx[981]} ,
-  {0, "str" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[980]} ,
-  {0, "db" ,128,1,0,0,0,0,0,0,NULL,&atx[981],NULL,0,NULL} ,
+  {0, "region" ,128,8,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[974]} ,
+  {0, "comment" ,128,9,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[975]} ,
+  {0, "bond" ,128,10,0,0,0,0,0,0,NULL,&atx[42],&avnx[426],0,&atx[976]} ,
+  {0, "site" ,128,11,0,0,0,0,0,0,NULL,&atx[42],&avnx[431],0,&atx[977]} ,
+  {0, "rsite" ,128,12,0,0,0,0,0,0,NULL,&atx[978],NULL,0,&atx[983]} ,
+  {414, "Rsite-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[979],NULL,0,&atx[986]} ,
+  {401, "Rsite-ref" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[980],0,&atx[982]} ,
+  {0, "str" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[981]} ,
+  {0, "db" ,128,1,0,0,0,0,0,0,NULL,&atx[982],NULL,0,NULL} ,
   {402, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,&atx[17],NULL,0,NULL} ,
-  {0, "user" ,128,13,0,0,0,0,0,0,NULL,&atx[983],NULL,0,&atx[984]} ,
-  {419, "User-object" ,1,0,0,0,0,0,1,0,NULL,&atx[46],NULL,0,&atx[887]} ,
-  {0, "txinit" ,128,14,0,0,0,0,0,0,NULL,&atx[985],NULL,0,&atx[1013]} ,
-  {415, "Txinit" ,1,0,0,0,0,0,1,0,NULL,&atx[986],NULL,0,&atx[1034]} ,
-  {401, "Txinit" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[987],0,&atx[992]} ,
-  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[988]} ,
-  {0, "syn" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[989],0,&atx[990]} ,
+  {0, "user" ,128,13,0,0,0,0,0,0,NULL,&atx[984],NULL,0,&atx[985]} ,
+  {419, "User-object" ,1,0,0,0,0,0,1,0,NULL,&atx[46],NULL,0,&atx[888]} ,
+  {0, "txinit" ,128,14,0,0,0,0,0,0,NULL,&atx[986],NULL,0,&atx[1014]} ,
+  {415, "Txinit" ,1,0,0,0,0,0,1,0,NULL,&atx[987],NULL,0,&atx[1035]} ,
+  {401, "Txinit" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[988],0,&atx[993]} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[989]} ,
+  {0, "syn" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[990],0,&atx[991]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "gene" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[991],0,&atx[993]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[992],NULL,0,NULL} ,
-  {402, "Gene-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[890],NULL,0,&atx[995]} ,
-  {0, "protein" ,128,3,0,1,0,0,0,0,NULL,&atx[66],&atx[994],0,&atx[996]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[995],NULL,0,NULL} ,
-  {403, "Prot-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[934],NULL,0,&atx[1002]} ,
-  {0, "rna" ,128,4,0,1,0,0,0,0,NULL,&atx[66],&atx[997],0,&atx[998]} ,
+  {0, "gene" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[992],0,&atx[994]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[993],NULL,0,NULL} ,
+  {402, "Gene-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[891],NULL,0,&atx[996]} ,
+  {0, "protein" ,128,3,0,1,0,0,0,0,NULL,&atx[66],&atx[995],0,&atx[997]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[996],NULL,0,NULL} ,
+  {403, "Prot-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[935],NULL,0,&atx[1003]} ,
+  {0, "rna" ,128,4,0,1,0,0,0,0,NULL,&atx[66],&atx[998],0,&atx[999]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "expression" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[999]} ,
-  {0, "txsystem" ,128,6,0,0,0,0,0,0,NULL,&atx[42],&avnx[454],0,&atx[1000]} ,
-  {0, "txdescr" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1001]} ,
-  {0, "txorg" ,128,8,0,1,0,0,0,0,NULL,&atx[1002],NULL,0,&atx[1003]} ,
-  {404, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[661],NULL,0,&atx[1008]} ,
-  {0, "mapping-precise" ,128,9,0,0,1,0,0,0,&avnx[463],&atx[60],NULL,0,&atx[1004]} ,
-  {0, "location-accurate" ,128,10,0,0,1,0,0,0,&avnx[464],&atx[60],NULL,0,&atx[1005]} ,
-  {0, "inittype" ,128,11,0,1,0,0,0,0,NULL,&atx[42],&avnx[465],0,&atx[1006]} ,
-  {0, "evidence" ,128,12,0,1,0,0,0,0,NULL,&atx[45],&atx[1007],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1008],NULL,0,NULL} ,
-  {405, "Tx-evidence" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1009],0,NULL} ,
-  {0, "exp-code" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[469],0,&atx[1010]} ,
-  {0, "expression-system" ,128,1,0,0,1,0,0,0,&avnx[488],&atx[42],&avnx[481],0,&atx[1011]} ,
-  {0, "low-prec-data" ,128,2,0,0,1,0,0,0,&avnx[489],&atx[60],NULL,0,&atx[1012]} ,
-  {0, "from-homolog" ,128,3,0,0,1,0,0,0,&avnx[490],&atx[60],NULL,0,NULL} ,
-  {0, "num" ,128,15,0,0,0,0,0,0,NULL,&atx[1014],NULL,0,&atx[1015]} ,
-  {412, "Numbering" ,1,0,0,0,0,0,1,0,NULL,&atx[447],NULL,0,&atx[1018]} ,
-  {0, "psec-str" ,128,16,0,0,0,0,0,0,NULL,&atx[42],&avnx[491],0,&atx[1016]} ,
-  {0, "non-std-residue" ,128,17,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1017]} ,
-  {0, "het" ,128,18,0,0,0,0,0,0,NULL,&atx[1018],NULL,0,&atx[1019]} ,
-  {413, "Heterogen" ,1,0,0,0,0,0,1,0,NULL,&atx[817],NULL,0,&atx[977]} ,
-  {0, "biosrc" ,128,19,0,0,0,0,0,0,NULL,&atx[1020],NULL,0,NULL} ,
-  {407, "BioSource" ,1,0,0,0,0,0,1,0,NULL,&atx[820],NULL,0,&atx[947]} ,
-  {0, "partial" ,128,2,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1022]} ,
-  {0, "except" ,128,3,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1023]} ,
-  {0, "comment" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1024]} ,
-  {0, "product" ,128,5,0,1,0,0,0,0,NULL,&atx[926],NULL,0,&atx[1025]} ,
-  {0, "location" ,128,6,0,0,0,0,0,0,NULL,&atx[926],NULL,0,&atx[1026]} ,
-  {0, "qual" ,128,7,0,1,0,0,0,0,NULL,&atx[66],&atx[1027],0,&atx[1031]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1028],NULL,0,NULL} ,
-  {421, "Gb-qual" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1029],0,&atx[1038]} ,
-  {0, "qual" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1030]} ,
+  {0, "expression" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1000]} ,
+  {0, "txsystem" ,128,6,0,0,0,0,0,0,NULL,&atx[42],&avnx[458],0,&atx[1001]} ,
+  {0, "txdescr" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1002]} ,
+  {0, "txorg" ,128,8,0,1,0,0,0,0,NULL,&atx[1003],NULL,0,&atx[1004]} ,
+  {404, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[661],NULL,0,&atx[1009]} ,
+  {0, "mapping-precise" ,128,9,0,0,1,0,0,0,&avnx[467],&atx[60],NULL,0,&atx[1005]} ,
+  {0, "location-accurate" ,128,10,0,0,1,0,0,0,&avnx[468],&atx[60],NULL,0,&atx[1006]} ,
+  {0, "inittype" ,128,11,0,1,0,0,0,0,NULL,&atx[42],&avnx[469],0,&atx[1007]} ,
+  {0, "evidence" ,128,12,0,1,0,0,0,0,NULL,&atx[45],&atx[1008],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1009],NULL,0,NULL} ,
+  {405, "Tx-evidence" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1010],0,NULL} ,
+  {0, "exp-code" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[473],0,&atx[1011]} ,
+  {0, "expression-system" ,128,1,0,0,1,0,0,0,&avnx[492],&atx[42],&avnx[485],0,&atx[1012]} ,
+  {0, "low-prec-data" ,128,2,0,0,1,0,0,0,&avnx[493],&atx[60],NULL,0,&atx[1013]} ,
+  {0, "from-homolog" ,128,3,0,0,1,0,0,0,&avnx[494],&atx[60],NULL,0,NULL} ,
+  {0, "num" ,128,15,0,0,0,0,0,0,NULL,&atx[1015],NULL,0,&atx[1016]} ,
+  {412, "Numbering" ,1,0,0,0,0,0,1,0,NULL,&atx[447],NULL,0,&atx[1019]} ,
+  {0, "psec-str" ,128,16,0,0,0,0,0,0,NULL,&atx[42],&avnx[495],0,&atx[1017]} ,
+  {0, "non-std-residue" ,128,17,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1018]} ,
+  {0, "het" ,128,18,0,0,0,0,0,0,NULL,&atx[1019],NULL,0,&atx[1020]} ,
+  {413, "Heterogen" ,1,0,0,0,0,0,1,0,NULL,&atx[817],NULL,0,&atx[978]} ,
+  {0, "biosrc" ,128,19,0,0,0,0,0,0,NULL,&atx[1021],NULL,0,NULL} ,
+  {407, "BioSource" ,1,0,0,0,0,0,1,0,NULL,&atx[820],NULL,0,&atx[948]} ,
+  {0, "partial" ,128,2,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1023]} ,
+  {0, "except" ,128,3,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1024]} ,
+  {0, "comment" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1025]} ,
+  {0, "product" ,128,5,0,1,0,0,0,0,NULL,&atx[927],NULL,0,&atx[1026]} ,
+  {0, "location" ,128,6,0,0,0,0,0,0,NULL,&atx[927],NULL,0,&atx[1027]} ,
+  {0, "qual" ,128,7,0,1,0,0,0,0,NULL,&atx[66],&atx[1028],0,&atx[1032]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1029],NULL,0,NULL} ,
+  {421, "Gb-qual" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1030],0,&atx[1039]} ,
+  {0, "qual" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1031]} ,
   {0, "val" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "title" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1032]} ,
-  {0, "ext" ,128,9,0,1,0,0,0,0,NULL,&atx[983],NULL,0,&atx[1033]} ,
-  {0, "cit" ,128,10,0,1,0,0,0,0,NULL,&atx[1034],NULL,0,&atx[1035]} ,
+  {0, "title" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1033]} ,
+  {0, "ext" ,128,9,0,1,0,0,0,0,NULL,&atx[984],NULL,0,&atx[1034]} ,
+  {0, "cit" ,128,10,0,1,0,0,0,0,NULL,&atx[1035],NULL,0,&atx[1036]} ,
   {416, "Pub-set" ,1,0,0,0,0,0,1,0,NULL,&atx[329],NULL,0,&atx[433]} ,
-  {0, "exp-ev" ,128,11,0,1,0,0,0,0,NULL,&atx[42],&avnx[494],0,&atx[1036]} ,
-  {0, "xref" ,128,12,0,1,0,0,0,0,NULL,&atx[45],&atx[1037],0,&atx[1041]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1038],NULL,0,NULL} ,
-  {422, "SeqFeatXref" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1039],0,&atx[905]} ,
-  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[428],NULL,0,&atx[1040]} ,
-  {0, "data" ,128,1,0,1,0,0,0,0,NULL,&atx[887],NULL,0,NULL} ,
-  {0, "dbxref" ,128,13,0,1,0,0,0,0,NULL,&atx[45],&atx[1042],0,&atx[1043]} ,
+  {0, "exp-ev" ,128,11,0,1,0,0,0,0,NULL,&atx[42],&avnx[498],0,&atx[1037]} ,
+  {0, "xref" ,128,12,0,1,0,0,0,0,NULL,&atx[45],&atx[1038],0,&atx[1042]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1039],NULL,0,NULL} ,
+  {422, "SeqFeatXref" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1040],0,&atx[906]} ,
+  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[428],NULL,0,&atx[1041]} ,
+  {0, "data" ,128,1,0,1,0,0,0,0,NULL,&atx[888],NULL,0,NULL} ,
+  {0, "dbxref" ,128,13,0,1,0,0,0,0,NULL,&atx[45],&atx[1043],0,&atx[1044]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[435],NULL,0,NULL} ,
-  {0, "pseudo" ,128,14,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1044]} ,
-  {0, "except-text" ,128,15,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1045]} ,
-  {0, "ids" ,128,16,0,1,0,0,0,0,NULL,&atx[45],&atx[1046],0,&atx[1047]} ,
+  {0, "pseudo" ,128,14,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1045]} ,
+  {0, "except-text" ,128,15,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1046]} ,
+  {0, "ids" ,128,16,0,1,0,0,0,0,NULL,&atx[45],&atx[1047],0,&atx[1048]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[428],NULL,0,NULL} ,
-  {0, "exts" ,128,17,0,1,0,0,0,0,NULL,&atx[45],&atx[1048],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[983],NULL,0,NULL} ,
-  {0, "delta" ,128,3,0,0,0,0,0,0,NULL,&atx[1050],NULL,0,NULL} ,
-  {417, "Delta-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[66],&atx[1051],0,&atx[630]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1052],NULL,0,NULL} ,
-  {446, "Delta-seq" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1053],0,&atx[1064]} ,
-  {0, "loc" ,128,0,0,0,0,0,0,0,NULL,&atx[640],NULL,0,&atx[1054]} ,
-  {0, "literal" ,128,1,0,0,0,0,0,0,NULL,&atx[1055],NULL,0,NULL} ,
-  {416, "Seq-literal" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1056],0,&atx[1050]} ,
-  {0, "length" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1057]} ,
-  {0, "fuzz" ,128,1,0,1,0,0,0,0,NULL,&atx[844],NULL,0,&atx[1058]} ,
-  {0, "seq-data" ,128,2,0,1,0,0,0,0,NULL,&atx[848],NULL,0,NULL} ,
-  {0, "hist" ,128,8,0,1,0,0,0,0,NULL,&atx[1060],NULL,0,NULL} ,
-  {414, "Seq-hist" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1061],0,&atx[839]} ,
-  {0, "assembly" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[1062],0,&atx[1063]} ,
+  {0, "exts" ,128,17,0,1,0,0,0,0,NULL,&atx[45],&atx[1049],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[984],NULL,0,NULL} ,
+  {0, "delta" ,128,3,0,0,0,0,0,0,NULL,&atx[1051],NULL,0,NULL} ,
+  {417, "Delta-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[66],&atx[1052],0,&atx[630]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1053],NULL,0,NULL} ,
+  {447, "Delta-seq" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1054],0,&atx[1065]} ,
+  {0, "loc" ,128,0,0,0,0,0,0,0,NULL,&atx[640],NULL,0,&atx[1055]} ,
+  {0, "literal" ,128,1,0,0,0,0,0,0,NULL,&atx[1056],NULL,0,NULL} ,
+  {416, "Seq-literal" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1057],0,&atx[1051]} ,
+  {0, "length" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1058]} ,
+  {0, "fuzz" ,128,1,0,1,0,0,0,0,NULL,&atx[845],NULL,0,&atx[1059]} ,
+  {0, "seq-data" ,128,2,0,1,0,0,0,0,NULL,&atx[849],NULL,0,NULL} ,
+  {0, "hist" ,128,8,0,1,0,0,0,0,NULL,&atx[1061],NULL,0,NULL} ,
+  {414, "Seq-hist" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1062],0,&atx[840]} ,
+  {0, "assembly" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[1063],0,&atx[1064]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[462],NULL,0,NULL} ,
-  {0, "replaces" ,128,1,0,1,0,0,0,0,NULL,&atx[1064],NULL,0,&atx[1068]} ,
-  {447, "Seq-hist-rec" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1065],0,&atx[850]} ,
-  {0, "date" ,128,0,0,1,0,0,0,0,NULL,&atx[630],NULL,0,&atx[1066]} ,
-  {0, "ids" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1067],0,NULL} ,
+  {0, "replaces" ,128,1,0,1,0,0,0,0,NULL,&atx[1065],NULL,0,&atx[1069]} ,
+  {448, "Seq-hist-rec" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1066],0,&atx[851]} ,
+  {0, "date" ,128,0,0,1,0,0,0,0,NULL,&atx[630],NULL,0,&atx[1067]} ,
+  {0, "ids" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1068],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[633],NULL,0,NULL} ,
-  {0, "replaced-by" ,128,2,0,1,0,0,0,0,NULL,&atx[1064],NULL,0,&atx[1069]} ,
-  {0, "deleted" ,128,3,0,1,0,0,0,0,NULL,&atx[14],&atx[1070],0,NULL} ,
-  {0, "bool" ,128,0,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1071]} ,
+  {0, "replaced-by" ,128,2,0,1,0,0,0,0,NULL,&atx[1065],NULL,0,&atx[1070]} ,
+  {0, "deleted" ,128,3,0,1,0,0,0,0,NULL,&atx[14],&atx[1071],0,NULL} ,
+  {0, "bool" ,128,0,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1072]} ,
   {0, "date" ,128,1,0,0,0,0,0,0,NULL,&atx[630],NULL,0,NULL} ,
-  {0, "annot" ,128,3,0,1,0,0,0,0,NULL,&atx[45],&atx[1073],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1074],NULL,0,NULL} ,
-  {409, "Seq-annot" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1075],0,&atx[848]} ,
-  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[1076],0,&atx[1082]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1077],NULL,0,NULL} ,
-  {459, "Annot-id" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1078],0,&atx[635]} ,
-  {0, "local" ,128,0,0,0,0,0,0,0,NULL,&atx[1079],NULL,0,&atx[1080]} ,
+  {0, "annot" ,128,3,0,1,0,0,0,0,NULL,&atx[45],&atx[1074],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1075],NULL,0,NULL} ,
+  {409, "Seq-annot" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1076],0,&atx[849]} ,
+  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[1077],0,&atx[1083]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1078],NULL,0,NULL} ,
+  {460, "Annot-id" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1079],0,&atx[635]} ,
+  {0, "local" ,128,0,0,0,0,0,0,0,NULL,&atx[1080],NULL,0,&atx[1081]} ,
   {421, "Object-id" ,1,0,0,0,0,0,1,0,NULL,&atx[20],NULL,0,&atx[628]} ,
-  {0, "ncbi" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1081]} ,
+  {0, "ncbi" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1082]} ,
   {0, "general" ,128,2,0,0,0,0,0,0,NULL,&atx[705],NULL,0,NULL} ,
-  {0, "db" ,128,1,0,1,0,0,0,0,NULL,&atx[6],&avnx[496],0,&atx[1083]} ,
-  {0, "name" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1084]} ,
-  {0, "desc" ,128,3,0,1,0,0,0,0,NULL,&atx[641],NULL,0,&atx[1085]} ,
-  {0, "data" ,128,4,0,0,0,0,0,0,NULL,&atx[14],&atx[1086],0,NULL} ,
-  {0, "ftable" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1087],0,&atx[1088]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[883],NULL,0,NULL} ,
-  {0, "align" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1089],0,&atx[1090]} ,
+  {0, "db" ,128,1,0,1,0,0,0,0,NULL,&atx[6],&avnx[500],0,&atx[1084]} ,
+  {0, "name" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1085]} ,
+  {0, "desc" ,128,3,0,1,0,0,0,0,NULL,&atx[641],NULL,0,&atx[1086]} ,
+  {0, "data" ,128,4,0,0,0,0,0,0,NULL,&atx[14],&atx[1087],0,NULL} ,
+  {0, "ftable" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1088],0,&atx[1089]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[884],NULL,0,NULL} ,
+  {0, "align" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1090],0,&atx[1091]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[462],NULL,0,NULL} ,
-  {0, "graph" ,128,2,0,0,0,0,0,0,NULL,&atx[45],&atx[1091],0,&atx[1125]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1092],NULL,0,NULL} ,
-  {425, "Seq-graph" ,1,0,0,0,0,0,1,0,NULL,&atx[1093],NULL,0,&atx[443]} ,
-  {401, "Seq-graph" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1094],0,&atx[1097]} ,
-  {0, "title" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1095]} ,
-  {0, "comment" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1096]} ,
-  {0, "loc" ,128,2,0,0,0,0,0,0,NULL,&atx[1097],NULL,0,&atx[1098]} ,
-  {402, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,&atx[385],NULL,0,&atx[1106]} ,
-  {0, "title-x" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1099]} ,
-  {0, "title-y" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1100]} ,
-  {0, "comp" ,128,5,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1101]} ,
-  {0, "a" ,128,6,0,1,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1102]} ,
-  {0, "b" ,128,7,0,1,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1103]} ,
-  {0, "numval" ,128,8,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1104]} ,
-  {0, "graph" ,128,9,0,0,0,0,0,0,NULL,&atx[14],&atx[1105],0,NULL} ,
-  {0, "real" ,128,0,0,0,0,0,0,0,NULL,&atx[1106],NULL,0,&atx[1112]} ,
-  {403, "Real-graph" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1107],0,&atx[1113]} ,
-  {0, "max" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1108]} ,
-  {0, "min" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1109]} ,
-  {0, "axis" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1110]} ,
-  {0, "values" ,128,3,0,0,0,0,0,0,NULL,&atx[66],&atx[1111],0,NULL} ,
+  {0, "graph" ,128,2,0,0,0,0,0,0,NULL,&atx[45],&atx[1092],0,&atx[1126]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1093],NULL,0,NULL} ,
+  {425, "Seq-graph" ,1,0,0,0,0,0,1,0,NULL,&atx[1094],NULL,0,&atx[443]} ,
+  {401, "Seq-graph" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1095],0,&atx[1098]} ,
+  {0, "title" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1096]} ,
+  {0, "comment" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1097]} ,
+  {0, "loc" ,128,2,0,0,0,0,0,0,NULL,&atx[1098],NULL,0,&atx[1099]} ,
+  {402, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,&atx[385],NULL,0,&atx[1107]} ,
+  {0, "title-x" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1100]} ,
+  {0, "title-y" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1101]} ,
+  {0, "comp" ,128,5,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1102]} ,
+  {0, "a" ,128,6,0,1,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1103]} ,
+  {0, "b" ,128,7,0,1,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1104]} ,
+  {0, "numval" ,128,8,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1105]} ,
+  {0, "graph" ,128,9,0,0,0,0,0,0,NULL,&atx[14],&atx[1106],0,NULL} ,
+  {0, "real" ,128,0,0,0,0,0,0,0,NULL,&atx[1107],NULL,0,&atx[1113]} ,
+  {403, "Real-graph" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1108],0,&atx[1114]} ,
+  {0, "max" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1109]} ,
+  {0, "min" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1110]} ,
+  {0, "axis" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1111]} ,
+  {0, "values" ,128,3,0,0,0,0,0,0,NULL,&atx[66],&atx[1112],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
-  {0, "int" ,128,1,0,0,0,0,0,0,NULL,&atx[1113],NULL,0,&atx[1119]} ,
-  {404, "Int-graph" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1114],0,&atx[1120]} ,
-  {0, "max" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1115]} ,
-  {0, "min" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1116]} ,
-  {0, "axis" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1117]} ,
-  {0, "values" ,128,3,0,0,0,0,0,0,NULL,&atx[66],&atx[1118],0,NULL} ,
+  {0, "int" ,128,1,0,0,0,0,0,0,NULL,&atx[1114],NULL,0,&atx[1120]} ,
+  {404, "Int-graph" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1115],0,&atx[1121]} ,
+  {0, "max" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1116]} ,
+  {0, "min" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1117]} ,
+  {0, "axis" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1118]} ,
+  {0, "values" ,128,3,0,0,0,0,0,0,NULL,&atx[66],&atx[1119],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "byte" ,128,2,0,0,0,0,0,0,NULL,&atx[1120],NULL,0,NULL} ,
-  {405, "Byte-graph" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1121],0,NULL} ,
-  {0, "max" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1122]} ,
-  {0, "min" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1123]} ,
-  {0, "axis" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1124]} ,
+  {0, "byte" ,128,2,0,0,0,0,0,0,NULL,&atx[1121],NULL,0,NULL} ,
+  {405, "Byte-graph" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1122],0,NULL} ,
+  {0, "max" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1123]} ,
+  {0, "min" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1124]} ,
+  {0, "axis" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1125]} ,
   {0, "values" ,128,3,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} ,
-  {0, "ids" ,128,3,0,0,0,0,0,0,NULL,&atx[45],&atx[1126],0,&atx[1127]} ,
+  {0, "ids" ,128,3,0,0,0,0,0,0,NULL,&atx[45],&atx[1127],0,&atx[1128]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[633],NULL,0,NULL} ,
-  {0, "locs" ,128,4,0,0,0,0,0,0,NULL,&atx[45],&atx[1128],0,NULL} ,
+  {0, "locs" ,128,4,0,0,0,0,0,0,NULL,&atx[45],&atx[1129],0,&atx[1130]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[640],NULL,0,NULL} ,
-  {401, "Bioseq-set" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1130],0,&atx[1143]} ,
-  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[1131],NULL,0,&atx[1132]} ,
-  {406, "Object-id" ,1,0,0,0,0,0,1,0,NULL,&atx[20],NULL,0,&atx[1133]} ,
-  {0, "coll" ,128,1,0,1,0,0,0,0,NULL,&atx[1133],NULL,0,&atx[1134]} ,
-  {407, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,&atx[17],NULL,0,&atx[1138]} ,
-  {0, "level" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1135]} ,
-  {0, "class" ,128,3,0,0,1,0,0,0,&avnx[524],&atx[42],&avnx[504],0,&atx[1136]} ,
-  {0, "release" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1137]} ,
-  {0, "date" ,128,5,0,1,0,0,0,0,NULL,&atx[1138],NULL,0,&atx[1139]} ,
+  {0, "seq-table" ,128,5,0,0,0,0,0,0,NULL,&atx[1131],NULL,0,NULL} ,
+  {437, "Seq-table" ,1,0,0,0,0,0,1,0,NULL,&atx[1132],NULL,0,&atx[654]} ,
+  {403, "Seq-table" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1133],0,&atx[1172]} ,
+  {0, "feat-type" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1134]} ,
+  {0, "feat-subtype" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1135]} ,
+  {0, "num-rows" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1136]} ,
+  {0, "columns" ,128,3,0,0,0,0,0,0,NULL,&atx[66],&atx[1137],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1138],NULL,0,NULL} ,
+  {402, "SeqTable-column" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1139],0,&atx[1132]} ,
+  {0, "header" ,128,0,0,0,0,0,0,0,NULL,&atx[1140],NULL,0,&atx[1144]} ,
+  {401, "SeqTable-column-info" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1141],0,&atx[1138]} ,
+  {0, "title" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1142]} ,
+  {0, "field-id" ,128,1,0,1,0,0,0,0,NULL,&atx[6],&avnx[508],0,&atx[1143]} ,
+  {0, "field-name" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "data" ,128,1,0,1,0,0,0,0,NULL,&atx[1145],NULL,0,&atx[1176]} ,
+  {409, "SeqTable-multi-data" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1146],0,&atx[1182]} ,
+  {0, "int" ,128,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1147],0,&atx[1148]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
+  {0, "real" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[1149],0,&atx[1150]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
+  {0, "string" ,128,2,0,0,0,0,0,0,NULL,&atx[66],&atx[1151],0,&atx[1152]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "bytes" ,128,3,0,0,0,0,0,0,NULL,&atx[66],&atx[1153],0,&atx[1154]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} ,
+  {0, "common-string" ,128,4,0,0,0,0,0,0,NULL,&atx[1155],NULL,0,&atx[1160]} ,
+  {407, "CommonString-table" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1156],0,&atx[1161]} ,
+  {0, "strings" ,128,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1157],0,&atx[1158]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "indexes" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[1159],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
+  {0, "common-bytes" ,128,5,0,0,0,0,0,0,NULL,&atx[1161],NULL,0,&atx[1166]} ,
+  {408, "CommonBytes-table" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1162],0,&atx[1145]} ,
+  {0, "bytes" ,128,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1163],0,&atx[1164]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} ,
+  {0, "indexes" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[1165],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
+  {0, "bit" ,128,6,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[1167]} ,
+  {0, "loc" ,128,7,0,0,0,0,0,0,NULL,&atx[66],&atx[1168],0,&atx[1170]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1169],NULL,0,NULL} ,
+  {405, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,&atx[385],NULL,0,&atx[1175]} ,
+  {0, "id" ,128,8,0,0,0,0,0,0,NULL,&atx[66],&atx[1171],0,&atx[1173]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1172],NULL,0,NULL} ,
+  {404, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,&atx[344],NULL,0,&atx[1169]} ,
+  {0, "interval" ,128,9,0,0,0,0,0,0,NULL,&atx[66],&atx[1174],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1175],NULL,0,NULL} ,
+  {406, "Seq-interval" ,1,0,0,0,0,0,1,0,NULL,&atx[391],NULL,0,&atx[1155]} ,
+  {0, "sparse" ,128,2,0,1,0,0,0,0,NULL,&atx[1177],NULL,0,&atx[1181]} ,
+  {411, "SeqTable-sparse-index" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1178],0,NULL} ,
+  {0, "indexes" ,128,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1179],0,&atx[1180]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
+  {0, "bit-set" ,128,1,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} ,
+  {0, "default" ,128,3,0,1,0,0,0,0,NULL,&atx[1182],NULL,0,&atx[1191]} ,
+  {410, "SeqTable-single-data" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1183],0,&atx[1177]} ,
+  {0, "int" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1184]} ,
+  {0, "real" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1185]} ,
+  {0, "string" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1186]} ,
+  {0, "bytes" ,128,3,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[1187]} ,
+  {0, "bit" ,128,4,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1188]} ,
+  {0, "loc" ,128,5,0,0,0,0,0,0,NULL,&atx[1169],NULL,0,&atx[1189]} ,
+  {0, "id" ,128,6,0,0,0,0,0,0,NULL,&atx[1172],NULL,0,&atx[1190]} ,
+  {0, "interval" ,128,7,0,0,0,0,0,0,NULL,&atx[1175],NULL,0,NULL} ,
+  {0, "sparse-other" ,128,4,0,1,0,0,0,0,NULL,&atx[1182],NULL,0,NULL} ,
+  {401, "Bioseq-set" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1193],0,&atx[1206]} ,
+  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[1194],NULL,0,&atx[1195]} ,
+  {406, "Object-id" ,1,0,0,0,0,0,1,0,NULL,&atx[20],NULL,0,&atx[1196]} ,
+  {0, "coll" ,128,1,0,1,0,0,0,0,NULL,&atx[1196],NULL,0,&atx[1197]} ,
+  {407, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,&atx[17],NULL,0,&atx[1201]} ,
+  {0, "level" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1198]} ,
+  {0, "class" ,128,3,0,0,1,0,0,0,&avnx[560],&atx[42],&avnx[540],0,&atx[1199]} ,
+  {0, "release" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1200]} ,
+  {0, "date" ,128,5,0,1,0,0,0,0,NULL,&atx[1201],NULL,0,&atx[1202]} ,
   {408, "Date" ,1,0,0,0,0,0,1,0,NULL,&atx[0],NULL,0,NULL} ,
-  {0, "descr" ,128,6,0,1,0,0,0,0,NULL,&atx[1140],NULL,0,&atx[1141]} ,
-  {405, "Seq-descr" ,1,0,0,0,0,0,1,0,NULL,&atx[647],NULL,0,&atx[1131]} ,
-  {0, "seq-set" ,128,7,0,0,0,0,0,0,NULL,&atx[66],&atx[1142],0,&atx[1147]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1143],NULL,0,NULL} ,
-  {402, "Seq-entry" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[1144],0,&atx[1145]} ,
-  {0, "seq" ,128,0,0,0,0,0,0,0,NULL,&atx[1145],NULL,0,&atx[1146]} ,
-  {403, "Bioseq" ,1,0,0,0,0,0,1,0,NULL,&atx[643],NULL,0,&atx[1149]} ,
-  {0, "set" ,128,1,0,0,0,0,0,0,NULL,&atx[1129],NULL,0,NULL} ,
-  {0, "annot" ,128,8,0,1,0,0,0,0,NULL,&atx[45],&atx[1148],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1149],NULL,0,NULL} ,
-  {404, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,&atx[1074],NULL,0,&atx[1140]} ,
-  {401, "Seq-code-table" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1151],0,&atx[1162]} ,
-  {0, "code" ,128,0,0,0,0,0,0,0,NULL,&atx[1152],NULL,0,&atx[1153]} ,
-  {404, "Seq-code-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[525],0,NULL} ,
-  {0, "num" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1154]} ,
-  {0, "one-letter" ,128,2,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1155]} ,
-  {0, "start-at" ,128,3,0,0,1,0,0,0,&avnx[536],&atx[6],NULL,0,&atx[1156]} ,
-  {0, "table" ,128,4,0,0,0,0,0,0,NULL,&atx[66],&atx[1157],0,&atx[1160]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[13],&atx[1158],0,NULL} ,
-  {0, "symbol" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1159]} ,
+  {0, "descr" ,128,6,0,1,0,0,0,0,NULL,&atx[1203],NULL,0,&atx[1204]} ,
+  {405, "Seq-descr" ,1,0,0,0,0,0,1,0,NULL,&atx[647],NULL,0,&atx[1194]} ,
+  {0, "seq-set" ,128,7,0,0,0,0,0,0,NULL,&atx[66],&atx[1205],0,&atx[1210]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1206],NULL,0,NULL} ,
+  {402, "Seq-entry" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[1207],0,&atx[1208]} ,
+  {0, "seq" ,128,0,0,0,0,0,0,0,NULL,&atx[1208],NULL,0,&atx[1209]} ,
+  {403, "Bioseq" ,1,0,0,0,0,0,1,0,NULL,&atx[643],NULL,0,&atx[1212]} ,
+  {0, "set" ,128,1,0,0,0,0,0,0,NULL,&atx[1192],NULL,0,NULL} ,
+  {0, "annot" ,128,8,0,1,0,0,0,0,NULL,&atx[45],&atx[1211],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1212],NULL,0,NULL} ,
+  {404, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,&atx[1075],NULL,0,&atx[1203]} ,
+  {401, "Seq-code-table" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1214],0,&atx[1225]} ,
+  {0, "code" ,128,0,0,0,0,0,0,0,NULL,&atx[1215],NULL,0,&atx[1216]} ,
+  {404, "Seq-code-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[561],0,NULL} ,
+  {0, "num" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1217]} ,
+  {0, "one-letter" ,128,2,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1218]} ,
+  {0, "start-at" ,128,3,0,0,1,0,0,0,&avnx[572],&atx[6],NULL,0,&atx[1219]} ,
+  {0, "table" ,128,4,0,0,0,0,0,0,NULL,&atx[66],&atx[1220],0,&atx[1223]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[13],&atx[1221],0,NULL} ,
+  {0, "symbol" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1222]} ,
   {0, "name" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "comps" ,128,5,0,1,0,0,0,0,NULL,&atx[66],&atx[1161],0,NULL} ,
+  {0, "comps" ,128,5,0,1,0,0,0,0,NULL,&atx[66],&atx[1224],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {402, "Seq-map-table" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1163],0,&atx[1169]} ,
-  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1152],NULL,0,&atx[1164]} ,
-  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1152],NULL,0,&atx[1165]} ,
-  {0, "num" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1166]} ,
-  {0, "start-at" ,128,3,0,0,1,0,0,0,&avnx[537],&atx[6],NULL,0,&atx[1167]} ,
-  {0, "table" ,128,4,0,0,0,0,0,0,NULL,&atx[66],&atx[1168],0,NULL} ,
+  {402, "Seq-map-table" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1226],0,&atx[1232]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1215],NULL,0,&atx[1227]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1215],NULL,0,&atx[1228]} ,
+  {0, "num" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1229]} ,
+  {0, "start-at" ,128,3,0,0,1,0,0,0,&avnx[573],&atx[6],NULL,0,&atx[1230]} ,
+  {0, "table" ,128,4,0,0,0,0,0,0,NULL,&atx[66],&atx[1231],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {403, "Seq-code-set" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1170],0,&atx[1152]} ,
-  {0, "codes" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[1171],0,&atx[1172]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1150],NULL,0,NULL} ,
-  {0, "maps" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[1173],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1162],NULL,0,NULL} ,
-  {426, "Genetic-code-table" ,1,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1175],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[912],NULL,0,NULL} ,
-  {401, "Seq-submit" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1177],0,&atx[1180]} ,
-  {0, "sub" ,128,0,0,0,0,0,0,0,NULL,&atx[1178],NULL,0,&atx[1205]} ,
-  {410, "Submit-block" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1179],0,NULL} ,
-  {0, "contact" ,128,0,0,0,0,0,0,0,NULL,&atx[1180],NULL,0,&atx[1196]} ,
-  {402, "Contact-info" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1181],0,&atx[1197]} ,
-  {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1182]} ,
-  {0, "address" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1183],0,&atx[1184]} ,
+  {403, "Seq-code-set" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1233],0,&atx[1215]} ,
+  {0, "codes" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[1234],0,&atx[1235]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1213],NULL,0,NULL} ,
+  {0, "maps" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[1236],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1225],NULL,0,NULL} ,
+  {426, "Genetic-code-table" ,1,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1238],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[913],NULL,0,NULL} ,
+  {401, "Seq-submit" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1240],0,&atx[1243]} ,
+  {0, "sub" ,128,0,0,0,0,0,0,0,NULL,&atx[1241],NULL,0,&atx[1268]} ,
+  {410, "Submit-block" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1242],0,NULL} ,
+  {0, "contact" ,128,0,0,0,0,0,0,0,NULL,&atx[1243],NULL,0,&atx[1259]} ,
+  {402, "Contact-info" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1244],0,&atx[1260]} ,
+  {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1245]} ,
+  {0, "address" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1246],0,&atx[1247]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "phone" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1185]} ,
-  {0, "fax" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1186]} ,
-  {0, "email" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1187]} ,
-  {0, "telex" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1188]} ,
-  {0, "owner-id" ,128,6,0,1,0,0,0,0,NULL,&atx[1189],NULL,0,&atx[1190]} ,
-  {406, "Object-id" ,1,0,0,0,0,0,1,0,NULL,&atx[20],NULL,0,&atx[1211]} ,
-  {0, "password" ,128,7,0,1,0,0,0,0,NULL,&atx[62],NULL,0,&atx[1191]} ,
-  {0, "last-name" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1192]} ,
-  {0, "first-name" ,128,9,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1193]} ,
-  {0, "middle-initial" ,128,10,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1194]} ,
-  {0, "contact" ,128,11,0,1,0,0,0,0,NULL,&atx[1195],NULL,0,NULL} ,
-  {404, "Author" ,1,0,0,0,0,0,1,0,NULL,&atx[96],NULL,0,&atx[1200]} ,
-  {0, "cit" ,128,1,0,0,0,0,0,0,NULL,&atx[1197],NULL,0,&atx[1198]} ,
-  {403, "Cit-sub" ,1,0,0,0,0,0,1,0,NULL,&atx[227],NULL,0,&atx[1195]} ,
-  {0, "hup" ,128,2,0,0,1,0,0,0,&avnx[538],&atx[60],NULL,0,&atx[1199]} ,
-  {0, "reldate" ,128,3,0,1,0,0,0,0,NULL,&atx[1200],NULL,0,&atx[1201]} ,
-  {405, "Date" ,1,0,0,0,0,0,1,0,NULL,&atx[0],NULL,0,&atx[1189]} ,
-  {0, "subtype" ,128,4,0,1,0,0,0,0,NULL,&atx[6],&avnx[539],0,&atx[1202]} ,
-  {0, "tool" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1203]} ,
-  {0, "user-tag" ,128,6,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1204]} ,
+  {0, "phone" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1248]} ,
+  {0, "fax" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1249]} ,
+  {0, "email" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1250]} ,
+  {0, "telex" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1251]} ,
+  {0, "owner-id" ,128,6,0,1,0,0,0,0,NULL,&atx[1252],NULL,0,&atx[1253]} ,
+  {406, "Object-id" ,1,0,0,0,0,0,1,0,NULL,&atx[20],NULL,0,&atx[1274]} ,
+  {0, "password" ,128,7,0,1,0,0,0,0,NULL,&atx[62],NULL,0,&atx[1254]} ,
+  {0, "last-name" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1255]} ,
+  {0, "first-name" ,128,9,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1256]} ,
+  {0, "middle-initial" ,128,10,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1257]} ,
+  {0, "contact" ,128,11,0,1,0,0,0,0,NULL,&atx[1258],NULL,0,NULL} ,
+  {404, "Author" ,1,0,0,0,0,0,1,0,NULL,&atx[96],NULL,0,&atx[1263]} ,
+  {0, "cit" ,128,1,0,0,0,0,0,0,NULL,&atx[1260],NULL,0,&atx[1261]} ,
+  {403, "Cit-sub" ,1,0,0,0,0,0,1,0,NULL,&atx[227],NULL,0,&atx[1258]} ,
+  {0, "hup" ,128,2,0,0,1,0,0,0,&avnx[574],&atx[60],NULL,0,&atx[1262]} ,
+  {0, "reldate" ,128,3,0,1,0,0,0,0,NULL,&atx[1263],NULL,0,&atx[1264]} ,
+  {405, "Date" ,1,0,0,0,0,0,1,0,NULL,&atx[0],NULL,0,&atx[1252]} ,
+  {0, "subtype" ,128,4,0,1,0,0,0,0,NULL,&atx[6],&avnx[575],0,&atx[1265]} ,
+  {0, "tool" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1266]} ,
+  {0, "user-tag" ,128,6,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1267]} ,
   {0, "comment" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "data" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[1206],0,NULL} ,
-  {0, "entrys" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1207],0,&atx[1209]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1208],NULL,0,NULL} ,
-  {409, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[1143],NULL,0,&atx[1178]} ,
-  {0, "annots" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1210],0,&atx[1212]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1211],NULL,0,NULL} ,
-  {407, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,&atx[1074],NULL,0,&atx[1214]} ,
-  {0, "delete" ,128,2,0,0,0,0,0,0,NULL,&atx[45],&atx[1213],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1214],NULL,0,NULL} ,
-  {408, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,&atx[344],NULL,0,&atx[1208]} ,
-  {401, "Cn3d-style-dictionary" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1216],0,&atx[1275]} ,
-  {0, "global-style" ,128,0,0,0,0,0,0,0,NULL,&atx[1217],NULL,0,&atx[1269]} ,
-  {413, "Cn3d-style-settings" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1218],0,&atx[1330]} ,
-  {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1219]} ,
-  {0, "protein-backbone" ,128,1,0,0,0,0,0,0,NULL,&atx[1220],NULL,0,&atx[1234]} ,
-  {410, "Cn3d-backbone-style" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1221],0,&atx[1236]} ,
-  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[1222],NULL,0,&atx[1223]} ,
-  {406, "Cn3d-backbone-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[543],0,&atx[1224]} ,
-  {0, "style" ,128,1,0,0,0,0,0,0,NULL,&atx[1224],NULL,0,&atx[1225]} ,
-  {407, "Cn3d-drawing-style" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[547],0,&atx[1226]} ,
-  {0, "color-scheme" ,128,2,0,0,0,0,0,0,NULL,&atx[1226],NULL,0,&atx[1227]} ,
-  {408, "Cn3d-color-scheme" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[555],0,&atx[1228]} ,
-  {0, "user-color" ,128,3,0,0,0,0,0,0,NULL,&atx[1228],NULL,0,NULL} ,
-  {409, "Cn3d-color" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1229],0,&atx[1220]} ,
-  {0, "scale-factor" ,128,0,0,0,1,0,0,0,&avnx[575],&atx[6],NULL,0,&atx[1230]} ,
-  {0, "red" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1231]} ,
-  {0, "green" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1232]} ,
-  {0, "blue" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1233]} ,
-  {0, "alpha" ,128,4,0,0,1,0,0,0,&avnx[576],&atx[6],NULL,0,NULL} ,
-  {0, "nucleotide-backbone" ,128,2,0,0,0,0,0,0,NULL,&atx[1220],NULL,0,&atx[1235]} ,
-  {0, "protein-sidechains" ,128,3,0,0,0,0,0,0,NULL,&atx[1236],NULL,0,&atx[1241]} ,
-  {411, "Cn3d-general-style" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1237],0,&atx[1261]} ,
-  {0, "is-on" ,128,0,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1238]} ,
-  {0, "style" ,128,1,0,0,0,0,0,0,NULL,&atx[1224],NULL,0,&atx[1239]} ,
-  {0, "color-scheme" ,128,2,0,0,0,0,0,0,NULL,&atx[1226],NULL,0,&atx[1240]} ,
-  {0, "user-color" ,128,3,0,0,0,0,0,0,NULL,&atx[1228],NULL,0,NULL} ,
-  {0, "nucleotide-sidechains" ,128,4,0,0,0,0,0,0,NULL,&atx[1236],NULL,0,&atx[1242]} ,
-  {0, "heterogens" ,128,5,0,0,0,0,0,0,NULL,&atx[1236],NULL,0,&atx[1243]} ,
-  {0, "solvents" ,128,6,0,0,0,0,0,0,NULL,&atx[1236],NULL,0,&atx[1244]} ,
-  {0, "connections" ,128,7,0,0,0,0,0,0,NULL,&atx[1236],NULL,0,&atx[1245]} ,
-  {0, "helix-objects" ,128,8,0,0,0,0,0,0,NULL,&atx[1236],NULL,0,&atx[1246]} ,
-  {0, "strand-objects" ,128,9,0,0,0,0,0,0,NULL,&atx[1236],NULL,0,&atx[1247]} ,
-  {0, "virtual-disulfides-on" ,128,10,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1248]} ,
-  {0, "virtual-disulfide-color" ,128,11,0,0,0,0,0,0,NULL,&atx[1228],NULL,0,&atx[1249]} ,
-  {0, "hydrogens-on" ,128,12,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1250]} ,
-  {0, "background-color" ,128,13,0,0,0,0,0,0,NULL,&atx[1228],NULL,0,&atx[1251]} ,
-  {0, "scale-factor" ,128,14,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1252]} ,
-  {0, "space-fill-proportion" ,128,15,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1253]} ,
-  {0, "ball-radius" ,128,16,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1254]} ,
-  {0, "stick-radius" ,128,17,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1255]} ,
-  {0, "tube-radius" ,128,18,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1256]} ,
-  {0, "tube-worm-radius" ,128,19,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1257]} ,
-  {0, "helix-radius" ,128,20,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1258]} ,
-  {0, "strand-width" ,128,21,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1259]} ,
-  {0, "strand-thickness" ,128,22,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1260]} ,
-  {0, "protein-labels" ,128,23,0,1,0,0,0,0,NULL,&atx[1261],NULL,0,&atx[1267]} ,
-  {412, "Cn3d-backbone-label-style" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1262],0,&atx[1217]} ,
-  {0, "spacing" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1263]} ,
-  {0, "type" ,128,1,0,0,0,0,0,0,NULL,&atx[42],&avnx[577],0,&atx[1264]} ,
-  {0, "number" ,128,2,0,0,0,0,0,0,NULL,&atx[42],&avnx[579],0,&atx[1265]} ,
-  {0, "termini" ,128,3,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1266]} ,
+  {0, "data" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[1269],0,NULL} ,
+  {0, "entrys" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1270],0,&atx[1272]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1271],NULL,0,NULL} ,
+  {409, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[1206],NULL,0,&atx[1241]} ,
+  {0, "annots" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1273],0,&atx[1275]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1274],NULL,0,NULL} ,
+  {407, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,&atx[1075],NULL,0,&atx[1277]} ,
+  {0, "delete" ,128,2,0,0,0,0,0,0,NULL,&atx[45],&atx[1276],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1277],NULL,0,NULL} ,
+  {408, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,&atx[344],NULL,0,&atx[1271]} ,
+  {401, "Cn3d-style-dictionary" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1279],0,&atx[1338]} ,
+  {0, "global-style" ,128,0,0,0,0,0,0,0,NULL,&atx[1280],NULL,0,&atx[1332]} ,
+  {413, "Cn3d-style-settings" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1281],0,&atx[1393]} ,
+  {0, "name" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1282]} ,
+  {0, "protein-backbone" ,128,1,0,0,0,0,0,0,NULL,&atx[1283],NULL,0,&atx[1297]} ,
+  {410, "Cn3d-backbone-style" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1284],0,&atx[1299]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[1285],NULL,0,&atx[1286]} ,
+  {406, "Cn3d-backbone-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[579],0,&atx[1287]} ,
+  {0, "style" ,128,1,0,0,0,0,0,0,NULL,&atx[1287],NULL,0,&atx[1288]} ,
+  {407, "Cn3d-drawing-style" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[583],0,&atx[1289]} ,
+  {0, "color-scheme" ,128,2,0,0,0,0,0,0,NULL,&atx[1289],NULL,0,&atx[1290]} ,
+  {408, "Cn3d-color-scheme" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[591],0,&atx[1291]} ,
+  {0, "user-color" ,128,3,0,0,0,0,0,0,NULL,&atx[1291],NULL,0,NULL} ,
+  {409, "Cn3d-color" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1292],0,&atx[1283]} ,
+  {0, "scale-factor" ,128,0,0,0,1,0,0,0,&avnx[611],&atx[6],NULL,0,&atx[1293]} ,
+  {0, "red" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1294]} ,
+  {0, "green" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1295]} ,
+  {0, "blue" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1296]} ,
+  {0, "alpha" ,128,4,0,0,1,0,0,0,&avnx[612],&atx[6],NULL,0,NULL} ,
+  {0, "nucleotide-backbone" ,128,2,0,0,0,0,0,0,NULL,&atx[1283],NULL,0,&atx[1298]} ,
+  {0, "protein-sidechains" ,128,3,0,0,0,0,0,0,NULL,&atx[1299],NULL,0,&atx[1304]} ,
+  {411, "Cn3d-general-style" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1300],0,&atx[1324]} ,
+  {0, "is-on" ,128,0,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1301]} ,
+  {0, "style" ,128,1,0,0,0,0,0,0,NULL,&atx[1287],NULL,0,&atx[1302]} ,
+  {0, "color-scheme" ,128,2,0,0,0,0,0,0,NULL,&atx[1289],NULL,0,&atx[1303]} ,
+  {0, "user-color" ,128,3,0,0,0,0,0,0,NULL,&atx[1291],NULL,0,NULL} ,
+  {0, "nucleotide-sidechains" ,128,4,0,0,0,0,0,0,NULL,&atx[1299],NULL,0,&atx[1305]} ,
+  {0, "heterogens" ,128,5,0,0,0,0,0,0,NULL,&atx[1299],NULL,0,&atx[1306]} ,
+  {0, "solvents" ,128,6,0,0,0,0,0,0,NULL,&atx[1299],NULL,0,&atx[1307]} ,
+  {0, "connections" ,128,7,0,0,0,0,0,0,NULL,&atx[1299],NULL,0,&atx[1308]} ,
+  {0, "helix-objects" ,128,8,0,0,0,0,0,0,NULL,&atx[1299],NULL,0,&atx[1309]} ,
+  {0, "strand-objects" ,128,9,0,0,0,0,0,0,NULL,&atx[1299],NULL,0,&atx[1310]} ,
+  {0, "virtual-disulfides-on" ,128,10,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1311]} ,
+  {0, "virtual-disulfide-color" ,128,11,0,0,0,0,0,0,NULL,&atx[1291],NULL,0,&atx[1312]} ,
+  {0, "hydrogens-on" ,128,12,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1313]} ,
+  {0, "background-color" ,128,13,0,0,0,0,0,0,NULL,&atx[1291],NULL,0,&atx[1314]} ,
+  {0, "scale-factor" ,128,14,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1315]} ,
+  {0, "space-fill-proportion" ,128,15,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1316]} ,
+  {0, "ball-radius" ,128,16,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1317]} ,
+  {0, "stick-radius" ,128,17,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1318]} ,
+  {0, "tube-radius" ,128,18,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1319]} ,
+  {0, "tube-worm-radius" ,128,19,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1320]} ,
+  {0, "helix-radius" ,128,20,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1321]} ,
+  {0, "strand-width" ,128,21,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1322]} ,
+  {0, "strand-thickness" ,128,22,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1323]} ,
+  {0, "protein-labels" ,128,23,0,1,0,0,0,0,NULL,&atx[1324],NULL,0,&atx[1330]} ,
+  {412, "Cn3d-backbone-label-style" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1325],0,&atx[1280]} ,
+  {0, "spacing" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1326]} ,
+  {0, "type" ,128,1,0,0,0,0,0,0,NULL,&atx[42],&avnx[613],0,&atx[1327]} ,
+  {0, "number" ,128,2,0,0,0,0,0,0,NULL,&atx[42],&avnx[615],0,&atx[1328]} ,
+  {0, "termini" ,128,3,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1329]} ,
   {0, "white" ,128,4,0,0,0,0,0,0,NULL,&atx[60],NULL,0,NULL} ,
-  {0, "nucleotide-labels" ,128,24,0,1,0,0,0,0,NULL,&atx[1261],NULL,0,&atx[1268]} ,
+  {0, "nucleotide-labels" ,128,24,0,1,0,0,0,0,NULL,&atx[1324],NULL,0,&atx[1331]} ,
   {0, "ion-labels" ,128,25,0,1,0,0,0,0,NULL,&atx[60],NULL,0,NULL} ,
-  {0, "style-table" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1270],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1271],NULL,0,NULL} ,
-  {416, "Cn3d-style-table-item" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1272],0,&atx[1294]} ,
-  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[1273],NULL,0,&atx[1274]} ,
-  {415, "Cn3d-style-table-id" ,1,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1271]} ,
-  {0, "style" ,128,1,0,0,0,0,0,0,NULL,&atx[1217],NULL,0,NULL} ,
-  {402, "Cn3d-user-annotations" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1276],0,&atx[1286]} ,
-  {0, "annotations" ,128,0,0,1,0,0,0,0,NULL,&atx[66],&atx[1277],0,&atx[1299]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1278],NULL,0,NULL} ,
-  {420, "Cn3d-user-annotation" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1279],0,&atx[1308]} ,
-  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1280]} ,
-  {0, "description" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1281]} ,
-  {0, "style-id" ,128,2,0,0,0,0,0,0,NULL,&atx[1273],NULL,0,&atx[1282]} ,
-  {0, "residues" ,128,3,0,0,0,0,0,0,NULL,&atx[66],&atx[1283],0,&atx[1298]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1284],NULL,0,NULL} ,
-  {419, "Cn3d-object-location" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1285],0,&atx[1278]} ,
-  {0, "structure-id" ,128,0,0,0,0,0,0,0,NULL,&atx[1286],NULL,0,&atx[1287]} ,
-  {403, "Biostruc-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1291]} ,
-  {0, "residues" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[1288],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1289],NULL,0,NULL} ,
-  {418, "Cn3d-molecule-location" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1290],0,&atx[1284]} ,
-  {0, "molecule-id" ,128,0,0,0,0,0,0,0,NULL,&atx[1291],NULL,0,&atx[1292]} ,
-  {404, "Molecule-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1296]} ,
-  {0, "residues" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1293],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1294],NULL,0,NULL} ,
-  {417, "Cn3d-residue-range" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1295],0,&atx[1289]} ,
-  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1296],NULL,0,&atx[1297]} ,
-  {405, "Residue-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1222]} ,
-  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1296],NULL,0,NULL} ,
+  {0, "style-table" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1333],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1334],NULL,0,NULL} ,
+  {416, "Cn3d-style-table-item" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1335],0,&atx[1357]} ,
+  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[1336],NULL,0,&atx[1337]} ,
+  {415, "Cn3d-style-table-id" ,1,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1334]} ,
+  {0, "style" ,128,1,0,0,0,0,0,0,NULL,&atx[1280],NULL,0,NULL} ,
+  {402, "Cn3d-user-annotations" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1339],0,&atx[1349]} ,
+  {0, "annotations" ,128,0,0,1,0,0,0,0,NULL,&atx[66],&atx[1340],0,&atx[1362]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1341],NULL,0,NULL} ,
+  {420, "Cn3d-user-annotation" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1342],0,&atx[1371]} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1343]} ,
+  {0, "description" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1344]} ,
+  {0, "style-id" ,128,2,0,0,0,0,0,0,NULL,&atx[1336],NULL,0,&atx[1345]} ,
+  {0, "residues" ,128,3,0,0,0,0,0,0,NULL,&atx[66],&atx[1346],0,&atx[1361]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1347],NULL,0,NULL} ,
+  {419, "Cn3d-object-location" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1348],0,&atx[1341]} ,
+  {0, "structure-id" ,128,0,0,0,0,0,0,0,NULL,&atx[1349],NULL,0,&atx[1350]} ,
+  {403, "Biostruc-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1354]} ,
+  {0, "residues" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[1351],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1352],NULL,0,NULL} ,
+  {418, "Cn3d-molecule-location" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1353],0,&atx[1347]} ,
+  {0, "molecule-id" ,128,0,0,0,0,0,0,0,NULL,&atx[1354],NULL,0,&atx[1355]} ,
+  {404, "Molecule-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1359]} ,
+  {0, "residues" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1356],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1357],NULL,0,NULL} ,
+  {417, "Cn3d-residue-range" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1358],0,&atx[1352]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1359],NULL,0,&atx[1360]} ,
+  {405, "Residue-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1285]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1359],NULL,0,NULL} ,
   {0, "is-on" ,128,4,0,0,0,0,0,0,NULL,&atx[60],NULL,0,NULL} ,
-  {0, "view" ,128,1,0,1,0,0,0,0,NULL,&atx[1300],NULL,0,NULL} ,
-  {423, "Cn3d-view-settings" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1301],0,NULL} ,
-  {0, "camera-distance" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1302]} ,
-  {0, "camera-angle-rad" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1303]} ,
-  {0, "camera-look-at-X" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1304]} ,
-  {0, "camera-look-at-Y" ,128,3,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1305]} ,
-  {0, "camera-clip-near" ,128,4,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1306]} ,
-  {0, "camera-clip-far" ,128,5,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1307]} ,
-  {0, "matrix" ,128,6,0,0,0,0,0,0,NULL,&atx[1308],NULL,0,&atx[1325]} ,
-  {421, "Cn3d-GL-matrix" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1309],0,&atx[1326]} ,
-  {0, "m0" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1310]} ,
-  {0, "m1" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1311]} ,
-  {0, "m2" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1312]} ,
-  {0, "m3" ,128,3,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1313]} ,
-  {0, "m4" ,128,4,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1314]} ,
-  {0, "m5" ,128,5,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1315]} ,
-  {0, "m6" ,128,6,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1316]} ,
-  {0, "m7" ,128,7,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1317]} ,
-  {0, "m8" ,128,8,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1318]} ,
-  {0, "m9" ,128,9,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1319]} ,
-  {0, "m10" ,128,10,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1320]} ,
-  {0, "m11" ,128,11,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1321]} ,
-  {0, "m12" ,128,12,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1322]} ,
-  {0, "m13" ,128,13,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1323]} ,
-  {0, "m14" ,128,14,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1324]} ,
+  {0, "view" ,128,1,0,1,0,0,0,0,NULL,&atx[1363],NULL,0,NULL} ,
+  {423, "Cn3d-view-settings" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1364],0,NULL} ,
+  {0, "camera-distance" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1365]} ,
+  {0, "camera-angle-rad" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1366]} ,
+  {0, "camera-look-at-X" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1367]} ,
+  {0, "camera-look-at-Y" ,128,3,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1368]} ,
+  {0, "camera-clip-near" ,128,4,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1369]} ,
+  {0, "camera-clip-far" ,128,5,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1370]} ,
+  {0, "matrix" ,128,6,0,0,0,0,0,0,NULL,&atx[1371],NULL,0,&atx[1388]} ,
+  {421, "Cn3d-GL-matrix" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1372],0,&atx[1389]} ,
+  {0, "m0" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1373]} ,
+  {0, "m1" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1374]} ,
+  {0, "m2" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1375]} ,
+  {0, "m3" ,128,3,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1376]} ,
+  {0, "m4" ,128,4,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1377]} ,
+  {0, "m5" ,128,5,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1378]} ,
+  {0, "m6" ,128,6,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1379]} ,
+  {0, "m7" ,128,7,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1380]} ,
+  {0, "m8" ,128,8,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1381]} ,
+  {0, "m9" ,128,9,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1382]} ,
+  {0, "m10" ,128,10,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1383]} ,
+  {0, "m11" ,128,11,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1384]} ,
+  {0, "m12" ,128,12,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1385]} ,
+  {0, "m13" ,128,13,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1386]} ,
+  {0, "m14" ,128,14,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1387]} ,
   {0, "m15" ,128,15,0,0,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
-  {0, "rotation-center" ,128,7,0,0,0,0,0,0,NULL,&atx[1326],NULL,0,NULL} ,
-  {422, "Cn3d-vector" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1327],0,&atx[1300]} ,
-  {0, "x" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1328]} ,
-  {0, "y" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1329]} ,
+  {0, "rotation-center" ,128,7,0,0,0,0,0,0,NULL,&atx[1389],NULL,0,NULL} ,
+  {422, "Cn3d-vector" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1390],0,&atx[1363]} ,
+  {0, "x" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1391]} ,
+  {0, "y" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1392]} ,
   {0, "z" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
-  {414, "Cn3d-style-settings-set" ,1,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1331],0,&atx[1273]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1217],NULL,0,NULL} ,
-  {401, "Project" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1333],0,&atx[1349]} ,
-  {0, "descr" ,128,0,0,1,0,0,0,0,NULL,&atx[1334],NULL,0,&atx[1348]} ,
-  {411, "Project-descr" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1335],0,&atx[1337]} ,
-  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1336],0,&atx[1338]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1337],NULL,0,NULL} ,
-  {412, "Project-id" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1341]} ,
-  {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1339]} ,
-  {0, "descr" ,128,2,0,1,0,0,0,0,NULL,&atx[45],&atx[1340],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1341],NULL,0,NULL} ,
-  {413, "Projdesc" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1342],0,NULL} ,
-  {0, "pub" ,128,0,0,0,0,0,0,0,NULL,&atx[1343],NULL,0,&atx[1344]} ,
-  {408, "Pubdesc" ,1,0,0,0,0,0,1,0,NULL,&atx[441],NULL,0,&atx[1380]} ,
-  {0, "date" ,128,1,0,0,0,0,0,0,NULL,&atx[1345],NULL,0,&atx[1346]} ,
-  {403, "Date" ,1,0,0,0,0,0,1,0,NULL,&atx[0],NULL,0,&atx[1364]} ,
-  {0, "comment" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1347]} ,
+  {414, "Cn3d-style-settings-set" ,1,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1394],0,&atx[1336]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1280],NULL,0,NULL} ,
+  {401, "Project" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1396],0,&atx[1412]} ,
+  {0, "descr" ,128,0,0,1,0,0,0,0,NULL,&atx[1397],NULL,0,&atx[1411]} ,
+  {411, "Project-descr" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1398],0,&atx[1400]} ,
+  {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1399],0,&atx[1401]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1400],NULL,0,NULL} ,
+  {412, "Project-id" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1404]} ,
+  {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1402]} ,
+  {0, "descr" ,128,2,0,1,0,0,0,0,NULL,&atx[45],&atx[1403],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1404],NULL,0,NULL} ,
+  {413, "Projdesc" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1405],0,NULL} ,
+  {0, "pub" ,128,0,0,0,0,0,0,0,NULL,&atx[1406],NULL,0,&atx[1407]} ,
+  {408, "Pubdesc" ,1,0,0,0,0,0,1,0,NULL,&atx[441],NULL,0,&atx[1443]} ,
+  {0, "date" ,128,1,0,0,0,0,0,0,NULL,&atx[1408],NULL,0,&atx[1409]} ,
+  {403, "Date" ,1,0,0,0,0,0,1,0,NULL,&atx[0],NULL,0,&atx[1427]} ,
+  {0, "comment" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1410]} ,
   {0, "title" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "data" ,128,1,0,0,0,0,0,0,NULL,&atx[1349],NULL,0,NULL} ,
-  {402, "Project-item" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[1350],0,&atx[1345]} ,
-  {0, "pmuid" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1351],0,&atx[1352]} ,
+  {0, "data" ,128,1,0,0,0,0,0,0,NULL,&atx[1412],NULL,0,NULL} ,
+  {402, "Project-item" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[1413],0,&atx[1408]} ,
+  {0, "pmuid" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1414],0,&atx[1415]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "protuid" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1353],0,&atx[1354]} ,
+  {0, "protuid" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1416],0,&atx[1417]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "nucuid" ,128,2,0,0,0,0,0,0,NULL,&atx[45],&atx[1355],0,&atx[1356]} ,
+  {0, "nucuid" ,128,2,0,0,0,0,0,0,NULL,&atx[45],&atx[1418],0,&atx[1419]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "sequid" ,128,3,0,0,0,0,0,0,NULL,&atx[45],&atx[1357],0,&atx[1358]} ,
+  {0, "sequid" ,128,3,0,0,0,0,0,0,NULL,&atx[45],&atx[1420],0,&atx[1421]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "genomeuid" ,128,4,0,0,0,0,0,0,NULL,&atx[45],&atx[1359],0,&atx[1360]} ,
+  {0, "genomeuid" ,128,4,0,0,0,0,0,0,NULL,&atx[45],&atx[1422],0,&atx[1423]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "structuid" ,128,5,0,0,0,0,0,0,NULL,&atx[45],&atx[1361],0,&atx[1362]} ,
+  {0, "structuid" ,128,5,0,0,0,0,0,0,NULL,&atx[45],&atx[1424],0,&atx[1425]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "pmid" ,128,6,0,0,0,0,0,0,NULL,&atx[45],&atx[1363],0,&atx[1365]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1364],NULL,0,NULL} ,
-  {404, "PubMedId" ,1,0,0,0,0,0,1,0,NULL,&atx[170],NULL,0,&atx[1367]} ,
-  {0, "protid" ,128,7,0,0,0,0,0,0,NULL,&atx[45],&atx[1366],0,&atx[1368]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1367],NULL,0,NULL} ,
-  {405, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,&atx[344],NULL,0,&atx[1393]} ,
-  {0, "nucid" ,128,8,0,0,0,0,0,0,NULL,&atx[45],&atx[1369],0,&atx[1370]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1367],NULL,0,NULL} ,
-  {0, "seqid" ,128,9,0,0,0,0,0,0,NULL,&atx[45],&atx[1371],0,&atx[1372]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1367],NULL,0,NULL} ,
-  {0, "genomeid" ,128,10,0,0,0,0,0,0,NULL,&atx[45],&atx[1373],0,&atx[1374]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1367],NULL,0,NULL} ,
-  {0, "structid" ,128,11,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1375]} ,
-  {0, "pment" ,128,12,0,0,0,0,0,0,NULL,&atx[45],&atx[1376],0,&atx[1378]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1377],NULL,0,NULL} ,
-  {410, "Pubmed-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[280],NULL,0,&atx[1334]} ,
-  {0, "protent" ,128,13,0,0,0,0,0,0,NULL,&atx[45],&atx[1379],0,&atx[1381]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1380],NULL,0,NULL} ,
-  {409, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[1143],NULL,0,&atx[1377]} ,
-  {0, "nucent" ,128,14,0,0,0,0,0,0,NULL,&atx[45],&atx[1382],0,&atx[1383]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1380],NULL,0,NULL} ,
-  {0, "seqent" ,128,15,0,0,0,0,0,0,NULL,&atx[45],&atx[1384],0,&atx[1385]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1380],NULL,0,NULL} ,
-  {0, "genomeent" ,128,16,0,0,0,0,0,0,NULL,&atx[45],&atx[1386],0,&atx[1387]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1380],NULL,0,NULL} ,
-  {0, "structent" ,128,17,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1388]} ,
-  {0, "seqannot" ,128,18,0,0,0,0,0,0,NULL,&atx[45],&atx[1389],0,&atx[1391]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1390],NULL,0,NULL} ,
-  {407, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,&atx[1074],NULL,0,&atx[1343]} ,
-  {0, "loc" ,128,19,0,0,0,0,0,0,NULL,&atx[45],&atx[1392],0,&atx[1394]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1393],NULL,0,NULL} ,
-  {406, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,&atx[385],NULL,0,&atx[1390]} ,
-  {0, "proj" ,128,20,0,0,0,0,0,0,NULL,&atx[45],&atx[1395],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1332],NULL,0,NULL} ,
-  {401, "Link-set" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1397],0,NULL} ,
-  {0, "num" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1398]} ,
-  {0, "uids" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1399],0,&atx[1400]} ,
+  {0, "pmid" ,128,6,0,0,0,0,0,0,NULL,&atx[45],&atx[1426],0,&atx[1428]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1427],NULL,0,NULL} ,
+  {404, "PubMedId" ,1,0,0,0,0,0,1,0,NULL,&atx[170],NULL,0,&atx[1430]} ,
+  {0, "protid" ,128,7,0,0,0,0,0,0,NULL,&atx[45],&atx[1429],0,&atx[1431]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1430],NULL,0,NULL} ,
+  {405, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,&atx[344],NULL,0,&atx[1456]} ,
+  {0, "nucid" ,128,8,0,0,0,0,0,0,NULL,&atx[45],&atx[1432],0,&atx[1433]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1430],NULL,0,NULL} ,
+  {0, "seqid" ,128,9,0,0,0,0,0,0,NULL,&atx[45],&atx[1434],0,&atx[1435]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1430],NULL,0,NULL} ,
+  {0, "genomeid" ,128,10,0,0,0,0,0,0,NULL,&atx[45],&atx[1436],0,&atx[1437]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1430],NULL,0,NULL} ,
+  {0, "structid" ,128,11,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1438]} ,
+  {0, "pment" ,128,12,0,0,0,0,0,0,NULL,&atx[45],&atx[1439],0,&atx[1441]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1440],NULL,0,NULL} ,
+  {410, "Pubmed-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[280],NULL,0,&atx[1397]} ,
+  {0, "protent" ,128,13,0,0,0,0,0,0,NULL,&atx[45],&atx[1442],0,&atx[1444]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1443],NULL,0,NULL} ,
+  {409, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[1206],NULL,0,&atx[1440]} ,
+  {0, "nucent" ,128,14,0,0,0,0,0,0,NULL,&atx[45],&atx[1445],0,&atx[1446]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1443],NULL,0,NULL} ,
+  {0, "seqent" ,128,15,0,0,0,0,0,0,NULL,&atx[45],&atx[1447],0,&atx[1448]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1443],NULL,0,NULL} ,
+  {0, "genomeent" ,128,16,0,0,0,0,0,0,NULL,&atx[45],&atx[1449],0,&atx[1450]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1443],NULL,0,NULL} ,
+  {0, "structent" ,128,17,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1451]} ,
+  {0, "seqannot" ,128,18,0,0,0,0,0,0,NULL,&atx[45],&atx[1452],0,&atx[1454]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1453],NULL,0,NULL} ,
+  {407, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,&atx[1075],NULL,0,&atx[1406]} ,
+  {0, "loc" ,128,19,0,0,0,0,0,0,NULL,&atx[45],&atx[1455],0,&atx[1457]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1456],NULL,0,NULL} ,
+  {406, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,&atx[385],NULL,0,&atx[1453]} ,
+  {0, "proj" ,128,20,0,0,0,0,0,0,NULL,&atx[45],&atx[1458],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1395],NULL,0,NULL} ,
+  {401, "Link-set" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1460],0,NULL} ,
+  {0, "num" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1461]} ,
+  {0, "uids" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1462],0,&atx[1463]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "weights" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1401],0,NULL} ,
+  {0, "weights" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1464],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {401, "FeatDef" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1403],0,&atx[1411]} ,
-  {0, "typelabel" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1404]} ,
-  {0, "menulabel" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1405]} ,
-  {0, "featdef-key" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1406]} ,
-  {0, "seqfeat-key" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1407]} ,
-  {0, "entrygroup" ,128,4,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1408]} ,
-  {0, "displaygroup" ,128,5,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1409]} ,
-  {0, "molgroup" ,128,6,0,0,0,0,0,0,NULL,&atx[1410],NULL,0,NULL} ,
-  {405, "FeatMolType" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[582],0,&atx[1418]} ,
-  {402, "FeatDefSet" ,1,0,0,0,0,1,0,0,NULL,&atx[66],&atx[1412],0,&atx[1413]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1402],NULL,0,NULL} ,
-  {403, "FeatDispGroup" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1414],0,&atx[1416]} ,
-  {0, "groupkey" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1415]} ,
+  {401, "FeatDef" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1466],0,&atx[1474]} ,
+  {0, "typelabel" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1467]} ,
+  {0, "menulabel" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1468]} ,
+  {0, "featdef-key" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1469]} ,
+  {0, "seqfeat-key" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1470]} ,
+  {0, "entrygroup" ,128,4,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1471]} ,
+  {0, "displaygroup" ,128,5,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1472]} ,
+  {0, "molgroup" ,128,6,0,0,0,0,0,0,NULL,&atx[1473],NULL,0,NULL} ,
+  {405, "FeatMolType" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[618],0,&atx[1481]} ,
+  {402, "FeatDefSet" ,1,0,0,0,0,1,0,0,NULL,&atx[66],&atx[1475],0,&atx[1476]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1465],NULL,0,NULL} ,
+  {403, "FeatDispGroup" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1477],0,&atx[1479]} ,
+  {0, "groupkey" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1478]} ,
   {0, "groupname" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {404, "FeatDispGroupSet" ,1,0,0,0,0,1,0,0,NULL,&atx[66],&atx[1417],0,&atx[1410]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1413],NULL,0,NULL} ,
-  {406, "FeatDefGroupSet" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1419],0,NULL} ,
-  {0, "groups" ,128,0,0,0,0,0,0,0,NULL,&atx[1416],NULL,0,&atx[1420]} ,
-  {0, "defs" ,128,1,0,0,0,0,0,0,NULL,&atx[1411],NULL,0,NULL} ,
-  {401, "Ncbi-mime-asn1" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[1422],0,&atx[1433]} ,
-  {0, "entrez" ,128,0,0,0,0,0,0,0,NULL,&atx[1423],NULL,0,&atx[1439]} ,
-  {410, "Entrez-general" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1424],0,&atx[1440]} ,
-  {0, "title" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1425]} ,
-  {0, "data" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[1426],0,&atx[1436]} ,
-  {0, "ml" ,128,0,0,0,0,0,0,0,NULL,&atx[1427],NULL,0,&atx[1428]} ,
-  {407, "Medline-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[233],NULL,0,&atx[1451]} ,
-  {0, "prot" ,128,1,0,0,0,0,0,0,NULL,&atx[1429],NULL,0,&atx[1430]} ,
-  {405, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[1143],NULL,0,&atx[1449]} ,
-  {0, "nuc" ,128,2,0,0,0,0,0,0,NULL,&atx[1429],NULL,0,&atx[1431]} ,
-  {0, "genome" ,128,3,0,0,0,0,0,0,NULL,&atx[1429],NULL,0,&atx[1432]} ,
-  {0, "structure" ,128,4,0,0,0,0,0,0,NULL,&atx[1433],NULL,0,&atx[1434]} ,
-  {402, "Biostruc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1435]} ,
-  {0, "strucAnnot" ,128,5,0,0,0,0,0,0,NULL,&atx[1435],NULL,0,NULL} ,
-  {403, "Biostruc-annot-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1493]} ,
-  {0, "style" ,128,2,0,0,0,0,0,0,NULL,&atx[1437],NULL,0,&atx[1438]} ,
-  {417, "Entrez-style" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[585],0,NULL} ,
+  {404, "FeatDispGroupSet" ,1,0,0,0,0,1,0,0,NULL,&atx[66],&atx[1480],0,&atx[1473]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1476],NULL,0,NULL} ,
+  {406, "FeatDefGroupSet" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1482],0,NULL} ,
+  {0, "groups" ,128,0,0,0,0,0,0,0,NULL,&atx[1479],NULL,0,&atx[1483]} ,
+  {0, "defs" ,128,1,0,0,0,0,0,0,NULL,&atx[1474],NULL,0,NULL} ,
+  {401, "Ncbi-mime-asn1" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[1485],0,&atx[1496]} ,
+  {0, "entrez" ,128,0,0,0,0,0,0,0,NULL,&atx[1486],NULL,0,&atx[1502]} ,
+  {410, "Entrez-general" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1487],0,&atx[1503]} ,
+  {0, "title" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1488]} ,
+  {0, "data" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[1489],0,&atx[1499]} ,
+  {0, "ml" ,128,0,0,0,0,0,0,0,NULL,&atx[1490],NULL,0,&atx[1491]} ,
+  {407, "Medline-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[233],NULL,0,&atx[1514]} ,
+  {0, "prot" ,128,1,0,0,0,0,0,0,NULL,&atx[1492],NULL,0,&atx[1493]} ,
+  {405, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[1206],NULL,0,&atx[1512]} ,
+  {0, "nuc" ,128,2,0,0,0,0,0,0,NULL,&atx[1492],NULL,0,&atx[1494]} ,
+  {0, "genome" ,128,3,0,0,0,0,0,0,NULL,&atx[1492],NULL,0,&atx[1495]} ,
+  {0, "structure" ,128,4,0,0,0,0,0,0,NULL,&atx[1496],NULL,0,&atx[1497]} ,
+  {402, "Biostruc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1498]} ,
+  {0, "strucAnnot" ,128,5,0,0,0,0,0,0,NULL,&atx[1498],NULL,0,NULL} ,
+  {403, "Biostruc-annot-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1556]} ,
+  {0, "style" ,128,2,0,0,0,0,0,0,NULL,&atx[1500],NULL,0,&atx[1501]} ,
+  {417, "Entrez-style" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[621],0,NULL} ,
   {0, "location" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "alignstruc" ,128,1,0,0,0,0,0,0,NULL,&atx[1440],NULL,0,&atx[1454]} ,
-  {411, "Biostruc-align" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1441],0,&atx[1455]} ,
-  {0, "master" ,128,0,0,0,0,0,0,0,NULL,&atx[1433],NULL,0,&atx[1442]} ,
-  {0, "slaves" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1443],0,&atx[1444]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1433],NULL,0,NULL} ,
-  {0, "alignments" ,128,2,0,0,0,0,0,0,NULL,&atx[1435],NULL,0,&atx[1445]} ,
-  {0, "sequences" ,128,3,0,0,0,0,0,0,NULL,&atx[45],&atx[1446],0,&atx[1447]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1429],NULL,0,NULL} ,
-  {0, "seqalign" ,128,4,0,0,0,0,0,0,NULL,&atx[45],&atx[1448],0,&atx[1450]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1449],NULL,0,NULL} ,
-  {406, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,&atx[1074],NULL,0,&atx[1427]} ,
-  {0, "style-dictionary" ,128,5,0,1,0,0,0,0,NULL,&atx[1451],NULL,0,&atx[1452]} ,
-  {408, "Cn3d-style-dictionary" ,1,0,0,0,0,0,1,0,NULL,&atx[1215],NULL,0,&atx[1453]} ,
-  {0, "user-annotations" ,128,6,0,1,0,0,0,0,NULL,&atx[1453],NULL,0,NULL} ,
-  {409, "Cn3d-user-annotations" ,1,0,0,0,0,0,1,0,NULL,&atx[1275],NULL,0,&atx[1423]} ,
-  {0, "alignseq" ,128,2,0,0,0,0,0,0,NULL,&atx[1455],NULL,0,&atx[1462]} ,
-  {412, "Biostruc-align-seq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1456],0,&atx[1463]} ,
-  {0, "sequences" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1457],0,&atx[1458]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1429],NULL,0,NULL} ,
-  {0, "seqalign" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1459],0,&atx[1460]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1449],NULL,0,NULL} ,
-  {0, "style-dictionary" ,128,2,0,1,0,0,0,0,NULL,&atx[1451],NULL,0,&atx[1461]} ,
-  {0, "user-annotations" ,128,3,0,1,0,0,0,0,NULL,&atx[1453],NULL,0,NULL} ,
-  {0, "strucseq" ,128,3,0,0,0,0,0,0,NULL,&atx[1463],NULL,0,&atx[1469]} ,
-  {413, "Biostruc-seq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1464],0,&atx[1470]} ,
-  {0, "structure" ,128,0,0,0,0,0,0,0,NULL,&atx[1433],NULL,0,&atx[1465]} ,
-  {0, "sequences" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1466],0,&atx[1467]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1429],NULL,0,NULL} ,
-  {0, "style-dictionary" ,128,2,0,1,0,0,0,0,NULL,&atx[1451],NULL,0,&atx[1468]} ,
-  {0, "user-annotations" ,128,3,0,1,0,0,0,0,NULL,&atx[1453],NULL,0,NULL} ,
-  {0, "strucseqs" ,128,4,0,0,0,0,0,0,NULL,&atx[1470],NULL,0,&atx[1478]} ,
-  {414, "Biostruc-seqs" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1471],0,&atx[1479]} ,
-  {0, "structure" ,128,0,0,0,0,0,0,0,NULL,&atx[1433],NULL,0,&atx[1472]} ,
-  {0, "sequences" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1473],0,&atx[1474]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1429],NULL,0,NULL} ,
-  {0, "seqalign" ,128,2,0,0,0,0,0,0,NULL,&atx[45],&atx[1475],0,&atx[1476]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1449],NULL,0,NULL} ,
-  {0, "style-dictionary" ,128,3,0,1,0,0,0,0,NULL,&atx[1451],NULL,0,&atx[1477]} ,
-  {0, "user-annotations" ,128,4,0,1,0,0,0,0,NULL,&atx[1453],NULL,0,NULL} ,
-  {0, "general" ,128,5,0,0,0,0,0,0,NULL,&atx[1479],NULL,0,NULL} ,
-  {415, "Biostruc-seqs-aligns-cdd" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1480],0,&atx[1482]} ,
-  {0, "seq-align-data" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1481],0,&atx[1494]} ,
-  {0, "bundle" ,128,0,0,0,0,0,0,0,NULL,&atx[1482],NULL,0,&atx[1492]} ,
-  {416, "Bundle-seqs-aligns" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1483],0,&atx[1437]} ,
-  {0, "sequences" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[1484],0,&atx[1485]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1429],NULL,0,NULL} ,
-  {0, "seqaligns" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[1486],0,&atx[1487]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1449],NULL,0,NULL} ,
-  {0, "strucaligns" ,128,2,0,1,0,0,0,0,NULL,&atx[1435],NULL,0,&atx[1488]} ,
-  {0, "imports" ,128,3,0,1,0,0,0,0,NULL,&atx[45],&atx[1489],0,&atx[1490]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1449],NULL,0,NULL} ,
-  {0, "style-dictionary" ,128,4,0,1,0,0,0,0,NULL,&atx[1451],NULL,0,&atx[1491]} ,
-  {0, "user-annotations" ,128,5,0,1,0,0,0,0,NULL,&atx[1453],NULL,0,NULL} ,
-  {0, "cdd" ,128,1,0,0,0,0,0,0,NULL,&atx[1493],NULL,0,NULL} ,
-  {404, "Cdd" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1429]} ,
-  {0, "structures" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[1495],0,&atx[1496]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1433],NULL,0,NULL} ,
-  {0, "structure-type" ,128,2,0,1,0,0,0,0,NULL,&atx[42],&avnx[598],0,NULL} ,
-  {401, "PrintTemplate" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1498],0,&atx[1531]} ,
-  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[1499],NULL,0,&atx[1500]} ,
-  {403, "TemplateName" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1502]} ,
-  {0, "labelfrom" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1501]} ,
-  {0, "format" ,128,2,0,0,0,0,0,0,NULL,&atx[1502],NULL,0,NULL} ,
-  {404, "PrintFormat" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1503],0,&atx[1508]} ,
-  {0, "asn1" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1504]} ,
-  {0, "label" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1505]} ,
-  {0, "prefix" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1506]} ,
-  {0, "suffix" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1507]} ,
-  {0, "form" ,128,4,0,0,0,0,0,0,NULL,&atx[1508],NULL,0,NULL} ,
-  {405, "PrintForm" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1509],0,&atx[1510]} ,
-  {0, "block" ,128,0,0,0,0,0,0,0,NULL,&atx[1510],NULL,0,&atx[1514]} ,
-  {406, "PrintFormBlock" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1511],0,&atx[1515]} ,
-  {0, "separator" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1512]} ,
-  {0, "components" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[1513],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1502],NULL,0,NULL} ,
-  {0, "boolean" ,128,1,0,0,0,0,0,0,NULL,&atx[1515],NULL,0,&atx[1518]} ,
-  {407, "PrintFormBoolean" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1516],0,&atx[1519]} ,
-  {0, "true" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1517]} ,
+  {0, "alignstruc" ,128,1,0,0,0,0,0,0,NULL,&atx[1503],NULL,0,&atx[1517]} ,
+  {411, "Biostruc-align" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1504],0,&atx[1518]} ,
+  {0, "master" ,128,0,0,0,0,0,0,0,NULL,&atx[1496],NULL,0,&atx[1505]} ,
+  {0, "slaves" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1506],0,&atx[1507]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1496],NULL,0,NULL} ,
+  {0, "alignments" ,128,2,0,0,0,0,0,0,NULL,&atx[1498],NULL,0,&atx[1508]} ,
+  {0, "sequences" ,128,3,0,0,0,0,0,0,NULL,&atx[45],&atx[1509],0,&atx[1510]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1492],NULL,0,NULL} ,
+  {0, "seqalign" ,128,4,0,0,0,0,0,0,NULL,&atx[45],&atx[1511],0,&atx[1513]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1512],NULL,0,NULL} ,
+  {406, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,&atx[1075],NULL,0,&atx[1490]} ,
+  {0, "style-dictionary" ,128,5,0,1,0,0,0,0,NULL,&atx[1514],NULL,0,&atx[1515]} ,
+  {408, "Cn3d-style-dictionary" ,1,0,0,0,0,0,1,0,NULL,&atx[1278],NULL,0,&atx[1516]} ,
+  {0, "user-annotations" ,128,6,0,1,0,0,0,0,NULL,&atx[1516],NULL,0,NULL} ,
+  {409, "Cn3d-user-annotations" ,1,0,0,0,0,0,1,0,NULL,&atx[1338],NULL,0,&atx[1486]} ,
+  {0, "alignseq" ,128,2,0,0,0,0,0,0,NULL,&atx[1518],NULL,0,&atx[1525]} ,
+  {412, "Biostruc-align-seq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1519],0,&atx[1526]} ,
+  {0, "sequences" ,128,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1520],0,&atx[1521]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1492],NULL,0,NULL} ,
+  {0, "seqalign" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1522],0,&atx[1523]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1512],NULL,0,NULL} ,
+  {0, "style-dictionary" ,128,2,0,1,0,0,0,0,NULL,&atx[1514],NULL,0,&atx[1524]} ,
+  {0, "user-annotations" ,128,3,0,1,0,0,0,0,NULL,&atx[1516],NULL,0,NULL} ,
+  {0, "strucseq" ,128,3,0,0,0,0,0,0,NULL,&atx[1526],NULL,0,&atx[1532]} ,
+  {413, "Biostruc-seq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1527],0,&atx[1533]} ,
+  {0, "structure" ,128,0,0,0,0,0,0,0,NULL,&atx[1496],NULL,0,&atx[1528]} ,
+  {0, "sequences" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1529],0,&atx[1530]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1492],NULL,0,NULL} ,
+  {0, "style-dictionary" ,128,2,0,1,0,0,0,0,NULL,&atx[1514],NULL,0,&atx[1531]} ,
+  {0, "user-annotations" ,128,3,0,1,0,0,0,0,NULL,&atx[1516],NULL,0,NULL} ,
+  {0, "strucseqs" ,128,4,0,0,0,0,0,0,NULL,&atx[1533],NULL,0,&atx[1541]} ,
+  {414, "Biostruc-seqs" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1534],0,&atx[1542]} ,
+  {0, "structure" ,128,0,0,0,0,0,0,0,NULL,&atx[1496],NULL,0,&atx[1535]} ,
+  {0, "sequences" ,128,1,0,0,0,0,0,0,NULL,&atx[45],&atx[1536],0,&atx[1537]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1492],NULL,0,NULL} ,
+  {0, "seqalign" ,128,2,0,0,0,0,0,0,NULL,&atx[45],&atx[1538],0,&atx[1539]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1512],NULL,0,NULL} ,
+  {0, "style-dictionary" ,128,3,0,1,0,0,0,0,NULL,&atx[1514],NULL,0,&atx[1540]} ,
+  {0, "user-annotations" ,128,4,0,1,0,0,0,0,NULL,&atx[1516],NULL,0,NULL} ,
+  {0, "general" ,128,5,0,0,0,0,0,0,NULL,&atx[1542],NULL,0,NULL} ,
+  {415, "Biostruc-seqs-aligns-cdd" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1543],0,&atx[1545]} ,
+  {0, "seq-align-data" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1544],0,&atx[1557]} ,
+  {0, "bundle" ,128,0,0,0,0,0,0,0,NULL,&atx[1545],NULL,0,&atx[1555]} ,
+  {416, "Bundle-seqs-aligns" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1546],0,&atx[1500]} ,
+  {0, "sequences" ,128,0,0,1,0,0,0,0,NULL,&atx[45],&atx[1547],0,&atx[1548]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1492],NULL,0,NULL} ,
+  {0, "seqaligns" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[1549],0,&atx[1550]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1512],NULL,0,NULL} ,
+  {0, "strucaligns" ,128,2,0,1,0,0,0,0,NULL,&atx[1498],NULL,0,&atx[1551]} ,
+  {0, "imports" ,128,3,0,1,0,0,0,0,NULL,&atx[45],&atx[1552],0,&atx[1553]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1512],NULL,0,NULL} ,
+  {0, "style-dictionary" ,128,4,0,1,0,0,0,0,NULL,&atx[1514],NULL,0,&atx[1554]} ,
+  {0, "user-annotations" ,128,5,0,1,0,0,0,0,NULL,&atx[1516],NULL,0,NULL} ,
+  {0, "cdd" ,128,1,0,0,0,0,0,0,NULL,&atx[1556],NULL,0,NULL} ,
+  {404, "Cdd" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[1492]} ,
+  {0, "structures" ,128,1,0,1,0,0,0,0,NULL,&atx[45],&atx[1558],0,&atx[1559]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1496],NULL,0,NULL} ,
+  {0, "structure-type" ,128,2,0,1,0,0,0,0,NULL,&atx[42],&avnx[634],0,NULL} ,
+  {401, "PrintTemplate" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1561],0,&atx[1594]} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[1562],NULL,0,&atx[1563]} ,
+  {403, "TemplateName" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1565]} ,
+  {0, "labelfrom" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1564]} ,
+  {0, "format" ,128,2,0,0,0,0,0,0,NULL,&atx[1565],NULL,0,NULL} ,
+  {404, "PrintFormat" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1566],0,&atx[1571]} ,
+  {0, "asn1" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1567]} ,
+  {0, "label" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1568]} ,
+  {0, "prefix" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1569]} ,
+  {0, "suffix" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1570]} ,
+  {0, "form" ,128,4,0,0,0,0,0,0,NULL,&atx[1571],NULL,0,NULL} ,
+  {405, "PrintForm" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1572],0,&atx[1573]} ,
+  {0, "block" ,128,0,0,0,0,0,0,0,NULL,&atx[1573],NULL,0,&atx[1577]} ,
+  {406, "PrintFormBlock" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1574],0,&atx[1578]} ,
+  {0, "separator" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1575]} ,
+  {0, "components" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[1576],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1565],NULL,0,NULL} ,
+  {0, "boolean" ,128,1,0,0,0,0,0,0,NULL,&atx[1578],NULL,0,&atx[1581]} ,
+  {407, "PrintFormBoolean" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1579],0,&atx[1582]} ,
+  {0, "true" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1580]} ,
   {0, "false" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "enum" ,128,2,0,0,0,0,0,0,NULL,&atx[1519],NULL,0,&atx[1522]} ,
-  {408, "PrintFormEnum" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1520],0,&atx[1523]} ,
-  {0, "values" ,128,0,0,1,0,0,0,0,NULL,&atx[66],&atx[1521],0,NULL} ,
+  {0, "enum" ,128,2,0,0,0,0,0,0,NULL,&atx[1582],NULL,0,&atx[1585]} ,
+  {408, "PrintFormEnum" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1583],0,&atx[1586]} ,
+  {0, "values" ,128,0,0,1,0,0,0,0,NULL,&atx[66],&atx[1584],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "text" ,128,3,0,0,0,0,0,0,NULL,&atx[1523],NULL,0,&atx[1525]} ,
-  {409, "PrintFormText" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1524],0,&atx[1527]} ,
+  {0, "text" ,128,3,0,0,0,0,0,0,NULL,&atx[1586],NULL,0,&atx[1588]} ,
+  {409, "PrintFormText" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1587],0,&atx[1590]} ,
   {0, "textfunc" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "use-template" ,128,4,0,0,0,0,0,0,NULL,&atx[1499],NULL,0,&atx[1526]} ,
-  {0, "user" ,128,5,0,0,0,0,0,0,NULL,&atx[1527],NULL,0,&atx[1530]} ,
-  {410, "UserFormat" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1528],0,NULL} ,
-  {0, "printfunc" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1529]} ,
+  {0, "use-template" ,128,4,0,0,0,0,0,0,NULL,&atx[1562],NULL,0,&atx[1589]} ,
+  {0, "user" ,128,5,0,0,0,0,0,0,NULL,&atx[1590],NULL,0,&atx[1593]} ,
+  {410, "UserFormat" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1591],0,NULL} ,
+  {0, "printfunc" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1592]} ,
   {0, "defaultfunc" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {0, "null" ,128,6,0,0,0,0,0,0,NULL,&atx[387],NULL,0,NULL} ,
-  {402, "PrintTemplateSet" ,1,0,0,0,0,1,0,0,NULL,&atx[66],&atx[1532],0,&atx[1499]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1497],NULL,0,NULL} ,
-  {401, "GBSeq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1534],0,&atx[1550]} ,
-  {0, "locus" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1535]} ,
-  {0, "length" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1536]} ,
-  {0, "strandedness" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1537]} ,
-  {0, "moltype" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1538]} ,
-  {0, "topology" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1539]} ,
-  {0, "division" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1540]} ,
-  {0, "update-date" ,128,6,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1541]} ,
-  {0, "create-date" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1542]} ,
-  {0, "update-release" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1543]} ,
-  {0, "create-release" ,128,9,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1544]} ,
-  {0, "definition" ,128,10,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1545]} ,
-  {0, "primary-accession" ,128,11,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1546]} ,
-  {0, "entry-version" ,128,12,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1547]} ,
-  {0, "accession-version" ,128,13,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1548]} ,
-  {0, "other-seqids" ,128,14,0,1,0,0,0,0,NULL,&atx[66],&atx[1549],0,&atx[1551]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1550],NULL,0,NULL} ,
-  {402, "GBSeqid" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1553]} ,
-  {0, "secondary-accessions" ,128,15,0,1,0,0,0,0,NULL,&atx[66],&atx[1552],0,&atx[1554]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1553],NULL,0,NULL} ,
-  {403, "GBSecondary-accn" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1557]} ,
-  {0, "project" ,128,16,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1555]} ,
-  {0, "keywords" ,128,17,0,1,0,0,0,0,NULL,&atx[66],&atx[1556],0,&atx[1558]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1557],NULL,0,NULL} ,
-  {404, "GBKeyword" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1564]} ,
-  {0, "segment" ,128,18,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1559]} ,
-  {0, "source" ,128,19,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1560]} ,
-  {0, "organism" ,128,20,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1561]} ,
-  {0, "taxonomy" ,128,21,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1562]} ,
-  {0, "references" ,128,22,0,1,0,0,0,0,NULL,&atx[66],&atx[1563],0,&atx[1580]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1564],NULL,0,NULL} ,
-  {405, "GBReference" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1565],0,&atx[1586]} ,
-  {0, "reference" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1566]} ,
-  {0, "position" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1567]} ,
-  {0, "authors" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1568],0,&atx[1570]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1569],NULL,0,NULL} ,
-  {407, "GBAuthor" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1575]} ,
-  {0, "consortium" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1571]} ,
-  {0, "title" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1572]} ,
-  {0, "journal" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1573]} ,
-  {0, "xref" ,128,6,0,1,0,0,0,0,NULL,&atx[45],&atx[1574],0,&atx[1578]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1575],NULL,0,NULL} ,
-  {408, "GBXref" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1576],0,&atx[1591]} ,
-  {0, "dbname" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1577]} ,
+  {402, "PrintTemplateSet" ,1,0,0,0,0,1,0,0,NULL,&atx[66],&atx[1595],0,&atx[1562]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1560],NULL,0,NULL} ,
+  {401, "GBSeq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1597],0,&atx[1613]} ,
+  {0, "locus" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1598]} ,
+  {0, "length" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1599]} ,
+  {0, "strandedness" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1600]} ,
+  {0, "moltype" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1601]} ,
+  {0, "topology" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1602]} ,
+  {0, "division" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1603]} ,
+  {0, "update-date" ,128,6,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1604]} ,
+  {0, "create-date" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1605]} ,
+  {0, "update-release" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1606]} ,
+  {0, "create-release" ,128,9,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1607]} ,
+  {0, "definition" ,128,10,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1608]} ,
+  {0, "primary-accession" ,128,11,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1609]} ,
+  {0, "entry-version" ,128,12,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1610]} ,
+  {0, "accession-version" ,128,13,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1611]} ,
+  {0, "other-seqids" ,128,14,0,1,0,0,0,0,NULL,&atx[66],&atx[1612],0,&atx[1614]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1613],NULL,0,NULL} ,
+  {402, "GBSeqid" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1616]} ,
+  {0, "secondary-accessions" ,128,15,0,1,0,0,0,0,NULL,&atx[66],&atx[1615],0,&atx[1617]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1616],NULL,0,NULL} ,
+  {403, "GBSecondary-accn" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1620]} ,
+  {0, "project" ,128,16,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1618]} ,
+  {0, "keywords" ,128,17,0,1,0,0,0,0,NULL,&atx[66],&atx[1619],0,&atx[1621]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1620],NULL,0,NULL} ,
+  {404, "GBKeyword" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1627]} ,
+  {0, "segment" ,128,18,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1622]} ,
+  {0, "source" ,128,19,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1623]} ,
+  {0, "organism" ,128,20,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1624]} ,
+  {0, "taxonomy" ,128,21,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1625]} ,
+  {0, "references" ,128,22,0,1,0,0,0,0,NULL,&atx[66],&atx[1626],0,&atx[1643]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1627],NULL,0,NULL} ,
+  {405, "GBReference" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1628],0,&atx[1649]} ,
+  {0, "reference" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1629]} ,
+  {0, "position" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1630]} ,
+  {0, "authors" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1631],0,&atx[1633]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1632],NULL,0,NULL} ,
+  {407, "GBAuthor" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1638]} ,
+  {0, "consortium" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1634]} ,
+  {0, "title" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1635]} ,
+  {0, "journal" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1636]} ,
+  {0, "xref" ,128,6,0,1,0,0,0,0,NULL,&atx[45],&atx[1637],0,&atx[1641]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1638],NULL,0,NULL} ,
+  {408, "GBXref" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1639],0,&atx[1654]} ,
+  {0, "dbname" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1640]} ,
   {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "pubmed" ,128,7,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1579]} ,
+  {0, "pubmed" ,128,7,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1642]} ,
   {0, "remark" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "comment" ,128,23,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1581]} ,
-  {0, "primary" ,128,24,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1582]} ,
-  {0, "source-db" ,128,25,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1583]} ,
-  {0, "database-reference" ,128,26,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1584]} ,
-  {0, "feature-table" ,128,27,0,1,0,0,0,0,NULL,&atx[66],&atx[1585],0,&atx[1606]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1586],NULL,0,NULL} ,
-  {406, "GBFeature" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1587],0,&atx[1569]} ,
-  {0, "key" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1588]} ,
-  {0, "location" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1589]} ,
-  {0, "intervals" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1590],0,&atx[1598]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1591],NULL,0,NULL} ,
-  {409, "GBInterval" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1592],0,&atx[1603]} ,
-  {0, "from" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1593]} ,
-  {0, "to" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1594]} ,
-  {0, "point" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1595]} ,
-  {0, "iscomp" ,128,3,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1596]} ,
-  {0, "interbp" ,128,4,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1597]} ,
+  {0, "comment" ,128,23,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1644]} ,
+  {0, "primary" ,128,24,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1645]} ,
+  {0, "source-db" ,128,25,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1646]} ,
+  {0, "database-reference" ,128,26,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1647]} ,
+  {0, "feature-table" ,128,27,0,1,0,0,0,0,NULL,&atx[66],&atx[1648],0,&atx[1669]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1649],NULL,0,NULL} ,
+  {406, "GBFeature" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1650],0,&atx[1632]} ,
+  {0, "key" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1651]} ,
+  {0, "location" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1652]} ,
+  {0, "intervals" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1653],0,&atx[1661]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1654],NULL,0,NULL} ,
+  {409, "GBInterval" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1655],0,&atx[1666]} ,
+  {0, "from" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1656]} ,
+  {0, "to" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1657]} ,
+  {0, "point" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1658]} ,
+  {0, "iscomp" ,128,3,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1659]} ,
+  {0, "interbp" ,128,4,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1660]} ,
   {0, "accession" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "operator" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1599]} ,
-  {0, "partial5" ,128,4,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1600]} ,
-  {0, "partial3" ,128,5,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1601]} ,
-  {0, "quals" ,128,6,0,1,0,0,0,0,NULL,&atx[66],&atx[1602],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1603],NULL,0,NULL} ,
-  {410, "GBQualifier" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1604],0,&atx[1608]} ,
-  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1605]} ,
+  {0, "operator" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1662]} ,
+  {0, "partial5" ,128,4,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1663]} ,
+  {0, "partial3" ,128,5,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1664]} ,
+  {0, "quals" ,128,6,0,1,0,0,0,0,NULL,&atx[66],&atx[1665],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1666],NULL,0,NULL} ,
+  {410, "GBQualifier" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1667],0,&atx[1671]} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1668]} ,
   {0, "value" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "sequence" ,128,28,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1607]} ,
+  {0, "sequence" ,128,28,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1670]} ,
   {0, "contig" ,128,29,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {411, "GBSet" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1609],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1533],NULL,0,NULL} ,
-  {401, "INSDSeq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1611],0,&atx[1627]} ,
-  {0, "locus" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1612]} ,
-  {0, "length" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1613]} ,
-  {0, "strandedness" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1614]} ,
-  {0, "moltype" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1615]} ,
-  {0, "topology" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1616]} ,
-  {0, "division" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1617]} ,
-  {0, "update-date" ,128,6,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1618]} ,
-  {0, "create-date" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1619]} ,
-  {0, "update-release" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1620]} ,
-  {0, "create-release" ,128,9,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1621]} ,
-  {0, "definition" ,128,10,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1622]} ,
-  {0, "primary-accession" ,128,11,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1623]} ,
-  {0, "entry-version" ,128,12,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1624]} ,
-  {0, "accession-version" ,128,13,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1625]} ,
-  {0, "other-seqids" ,128,14,0,1,0,0,0,0,NULL,&atx[66],&atx[1626],0,&atx[1628]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1627],NULL,0,NULL} ,
-  {402, "INSDSeqid" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1630]} ,
-  {0, "secondary-accessions" ,128,15,0,1,0,0,0,0,NULL,&atx[66],&atx[1629],0,&atx[1631]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1630],NULL,0,NULL} ,
-  {403, "INSDSecondary-accn" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1634]} ,
-  {0, "project" ,128,16,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1632]} ,
-  {0, "keywords" ,128,17,0,1,0,0,0,0,NULL,&atx[66],&atx[1633],0,&atx[1635]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1634],NULL,0,NULL} ,
-  {404, "INSDKeyword" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1641]} ,
-  {0, "segment" ,128,18,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1636]} ,
-  {0, "source" ,128,19,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1637]} ,
-  {0, "organism" ,128,20,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1638]} ,
-  {0, "taxonomy" ,128,21,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1639]} ,
-  {0, "references" ,128,22,0,1,0,0,0,0,NULL,&atx[66],&atx[1640],0,&atx[1657]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1641],NULL,0,NULL} ,
-  {405, "INSDReference" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1642],0,&atx[1663]} ,
-  {0, "reference" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1643]} ,
-  {0, "position" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1644]} ,
-  {0, "authors" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1645],0,&atx[1647]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1646],NULL,0,NULL} ,
-  {407, "INSDAuthor" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1652]} ,
-  {0, "consortium" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1648]} ,
-  {0, "title" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1649]} ,
-  {0, "journal" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1650]} ,
-  {0, "xref" ,128,6,0,1,0,0,0,0,NULL,&atx[45],&atx[1651],0,&atx[1655]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1652],NULL,0,NULL} ,
-  {408, "INSDXref" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1653],0,&atx[1668]} ,
-  {0, "dbname" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1654]} ,
+  {411, "GBSet" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1672],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1596],NULL,0,NULL} ,
+  {401, "INSDSeq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1674],0,&atx[1690]} ,
+  {0, "locus" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1675]} ,
+  {0, "length" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1676]} ,
+  {0, "strandedness" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1677]} ,
+  {0, "moltype" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1678]} ,
+  {0, "topology" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1679]} ,
+  {0, "division" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1680]} ,
+  {0, "update-date" ,128,6,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1681]} ,
+  {0, "create-date" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1682]} ,
+  {0, "update-release" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1683]} ,
+  {0, "create-release" ,128,9,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1684]} ,
+  {0, "definition" ,128,10,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1685]} ,
+  {0, "primary-accession" ,128,11,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1686]} ,
+  {0, "entry-version" ,128,12,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1687]} ,
+  {0, "accession-version" ,128,13,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1688]} ,
+  {0, "other-seqids" ,128,14,0,1,0,0,0,0,NULL,&atx[66],&atx[1689],0,&atx[1691]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1690],NULL,0,NULL} ,
+  {402, "INSDSeqid" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1693]} ,
+  {0, "secondary-accessions" ,128,15,0,1,0,0,0,0,NULL,&atx[66],&atx[1692],0,&atx[1694]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1693],NULL,0,NULL} ,
+  {403, "INSDSecondary-accn" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1697]} ,
+  {0, "project" ,128,16,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1695]} ,
+  {0, "keywords" ,128,17,0,1,0,0,0,0,NULL,&atx[66],&atx[1696],0,&atx[1698]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1697],NULL,0,NULL} ,
+  {404, "INSDKeyword" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1704]} ,
+  {0, "segment" ,128,18,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1699]} ,
+  {0, "source" ,128,19,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1700]} ,
+  {0, "organism" ,128,20,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1701]} ,
+  {0, "taxonomy" ,128,21,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1702]} ,
+  {0, "references" ,128,22,0,1,0,0,0,0,NULL,&atx[66],&atx[1703],0,&atx[1720]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1704],NULL,0,NULL} ,
+  {405, "INSDReference" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1705],0,&atx[1726]} ,
+  {0, "reference" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1706]} ,
+  {0, "position" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1707]} ,
+  {0, "authors" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1708],0,&atx[1710]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1709],NULL,0,NULL} ,
+  {407, "INSDAuthor" ,1,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1715]} ,
+  {0, "consortium" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1711]} ,
+  {0, "title" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1712]} ,
+  {0, "journal" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1713]} ,
+  {0, "xref" ,128,6,0,1,0,0,0,0,NULL,&atx[45],&atx[1714],0,&atx[1718]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1715],NULL,0,NULL} ,
+  {408, "INSDXref" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1716],0,&atx[1731]} ,
+  {0, "dbname" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1717]} ,
   {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "pubmed" ,128,7,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1656]} ,
+  {0, "pubmed" ,128,7,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1719]} ,
   {0, "remark" ,128,8,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "comment" ,128,23,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1658]} ,
-  {0, "primary" ,128,24,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1659]} ,
-  {0, "source-db" ,128,25,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1660]} ,
-  {0, "database-reference" ,128,26,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1661]} ,
-  {0, "feature-table" ,128,27,0,1,0,0,0,0,NULL,&atx[66],&atx[1662],0,&atx[1683]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1663],NULL,0,NULL} ,
-  {406, "INSDFeature" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1664],0,&atx[1646]} ,
-  {0, "key" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1665]} ,
-  {0, "location" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1666]} ,
-  {0, "intervals" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1667],0,&atx[1675]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1668],NULL,0,NULL} ,
-  {409, "INSDInterval" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1669],0,&atx[1680]} ,
-  {0, "from" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1670]} ,
-  {0, "to" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1671]} ,
-  {0, "point" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1672]} ,
-  {0, "iscomp" ,128,3,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1673]} ,
-  {0, "interbp" ,128,4,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1674]} ,
+  {0, "comment" ,128,23,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1721]} ,
+  {0, "primary" ,128,24,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1722]} ,
+  {0, "source-db" ,128,25,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1723]} ,
+  {0, "database-reference" ,128,26,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1724]} ,
+  {0, "feature-table" ,128,27,0,1,0,0,0,0,NULL,&atx[66],&atx[1725],0,&atx[1746]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1726],NULL,0,NULL} ,
+  {406, "INSDFeature" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1727],0,&atx[1709]} ,
+  {0, "key" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1728]} ,
+  {0, "location" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1729]} ,
+  {0, "intervals" ,128,2,0,1,0,0,0,0,NULL,&atx[66],&atx[1730],0,&atx[1738]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1731],NULL,0,NULL} ,
+  {409, "INSDInterval" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1732],0,&atx[1743]} ,
+  {0, "from" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1733]} ,
+  {0, "to" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1734]} ,
+  {0, "point" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1735]} ,
+  {0, "iscomp" ,128,3,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1736]} ,
+  {0, "interbp" ,128,4,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1737]} ,
   {0, "accession" ,128,5,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "operator" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1676]} ,
-  {0, "partial5" ,128,4,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1677]} ,
-  {0, "partial3" ,128,5,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1678]} ,
-  {0, "quals" ,128,6,0,1,0,0,0,0,NULL,&atx[66],&atx[1679],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1680],NULL,0,NULL} ,
-  {410, "INSDQualifier" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1681],0,&atx[1685]} ,
-  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1682]} ,
+  {0, "operator" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1739]} ,
+  {0, "partial5" ,128,4,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1740]} ,
+  {0, "partial3" ,128,5,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1741]} ,
+  {0, "quals" ,128,6,0,1,0,0,0,0,NULL,&atx[66],&atx[1742],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1743],NULL,0,NULL} ,
+  {410, "INSDQualifier" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1744],0,&atx[1748]} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1745]} ,
   {0, "value" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "sequence" ,128,28,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1684]} ,
+  {0, "sequence" ,128,28,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1747]} ,
   {0, "contig" ,128,29,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {411, "INSDSet" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1686],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1610],NULL,0,NULL} ,
-  {401, "TSeq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1688],0,&atx[1698]} ,
-  {0, "seqtype" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[601],0,&atx[1689]} ,
-  {0, "gi" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1690]} ,
-  {0, "accver" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1691]} ,
-  {0, "sid" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1692]} ,
-  {0, "local" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1693]} ,
-  {0, "taxid" ,128,5,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1694]} ,
-  {0, "orgname" ,128,6,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1695]} ,
-  {0, "defline" ,128,7,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1696]} ,
-  {0, "length" ,128,8,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1697]} ,
+  {411, "INSDSet" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1749],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1673],NULL,0,NULL} ,
+  {401, "TSeq" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1751],0,&atx[1761]} ,
+  {0, "seqtype" ,128,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[637],0,&atx[1752]} ,
+  {0, "gi" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1753]} ,
+  {0, "accver" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1754]} ,
+  {0, "sid" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1755]} ,
+  {0, "local" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1756]} ,
+  {0, "taxid" ,128,5,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1757]} ,
+  {0, "orgname" ,128,6,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1758]} ,
+  {0, "defline" ,128,7,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1759]} ,
+  {0, "length" ,128,8,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1760]} ,
   {0, "sequence" ,128,9,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {402, "TSeqSet" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1699],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1687],NULL,0,NULL} ,
-  {401, "Pssm" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1701],0,&atx[1712]} ,
-  {0, "isProtein" ,128,0,0,0,1,0,0,0,&avnx[603],&atx[60],NULL,0,&atx[1702]} ,
-  {0, "identifier" ,128,1,0,1,0,0,0,0,NULL,&atx[1703],NULL,0,&atx[1704]} ,
-  {406, "Object-id" ,1,0,0,0,0,0,1,0,NULL,&atx[20],NULL,0,&atx[1710]} ,
-  {0, "numRows" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1705]} ,
-  {0, "numColumns" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1706]} ,
-  {0, "rowLabels" ,128,4,0,1,0,0,0,0,NULL,&atx[66],&atx[1707],0,&atx[1708]} ,
+  {402, "TSeqSet" ,1,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1762],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1750],NULL,0,NULL} ,
+  {401, "Pssm" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1764],0,&atx[1775]} ,
+  {0, "isProtein" ,128,0,0,0,1,0,0,0,&avnx[639],&atx[60],NULL,0,&atx[1765]} ,
+  {0, "identifier" ,128,1,0,1,0,0,0,0,NULL,&atx[1766],NULL,0,&atx[1767]} ,
+  {406, "Object-id" ,1,0,0,0,0,0,1,0,NULL,&atx[20],NULL,0,&atx[1773]} ,
+  {0, "numRows" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1768]} ,
+  {0, "numColumns" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1769]} ,
+  {0, "rowLabels" ,128,4,0,1,0,0,0,0,NULL,&atx[66],&atx[1770],0,&atx[1771]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "byRow" ,128,5,0,0,1,0,0,0,&avnx[604],&atx[60],NULL,0,&atx[1709]} ,
-  {0, "query" ,128,6,0,1,0,0,0,0,NULL,&atx[1710],NULL,0,&atx[1711]} ,
-  {407, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[1143],NULL,0,&atx[1746]} ,
-  {0, "intermediateData" ,128,7,0,1,0,0,0,0,NULL,&atx[1712],NULL,0,&atx[1719]} ,
-  {402, "PssmIntermediateData" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1713],0,&atx[1720]} ,
-  {0, "resFreqsPerPos" ,128,0,0,1,0,0,0,0,NULL,&atx[66],&atx[1714],0,&atx[1715]} ,
+  {0, "byRow" ,128,5,0,0,1,0,0,0,&avnx[640],&atx[60],NULL,0,&atx[1772]} ,
+  {0, "query" ,128,6,0,1,0,0,0,0,NULL,&atx[1773],NULL,0,&atx[1774]} ,
+  {407, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,&atx[1206],NULL,0,&atx[1809]} ,
+  {0, "intermediateData" ,128,7,0,1,0,0,0,0,NULL,&atx[1775],NULL,0,&atx[1782]} ,
+  {402, "PssmIntermediateData" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1776],0,&atx[1783]} ,
+  {0, "resFreqsPerPos" ,128,0,0,1,0,0,0,0,NULL,&atx[66],&atx[1777],0,&atx[1778]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "weightedResFreqsPerPos" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1716],0,&atx[1717]} ,
+  {0, "weightedResFreqsPerPos" ,128,1,0,1,0,0,0,0,NULL,&atx[66],&atx[1779],0,&atx[1780]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
-  {0, "freqRatios" ,128,2,0,0,0,0,0,0,NULL,&atx[66],&atx[1718],0,NULL} ,
+  {0, "freqRatios" ,128,2,0,0,0,0,0,0,NULL,&atx[66],&atx[1781],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
-  {0, "finalData" ,128,8,0,1,0,0,0,0,NULL,&atx[1720],NULL,0,NULL} ,
-  {403, "PssmFinalData" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1721],0,&atx[1727]} ,
-  {0, "scores" ,128,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1722],0,&atx[1723]} ,
+  {0, "finalData" ,128,8,0,1,0,0,0,0,NULL,&atx[1783],NULL,0,NULL} ,
+  {403, "PssmFinalData" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1784],0,&atx[1790]} ,
+  {0, "scores" ,128,0,0,0,0,0,0,0,NULL,&atx[66],&atx[1785],0,&atx[1786]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "lambda" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1724]} ,
-  {0, "kappa" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1725]} ,
-  {0, "h" ,128,3,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1726]} ,
-  {0, "scalingFactor" ,128,4,0,0,1,0,0,0,&avnx[605],&atx[6],NULL,0,NULL} ,
-  {404, "PssmParameters" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1728],0,&atx[1755]} ,
-  {0, "pseudocount" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1729]} ,
-  {0, "rpsdbparams" ,128,1,0,1,0,0,0,0,NULL,&atx[1730],NULL,0,&atx[1734]} ,
-  {412, "FormatRpsDbParameters" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1731],0,NULL} ,
-  {0, "matrixName" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1732]} ,
-  {0, "gapOpen" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1733]} ,
+  {0, "lambda" ,128,1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1787]} ,
+  {0, "kappa" ,128,2,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1788]} ,
+  {0, "h" ,128,3,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[1789]} ,
+  {0, "scalingFactor" ,128,4,0,0,1,0,0,0,&avnx[641],&atx[6],NULL,0,NULL} ,
+  {404, "PssmParameters" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1791],0,&atx[1818]} ,
+  {0, "pseudocount" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1792]} ,
+  {0, "rpsdbparams" ,128,1,0,1,0,0,0,0,NULL,&atx[1793],NULL,0,&atx[1797]} ,
+  {412, "FormatRpsDbParameters" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1794],0,NULL} ,
+  {0, "matrixName" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1795]} ,
+  {0, "gapOpen" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1796]} ,
   {0, "gapExtend" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "constraints" ,128,2,0,1,0,0,0,0,NULL,&atx[1735],NULL,0,NULL} ,
-  {411, "CoreDef" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1736],0,&atx[1730]} ,
-  {0, "nblocks" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1737]} ,
-  {0, "blocks" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[1738],0,&atx[1750]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1739],NULL,0,NULL} ,
-  {409, "CoreBlock" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1740],0,&atx[1752]} ,
-  {0, "start" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1741]} ,
-  {0, "stop" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1742]} ,
-  {0, "minstart" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1743]} ,
-  {0, "maxstop" ,128,3,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1744]} ,
-  {0, "property" ,128,4,0,1,0,0,0,0,NULL,&atx[66],&atx[1745],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1746],NULL,0,NULL} ,
-  {408, "BlockProperty" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1747],0,&atx[1739]} ,
-  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[6],&avnx[606],0,&atx[1748]} ,
-  {0, "intvalue" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1749]} ,
+  {0, "constraints" ,128,2,0,1,0,0,0,0,NULL,&atx[1798],NULL,0,NULL} ,
+  {411, "CoreDef" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1799],0,&atx[1793]} ,
+  {0, "nblocks" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1800]} ,
+  {0, "blocks" ,128,1,0,0,0,0,0,0,NULL,&atx[66],&atx[1801],0,&atx[1813]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1802],NULL,0,NULL} ,
+  {409, "CoreBlock" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1803],0,&atx[1815]} ,
+  {0, "start" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1804]} ,
+  {0, "stop" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1805]} ,
+  {0, "minstart" ,128,2,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1806]} ,
+  {0, "maxstop" ,128,3,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1807]} ,
+  {0, "property" ,128,4,0,1,0,0,0,0,NULL,&atx[66],&atx[1808],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1809],NULL,0,NULL} ,
+  {408, "BlockProperty" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1810],0,&atx[1802]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[6],&avnx[642],0,&atx[1811]} ,
+  {0, "intvalue" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[1812]} ,
   {0, "textvalue" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "loops" ,128,2,0,0,0,0,0,0,NULL,&atx[66],&atx[1751],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1752],NULL,0,NULL} ,
-  {410, "LoopConstraint" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1753],0,&atx[1735]} ,
-  {0, "minlength" ,128,0,0,0,1,0,0,0,&avnx[615],&atx[6],NULL,0,&atx[1754]} ,
-  {0, "maxlength" ,128,1,0,0,1,0,0,0,&avnx[616],&atx[6],NULL,0,NULL} ,
-  {405, "PssmWithParameters" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1756],0,&atx[1703]} ,
-  {0, "pssm" ,128,0,0,0,0,0,0,0,NULL,&atx[1700],NULL,0,&atx[1757]} ,
-  {0, "params" ,128,1,0,1,0,0,0,0,NULL,&atx[1727],NULL,0,NULL} };
-
-static AsnModule ampx[37] = {
+  {0, "loops" ,128,2,0,0,0,0,0,0,NULL,&atx[66],&atx[1814],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1815],NULL,0,NULL} ,
+  {410, "LoopConstraint" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1816],0,&atx[1798]} ,
+  {0, "minlength" ,128,0,0,0,1,0,0,0,&avnx[651],&atx[6],NULL,0,&atx[1817]} ,
+  {0, "maxlength" ,128,1,0,0,1,0,0,0,&avnx[652],&atx[6],NULL,0,NULL} ,
+  {405, "PssmWithParameters" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1819],0,&atx[1766]} ,
+  {0, "pssm" ,128,0,0,0,0,0,0,0,NULL,&atx[1763],NULL,0,&atx[1820]} ,
+  {0, "params" ,128,1,0,1,0,0,0,0,NULL,&atx[1790],NULL,0,NULL} ,
+  {401, "AECR-action" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1822],0,&atx[1991]} ,
+  {0, "action" ,128,0,0,0,0,0,0,0,NULL,&atx[1823],NULL,0,&atx[1949]} ,
+  {463, "Action-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1824],0,&atx[2022]} ,
+  {0, "apply" ,128,0,0,0,0,0,0,0,NULL,&atx[1825],NULL,0,&atx[1871]} ,
+  {456, "Apply-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1826],0,&atx[1872]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[1827],NULL,0,&atx[1868]} ,
+  {453, "Field-type" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1828],0,&atx[1883]} ,
+  {0, "source-qual" ,128,0,0,0,0,0,0,0,NULL,&atx[1829],NULL,0,&atx[1836]} ,
+  {423, "Source-qual-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1830],0,&atx[1853]} ,
+  {0, "textqual" ,128,0,0,0,0,0,0,0,NULL,&atx[1831],NULL,0,&atx[1832]} ,
+  {419, "Source-qual" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[653],0,&atx[1885]} ,
+  {0, "location" ,128,1,0,0,0,0,0,0,NULL,&atx[1833],NULL,0,&atx[1834]} ,
+  {421, "Source-location" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[734],0,&atx[1835]} ,
+  {0, "origin" ,128,2,0,0,0,0,0,0,NULL,&atx[1835],NULL,0,NULL} ,
+  {422, "Source-origin" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[757],0,&atx[1829]} ,
+  {0, "feature-field" ,128,1,0,0,0,0,0,0,NULL,&atx[1837],NULL,0,&atx[1852]} ,
+  {416, "Feature-field" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1838],0,&atx[2017]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[1839],NULL,0,&atx[1840]} ,
+  {410, "Feature-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[764],0,&atx[1843]} ,
+  {0, "field" ,128,1,0,0,0,0,0,0,NULL,&atx[1841],NULL,0,NULL} ,
+  {415, "Feat-qual-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1842],0,&atx[1837]} ,
+  {0, "legal-qual" ,128,0,0,0,0,0,0,0,NULL,&atx[1843],NULL,0,&atx[1844]} ,
+  {411, "Feat-qual-legal" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[860],0,&atx[2058]} ,
+  {0, "illegal-qual" ,128,1,0,0,0,0,0,0,NULL,&atx[1845],NULL,0,NULL} ,
+  {405, "String-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1846],0,&atx[1957]} ,
+  {0, "match-text" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1847]} ,
+  {0, "match-location" ,128,1,0,0,1,0,0,0,&avnx[921],&atx[1848],NULL,0,&atx[1849]} ,
+  {404, "String-location" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[922],0,&atx[1845]} ,
+  {0, "case-sensitive" ,128,2,0,0,1,0,0,0,&avnx[927],&atx[60],NULL,0,&atx[1850]} ,
+  {0, "whole-word" ,128,3,0,0,1,0,0,0,&avnx[928],&atx[60],NULL,0,&atx[1851]} ,
+  {0, "not-present" ,128,4,0,0,1,0,0,0,&avnx[929],&atx[60],NULL,0,NULL} ,
+  {0, "cds-gene-prot" ,128,2,0,0,0,0,0,0,NULL,&atx[1853],NULL,0,&atx[1854]} ,
+  {424, "CDSGeneProt-field" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[930],0,&atx[1894]} ,
+  {0, "molinfo-field" ,128,3,0,0,0,0,0,0,NULL,&atx[1855],NULL,0,NULL} ,
+  {432, "Molinfo-field" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1856],0,&atx[1900]} ,
+  {0, "molecule" ,128,0,0,0,0,0,0,0,NULL,&atx[1857],NULL,0,&atx[1858]} ,
+  {426, "Molecule-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[951],0,&atx[1859]} ,
+  {0, "technique" ,128,1,0,0,0,0,0,0,NULL,&atx[1859],NULL,0,&atx[1860]} ,
+  {427, "Technique-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[966],0,&atx[1861]} ,
+  {0, "completedness" ,128,2,0,0,0,0,0,0,NULL,&atx[1861],NULL,0,&atx[1862]} ,
+  {428, "Completedness-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[991],0,&atx[1863]} ,
+  {0, "mol-class" ,128,3,0,0,0,0,0,0,NULL,&atx[1863],NULL,0,&atx[1864]} ,
+  {429, "Molecule-class-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1000],0,&atx[1865]} ,
+  {0, "topology" ,128,4,0,0,0,0,0,0,NULL,&atx[1865],NULL,0,&atx[1866]} ,
+  {430, "Topology-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1006],0,&atx[1867]} ,
+  {0, "strand" ,128,5,0,0,0,0,0,0,NULL,&atx[1867],NULL,0,NULL} ,
+  {431, "Strand-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1011],0,&atx[1855]} ,
+  {0, "value" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1869]} ,
+  {0, "existing-text" ,128,2,0,0,0,0,0,0,NULL,&atx[1870],NULL,0,NULL} ,
+  {455, "ExistingTextOption" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1017],0,&atx[1825]} ,
+  {0, "edit" ,128,1,0,0,0,0,0,0,NULL,&atx[1872],NULL,0,&atx[1880]} ,
+  {457, "Edit-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1873],0,&atx[1881]} ,
+  {0, "edit" ,128,0,0,0,0,0,0,0,NULL,&atx[1874],NULL,0,&atx[1879]} ,
+  {452, "Field-edit" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1875],0,&atx[1827]} ,
+  {0, "find-txt" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1876]} ,
+  {0, "repl-txt" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1877]} ,
+  {0, "location" ,128,2,0,0,1,0,0,0,&avnx[1027],&atx[1878],NULL,0,NULL} ,
+  {451, "Field-edit-location" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1028],0,&atx[1874]} ,
+  {0, "field" ,128,1,0,0,0,0,0,0,NULL,&atx[1827],NULL,0,NULL} ,
+  {0, "convert" ,128,2,0,0,0,0,0,0,NULL,&atx[1881],NULL,0,&atx[1924]} ,
+  {458, "Convert-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1882],0,&atx[1925]} ,
+  {0, "fields" ,128,0,0,0,0,0,0,0,NULL,&atx[1883],NULL,0,&atx[1923]} ,
+  {454, "Field-pair-type" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1884],0,&atx[1870]} ,
+  {0, "source-qual" ,128,0,0,0,0,0,0,0,NULL,&atx[1885],NULL,0,&atx[1888]} ,
+  {420, "Source-qual-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1886],0,&atx[1833]} ,
+  {0, "field-from" ,128,0,0,0,0,0,0,0,NULL,&atx[1831],NULL,0,&atx[1887]} ,
+  {0, "field-to" ,128,1,0,0,0,0,0,0,NULL,&atx[1831],NULL,0,NULL} ,
+  {0, "feature-field" ,128,1,0,0,0,0,0,0,NULL,&atx[1889],NULL,0,&atx[1893]} ,
+  {418, "Feature-field-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1890],0,&atx[1831]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[1839],NULL,0,&atx[1891]} ,
+  {0, "field-from" ,128,1,0,0,0,0,0,0,NULL,&atx[1841],NULL,0,&atx[1892]} ,
+  {0, "field-to" ,128,2,0,0,0,0,0,0,NULL,&atx[1841],NULL,0,NULL} ,
+  {0, "cds-gene-prot" ,128,2,0,0,0,0,0,0,NULL,&atx[1894],NULL,0,&atx[1897]} ,
+  {425, "CDSGeneProt-field-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1895],0,&atx[1857]} ,
+  {0, "field-from" ,128,0,0,0,0,0,0,0,NULL,&atx[1853],NULL,0,&atx[1896]} ,
+  {0, "field-to" ,128,1,0,0,0,0,0,0,NULL,&atx[1853],NULL,0,NULL} ,
+  {0, "molinfo-field" ,128,3,0,0,0,0,0,0,NULL,&atx[1898],NULL,0,NULL} ,
+  {439, "Molinfo-field-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1899],0,&atx[1961]} ,
+  {0, "molecule" ,128,0,0,0,0,0,0,0,NULL,&atx[1900],NULL,0,&atx[1903]} ,
+  {433, "Molinfo-molecule-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1901],0,&atx[1904]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1857],NULL,0,&atx[1902]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1857],NULL,0,NULL} ,
+  {0, "technique" ,128,1,0,0,0,0,0,0,NULL,&atx[1904],NULL,0,&atx[1907]} ,
+  {434, "Molinfo-technique-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1905],0,&atx[1908]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1859],NULL,0,&atx[1906]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1859],NULL,0,NULL} ,
+  {0, "completedness" ,128,2,0,0,0,0,0,0,NULL,&atx[1908],NULL,0,&atx[1911]} ,
+  {435, "Molinfo-completedness-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1909],0,&atx[1912]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1861],NULL,0,&atx[1910]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1861],NULL,0,NULL} ,
+  {0, "mol-class" ,128,3,0,0,0,0,0,0,NULL,&atx[1912],NULL,0,&atx[1915]} ,
+  {436, "Molinfo-mol-class-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1913],0,&atx[1916]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1863],NULL,0,&atx[1914]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1863],NULL,0,NULL} ,
+  {0, "topology" ,128,4,0,0,0,0,0,0,NULL,&atx[1916],NULL,0,&atx[1919]} ,
+  {437, "Molinfo-topology-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1917],0,&atx[1920]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1865],NULL,0,&atx[1918]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1865],NULL,0,NULL} ,
+  {0, "strand" ,128,5,0,0,0,0,0,0,NULL,&atx[1920],NULL,0,NULL} ,
+  {438, "Molinfo-strand-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1921],0,&atx[1898]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[1867],NULL,0,&atx[1922]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[1867],NULL,0,NULL} ,
+  {0, "existing-text" ,128,1,0,0,0,0,0,0,NULL,&atx[1870],NULL,0,NULL} ,
+  {0, "copy" ,128,3,0,0,0,0,0,0,NULL,&atx[1925],NULL,0,&atx[1928]} ,
+  {459, "Copy-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1926],0,&atx[1929]} ,
+  {0, "fields" ,128,0,0,0,0,0,0,0,NULL,&atx[1883],NULL,0,&atx[1927]} ,
+  {0, "existing-text" ,128,1,0,0,0,0,0,0,NULL,&atx[1870],NULL,0,NULL} ,
+  {0, "swap" ,128,4,0,0,0,0,0,0,NULL,&atx[1929],NULL,0,&atx[1932]} ,
+  {460, "Swap-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1930],0,&atx[1936]} ,
+  {0, "fields" ,128,0,0,0,0,0,0,0,NULL,&atx[1883],NULL,0,&atx[1931]} ,
+  {0, "field-to" ,128,1,0,0,0,0,0,0,NULL,&atx[1827],NULL,0,NULL} ,
+  {0, "remove" ,128,5,0,0,0,0,0,0,NULL,&atx[1933],NULL,0,&atx[1935]} ,
+  {462, "Remove-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1934],0,&atx[1823]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[1827],NULL,0,NULL} ,
+  {0, "parse" ,128,6,0,0,0,0,0,0,NULL,&atx[1936],NULL,0,NULL} ,
+  {461, "AECRParse-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1937],0,&atx[1933]} ,
+  {0, "portion" ,128,0,0,0,0,0,0,0,NULL,&atx[1938],NULL,0,&atx[1946]} ,
+  {450, "Text-portion" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1939],0,&atx[1878]} ,
+  {0, "left-text" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1940]} ,
+  {0, "include-left" ,128,1,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1941]} ,
+  {0, "right-text" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[1942]} ,
+  {0, "include-right" ,128,3,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1943]} ,
+  {0, "inside" ,128,4,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[1944]} ,
+  {0, "case-sensitive" ,128,5,0,0,1,0,0,0,&avnx[1031],&atx[60],NULL,0,&atx[1945]} ,
+  {0, "whole-word" ,128,6,0,0,1,0,0,0,&avnx[1032],&atx[60],NULL,0,NULL} ,
+  {0, "fields" ,128,1,0,0,0,0,0,0,NULL,&atx[1883],NULL,0,&atx[1947]} ,
+  {0, "remove-from-parsed" ,128,2,0,0,1,0,0,0,&avnx[1033],&atx[60],NULL,0,&atx[1948]} ,
+  {0, "existing-text" ,128,3,0,0,0,0,0,0,NULL,&atx[1870],NULL,0,NULL} ,
+  {0, "constraint" ,128,1,0,1,0,0,0,0,NULL,&atx[1950],NULL,0,NULL} ,
+  {449, "Constraint-choice-set" ,1,0,0,0,0,0,0,0,NULL,&atx[45],&atx[1951],0,&atx[1938]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[1952],NULL,0,NULL} ,
+  {448, "Constraint-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1953],0,&atx[1950]} ,
+  {0, "string" ,128,0,0,0,0,0,0,0,NULL,&atx[1845],NULL,0,&atx[1954]} ,
+  {0, "location" ,128,1,0,0,0,0,0,0,NULL,&atx[1955],NULL,0,&atx[1960]} ,
+  {408, "Location-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1956],0,&atx[1966]} ,
+  {0, "strand" ,128,0,0,0,1,0,0,0,&avnx[1034],&atx[1957],NULL,0,&atx[1958]} ,
+  {406, "Strand-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1035],0,&atx[1959]} ,
+  {0, "seq-type" ,128,1,0,0,1,0,0,0,&avnx[1038],&atx[1959],NULL,0,NULL} ,
+  {407, "Seqtype-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1039],0,&atx[1955]} ,
+  {0, "source" ,128,2,0,0,0,0,0,0,NULL,&atx[1961],NULL,0,&atx[1967]} ,
+  {440, "Source-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1962],0,&atx[1977]} ,
+  {0, "field1" ,128,0,0,1,0,0,0,0,NULL,&atx[1829],NULL,0,&atx[1963]} ,
+  {0, "field2" ,128,1,0,1,0,0,0,0,NULL,&atx[1829],NULL,0,&atx[1964]} ,
+  {0, "constraint" ,128,2,0,1,0,0,0,0,NULL,&atx[1845],NULL,0,&atx[1965]} ,
+  {0, "type-constraint" ,128,3,0,1,0,0,0,0,NULL,&atx[1966],NULL,0,NULL} ,
+  {409, "Object-type-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1042],0,&atx[1839]} ,
+  {0, "cdsgeneprot-qual" ,128,3,0,0,0,0,0,0,NULL,&atx[1968],NULL,0,&atx[1974]} ,
+  {444, "CDSGeneProt-qual-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1969],0,&atx[1987]} ,
+  {0, "field1" ,128,0,0,1,0,0,0,0,NULL,&atx[1970],NULL,0,&atx[1972]} ,
+  {443, "CDSGeneProt-constraint-field" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1971],0,&atx[1968]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[1853],NULL,0,NULL} ,
+  {0, "field2" ,128,1,0,1,0,0,0,0,NULL,&atx[1970],NULL,0,&atx[1973]} ,
+  {0, "constraint" ,128,2,0,1,0,0,0,0,NULL,&atx[1845],NULL,0,NULL} ,
+  {0, "cdsgeneprot-pseudo" ,128,4,0,0,0,0,0,0,NULL,&atx[1975],NULL,0,&atx[1979]} ,
+  {442, "CDSGeneProt-pseudo-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1976],0,&atx[1970]} ,
+  {0, "feature" ,128,0,0,0,0,0,0,0,NULL,&atx[1977],NULL,0,&atx[1978]} ,
+  {441, "CDSGeneProt-feature-type-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1045],0,&atx[1975]} ,
+  {0, "is-pseudo" ,128,1,0,0,1,0,0,0,&avnx[1051],&atx[60],NULL,0,NULL} ,
+  {0, "sequence" ,128,5,0,0,0,0,0,0,NULL,&atx[1980],NULL,0,NULL} ,
+  {447, "Sequence-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[1981],0,&atx[1952]} ,
+  {0, "seqtype" ,128,0,0,1,0,0,0,0,NULL,&atx[1982],NULL,0,&atx[1989]} ,
+  {446, "Sequence-constraint-mol-type-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1983],0,&atx[1980]} ,
+  {0, "any" ,128,0,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1984]} ,
+  {0, "nucleotide" ,128,1,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1985]} ,
+  {0, "dna" ,128,2,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1986]} ,
+  {0, "rna" ,128,3,0,0,0,0,0,0,NULL,&atx[1987],NULL,0,&atx[1988]} ,
+  {445, "Sequence-constraint-rnamol" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1052],0,&atx[1982]} ,
+  {0, "protein" ,128,4,0,0,0,0,0,0,NULL,&atx[387],NULL,0,NULL} ,
+  {0, "id" ,128,1,0,1,0,0,0,0,NULL,&atx[1845],NULL,0,&atx[1990]} ,
+  {0, "feature" ,128,2,0,0,0,0,0,0,NULL,&atx[1839],NULL,0,NULL} ,
+  {402, "Parse-action" ,1,0,0,0,0,1,0,0,NULL,&atx[13],&atx[1992],0,&atx[2025]} ,
+  {0, "portion" ,128,0,0,0,0,0,0,0,NULL,&atx[1938],NULL,0,&atx[1993]} ,
+  {0, "src" ,128,1,0,0,0,0,0,0,NULL,&atx[1994],NULL,0,&atx[2009]} ,
+  {467, "Parse-src" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[1995],0,&atx[2013]} ,
+  {0, "defline" ,128,0,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1996]} ,
+  {0, "flatfile" ,128,1,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1997]} ,
+  {0, "local-id" ,128,2,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[1998]} ,
+  {0, "org" ,128,3,0,0,0,0,0,0,NULL,&atx[1999],NULL,0,&atx[2005]} ,
+  {466, "Parse-src-org" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2000],0,&atx[1994]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[2001],NULL,0,&atx[2004]} ,
+  {465, "Parse-src-org-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[2002],0,&atx[1999]} ,
+  {0, "source-qual" ,128,0,0,0,0,0,0,0,NULL,&atx[1831],NULL,0,&atx[2003]} ,
+  {0, "taxname-after-binomial" ,128,1,0,0,0,0,0,0,NULL,&atx[387],NULL,0,NULL} ,
+  {0, "type" ,128,1,0,0,1,0,0,0,&avnx[1066],&atx[1966],NULL,0,NULL} ,
+  {0, "comment" ,128,4,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[2006]} ,
+  {0, "bankit-comment" ,128,5,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[2007]} ,
+  {0, "structured-comment" ,128,6,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[2008]} ,
+  {0, "file-id" ,128,7,0,0,0,0,0,0,NULL,&atx[387],NULL,0,NULL} ,
+  {0, "dest" ,128,2,0,0,0,0,0,0,NULL,&atx[2010],NULL,0,&atx[2021]} ,
+  {469, "Parse-dest" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[2011],0,&atx[2039]} ,
+  {0, "defline" ,128,0,0,0,0,0,0,0,NULL,&atx[387],NULL,0,&atx[2012]} ,
+  {0, "org" ,128,1,0,0,0,0,0,0,NULL,&atx[2013],NULL,0,&atx[2016]} ,
+  {468, "Parse-dst-org" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2014],0,&atx[2010]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[1829],NULL,0,&atx[2015]} ,
+  {0, "type" ,128,1,0,0,1,0,0,0,&avnx[1067],&atx[1966],NULL,0,NULL} ,
+  {0, "featqual" ,128,2,0,0,0,0,0,0,NULL,&atx[2017],NULL,0,&atx[2020]} ,
+  {417, "Feature-field-legal" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2018],0,&atx[1889]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[1839],NULL,0,&atx[2019]} ,
+  {0, "field" ,128,1,0,0,0,0,0,0,NULL,&atx[1843],NULL,0,NULL} ,
+  {0, "dbxref" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "capitalization" ,128,3,0,0,1,0,0,0,&avnx[1068],&atx[2022],NULL,0,&atx[2023]} ,
+  {464, "Cap-change" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1069],0,&atx[2001]} ,
+  {0, "remove-from-parsed" ,128,4,0,0,1,0,0,0,&avnx[1073],&atx[60],NULL,0,&atx[2024]} ,
+  {0, "existing-text" ,128,5,0,0,0,0,0,0,NULL,&atx[1870],NULL,0,NULL} ,
+  {403, "Macro-action-list" ,1,0,0,0,0,1,0,0,NULL,&atx[45],&atx[2026],0,&atx[1848]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2027],NULL,0,NULL} ,
+  {488, "Macro-action-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[2028],0,NULL} ,
+  {0, "aecr" ,128,0,0,0,0,0,0,0,NULL,&atx[1821],NULL,0,&atx[2029]} ,
+  {0, "parse" ,128,1,0,0,0,0,0,0,NULL,&atx[1991],NULL,0,&atx[2030]} ,
+  {0, "add-feature" ,128,2,0,0,0,0,0,0,NULL,&atx[2031],NULL,0,&atx[2061]} ,
+  {474, "Apply-feature-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2032],0,&atx[2062]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[1839],NULL,0,&atx[2033]} ,
+  {0, "partial5" ,128,1,0,0,1,0,0,0,&avnx[1074],&atx[60],NULL,0,&atx[2034]} ,
+  {0, "partial3" ,128,2,0,0,1,0,0,0,&avnx[1075],&atx[60],NULL,0,&atx[2035]} ,
+  {0, "plus-strand" ,128,3,0,0,1,0,0,0,&avnx[1076],&atx[60],NULL,0,&atx[2036]} ,
+  {0, "location" ,128,4,0,0,0,0,0,0,NULL,&atx[2037],NULL,0,&atx[2043]} ,
+  {471, "Location-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[2038],0,&atx[2046]} ,
+  {0, "interval" ,128,0,0,0,0,0,0,0,NULL,&atx[2039],NULL,0,&atx[2042]} ,
+  {470, "Location-interval" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2040],0,&atx[2037]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[2041]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
+  {0, "whole-sequence" ,128,1,0,0,0,0,0,0,NULL,&atx[387],NULL,0,NULL} ,
+  {0, "seq-list" ,128,5,0,0,0,0,0,0,NULL,&atx[2044],NULL,0,&atx[2049]} ,
+  {473, "Sequence-list-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[2045],0,&atx[2031]} ,
+  {0, "list" ,128,0,0,0,0,0,0,0,NULL,&atx[2046],NULL,0,&atx[2048]} ,
+  {472, "Sequence-list" ,1,0,0,0,0,0,0,0,NULL,&atx[45],&atx[2047],0,&atx[2044]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "all" ,128,1,0,0,0,0,0,0,NULL,&atx[387],NULL,0,NULL} ,
+  {0, "add-redundant" ,128,6,0,0,1,0,0,0,&avnx[1077],&atx[60],NULL,0,&atx[2050]} ,
+  {0, "add-mrna" ,128,7,0,0,1,0,0,0,&avnx[1078],&atx[60],NULL,0,&atx[2051]} ,
+  {0, "apply-to-parts" ,128,8,0,0,1,0,0,0,&avnx[1079],&atx[60],NULL,0,&atx[2052]} ,
+  {0, "only-seg-num" ,128,9,0,0,1,0,0,0,&avnx[1080],&atx[6],NULL,0,&atx[2053]} ,
+  {0, "fields" ,128,10,0,1,0,0,0,0,NULL,&atx[2054],NULL,0,NULL} ,
+  {414, "Feat-qual-legal-set" ,1,0,0,0,0,0,0,0,NULL,&atx[45],&atx[2055],0,&atx[1841]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2056],NULL,0,NULL} ,
+  {413, "Feat-qual-legal-val-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[2057],0,&atx[2054]} ,
+  {0, "qual" ,128,0,0,0,0,0,0,0,NULL,&atx[2058],NULL,0,NULL} ,
+  {412, "Feat-qual-legal-val" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2059],0,&atx[2056]} ,
+  {0, "qual" ,128,0,0,0,0,0,0,0,NULL,&atx[1843],NULL,0,&atx[2060]} ,
+  {0, "val" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "remove-feature" ,128,3,0,0,0,0,0,0,NULL,&atx[2062],NULL,0,&atx[2065]} ,
+  {475, "Remove-feature-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2063],0,&atx[2073]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[1839],NULL,0,&atx[2064]} ,
+  {0, "constraint" ,128,1,0,1,0,0,0,0,NULL,&atx[1950],NULL,0,NULL} ,
+  {0, "edit-location" ,128,4,0,0,0,0,0,0,NULL,&atx[2066],NULL,0,NULL} ,
+  {487, "Edit-feature-location-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2067],0,&atx[2027]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[1839],NULL,0,&atx[2068]} ,
+  {0, "action" ,128,1,0,0,0,0,0,0,NULL,&atx[2069],NULL,0,&atx[2092]} ,
+  {486, "Location-edit-type" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[2070],0,&atx[2066]} ,
+  {0, "strand" ,128,0,0,0,0,0,0,0,NULL,&atx[2071],NULL,0,&atx[2076]} ,
+  {478, "Edit-location-strand" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2072],0,&atx[2079]} ,
+  {0, "strand-from" ,128,0,0,0,0,0,0,0,NULL,&atx[2073],NULL,0,&atx[2074]} ,
+  {476, "Feature-location-strand-from" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1081],0,&atx[2075]} ,
+  {0, "strand-to" ,128,1,0,0,0,0,0,0,NULL,&atx[2075],NULL,0,NULL} ,
+  {477, "Feature-location-strand-to" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1086],0,&atx[2071]} ,
+  {0, "set-5-partial" ,128,1,0,0,0,0,0,0,NULL,&atx[2077],NULL,0,&atx[2081]} ,
+  {480, "Partial-5-set-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2078],0,&atx[2082]} ,
+  {0, "constraint" ,128,0,0,0,0,0,0,0,NULL,&atx[2079],NULL,0,&atx[2080]} ,
+  {479, "Partial-5-set-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1091],0,&atx[2077]} ,
+  {0, "extend" ,128,1,0,0,0,0,0,0,NULL,&atx[60],NULL,0,NULL} ,
+  {0, "clear-5-partial" ,128,2,0,0,0,0,0,0,NULL,&atx[2082],NULL,0,&atx[2083]} ,
+  {481, "Partial-5-clear-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1095],0,&atx[2086]} ,
+  {0, "set-3-partial" ,128,3,0,0,0,0,0,0,NULL,&atx[2084],NULL,0,&atx[2088]} ,
+  {483, "Partial-3-set-action" ,1,0,0,0,0,0,0,0,NULL,&atx[13],&atx[2085],0,&atx[2089]} ,
+  {0, "constraint" ,128,0,0,0,0,0,0,0,NULL,&atx[2086],NULL,0,&atx[2087]} ,
+  {482, "Partial-3-set-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1098],0,&atx[2084]} ,
+  {0, "extend" ,128,1,0,0,0,0,0,0,NULL,&atx[60],NULL,0,NULL} ,
+  {0, "clear-3-partial" ,128,4,0,0,0,0,0,0,NULL,&atx[2089],NULL,0,&atx[2090]} ,
+  {484, "Partial-3-clear-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1101],0,&atx[2091]} ,
+  {0, "convert" ,128,5,0,0,0,0,0,0,NULL,&atx[2091],NULL,0,NULL} ,
+  {485, "Convert-location-type" ,1,0,0,0,0,0,0,0,NULL,&atx[42],&avnx[1104],0,&atx[2069]} ,
+  {0, "constraint" ,128,2,0,1,0,0,0,0,NULL,&atx[1950],NULL,0,NULL} };
+
+static AsnModule ampx[39] = {
   { "NCBI-General" , "all.h60",&atx[0],NULL,&ampx[1],0,0} ,
   { "NCBI-Biblio" , NULL,&atx[77],NULL,&ampx[2],0,0} ,
   { "NCBI-Medline" , NULL,&atx[233],NULL,&ampx[3],0,0} ,
@@ -2398,35 +3223,37 @@ static AsnModule ampx[37] = {
   { "NCBI-Pub" , NULL,&atx[302],NULL,&ampx[6],0,0} ,
   { "NCBI-Seqloc" , NULL,&atx[344],NULL,&ampx[7],0,0} ,
   { "NCBI-Sequence" , NULL,&atx[436],NULL,&ampx[8],0,0} ,
-  { "NCBI-Seqset" , NULL,&atx[1129],NULL,&ampx[9],0,0} ,
-  { "NCBI-SeqCode" , NULL,&atx[1150],NULL,&ampx[10],0,0} ,
+  { "NCBI-Seqset" , NULL,&atx[1192],NULL,&ampx[9],0,0} ,
+  { "NCBI-SeqCode" , NULL,&atx[1213],NULL,&ampx[10],0,0} ,
   { "EMBL-General" , NULL,&atx[780],NULL,&ampx[11],0,0} ,
   { "SP-General" , NULL,&atx[744],NULL,&ampx[12],0,0} ,
   { "PIR-General" , NULL,&atx[708],NULL,&ampx[13],0,0} ,
   { "GenBank-General" , NULL,&atx[727],NULL,&ampx[14],0,0} ,
   { "PRF-General" , NULL,&atx[790],NULL,&ampx[15],0,0} ,
   { "PDB-General" , NULL,&atx[802],NULL,&ampx[16],0,0} ,
-  { "NCBI-Seqfeat" , NULL,&atx[884],NULL,&ampx[17],0,0} ,
-  { "NCBI-Rsite" , NULL,&atx[978],NULL,&ampx[18],0,0} ,
-  { "NCBI-RNA" , NULL,&atx[948],NULL,&ampx[19],0,0} ,
-  { "NCBI-Gene" , NULL,&atx[890],NULL,&ampx[20],0,0} ,
+  { "NCBI-Seqfeat" , NULL,&atx[885],NULL,&ampx[17],0,0} ,
+  { "NCBI-Rsite" , NULL,&atx[979],NULL,&ampx[18],0,0} ,
+  { "NCBI-RNA" , NULL,&atx[949],NULL,&ampx[19],0,0} ,
+  { "NCBI-Gene" , NULL,&atx[891],NULL,&ampx[20],0,0} ,
   { "NCBI-Organism" , NULL,&atx[661],NULL,&ampx[21],0,0} ,
   { "NCBI-BioSource" , NULL,&atx[820],NULL,&ampx[22],0,0} ,
-  { "NCBI-Protein" , NULL,&atx[934],NULL,&ampx[23],0,0} ,
-  { "NCBI-TxInit" , NULL,&atx[986],NULL,&ampx[24],0,0} ,
-  { "NCBI-Seqalign" , NULL,&atx[463],NULL,&ampx[25],0,0} ,
-  { "NCBI-Seqres" , NULL,&atx[1093],NULL,&ampx[26],0,0} ,
-  { "NCBI-Submit" , NULL,&atx[1176],NULL,&ampx[27],0,0} ,
-  { "NCBI-Cn3d" , NULL,&atx[1215],NULL,&ampx[28],0,0} ,
-  { "NCBI-Project" , NULL,&atx[1332],NULL,&ampx[29],0,0} ,
-  { "NCBI-Access" , NULL,&atx[1396],NULL,&ampx[30],0,0} ,
-  { "NCBI-FeatDef" , NULL,&atx[1402],NULL,&ampx[31],0,0} ,
-  { "NCBI-Mime" , NULL,&atx[1421],NULL,&ampx[32],0,0} ,
-  { "NCBI-ObjPrt" , NULL,&atx[1497],NULL,&ampx[33],0,0} ,
-  { "NCBI-GBSeq" , NULL,&atx[1533],NULL,&ampx[34],0,0} ,
-  { "INSD-INSDSeq" , NULL,&atx[1610],NULL,&ampx[35],0,0} ,
-  { "NCBI-TSeq" , NULL,&atx[1687],NULL,&ampx[36],0,0} ,
-  { "NCBI-ScoreMat" , NULL,&atx[1700],NULL,NULL,0,0} };
+  { "NCBI-Protein" , NULL,&atx[935],NULL,&ampx[23],0,0} ,
+  { "NCBI-TxInit" , NULL,&atx[987],NULL,&ampx[24],0,0} ,
+  { "NCBI-SeqTable" , NULL,&atx[1140],NULL,&ampx[25],0,0} ,
+  { "NCBI-Seqalign" , NULL,&atx[463],NULL,&ampx[26],0,0} ,
+  { "NCBI-Seqres" , NULL,&atx[1094],NULL,&ampx[27],0,0} ,
+  { "NCBI-Submit" , NULL,&atx[1239],NULL,&ampx[28],0,0} ,
+  { "NCBI-Cn3d" , NULL,&atx[1278],NULL,&ampx[29],0,0} ,
+  { "NCBI-Project" , NULL,&atx[1395],NULL,&ampx[30],0,0} ,
+  { "NCBI-Access" , NULL,&atx[1459],NULL,&ampx[31],0,0} ,
+  { "NCBI-FeatDef" , NULL,&atx[1465],NULL,&ampx[32],0,0} ,
+  { "NCBI-Mime" , NULL,&atx[1484],NULL,&ampx[33],0,0} ,
+  { "NCBI-ObjPrt" , NULL,&atx[1560],NULL,&ampx[34],0,0} ,
+  { "NCBI-GBSeq" , NULL,&atx[1596],NULL,&ampx[35],0,0} ,
+  { "INSD-INSDSeq" , NULL,&atx[1673],NULL,&ampx[36],0,0} ,
+  { "NCBI-TSeq" , NULL,&atx[1750],NULL,&ampx[37],0,0} ,
+  { "NCBI-ScoreMat" , NULL,&atx[1763],NULL,&ampx[38],0,0} ,
+  { "NCBI-Macro" , NULL,&atx[1821],NULL,NULL,0,0} };
 
 static AsnValxNodePtr avn = avnx;
 static AsnTypePtr at = atx;
@@ -2966,9 +3793,9 @@ static AsnModulePtr amp = ampx;
 #define BIOSEQ_id &at[644]
 #define BIOSEQ_id_E &at[645]
 #define BIOSEQ_descr &at[646]
-#define BIOSEQ_inst &at[838]
-#define BIOSEQ_annot &at[1072]
-#define BIOSEQ_annot_E &at[1073]
+#define BIOSEQ_inst &at[839]
+#define BIOSEQ_annot &at[1073]
+#define BIOSEQ_annot_E &at[1074]
 
 #define GIBB_MOL &at[651]
 
@@ -2979,6 +3806,7 @@ static AsnModulePtr amp = ampx;
 #define MOLINFO_tech &at[835]
 #define MOLINFO_techexp &at[836]
 #define MOLINFO_completeness &at[837]
+#define MOLINFO_gbmoltype &at[838]
 
 #define NUMBERING &at[447]
 #define NUMBERING_cont &at[448]
@@ -2999,36 +3827,37 @@ static AsnModulePtr amp = ampx;
 #define PUBDESC_comment &at[625]
 #define PUBDESC_reftype &at[626]
 
-#define SEQ_ANNOT &at[1074]
-#define SEQ_ANNOT_id &at[1075]
-#define SEQ_ANNOT_id_E &at[1076]
-#define SEQ_ANNOT_db &at[1082]
-#define SEQ_ANNOT_name &at[1083]
-#define SEQ_ANNOT_desc &at[1084]
-#define SEQ_ANNOT_data &at[1085]
-#define SEQ_ANNOT_data_ftable &at[1086]
-#define SEQ_ANNOT_data_ftable_E &at[1087]
-#define SEQ_ANNOT_data_align &at[1088]
-#define SEQ_ANNOT_data_align_E &at[1089]
-#define SEQ_ANNOT_data_graph &at[1090]
-#define SEQ_ANNOT_data_graph_E &at[1091]
-#define SEQ_ANNOT_data_ids &at[1125]
-#define SEQ_ANNOT_data_ids_E &at[1126]
-#define SEQ_ANNOT_data_locs &at[1127]
-#define SEQ_ANNOT_data_locs_E &at[1128]
-
-#define SEQ_DATA &at[848]
-#define SEQ_DATA_iupacna &at[849]
-#define SEQ_DATA_iupacaa &at[851]
-#define SEQ_DATA_ncbi2na &at[853]
-#define SEQ_DATA_ncbi4na &at[855]
-#define SEQ_DATA_ncbi8na &at[857]
-#define SEQ_DATA_ncbipna &at[859]
-#define SEQ_DATA_ncbi8aa &at[861]
-#define SEQ_DATA_ncbieaa &at[863]
-#define SEQ_DATA_ncbipaa &at[865]
-#define SEQ_DATA_ncbistdaa &at[867]
-#define SEQ_DATA_gap &at[869]
+#define SEQ_ANNOT &at[1075]
+#define SEQ_ANNOT_id &at[1076]
+#define SEQ_ANNOT_id_E &at[1077]
+#define SEQ_ANNOT_db &at[1083]
+#define SEQ_ANNOT_name &at[1084]
+#define SEQ_ANNOT_desc &at[1085]
+#define SEQ_ANNOT_data &at[1086]
+#define SEQ_ANNOT_data_ftable &at[1087]
+#define SEQ_ANNOT_data_ftable_E &at[1088]
+#define SEQ_ANNOT_data_align &at[1089]
+#define SEQ_ANNOT_data_align_E &at[1090]
+#define SEQ_ANNOT_data_graph &at[1091]
+#define SEQ_ANNOT_data_graph_E &at[1092]
+#define SEQ_ANNOT_data_ids &at[1126]
+#define SEQ_ANNOT_data_ids_E &at[1127]
+#define SEQ_ANNOT_data_locs &at[1128]
+#define SEQ_ANNOT_data_locs_E &at[1129]
+#define SEQ_ANNOT_data_seq_table &at[1130]
+
+#define SEQ_DATA &at[849]
+#define SEQ_DATA_iupacna &at[850]
+#define SEQ_DATA_iupacaa &at[852]
+#define SEQ_DATA_ncbi2na &at[854]
+#define SEQ_DATA_ncbi4na &at[856]
+#define SEQ_DATA_ncbi8na &at[858]
+#define SEQ_DATA_ncbipna &at[860]
+#define SEQ_DATA_ncbi8aa &at[862]
+#define SEQ_DATA_ncbieaa &at[864]
+#define SEQ_DATA_ncbipaa &at[866]
+#define SEQ_DATA_ncbistdaa &at[868]
+#define SEQ_DATA_gap &at[870]
 
 #define SEQDESC &at[649]
 #define SEQDESC_mol_type &at[650]
@@ -3060,39 +3889,39 @@ static AsnModulePtr amp = ampx;
 #define SEQ_DESCR &at[647]
 #define SEQ_DESCR_E &at[648]
 
-#define SEQ_EXT &at[874]
-#define SEQ_EXT_seg &at[875]
-#define SEQ_EXT_ref &at[878]
-#define SEQ_EXT_map &at[880]
-#define SEQ_EXT_delta &at[1049]
-
-#define SEQ_HIST &at[1060]
-#define SEQ_HIST_assembly &at[1061]
-#define SEQ_HIST_assembly_E &at[1062]
-#define SEQ_HIST_replaces &at[1063]
-#define SEQ_HIST_replaced_by &at[1068]
-#define SEQ_HIST_deleted &at[1069]
-#define SEQ_HIST_deleted_bool &at[1070]
-#define SEQ_HIST_deleted_date &at[1071]
-
-#define SEQ_INST &at[839]
-#define SEQ_INST_repr &at[840]
-#define SEQ_INST_mol &at[841]
-#define SEQ_INST_length &at[842]
-#define SEQ_INST_fuzz &at[843]
-#define SEQ_INST_topology &at[845]
-#define SEQ_INST_strand &at[846]
-#define SEQ_INST_seq_data &at[847]
-#define SEQ_INST_ext &at[873]
-#define SEQ_INST_hist &at[1059]
-
-#define SEQ_LITERAL &at[1055]
-#define SEQ_LITERAL_length &at[1056]
-#define SEQ_LITERAL_fuzz &at[1057]
-#define SEQ_LITERAL_seq_data &at[1058]
-
-#define DELTA_EXT &at[1050]
-#define DELTA_EXT_E &at[1051]
+#define SEQ_EXT &at[875]
+#define SEQ_EXT_seg &at[876]
+#define SEQ_EXT_ref &at[879]
+#define SEQ_EXT_map &at[881]
+#define SEQ_EXT_delta &at[1050]
+
+#define SEQ_HIST &at[1061]
+#define SEQ_HIST_assembly &at[1062]
+#define SEQ_HIST_assembly_E &at[1063]
+#define SEQ_HIST_replaces &at[1064]
+#define SEQ_HIST_replaced_by &at[1069]
+#define SEQ_HIST_deleted &at[1070]
+#define SEQ_HIST_deleted_bool &at[1071]
+#define SEQ_HIST_deleted_date &at[1072]
+
+#define SEQ_INST &at[840]
+#define SEQ_INST_repr &at[841]
+#define SEQ_INST_mol &at[842]
+#define SEQ_INST_length &at[843]
+#define SEQ_INST_fuzz &at[844]
+#define SEQ_INST_topology &at[846]
+#define SEQ_INST_strand &at[847]
+#define SEQ_INST_seq_data &at[848]
+#define SEQ_INST_ext &at[874]
+#define SEQ_INST_hist &at[1060]
+
+#define SEQ_LITERAL &at[1056]
+#define SEQ_LITERAL_length &at[1057]
+#define SEQ_LITERAL_fuzz &at[1058]
+#define SEQ_LITERAL_seq_data &at[1059]
+
+#define DELTA_EXT &at[1051]
+#define DELTA_EXT_E &at[1052]
 
 #define GIBB_MOD &at[654]
 
@@ -3117,51 +3946,51 @@ static AsnModulePtr amp = ampx;
 #define NUM_REAL_b &at[617]
 #define NUM_REAL_units &at[618]
 
-#define SEG_EXT &at[876]
-#define SEG_EXT_E &at[877]
+#define SEG_EXT &at[877]
+#define SEG_EXT_E &at[878]
 
-#define REF_EXT &at[879]
+#define REF_EXT &at[880]
 
-#define MAP_EXT &at[881]
-#define MAP_EXT_E &at[882]
+#define MAP_EXT &at[882]
+#define MAP_EXT_E &at[883]
 
-#define DELTA_SEQ &at[1052]
-#define DELTA_SEQ_loc &at[1053]
-#define DELTA_SEQ_literal &at[1054]
+#define DELTA_SEQ &at[1053]
+#define DELTA_SEQ_loc &at[1054]
+#define DELTA_SEQ_literal &at[1055]
 
-#define SEQ_HIST_REC &at[1064]
-#define SEQ_HIST_REC_date &at[1065]
-#define SEQ_HIST_REC_ids &at[1066]
-#define SEQ_HIST_REC_ids_E &at[1067]
+#define SEQ_HIST_REC &at[1065]
+#define SEQ_HIST_REC_date &at[1066]
+#define SEQ_HIST_REC_ids &at[1067]
+#define SEQ_HIST_REC_ids_E &at[1068]
 
-#define IUPACNA &at[850]
+#define IUPACNA &at[851]
 
-#define IUPACAA &at[852]
+#define IUPACAA &at[853]
 
-#define NCBI2NA &at[854]
+#define NCBI2NA &at[855]
 
-#define NCBI4NA &at[856]
+#define NCBI4NA &at[857]
 
-#define NCBI8NA &at[858]
+#define NCBI8NA &at[859]
 
-#define NCBIPNA &at[860]
+#define NCBIPNA &at[861]
 
-#define NCBI8AA &at[862]
+#define NCBI8AA &at[863]
 
-#define NCBIEAA &at[864]
+#define NCBIEAA &at[865]
 
-#define NCBIPAA &at[866]
+#define NCBIPAA &at[867]
 
-#define NCBISTDAA &at[868]
+#define NCBISTDAA &at[869]
 
-#define SEQ_GAP &at[870]
-#define SEQ_GAP_type &at[871]
-#define SEQ_GAP_linkage &at[872]
+#define SEQ_GAP &at[871]
+#define SEQ_GAP_type &at[872]
+#define SEQ_GAP_linkage &at[873]
 
-#define ANNOT_ID &at[1077]
-#define ANNOT_ID_local &at[1078]
-#define ANNOT_ID_ncbi &at[1080]
-#define ANNOT_ID_general &at[1081]
+#define ANNOT_ID &at[1078]
+#define ANNOT_ID_local &at[1079]
+#define ANNOT_ID_ncbi &at[1081]
+#define ANNOT_ID_general &at[1082]
 
 #define ALIGN_DEF &at[635]
 #define ALIGN_DEF_align_type &at[636]
@@ -3175,22 +4004,22 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define BIOSEQ_SET &at[1129]
-#define BIOSEQ_SET_id &at[1130]
-#define BIOSEQ_SET_coll &at[1132]
-#define BIOSEQ_SET_level &at[1134]
-#define BIOSEQ_SET_class &at[1135]
-#define BIOSEQ_SET_release &at[1136]
-#define BIOSEQ_SET_date &at[1137]
-#define BIOSEQ_SET_descr &at[1139]
-#define BIOSEQ_SET_seq_set &at[1141]
-#define BIOSEQ_SET_seq_set_E &at[1142]
-#define BIOSEQ_SET_annot &at[1147]
-#define BIOSEQ_SET_annot_E &at[1148]
+#define BIOSEQ_SET &at[1192]
+#define BIOSEQ_SET_id &at[1193]
+#define BIOSEQ_SET_coll &at[1195]
+#define BIOSEQ_SET_level &at[1197]
+#define BIOSEQ_SET_class &at[1198]
+#define BIOSEQ_SET_release &at[1199]
+#define BIOSEQ_SET_date &at[1200]
+#define BIOSEQ_SET_descr &at[1202]
+#define BIOSEQ_SET_seq_set &at[1204]
+#define BIOSEQ_SET_seq_set_E &at[1205]
+#define BIOSEQ_SET_annot &at[1210]
+#define BIOSEQ_SET_annot_E &at[1211]
 
-#define SEQ_ENTRY &at[1143]
-#define SEQ_ENTRY_seq &at[1144]
-#define SEQ_ENTRY_set &at[1146]
+#define SEQ_ENTRY &at[1206]
+#define SEQ_ENTRY_seq &at[1207]
+#define SEQ_ENTRY_set &at[1209]
 
 
 /**************************************************
@@ -3199,33 +4028,33 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define SEQ_CODE_TABLE &at[1150]
-#define SEQ_CODE_TABLE_code &at[1151]
-#define SEQ_CODE_TABLE_num &at[1153]
-#define SEQ_CODE_TABLE_one_letter &at[1154]
-#define SEQ_CODE_TABLE_start_at &at[1155]
-#define SEQ_CODE_TABLE_table &at[1156]
-#define SEQ_CODE_TABLE_table_E &at[1157]
-#define SEQ_CODE_TABLE_table_E_symbol &at[1158]
-#define SEQ_CODE_TABLE_table_E_name &at[1159]
-#define SEQ_CODE_TABLE_comps &at[1160]
-#define SEQ_CODE_TABLE_comps_E &at[1161]
-
-#define SEQ_MAP_TABLE &at[1162]
-#define SEQ_MAP_TABLE_from &at[1163]
-#define SEQ_MAP_TABLE_to &at[1164]
-#define SEQ_MAP_TABLE_num &at[1165]
-#define SEQ_MAP_TABLE_start_at &at[1166]
-#define SEQ_MAP_TABLE_table &at[1167]
-#define SEQ_MAP_TABLE_table_E &at[1168]
-
-#define SEQ_CODE_SET &at[1169]
-#define SEQ_CODE_SET_codes &at[1170]
-#define SEQ_CODE_SET_codes_E &at[1171]
-#define SEQ_CODE_SET_maps &at[1172]
-#define SEQ_CODE_SET_maps_E &at[1173]
-
-#define SEQ_CODE_TYPE &at[1152]
+#define SEQ_CODE_TABLE &at[1213]
+#define SEQ_CODE_TABLE_code &at[1214]
+#define SEQ_CODE_TABLE_num &at[1216]
+#define SEQ_CODE_TABLE_one_letter &at[1217]
+#define SEQ_CODE_TABLE_start_at &at[1218]
+#define SEQ_CODE_TABLE_table &at[1219]
+#define SEQ_CODE_TABLE_table_E &at[1220]
+#define SEQ_CODE_TABLE_table_E_symbol &at[1221]
+#define SEQ_CODE_TABLE_table_E_name &at[1222]
+#define SEQ_CODE_TABLE_comps &at[1223]
+#define SEQ_CODE_TABLE_comps_E &at[1224]
+
+#define SEQ_MAP_TABLE &at[1225]
+#define SEQ_MAP_TABLE_from &at[1226]
+#define SEQ_MAP_TABLE_to &at[1227]
+#define SEQ_MAP_TABLE_num &at[1228]
+#define SEQ_MAP_TABLE_start_at &at[1229]
+#define SEQ_MAP_TABLE_table &at[1230]
+#define SEQ_MAP_TABLE_table_E &at[1231]
+
+#define SEQ_CODE_SET &at[1232]
+#define SEQ_CODE_SET_codes &at[1233]
+#define SEQ_CODE_SET_codes_E &at[1234]
+#define SEQ_CODE_SET_maps &at[1235]
+#define SEQ_CODE_SET_maps_E &at[1236]
+
+#define SEQ_CODE_TYPE &at[1215]
 
 
 /**************************************************
@@ -3370,30 +4199,30 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define SEQ_FEAT &at[884]
-#define SEQ_FEAT_id &at[885]
-#define SEQ_FEAT_data &at[886]
-#define SEQ_FEAT_partial &at[1021]
-#define SEQ_FEAT_except &at[1022]
-#define SEQ_FEAT_comment &at[1023]
-#define SEQ_FEAT_product &at[1024]
-#define SEQ_FEAT_location &at[1025]
-#define SEQ_FEAT_qual &at[1026]
-#define SEQ_FEAT_qual_E &at[1027]
-#define SEQ_FEAT_title &at[1031]
-#define SEQ_FEAT_ext &at[1032]
-#define SEQ_FEAT_cit &at[1033]
-#define SEQ_FEAT_exp_ev &at[1035]
-#define SEQ_FEAT_xref &at[1036]
-#define SEQ_FEAT_xref_E &at[1037]
-#define SEQ_FEAT_dbxref &at[1041]
-#define SEQ_FEAT_dbxref_E &at[1042]
-#define SEQ_FEAT_pseudo &at[1043]
-#define SEQ_FEAT_except_text &at[1044]
-#define SEQ_FEAT_ids &at[1045]
-#define SEQ_FEAT_ids_E &at[1046]
-#define SEQ_FEAT_exts &at[1047]
-#define SEQ_FEAT_exts_E &at[1048]
+#define SEQ_FEAT &at[885]
+#define SEQ_FEAT_id &at[886]
+#define SEQ_FEAT_data &at[887]
+#define SEQ_FEAT_partial &at[1022]
+#define SEQ_FEAT_except &at[1023]
+#define SEQ_FEAT_comment &at[1024]
+#define SEQ_FEAT_product &at[1025]
+#define SEQ_FEAT_location &at[1026]
+#define SEQ_FEAT_qual &at[1027]
+#define SEQ_FEAT_qual_E &at[1028]
+#define SEQ_FEAT_title &at[1032]
+#define SEQ_FEAT_ext &at[1033]
+#define SEQ_FEAT_cit &at[1034]
+#define SEQ_FEAT_exp_ev &at[1036]
+#define SEQ_FEAT_xref &at[1037]
+#define SEQ_FEAT_xref_E &at[1038]
+#define SEQ_FEAT_dbxref &at[1042]
+#define SEQ_FEAT_dbxref_E &at[1043]
+#define SEQ_FEAT_pseudo &at[1044]
+#define SEQ_FEAT_except_text &at[1045]
+#define SEQ_FEAT_ids &at[1046]
+#define SEQ_FEAT_ids_E &at[1047]
+#define SEQ_FEAT_exts &at[1048]
+#define SEQ_FEAT_exts_E &at[1049]
 
 #define FEAT_ID &at[428]
 #define FEAT_ID_gibb &at[429]
@@ -3401,72 +4230,72 @@ static AsnModulePtr amp = ampx;
 #define FEAT_ID_local &at[432]
 #define FEAT_ID_general &at[434]
 
-#define GENETIC_CODE &at[912]
-#define GENETIC_CODE_E &at[913]
-#define GENETIC_CODE_E_name &at[914]
-#define GENETIC_CODE_E_id &at[915]
-#define GENETIC_CODE_E_ncbieaa &at[916]
-#define GENETIC_CODE_E_ncbi8aa &at[917]
-#define GENETIC_CODE_E_ncbistdaa &at[918]
-#define GENETIC_CODE_E_sncbieaa &at[919]
-#define GENETIC_CODE_E_sncbi8aa &at[920]
-#define GENETIC_CODE_E_sncbistdaa &at[921]
-
-#define SEQFEATDATA &at[887]
-#define SEQFEATDATA_gene &at[888]
-#define SEQFEATDATA_org &at[902]
-#define SEQFEATDATA_cdregion &at[904]
-#define SEQFEATDATA_prot &at[932]
-#define SEQFEATDATA_rna &at[946]
-#define SEQFEATDATA_pub &at[964]
-#define SEQFEATDATA_seq &at[966]
-#define SEQFEATDATA_imp &at[967]
-#define SEQFEATDATA_region &at[972]
-#define SEQFEATDATA_comment &at[973]
-#define SEQFEATDATA_bond &at[974]
-#define SEQFEATDATA_site &at[975]
-#define SEQFEATDATA_rsite &at[976]
-#define SEQFEATDATA_user &at[982]
-#define SEQFEATDATA_txinit &at[984]
-#define SEQFEATDATA_num &at[1013]
-#define SEQFEATDATA_psec_str &at[1015]
-#define SEQFEATDATA_non_std_residue &at[1016]
-#define SEQFEATDATA_het &at[1017]
-#define SEQFEATDATA_biosrc &at[1019]
-
-#define GB_QUAL &at[1028]
-#define GB_QUAL_qual &at[1029]
-#define GB_QUAL_val &at[1030]
-
-#define SEQFEATXREF &at[1038]
-#define SEQFEATXREF_id &at[1039]
-#define SEQFEATXREF_data &at[1040]
-
-#define CDREGION &at[905]
-#define CDREGION_orf &at[906]
-#define CDREGION_frame &at[907]
-#define CDREGION_conflict &at[908]
-#define CDREGION_gaps &at[909]
-#define CDREGION_mismatch &at[910]
-#define CDREGION_code &at[911]
-#define CDREGION_code_break &at[922]
-#define CDREGION_code_break_E &at[923]
-#define CDREGION_stops &at[931]
-
-#define IMP_FEAT &at[968]
-#define IMP_FEAT_key &at[969]
-#define IMP_FEAT_loc &at[970]
-#define IMP_FEAT_descr &at[971]
-
-#define CODE_BREAK &at[924]
-#define CODE_BREAK_loc &at[925]
-#define CODE_BREAK_aa &at[927]
-#define CODE_BREAK_aa_ncbieaa &at[928]
-#define CODE_BREAK_aa_ncbi8aa &at[929]
-#define CODE_BREAK_aa_ncbistdaa &at[930]
-
-#define GENETIC_CODE_TABLE &at[1174]
-#define GENETIC_CODE_TABLE_E &at[1175]
+#define GENETIC_CODE &at[913]
+#define GENETIC_CODE_E &at[914]
+#define GENETIC_CODE_E_name &at[915]
+#define GENETIC_CODE_E_id &at[916]
+#define GENETIC_CODE_E_ncbieaa &at[917]
+#define GENETIC_CODE_E_ncbi8aa &at[918]
+#define GENETIC_CODE_E_ncbistdaa &at[919]
+#define GENETIC_CODE_E_sncbieaa &at[920]
+#define GENETIC_CODE_E_sncbi8aa &at[921]
+#define GENETIC_CODE_E_sncbistdaa &at[922]
+
+#define SEQFEATDATA &at[888]
+#define SEQFEATDATA_gene &at[889]
+#define SEQFEATDATA_org &at[903]
+#define SEQFEATDATA_cdregion &at[905]
+#define SEQFEATDATA_prot &at[933]
+#define SEQFEATDATA_rna &at[947]
+#define SEQFEATDATA_pub &at[965]
+#define SEQFEATDATA_seq &at[967]
+#define SEQFEATDATA_imp &at[968]
+#define SEQFEATDATA_region &at[973]
+#define SEQFEATDATA_comment &at[974]
+#define SEQFEATDATA_bond &at[975]
+#define SEQFEATDATA_site &at[976]
+#define SEQFEATDATA_rsite &at[977]
+#define SEQFEATDATA_user &at[983]
+#define SEQFEATDATA_txinit &at[985]
+#define SEQFEATDATA_num &at[1014]
+#define SEQFEATDATA_psec_str &at[1016]
+#define SEQFEATDATA_non_std_residue &at[1017]
+#define SEQFEATDATA_het &at[1018]
+#define SEQFEATDATA_biosrc &at[1020]
+
+#define GB_QUAL &at[1029]
+#define GB_QUAL_qual &at[1030]
+#define GB_QUAL_val &at[1031]
+
+#define SEQFEATXREF &at[1039]
+#define SEQFEATXREF_id &at[1040]
+#define SEQFEATXREF_data &at[1041]
+
+#define CDREGION &at[906]
+#define CDREGION_orf &at[907]
+#define CDREGION_frame &at[908]
+#define CDREGION_conflict &at[909]
+#define CDREGION_gaps &at[910]
+#define CDREGION_mismatch &at[911]
+#define CDREGION_code &at[912]
+#define CDREGION_code_break &at[923]
+#define CDREGION_code_break_E &at[924]
+#define CDREGION_stops &at[932]
+
+#define IMP_FEAT &at[969]
+#define IMP_FEAT_key &at[970]
+#define IMP_FEAT_loc &at[971]
+#define IMP_FEAT_descr &at[972]
+
+#define CODE_BREAK &at[925]
+#define CODE_BREAK_loc &at[926]
+#define CODE_BREAK_aa &at[928]
+#define CODE_BREAK_aa_ncbieaa &at[929]
+#define CODE_BREAK_aa_ncbi8aa &at[930]
+#define CODE_BREAK_aa_ncbistdaa &at[931]
+
+#define GENETIC_CODE_TABLE &at[1237]
+#define GENETIC_CODE_TABLE_E &at[1238]
 
 
 /**************************************************
@@ -3475,9 +4304,9 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define RSITE_REF &at[978]
-#define RSITE_REF_str &at[979]
-#define RSITE_REF_db &at[980]
+#define RSITE_REF &at[979]
+#define RSITE_REF_str &at[980]
+#define RSITE_REF_db &at[981]
 
 
 /**************************************************
@@ -3486,22 +4315,22 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define RNA_REF &at[948]
-#define RNA_REF_type &at[949]
-#define RNA_REF_pseudo &at[950]
-#define RNA_REF_ext &at[951]
-#define RNA_REF_ext_name &at[952]
-#define RNA_REF_ext_tRNA &at[953]
+#define RNA_REF &at[949]
+#define RNA_REF_type &at[950]
+#define RNA_REF_pseudo &at[951]
+#define RNA_REF_ext &at[952]
+#define RNA_REF_ext_name &at[953]
+#define RNA_REF_ext_tRNA &at[954]
 
-#define TRNA_EXT &at[954]
-#define TRNA_EXT_aa &at[955]
-#define TRNA_EXT_aa_iupacaa &at[956]
-#define TRNA_EXT_aa_ncbieaa &at[957]
-#define TRNA_EXT_aa_ncbi8aa &at[958]
-#define TRNA_EXT_aa_ncbistdaa &at[959]
-#define TRNA_EXT_codon &at[960]
-#define TRNA_EXT_codon_E &at[961]
-#define TRNA_EXT_anticodon &at[962]
+#define TRNA_EXT &at[955]
+#define TRNA_EXT_aa &at[956]
+#define TRNA_EXT_aa_iupacaa &at[957]
+#define TRNA_EXT_aa_ncbieaa &at[958]
+#define TRNA_EXT_aa_ncbi8aa &at[959]
+#define TRNA_EXT_aa_ncbistdaa &at[960]
+#define TRNA_EXT_codon &at[961]
+#define TRNA_EXT_codon_E &at[962]
+#define TRNA_EXT_anticodon &at[963]
 
 
 /**************************************************
@@ -3510,17 +4339,17 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define GENE_REF &at[890]
-#define GENE_REF_locus &at[891]
-#define GENE_REF_allele &at[892]
-#define GENE_REF_desc &at[893]
-#define GENE_REF_maploc &at[894]
-#define GENE_REF_pseudo &at[895]
-#define GENE_REF_db &at[896]
-#define GENE_REF_db_E &at[897]
-#define GENE_REF_syn &at[899]
-#define GENE_REF_syn_E &at[900]
-#define GENE_REF_locus_tag &at[901]
+#define GENE_REF &at[891]
+#define GENE_REF_locus &at[892]
+#define GENE_REF_allele &at[893]
+#define GENE_REF_desc &at[894]
+#define GENE_REF_maploc &at[895]
+#define GENE_REF_pseudo &at[896]
+#define GENE_REF_db &at[897]
+#define GENE_REF_db_E &at[898]
+#define GENE_REF_syn &at[900]
+#define GENE_REF_syn_E &at[901]
+#define GENE_REF_locus_tag &at[902]
 
 
 /**************************************************
@@ -3603,17 +4432,17 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define PROT_REF &at[934]
-#define PROT_REF_name &at[935]
-#define PROT_REF_name_E &at[936]
-#define PROT_REF_desc &at[937]
-#define PROT_REF_ec &at[938]
-#define PROT_REF_ec_E &at[939]
-#define PROT_REF_activity &at[940]
-#define PROT_REF_activity_E &at[941]
-#define PROT_REF_db &at[942]
-#define PROT_REF_db_E &at[943]
-#define PROT_REF_processed &at[945]
+#define PROT_REF &at[935]
+#define PROT_REF_name &at[936]
+#define PROT_REF_name_E &at[937]
+#define PROT_REF_desc &at[938]
+#define PROT_REF_ec &at[939]
+#define PROT_REF_ec_E &at[940]
+#define PROT_REF_activity &at[941]
+#define PROT_REF_activity_E &at[942]
+#define PROT_REF_db &at[943]
+#define PROT_REF_db_E &at[944]
+#define PROT_REF_processed &at[946]
 
 
 /**************************************************
@@ -3622,31 +4451,103 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define TXINIT &at[986]
-#define TXINIT_name &at[987]
-#define TXINIT_syn &at[988]
-#define TXINIT_syn_E &at[989]
-#define TXINIT_gene &at[990]
-#define TXINIT_gene_E &at[991]
-#define TXINIT_protein &at[993]
-#define TXINIT_protein_E &at[994]
-#define TXINIT_rna &at[996]
-#define TXINIT_rna_E &at[997]
-#define TXINIT_expression &at[998]
-#define TXINIT_txsystem &at[999]
-#define TXINIT_txdescr &at[1000]
-#define TXINIT_txorg &at[1001]
-#define TXINIT_mapping_precise &at[1003]
-#define TXINIT_location_accurate &at[1004]
-#define TXINIT_inittype &at[1005]
-#define TXINIT_evidence &at[1006]
-#define TXINIT_evidence_E &at[1007]
-
-#define TX_EVIDENCE &at[1008]
-#define TX_EVIDENCE_exp_code &at[1009]
-#define TX_EVIDENCE_expression_system &at[1010]
-#define TX_EVIDENCE_low_prec_data &at[1011]
-#define TX_EVIDENCE_from_homolog &at[1012]
+#define TXINIT &at[987]
+#define TXINIT_name &at[988]
+#define TXINIT_syn &at[989]
+#define TXINIT_syn_E &at[990]
+#define TXINIT_gene &at[991]
+#define TXINIT_gene_E &at[992]
+#define TXINIT_protein &at[994]
+#define TXINIT_protein_E &at[995]
+#define TXINIT_rna &at[997]
+#define TXINIT_rna_E &at[998]
+#define TXINIT_expression &at[999]
+#define TXINIT_txsystem &at[1000]
+#define TXINIT_txdescr &at[1001]
+#define TXINIT_txorg &at[1002]
+#define TXINIT_mapping_precise &at[1004]
+#define TXINIT_location_accurate &at[1005]
+#define TXINIT_inittype &at[1006]
+#define TXINIT_evidence &at[1007]
+#define TXINIT_evidence_E &at[1008]
+
+#define TX_EVIDENCE &at[1009]
+#define TX_EVIDENCE_exp_code &at[1010]
+#define TX_EVIDENCE_expression_system &at[1011]
+#define TX_EVIDENCE_low_prec_data &at[1012]
+#define TX_EVIDENCE_from_homolog &at[1013]
+
+
+/**************************************************
+*
+*    Defines for Module NCBI-SeqTable
+*
+**************************************************/
+
+#define SEQTABLE_COLUMN_INFO &at[1140]
+#define SEQTABLE_COLUMN_INFO_title &at[1141]
+#define SEQTABLE_COLUMN_INFO_field_id &at[1142]
+#define SEQTABLE_COLUMN_INFO_field_name &at[1143]
+
+#define SEQTABLE_COLUMN &at[1138]
+#define SEQTABLE_COLUMN_header &at[1139]
+#define SEQTABLE_COLUMN_data &at[1144]
+#define SEQTABLE_COLUMN_sparse &at[1176]
+#define SEQTABLE_COLUMN_default &at[1181]
+#define SEQTABLE_COLUMN_sparse_other &at[1191]
+
+#define SEQ_TABLE &at[1132]
+#define SEQ_TABLE_feat_type &at[1133]
+#define SEQ_TABLE_feat_subtype &at[1134]
+#define SEQ_TABLE_num_rows &at[1135]
+#define SEQ_TABLE_columns &at[1136]
+#define SEQ_TABLE_columns_E &at[1137]
+
+#define COMMONSTRING_TABLE &at[1155]
+#define COMMONSTRING_TABLE_strings &at[1156]
+#define COMMONSTRING_TABLE_strings_E &at[1157]
+#define COMMONSTRING_TABLE_indexes &at[1158]
+#define COMMONSTRING_TABLE_indexes_E &at[1159]
+
+#define COMMONBYTES_TABLE &at[1161]
+#define COMMONBYTES_TABLE_bytes &at[1162]
+#define COMMONBYTES_TABLE_bytes_E &at[1163]
+#define COMMONBYTES_TABLE_indexes &at[1164]
+#define COMMONBYTES_TABLE_indexes_E &at[1165]
+
+#define SEQTABLE_MULTI_DATA &at[1145]
+#define SEQTABLE_MULTI_DATA_int &at[1146]
+#define SEQTABLE_MULTI_DATA_int_E &at[1147]
+#define SEQTABLE_MULTI_DATA_real &at[1148]
+#define SEQTABLE_MULTI_DATA_real_E &at[1149]
+#define SEQTABLE_MULTI_DATA_string &at[1150]
+#define SEQTABLE_MULTI_DATA_string_E &at[1151]
+#define SEQTABLE_MULTI_DATA_bytes &at[1152]
+#define SEQTABLE_MULTI_DATA_bytes_E &at[1153]
+#define MULTI_DATA_common_string &at[1154]
+#define MULTI_DATA_common_bytes &at[1160]
+#define SEQTABLE_MULTI_DATA_bit &at[1166]
+#define SEQTABLE_MULTI_DATA_loc &at[1167]
+#define SEQTABLE_MULTI_DATA_loc_E &at[1168]
+#define SEQTABLE_MULTI_DATA_id &at[1170]
+#define SEQTABLE_MULTI_DATA_id_E &at[1171]
+#define SEQTABLE_MULTI_DATA_interval &at[1173]
+#define SEQTABLE_MULTI_DATA_interval_E &at[1174]
+
+#define SEQTABLE_SINGLE_DATA &at[1182]
+#define SEQTABLE_SINGLE_DATA_int &at[1183]
+#define SEQTABLE_SINGLE_DATA_real &at[1184]
+#define SEQTABLE_SINGLE_DATA_string &at[1185]
+#define SEQTABLE_SINGLE_DATA_bytes &at[1186]
+#define SEQTABLE_SINGLE_DATA_bit &at[1187]
+#define SEQTABLE_SINGLE_DATA_loc &at[1188]
+#define SEQTABLE_SINGLE_DATA_id &at[1189]
+#define SEQTABLE_SINGLE_DATA_interval &at[1190]
+
+#define SEQTABLE_SPARSE_INDEX &at[1177]
+#define SEQTABLE_SPARSE_INDEX_indexes &at[1178]
+#define SEQTABLE_SPARSE_INDEX_indexes_E &at[1179]
+#define SEQTABLE_SPARSE_INDEX_bit_set &at[1180]
 
 
 /**************************************************
@@ -3826,40 +4727,40 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define SEQ_GRAPH &at[1093]
-#define SEQ_GRAPH_title &at[1094]
-#define SEQ_GRAPH_comment &at[1095]
-#define SEQ_GRAPH_loc &at[1096]
-#define SEQ_GRAPH_title_x &at[1098]
-#define SEQ_GRAPH_title_y &at[1099]
-#define SEQ_GRAPH_comp &at[1100]
-#define SEQ_GRAPH_a &at[1101]
-#define SEQ_GRAPH_b &at[1102]
-#define SEQ_GRAPH_numval &at[1103]
-#define SEQ_GRAPH_graph &at[1104]
-#define SEQ_GRAPH_graph_real &at[1105]
-#define SEQ_GRAPH_graph_int &at[1112]
-#define SEQ_GRAPH_graph_byte &at[1119]
-
-#define REAL_GRAPH &at[1106]
-#define REAL_GRAPH_max &at[1107]
-#define REAL_GRAPH_min &at[1108]
-#define REAL_GRAPH_axis &at[1109]
-#define REAL_GRAPH_values &at[1110]
-#define REAL_GRAPH_values_E &at[1111]
-
-#define INT_GRAPH &at[1113]
-#define INT_GRAPH_max &at[1114]
-#define INT_GRAPH_min &at[1115]
-#define INT_GRAPH_axis &at[1116]
-#define INT_GRAPH_values &at[1117]
-#define INT_GRAPH_values_E &at[1118]
-
-#define BYTE_GRAPH &at[1120]
-#define BYTE_GRAPH_max &at[1121]
-#define BYTE_GRAPH_min &at[1122]
-#define BYTE_GRAPH_axis &at[1123]
-#define BYTE_GRAPH_values &at[1124]
+#define SEQ_GRAPH &at[1094]
+#define SEQ_GRAPH_title &at[1095]
+#define SEQ_GRAPH_comment &at[1096]
+#define SEQ_GRAPH_loc &at[1097]
+#define SEQ_GRAPH_title_x &at[1099]
+#define SEQ_GRAPH_title_y &at[1100]
+#define SEQ_GRAPH_comp &at[1101]
+#define SEQ_GRAPH_a &at[1102]
+#define SEQ_GRAPH_b &at[1103]
+#define SEQ_GRAPH_numval &at[1104]
+#define SEQ_GRAPH_graph &at[1105]
+#define SEQ_GRAPH_graph_real &at[1106]
+#define SEQ_GRAPH_graph_int &at[1113]
+#define SEQ_GRAPH_graph_byte &at[1120]
+
+#define REAL_GRAPH &at[1107]
+#define REAL_GRAPH_max &at[1108]
+#define REAL_GRAPH_min &at[1109]
+#define REAL_GRAPH_axis &at[1110]
+#define REAL_GRAPH_values &at[1111]
+#define REAL_GRAPH_values_E &at[1112]
+
+#define INT_GRAPH &at[1114]
+#define INT_GRAPH_max &at[1115]
+#define INT_GRAPH_min &at[1116]
+#define INT_GRAPH_axis &at[1117]
+#define INT_GRAPH_values &at[1118]
+#define INT_GRAPH_values_E &at[1119]
+
+#define BYTE_GRAPH &at[1121]
+#define BYTE_GRAPH_max &at[1122]
+#define BYTE_GRAPH_min &at[1123]
+#define BYTE_GRAPH_axis &at[1124]
+#define BYTE_GRAPH_values &at[1125]
 
 
 /**************************************************
@@ -3868,40 +4769,40 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define SEQ_SUBMIT &at[1176]
-#define SEQ_SUBMIT_sub &at[1177]
-#define SEQ_SUBMIT_data &at[1205]
-#define SEQ_SUBMIT_data_entrys &at[1206]
-#define SEQ_SUBMIT_data_entrys_E &at[1207]
-#define SEQ_SUBMIT_data_annots &at[1209]
-#define SEQ_SUBMIT_data_annots_E &at[1210]
-#define SEQ_SUBMIT_data_delete &at[1212]
-#define SEQ_SUBMIT_data_delete_E &at[1213]
-
-#define CONTACT_INFO &at[1180]
-#define CONTACT_INFO_name &at[1181]
-#define CONTACT_INFO_address &at[1182]
-#define CONTACT_INFO_address_E &at[1183]
-#define CONTACT_INFO_phone &at[1184]
-#define CONTACT_INFO_fax &at[1185]
-#define CONTACT_INFO_email &at[1186]
-#define CONTACT_INFO_telex &at[1187]
-#define CONTACT_INFO_owner_id &at[1188]
-#define CONTACT_INFO_password &at[1190]
-#define CONTACT_INFO_last_name &at[1191]
-#define CONTACT_INFO_first_name &at[1192]
-#define CONTACT_INFO_middle_initial &at[1193]
-#define CONTACT_INFO_contact &at[1194]
-
-#define SUBMIT_BLOCK &at[1178]
-#define SUBMIT_BLOCK_contact &at[1179]
-#define SUBMIT_BLOCK_cit &at[1196]
-#define SUBMIT_BLOCK_hup &at[1198]
-#define SUBMIT_BLOCK_reldate &at[1199]
-#define SUBMIT_BLOCK_subtype &at[1201]
-#define SUBMIT_BLOCK_tool &at[1202]
-#define SUBMIT_BLOCK_user_tag &at[1203]
-#define SUBMIT_BLOCK_comment &at[1204]
+#define SEQ_SUBMIT &at[1239]
+#define SEQ_SUBMIT_sub &at[1240]
+#define SEQ_SUBMIT_data &at[1268]
+#define SEQ_SUBMIT_data_entrys &at[1269]
+#define SEQ_SUBMIT_data_entrys_E &at[1270]
+#define SEQ_SUBMIT_data_annots &at[1272]
+#define SEQ_SUBMIT_data_annots_E &at[1273]
+#define SEQ_SUBMIT_data_delete &at[1275]
+#define SEQ_SUBMIT_data_delete_E &at[1276]
+
+#define CONTACT_INFO &at[1243]
+#define CONTACT_INFO_name &at[1244]
+#define CONTACT_INFO_address &at[1245]
+#define CONTACT_INFO_address_E &at[1246]
+#define CONTACT_INFO_phone &at[1247]
+#define CONTACT_INFO_fax &at[1248]
+#define CONTACT_INFO_email &at[1249]
+#define CONTACT_INFO_telex &at[1250]
+#define CONTACT_INFO_owner_id &at[1251]
+#define CONTACT_INFO_password &at[1253]
+#define CONTACT_INFO_last_name &at[1254]
+#define CONTACT_INFO_first_name &at[1255]
+#define CONTACT_INFO_middle_initial &at[1256]
+#define CONTACT_INFO_contact &at[1257]
+
+#define SUBMIT_BLOCK &at[1241]
+#define SUBMIT_BLOCK_contact &at[1242]
+#define SUBMIT_BLOCK_cit &at[1259]
+#define SUBMIT_BLOCK_hup &at[1261]
+#define SUBMIT_BLOCK_reldate &at[1262]
+#define SUBMIT_BLOCK_subtype &at[1264]
+#define SUBMIT_BLOCK_tool &at[1265]
+#define SUBMIT_BLOCK_user_tag &at[1266]
+#define SUBMIT_BLOCK_comment &at[1267]
 
 
 /**************************************************
@@ -3910,139 +4811,139 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define CN3D_STYLE_DICTIONARY &at[1215]
-#define STYLE_DICTIONARY_global_style &at[1216]
-#define STYLE_DICTIONARY_style_table &at[1269]
-#define STYLE_DICTIONARY_style_table_E &at[1270]
-
-#define CN3D_USER_ANNOTATIONS &at[1275]
-#define USER_ANNOTATIONS_annotations &at[1276]
-#define USER_ANNOTATIONS_annotations_E &at[1277]
-#define CN3D_USER_ANNOTATIONS_view &at[1299]
-
-#define CN3D_BACKBONE_TYPE &at[1222]
-
-#define CN3D_DRAWING_STYLE &at[1224]
-
-#define CN3D_COLOR_SCHEME &at[1226]
-
-#define CN3D_COLOR &at[1228]
-#define CN3D_COLOR_scale_factor &at[1229]
-#define CN3D_COLOR_red &at[1230]
-#define CN3D_COLOR_green &at[1231]
-#define CN3D_COLOR_blue &at[1232]
-#define CN3D_COLOR_alpha &at[1233]
-
-#define CN3D_BACKBONE_STYLE &at[1220]
-#define CN3D_BACKBONE_STYLE_type &at[1221]
-#define CN3D_BACKBONE_STYLE_style &at[1223]
-#define BACKBONE_STYLE_color_scheme &at[1225]
-#define CN3D_BACKBONE_STYLE_user_color &at[1227]
-
-#define CN3D_GENERAL_STYLE &at[1236]
-#define CN3D_GENERAL_STYLE_is_on &at[1237]
-#define CN3D_GENERAL_STYLE_style &at[1238]
-#define CN3D_GENERAL_STYLE_color_scheme &at[1239]
-#define CN3D_GENERAL_STYLE_user_color &at[1240]
-
-#define CN3D_BACKBONE_LABEL_STYLE &at[1261]
-#define BACKBONE_LABEL_STYLE_spacing &at[1262]
-#define CN3D_BACKBONE_LABEL_STYLE_type &at[1263]
-#define BACKBONE_LABEL_STYLE_number &at[1264]
-#define BACKBONE_LABEL_STYLE_termini &at[1265]
-#define CN3D_BACKBONE_LABEL_STYLE_white &at[1266]
-
-#define CN3D_STYLE_SETTINGS &at[1217]
-#define CN3D_STYLE_SETTINGS_name &at[1218]
-#define SETTINGS_protein_backbone &at[1219]
-#define SETTINGS_nucleotide_backbone &at[1234]
-#define SETTINGS_protein_sidechains &at[1235]
-#define SETTINGS_nucleotide_sidechains &at[1241]
-#define CN3D_STYLE_SETTINGS_heterogens &at[1242]
-#define CN3D_STYLE_SETTINGS_solvents &at[1243]
-#define CN3D_STYLE_SETTINGS_connections &at[1244]
-#define STYLE_SETTINGS_helix_objects &at[1245]
-#define STYLE_SETTINGS_strand_objects &at[1246]
-#define SETTINGS_virtual_disulfides_on &at[1247]
-#define virtual_disulfide_color &at[1248]
-#define STYLE_SETTINGS_hydrogens_on &at[1249]
-#define SETTINGS_background_color &at[1250]
-#define STYLE_SETTINGS_scale_factor &at[1251]
-#define SETTINGS_space_fill_proportion &at[1252]
-#define CN3D_STYLE_SETTINGS_ball_radius &at[1253]
-#define STYLE_SETTINGS_stick_radius &at[1254]
-#define CN3D_STYLE_SETTINGS_tube_radius &at[1255]
-#define SETTINGS_tube_worm_radius &at[1256]
-#define STYLE_SETTINGS_helix_radius &at[1257]
-#define STYLE_SETTINGS_strand_width &at[1258]
-#define SETTINGS_strand_thickness &at[1259]
-#define STYLE_SETTINGS_protein_labels &at[1260]
-#define SETTINGS_nucleotide_labels &at[1267]
-#define CN3D_STYLE_SETTINGS_ion_labels &at[1268]
-
-#define CN3D_STYLE_SETTINGS_SET &at[1330]
-#define CN3D_STYLE_SETTINGS_SET_E &at[1331]
-
-#define CN3D_STYLE_TABLE_ID &at[1273]
-
-#define CN3D_STYLE_TABLE_ITEM &at[1271]
-#define CN3D_STYLE_TABLE_ITEM_id &at[1272]
-#define CN3D_STYLE_TABLE_ITEM_style &at[1274]
-
-#define CN3D_RESIDUE_RANGE &at[1294]
-#define CN3D_RESIDUE_RANGE_from &at[1295]
-#define CN3D_RESIDUE_RANGE_to &at[1297]
-
-#define CN3D_MOLECULE_LOCATION &at[1289]
-#define MOLECULE_LOCATION_molecule_id &at[1290]
-#define CN3D_MOLECULE_LOCATION_residues &at[1292]
-#define MOLECULE_LOCATION_residues_E &at[1293]
-
-#define CN3D_OBJECT_LOCATION &at[1284]
-#define OBJECT_LOCATION_structure_id &at[1285]
-#define CN3D_OBJECT_LOCATION_residues &at[1287]
-#define CN3D_OBJECT_LOCATION_residues_E &at[1288]
-
-#define CN3D_USER_ANNOTATION &at[1278]
-#define CN3D_USER_ANNOTATION_name &at[1279]
-#define USER_ANNOTATION_description &at[1280]
-#define CN3D_USER_ANNOTATION_style_id &at[1281]
-#define CN3D_USER_ANNOTATION_residues &at[1282]
-#define CN3D_USER_ANNOTATION_residues_E &at[1283]
-#define CN3D_USER_ANNOTATION_is_on &at[1298]
-
-#define CN3D_GL_MATRIX &at[1308]
-#define CN3D_GL_MATRIX_m0 &at[1309]
-#define CN3D_GL_MATRIX_m1 &at[1310]
-#define CN3D_GL_MATRIX_m2 &at[1311]
-#define CN3D_GL_MATRIX_m3 &at[1312]
-#define CN3D_GL_MATRIX_m4 &at[1313]
-#define CN3D_GL_MATRIX_m5 &at[1314]
-#define CN3D_GL_MATRIX_m6 &at[1315]
-#define CN3D_GL_MATRIX_m7 &at[1316]
-#define CN3D_GL_MATRIX_m8 &at[1317]
-#define CN3D_GL_MATRIX_m9 &at[1318]
-#define CN3D_GL_MATRIX_m10 &at[1319]
-#define CN3D_GL_MATRIX_m11 &at[1320]
-#define CN3D_GL_MATRIX_m12 &at[1321]
-#define CN3D_GL_MATRIX_m13 &at[1322]
-#define CN3D_GL_MATRIX_m14 &at[1323]
-#define CN3D_GL_MATRIX_m15 &at[1324]
-
-#define CN3D_VECTOR &at[1326]
-#define CN3D_VECTOR_x &at[1327]
-#define CN3D_VECTOR_y &at[1328]
-#define CN3D_VECTOR_z &at[1329]
-
-#define CN3D_VIEW_SETTINGS &at[1300]
-#define VIEW_SETTINGS_camera_distance &at[1301]
-#define VIEW_SETTINGS_camera_angle_rad &at[1302]
-#define VIEW_SETTINGS_camera_look_at_X &at[1303]
-#define VIEW_SETTINGS_camera_look_at_Y &at[1304]
-#define VIEW_SETTINGS_camera_clip_near &at[1305]
-#define VIEW_SETTINGS_camera_clip_far &at[1306]
-#define CN3D_VIEW_SETTINGS_matrix &at[1307]
-#define VIEW_SETTINGS_rotation_center &at[1325]
+#define CN3D_STYLE_DICTIONARY &at[1278]
+#define STYLE_DICTIONARY_global_style &at[1279]
+#define STYLE_DICTIONARY_style_table &at[1332]
+#define STYLE_DICTIONARY_style_table_E &at[1333]
+
+#define CN3D_USER_ANNOTATIONS &at[1338]
+#define USER_ANNOTATIONS_annotations &at[1339]
+#define USER_ANNOTATIONS_annotations_E &at[1340]
+#define CN3D_USER_ANNOTATIONS_view &at[1362]
+
+#define CN3D_BACKBONE_TYPE &at[1285]
+
+#define CN3D_DRAWING_STYLE &at[1287]
+
+#define CN3D_COLOR_SCHEME &at[1289]
+
+#define CN3D_COLOR &at[1291]
+#define CN3D_COLOR_scale_factor &at[1292]
+#define CN3D_COLOR_red &at[1293]
+#define CN3D_COLOR_green &at[1294]
+#define CN3D_COLOR_blue &at[1295]
+#define CN3D_COLOR_alpha &at[1296]
+
+#define CN3D_BACKBONE_STYLE &at[1283]
+#define CN3D_BACKBONE_STYLE_type &at[1284]
+#define CN3D_BACKBONE_STYLE_style &at[1286]
+#define BACKBONE_STYLE_color_scheme &at[1288]
+#define CN3D_BACKBONE_STYLE_user_color &at[1290]
+
+#define CN3D_GENERAL_STYLE &at[1299]
+#define CN3D_GENERAL_STYLE_is_on &at[1300]
+#define CN3D_GENERAL_STYLE_style &at[1301]
+#define CN3D_GENERAL_STYLE_color_scheme &at[1302]
+#define CN3D_GENERAL_STYLE_user_color &at[1303]
+
+#define CN3D_BACKBONE_LABEL_STYLE &at[1324]
+#define BACKBONE_LABEL_STYLE_spacing &at[1325]
+#define CN3D_BACKBONE_LABEL_STYLE_type &at[1326]
+#define BACKBONE_LABEL_STYLE_number &at[1327]
+#define BACKBONE_LABEL_STYLE_termini &at[1328]
+#define CN3D_BACKBONE_LABEL_STYLE_white &at[1329]
+
+#define CN3D_STYLE_SETTINGS &at[1280]
+#define CN3D_STYLE_SETTINGS_name &at[1281]
+#define SETTINGS_protein_backbone &at[1282]
+#define SETTINGS_nucleotide_backbone &at[1297]
+#define SETTINGS_protein_sidechains &at[1298]
+#define SETTINGS_nucleotide_sidechains &at[1304]
+#define CN3D_STYLE_SETTINGS_heterogens &at[1305]
+#define CN3D_STYLE_SETTINGS_solvents &at[1306]
+#define CN3D_STYLE_SETTINGS_connections &at[1307]
+#define STYLE_SETTINGS_helix_objects &at[1308]
+#define STYLE_SETTINGS_strand_objects &at[1309]
+#define SETTINGS_virtual_disulfides_on &at[1310]
+#define virtual_disulfide_color &at[1311]
+#define STYLE_SETTINGS_hydrogens_on &at[1312]
+#define SETTINGS_background_color &at[1313]
+#define STYLE_SETTINGS_scale_factor &at[1314]
+#define SETTINGS_space_fill_proportion &at[1315]
+#define CN3D_STYLE_SETTINGS_ball_radius &at[1316]
+#define STYLE_SETTINGS_stick_radius &at[1317]
+#define CN3D_STYLE_SETTINGS_tube_radius &at[1318]
+#define SETTINGS_tube_worm_radius &at[1319]
+#define STYLE_SETTINGS_helix_radius &at[1320]
+#define STYLE_SETTINGS_strand_width &at[1321]
+#define SETTINGS_strand_thickness &at[1322]
+#define STYLE_SETTINGS_protein_labels &at[1323]
+#define SETTINGS_nucleotide_labels &at[1330]
+#define CN3D_STYLE_SETTINGS_ion_labels &at[1331]
+
+#define CN3D_STYLE_SETTINGS_SET &at[1393]
+#define CN3D_STYLE_SETTINGS_SET_E &at[1394]
+
+#define CN3D_STYLE_TABLE_ID &at[1336]
+
+#define CN3D_STYLE_TABLE_ITEM &at[1334]
+#define CN3D_STYLE_TABLE_ITEM_id &at[1335]
+#define CN3D_STYLE_TABLE_ITEM_style &at[1337]
+
+#define CN3D_RESIDUE_RANGE &at[1357]
+#define CN3D_RESIDUE_RANGE_from &at[1358]
+#define CN3D_RESIDUE_RANGE_to &at[1360]
+
+#define CN3D_MOLECULE_LOCATION &at[1352]
+#define MOLECULE_LOCATION_molecule_id &at[1353]
+#define CN3D_MOLECULE_LOCATION_residues &at[1355]
+#define MOLECULE_LOCATION_residues_E &at[1356]
+
+#define CN3D_OBJECT_LOCATION &at[1347]
+#define OBJECT_LOCATION_structure_id &at[1348]
+#define CN3D_OBJECT_LOCATION_residues &at[1350]
+#define CN3D_OBJECT_LOCATION_residues_E &at[1351]
+
+#define CN3D_USER_ANNOTATION &at[1341]
+#define CN3D_USER_ANNOTATION_name &at[1342]
+#define USER_ANNOTATION_description &at[1343]
+#define CN3D_USER_ANNOTATION_style_id &at[1344]
+#define CN3D_USER_ANNOTATION_residues &at[1345]
+#define CN3D_USER_ANNOTATION_residues_E &at[1346]
+#define CN3D_USER_ANNOTATION_is_on &at[1361]
+
+#define CN3D_GL_MATRIX &at[1371]
+#define CN3D_GL_MATRIX_m0 &at[1372]
+#define CN3D_GL_MATRIX_m1 &at[1373]
+#define CN3D_GL_MATRIX_m2 &at[1374]
+#define CN3D_GL_MATRIX_m3 &at[1375]
+#define CN3D_GL_MATRIX_m4 &at[1376]
+#define CN3D_GL_MATRIX_m5 &at[1377]
+#define CN3D_GL_MATRIX_m6 &at[1378]
+#define CN3D_GL_MATRIX_m7 &at[1379]
+#define CN3D_GL_MATRIX_m8 &at[1380]
+#define CN3D_GL_MATRIX_m9 &at[1381]
+#define CN3D_GL_MATRIX_m10 &at[1382]
+#define CN3D_GL_MATRIX_m11 &at[1383]
+#define CN3D_GL_MATRIX_m12 &at[1384]
+#define CN3D_GL_MATRIX_m13 &at[1385]
+#define CN3D_GL_MATRIX_m14 &at[1386]
+#define CN3D_GL_MATRIX_m15 &at[1387]
+
+#define CN3D_VECTOR &at[1389]
+#define CN3D_VECTOR_x &at[1390]
+#define CN3D_VECTOR_y &at[1391]
+#define CN3D_VECTOR_z &at[1392]
+
+#define CN3D_VIEW_SETTINGS &at[1363]
+#define VIEW_SETTINGS_camera_distance &at[1364]
+#define VIEW_SETTINGS_camera_angle_rad &at[1365]
+#define VIEW_SETTINGS_camera_look_at_X &at[1366]
+#define VIEW_SETTINGS_camera_look_at_Y &at[1367]
+#define VIEW_SETTINGS_camera_clip_near &at[1368]
+#define VIEW_SETTINGS_camera_clip_far &at[1369]
+#define CN3D_VIEW_SETTINGS_matrix &at[1370]
+#define VIEW_SETTINGS_rotation_center &at[1388]
 
 
 /**************************************************
@@ -4051,66 +4952,66 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define PROJECT &at[1332]
-#define PROJECT_descr &at[1333]
-#define PROJECT_data &at[1348]
-
-#define PROJECT_ITEM &at[1349]
-#define PROJECT_ITEM_pmuid &at[1350]
-#define PROJECT_ITEM_pmuid_E &at[1351]
-#define PROJECT_ITEM_protuid &at[1352]
-#define PROJECT_ITEM_protuid_E &at[1353]
-#define PROJECT_ITEM_nucuid &at[1354]
-#define PROJECT_ITEM_nucuid_E &at[1355]
-#define PROJECT_ITEM_sequid &at[1356]
-#define PROJECT_ITEM_sequid_E &at[1357]
-#define PROJECT_ITEM_genomeuid &at[1358]
-#define PROJECT_ITEM_genomeuid_E &at[1359]
-#define PROJECT_ITEM_structuid &at[1360]
-#define PROJECT_ITEM_structuid_E &at[1361]
-#define PROJECT_ITEM_pmid &at[1362]
-#define PROJECT_ITEM_pmid_E &at[1363]
-#define PROJECT_ITEM_protid &at[1365]
-#define PROJECT_ITEM_protid_E &at[1366]
-#define PROJECT_ITEM_nucid &at[1368]
-#define PROJECT_ITEM_nucid_E &at[1369]
-#define PROJECT_ITEM_seqid &at[1370]
-#define PROJECT_ITEM_seqid_E &at[1371]
-#define PROJECT_ITEM_genomeid &at[1372]
-#define PROJECT_ITEM_genomeid_E &at[1373]
-#define PROJECT_ITEM_structid &at[1374]
-#define PROJECT_ITEM_pment &at[1375]
-#define PROJECT_ITEM_pment_E &at[1376]
-#define PROJECT_ITEM_protent &at[1378]
-#define PROJECT_ITEM_protent_E &at[1379]
-#define PROJECT_ITEM_nucent &at[1381]
-#define PROJECT_ITEM_nucent_E &at[1382]
-#define PROJECT_ITEM_seqent &at[1383]
-#define PROJECT_ITEM_seqent_E &at[1384]
-#define PROJECT_ITEM_genomeent &at[1385]
-#define PROJECT_ITEM_genomeent_E &at[1386]
-#define PROJECT_ITEM_structent &at[1387]
-#define PROJECT_ITEM_seqannot &at[1388]
-#define PROJECT_ITEM_seqannot_E &at[1389]
-#define PROJECT_ITEM_loc &at[1391]
-#define PROJECT_ITEM_loc_E &at[1392]
-#define PROJECT_ITEM_proj &at[1394]
-#define PROJECT_ITEM_proj_E &at[1395]
-
-#define PROJECT_DESCR &at[1334]
-#define PROJECT_DESCR_id &at[1335]
-#define PROJECT_DESCR_id_E &at[1336]
-#define PROJECT_DESCR_name &at[1338]
-#define PROJECT_DESCR_descr &at[1339]
-#define PROJECT_DESCR_descr_E &at[1340]
-
-#define PROJECT_ID &at[1337]
-
-#define PROJDESC &at[1341]
-#define PROJDESC_pub &at[1342]
-#define PROJDESC_date &at[1344]
-#define PROJDESC_comment &at[1346]
-#define PROJDESC_title &at[1347]
+#define PROJECT &at[1395]
+#define PROJECT_descr &at[1396]
+#define PROJECT_data &at[1411]
+
+#define PROJECT_ITEM &at[1412]
+#define PROJECT_ITEM_pmuid &at[1413]
+#define PROJECT_ITEM_pmuid_E &at[1414]
+#define PROJECT_ITEM_protuid &at[1415]
+#define PROJECT_ITEM_protuid_E &at[1416]
+#define PROJECT_ITEM_nucuid &at[1417]
+#define PROJECT_ITEM_nucuid_E &at[1418]
+#define PROJECT_ITEM_sequid &at[1419]
+#define PROJECT_ITEM_sequid_E &at[1420]
+#define PROJECT_ITEM_genomeuid &at[1421]
+#define PROJECT_ITEM_genomeuid_E &at[1422]
+#define PROJECT_ITEM_structuid &at[1423]
+#define PROJECT_ITEM_structuid_E &at[1424]
+#define PROJECT_ITEM_pmid &at[1425]
+#define PROJECT_ITEM_pmid_E &at[1426]
+#define PROJECT_ITEM_protid &at[1428]
+#define PROJECT_ITEM_protid_E &at[1429]
+#define PROJECT_ITEM_nucid &at[1431]
+#define PROJECT_ITEM_nucid_E &at[1432]
+#define PROJECT_ITEM_seqid &at[1433]
+#define PROJECT_ITEM_seqid_E &at[1434]
+#define PROJECT_ITEM_genomeid &at[1435]
+#define PROJECT_ITEM_genomeid_E &at[1436]
+#define PROJECT_ITEM_structid &at[1437]
+#define PROJECT_ITEM_pment &at[1438]
+#define PROJECT_ITEM_pment_E &at[1439]
+#define PROJECT_ITEM_protent &at[1441]
+#define PROJECT_ITEM_protent_E &at[1442]
+#define PROJECT_ITEM_nucent &at[1444]
+#define PROJECT_ITEM_nucent_E &at[1445]
+#define PROJECT_ITEM_seqent &at[1446]
+#define PROJECT_ITEM_seqent_E &at[1447]
+#define PROJECT_ITEM_genomeent &at[1448]
+#define PROJECT_ITEM_genomeent_E &at[1449]
+#define PROJECT_ITEM_structent &at[1450]
+#define PROJECT_ITEM_seqannot &at[1451]
+#define PROJECT_ITEM_seqannot_E &at[1452]
+#define PROJECT_ITEM_loc &at[1454]
+#define PROJECT_ITEM_loc_E &at[1455]
+#define PROJECT_ITEM_proj &at[1457]
+#define PROJECT_ITEM_proj_E &at[1458]
+
+#define PROJECT_DESCR &at[1397]
+#define PROJECT_DESCR_id &at[1398]
+#define PROJECT_DESCR_id_E &at[1399]
+#define PROJECT_DESCR_name &at[1401]
+#define PROJECT_DESCR_descr &at[1402]
+#define PROJECT_DESCR_descr_E &at[1403]
+
+#define PROJECT_ID &at[1400]
+
+#define PROJDESC &at[1404]
+#define PROJDESC_pub &at[1405]
+#define PROJDESC_date &at[1407]
+#define PROJDESC_comment &at[1409]
+#define PROJDESC_title &at[1410]
 
 
 /**************************************************
@@ -4119,12 +5020,12 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define LINK_SET &at[1396]
-#define LINK_SET_num &at[1397]
-#define LINK_SET_uids &at[1398]
-#define LINK_SET_uids_E &at[1399]
-#define LINK_SET_weights &at[1400]
-#define LINK_SET_weights_E &at[1401]
+#define LINK_SET &at[1459]
+#define LINK_SET_num &at[1460]
+#define LINK_SET_uids &at[1461]
+#define LINK_SET_uids_E &at[1462]
+#define LINK_SET_weights &at[1463]
+#define LINK_SET_weights_E &at[1464]
 
 
 /**************************************************
@@ -4133,30 +5034,30 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define FEATDEF &at[1402]
-#define FEATDEF_typelabel &at[1403]
-#define FEATDEF_menulabel &at[1404]
-#define FEATDEF_featdef_key &at[1405]
-#define FEATDEF_seqfeat_key &at[1406]
-#define FEATDEF_entrygroup &at[1407]
-#define FEATDEF_displaygroup &at[1408]
-#define FEATDEF_molgroup &at[1409]
+#define FEATDEF &at[1465]
+#define FEATDEF_typelabel &at[1466]
+#define FEATDEF_menulabel &at[1467]
+#define FEATDEF_featdef_key &at[1468]
+#define FEATDEF_seqfeat_key &at[1469]
+#define FEATDEF_entrygroup &at[1470]
+#define FEATDEF_displaygroup &at[1471]
+#define FEATDEF_molgroup &at[1472]
 
-#define FEATDEFSET &at[1411]
-#define FEATDEFSET_E &at[1412]
+#define FEATDEFSET &at[1474]
+#define FEATDEFSET_E &at[1475]
 
-#define FEATDISPGROUP &at[1413]
-#define FEATDISPGROUP_groupkey &at[1414]
-#define FEATDISPGROUP_groupname &at[1415]
+#define FEATDISPGROUP &at[1476]
+#define FEATDISPGROUP_groupkey &at[1477]
+#define FEATDISPGROUP_groupname &at[1478]
 
-#define FEATDISPGROUPSET &at[1416]
-#define FEATDISPGROUPSET_E &at[1417]
+#define FEATDISPGROUPSET &at[1479]
+#define FEATDISPGROUPSET_E &at[1480]
 
-#define FEATMOLTYPE &at[1410]
+#define FEATMOLTYPE &at[1473]
 
-#define FEATDEFGROUPSET &at[1418]
-#define FEATDEFGROUPSET_groups &at[1419]
-#define FEATDEFGROUPSET_defs &at[1420]
+#define FEATDEFGROUPSET &at[1481]
+#define FEATDEFGROUPSET_groups &at[1482]
+#define FEATDEFGROUPSET_defs &at[1483]
 
 
 /**************************************************
@@ -4165,82 +5066,82 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define NCBI_MIME_ASN1 &at[1421]
-#define NCBI_MIME_ASN1_entrez &at[1422]
-#define NCBI_MIME_ASN1_alignstruc &at[1439]
-#define NCBI_MIME_ASN1_alignseq &at[1454]
-#define NCBI_MIME_ASN1_strucseq &at[1462]
-#define NCBI_MIME_ASN1_strucseqs &at[1469]
-#define NCBI_MIME_ASN1_general &at[1478]
-
-#define ENTREZ_GENERAL &at[1423]
-#define ENTREZ_GENERAL_title &at[1424]
-#define ENTREZ_GENERAL_data &at[1425]
-#define ENTREZ_GENERAL_data_ml &at[1426]
-#define ENTREZ_GENERAL_data_prot &at[1428]
-#define ENTREZ_GENERAL_data_nuc &at[1430]
-#define ENTREZ_GENERAL_data_genome &at[1431]
-#define ENTREZ_GENERAL_data_structure &at[1432]
-#define ENTREZ_GENERAL_data_strucAnnot &at[1434]
-#define ENTREZ_GENERAL_style &at[1436]
-#define ENTREZ_GENERAL_location &at[1438]
-
-#define BIOSTRUC_ALIGN &at[1440]
-#define BIOSTRUC_ALIGN_master &at[1441]
-#define BIOSTRUC_ALIGN_slaves &at[1442]
-#define BIOSTRUC_ALIGN_slaves_E &at[1443]
-#define BIOSTRUC_ALIGN_alignments &at[1444]
-#define BIOSTRUC_ALIGN_sequences &at[1445]
-#define BIOSTRUC_ALIGN_sequences_E &at[1446]
-#define BIOSTRUC_ALIGN_seqalign &at[1447]
-#define BIOSTRUC_ALIGN_seqalign_E &at[1448]
-#define BIOSTRUC_ALIGN_style_dictionary &at[1450]
-#define BIOSTRUC_ALIGN_user_annotations &at[1452]
-
-#define BIOSTRUC_ALIGN_SEQ &at[1455]
-#define BIOSTRUC_ALIGN_SEQ_sequences &at[1456]
-#define BIOSTRUC_ALIGN_SEQ_sequences_E &at[1457]
-#define BIOSTRUC_ALIGN_SEQ_seqalign &at[1458]
-#define BIOSTRUC_ALIGN_SEQ_seqalign_E &at[1459]
-#define ALIGN_SEQ_style_dictionary &at[1460]
-#define ALIGN_SEQ_user_annotations &at[1461]
-
-#define BIOSTRUC_SEQ &at[1463]
-#define BIOSTRUC_SEQ_structure &at[1464]
-#define BIOSTRUC_SEQ_sequences &at[1465]
-#define BIOSTRUC_SEQ_sequences_E &at[1466]
-#define BIOSTRUC_SEQ_style_dictionary &at[1467]
-#define BIOSTRUC_SEQ_user_annotations &at[1468]
-
-#define BIOSTRUC_SEQS &at[1470]
-#define BIOSTRUC_SEQS_structure &at[1471]
-#define BIOSTRUC_SEQS_sequences &at[1472]
-#define BIOSTRUC_SEQS_sequences_E &at[1473]
-#define BIOSTRUC_SEQS_seqalign &at[1474]
-#define BIOSTRUC_SEQS_seqalign_E &at[1475]
-#define BIOSTRUC_SEQS_style_dictionary &at[1476]
-#define BIOSTRUC_SEQS_user_annotations &at[1477]
-
-#define BIOSTRUC_SEQS_ALIGNS_CDD &at[1479]
-#define SEQS_ALIGNS_CDD_seq_align_data &at[1480]
-#define CDD_seq_align_data_bundle &at[1481]
-#define ALIGNS_CDD_seq_align_data_cdd &at[1492]
-#define SEQS_ALIGNS_CDD_structures &at[1494]
-#define SEQS_ALIGNS_CDD_structures_E &at[1495]
-#define SEQS_ALIGNS_CDD_structure_type &at[1496]
-
-#define BUNDLE_SEQS_ALIGNS &at[1482]
-#define BUNDLE_SEQS_ALIGNS_sequences &at[1483]
-#define BUNDLE_SEQS_ALIGNS_sequences_E &at[1484]
-#define BUNDLE_SEQS_ALIGNS_seqaligns &at[1485]
-#define BUNDLE_SEQS_ALIGNS_seqaligns_E &at[1486]
-#define BUNDLE_SEQS_ALIGNS_strucaligns &at[1487]
-#define BUNDLE_SEQS_ALIGNS_imports &at[1488]
-#define BUNDLE_SEQS_ALIGNS_imports_E &at[1489]
-#define SEQS_ALIGNS_style_dictionary &at[1490]
-#define SEQS_ALIGNS_user_annotations &at[1491]
-
-#define ENTREZ_STYLE &at[1437]
+#define NCBI_MIME_ASN1 &at[1484]
+#define NCBI_MIME_ASN1_entrez &at[1485]
+#define NCBI_MIME_ASN1_alignstruc &at[1502]
+#define NCBI_MIME_ASN1_alignseq &at[1517]
+#define NCBI_MIME_ASN1_strucseq &at[1525]
+#define NCBI_MIME_ASN1_strucseqs &at[1532]
+#define NCBI_MIME_ASN1_general &at[1541]
+
+#define ENTREZ_GENERAL &at[1486]
+#define ENTREZ_GENERAL_title &at[1487]
+#define ENTREZ_GENERAL_data &at[1488]
+#define ENTREZ_GENERAL_data_ml &at[1489]
+#define ENTREZ_GENERAL_data_prot &at[1491]
+#define ENTREZ_GENERAL_data_nuc &at[1493]
+#define ENTREZ_GENERAL_data_genome &at[1494]
+#define ENTREZ_GENERAL_data_structure &at[1495]
+#define ENTREZ_GENERAL_data_strucAnnot &at[1497]
+#define ENTREZ_GENERAL_style &at[1499]
+#define ENTREZ_GENERAL_location &at[1501]
+
+#define BIOSTRUC_ALIGN &at[1503]
+#define BIOSTRUC_ALIGN_master &at[1504]
+#define BIOSTRUC_ALIGN_slaves &at[1505]
+#define BIOSTRUC_ALIGN_slaves_E &at[1506]
+#define BIOSTRUC_ALIGN_alignments &at[1507]
+#define BIOSTRUC_ALIGN_sequences &at[1508]
+#define BIOSTRUC_ALIGN_sequences_E &at[1509]
+#define BIOSTRUC_ALIGN_seqalign &at[1510]
+#define BIOSTRUC_ALIGN_seqalign_E &at[1511]
+#define BIOSTRUC_ALIGN_style_dictionary &at[1513]
+#define BIOSTRUC_ALIGN_user_annotations &at[1515]
+
+#define BIOSTRUC_ALIGN_SEQ &at[1518]
+#define BIOSTRUC_ALIGN_SEQ_sequences &at[1519]
+#define BIOSTRUC_ALIGN_SEQ_sequences_E &at[1520]
+#define BIOSTRUC_ALIGN_SEQ_seqalign &at[1521]
+#define BIOSTRUC_ALIGN_SEQ_seqalign_E &at[1522]
+#define ALIGN_SEQ_style_dictionary &at[1523]
+#define ALIGN_SEQ_user_annotations &at[1524]
+
+#define BIOSTRUC_SEQ &at[1526]
+#define BIOSTRUC_SEQ_structure &at[1527]
+#define BIOSTRUC_SEQ_sequences &at[1528]
+#define BIOSTRUC_SEQ_sequences_E &at[1529]
+#define BIOSTRUC_SEQ_style_dictionary &at[1530]
+#define BIOSTRUC_SEQ_user_annotations &at[1531]
+
+#define BIOSTRUC_SEQS &at[1533]
+#define BIOSTRUC_SEQS_structure &at[1534]
+#define BIOSTRUC_SEQS_sequences &at[1535]
+#define BIOSTRUC_SEQS_sequences_E &at[1536]
+#define BIOSTRUC_SEQS_seqalign &at[1537]
+#define BIOSTRUC_SEQS_seqalign_E &at[1538]
+#define BIOSTRUC_SEQS_style_dictionary &at[1539]
+#define BIOSTRUC_SEQS_user_annotations &at[1540]
+
+#define BIOSTRUC_SEQS_ALIGNS_CDD &at[1542]
+#define SEQS_ALIGNS_CDD_seq_align_data &at[1543]
+#define CDD_seq_align_data_bundle &at[1544]
+#define ALIGNS_CDD_seq_align_data_cdd &at[1555]
+#define SEQS_ALIGNS_CDD_structures &at[1557]
+#define SEQS_ALIGNS_CDD_structures_E &at[1558]
+#define SEQS_ALIGNS_CDD_structure_type &at[1559]
+
+#define BUNDLE_SEQS_ALIGNS &at[1545]
+#define BUNDLE_SEQS_ALIGNS_sequences &at[1546]
+#define BUNDLE_SEQS_ALIGNS_sequences_E &at[1547]
+#define BUNDLE_SEQS_ALIGNS_seqaligns &at[1548]
+#define BUNDLE_SEQS_ALIGNS_seqaligns_E &at[1549]
+#define BUNDLE_SEQS_ALIGNS_strucaligns &at[1550]
+#define BUNDLE_SEQS_ALIGNS_imports &at[1551]
+#define BUNDLE_SEQS_ALIGNS_imports_E &at[1552]
+#define SEQS_ALIGNS_style_dictionary &at[1553]
+#define SEQS_ALIGNS_user_annotations &at[1554]
+
+#define ENTREZ_STYLE &at[1500]
 
 
 /**************************************************
@@ -4249,51 +5150,51 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define PRINTTEMPLATE &at[1497]
-#define PRINTTEMPLATE_name &at[1498]
-#define PRINTTEMPLATE_labelfrom &at[1500]
-#define PRINTTEMPLATE_format &at[1501]
+#define PRINTTEMPLATE &at[1560]
+#define PRINTTEMPLATE_name &at[1561]
+#define PRINTTEMPLATE_labelfrom &at[1563]
+#define PRINTTEMPLATE_format &at[1564]
 
-#define PRINTTEMPLATESET &at[1531]
-#define PRINTTEMPLATESET_E &at[1532]
+#define PRINTTEMPLATESET &at[1594]
+#define PRINTTEMPLATESET_E &at[1595]
 
-#define TEMPLATENAME &at[1499]
+#define TEMPLATENAME &at[1562]
 
-#define PRINTFORMAT &at[1502]
-#define PRINTFORMAT_asn1 &at[1503]
-#define PRINTFORMAT_label &at[1504]
-#define PRINTFORMAT_prefix &at[1505]
-#define PRINTFORMAT_suffix &at[1506]
-#define PRINTFORMAT_form &at[1507]
+#define PRINTFORMAT &at[1565]
+#define PRINTFORMAT_asn1 &at[1566]
+#define PRINTFORMAT_label &at[1567]
+#define PRINTFORMAT_prefix &at[1568]
+#define PRINTFORMAT_suffix &at[1569]
+#define PRINTFORMAT_form &at[1570]
 
-#define PRINTFORM &at[1508]
-#define PRINTFORM_block &at[1509]
-#define PRINTFORM_boolean &at[1514]
-#define PRINTFORM_enum &at[1518]
-#define PRINTFORM_text &at[1522]
-#define PRINTFORM_use_template &at[1525]
-#define PRINTFORM_user &at[1526]
-#define PRINTFORM_null &at[1530]
+#define PRINTFORM &at[1571]
+#define PRINTFORM_block &at[1572]
+#define PRINTFORM_boolean &at[1577]
+#define PRINTFORM_enum &at[1581]
+#define PRINTFORM_text &at[1585]
+#define PRINTFORM_use_template &at[1588]
+#define PRINTFORM_user &at[1589]
+#define PRINTFORM_null &at[1593]
 
-#define PRINTFORMBLOCK &at[1510]
-#define PRINTFORMBLOCK_separator &at[1511]
-#define PRINTFORMBLOCK_components &at[1512]
-#define PRINTFORMBLOCK_components_E &at[1513]
+#define PRINTFORMBLOCK &at[1573]
+#define PRINTFORMBLOCK_separator &at[1574]
+#define PRINTFORMBLOCK_components &at[1575]
+#define PRINTFORMBLOCK_components_E &at[1576]
 
-#define PRINTFORMBOOLEAN &at[1515]
-#define PRINTFORMBOOLEAN_true &at[1516]
-#define PRINTFORMBOOLEAN_false &at[1517]
+#define PRINTFORMBOOLEAN &at[1578]
+#define PRINTFORMBOOLEAN_true &at[1579]
+#define PRINTFORMBOOLEAN_false &at[1580]
 
-#define PRINTFORMENUM &at[1519]
-#define PRINTFORMENUM_values &at[1520]
-#define PRINTFORMENUM_values_E &at[1521]
+#define PRINTFORMENUM &at[1582]
+#define PRINTFORMENUM_values &at[1583]
+#define PRINTFORMENUM_values_E &at[1584]
 
-#define PRINTFORMTEXT &at[1523]
-#define PRINTFORMTEXT_textfunc &at[1524]
+#define PRINTFORMTEXT &at[1586]
+#define PRINTFORMTEXT_textfunc &at[1587]
 
-#define USERFORMAT &at[1527]
-#define USERFORMAT_printfunc &at[1528]
-#define USERFORMAT_defaultfunc &at[1529]
+#define USERFORMAT &at[1590]
+#define USERFORMAT_printfunc &at[1591]
+#define USERFORMAT_defaultfunc &at[1592]
 
 
 /**************************************************
@@ -4302,93 +5203,93 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define GBSEQ &at[1533]
-#define GBSEQ_locus &at[1534]
-#define GBSEQ_length &at[1535]
-#define GBSEQ_strandedness &at[1536]
-#define GBSEQ_moltype &at[1537]
-#define GBSEQ_topology &at[1538]
-#define GBSEQ_division &at[1539]
-#define GBSEQ_update_date &at[1540]
-#define GBSEQ_create_date &at[1541]
-#define GBSEQ_update_release &at[1542]
-#define GBSEQ_create_release &at[1543]
-#define GBSEQ_definition &at[1544]
-#define GBSEQ_primary_accession &at[1545]
-#define GBSEQ_entry_version &at[1546]
-#define GBSEQ_accession_version &at[1547]
-#define GBSEQ_other_seqids &at[1548]
-#define GBSEQ_other_seqids_E &at[1549]
-#define GBSEQ_secondary_accessions &at[1551]
-#define GBSEQ_secondary_accessions_E &at[1552]
-#define GBSEQ_project &at[1554]
-#define GBSEQ_keywords &at[1555]
-#define GBSEQ_keywords_E &at[1556]
-#define GBSEQ_segment &at[1558]
-#define GBSEQ_source &at[1559]
-#define GBSEQ_organism &at[1560]
-#define GBSEQ_taxonomy &at[1561]
-#define GBSEQ_references &at[1562]
-#define GBSEQ_references_E &at[1563]
-#define GBSEQ_comment &at[1580]
-#define GBSEQ_primary &at[1581]
-#define GBSEQ_source_db &at[1582]
-#define GBSEQ_database_reference &at[1583]
-#define GBSEQ_feature_table &at[1584]
-#define GBSEQ_feature_table_E &at[1585]
-#define GBSEQ_sequence &at[1606]
-#define GBSEQ_contig &at[1607]
-
-#define GBSEQID &at[1550]
-
-#define GBSECONDARY_ACCN &at[1553]
-
-#define GBKEYWORD &at[1557]
-
-#define GBREFERENCE &at[1564]
-#define GBREFERENCE_reference &at[1565]
-#define GBREFERENCE_position &at[1566]
-#define GBREFERENCE_authors &at[1567]
-#define GBREFERENCE_authors_E &at[1568]
-#define GBREFERENCE_consortium &at[1570]
-#define GBREFERENCE_title &at[1571]
-#define GBREFERENCE_journal &at[1572]
-#define GBREFERENCE_xref &at[1573]
-#define GBREFERENCE_xref_E &at[1574]
-#define GBREFERENCE_pubmed &at[1578]
-#define GBREFERENCE_remark &at[1579]
-
-#define GBFEATURE &at[1586]
-#define GBFEATURE_key &at[1587]
-#define GBFEATURE_location &at[1588]
-#define GBFEATURE_intervals &at[1589]
-#define GBFEATURE_intervals_E &at[1590]
-#define GBFEATURE_operator &at[1598]
-#define GBFEATURE_partial5 &at[1599]
-#define GBFEATURE_partial3 &at[1600]
-#define GBFEATURE_quals &at[1601]
-#define GBFEATURE_quals_E &at[1602]
-
-#define GBAUTHOR &at[1569]
-
-#define GBXREF &at[1575]
-#define GBXREF_dbname &at[1576]
-#define GBXREF_id &at[1577]
-
-#define GBINTERVAL &at[1591]
-#define GBINTERVAL_from &at[1592]
-#define GBINTERVAL_to &at[1593]
-#define GBINTERVAL_point &at[1594]
-#define GBINTERVAL_iscomp &at[1595]
-#define GBINTERVAL_interbp &at[1596]
-#define GBINTERVAL_accession &at[1597]
-
-#define GBQUALIFIER &at[1603]
-#define GBQUALIFIER_name &at[1604]
-#define GBQUALIFIER_value &at[1605]
-
-#define GBSET &at[1608]
-#define GBSET_E &at[1609]
+#define GBSEQ &at[1596]
+#define GBSEQ_locus &at[1597]
+#define GBSEQ_length &at[1598]
+#define GBSEQ_strandedness &at[1599]
+#define GBSEQ_moltype &at[1600]
+#define GBSEQ_topology &at[1601]
+#define GBSEQ_division &at[1602]
+#define GBSEQ_update_date &at[1603]
+#define GBSEQ_create_date &at[1604]
+#define GBSEQ_update_release &at[1605]
+#define GBSEQ_create_release &at[1606]
+#define GBSEQ_definition &at[1607]
+#define GBSEQ_primary_accession &at[1608]
+#define GBSEQ_entry_version &at[1609]
+#define GBSEQ_accession_version &at[1610]
+#define GBSEQ_other_seqids &at[1611]
+#define GBSEQ_other_seqids_E &at[1612]
+#define GBSEQ_secondary_accessions &at[1614]
+#define GBSEQ_secondary_accessions_E &at[1615]
+#define GBSEQ_project &at[1617]
+#define GBSEQ_keywords &at[1618]
+#define GBSEQ_keywords_E &at[1619]
+#define GBSEQ_segment &at[1621]
+#define GBSEQ_source &at[1622]
+#define GBSEQ_organism &at[1623]
+#define GBSEQ_taxonomy &at[1624]
+#define GBSEQ_references &at[1625]
+#define GBSEQ_references_E &at[1626]
+#define GBSEQ_comment &at[1643]
+#define GBSEQ_primary &at[1644]
+#define GBSEQ_source_db &at[1645]
+#define GBSEQ_database_reference &at[1646]
+#define GBSEQ_feature_table &at[1647]
+#define GBSEQ_feature_table_E &at[1648]
+#define GBSEQ_sequence &at[1669]
+#define GBSEQ_contig &at[1670]
+
+#define GBSEQID &at[1613]
+
+#define GBSECONDARY_ACCN &at[1616]
+
+#define GBKEYWORD &at[1620]
+
+#define GBREFERENCE &at[1627]
+#define GBREFERENCE_reference &at[1628]
+#define GBREFERENCE_position &at[1629]
+#define GBREFERENCE_authors &at[1630]
+#define GBREFERENCE_authors_E &at[1631]
+#define GBREFERENCE_consortium &at[1633]
+#define GBREFERENCE_title &at[1634]
+#define GBREFERENCE_journal &at[1635]
+#define GBREFERENCE_xref &at[1636]
+#define GBREFERENCE_xref_E &at[1637]
+#define GBREFERENCE_pubmed &at[1641]
+#define GBREFERENCE_remark &at[1642]
+
+#define GBFEATURE &at[1649]
+#define GBFEATURE_key &at[1650]
+#define GBFEATURE_location &at[1651]
+#define GBFEATURE_intervals &at[1652]
+#define GBFEATURE_intervals_E &at[1653]
+#define GBFEATURE_operator &at[1661]
+#define GBFEATURE_partial5 &at[1662]
+#define GBFEATURE_partial3 &at[1663]
+#define GBFEATURE_quals &at[1664]
+#define GBFEATURE_quals_E &at[1665]
+
+#define GBAUTHOR &at[1632]
+
+#define GBXREF &at[1638]
+#define GBXREF_dbname &at[1639]
+#define GBXREF_id &at[1640]
+
+#define GBINTERVAL &at[1654]
+#define GBINTERVAL_from &at[1655]
+#define GBINTERVAL_to &at[1656]
+#define GBINTERVAL_point &at[1657]
+#define GBINTERVAL_iscomp &at[1658]
+#define GBINTERVAL_interbp &at[1659]
+#define GBINTERVAL_accession &at[1660]
+
+#define GBQUALIFIER &at[1666]
+#define GBQUALIFIER_name &at[1667]
+#define GBQUALIFIER_value &at[1668]
+
+#define GBSET &at[1671]
+#define GBSET_E &at[1672]
 
 
 /**************************************************
@@ -4397,93 +5298,93 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define INSDSEQ &at[1610]
-#define INSDSEQ_locus &at[1611]
-#define INSDSEQ_length &at[1612]
-#define INSDSEQ_strandedness &at[1613]
-#define INSDSEQ_moltype &at[1614]
-#define INSDSEQ_topology &at[1615]
-#define INSDSEQ_division &at[1616]
-#define INSDSEQ_update_date &at[1617]
-#define INSDSEQ_create_date &at[1618]
-#define INSDSEQ_update_release &at[1619]
-#define INSDSEQ_create_release &at[1620]
-#define INSDSEQ_definition &at[1621]
-#define INSDSEQ_primary_accession &at[1622]
-#define INSDSEQ_entry_version &at[1623]
-#define INSDSEQ_accession_version &at[1624]
-#define INSDSEQ_other_seqids &at[1625]
-#define INSDSEQ_other_seqids_E &at[1626]
-#define INSDSEQ_secondary_accessions &at[1628]
-#define INSDSEQ_secondary_accessions_E &at[1629]
-#define INSDSEQ_project &at[1631]
-#define INSDSEQ_keywords &at[1632]
-#define INSDSEQ_keywords_E &at[1633]
-#define INSDSEQ_segment &at[1635]
-#define INSDSEQ_source &at[1636]
-#define INSDSEQ_organism &at[1637]
-#define INSDSEQ_taxonomy &at[1638]
-#define INSDSEQ_references &at[1639]
-#define INSDSEQ_references_E &at[1640]
-#define INSDSEQ_comment &at[1657]
-#define INSDSEQ_primary &at[1658]
-#define INSDSEQ_source_db &at[1659]
-#define INSDSEQ_database_reference &at[1660]
-#define INSDSEQ_feature_table &at[1661]
-#define INSDSEQ_feature_table_E &at[1662]
-#define INSDSEQ_sequence &at[1683]
-#define INSDSEQ_contig &at[1684]
-
-#define INSDSEQID &at[1627]
-
-#define INSDSECONDARY_ACCN &at[1630]
-
-#define INSDKEYWORD &at[1634]
-
-#define INSDREFERENCE &at[1641]
-#define INSDREFERENCE_reference &at[1642]
-#define INSDREFERENCE_position &at[1643]
-#define INSDREFERENCE_authors &at[1644]
-#define INSDREFERENCE_authors_E &at[1645]
-#define INSDREFERENCE_consortium &at[1647]
-#define INSDREFERENCE_title &at[1648]
-#define INSDREFERENCE_journal &at[1649]
-#define INSDREFERENCE_xref &at[1650]
-#define INSDREFERENCE_xref_E &at[1651]
-#define INSDREFERENCE_pubmed &at[1655]
-#define INSDREFERENCE_remark &at[1656]
-
-#define INSDFEATURE &at[1663]
-#define INSDFEATURE_key &at[1664]
-#define INSDFEATURE_location &at[1665]
-#define INSDFEATURE_intervals &at[1666]
-#define INSDFEATURE_intervals_E &at[1667]
-#define INSDFEATURE_operator &at[1675]
-#define INSDFEATURE_partial5 &at[1676]
-#define INSDFEATURE_partial3 &at[1677]
-#define INSDFEATURE_quals &at[1678]
-#define INSDFEATURE_quals_E &at[1679]
-
-#define INSDAUTHOR &at[1646]
-
-#define INSDXREF &at[1652]
-#define INSDXREF_dbname &at[1653]
-#define INSDXREF_id &at[1654]
-
-#define INSDINTERVAL &at[1668]
-#define INSDINTERVAL_from &at[1669]
-#define INSDINTERVAL_to &at[1670]
-#define INSDINTERVAL_point &at[1671]
-#define INSDINTERVAL_iscomp &at[1672]
-#define INSDINTERVAL_interbp &at[1673]
-#define INSDINTERVAL_accession &at[1674]
-
-#define INSDQUALIFIER &at[1680]
-#define INSDQUALIFIER_name &at[1681]
-#define INSDQUALIFIER_value &at[1682]
-
-#define INSDSET &at[1685]
-#define INSDSET_E &at[1686]
+#define INSDSEQ &at[1673]
+#define INSDSEQ_locus &at[1674]
+#define INSDSEQ_length &at[1675]
+#define INSDSEQ_strandedness &at[1676]
+#define INSDSEQ_moltype &at[1677]
+#define INSDSEQ_topology &at[1678]
+#define INSDSEQ_division &at[1679]
+#define INSDSEQ_update_date &at[1680]
+#define INSDSEQ_create_date &at[1681]
+#define INSDSEQ_update_release &at[1682]
+#define INSDSEQ_create_release &at[1683]
+#define INSDSEQ_definition &at[1684]
+#define INSDSEQ_primary_accession &at[1685]
+#define INSDSEQ_entry_version &at[1686]
+#define INSDSEQ_accession_version &at[1687]
+#define INSDSEQ_other_seqids &at[1688]
+#define INSDSEQ_other_seqids_E &at[1689]
+#define INSDSEQ_secondary_accessions &at[1691]
+#define INSDSEQ_secondary_accessions_E &at[1692]
+#define INSDSEQ_project &at[1694]
+#define INSDSEQ_keywords &at[1695]
+#define INSDSEQ_keywords_E &at[1696]
+#define INSDSEQ_segment &at[1698]
+#define INSDSEQ_source &at[1699]
+#define INSDSEQ_organism &at[1700]
+#define INSDSEQ_taxonomy &at[1701]
+#define INSDSEQ_references &at[1702]
+#define INSDSEQ_references_E &at[1703]
+#define INSDSEQ_comment &at[1720]
+#define INSDSEQ_primary &at[1721]
+#define INSDSEQ_source_db &at[1722]
+#define INSDSEQ_database_reference &at[1723]
+#define INSDSEQ_feature_table &at[1724]
+#define INSDSEQ_feature_table_E &at[1725]
+#define INSDSEQ_sequence &at[1746]
+#define INSDSEQ_contig &at[1747]
+
+#define INSDSEQID &at[1690]
+
+#define INSDSECONDARY_ACCN &at[1693]
+
+#define INSDKEYWORD &at[1697]
+
+#define INSDREFERENCE &at[1704]
+#define INSDREFERENCE_reference &at[1705]
+#define INSDREFERENCE_position &at[1706]
+#define INSDREFERENCE_authors &at[1707]
+#define INSDREFERENCE_authors_E &at[1708]
+#define INSDREFERENCE_consortium &at[1710]
+#define INSDREFERENCE_title &at[1711]
+#define INSDREFERENCE_journal &at[1712]
+#define INSDREFERENCE_xref &at[1713]
+#define INSDREFERENCE_xref_E &at[1714]
+#define INSDREFERENCE_pubmed &at[1718]
+#define INSDREFERENCE_remark &at[1719]
+
+#define INSDFEATURE &at[1726]
+#define INSDFEATURE_key &at[1727]
+#define INSDFEATURE_location &at[1728]
+#define INSDFEATURE_intervals &at[1729]
+#define INSDFEATURE_intervals_E &at[1730]
+#define INSDFEATURE_operator &at[1738]
+#define INSDFEATURE_partial5 &at[1739]
+#define INSDFEATURE_partial3 &at[1740]
+#define INSDFEATURE_quals &at[1741]
+#define INSDFEATURE_quals_E &at[1742]
+
+#define INSDAUTHOR &at[1709]
+
+#define INSDXREF &at[1715]
+#define INSDXREF_dbname &at[1716]
+#define INSDXREF_id &at[1717]
+
+#define INSDINTERVAL &at[1731]
+#define INSDINTERVAL_from &at[1732]
+#define INSDINTERVAL_to &at[1733]
+#define INSDINTERVAL_point &at[1734]
+#define INSDINTERVAL_iscomp &at[1735]
+#define INSDINTERVAL_interbp &at[1736]
+#define INSDINTERVAL_accession &at[1737]
+
+#define INSDQUALIFIER &at[1743]
+#define INSDQUALIFIER_name &at[1744]
+#define INSDQUALIFIER_value &at[1745]
+
+#define INSDSET &at[1748]
+#define INSDSET_E &at[1749]
 
 
 /**************************************************
@@ -4492,20 +5393,20 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define TSEQ &at[1687]
-#define TSEQ_seqtype &at[1688]
-#define TSEQ_gi &at[1689]
-#define TSEQ_accver &at[1690]
-#define TSEQ_sid &at[1691]
-#define TSEQ_local &at[1692]
-#define TSEQ_taxid &at[1693]
-#define TSEQ_orgname &at[1694]
-#define TSEQ_defline &at[1695]
-#define TSEQ_length &at[1696]
-#define TSEQ_sequence &at[1697]
+#define TSEQ &at[1750]
+#define TSEQ_seqtype &at[1751]
+#define TSEQ_gi &at[1752]
+#define TSEQ_accver &at[1753]
+#define TSEQ_sid &at[1754]
+#define TSEQ_local &at[1755]
+#define TSEQ_taxid &at[1756]
+#define TSEQ_orgname &at[1757]
+#define TSEQ_defline &at[1758]
+#define TSEQ_length &at[1759]
+#define TSEQ_sequence &at[1760]
 
-#define TSEQSET &at[1698]
-#define TSEQSET_E &at[1699]
+#define TSEQSET &at[1761]
+#define TSEQSET_E &at[1762]
 
 
 /**************************************************
@@ -4514,68 +5415,435 @@ static AsnModulePtr amp = ampx;
 *
 **************************************************/
 
-#define PSSM &at[1700]
-#define PSSM_isProtein &at[1701]
-#define PSSM_identifier &at[1702]
-#define PSSM_numRows &at[1704]
-#define PSSM_numColumns &at[1705]
-#define PSSM_rowLabels &at[1706]
-#define PSSM_rowLabels_E &at[1707]
-#define PSSM_byRow &at[1708]
-#define PSSM_query &at[1709]
-#define PSSM_intermediateData &at[1711]
-#define PSSM_finalData &at[1719]
-
-#define PSSMINTERMEDIATEDATA &at[1712]
-#define resFreqsPerPos &at[1713]
-#define resFreqsPerPos_E &at[1714]
-#define weightedResFreqsPerPos &at[1715]
-#define weightedResFreqsPerPos_E &at[1716]
-#define PSSMINTERMEDIATEDATA_freqRatios &at[1717]
-#define freqRatios_E &at[1718]
-
-#define PSSMFINALDATA &at[1720]
-#define PSSMFINALDATA_scores &at[1721]
-#define PSSMFINALDATA_scores_E &at[1722]
-#define PSSMFINALDATA_lambda &at[1723]
-#define PSSMFINALDATA_kappa &at[1724]
-#define PSSMFINALDATA_h &at[1725]
-#define PSSMFINALDATA_scalingFactor &at[1726]
-
-#define PSSMPARAMETERS &at[1727]
-#define PSSMPARAMETERS_pseudocount &at[1728]
-#define PSSMPARAMETERS_rpsdbparams &at[1729]
-#define PSSMPARAMETERS_constraints &at[1734]
-
-#define PSSMWITHPARAMETERS &at[1755]
-#define PSSMWITHPARAMETERS_pssm &at[1756]
-#define PSSMWITHPARAMETERS_params &at[1757]
-
-#define BLOCKPROPERTY &at[1746]
-#define BLOCKPROPERTY_type &at[1747]
-#define BLOCKPROPERTY_intvalue &at[1748]
-#define BLOCKPROPERTY_textvalue &at[1749]
-
-#define COREBLOCK &at[1739]
-#define COREBLOCK_start &at[1740]
-#define COREBLOCK_stop &at[1741]
-#define COREBLOCK_minstart &at[1742]
-#define COREBLOCK_maxstop &at[1743]
-#define COREBLOCK_property &at[1744]
-#define COREBLOCK_property_E &at[1745]
-
-#define LOOPCONSTRAINT &at[1752]
-#define LOOPCONSTRAINT_minlength &at[1753]
-#define LOOPCONSTRAINT_maxlength &at[1754]
-
-#define COREDEF &at[1735]
-#define COREDEF_nblocks &at[1736]
-#define COREDEF_blocks &at[1737]
-#define COREDEF_blocks_E &at[1738]
-#define COREDEF_loops &at[1750]
-#define COREDEF_loops_E &at[1751]
-
-#define FORMATRPSDBPARAMETERS &at[1730]
-#define matrixName &at[1731]
-#define FORMATRPSDBPARAMETERS_gapOpen &at[1732]
-#define FORMATRPSDBPARAMETERS_gapExtend &at[1733]
+#define PSSM &at[1763]
+#define PSSM_isProtein &at[1764]
+#define PSSM_identifier &at[1765]
+#define PSSM_numRows &at[1767]
+#define PSSM_numColumns &at[1768]
+#define PSSM_rowLabels &at[1769]
+#define PSSM_rowLabels_E &at[1770]
+#define PSSM_byRow &at[1771]
+#define PSSM_query &at[1772]
+#define PSSM_intermediateData &at[1774]
+#define PSSM_finalData &at[1782]
+
+#define PSSMINTERMEDIATEDATA &at[1775]
+#define resFreqsPerPos &at[1776]
+#define resFreqsPerPos_E &at[1777]
+#define weightedResFreqsPerPos &at[1778]
+#define weightedResFreqsPerPos_E &at[1779]
+#define PSSMINTERMEDIATEDATA_freqRatios &at[1780]
+#define freqRatios_E &at[1781]
+
+#define PSSMFINALDATA &at[1783]
+#define PSSMFINALDATA_scores &at[1784]
+#define PSSMFINALDATA_scores_E &at[1785]
+#define PSSMFINALDATA_lambda &at[1786]
+#define PSSMFINALDATA_kappa &at[1787]
+#define PSSMFINALDATA_h &at[1788]
+#define PSSMFINALDATA_scalingFactor &at[1789]
+
+#define PSSMPARAMETERS &at[1790]
+#define PSSMPARAMETERS_pseudocount &at[1791]
+#define PSSMPARAMETERS_rpsdbparams &at[1792]
+#define PSSMPARAMETERS_constraints &at[1797]
+
+#define PSSMWITHPARAMETERS &at[1818]
+#define PSSMWITHPARAMETERS_pssm &at[1819]
+#define PSSMWITHPARAMETERS_params &at[1820]
+
+#define BLOCKPROPERTY &at[1809]
+#define BLOCKPROPERTY_type &at[1810]
+#define BLOCKPROPERTY_intvalue &at[1811]
+#define BLOCKPROPERTY_textvalue &at[1812]
+
+#define COREBLOCK &at[1802]
+#define COREBLOCK_start &at[1803]
+#define COREBLOCK_stop &at[1804]
+#define COREBLOCK_minstart &at[1805]
+#define COREBLOCK_maxstop &at[1806]
+#define COREBLOCK_property &at[1807]
+#define COREBLOCK_property_E &at[1808]
+
+#define LOOPCONSTRAINT &at[1815]
+#define LOOPCONSTRAINT_minlength &at[1816]
+#define LOOPCONSTRAINT_maxlength &at[1817]
+
+#define COREDEF &at[1798]
+#define COREDEF_nblocks &at[1799]
+#define COREDEF_blocks &at[1800]
+#define COREDEF_blocks_E &at[1801]
+#define COREDEF_loops &at[1813]
+#define COREDEF_loops_E &at[1814]
+
+#define FORMATRPSDBPARAMETERS &at[1793]
+#define matrixName &at[1794]
+#define FORMATRPSDBPARAMETERS_gapOpen &at[1795]
+#define FORMATRPSDBPARAMETERS_gapExtend &at[1796]
+
+
+/**************************************************
+*
+*    Defines for Module NCBI-Macro
+*
+**************************************************/
+
+#define AECR_ACTION &at[1821]
+#define AECR_ACTION_action &at[1822]
+#define AECR_ACTION_constraint &at[1949]
+
+#define PARSE_ACTION &at[1991]
+#define PARSE_ACTION_portion &at[1992]
+#define PARSE_ACTION_src &at[1993]
+#define PARSE_ACTION_dest &at[2009]
+#define PARSE_ACTION_capitalization &at[2021]
+#define PARSE_ACTION_remove_from_parsed &at[2023]
+#define PARSE_ACTION_existing_text &at[2024]
+
+#define MACRO_ACTION_LIST &at[2025]
+#define MACRO_ACTION_LIST_E &at[2026]
+
+#define STRING_LOCATION &at[1848]
+
+#define STRING_CONSTRAINT &at[1845]
+#define STRING_CONSTRAINT_match_text &at[1846]
+#define CONSTRAINT_match_location &at[1847]
+#define CONSTRAINT_case_sensitive &at[1849]
+#define STRING_CONSTRAINT_whole_word &at[1850]
+#define STRING_CONSTRAINT_not_present &at[1851]
+
+#define STRAND_CONSTRAINT &at[1957]
+
+#define SEQTYPE_CONSTRAINT &at[1959]
+
+#define LOCATION_CONSTRAINT &at[1955]
+#define LOCATION_CONSTRAINT_strand &at[1956]
+#define LOCATION_CONSTRAINT_seq_type &at[1958]
+
+#define OBJECT_TYPE_CONSTRAINT &at[1966]
+
+#define FEATURE_TYPE &at[1839]
+
+#define FEAT_QUAL_LEGAL &at[1843]
+
+#define FEAT_QUAL_LEGAL_VAL &at[2058]
+#define FEAT_QUAL_LEGAL_VAL_qual &at[2059]
+#define FEAT_QUAL_LEGAL_VAL_val &at[2060]
+
+#define FEAT_QUAL_LEGAL_VAL_CHOICE &at[2056]
+#define FEAT_QUAL_LEGAL_VAL_CHOICE_qual &at[2057]
+
+#define FEAT_QUAL_LEGAL_SET &at[2054]
+#define FEAT_QUAL_LEGAL_SET_E &at[2055]
+
+#define FEAT_QUAL_CHOICE &at[1841]
+#define FEAT_QUAL_CHOICE_legal_qual &at[1842]
+#define FEAT_QUAL_CHOICE_illegal_qual &at[1844]
+
+#define FEATURE_FIELD &at[1837]
+#define FEATURE_FIELD_type &at[1838]
+#define FEATURE_FIELD_field &at[1840]
+
+#define FEATURE_FIELD_LEGAL &at[2017]
+#define FEATURE_FIELD_LEGAL_type &at[2018]
+#define FEATURE_FIELD_LEGAL_field &at[2019]
+
+#define FEATURE_FIELD_PAIR &at[1889]
+#define FEATURE_FIELD_PAIR_type &at[1890]
+#define FEATURE_FIELD_PAIR_field_from &at[1891]
+#define FEATURE_FIELD_PAIR_field_to &at[1892]
+
+#define SOURCE_QUAL &at[1831]
+
+#define SOURCE_QUAL_PAIR &at[1885]
+#define SOURCE_QUAL_PAIR_field_from &at[1886]
+#define SOURCE_QUAL_PAIR_field_to &at[1887]
+
+#define SOURCE_LOCATION &at[1833]
+
+#define SOURCE_ORIGIN &at[1835]
+
+#define SOURCE_QUAL_CHOICE &at[1829]
+#define SOURCE_QUAL_CHOICE_textqual &at[1830]
+#define SOURCE_QUAL_CHOICE_location &at[1832]
+#define SOURCE_QUAL_CHOICE_origin &at[1834]
+
+#define CDSGENEPROT_FIELD &at[1853]
+
+#define CDSGENEPROT_FIELD_PAIR &at[1894]
+#define FIELD_PAIR_field_from &at[1895]
+#define CDSGENEPROT_FIELD_PAIR_field_to &at[1896]
+
+#define MOLECULE_TYPE &at[1857]
+
+#define TECHNIQUE_TYPE &at[1859]
+
+#define COMPLETEDNESS_TYPE &at[1861]
+
+#define MOLECULE_CLASS_TYPE &at[1863]
+
+#define TOPOLOGY_TYPE &at[1865]
+
+#define STRAND_TYPE &at[1867]
+
+#define MOLINFO_FIELD &at[1855]
+#define MOLINFO_FIELD_molecule &at[1856]
+#define MOLINFO_FIELD_technique &at[1858]
+#define MOLINFO_FIELD_completedness &at[1860]
+#define MOLINFO_FIELD_mol_class &at[1862]
+#define MOLINFO_FIELD_topology &at[1864]
+#define MOLINFO_FIELD_strand &at[1866]
+
+#define MOLINFO_MOLECULE_PAIR &at[1900]
+#define MOLINFO_MOLECULE_PAIR_from &at[1901]
+#define MOLINFO_MOLECULE_PAIR_to &at[1902]
+
+#define MOLINFO_TECHNIQUE_PAIR &at[1904]
+#define MOLINFO_TECHNIQUE_PAIR_from &at[1905]
+#define MOLINFO_TECHNIQUE_PAIR_to &at[1906]
+
+#define MOLINFO_COMPLETEDNESS_PAIR &at[1908]
+#define MOLINFO_COMPLETEDNESS_PAIR_from &at[1909]
+#define MOLINFO_COMPLETEDNESS_PAIR_to &at[1910]
+
+#define MOLINFO_MOL_CLASS_PAIR &at[1912]
+#define MOLINFO_MOL_CLASS_PAIR_from &at[1913]
+#define MOLINFO_MOL_CLASS_PAIR_to &at[1914]
+
+#define MOLINFO_TOPOLOGY_PAIR &at[1916]
+#define MOLINFO_TOPOLOGY_PAIR_from &at[1917]
+#define MOLINFO_TOPOLOGY_PAIR_to &at[1918]
+
+#define MOLINFO_STRAND_PAIR &at[1920]
+#define MOLINFO_STRAND_PAIR_from &at[1921]
+#define MOLINFO_STRAND_PAIR_to &at[1922]
+
+#define MOLINFO_FIELD_PAIR &at[1898]
+#define MOLINFO_FIELD_PAIR_molecule &at[1899]
+#define MOLINFO_FIELD_PAIR_technique &at[1903]
+#define FIELD_PAIR_completedness &at[1907]
+#define MOLINFO_FIELD_PAIR_mol_class &at[1911]
+#define MOLINFO_FIELD_PAIR_topology &at[1915]
+#define MOLINFO_FIELD_PAIR_strand &at[1919]
+
+#define SOURCE_CONSTRAINT &at[1961]
+#define SOURCE_CONSTRAINT_field1 &at[1962]
+#define SOURCE_CONSTRAINT_field2 &at[1963]
+#define SOURCE_CONSTRAINT_constraint &at[1964]
+#define CONSTRAINT_type_constraint &at[1965]
+
+#define FEATURE_TYPE_CONSTRAINT &at[1977]
+
+#define CDSGENEPROT_PSEUDO_CONSTRAINT &at[1975]
+#define PSEUDO_CONSTRAINT_feature &at[1976]
+#define PSEUDO_CONSTRAINT_is_pseudo &at[1978]
+
+#define CDSGENEPROT_CONSTRAINT_FIELD &at[1970]
+#define CONSTRAINT_FIELD_field &at[1971]
+
+#define CDSGENEPROT_QUAL_CONSTRAINT &at[1968]
+#define QUAL_CONSTRAINT_field1 &at[1969]
+#define QUAL_CONSTRAINT_field2 &at[1972]
+#define QUAL_CONSTRAINT_constraint &at[1973]
+
+#define SEQUENCE_CONSTRAINT_RNAMOL &at[1987]
+
+#define CONSTRAINT_MOL_TYPE_CONSTRAINT &at[1982]
+#define MOL_TYPE_CONSTRAINT_any &at[1983]
+#define MOL_TYPE_CONSTRAINT_nucleotide &at[1984]
+#define MOL_TYPE_CONSTRAINT_dna &at[1985]
+#define MOL_TYPE_CONSTRAINT_rna &at[1986]
+#define MOL_TYPE_CONSTRAINT_protein &at[1988]
+
+#define SEQUENCE_CONSTRAINT &at[1980]
+#define SEQUENCE_CONSTRAINT_seqtype &at[1981]
+#define SEQUENCE_CONSTRAINT_id &at[1989]
+#define SEQUENCE_CONSTRAINT_feature &at[1990]
+
+#define CONSTRAINT_CHOICE &at[1952]
+#define CONSTRAINT_CHOICE_string &at[1953]
+#define CONSTRAINT_CHOICE_location &at[1954]
+#define CONSTRAINT_CHOICE_source &at[1960]
+#define CHOICE_cdsgeneprot_qual &at[1967]
+#define CHOICE_cdsgeneprot_pseudo &at[1974]
+#define CONSTRAINT_CHOICE_sequence &at[1979]
+
+#define CONSTRAINT_CHOICE_SET &at[1950]
+#define CONSTRAINT_CHOICE_SET_E &at[1951]
+
+#define TEXT_PORTION &at[1938]
+#define TEXT_PORTION_left_text &at[1939]
+#define TEXT_PORTION_include_left &at[1940]
+#define TEXT_PORTION_right_text &at[1941]
+#define TEXT_PORTION_include_right &at[1942]
+#define TEXT_PORTION_inside &at[1943]
+#define TEXT_PORTION_case_sensitive &at[1944]
+#define TEXT_PORTION_whole_word &at[1945]
+
+#define FIELD_EDIT_LOCATION &at[1878]
+
+#define FIELD_EDIT &at[1874]
+#define FIELD_EDIT_find_txt &at[1875]
+#define FIELD_EDIT_repl_txt &at[1876]
+#define FIELD_EDIT_location &at[1877]
+
+#define FIELD_TYPE &at[1827]
+#define FIELD_TYPE_source_qual &at[1828]
+#define FIELD_TYPE_feature_field &at[1836]
+#define FIELD_TYPE_cds_gene_prot &at[1852]
+#define FIELD_TYPE_molinfo_field &at[1854]
+
+#define FIELD_PAIR_TYPE &at[1883]
+#define FIELD_PAIR_TYPE_source_qual &at[1884]
+#define FIELD_PAIR_TYPE_feature_field &at[1888]
+#define FIELD_PAIR_TYPE_cds_gene_prot &at[1893]
+#define FIELD_PAIR_TYPE_molinfo_field &at[1897]
+
+#define EXISTINGTEXTOPTION &at[1870]
+
+#define APPLY_ACTION &at[1825]
+#define APPLY_ACTION_field &at[1826]
+#define APPLY_ACTION_value &at[1868]
+#define APPLY_ACTION_existing_text &at[1869]
+
+#define EDIT_ACTION &at[1872]
+#define EDIT_ACTION_edit &at[1873]
+#define EDIT_ACTION_field &at[1879]
+
+#define CONVERT_ACTION &at[1881]
+#define CONVERT_ACTION_fields &at[1882]
+#define CONVERT_ACTION_existing_text &at[1923]
+
+#define COPY_ACTION &at[1925]
+#define COPY_ACTION_fields &at[1926]
+#define COPY_ACTION_existing_text &at[1927]
+
+#define SWAP_ACTION &at[1929]
+#define SWAP_ACTION_fields &at[1930]
+#define SWAP_ACTION_field_to &at[1931]
+
+#define AECRPARSE_ACTION &at[1936]
+#define AECRPARSE_ACTION_portion &at[1937]
+#define AECRPARSE_ACTION_fields &at[1946]
+#define ACTION_remove_from_parsed &at[1947]
+#define AECRPARSE_ACTION_existing_text &at[1948]
+
+#define REMOVE_ACTION &at[1933]
+#define REMOVE_ACTION_field &at[1934]
+
+#define ACTION_CHOICE &at[1823]
+#define ACTION_CHOICE_apply &at[1824]
+#define ACTION_CHOICE_edit &at[1871]
+#define ACTION_CHOICE_convert &at[1880]
+#define ACTION_CHOICE_copy &at[1924]
+#define ACTION_CHOICE_swap &at[1928]
+#define ACTION_CHOICE_remove &at[1932]
+#define ACTION_CHOICE_parse &at[1935]
+
+#define CAP_CHANGE &at[2022]
+
+#define PARSE_SRC_ORG_CHOICE &at[2001]
+#define SRC_ORG_CHOICE_source_qual &at[2002]
+#define CHOICE_taxname_after_binomial &at[2003]
+
+#define PARSE_SRC_ORG &at[1999]
+#define PARSE_SRC_ORG_field &at[2000]
+#define PARSE_SRC_ORG_type &at[2004]
+
+#define PARSE_SRC &at[1994]
+#define PARSE_SRC_defline &at[1995]
+#define PARSE_SRC_flatfile &at[1996]
+#define PARSE_SRC_local_id &at[1997]
+#define PARSE_SRC_org &at[1998]
+#define PARSE_SRC_comment &at[2005]
+#define PARSE_SRC_bankit_comment &at[2006]
+#define PARSE_SRC_structured_comment &at[2007]
+#define PARSE_SRC_file_id &at[2008]
+
+#define PARSE_DST_ORG &at[2013]
+#define PARSE_DST_ORG_field &at[2014]
+#define PARSE_DST_ORG_type &at[2015]
+
+#define PARSE_DEST &at[2010]
+#define PARSE_DEST_defline &at[2011]
+#define PARSE_DEST_org &at[2012]
+#define PARSE_DEST_featqual &at[2016]
+#define PARSE_DEST_dbxref &at[2020]
+
+#define LOCATION_INTERVAL &at[2039]
+#define LOCATION_INTERVAL_from &at[2040]
+#define LOCATION_INTERVAL_to &at[2041]
+
+#define LOCATION_CHOICE &at[2037]
+#define LOCATION_CHOICE_interval &at[2038]
+#define LOCATION_CHOICE_whole_sequence &at[2042]
+
+#define SEQUENCE_LIST &at[2046]
+#define SEQUENCE_LIST_E &at[2047]
+
+#define SEQUENCE_LIST_CHOICE &at[2044]
+#define SEQUENCE_LIST_CHOICE_list &at[2045]
+#define SEQUENCE_LIST_CHOICE_all &at[2048]
+
+#define APPLY_FEATURE_ACTION &at[2031]
+#define APPLY_FEATURE_ACTION_type &at[2032]
+#define APPLY_FEATURE_ACTION_partial5 &at[2033]
+#define APPLY_FEATURE_ACTION_partial3 &at[2034]
+#define FEATURE_ACTION_plus_strand &at[2035]
+#define APPLY_FEATURE_ACTION_location &at[2036]
+#define APPLY_FEATURE_ACTION_seq_list &at[2043]
+#define FEATURE_ACTION_add_redundant &at[2049]
+#define APPLY_FEATURE_ACTION_add_mrna &at[2050]
+#define FEATURE_ACTION_apply_to_parts &at[2051]
+#define FEATURE_ACTION_only_seg_num &at[2052]
+#define APPLY_FEATURE_ACTION_fields &at[2053]
+
+#define REMOVE_FEATURE_ACTION &at[2062]
+#define REMOVE_FEATURE_ACTION_type &at[2063]
+#define FEATURE_ACTION_constraint &at[2064]
+
+#define FEATURE_LOCATION_STRAND_FROM &at[2073]
+
+#define FEATURE_LOCATION_STRAND_TO &at[2075]
+
+#define EDIT_LOCATION_STRAND &at[2071]
+#define LOCATION_STRAND_strand_from &at[2072]
+#define EDIT_LOCATION_STRAND_strand_to &at[2074]
+
+#define PARTIAL_5_SET_CONSTRAINT &at[2079]
+
+#define PARTIAL_5_SET_ACTION &at[2077]
+#define PARTIAL_5_SET_ACTION_constraint &at[2078]
+#define PARTIAL_5_SET_ACTION_extend &at[2080]
+
+#define PARTIAL_5_CLEAR_CONSTRAINT &at[2082]
+
+#define PARTIAL_3_SET_CONSTRAINT &at[2086]
+
+#define PARTIAL_3_SET_ACTION &at[2084]
+#define PARTIAL_3_SET_ACTION_constraint &at[2085]
+#define PARTIAL_3_SET_ACTION_extend &at[2087]
+
+#define PARTIAL_3_CLEAR_CONSTRAINT &at[2089]
+
+#define CONVERT_LOCATION_TYPE &at[2091]
+
+#define LOCATION_EDIT_TYPE &at[2069]
+#define LOCATION_EDIT_TYPE_strand &at[2070]
+#define EDIT_TYPE_set_5_partial &at[2076]
+#define EDIT_TYPE_clear_5_partial &at[2081]
+#define EDIT_TYPE_set_3_partial &at[2083]
+#define EDIT_TYPE_clear_3_partial &at[2088]
+#define LOCATION_EDIT_TYPE_convert &at[2090]
+
+#define EDIT_FEATURE_LOCATION_ACTION &at[2066]
+#define FEATURE_LOCATION_ACTION_type &at[2067]
+#define FEATURE_LOCATION_ACTION_action &at[2068]
+#define LOCATION_ACTION_constraint &at[2092]
+
+#define MACRO_ACTION_CHOICE &at[2027]
+#define MACRO_ACTION_CHOICE_aecr &at[2028]
+#define MACRO_ACTION_CHOICE_parse &at[2029]
+#define MACRO_ACTION_CHOICE_add_feature &at[2030]
+#define ACTION_CHOICE_remove_feature &at[2061]
+#define ACTION_CHOICE_edit_location &at[2065]
diff --git a/asnstat/asnfeat.h b/asnstat/asnfeat.h
index c0db8a96..819471e8 100644
--- a/asnstat/asnfeat.h
+++ b/asnstat/asnfeat.h
@@ -9,8 +9,8 @@
 #include <asn.h>
 #endif
 
-static char * asnfilename = "asnfeat.h18";
-static AsnValxNode avnx[207] = {
+static char * asnfilename = "asnfeat.h19";
+static AsnValxNode avnx[208] = {
     {2,NULL,0,0.0,NULL } ,
     {20,"other" ,0,0.0,&avnx[2] } ,
     {20,"family" ,1,0.0,&avnx[3] } ,
@@ -168,55 +168,56 @@ static AsnValxNode avnx[207] = {
     {20,"proplastid" ,18,0.0,&avnx[155] } ,
     {20,"endogenous-virus" ,19,0.0,&avnx[156] } ,
     {20,"hydrogenosome" ,20,0.0,&avnx[157] } ,
-    {20,"chromosome" ,21,0.0,NULL } ,
+    {20,"chromosome" ,21,0.0,&avnx[158] } ,
+    {20,"chromatophore" ,22,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[160] } ,
-    {20,"natural" ,1,0.0,&avnx[161] } ,
-    {20,"natmut" ,2,0.0,&avnx[162] } ,
-    {20,"mut" ,3,0.0,&avnx[163] } ,
-    {20,"artificial" ,4,0.0,&avnx[164] } ,
-    {20,"synthetic" ,5,0.0,&avnx[165] } ,
+    {20,"unknown" ,0,0.0,&avnx[161] } ,
+    {20,"natural" ,1,0.0,&avnx[162] } ,
+    {20,"natmut" ,2,0.0,&avnx[163] } ,
+    {20,"mut" ,3,0.0,&avnx[164] } ,
+    {20,"artificial" ,4,0.0,&avnx[165] } ,
+    {20,"synthetic" ,5,0.0,&avnx[166] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"chromosome" ,1,0.0,&avnx[168] } ,
-    {20,"map" ,2,0.0,&avnx[169] } ,
-    {20,"clone" ,3,0.0,&avnx[170] } ,
-    {20,"subclone" ,4,0.0,&avnx[171] } ,
-    {20,"haplotype" ,5,0.0,&avnx[172] } ,
-    {20,"genotype" ,6,0.0,&avnx[173] } ,
-    {20,"sex" ,7,0.0,&avnx[174] } ,
-    {20,"cell-line" ,8,0.0,&avnx[175] } ,
-    {20,"cell-type" ,9,0.0,&avnx[176] } ,
-    {20,"tissue-type" ,10,0.0,&avnx[177] } ,
-    {20,"clone-lib" ,11,0.0,&avnx[178] } ,
-    {20,"dev-stage" ,12,0.0,&avnx[179] } ,
-    {20,"frequency" ,13,0.0,&avnx[180] } ,
-    {20,"germline" ,14,0.0,&avnx[181] } ,
-    {20,"rearranged" ,15,0.0,&avnx[182] } ,
-    {20,"lab-host" ,16,0.0,&avnx[183] } ,
-    {20,"pop-variant" ,17,0.0,&avnx[184] } ,
-    {20,"tissue-lib" ,18,0.0,&avnx[185] } ,
-    {20,"plasmid-name" ,19,0.0,&avnx[186] } ,
-    {20,"transposon-name" ,20,0.0,&avnx[187] } ,
-    {20,"insertion-seq-name" ,21,0.0,&avnx[188] } ,
-    {20,"plastid-name" ,22,0.0,&avnx[189] } ,
-    {20,"country" ,23,0.0,&avnx[190] } ,
-    {20,"segment" ,24,0.0,&avnx[191] } ,
-    {20,"endogenous-virus-name" ,25,0.0,&avnx[192] } ,
-    {20,"transgenic" ,26,0.0,&avnx[193] } ,
-    {20,"environmental-sample" ,27,0.0,&avnx[194] } ,
-    {20,"isolation-source" ,28,0.0,&avnx[195] } ,
-    {20,"lat-lon" ,29,0.0,&avnx[196] } ,
-    {20,"collection-date" ,30,0.0,&avnx[197] } ,
-    {20,"collected-by" ,31,0.0,&avnx[198] } ,
-    {20,"identified-by" ,32,0.0,&avnx[199] } ,
-    {20,"fwd-primer-seq" ,33,0.0,&avnx[200] } ,
-    {20,"rev-primer-seq" ,34,0.0,&avnx[201] } ,
-    {20,"fwd-primer-name" ,35,0.0,&avnx[202] } ,
-    {20,"rev-primer-name" ,36,0.0,&avnx[203] } ,
-    {20,"metagenomic" ,37,0.0,&avnx[204] } ,
+    {20,"chromosome" ,1,0.0,&avnx[169] } ,
+    {20,"map" ,2,0.0,&avnx[170] } ,
+    {20,"clone" ,3,0.0,&avnx[171] } ,
+    {20,"subclone" ,4,0.0,&avnx[172] } ,
+    {20,"haplotype" ,5,0.0,&avnx[173] } ,
+    {20,"genotype" ,6,0.0,&avnx[174] } ,
+    {20,"sex" ,7,0.0,&avnx[175] } ,
+    {20,"cell-line" ,8,0.0,&avnx[176] } ,
+    {20,"cell-type" ,9,0.0,&avnx[177] } ,
+    {20,"tissue-type" ,10,0.0,&avnx[178] } ,
+    {20,"clone-lib" ,11,0.0,&avnx[179] } ,
+    {20,"dev-stage" ,12,0.0,&avnx[180] } ,
+    {20,"frequency" ,13,0.0,&avnx[181] } ,
+    {20,"germline" ,14,0.0,&avnx[182] } ,
+    {20,"rearranged" ,15,0.0,&avnx[183] } ,
+    {20,"lab-host" ,16,0.0,&avnx[184] } ,
+    {20,"pop-variant" ,17,0.0,&avnx[185] } ,
+    {20,"tissue-lib" ,18,0.0,&avnx[186] } ,
+    {20,"plasmid-name" ,19,0.0,&avnx[187] } ,
+    {20,"transposon-name" ,20,0.0,&avnx[188] } ,
+    {20,"insertion-seq-name" ,21,0.0,&avnx[189] } ,
+    {20,"plastid-name" ,22,0.0,&avnx[190] } ,
+    {20,"country" ,23,0.0,&avnx[191] } ,
+    {20,"segment" ,24,0.0,&avnx[192] } ,
+    {20,"endogenous-virus-name" ,25,0.0,&avnx[193] } ,
+    {20,"transgenic" ,26,0.0,&avnx[194] } ,
+    {20,"environmental-sample" ,27,0.0,&avnx[195] } ,
+    {20,"isolation-source" ,28,0.0,&avnx[196] } ,
+    {20,"lat-lon" ,29,0.0,&avnx[197] } ,
+    {20,"collection-date" ,30,0.0,&avnx[198] } ,
+    {20,"collected-by" ,31,0.0,&avnx[199] } ,
+    {20,"identified-by" ,32,0.0,&avnx[200] } ,
+    {20,"fwd-primer-seq" ,33,0.0,&avnx[201] } ,
+    {20,"rev-primer-seq" ,34,0.0,&avnx[202] } ,
+    {20,"fwd-primer-name" ,35,0.0,&avnx[203] } ,
+    {20,"rev-primer-name" ,36,0.0,&avnx[204] } ,
+    {20,"metagenomic" ,37,0.0,&avnx[205] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"experimental" ,1,0.0,&avnx[206] } ,
+    {20,"experimental" ,1,0.0,&avnx[207] } ,
     {20,"not-experimental" ,2,0.0,NULL } };
 
 static AsnType atx[238] = {
@@ -417,14 +418,14 @@ static AsnType atx[238] = {
   {0, "biosrc" ,128,19,0,0,0,0,0,0,NULL,&atx[195],NULL,0,NULL} ,
   {407, "BioSource" ,1,0,0,0,0,0,1,0,NULL,&atx[196],NULL,0,&atx[121]} ,
   {401, "BioSource" ,1,0,0,0,0,1,0,0,NULL,&atx[31],&atx[197],0,&atx[200]} ,
-  {0, "genome" ,128,0,0,0,1,0,0,0,&avnx[158],&atx[4],&avnx[136],0,&atx[198]} ,
-  {0, "origin" ,128,1,0,0,1,0,0,0,&avnx[166],&atx[4],&avnx[159],0,&atx[199]} ,
+  {0, "genome" ,128,0,0,0,1,0,0,0,&avnx[159],&atx[4],&avnx[136],0,&atx[198]} ,
+  {0, "origin" ,128,1,0,0,1,0,0,0,&avnx[167],&atx[4],&avnx[160],0,&atx[199]} ,
   {0, "org" ,128,2,0,0,0,0,0,0,NULL,&atx[200],NULL,0,&atx[201]} ,
   {402, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,&atx[34],NULL,0,&atx[203]} ,
   {0, "subtype" ,128,3,0,1,0,0,0,0,NULL,&atx[56],&atx[202],0,&atx[207]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[203],NULL,0,NULL} ,
   {403, "SubSource" ,1,0,0,0,0,0,0,0,NULL,&atx[31],&atx[204],0,NULL} ,
-  {0, "subtype" ,128,0,0,0,0,0,0,0,NULL,&atx[4],&avnx[167],0,&atx[205]} ,
+  {0, "subtype" ,128,0,0,0,0,0,0,0,NULL,&atx[4],&avnx[168],0,&atx[205]} ,
   {0, "name" ,128,1,0,0,0,0,0,0,NULL,&atx[18],NULL,0,&atx[206]} ,
   {0, "attrib" ,128,2,0,1,0,0,0,0,NULL,&atx[18],NULL,0,NULL} ,
   {0, "is-focus" ,128,4,0,1,0,0,0,0,NULL,&atx[148],NULL,0,NULL} ,
@@ -442,7 +443,7 @@ static AsnType atx[238] = {
   {0, "ext" ,128,9,0,1,0,0,0,0,NULL,&atx[158],NULL,0,&atx[220]} ,
   {0, "cit" ,128,10,0,1,0,0,0,0,NULL,&atx[221],NULL,0,&atx[222]} ,
   {416, "Pub-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[8]} ,
-  {0, "exp-ev" ,128,11,0,1,0,0,0,0,NULL,&atx[80],&avnx[205],0,&atx[223]} ,
+  {0, "exp-ev" ,128,11,0,1,0,0,0,0,NULL,&atx[80],&avnx[206],0,&atx[223]} ,
   {0, "xref" ,128,12,0,1,0,0,0,0,NULL,&atx[27],&atx[224],0,&atx[228]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[225],NULL,0,NULL} ,
   {422, "SeqFeatXref" ,1,0,0,0,0,0,0,0,NULL,&atx[31],&atx[226],0,&atx[77]} ,
@@ -460,7 +461,7 @@ static AsnType atx[238] = {
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[85],NULL,0,NULL} };
 
 static AsnModule ampx[8] = {
-  { "NCBI-Seqfeat" , "asnfeat.h18",&atx[0],NULL,&ampx[1],0,0} ,
+  { "NCBI-Seqfeat" , "asnfeat.h19",&atx[0],NULL,&ampx[1],0,0} ,
   { "NCBI-Rsite" , NULL,&atx[153],NULL,&ampx[2],0,0} ,
   { "NCBI-RNA" , NULL,&atx[122],NULL,&ampx[3],0,0} ,
   { "NCBI-Gene" , NULL,&atx[16],NULL,&ampx[4],0,0} ,
diff --git a/asnstat/asnmacro.h b/asnstat/asnmacro.h
new file mode 100644
index 00000000..33b54494
--- /dev/null
+++ b/asnstat/asnmacro.h
@@ -0,0 +1,1124 @@
+/***********************************************************************
+*
+**
+*        Automatic header module from ASNTOOL
+*
+************************************************************************/
+
+#ifndef _ASNTOOL_
+#include <asn.h>
+#endif
+
+static char * asnfilename = "asnmacro.h13";
+static AsnValxNode avnx[454] = {
+    {20,"acronym" ,1,0.0,&avnx[1] } ,
+    {20,"anamorph" ,2,0.0,&avnx[2] } ,
+    {20,"authority" ,3,0.0,&avnx[3] } ,
+    {20,"bio-material" ,4,0.0,&avnx[4] } ,
+    {20,"biotype" ,5,0.0,&avnx[5] } ,
+    {20,"biovar" ,6,0.0,&avnx[6] } ,
+    {20,"breed" ,7,0.0,&avnx[7] } ,
+    {20,"cell-line" ,8,0.0,&avnx[8] } ,
+    {20,"cell-type" ,9,0.0,&avnx[9] } ,
+    {20,"chemovar" ,10,0.0,&avnx[10] } ,
+    {20,"chromosome" ,11,0.0,&avnx[11] } ,
+    {20,"clone" ,12,0.0,&avnx[12] } ,
+    {20,"clone-lib" ,13,0.0,&avnx[13] } ,
+    {20,"collected-by" ,14,0.0,&avnx[14] } ,
+    {20,"collection-date" ,15,0.0,&avnx[15] } ,
+    {20,"common" ,16,0.0,&avnx[16] } ,
+    {20,"common-name" ,17,0.0,&avnx[17] } ,
+    {20,"country" ,18,0.0,&avnx[18] } ,
+    {20,"cultivar" ,19,0.0,&avnx[19] } ,
+    {20,"culture-collection" ,20,0.0,&avnx[20] } ,
+    {20,"dev-stage" ,21,0.0,&avnx[21] } ,
+    {20,"division" ,22,0.0,&avnx[22] } ,
+    {20,"dosage" ,23,0.0,&avnx[23] } ,
+    {20,"ecotype" ,24,0.0,&avnx[24] } ,
+    {20,"endogenous-virus-name" ,25,0.0,&avnx[25] } ,
+    {20,"environmental-sample" ,26,0.0,&avnx[26] } ,
+    {20,"forma" ,27,0.0,&avnx[27] } ,
+    {20,"forma-specialis" ,28,0.0,&avnx[28] } ,
+    {20,"frequency" ,29,0.0,&avnx[29] } ,
+    {20,"fwd-primer-name" ,30,0.0,&avnx[30] } ,
+    {20,"fwd-primer-seq" ,31,0.0,&avnx[31] } ,
+    {20,"gb-acronym" ,32,0.0,&avnx[32] } ,
+    {20,"gb-anamorph" ,33,0.0,&avnx[33] } ,
+    {20,"gb-synonym" ,34,0.0,&avnx[34] } ,
+    {20,"genotype" ,35,0.0,&avnx[35] } ,
+    {20,"germline" ,36,0.0,&avnx[36] } ,
+    {20,"group" ,37,0.0,&avnx[37] } ,
+    {20,"haplotype" ,38,0.0,&avnx[38] } ,
+    {20,"identified-by" ,39,0.0,&avnx[39] } ,
+    {20,"insertion-seq-name" ,40,0.0,&avnx[40] } ,
+    {20,"isolate" ,41,0.0,&avnx[41] } ,
+    {20,"isolation-source" ,42,0.0,&avnx[42] } ,
+    {20,"lab-host" ,43,0.0,&avnx[43] } ,
+    {20,"lat-lon" ,44,0.0,&avnx[44] } ,
+    {20,"lineage" ,45,0.0,&avnx[45] } ,
+    {20,"map" ,46,0.0,&avnx[46] } ,
+    {20,"metagenome-source" ,47,0.0,&avnx[47] } ,
+    {20,"metagenomic" ,48,0.0,&avnx[48] } ,
+    {20,"old-lineage" ,49,0.0,&avnx[49] } ,
+    {20,"old-name" ,50,0.0,&avnx[50] } ,
+    {20,"orgmod-note" ,51,0.0,&avnx[51] } ,
+    {20,"nat-host" ,52,0.0,&avnx[52] } ,
+    {20,"pathovar" ,53,0.0,&avnx[53] } ,
+    {20,"plasmid-name" ,54,0.0,&avnx[54] } ,
+    {20,"plastid-name" ,55,0.0,&avnx[55] } ,
+    {20,"pop-variant" ,56,0.0,&avnx[56] } ,
+    {20,"rearranged" ,57,0.0,&avnx[57] } ,
+    {20,"rev-primer-name" ,58,0.0,&avnx[58] } ,
+    {20,"rev-primer-seq" ,59,0.0,&avnx[59] } ,
+    {20,"segment" ,60,0.0,&avnx[60] } ,
+    {20,"serogroup" ,61,0.0,&avnx[61] } ,
+    {20,"serotype" ,62,0.0,&avnx[62] } ,
+    {20,"serovar" ,63,0.0,&avnx[63] } ,
+    {20,"sex" ,64,0.0,&avnx[64] } ,
+    {20,"specimen-voucher" ,65,0.0,&avnx[65] } ,
+    {20,"strain" ,66,0.0,&avnx[66] } ,
+    {20,"subclone" ,67,0.0,&avnx[67] } ,
+    {20,"subgroup" ,68,0.0,&avnx[68] } ,
+    {20,"subsource-note" ,69,0.0,&avnx[69] } ,
+    {20,"sub-species" ,70,0.0,&avnx[70] } ,
+    {20,"substrain" ,71,0.0,&avnx[71] } ,
+    {20,"subtype" ,72,0.0,&avnx[72] } ,
+    {20,"synonym" ,73,0.0,&avnx[73] } ,
+    {20,"taxname" ,74,0.0,&avnx[74] } ,
+    {20,"teleomorph" ,75,0.0,&avnx[75] } ,
+    {20,"tissue-lib" ,76,0.0,&avnx[76] } ,
+    {20,"tissue-type" ,77,0.0,&avnx[77] } ,
+    {20,"transgenic" ,78,0.0,&avnx[78] } ,
+    {20,"transposon-name" ,79,0.0,&avnx[79] } ,
+    {20,"type" ,80,0.0,&avnx[80] } ,
+    {20,"variety" ,81,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[82] } ,
+    {20,"genomic" ,1,0.0,&avnx[83] } ,
+    {20,"chloroplast" ,2,0.0,&avnx[84] } ,
+    {20,"chromoplast" ,3,0.0,&avnx[85] } ,
+    {20,"kinetoplast" ,4,0.0,&avnx[86] } ,
+    {20,"mitochondrion" ,5,0.0,&avnx[87] } ,
+    {20,"plastid" ,6,0.0,&avnx[88] } ,
+    {20,"macronuclear" ,7,0.0,&avnx[89] } ,
+    {20,"extrachrom" ,8,0.0,&avnx[90] } ,
+    {20,"plasmid" ,9,0.0,&avnx[91] } ,
+    {20,"transposon" ,10,0.0,&avnx[92] } ,
+    {20,"insertion-seq" ,11,0.0,&avnx[93] } ,
+    {20,"cyanelle" ,12,0.0,&avnx[94] } ,
+    {20,"proviral" ,13,0.0,&avnx[95] } ,
+    {20,"virion" ,14,0.0,&avnx[96] } ,
+    {20,"nucleomorph" ,15,0.0,&avnx[97] } ,
+    {20,"apicoplast" ,16,0.0,&avnx[98] } ,
+    {20,"leucoplast" ,17,0.0,&avnx[99] } ,
+    {20,"proplastid" ,18,0.0,&avnx[100] } ,
+    {20,"endogenous-virus" ,19,0.0,&avnx[101] } ,
+    {20,"hydrogenosome" ,20,0.0,&avnx[102] } ,
+    {20,"chromosome" ,21,0.0,&avnx[103] } ,
+    {20,"chromatophore" ,22,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[105] } ,
+    {20,"natural" ,1,0.0,&avnx[106] } ,
+    {20,"natmut" ,2,0.0,&avnx[107] } ,
+    {20,"mut" ,3,0.0,&avnx[108] } ,
+    {20,"artificial" ,4,0.0,&avnx[109] } ,
+    {20,"synthetic" ,5,0.0,&avnx[110] } ,
+    {20,"other" ,255,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[112] } ,
+    {20,"gene" ,1,0.0,&avnx[113] } ,
+    {20,"org" ,2,0.0,&avnx[114] } ,
+    {20,"cds" ,3,0.0,&avnx[115] } ,
+    {20,"prot" ,4,0.0,&avnx[116] } ,
+    {20,"preRNA" ,5,0.0,&avnx[117] } ,
+    {20,"mRNA" ,6,0.0,&avnx[118] } ,
+    {20,"tRNA" ,7,0.0,&avnx[119] } ,
+    {20,"rRNA" ,8,0.0,&avnx[120] } ,
+    {20,"snRNA" ,9,0.0,&avnx[121] } ,
+    {20,"scRNA" ,10,0.0,&avnx[122] } ,
+    {20,"otherRNA" ,11,0.0,&avnx[123] } ,
+    {20,"pub" ,12,0.0,&avnx[124] } ,
+    {20,"seq" ,13,0.0,&avnx[125] } ,
+    {20,"imp" ,14,0.0,&avnx[126] } ,
+    {20,"allele" ,15,0.0,&avnx[127] } ,
+    {20,"attenuator" ,16,0.0,&avnx[128] } ,
+    {20,"c-region" ,17,0.0,&avnx[129] } ,
+    {20,"caat-signal" ,18,0.0,&avnx[130] } ,
+    {20,"imp-CDS" ,19,0.0,&avnx[131] } ,
+    {20,"conflict" ,20,0.0,&avnx[132] } ,
+    {20,"d-loop" ,21,0.0,&avnx[133] } ,
+    {20,"d-segment" ,22,0.0,&avnx[134] } ,
+    {20,"enhancer" ,23,0.0,&avnx[135] } ,
+    {20,"exon" ,24,0.0,&avnx[136] } ,
+    {20,"gC-signal" ,25,0.0,&avnx[137] } ,
+    {20,"iDNA" ,26,0.0,&avnx[138] } ,
+    {20,"intron" ,27,0.0,&avnx[139] } ,
+    {20,"j-segment" ,28,0.0,&avnx[140] } ,
+    {20,"ltr" ,29,0.0,&avnx[141] } ,
+    {20,"mat-peptide" ,30,0.0,&avnx[142] } ,
+    {20,"misc-binding" ,31,0.0,&avnx[143] } ,
+    {20,"misc-difference" ,32,0.0,&avnx[144] } ,
+    {20,"misc-feature" ,33,0.0,&avnx[145] } ,
+    {20,"misc-recomb" ,34,0.0,&avnx[146] } ,
+    {20,"misc-RNA" ,35,0.0,&avnx[147] } ,
+    {20,"misc-signal" ,36,0.0,&avnx[148] } ,
+    {20,"misc-structure" ,37,0.0,&avnx[149] } ,
+    {20,"modified-base" ,38,0.0,&avnx[150] } ,
+    {20,"mutation" ,39,0.0,&avnx[151] } ,
+    {20,"n-region" ,40,0.0,&avnx[152] } ,
+    {20,"old-sequence" ,41,0.0,&avnx[153] } ,
+    {20,"polyA-signal" ,42,0.0,&avnx[154] } ,
+    {20,"polyA-site" ,43,0.0,&avnx[155] } ,
+    {20,"precursor-RNA" ,44,0.0,&avnx[156] } ,
+    {20,"prim-transcript" ,45,0.0,&avnx[157] } ,
+    {20,"primer-bind" ,46,0.0,&avnx[158] } ,
+    {20,"promoter" ,47,0.0,&avnx[159] } ,
+    {20,"protein-bind" ,48,0.0,&avnx[160] } ,
+    {20,"rbs" ,49,0.0,&avnx[161] } ,
+    {20,"repeat-region" ,50,0.0,&avnx[162] } ,
+    {20,"repeat-unit" ,51,0.0,&avnx[163] } ,
+    {20,"rep-origin" ,52,0.0,&avnx[164] } ,
+    {20,"s-region" ,53,0.0,&avnx[165] } ,
+    {20,"satellite" ,54,0.0,&avnx[166] } ,
+    {20,"sig-peptide" ,55,0.0,&avnx[167] } ,
+    {20,"source" ,56,0.0,&avnx[168] } ,
+    {20,"stem-loop" ,57,0.0,&avnx[169] } ,
+    {20,"sts" ,58,0.0,&avnx[170] } ,
+    {20,"tata-signal" ,59,0.0,&avnx[171] } ,
+    {20,"terminator" ,60,0.0,&avnx[172] } ,
+    {20,"transit-peptide" ,61,0.0,&avnx[173] } ,
+    {20,"unsure" ,62,0.0,&avnx[174] } ,
+    {20,"v-region" ,63,0.0,&avnx[175] } ,
+    {20,"v-segment" ,64,0.0,&avnx[176] } ,
+    {20,"variation" ,65,0.0,&avnx[177] } ,
+    {20,"virion" ,66,0.0,&avnx[178] } ,
+    {20,"n3clip" ,67,0.0,&avnx[179] } ,
+    {20,"n3UTR" ,68,0.0,&avnx[180] } ,
+    {20,"n5clip" ,69,0.0,&avnx[181] } ,
+    {20,"n5UTR" ,70,0.0,&avnx[182] } ,
+    {20,"n10-signal" ,71,0.0,&avnx[183] } ,
+    {20,"n35-signal" ,72,0.0,&avnx[184] } ,
+    {20,"site-ref" ,73,0.0,&avnx[185] } ,
+    {20,"region" ,74,0.0,&avnx[186] } ,
+    {20,"comment" ,75,0.0,&avnx[187] } ,
+    {20,"bond" ,76,0.0,&avnx[188] } ,
+    {20,"site" ,77,0.0,&avnx[189] } ,
+    {20,"rsite" ,78,0.0,&avnx[190] } ,
+    {20,"user" ,79,0.0,&avnx[191] } ,
+    {20,"txinit" ,80,0.0,&avnx[192] } ,
+    {20,"num" ,81,0.0,&avnx[193] } ,
+    {20,"psec-str" ,82,0.0,&avnx[194] } ,
+    {20,"non-std-residue" ,83,0.0,&avnx[195] } ,
+    {20,"het" ,84,0.0,&avnx[196] } ,
+    {20,"biosrc" ,85,0.0,&avnx[197] } ,
+    {20,"preprotein" ,86,0.0,&avnx[198] } ,
+    {20,"mat-peptide-aa" ,87,0.0,&avnx[199] } ,
+    {20,"sig-peptide-aa" ,88,0.0,&avnx[200] } ,
+    {20,"transit-peptide-aa" ,89,0.0,&avnx[201] } ,
+    {20,"snoRNA" ,90,0.0,&avnx[202] } ,
+    {20,"gap" ,91,0.0,&avnx[203] } ,
+    {20,"operon" ,92,0.0,&avnx[204] } ,
+    {20,"oriT" ,93,0.0,&avnx[205] } ,
+    {20,"ncRNA" ,94,0.0,&avnx[206] } ,
+    {20,"tmRNA" ,95,0.0,NULL } ,
+    {20,"allele" ,1,0.0,&avnx[208] } ,
+    {20,"activity" ,2,0.0,&avnx[209] } ,
+    {20,"anticodon" ,3,0.0,&avnx[210] } ,
+    {20,"bound-moiety" ,4,0.0,&avnx[211] } ,
+    {20,"chromosome" ,5,0.0,&avnx[212] } ,
+    {20,"citation" ,6,0.0,&avnx[213] } ,
+    {20,"codon" ,7,0.0,&avnx[214] } ,
+    {20,"codon-start" ,8,0.0,&avnx[215] } ,
+    {20,"codons-recognized" ,9,0.0,&avnx[216] } ,
+    {20,"compare" ,10,0.0,&avnx[217] } ,
+    {20,"cons-splice" ,11,0.0,&avnx[218] } ,
+    {20,"db-xref" ,12,0.0,&avnx[219] } ,
+    {20,"description" ,13,0.0,&avnx[220] } ,
+    {20,"direction" ,14,0.0,&avnx[221] } ,
+    {20,"ec-number" ,15,0.0,&avnx[222] } ,
+    {20,"environmental-sample" ,16,0.0,&avnx[223] } ,
+    {20,"evidence" ,17,0.0,&avnx[224] } ,
+    {20,"exception" ,18,0.0,&avnx[225] } ,
+    {20,"experiment" ,19,0.0,&avnx[226] } ,
+    {20,"focus" ,20,0.0,&avnx[227] } ,
+    {20,"frequency" ,21,0.0,&avnx[228] } ,
+    {20,"function" ,22,0.0,&avnx[229] } ,
+    {20,"gene" ,23,0.0,&avnx[230] } ,
+    {20,"gene-description" ,24,0.0,&avnx[231] } ,
+    {20,"inference" ,25,0.0,&avnx[232] } ,
+    {20,"label" ,26,0.0,&avnx[233] } ,
+    {20,"locus-tag" ,27,0.0,&avnx[234] } ,
+    {20,"map" ,28,0.0,&avnx[235] } ,
+    {20,"mobile-element" ,29,0.0,&avnx[236] } ,
+    {20,"mod-base" ,30,0.0,&avnx[237] } ,
+    {20,"mol-type" ,31,0.0,&avnx[238] } ,
+    {20,"ncRNA-class" ,32,0.0,&avnx[239] } ,
+    {20,"note" ,33,0.0,&avnx[240] } ,
+    {20,"number" ,34,0.0,&avnx[241] } ,
+    {20,"old-locus-tag" ,35,0.0,&avnx[242] } ,
+    {20,"operon" ,36,0.0,&avnx[243] } ,
+    {20,"organism" ,37,0.0,&avnx[244] } ,
+    {20,"organelle" ,38,0.0,&avnx[245] } ,
+    {20,"partial" ,39,0.0,&avnx[246] } ,
+    {20,"phenotype" ,40,0.0,&avnx[247] } ,
+    {20,"plasmid" ,41,0.0,&avnx[248] } ,
+    {20,"product" ,42,0.0,&avnx[249] } ,
+    {20,"protein-id" ,43,0.0,&avnx[250] } ,
+    {20,"pseudo" ,44,0.0,&avnx[251] } ,
+    {20,"rearranged" ,45,0.0,&avnx[252] } ,
+    {20,"replace" ,46,0.0,&avnx[253] } ,
+    {20,"rpt-family" ,47,0.0,&avnx[254] } ,
+    {20,"rpt-type" ,48,0.0,&avnx[255] } ,
+    {20,"rpt-unit" ,49,0.0,&avnx[256] } ,
+    {20,"rpt-unit-seq" ,50,0.0,&avnx[257] } ,
+    {20,"rpt-unit-range" ,51,0.0,&avnx[258] } ,
+    {20,"segment" ,52,0.0,&avnx[259] } ,
+    {20,"sequenced-mol" ,53,0.0,&avnx[260] } ,
+    {20,"standard-name" ,54,0.0,&avnx[261] } ,
+    {20,"synonym" ,55,0.0,&avnx[262] } ,
+    {20,"transcript-id" ,56,0.0,&avnx[263] } ,
+    {20,"transgenic" ,57,0.0,&avnx[264] } ,
+    {20,"translation" ,58,0.0,&avnx[265] } ,
+    {20,"transl-except" ,59,0.0,&avnx[266] } ,
+    {20,"transl-table" ,60,0.0,&avnx[267] } ,
+    {20,"usedin" ,61,0.0,NULL } ,
+    {3,NULL,1,0.0,NULL } ,
+    {20,"contains" ,1,0.0,&avnx[270] } ,
+    {20,"equals" ,2,0.0,&avnx[271] } ,
+    {20,"starts" ,3,0.0,&avnx[272] } ,
+    {20,"ends" ,4,0.0,&avnx[273] } ,
+    {20,"inlist" ,5,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {20,"cds-comment" ,1,0.0,&avnx[278] } ,
+    {20,"gene-locus" ,2,0.0,&avnx[279] } ,
+    {20,"gene-description" ,3,0.0,&avnx[280] } ,
+    {20,"gene-comment" ,4,0.0,&avnx[281] } ,
+    {20,"gene-allele" ,5,0.0,&avnx[282] } ,
+    {20,"gene-maploc" ,6,0.0,&avnx[283] } ,
+    {20,"gene-locus-tag" ,7,0.0,&avnx[284] } ,
+    {20,"gene-synonym" ,8,0.0,&avnx[285] } ,
+    {20,"gene-old-locus-tag" ,9,0.0,&avnx[286] } ,
+    {20,"mrna-product" ,10,0.0,&avnx[287] } ,
+    {20,"mrna-comment" ,11,0.0,&avnx[288] } ,
+    {20,"prot-name" ,12,0.0,&avnx[289] } ,
+    {20,"prot-description" ,13,0.0,&avnx[290] } ,
+    {20,"prot-ec-number" ,14,0.0,&avnx[291] } ,
+    {20,"prot-activity" ,15,0.0,&avnx[292] } ,
+    {20,"prot-comment" ,16,0.0,&avnx[293] } ,
+    {20,"mat-peptide-name" ,17,0.0,&avnx[294] } ,
+    {20,"mat-peptide-description" ,18,0.0,&avnx[295] } ,
+    {20,"mat-peptide-ec-number" ,19,0.0,&avnx[296] } ,
+    {20,"mat-peptide-activity" ,20,0.0,&avnx[297] } ,
+    {20,"mat-peptide-comment" ,21,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[299] } ,
+    {20,"genomic" ,1,0.0,&avnx[300] } ,
+    {20,"precursor-RNA" ,2,0.0,&avnx[301] } ,
+    {20,"mRNA" ,3,0.0,&avnx[302] } ,
+    {20,"rRNA" ,4,0.0,&avnx[303] } ,
+    {20,"tRNA" ,5,0.0,&avnx[304] } ,
+    {20,"snRNA" ,6,0.0,&avnx[305] } ,
+    {20,"scRNA" ,7,0.0,&avnx[306] } ,
+    {20,"genomic-mRNA" ,8,0.0,&avnx[307] } ,
+    {20,"cRNA" ,9,0.0,&avnx[308] } ,
+    {20,"snoRNA" ,10,0.0,&avnx[309] } ,
+    {20,"transcribed-RNA" ,11,0.0,&avnx[310] } ,
+    {20,"ncRNA" ,12,0.0,&avnx[311] } ,
+    {20,"transfer-messenger-RNA" ,13,0.0,&avnx[312] } ,
+    {20,"other" ,14,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[314] } ,
+    {20,"standard" ,1,0.0,&avnx[315] } ,
+    {20,"est" ,2,0.0,&avnx[316] } ,
+    {20,"sts" ,3,0.0,&avnx[317] } ,
+    {20,"survey" ,4,0.0,&avnx[318] } ,
+    {20,"genetic-map" ,5,0.0,&avnx[319] } ,
+    {20,"physical-map" ,6,0.0,&avnx[320] } ,
+    {20,"derived" ,7,0.0,&avnx[321] } ,
+    {20,"concept-trans" ,8,0.0,&avnx[322] } ,
+    {20,"seq-pept" ,9,0.0,&avnx[323] } ,
+    {20,"both" ,10,0.0,&avnx[324] } ,
+    {20,"seq-pept-overlap" ,11,0.0,&avnx[325] } ,
+    {20,"seq-pept-homol" ,12,0.0,&avnx[326] } ,
+    {20,"concept-trans-a" ,13,0.0,&avnx[327] } ,
+    {20,"htgs-1" ,14,0.0,&avnx[328] } ,
+    {20,"htgs-2" ,15,0.0,&avnx[329] } ,
+    {20,"htgs-3" ,16,0.0,&avnx[330] } ,
+    {20,"fli-cDNA" ,17,0.0,&avnx[331] } ,
+    {20,"htgs-0" ,18,0.0,&avnx[332] } ,
+    {20,"htc" ,19,0.0,&avnx[333] } ,
+    {20,"wgs" ,20,0.0,&avnx[334] } ,
+    {20,"barcode" ,21,0.0,&avnx[335] } ,
+    {20,"composite-wgs-htgs" ,22,0.0,&avnx[336] } ,
+    {20,"tsa" ,23,0.0,&avnx[337] } ,
+    {20,"other" ,24,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[339] } ,
+    {20,"complete" ,1,0.0,&avnx[340] } ,
+    {20,"partial" ,2,0.0,&avnx[341] } ,
+    {20,"no-left" ,3,0.0,&avnx[342] } ,
+    {20,"no-right" ,4,0.0,&avnx[343] } ,
+    {20,"no-ends" ,5,0.0,&avnx[344] } ,
+    {20,"has-left" ,6,0.0,&avnx[345] } ,
+    {20,"has-right" ,7,0.0,&avnx[346] } ,
+    {20,"other" ,6,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[348] } ,
+    {20,"dna" ,1,0.0,&avnx[349] } ,
+    {20,"rna" ,2,0.0,&avnx[350] } ,
+    {20,"protein" ,3,0.0,&avnx[351] } ,
+    {20,"nucleotide" ,4,0.0,&avnx[352] } ,
+    {20,"other" ,5,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[354] } ,
+    {20,"linear" ,1,0.0,&avnx[355] } ,
+    {20,"circular" ,2,0.0,&avnx[356] } ,
+    {20,"tandem" ,3,0.0,&avnx[357] } ,
+    {20,"other" ,4,0.0,NULL } ,
+    {20,"unknown" ,0,0.0,&avnx[359] } ,
+    {20,"single" ,1,0.0,&avnx[360] } ,
+    {20,"double" ,2,0.0,&avnx[361] } ,
+    {20,"mixed" ,3,0.0,&avnx[362] } ,
+    {20,"mixed-rev" ,4,0.0,&avnx[363] } ,
+    {20,"other" ,5,0.0,NULL } ,
+    {20,"replace-old" ,1,0.0,&avnx[365] } ,
+    {20,"append-semi" ,2,0.0,&avnx[366] } ,
+    {20,"append-space" ,3,0.0,&avnx[367] } ,
+    {20,"append-colon" ,4,0.0,&avnx[368] } ,
+    {20,"append-none" ,5,0.0,&avnx[369] } ,
+    {20,"prefix-semi" ,6,0.0,&avnx[370] } ,
+    {20,"prefix-space" ,7,0.0,&avnx[371] } ,
+    {20,"prefix-colon" ,8,0.0,&avnx[372] } ,
+    {20,"prefix-none" ,9,0.0,&avnx[373] } ,
+    {20,"leave-old" ,10,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"anywhere" ,0,0.0,&avnx[376] } ,
+    {20,"beginning" ,1,0.0,&avnx[377] } ,
+    {20,"end" ,2,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[383] } ,
+    {20,"plus" ,1,0.0,&avnx[384] } ,
+    {20,"minus" ,2,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[387] } ,
+    {20,"nuc" ,1,0.0,&avnx[388] } ,
+    {20,"prot" ,2,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[390] } ,
+    {20,"feature" ,1,0.0,&avnx[391] } ,
+    {20,"descriptor" ,2,0.0,NULL } ,
+    {20,"gene" ,1,0.0,&avnx[393] } ,
+    {20,"mRNA" ,2,0.0,&avnx[394] } ,
+    {20,"cds" ,3,0.0,&avnx[395] } ,
+    {20,"prot" ,4,0.0,&avnx[396] } ,
+    {20,"exon" ,5,0.0,&avnx[397] } ,
+    {20,"mat-peptide" ,6,0.0,NULL } ,
+    {2,NULL,1,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[400] } ,
+    {20,"genomic" ,1,0.0,&avnx[401] } ,
+    {20,"precursor-RNA" ,2,0.0,&avnx[402] } ,
+    {20,"mRNA" ,3,0.0,&avnx[403] } ,
+    {20,"rRNA" ,4,0.0,&avnx[404] } ,
+    {20,"tRNA" ,5,0.0,&avnx[405] } ,
+    {20,"snRNA" ,6,0.0,&avnx[406] } ,
+    {20,"scRNA" ,7,0.0,&avnx[407] } ,
+    {20,"genomic-mRNA" ,8,0.0,&avnx[408] } ,
+    {20,"cRNA" ,9,0.0,&avnx[409] } ,
+    {20,"snoRNA" ,10,0.0,&avnx[410] } ,
+    {20,"transcribed-RNA" ,11,0.0,&avnx[411] } ,
+    {20,"ncRNA" ,12,0.0,&avnx[412] } ,
+    {20,"transfer-messenger-RNA" ,13,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {3,NULL,0,0.0,NULL } ,
+    {20,"none" ,0,0.0,&avnx[417] } ,
+    {20,"tolower" ,1,0.0,&avnx[418] } ,
+    {20,"toupper" ,2,0.0,&avnx[419] } ,
+    {20,"firstcap" ,3,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,1,0.0,NULL } ,
+    {2,NULL,1,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {2,NULL,0,0.0,NULL } ,
+    {3,NULL,-1,0.0,NULL } ,
+    {20,"any" ,0,0.0,&avnx[429] } ,
+    {20,"plus" ,1,0.0,&avnx[430] } ,
+    {20,"minus" ,2,0.0,&avnx[431] } ,
+    {20,"unknown" ,3,0.0,&avnx[432] } ,
+    {20,"both" ,4,0.0,NULL } ,
+    {20,"plus" ,1,0.0,&avnx[434] } ,
+    {20,"minus" ,2,0.0,&avnx[435] } ,
+    {20,"unknown" ,3,0.0,&avnx[436] } ,
+    {20,"both" ,4,0.0,&avnx[437] } ,
+    {20,"reverse" ,5,0.0,NULL } ,
+    {20,"all" ,0,0.0,&avnx[439] } ,
+    {20,"at-end" ,1,0.0,&avnx[440] } ,
+    {20,"bad-start" ,2,0.0,&avnx[441] } ,
+    {20,"frame-not-one" ,3,0.0,NULL } ,
+    {20,"all" ,0,0.0,&avnx[443] } ,
+    {20,"not-at-end" ,1,0.0,&avnx[444] } ,
+    {20,"good-start" ,2,0.0,NULL } ,
+    {20,"all" ,0,0.0,&avnx[446] } ,
+    {20,"at-end" ,1,0.0,&avnx[447] } ,
+    {20,"bad-end" ,2,0.0,NULL } ,
+    {20,"all" ,0,0.0,&avnx[449] } ,
+    {20,"not-at-end" ,1,0.0,&avnx[450] } ,
+    {20,"good-end" ,2,0.0,NULL } ,
+    {20,"join" ,1,0.0,&avnx[452] } ,
+    {20,"order" ,2,0.0,&avnx[453] } ,
+    {20,"merge" ,3,0.0,NULL } };
+
+static AsnType atx[280] = {
+  {401, "AECR-action" ,1,0,0,0,0,1,0,0,NULL,&atx[35],&atx[1],0,&atx[177]} ,
+  {0, "action" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[133]} ,
+  {463, "Action-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[3],0,&atx[208]} ,
+  {0, "apply" ,128,0,0,0,0,0,0,0,NULL,&atx[4],NULL,0,&atx[55]} ,
+  {456, "Apply-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[5],0,&atx[56]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[52]} ,
+  {453, "Field-type" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[7],0,&atx[67]} ,
+  {0, "source-qual" ,128,0,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[17]} ,
+  {423, "Source-qual-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[9],0,&atx[37]} ,
+  {0, "textqual" ,128,0,0,0,0,0,0,0,NULL,&atx[10],NULL,0,&atx[12]} ,
+  {419, "Source-qual" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[0],0,&atx[69]} ,
+  {310, "ENUMERATED" ,0,10,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "location" ,128,1,0,0,0,0,0,0,NULL,&atx[13],NULL,0,&atx[14]} ,
+  {421, "Source-location" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[81],0,&atx[15]} ,
+  {0, "origin" ,128,2,0,0,0,0,0,0,NULL,&atx[15],NULL,0,NULL} ,
+  {422, "Source-origin" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[104],0,&atx[8]} ,
+  {315, "CHOICE" ,0,-1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "feature-field" ,128,1,0,0,0,0,0,0,NULL,&atx[18],NULL,0,&atx[36]} ,
+  {416, "Feature-field" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[19],0,&atx[203]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[20],NULL,0,&atx[21]} ,
+  {410, "Feature-type" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[111],0,&atx[24]} ,
+  {0, "field" ,128,1,0,0,0,0,0,0,NULL,&atx[22],NULL,0,NULL} ,
+  {415, "Feat-qual-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[23],0,&atx[18]} ,
+  {0, "legal-qual" ,128,0,0,0,0,0,0,0,NULL,&atx[24],NULL,0,&atx[25]} ,
+  {411, "Feat-qual-legal" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[207],0,&atx[245]} ,
+  {0, "illegal-qual" ,128,1,0,0,0,0,0,0,NULL,&atx[26],NULL,0,NULL} ,
+  {405, "String-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[27],0,&atx[141]} ,
+  {0, "match-text" ,128,0,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[29]} ,
+  {323, "VisibleString" ,0,26,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "match-location" ,128,1,0,0,1,0,0,0,&avnx[268],&atx[30],NULL,0,&atx[31]} ,
+  {404, "String-location" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[269],0,&atx[26]} ,
+  {0, "case-sensitive" ,128,2,0,0,1,0,0,0,&avnx[274],&atx[32],NULL,0,&atx[33]} ,
+  {301, "BOOLEAN" ,0,1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "whole-word" ,128,3,0,0,1,0,0,0,&avnx[275],&atx[32],NULL,0,&atx[34]} ,
+  {0, "not-present" ,128,4,0,0,1,0,0,0,&avnx[276],&atx[32],NULL,0,NULL} ,
+  {311, "SEQUENCE" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "cds-gene-prot" ,128,2,0,0,0,0,0,0,NULL,&atx[37],NULL,0,&atx[38]} ,
+  {424, "CDSGeneProt-field" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[277],0,&atx[78]} ,
+  {0, "molinfo-field" ,128,3,0,0,0,0,0,0,NULL,&atx[39],NULL,0,NULL} ,
+  {432, "Molinfo-field" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[40],0,&atx[84]} ,
+  {0, "molecule" ,128,0,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[42]} ,
+  {426, "Molecule-type" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[298],0,&atx[43]} ,
+  {0, "technique" ,128,1,0,0,0,0,0,0,NULL,&atx[43],NULL,0,&atx[44]} ,
+  {427, "Technique-type" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[313],0,&atx[45]} ,
+  {0, "completedness" ,128,2,0,0,0,0,0,0,NULL,&atx[45],NULL,0,&atx[46]} ,
+  {428, "Completedness-type" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[338],0,&atx[47]} ,
+  {0, "mol-class" ,128,3,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[48]} ,
+  {429, "Molecule-class-type" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[347],0,&atx[49]} ,
+  {0, "topology" ,128,4,0,0,0,0,0,0,NULL,&atx[49],NULL,0,&atx[50]} ,
+  {430, "Topology-type" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[353],0,&atx[51]} ,
+  {0, "strand" ,128,5,0,0,0,0,0,0,NULL,&atx[51],NULL,0,NULL} ,
+  {431, "Strand-type" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[358],0,&atx[39]} ,
+  {0, "value" ,128,1,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[53]} ,
+  {0, "existing-text" ,128,2,0,0,0,0,0,0,NULL,&atx[54],NULL,0,NULL} ,
+  {455, "ExistingTextOption" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[364],0,&atx[4]} ,
+  {0, "edit" ,128,1,0,0,0,0,0,0,NULL,&atx[56],NULL,0,&atx[64]} ,
+  {457, "Edit-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[57],0,&atx[65]} ,
+  {0, "edit" ,128,0,0,0,0,0,0,0,NULL,&atx[58],NULL,0,&atx[63]} ,
+  {452, "Field-edit" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[59],0,&atx[6]} ,
+  {0, "find-txt" ,128,0,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[60]} ,
+  {0, "repl-txt" ,128,1,0,1,0,0,0,0,NULL,&atx[28],NULL,0,&atx[61]} ,
+  {0, "location" ,128,2,0,0,1,0,0,0,&avnx[374],&atx[62],NULL,0,NULL} ,
+  {451, "Field-edit-location" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[375],0,&atx[58]} ,
+  {0, "field" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
+  {0, "convert" ,128,2,0,0,0,0,0,0,NULL,&atx[65],NULL,0,&atx[108]} ,
+  {458, "Convert-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[66],0,&atx[109]} ,
+  {0, "fields" ,128,0,0,0,0,0,0,0,NULL,&atx[67],NULL,0,&atx[107]} ,
+  {454, "Field-pair-type" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[68],0,&atx[54]} ,
+  {0, "source-qual" ,128,0,0,0,0,0,0,0,NULL,&atx[69],NULL,0,&atx[72]} ,
+  {420, "Source-qual-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[70],0,&atx[13]} ,
+  {0, "field-from" ,128,0,0,0,0,0,0,0,NULL,&atx[10],NULL,0,&atx[71]} ,
+  {0, "field-to" ,128,1,0,0,0,0,0,0,NULL,&atx[10],NULL,0,NULL} ,
+  {0, "feature-field" ,128,1,0,0,0,0,0,0,NULL,&atx[73],NULL,0,&atx[77]} ,
+  {418, "Feature-field-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[74],0,&atx[10]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[20],NULL,0,&atx[75]} ,
+  {0, "field-from" ,128,1,0,0,0,0,0,0,NULL,&atx[22],NULL,0,&atx[76]} ,
+  {0, "field-to" ,128,2,0,0,0,0,0,0,NULL,&atx[22],NULL,0,NULL} ,
+  {0, "cds-gene-prot" ,128,2,0,0,0,0,0,0,NULL,&atx[78],NULL,0,&atx[81]} ,
+  {425, "CDSGeneProt-field-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[79],0,&atx[41]} ,
+  {0, "field-from" ,128,0,0,0,0,0,0,0,NULL,&atx[37],NULL,0,&atx[80]} ,
+  {0, "field-to" ,128,1,0,0,0,0,0,0,NULL,&atx[37],NULL,0,NULL} ,
+  {0, "molinfo-field" ,128,3,0,0,0,0,0,0,NULL,&atx[82],NULL,0,NULL} ,
+  {439, "Molinfo-field-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[83],0,&atx[145]} ,
+  {0, "molecule" ,128,0,0,0,0,0,0,0,NULL,&atx[84],NULL,0,&atx[87]} ,
+  {433, "Molinfo-molecule-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[85],0,&atx[88]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[86]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[41],NULL,0,NULL} ,
+  {0, "technique" ,128,1,0,0,0,0,0,0,NULL,&atx[88],NULL,0,&atx[91]} ,
+  {434, "Molinfo-technique-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[89],0,&atx[92]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[43],NULL,0,&atx[90]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[43],NULL,0,NULL} ,
+  {0, "completedness" ,128,2,0,0,0,0,0,0,NULL,&atx[92],NULL,0,&atx[95]} ,
+  {435, "Molinfo-completedness-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[93],0,&atx[96]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[45],NULL,0,&atx[94]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[45],NULL,0,NULL} ,
+  {0, "mol-class" ,128,3,0,0,0,0,0,0,NULL,&atx[96],NULL,0,&atx[99]} ,
+  {436, "Molinfo-mol-class-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[97],0,&atx[100]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[98]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[47],NULL,0,NULL} ,
+  {0, "topology" ,128,4,0,0,0,0,0,0,NULL,&atx[100],NULL,0,&atx[103]} ,
+  {437, "Molinfo-topology-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[101],0,&atx[104]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[49],NULL,0,&atx[102]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[49],NULL,0,NULL} ,
+  {0, "strand" ,128,5,0,0,0,0,0,0,NULL,&atx[104],NULL,0,NULL} ,
+  {438, "Molinfo-strand-pair" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[105],0,&atx[82]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[51],NULL,0,&atx[106]} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[51],NULL,0,NULL} ,
+  {0, "existing-text" ,128,1,0,0,0,0,0,0,NULL,&atx[54],NULL,0,NULL} ,
+  {0, "copy" ,128,3,0,0,0,0,0,0,NULL,&atx[109],NULL,0,&atx[112]} ,
+  {459, "Copy-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[110],0,&atx[113]} ,
+  {0, "fields" ,128,0,0,0,0,0,0,0,NULL,&atx[67],NULL,0,&atx[111]} ,
+  {0, "existing-text" ,128,1,0,0,0,0,0,0,NULL,&atx[54],NULL,0,NULL} ,
+  {0, "swap" ,128,4,0,0,0,0,0,0,NULL,&atx[113],NULL,0,&atx[116]} ,
+  {460, "Swap-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[114],0,&atx[120]} ,
+  {0, "fields" ,128,0,0,0,0,0,0,0,NULL,&atx[67],NULL,0,&atx[115]} ,
+  {0, "field-to" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
+  {0, "remove" ,128,5,0,0,0,0,0,0,NULL,&atx[117],NULL,0,&atx[119]} ,
+  {462, "Remove-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[118],0,&atx[2]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
+  {0, "parse" ,128,6,0,0,0,0,0,0,NULL,&atx[120],NULL,0,NULL} ,
+  {461, "AECRParse-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[121],0,&atx[117]} ,
+  {0, "portion" ,128,0,0,0,0,0,0,0,NULL,&atx[122],NULL,0,&atx[130]} ,
+  {450, "Text-portion" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[123],0,&atx[62]} ,
+  {0, "left-text" ,128,0,0,1,0,0,0,0,NULL,&atx[28],NULL,0,&atx[124]} ,
+  {0, "include-left" ,128,1,0,0,0,0,0,0,NULL,&atx[32],NULL,0,&atx[125]} ,
+  {0, "right-text" ,128,2,0,1,0,0,0,0,NULL,&atx[28],NULL,0,&atx[126]} ,
+  {0, "include-right" ,128,3,0,0,0,0,0,0,NULL,&atx[32],NULL,0,&atx[127]} ,
+  {0, "inside" ,128,4,0,0,0,0,0,0,NULL,&atx[32],NULL,0,&atx[128]} ,
+  {0, "case-sensitive" ,128,5,0,0,1,0,0,0,&avnx[378],&atx[32],NULL,0,&atx[129]} ,
+  {0, "whole-word" ,128,6,0,0,1,0,0,0,&avnx[379],&atx[32],NULL,0,NULL} ,
+  {0, "fields" ,128,1,0,0,0,0,0,0,NULL,&atx[67],NULL,0,&atx[131]} ,
+  {0, "remove-from-parsed" ,128,2,0,0,1,0,0,0,&avnx[380],&atx[32],NULL,0,&atx[132]} ,
+  {0, "existing-text" ,128,3,0,0,0,0,0,0,NULL,&atx[54],NULL,0,NULL} ,
+  {0, "constraint" ,128,1,0,1,0,0,0,0,NULL,&atx[134],NULL,0,NULL} ,
+  {449, "Constraint-choice-set" ,1,0,0,0,0,0,0,0,NULL,&atx[176],&atx[135],0,&atx[122]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[136],NULL,0,NULL} ,
+  {448, "Constraint-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[137],0,&atx[134]} ,
+  {0, "string" ,128,0,0,0,0,0,0,0,NULL,&atx[26],NULL,0,&atx[138]} ,
+  {0, "location" ,128,1,0,0,0,0,0,0,NULL,&atx[139],NULL,0,&atx[144]} ,
+  {408, "Location-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[140],0,&atx[150]} ,
+  {0, "strand" ,128,0,0,0,1,0,0,0,&avnx[381],&atx[141],NULL,0,&atx[142]} ,
+  {406, "Strand-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[382],0,&atx[143]} ,
+  {0, "seq-type" ,128,1,0,0,1,0,0,0,&avnx[385],&atx[143],NULL,0,NULL} ,
+  {407, "Seqtype-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[386],0,&atx[139]} ,
+  {0, "source" ,128,2,0,0,0,0,0,0,NULL,&atx[145],NULL,0,&atx[151]} ,
+  {440, "Source-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[146],0,&atx[161]} ,
+  {0, "field1" ,128,0,0,1,0,0,0,0,NULL,&atx[8],NULL,0,&atx[147]} ,
+  {0, "field2" ,128,1,0,1,0,0,0,0,NULL,&atx[8],NULL,0,&atx[148]} ,
+  {0, "constraint" ,128,2,0,1,0,0,0,0,NULL,&atx[26],NULL,0,&atx[149]} ,
+  {0, "type-constraint" ,128,3,0,1,0,0,0,0,NULL,&atx[150],NULL,0,NULL} ,
+  {409, "Object-type-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[389],0,&atx[20]} ,
+  {0, "cdsgeneprot-qual" ,128,3,0,0,0,0,0,0,NULL,&atx[152],NULL,0,&atx[158]} ,
+  {444, "CDSGeneProt-qual-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[153],0,&atx[172]} ,
+  {0, "field1" ,128,0,0,1,0,0,0,0,NULL,&atx[154],NULL,0,&atx[156]} ,
+  {443, "CDSGeneProt-constraint-field" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[155],0,&atx[152]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[37],NULL,0,NULL} ,
+  {0, "field2" ,128,1,0,1,0,0,0,0,NULL,&atx[154],NULL,0,&atx[157]} ,
+  {0, "constraint" ,128,2,0,1,0,0,0,0,NULL,&atx[26],NULL,0,NULL} ,
+  {0, "cdsgeneprot-pseudo" ,128,4,0,0,0,0,0,0,NULL,&atx[159],NULL,0,&atx[163]} ,
+  {442, "CDSGeneProt-pseudo-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[160],0,&atx[154]} ,
+  {0, "feature" ,128,0,0,0,0,0,0,0,NULL,&atx[161],NULL,0,&atx[162]} ,
+  {441, "CDSGeneProt-feature-type-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[392],0,&atx[159]} ,
+  {0, "is-pseudo" ,128,1,0,0,1,0,0,0,&avnx[398],&atx[32],NULL,0,NULL} ,
+  {0, "sequence" ,128,5,0,0,0,0,0,0,NULL,&atx[164],NULL,0,NULL} ,
+  {447, "Sequence-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[165],0,&atx[136]} ,
+  {0, "seqtype" ,128,0,0,1,0,0,0,0,NULL,&atx[166],NULL,0,&atx[174]} ,
+  {446, "Sequence-constraint-mol-type-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[167],0,&atx[164]} ,
+  {0, "any" ,128,0,0,0,0,0,0,0,NULL,&atx[168],NULL,0,&atx[169]} ,
+  {305, "NULL" ,0,5,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "nucleotide" ,128,1,0,0,0,0,0,0,NULL,&atx[168],NULL,0,&atx[170]} ,
+  {0, "dna" ,128,2,0,0,0,0,0,0,NULL,&atx[168],NULL,0,&atx[171]} ,
+  {0, "rna" ,128,3,0,0,0,0,0,0,NULL,&atx[172],NULL,0,&atx[173]} ,
+  {445, "Sequence-constraint-rnamol" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[399],0,&atx[166]} ,
+  {0, "protein" ,128,4,0,0,0,0,0,0,NULL,&atx[168],NULL,0,NULL} ,
+  {0, "id" ,128,1,0,1,0,0,0,0,NULL,&atx[26],NULL,0,&atx[175]} ,
+  {0, "feature" ,128,2,0,0,0,0,0,0,NULL,&atx[20],NULL,0,NULL} ,
+  {314, "SET OF" ,0,17,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {402, "Parse-action" ,1,0,0,0,0,1,0,0,NULL,&atx[35],&atx[178],0,&atx[211]} ,
+  {0, "portion" ,128,0,0,0,0,0,0,0,NULL,&atx[122],NULL,0,&atx[179]} ,
+  {0, "src" ,128,1,0,0,0,0,0,0,NULL,&atx[180],NULL,0,&atx[195]} ,
+  {467, "Parse-src" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[181],0,&atx[199]} ,
+  {0, "defline" ,128,0,0,0,0,0,0,0,NULL,&atx[168],NULL,0,&atx[182]} ,
+  {0, "flatfile" ,128,1,0,0,0,0,0,0,NULL,&atx[168],NULL,0,&atx[183]} ,
+  {0, "local-id" ,128,2,0,0,0,0,0,0,NULL,&atx[168],NULL,0,&atx[184]} ,
+  {0, "org" ,128,3,0,0,0,0,0,0,NULL,&atx[185],NULL,0,&atx[191]} ,
+  {466, "Parse-src-org" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[186],0,&atx[180]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[187],NULL,0,&atx[190]} ,
+  {465, "Parse-src-org-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[188],0,&atx[185]} ,
+  {0, "source-qual" ,128,0,0,0,0,0,0,0,NULL,&atx[10],NULL,0,&atx[189]} ,
+  {0, "taxname-after-binomial" ,128,1,0,0,0,0,0,0,NULL,&atx[168],NULL,0,NULL} ,
+  {0, "type" ,128,1,0,0,1,0,0,0,&avnx[413],&atx[150],NULL,0,NULL} ,
+  {0, "comment" ,128,4,0,0,0,0,0,0,NULL,&atx[168],NULL,0,&atx[192]} ,
+  {0, "bankit-comment" ,128,5,0,0,0,0,0,0,NULL,&atx[168],NULL,0,&atx[193]} ,
+  {0, "structured-comment" ,128,6,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[194]} ,
+  {0, "file-id" ,128,7,0,0,0,0,0,0,NULL,&atx[168],NULL,0,NULL} ,
+  {0, "dest" ,128,2,0,0,0,0,0,0,NULL,&atx[196],NULL,0,&atx[207]} ,
+  {469, "Parse-dest" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[197],0,&atx[225]} ,
+  {0, "defline" ,128,0,0,0,0,0,0,0,NULL,&atx[168],NULL,0,&atx[198]} ,
+  {0, "org" ,128,1,0,0,0,0,0,0,NULL,&atx[199],NULL,0,&atx[202]} ,
+  {468, "Parse-dst-org" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[200],0,&atx[196]} ,
+  {0, "field" ,128,0,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[201]} ,
+  {0, "type" ,128,1,0,0,1,0,0,0,&avnx[414],&atx[150],NULL,0,NULL} ,
+  {0, "featqual" ,128,2,0,0,0,0,0,0,NULL,&atx[203],NULL,0,&atx[206]} ,
+  {417, "Feature-field-legal" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[204],0,&atx[73]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[20],NULL,0,&atx[205]} ,
+  {0, "field" ,128,1,0,0,0,0,0,0,NULL,&atx[24],NULL,0,NULL} ,
+  {0, "dbxref" ,128,3,0,0,0,0,0,0,NULL,&atx[28],NULL,0,NULL} ,
+  {0, "capitalization" ,128,3,0,0,1,0,0,0,&avnx[415],&atx[208],NULL,0,&atx[209]} ,
+  {464, "Cap-change" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[416],0,&atx[187]} ,
+  {0, "remove-from-parsed" ,128,4,0,0,1,0,0,0,&avnx[420],&atx[32],NULL,0,&atx[210]} ,
+  {0, "existing-text" ,128,5,0,0,0,0,0,0,NULL,&atx[54],NULL,0,NULL} ,
+  {403, "Macro-action-list" ,1,0,0,0,0,1,0,0,NULL,&atx[176],&atx[212],0,&atx[30]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[213],NULL,0,NULL} ,
+  {488, "Macro-action-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[214],0,NULL} ,
+  {0, "aecr" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[215]} ,
+  {0, "parse" ,128,1,0,0,0,0,0,0,NULL,&atx[177],NULL,0,&atx[216]} ,
+  {0, "add-feature" ,128,2,0,0,0,0,0,0,NULL,&atx[217],NULL,0,&atx[248]} ,
+  {474, "Apply-feature-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[218],0,&atx[249]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[20],NULL,0,&atx[219]} ,
+  {0, "partial5" ,128,1,0,0,1,0,0,0,&avnx[421],&atx[32],NULL,0,&atx[220]} ,
+  {0, "partial3" ,128,2,0,0,1,0,0,0,&avnx[422],&atx[32],NULL,0,&atx[221]} ,
+  {0, "plus-strand" ,128,3,0,0,1,0,0,0,&avnx[423],&atx[32],NULL,0,&atx[222]} ,
+  {0, "location" ,128,4,0,0,0,0,0,0,NULL,&atx[223],NULL,0,&atx[230]} ,
+  {471, "Location-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[224],0,&atx[233]} ,
+  {0, "interval" ,128,0,0,0,0,0,0,0,NULL,&atx[225],NULL,0,&atx[229]} ,
+  {470, "Location-interval" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[226],0,&atx[223]} ,
+  {0, "from" ,128,0,0,0,0,0,0,0,NULL,&atx[227],NULL,0,&atx[228]} ,
+  {302, "INTEGER" ,0,2,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "to" ,128,1,0,0,0,0,0,0,NULL,&atx[227],NULL,0,NULL} ,
+  {0, "whole-sequence" ,128,1,0,0,0,0,0,0,NULL,&atx[168],NULL,0,NULL} ,
+  {0, "seq-list" ,128,5,0,0,0,0,0,0,NULL,&atx[231],NULL,0,&atx[236]} ,
+  {473, "Sequence-list-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[232],0,&atx[217]} ,
+  {0, "list" ,128,0,0,0,0,0,0,0,NULL,&atx[233],NULL,0,&atx[235]} ,
+  {472, "Sequence-list" ,1,0,0,0,0,0,0,0,NULL,&atx[176],&atx[234],0,&atx[231]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[28],NULL,0,NULL} ,
+  {0, "all" ,128,1,0,0,0,0,0,0,NULL,&atx[168],NULL,0,NULL} ,
+  {0, "add-redundant" ,128,6,0,0,1,0,0,0,&avnx[424],&atx[32],NULL,0,&atx[237]} ,
+  {0, "add-mrna" ,128,7,0,0,1,0,0,0,&avnx[425],&atx[32],NULL,0,&atx[238]} ,
+  {0, "apply-to-parts" ,128,8,0,0,1,0,0,0,&avnx[426],&atx[32],NULL,0,&atx[239]} ,
+  {0, "only-seg-num" ,128,9,0,0,1,0,0,0,&avnx[427],&atx[227],NULL,0,&atx[240]} ,
+  {0, "fields" ,128,10,0,1,0,0,0,0,NULL,&atx[241],NULL,0,NULL} ,
+  {414, "Feat-qual-legal-set" ,1,0,0,0,0,0,0,0,NULL,&atx[176],&atx[242],0,&atx[22]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[243],NULL,0,NULL} ,
+  {413, "Feat-qual-legal-val-choice" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[244],0,&atx[241]} ,
+  {0, "qual" ,128,0,0,0,0,0,0,0,NULL,&atx[245],NULL,0,NULL} ,
+  {412, "Feat-qual-legal-val" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[246],0,&atx[243]} ,
+  {0, "qual" ,128,0,0,0,0,0,0,0,NULL,&atx[24],NULL,0,&atx[247]} ,
+  {0, "val" ,128,1,0,0,0,0,0,0,NULL,&atx[28],NULL,0,NULL} ,
+  {0, "remove-feature" ,128,3,0,0,0,0,0,0,NULL,&atx[249],NULL,0,&atx[252]} ,
+  {475, "Remove-feature-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[250],0,&atx[260]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[20],NULL,0,&atx[251]} ,
+  {0, "constraint" ,128,1,0,1,0,0,0,0,NULL,&atx[134],NULL,0,NULL} ,
+  {0, "edit-location" ,128,4,0,0,0,0,0,0,NULL,&atx[253],NULL,0,NULL} ,
+  {487, "Edit-feature-location-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[254],0,&atx[213]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[20],NULL,0,&atx[255]} ,
+  {0, "action" ,128,1,0,0,0,0,0,0,NULL,&atx[256],NULL,0,&atx[279]} ,
+  {486, "Location-edit-type" ,1,0,0,0,0,0,0,0,NULL,&atx[16],&atx[257],0,&atx[253]} ,
+  {0, "strand" ,128,0,0,0,0,0,0,0,NULL,&atx[258],NULL,0,&atx[263]} ,
+  {478, "Edit-location-strand" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[259],0,&atx[266]} ,
+  {0, "strand-from" ,128,0,0,0,0,0,0,0,NULL,&atx[260],NULL,0,&atx[261]} ,
+  {476, "Feature-location-strand-from" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[428],0,&atx[262]} ,
+  {0, "strand-to" ,128,1,0,0,0,0,0,0,NULL,&atx[262],NULL,0,NULL} ,
+  {477, "Feature-location-strand-to" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[433],0,&atx[258]} ,
+  {0, "set-5-partial" ,128,1,0,0,0,0,0,0,NULL,&atx[264],NULL,0,&atx[268]} ,
+  {480, "Partial-5-set-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[265],0,&atx[269]} ,
+  {0, "constraint" ,128,0,0,0,0,0,0,0,NULL,&atx[266],NULL,0,&atx[267]} ,
+  {479, "Partial-5-set-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[438],0,&atx[264]} ,
+  {0, "extend" ,128,1,0,0,0,0,0,0,NULL,&atx[32],NULL,0,NULL} ,
+  {0, "clear-5-partial" ,128,2,0,0,0,0,0,0,NULL,&atx[269],NULL,0,&atx[270]} ,
+  {481, "Partial-5-clear-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[442],0,&atx[273]} ,
+  {0, "set-3-partial" ,128,3,0,0,0,0,0,0,NULL,&atx[271],NULL,0,&atx[275]} ,
+  {483, "Partial-3-set-action" ,1,0,0,0,0,0,0,0,NULL,&atx[35],&atx[272],0,&atx[276]} ,
+  {0, "constraint" ,128,0,0,0,0,0,0,0,NULL,&atx[273],NULL,0,&atx[274]} ,
+  {482, "Partial-3-set-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[445],0,&atx[271]} ,
+  {0, "extend" ,128,1,0,0,0,0,0,0,NULL,&atx[32],NULL,0,NULL} ,
+  {0, "clear-3-partial" ,128,4,0,0,0,0,0,0,NULL,&atx[276],NULL,0,&atx[277]} ,
+  {484, "Partial-3-clear-constraint" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[448],0,&atx[278]} ,
+  {0, "convert" ,128,5,0,0,0,0,0,0,NULL,&atx[278],NULL,0,NULL} ,
+  {485, "Convert-location-type" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&avnx[451],0,&atx[256]} ,
+  {0, "constraint" ,128,2,0,1,0,0,0,0,NULL,&atx[134],NULL,0,NULL} };
+
+static AsnModule ampx[1] = {
+  { "NCBI-Macro" , "asnmacro.h13",&atx[0],NULL,NULL,0,0} };
+
+static AsnValxNodePtr avn = avnx;
+static AsnTypePtr at = atx;
+static AsnModulePtr amp = ampx;
+
+
+
+/**************************************************
+*
+*    Defines for Module NCBI-Macro
+*
+**************************************************/
+
+#define AECR_ACTION &at[0]
+#define AECR_ACTION_action &at[1]
+#define AECR_ACTION_constraint &at[133]
+
+#define PARSE_ACTION &at[177]
+#define PARSE_ACTION_portion &at[178]
+#define PARSE_ACTION_src &at[179]
+#define PARSE_ACTION_dest &at[195]
+#define PARSE_ACTION_capitalization &at[207]
+#define PARSE_ACTION_remove_from_parsed &at[209]
+#define PARSE_ACTION_existing_text &at[210]
+
+#define MACRO_ACTION_LIST &at[211]
+#define MACRO_ACTION_LIST_E &at[212]
+
+#define STRING_LOCATION &at[30]
+
+#define STRING_CONSTRAINT &at[26]
+#define STRING_CONSTRAINT_match_text &at[27]
+#define CONSTRAINT_match_location &at[29]
+#define CONSTRAINT_case_sensitive &at[31]
+#define STRING_CONSTRAINT_whole_word &at[33]
+#define STRING_CONSTRAINT_not_present &at[34]
+
+#define STRAND_CONSTRAINT &at[141]
+
+#define SEQTYPE_CONSTRAINT &at[143]
+
+#define LOCATION_CONSTRAINT &at[139]
+#define LOCATION_CONSTRAINT_strand &at[140]
+#define LOCATION_CONSTRAINT_seq_type &at[142]
+
+#define OBJECT_TYPE_CONSTRAINT &at[150]
+
+#define FEATURE_TYPE &at[20]
+
+#define FEAT_QUAL_LEGAL &at[24]
+
+#define FEAT_QUAL_LEGAL_VAL &at[245]
+#define FEAT_QUAL_LEGAL_VAL_qual &at[246]
+#define FEAT_QUAL_LEGAL_VAL_val &at[247]
+
+#define FEAT_QUAL_LEGAL_VAL_CHOICE &at[243]
+#define FEAT_QUAL_LEGAL_VAL_CHOICE_qual &at[244]
+
+#define FEAT_QUAL_LEGAL_SET &at[241]
+#define FEAT_QUAL_LEGAL_SET_E &at[242]
+
+#define FEAT_QUAL_CHOICE &at[22]
+#define FEAT_QUAL_CHOICE_legal_qual &at[23]
+#define FEAT_QUAL_CHOICE_illegal_qual &at[25]
+
+#define FEATURE_FIELD &at[18]
+#define FEATURE_FIELD_type &at[19]
+#define FEATURE_FIELD_field &at[21]
+
+#define FEATURE_FIELD_LEGAL &at[203]
+#define FEATURE_FIELD_LEGAL_type &at[204]
+#define FEATURE_FIELD_LEGAL_field &at[205]
+
+#define FEATURE_FIELD_PAIR &at[73]
+#define FEATURE_FIELD_PAIR_type &at[74]
+#define FEATURE_FIELD_PAIR_field_from &at[75]
+#define FEATURE_FIELD_PAIR_field_to &at[76]
+
+#define SOURCE_QUAL &at[10]
+
+#define SOURCE_QUAL_PAIR &at[69]
+#define SOURCE_QUAL_PAIR_field_from &at[70]
+#define SOURCE_QUAL_PAIR_field_to &at[71]
+
+#define SOURCE_LOCATION &at[13]
+
+#define SOURCE_ORIGIN &at[15]
+
+#define SOURCE_QUAL_CHOICE &at[8]
+#define SOURCE_QUAL_CHOICE_textqual &at[9]
+#define SOURCE_QUAL_CHOICE_location &at[12]
+#define SOURCE_QUAL_CHOICE_origin &at[14]
+
+#define CDSGENEPROT_FIELD &at[37]
+
+#define CDSGENEPROT_FIELD_PAIR &at[78]
+#define FIELD_PAIR_field_from &at[79]
+#define CDSGENEPROT_FIELD_PAIR_field_to &at[80]
+
+#define MOLECULE_TYPE &at[41]
+
+#define TECHNIQUE_TYPE &at[43]
+
+#define COMPLETEDNESS_TYPE &at[45]
+
+#define MOLECULE_CLASS_TYPE &at[47]
+
+#define TOPOLOGY_TYPE &at[49]
+
+#define STRAND_TYPE &at[51]
+
+#define MOLINFO_FIELD &at[39]
+#define MOLINFO_FIELD_molecule &at[40]
+#define MOLINFO_FIELD_technique &at[42]
+#define MOLINFO_FIELD_completedness &at[44]
+#define MOLINFO_FIELD_mol_class &at[46]
+#define MOLINFO_FIELD_topology &at[48]
+#define MOLINFO_FIELD_strand &at[50]
+
+#define MOLINFO_MOLECULE_PAIR &at[84]
+#define MOLINFO_MOLECULE_PAIR_from &at[85]
+#define MOLINFO_MOLECULE_PAIR_to &at[86]
+
+#define MOLINFO_TECHNIQUE_PAIR &at[88]
+#define MOLINFO_TECHNIQUE_PAIR_from &at[89]
+#define MOLINFO_TECHNIQUE_PAIR_to &at[90]
+
+#define MOLINFO_COMPLETEDNESS_PAIR &at[92]
+#define MOLINFO_COMPLETEDNESS_PAIR_from &at[93]
+#define MOLINFO_COMPLETEDNESS_PAIR_to &at[94]
+
+#define MOLINFO_MOL_CLASS_PAIR &at[96]
+#define MOLINFO_MOL_CLASS_PAIR_from &at[97]
+#define MOLINFO_MOL_CLASS_PAIR_to &at[98]
+
+#define MOLINFO_TOPOLOGY_PAIR &at[100]
+#define MOLINFO_TOPOLOGY_PAIR_from &at[101]
+#define MOLINFO_TOPOLOGY_PAIR_to &at[102]
+
+#define MOLINFO_STRAND_PAIR &at[104]
+#define MOLINFO_STRAND_PAIR_from &at[105]
+#define MOLINFO_STRAND_PAIR_to &at[106]
+
+#define MOLINFO_FIELD_PAIR &at[82]
+#define MOLINFO_FIELD_PAIR_molecule &at[83]
+#define MOLINFO_FIELD_PAIR_technique &at[87]
+#define FIELD_PAIR_completedness &at[91]
+#define MOLINFO_FIELD_PAIR_mol_class &at[95]
+#define MOLINFO_FIELD_PAIR_topology &at[99]
+#define MOLINFO_FIELD_PAIR_strand &at[103]
+
+#define SOURCE_CONSTRAINT &at[145]
+#define SOURCE_CONSTRAINT_field1 &at[146]
+#define SOURCE_CONSTRAINT_field2 &at[147]
+#define SOURCE_CONSTRAINT_constraint &at[148]
+#define CONSTRAINT_type_constraint &at[149]
+
+#define FEATURE_TYPE_CONSTRAINT &at[161]
+
+#define CDSGENEPROT_PSEUDO_CONSTRAINT &at[159]
+#define PSEUDO_CONSTRAINT_feature &at[160]
+#define PSEUDO_CONSTRAINT_is_pseudo &at[162]
+
+#define CDSGENEPROT_CONSTRAINT_FIELD &at[154]
+#define CONSTRAINT_FIELD_field &at[155]
+
+#define CDSGENEPROT_QUAL_CONSTRAINT &at[152]
+#define QUAL_CONSTRAINT_field1 &at[153]
+#define QUAL_CONSTRAINT_field2 &at[156]
+#define QUAL_CONSTRAINT_constraint &at[157]
+
+#define SEQUENCE_CONSTRAINT_RNAMOL &at[172]
+
+#define CONSTRAINT_MOL_TYPE_CONSTRAINT &at[166]
+#define MOL_TYPE_CONSTRAINT_any &at[167]
+#define MOL_TYPE_CONSTRAINT_nucleotide &at[169]
+#define MOL_TYPE_CONSTRAINT_dna &at[170]
+#define MOL_TYPE_CONSTRAINT_rna &at[171]
+#define MOL_TYPE_CONSTRAINT_protein &at[173]
+
+#define SEQUENCE_CONSTRAINT &at[164]
+#define SEQUENCE_CONSTRAINT_seqtype &at[165]
+#define SEQUENCE_CONSTRAINT_id &at[174]
+#define SEQUENCE_CONSTRAINT_feature &at[175]
+
+#define CONSTRAINT_CHOICE &at[136]
+#define CONSTRAINT_CHOICE_string &at[137]
+#define CONSTRAINT_CHOICE_location &at[138]
+#define CONSTRAINT_CHOICE_source &at[144]
+#define CHOICE_cdsgeneprot_qual &at[151]
+#define CHOICE_cdsgeneprot_pseudo &at[158]
+#define CONSTRAINT_CHOICE_sequence &at[163]
+
+#define CONSTRAINT_CHOICE_SET &at[134]
+#define CONSTRAINT_CHOICE_SET_E &at[135]
+
+#define TEXT_PORTION &at[122]
+#define TEXT_PORTION_left_text &at[123]
+#define TEXT_PORTION_include_left &at[124]
+#define TEXT_PORTION_right_text &at[125]
+#define TEXT_PORTION_include_right &at[126]
+#define TEXT_PORTION_inside &at[127]
+#define TEXT_PORTION_case_sensitive &at[128]
+#define TEXT_PORTION_whole_word &at[129]
+
+#define FIELD_EDIT_LOCATION &at[62]
+
+#define FIELD_EDIT &at[58]
+#define FIELD_EDIT_find_txt &at[59]
+#define FIELD_EDIT_repl_txt &at[60]
+#define FIELD_EDIT_location &at[61]
+
+#define FIELD_TYPE &at[6]
+#define FIELD_TYPE_source_qual &at[7]
+#define FIELD_TYPE_feature_field &at[17]
+#define FIELD_TYPE_cds_gene_prot &at[36]
+#define FIELD_TYPE_molinfo_field &at[38]
+
+#define FIELD_PAIR_TYPE &at[67]
+#define FIELD_PAIR_TYPE_source_qual &at[68]
+#define FIELD_PAIR_TYPE_feature_field &at[72]
+#define FIELD_PAIR_TYPE_cds_gene_prot &at[77]
+#define FIELD_PAIR_TYPE_molinfo_field &at[81]
+
+#define EXISTINGTEXTOPTION &at[54]
+
+#define APPLY_ACTION &at[4]
+#define APPLY_ACTION_field &at[5]
+#define APPLY_ACTION_value &at[52]
+#define APPLY_ACTION_existing_text &at[53]
+
+#define EDIT_ACTION &at[56]
+#define EDIT_ACTION_edit &at[57]
+#define EDIT_ACTION_field &at[63]
+
+#define CONVERT_ACTION &at[65]
+#define CONVERT_ACTION_fields &at[66]
+#define CONVERT_ACTION_existing_text &at[107]
+
+#define COPY_ACTION &at[109]
+#define COPY_ACTION_fields &at[110]
+#define COPY_ACTION_existing_text &at[111]
+
+#define SWAP_ACTION &at[113]
+#define SWAP_ACTION_fields &at[114]
+#define SWAP_ACTION_field_to &at[115]
+
+#define AECRPARSE_ACTION &at[120]
+#define AECRPARSE_ACTION_portion &at[121]
+#define AECRPARSE_ACTION_fields &at[130]
+#define ACTION_remove_from_parsed &at[131]
+#define AECRPARSE_ACTION_existing_text &at[132]
+
+#define REMOVE_ACTION &at[117]
+#define REMOVE_ACTION_field &at[118]
+
+#define ACTION_CHOICE &at[2]
+#define ACTION_CHOICE_apply &at[3]
+#define ACTION_CHOICE_edit &at[55]
+#define ACTION_CHOICE_convert &at[64]
+#define ACTION_CHOICE_copy &at[108]
+#define ACTION_CHOICE_swap &at[112]
+#define ACTION_CHOICE_remove &at[116]
+#define ACTION_CHOICE_parse &at[119]
+
+#define CAP_CHANGE &at[208]
+
+#define PARSE_SRC_ORG_CHOICE &at[187]
+#define SRC_ORG_CHOICE_source_qual &at[188]
+#define CHOICE_taxname_after_binomial &at[189]
+
+#define PARSE_SRC_ORG &at[185]
+#define PARSE_SRC_ORG_field &at[186]
+#define PARSE_SRC_ORG_type &at[190]
+
+#define PARSE_SRC &at[180]
+#define PARSE_SRC_defline &at[181]
+#define PARSE_SRC_flatfile &at[182]
+#define PARSE_SRC_local_id &at[183]
+#define PARSE_SRC_org &at[184]
+#define PARSE_SRC_comment &at[191]
+#define PARSE_SRC_bankit_comment &at[192]
+#define PARSE_SRC_structured_comment &at[193]
+#define PARSE_SRC_file_id &at[194]
+
+#define PARSE_DST_ORG &at[199]
+#define PARSE_DST_ORG_field &at[200]
+#define PARSE_DST_ORG_type &at[201]
+
+#define PARSE_DEST &at[196]
+#define PARSE_DEST_defline &at[197]
+#define PARSE_DEST_org &at[198]
+#define PARSE_DEST_featqual &at[202]
+#define PARSE_DEST_dbxref &at[206]
+
+#define LOCATION_INTERVAL &at[225]
+#define LOCATION_INTERVAL_from &at[226]
+#define LOCATION_INTERVAL_to &at[228]
+
+#define LOCATION_CHOICE &at[223]
+#define LOCATION_CHOICE_interval &at[224]
+#define LOCATION_CHOICE_whole_sequence &at[229]
+
+#define SEQUENCE_LIST &at[233]
+#define SEQUENCE_LIST_E &at[234]
+
+#define SEQUENCE_LIST_CHOICE &at[231]
+#define SEQUENCE_LIST_CHOICE_list &at[232]
+#define SEQUENCE_LIST_CHOICE_all &at[235]
+
+#define APPLY_FEATURE_ACTION &at[217]
+#define APPLY_FEATURE_ACTION_type &at[218]
+#define APPLY_FEATURE_ACTION_partial5 &at[219]
+#define APPLY_FEATURE_ACTION_partial3 &at[220]
+#define FEATURE_ACTION_plus_strand &at[221]
+#define APPLY_FEATURE_ACTION_location &at[222]
+#define APPLY_FEATURE_ACTION_seq_list &at[230]
+#define FEATURE_ACTION_add_redundant &at[236]
+#define APPLY_FEATURE_ACTION_add_mrna &at[237]
+#define FEATURE_ACTION_apply_to_parts &at[238]
+#define FEATURE_ACTION_only_seg_num &at[239]
+#define APPLY_FEATURE_ACTION_fields &at[240]
+
+#define REMOVE_FEATURE_ACTION &at[249]
+#define REMOVE_FEATURE_ACTION_type &at[250]
+#define FEATURE_ACTION_constraint &at[251]
+
+#define FEATURE_LOCATION_STRAND_FROM &at[260]
+
+#define FEATURE_LOCATION_STRAND_TO &at[262]
+
+#define EDIT_LOCATION_STRAND &at[258]
+#define LOCATION_STRAND_strand_from &at[259]
+#define EDIT_LOCATION_STRAND_strand_to &at[261]
+
+#define PARTIAL_5_SET_CONSTRAINT &at[266]
+
+#define PARTIAL_5_SET_ACTION &at[264]
+#define PARTIAL_5_SET_ACTION_constraint &at[265]
+#define PARTIAL_5_SET_ACTION_extend &at[267]
+
+#define PARTIAL_5_CLEAR_CONSTRAINT &at[269]
+
+#define PARTIAL_3_SET_CONSTRAINT &at[273]
+
+#define PARTIAL_3_SET_ACTION &at[271]
+#define PARTIAL_3_SET_ACTION_constraint &at[272]
+#define PARTIAL_3_SET_ACTION_extend &at[274]
+
+#define PARTIAL_3_CLEAR_CONSTRAINT &at[276]
+
+#define CONVERT_LOCATION_TYPE &at[278]
+
+#define LOCATION_EDIT_TYPE &at[256]
+#define LOCATION_EDIT_TYPE_strand &at[257]
+#define EDIT_TYPE_set_5_partial &at[263]
+#define EDIT_TYPE_clear_5_partial &at[268]
+#define EDIT_TYPE_set_3_partial &at[270]
+#define EDIT_TYPE_clear_3_partial &at[275]
+#define LOCATION_EDIT_TYPE_convert &at[277]
+
+#define EDIT_FEATURE_LOCATION_ACTION &at[253]
+#define FEATURE_LOCATION_ACTION_type &at[254]
+#define FEATURE_LOCATION_ACTION_action &at[255]
+#define LOCATION_ACTION_constraint &at[279]
+
+#define MACRO_ACTION_CHOICE &at[213]
+#define MACRO_ACTION_CHOICE_aecr &at[214]
+#define MACRO_ACTION_CHOICE_parse &at[215]
+#define MACRO_ACTION_CHOICE_add_feature &at[216]
+#define ACTION_CHOICE_remove_feature &at[248]
+#define ACTION_CHOICE_edit_location &at[252]
diff --git a/asnstat/asnseq.h b/asnstat/asnseq.h
index 857aa20f..f8dad1af 100644
--- a/asnstat/asnseq.h
+++ b/asnstat/asnseq.h
@@ -9,8 +9,8 @@
 #include <asn.h>
 #endif
 
-static char * asnfilename = "asnseq.h16";
-static AsnValxNode avnx[161] = {
+static char * asnfilename = "asnseq.h19";
+static AsnValxNode avnx[164] = {
     {3,NULL,1,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
     {2,NULL,1,0.0,NULL } ,
@@ -87,100 +87,103 @@ static AsnValxNode avnx[161] = {
     {20,"cRNA" ,11,0.0,&avnx[74] } ,
     {20,"snoRNA" ,12,0.0,&avnx[75] } ,
     {20,"transcribed-RNA" ,13,0.0,&avnx[76] } ,
+    {20,"ncRNA" ,14,0.0,&avnx[77] } ,
+    {20,"tmRNA" ,15,0.0,&avnx[78] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[79] } ,
-    {20,"standard" ,1,0.0,&avnx[80] } ,
-    {20,"est" ,2,0.0,&avnx[81] } ,
-    {20,"sts" ,3,0.0,&avnx[82] } ,
-    {20,"survey" ,4,0.0,&avnx[83] } ,
-    {20,"genemap" ,5,0.0,&avnx[84] } ,
-    {20,"physmap" ,6,0.0,&avnx[85] } ,
-    {20,"derived" ,7,0.0,&avnx[86] } ,
-    {20,"concept-trans" ,8,0.0,&avnx[87] } ,
-    {20,"seq-pept" ,9,0.0,&avnx[88] } ,
-    {20,"both" ,10,0.0,&avnx[89] } ,
-    {20,"seq-pept-overlap" ,11,0.0,&avnx[90] } ,
-    {20,"seq-pept-homol" ,12,0.0,&avnx[91] } ,
-    {20,"concept-trans-a" ,13,0.0,&avnx[92] } ,
-    {20,"htgs-1" ,14,0.0,&avnx[93] } ,
-    {20,"htgs-2" ,15,0.0,&avnx[94] } ,
-    {20,"htgs-3" ,16,0.0,&avnx[95] } ,
-    {20,"fli-cdna" ,17,0.0,&avnx[96] } ,
-    {20,"htgs-0" ,18,0.0,&avnx[97] } ,
-    {20,"htc" ,19,0.0,&avnx[98] } ,
-    {20,"wgs" ,20,0.0,&avnx[99] } ,
-    {20,"barcode" ,21,0.0,&avnx[100] } ,
-    {20,"composite-wgs-htgs" ,22,0.0,&avnx[101] } ,
+    {20,"unknown" ,0,0.0,&avnx[81] } ,
+    {20,"standard" ,1,0.0,&avnx[82] } ,
+    {20,"est" ,2,0.0,&avnx[83] } ,
+    {20,"sts" ,3,0.0,&avnx[84] } ,
+    {20,"survey" ,4,0.0,&avnx[85] } ,
+    {20,"genemap" ,5,0.0,&avnx[86] } ,
+    {20,"physmap" ,6,0.0,&avnx[87] } ,
+    {20,"derived" ,7,0.0,&avnx[88] } ,
+    {20,"concept-trans" ,8,0.0,&avnx[89] } ,
+    {20,"seq-pept" ,9,0.0,&avnx[90] } ,
+    {20,"both" ,10,0.0,&avnx[91] } ,
+    {20,"seq-pept-overlap" ,11,0.0,&avnx[92] } ,
+    {20,"seq-pept-homol" ,12,0.0,&avnx[93] } ,
+    {20,"concept-trans-a" ,13,0.0,&avnx[94] } ,
+    {20,"htgs-1" ,14,0.0,&avnx[95] } ,
+    {20,"htgs-2" ,15,0.0,&avnx[96] } ,
+    {20,"htgs-3" ,16,0.0,&avnx[97] } ,
+    {20,"fli-cdna" ,17,0.0,&avnx[98] } ,
+    {20,"htgs-0" ,18,0.0,&avnx[99] } ,
+    {20,"htc" ,19,0.0,&avnx[100] } ,
+    {20,"wgs" ,20,0.0,&avnx[101] } ,
+    {20,"barcode" ,21,0.0,&avnx[102] } ,
+    {20,"composite-wgs-htgs" ,22,0.0,&avnx[103] } ,
+    {20,"tsa" ,23,0.0,&avnx[104] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[104] } ,
-    {20,"complete" ,1,0.0,&avnx[105] } ,
-    {20,"partial" ,2,0.0,&avnx[106] } ,
-    {20,"no-left" ,3,0.0,&avnx[107] } ,
-    {20,"no-right" ,4,0.0,&avnx[108] } ,
-    {20,"no-ends" ,5,0.0,&avnx[109] } ,
-    {20,"has-left" ,6,0.0,&avnx[110] } ,
-    {20,"has-right" ,7,0.0,&avnx[111] } ,
+    {20,"unknown" ,0,0.0,&avnx[107] } ,
+    {20,"complete" ,1,0.0,&avnx[108] } ,
+    {20,"partial" ,2,0.0,&avnx[109] } ,
+    {20,"no-left" ,3,0.0,&avnx[110] } ,
+    {20,"no-right" ,4,0.0,&avnx[111] } ,
+    {20,"no-ends" ,5,0.0,&avnx[112] } ,
+    {20,"has-left" ,6,0.0,&avnx[113] } ,
+    {20,"has-right" ,7,0.0,&avnx[114] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[114] } ,
-    {20,"virtual" ,1,0.0,&avnx[115] } ,
-    {20,"raw" ,2,0.0,&avnx[116] } ,
-    {20,"seg" ,3,0.0,&avnx[117] } ,
-    {20,"const" ,4,0.0,&avnx[118] } ,
-    {20,"ref" ,5,0.0,&avnx[119] } ,
-    {20,"consen" ,6,0.0,&avnx[120] } ,
-    {20,"map" ,7,0.0,&avnx[121] } ,
-    {20,"delta" ,8,0.0,&avnx[122] } ,
+    {20,"not-set" ,0,0.0,&avnx[117] } ,
+    {20,"virtual" ,1,0.0,&avnx[118] } ,
+    {20,"raw" ,2,0.0,&avnx[119] } ,
+    {20,"seg" ,3,0.0,&avnx[120] } ,
+    {20,"const" ,4,0.0,&avnx[121] } ,
+    {20,"ref" ,5,0.0,&avnx[122] } ,
+    {20,"consen" ,6,0.0,&avnx[123] } ,
+    {20,"map" ,7,0.0,&avnx[124] } ,
+    {20,"delta" ,8,0.0,&avnx[125] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[124] } ,
-    {20,"dna" ,1,0.0,&avnx[125] } ,
-    {20,"rna" ,2,0.0,&avnx[126] } ,
-    {20,"aa" ,3,0.0,&avnx[127] } ,
-    {20,"na" ,4,0.0,&avnx[128] } ,
+    {20,"not-set" ,0,0.0,&avnx[127] } ,
+    {20,"dna" ,1,0.0,&avnx[128] } ,
+    {20,"rna" ,2,0.0,&avnx[129] } ,
+    {20,"aa" ,3,0.0,&avnx[130] } ,
+    {20,"na" ,4,0.0,&avnx[131] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[130] } ,
-    {20,"linear" ,1,0.0,&avnx[131] } ,
-    {20,"circular" ,2,0.0,&avnx[132] } ,
-    {20,"tandem" ,3,0.0,&avnx[133] } ,
+    {20,"not-set" ,0,0.0,&avnx[133] } ,
+    {20,"linear" ,1,0.0,&avnx[134] } ,
+    {20,"circular" ,2,0.0,&avnx[135] } ,
+    {20,"tandem" ,3,0.0,&avnx[136] } ,
     {20,"other" ,255,0.0,NULL } ,
     {3,NULL,1,0.0,NULL } ,
-    {20,"not-set" ,0,0.0,&avnx[136] } ,
-    {20,"ss" ,1,0.0,&avnx[137] } ,
-    {20,"ds" ,2,0.0,&avnx[138] } ,
-    {20,"mixed" ,3,0.0,&avnx[139] } ,
+    {20,"not-set" ,0,0.0,&avnx[139] } ,
+    {20,"ss" ,1,0.0,&avnx[140] } ,
+    {20,"ds" ,2,0.0,&avnx[141] } ,
+    {20,"mixed" ,3,0.0,&avnx[142] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unknown" ,0,0.0,&avnx[141] } ,
-    {20,"fragment" ,1,0.0,&avnx[142] } ,
-    {20,"clone" ,2,0.0,&avnx[143] } ,
-    {20,"short-arm" ,3,0.0,&avnx[144] } ,
-    {20,"heterochromatin" ,4,0.0,&avnx[145] } ,
-    {20,"centromere" ,5,0.0,&avnx[146] } ,
-    {20,"telomere" ,6,0.0,&avnx[147] } ,
-    {20,"repeat" ,7,0.0,&avnx[148] } ,
-    {20,"contig" ,8,0.0,&avnx[149] } ,
+    {20,"unknown" ,0,0.0,&avnx[144] } ,
+    {20,"fragment" ,1,0.0,&avnx[145] } ,
+    {20,"clone" ,2,0.0,&avnx[146] } ,
+    {20,"short-arm" ,3,0.0,&avnx[147] } ,
+    {20,"heterochromatin" ,4,0.0,&avnx[148] } ,
+    {20,"centromere" ,5,0.0,&avnx[149] } ,
+    {20,"telomere" ,6,0.0,&avnx[150] } ,
+    {20,"repeat" ,7,0.0,&avnx[151] } ,
+    {20,"contig" ,8,0.0,&avnx[152] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unlinked" ,0,0.0,&avnx[151] } ,
-    {20,"linked" ,1,0.0,&avnx[152] } ,
+    {20,"unlinked" ,0,0.0,&avnx[154] } ,
+    {20,"linked" ,1,0.0,&avnx[155] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"genbank" ,1,0.0,&avnx[154] } ,
-    {20,"embl" ,2,0.0,&avnx[155] } ,
-    {20,"ddbj" ,3,0.0,&avnx[156] } ,
-    {20,"pir" ,4,0.0,&avnx[157] } ,
-    {20,"sp" ,5,0.0,&avnx[158] } ,
-    {20,"bbone" ,6,0.0,&avnx[159] } ,
-    {20,"pdb" ,7,0.0,&avnx[160] } ,
+    {20,"genbank" ,1,0.0,&avnx[157] } ,
+    {20,"embl" ,2,0.0,&avnx[158] } ,
+    {20,"ddbj" ,3,0.0,&avnx[159] } ,
+    {20,"pir" ,4,0.0,&avnx[160] } ,
+    {20,"sp" ,5,0.0,&avnx[161] } ,
+    {20,"bbone" ,6,0.0,&avnx[162] } ,
+    {20,"pdb" ,7,0.0,&avnx[163] } ,
     {20,"other" ,255,0.0,NULL } };
 
-static AsnType atx[210] = {
+static AsnType atx[213] = {
   {401, "Annotdesc" ,1,0,0,0,0,1,0,0,NULL,&atx[39],&atx[1],0,&atx[63]} ,
   {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[3]} ,
   {323, "VisibleString" ,0,26,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "title" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[4]} ,
   {0, "comment" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[5]} ,
   {0, "pub" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[48]} ,
-  {408, "Pubdesc" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[7],0,&atx[187]} ,
+  {408, "Pubdesc" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[7],0,&atx[188]} ,
   {0, "pub" ,128,0,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[9]} ,
   {426, "Pub-equiv" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[82]} ,
   {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[10]} ,
@@ -188,7 +191,7 @@ static AsnType atx[210] = {
   {0, "num" ,128,3,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[40]} ,
   {407, "Numbering" ,1,0,0,0,0,1,0,0,NULL,&atx[39],&atx[13],0,&atx[6]} ,
   {0, "cont" ,128,0,0,0,0,0,0,0,NULL,&atx[14],NULL,0,&atx[21]} ,
-  {439, "Num-cont" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[15],0,&atx[22]} ,
+  {440, "Num-cont" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[15],0,&atx[22]} ,
   {0, "refnum" ,128,0,0,0,1,0,0,0,&avnx[0],&atx[16],NULL,0,&atx[17]} ,
   {302, "INTEGER" ,0,2,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "has-zero" ,128,1,0,0,1,0,0,0,&avnx[1],&atx[18],NULL,0,&atx[19]} ,
@@ -196,19 +199,19 @@ static AsnType atx[210] = {
   {0, "ascending" ,128,2,0,0,1,0,0,0,&avnx[2],&atx[18],NULL,0,NULL} ,
   {311, "SEQUENCE" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "enum" ,128,1,0,0,0,0,0,0,NULL,&atx[22],NULL,0,&atx[27]} ,
-  {440, "Num-enum" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[23],0,&atx[28]} ,
+  {441, "Num-enum" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[23],0,&atx[28]} ,
   {0, "num" ,128,0,0,0,0,0,0,0,NULL,&atx[16],NULL,0,&atx[24]} ,
   {0, "names" ,128,1,0,0,0,0,0,0,NULL,&atx[26],&atx[25],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {312, "SEQUENCE OF" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "ref" ,128,2,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[33]} ,
-  {441, "Num-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[29],0,&atx[34]} ,
+  {442, "Num-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[29],0,&atx[34]} ,
   {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[30],&avnx[3],0,&atx[31]} ,
   {310, "ENUMERATED" ,0,10,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "aligns" ,128,1,0,1,0,0,0,0,NULL,&atx[32],NULL,0,NULL} ,
-  {423, "Seq-align" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[161]} ,
+  {423, "Seq-align" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[162]} ,
   {0, "real" ,128,3,0,0,0,0,0,0,NULL,&atx[34],NULL,0,NULL} ,
-  {442, "Num-real" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[35],0,&atx[154]} ,
+  {443, "Num-real" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[35],0,&atx[155]} ,
   {0, "a" ,128,0,0,0,0,0,0,0,NULL,&atx[36],NULL,0,&atx[37]} ,
   {309, "REAL" ,0,9,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "b" ,128,1,0,0,0,0,0,0,NULL,&atx[36],NULL,0,&atx[38]} ,
@@ -225,12 +228,12 @@ static AsnType atx[210] = {
   {0, "user" ,128,4,0,0,0,0,0,0,NULL,&atx[49],NULL,0,&atx[50]} ,
   {422, "User-object" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[32]} ,
   {0, "create-date" ,128,5,0,0,0,0,0,0,NULL,&atx[51],NULL,0,&atx[52]} ,
-  {418, "Date" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[121]} ,
+  {418, "Date" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[122]} ,
   {0, "update-date" ,128,6,0,0,0,0,0,0,NULL,&atx[51],NULL,0,&atx[53]} ,
   {0, "src" ,128,7,0,0,0,0,0,0,NULL,&atx[54],NULL,0,&atx[55]} ,
   {429, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[62]} ,
   {0, "align" ,128,8,0,0,0,0,0,0,NULL,&atx[56],NULL,0,&atx[61]} ,
-  {460, "Align-def" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[57],0,NULL} ,
+  {461, "Align-def" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[57],0,NULL} ,
   {0, "align-type" ,128,0,0,0,0,0,0,0,NULL,&atx[16],&avnx[11],0,&atx[58]} ,
   {0, "ids" ,128,1,0,1,0,0,0,0,NULL,&atx[60],&atx[59],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[54],NULL,0,NULL} ,
@@ -242,17 +245,17 @@ static AsnType atx[210] = {
   {403, "Bioseq" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[66],0,&atx[73]} ,
   {0, "id" ,128,0,0,0,0,0,0,0,NULL,&atx[60],&atx[67],0,&atx[68]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[54],NULL,0,NULL} ,
-  {0, "descr" ,128,1,0,1,0,0,0,0,NULL,&atx[69],NULL,0,&atx[115]} ,
-  {412, "Seq-descr" ,1,0,0,0,0,1,0,0,NULL,&atx[60],&atx[70],0,&atx[152]} ,
+  {0, "descr" ,128,1,0,1,0,0,0,0,NULL,&atx[69],NULL,0,&atx[116]} ,
+  {412, "Seq-descr" ,1,0,0,0,0,1,0,0,NULL,&atx[60],&atx[70],0,&atx[153]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[71],NULL,0,NULL} ,
   {411, "Seqdesc" ,1,0,0,0,0,1,0,0,NULL,&atx[39],&atx[72],0,&atx[69]} ,
   {0, "mol-type" ,128,0,0,0,0,0,0,0,NULL,&atx[73],NULL,0,&atx[74]} ,
   {404, "GIBB-mol" ,1,0,0,0,0,1,0,0,NULL,&atx[30],&avnx[15],0,&atx[106]} ,
   {0, "modif" ,128,1,0,0,0,0,0,0,NULL,&atx[60],&atx[75],0,&atx[77]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[76],NULL,0,NULL} ,
-  {437, "GIBB-mod" ,1,0,0,0,0,0,0,0,NULL,&atx[30],&avnx[27],0,&atx[78]} ,
+  {438, "GIBB-mod" ,1,0,0,0,0,0,0,0,NULL,&atx[30],&avnx[27],0,&atx[78]} ,
   {0, "method" ,128,2,0,0,0,0,0,0,NULL,&atx[78],NULL,0,&atx[79]} ,
-  {438, "GIBB-method" ,1,0,0,0,0,0,0,0,NULL,&atx[30],&avnx[55],0,&atx[14]} ,
+  {439, "GIBB-method" ,1,0,0,0,0,0,0,0,NULL,&atx[30],&avnx[55],0,&atx[14]} ,
   {0, "name" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[80]} ,
   {0, "title" ,128,4,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[81]} ,
   {0, "org" ,128,5,0,0,0,0,0,0,NULL,&atx[82],NULL,0,&atx[83]} ,
@@ -260,7 +263,7 @@ static AsnType atx[210] = {
   {0, "comment" ,128,6,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[84]} ,
   {0, "num" ,128,7,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[85]} ,
   {0, "maploc" ,128,8,0,0,0,0,0,0,NULL,&atx[86],NULL,0,&atx[87]} ,
-  {420, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[192]} ,
+  {420, "Dbtag" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[193]} ,
   {0, "pir" ,128,9,0,0,0,0,0,0,NULL,&atx[88],NULL,0,&atx[89]} ,
   {432, "PIR-block" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[98]} ,
   {0, "genbank" ,128,10,0,0,0,0,0,0,NULL,&atx[90],NULL,0,&atx[91]} ,
@@ -278,115 +281,118 @@ static AsnType atx[210] = {
   {0, "prf" ,128,19,0,0,0,0,0,0,NULL,&atx[102],NULL,0,&atx[103]} ,
   {435, "PRF-block" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[104]} ,
   {0, "pdb" ,128,20,0,0,0,0,0,0,NULL,&atx[104],NULL,0,&atx[105]} ,
-  {436, "PDB-block" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[76]} ,
+  {436, "PDB-block" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[212]} ,
   {0, "het" ,128,21,0,0,0,0,0,0,NULL,&atx[106],NULL,0,&atx[107]} ,
   {405, "Heterogen" ,1,0,0,0,0,1,0,0,NULL,&atx[2],NULL,0,&atx[110]} ,
   {0, "source" ,128,22,0,0,0,0,0,0,NULL,&atx[108],NULL,0,&atx[109]} ,
   {428, "BioSource" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[54]} ,
   {0, "molinfo" ,128,23,0,0,0,0,0,0,NULL,&atx[110],NULL,0,NULL} ,
   {406, "MolInfo" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[111],0,&atx[12]} ,
-  {0, "biomol" ,128,0,0,0,1,0,0,0,&avnx[77],&atx[16],&avnx[62],0,&atx[112]} ,
-  {0, "tech" ,128,1,0,0,1,0,0,0,&avnx[102],&atx[16],&avnx[78],0,&atx[113]} ,
+  {0, "biomol" ,128,0,0,0,1,0,0,0,&avnx[79],&atx[16],&avnx[62],0,&atx[112]} ,
+  {0, "tech" ,128,1,0,0,1,0,0,0,&avnx[105],&atx[16],&avnx[80],0,&atx[113]} ,
   {0, "techexp" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[114]} ,
-  {0, "completeness" ,128,3,0,0,1,0,0,0,&avnx[112],&atx[16],&avnx[103],0,NULL} ,
-  {0, "inst" ,128,2,0,0,0,0,0,0,NULL,&atx[116],NULL,0,&atx[185]} ,
-  {415, "Seq-inst" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[117],0,&atx[168]} ,
-  {0, "repr" ,128,0,0,0,0,0,0,0,NULL,&atx[30],&avnx[113],0,&atx[118]} ,
-  {0, "mol" ,128,1,0,0,0,0,0,0,NULL,&atx[30],&avnx[123],0,&atx[119]} ,
-  {0, "length" ,128,2,0,1,0,0,0,0,NULL,&atx[16],NULL,0,&atx[120]} ,
-  {0, "fuzz" ,128,3,0,1,0,0,0,0,NULL,&atx[121],NULL,0,&atx[122]} ,
+  {0, "completeness" ,128,3,0,0,1,0,0,0,&avnx[115],&atx[16],&avnx[106],0,&atx[115]} ,
+  {0, "gbmoltype" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "inst" ,128,2,0,0,0,0,0,0,NULL,&atx[117],NULL,0,&atx[186]} ,
+  {415, "Seq-inst" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[118],0,&atx[169]} ,
+  {0, "repr" ,128,0,0,0,0,0,0,0,NULL,&atx[30],&avnx[116],0,&atx[119]} ,
+  {0, "mol" ,128,1,0,0,0,0,0,0,NULL,&atx[30],&avnx[126],0,&atx[120]} ,
+  {0, "length" ,128,2,0,1,0,0,0,0,NULL,&atx[16],NULL,0,&atx[121]} ,
+  {0, "fuzz" ,128,3,0,1,0,0,0,0,NULL,&atx[122],NULL,0,&atx[123]} ,
   {419, "Int-fuzz" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[86]} ,
-  {0, "topology" ,128,4,0,0,1,0,0,0,&avnx[134],&atx[30],&avnx[129],0,&atx[123]} ,
-  {0, "strand" ,128,5,0,1,0,0,0,0,NULL,&atx[30],&avnx[135],0,&atx[124]} ,
-  {0, "seq-data" ,128,6,0,1,0,0,0,0,NULL,&atx[125],NULL,0,&atx[151]} ,
-  {410, "Seq-data" ,1,0,0,0,0,1,0,0,NULL,&atx[39],&atx[126],0,&atx[71]} ,
-  {0, "iupacna" ,128,0,0,0,0,0,0,0,NULL,&atx[127],NULL,0,&atx[128]} ,
-  {448, "IUPACna" ,1,0,0,0,0,0,0,0,NULL,&atx[44],NULL,0,&atx[129]} ,
-  {0, "iupacaa" ,128,1,0,0,0,0,0,0,NULL,&atx[129],NULL,0,&atx[130]} ,
-  {449, "IUPACaa" ,1,0,0,0,0,0,0,0,NULL,&atx[44],NULL,0,&atx[131]} ,
-  {0, "ncbi2na" ,128,2,0,0,0,0,0,0,NULL,&atx[131],NULL,0,&atx[133]} ,
-  {450, "NCBI2na" ,1,0,0,0,0,0,0,0,NULL,&atx[132],NULL,0,&atx[134]} ,
+  {0, "topology" ,128,4,0,0,1,0,0,0,&avnx[137],&atx[30],&avnx[132],0,&atx[124]} ,
+  {0, "strand" ,128,5,0,1,0,0,0,0,NULL,&atx[30],&avnx[138],0,&atx[125]} ,
+  {0, "seq-data" ,128,6,0,1,0,0,0,0,NULL,&atx[126],NULL,0,&atx[152]} ,
+  {410, "Seq-data" ,1,0,0,0,0,1,0,0,NULL,&atx[39],&atx[127],0,&atx[71]} ,
+  {0, "iupacna" ,128,0,0,0,0,0,0,0,NULL,&atx[128],NULL,0,&atx[129]} ,
+  {449, "IUPACna" ,1,0,0,0,0,0,0,0,NULL,&atx[44],NULL,0,&atx[130]} ,
+  {0, "iupacaa" ,128,1,0,0,0,0,0,0,NULL,&atx[130],NULL,0,&atx[131]} ,
+  {450, "IUPACaa" ,1,0,0,0,0,0,0,0,NULL,&atx[44],NULL,0,&atx[132]} ,
+  {0, "ncbi2na" ,128,2,0,0,0,0,0,0,NULL,&atx[132],NULL,0,&atx[134]} ,
+  {451, "NCBI2na" ,1,0,0,0,0,0,0,0,NULL,&atx[133],NULL,0,&atx[135]} ,
   {304, "OCTET STRING" ,0,4,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {0, "ncbi4na" ,128,3,0,0,0,0,0,0,NULL,&atx[134],NULL,0,&atx[135]} ,
-  {451, "NCBI4na" ,1,0,0,0,0,0,0,0,NULL,&atx[132],NULL,0,&atx[136]} ,
-  {0, "ncbi8na" ,128,4,0,0,0,0,0,0,NULL,&atx[136],NULL,0,&atx[137]} ,
-  {452, "NCBI8na" ,1,0,0,0,0,0,0,0,NULL,&atx[132],NULL,0,&atx[138]} ,
-  {0, "ncbipna" ,128,5,0,0,0,0,0,0,NULL,&atx[138],NULL,0,&atx[139]} ,
-  {453, "NCBIpna" ,1,0,0,0,0,0,0,0,NULL,&atx[132],NULL,0,&atx[140]} ,
-  {0, "ncbi8aa" ,128,6,0,0,0,0,0,0,NULL,&atx[140],NULL,0,&atx[141]} ,
-  {454, "NCBI8aa" ,1,0,0,0,0,0,0,0,NULL,&atx[132],NULL,0,&atx[142]} ,
-  {0, "ncbieaa" ,128,7,0,0,0,0,0,0,NULL,&atx[142],NULL,0,&atx[143]} ,
-  {455, "NCBIeaa" ,1,0,0,0,0,0,0,0,NULL,&atx[44],NULL,0,&atx[144]} ,
-  {0, "ncbipaa" ,128,8,0,0,0,0,0,0,NULL,&atx[144],NULL,0,&atx[145]} ,
-  {456, "NCBIpaa" ,1,0,0,0,0,0,0,0,NULL,&atx[132],NULL,0,&atx[146]} ,
-  {0, "ncbistdaa" ,128,9,0,0,0,0,0,0,NULL,&atx[146],NULL,0,&atx[147]} ,
-  {457, "NCBIstdaa" ,1,0,0,0,0,0,0,0,NULL,&atx[132],NULL,0,&atx[148]} ,
-  {0, "gap" ,128,10,0,0,0,0,0,0,NULL,&atx[148],NULL,0,NULL} ,
-  {458, "Seq-gap" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[149],0,&atx[190]} ,
-  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[16],&avnx[140],0,&atx[150]} ,
-  {0, "linkage" ,128,1,0,1,0,0,0,0,NULL,&atx[16],&avnx[150],0,NULL} ,
-  {0, "ext" ,128,7,0,1,0,0,0,0,NULL,&atx[152],NULL,0,&atx[172]} ,
-  {413, "Seq-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[39],&atx[153],0,&atx[173]} ,
-  {0, "seg" ,128,0,0,0,0,0,0,0,NULL,&atx[154],NULL,0,&atx[156]} ,
-  {443, "Seg-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[26],&atx[155],0,&atx[157]} ,
+  {0, "ncbi4na" ,128,3,0,0,0,0,0,0,NULL,&atx[135],NULL,0,&atx[136]} ,
+  {452, "NCBI4na" ,1,0,0,0,0,0,0,0,NULL,&atx[133],NULL,0,&atx[137]} ,
+  {0, "ncbi8na" ,128,4,0,0,0,0,0,0,NULL,&atx[137],NULL,0,&atx[138]} ,
+  {453, "NCBI8na" ,1,0,0,0,0,0,0,0,NULL,&atx[133],NULL,0,&atx[139]} ,
+  {0, "ncbipna" ,128,5,0,0,0,0,0,0,NULL,&atx[139],NULL,0,&atx[140]} ,
+  {454, "NCBIpna" ,1,0,0,0,0,0,0,0,NULL,&atx[133],NULL,0,&atx[141]} ,
+  {0, "ncbi8aa" ,128,6,0,0,0,0,0,0,NULL,&atx[141],NULL,0,&atx[142]} ,
+  {455, "NCBI8aa" ,1,0,0,0,0,0,0,0,NULL,&atx[133],NULL,0,&atx[143]} ,
+  {0, "ncbieaa" ,128,7,0,0,0,0,0,0,NULL,&atx[143],NULL,0,&atx[144]} ,
+  {456, "NCBIeaa" ,1,0,0,0,0,0,0,0,NULL,&atx[44],NULL,0,&atx[145]} ,
+  {0, "ncbipaa" ,128,8,0,0,0,0,0,0,NULL,&atx[145],NULL,0,&atx[146]} ,
+  {457, "NCBIpaa" ,1,0,0,0,0,0,0,0,NULL,&atx[133],NULL,0,&atx[147]} ,
+  {0, "ncbistdaa" ,128,9,0,0,0,0,0,0,NULL,&atx[147],NULL,0,&atx[148]} ,
+  {458, "NCBIstdaa" ,1,0,0,0,0,0,0,0,NULL,&atx[133],NULL,0,&atx[149]} ,
+  {0, "gap" ,128,10,0,0,0,0,0,0,NULL,&atx[149],NULL,0,NULL} ,
+  {459, "Seq-gap" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[150],0,&atx[191]} ,
+  {0, "type" ,128,0,0,0,0,0,0,0,NULL,&atx[16],&avnx[143],0,&atx[151]} ,
+  {0, "linkage" ,128,1,0,1,0,0,0,0,NULL,&atx[16],&avnx[153],0,NULL} ,
+  {0, "ext" ,128,7,0,1,0,0,0,0,NULL,&atx[153],NULL,0,&atx[173]} ,
+  {413, "Seq-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[39],&atx[154],0,&atx[174]} ,
+  {0, "seg" ,128,0,0,0,0,0,0,0,NULL,&atx[155],NULL,0,&atx[157]} ,
+  {444, "Seg-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[26],&atx[156],0,&atx[158]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} ,
-  {0, "ref" ,128,1,0,0,0,0,0,0,NULL,&atx[157],NULL,0,&atx[158]} ,
-  {444, "Ref-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[159]} ,
-  {0, "map" ,128,2,0,0,0,0,0,0,NULL,&atx[159],NULL,0,&atx[162]} ,
-  {445, "Map-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[26],&atx[160],0,&atx[165]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[161],NULL,0,NULL} ,
-  {424, "Seq-feat" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[205]} ,
-  {0, "delta" ,128,3,0,0,0,0,0,0,NULL,&atx[163],NULL,0,NULL} ,
-  {417, "Delta-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[26],&atx[164],0,&atx[51]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[165],NULL,0,NULL} ,
-  {446, "Delta-seq" ,1,0,0,0,0,0,0,0,NULL,&atx[39],&atx[166],0,&atx[177]} ,
-  {0, "loc" ,128,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[167]} ,
-  {0, "literal" ,128,1,0,0,0,0,0,0,NULL,&atx[168],NULL,0,NULL} ,
-  {416, "Seq-literal" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[169],0,&atx[163]} ,
-  {0, "length" ,128,0,0,0,0,0,0,0,NULL,&atx[16],NULL,0,&atx[170]} ,
-  {0, "fuzz" ,128,1,0,1,0,0,0,0,NULL,&atx[121],NULL,0,&atx[171]} ,
-  {0, "seq-data" ,128,2,0,1,0,0,0,0,NULL,&atx[125],NULL,0,NULL} ,
-  {0, "hist" ,128,8,0,1,0,0,0,0,NULL,&atx[173],NULL,0,NULL} ,
-  {414, "Seq-hist" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[174],0,&atx[116]} ,
-  {0, "assembly" ,128,0,0,1,0,0,0,0,NULL,&atx[60],&atx[175],0,&atx[176]} ,
+  {0, "ref" ,128,1,0,0,0,0,0,0,NULL,&atx[158],NULL,0,&atx[159]} ,
+  {445, "Ref-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[160]} ,
+  {0, "map" ,128,2,0,0,0,0,0,0,NULL,&atx[160],NULL,0,&atx[163]} ,
+  {446, "Map-ext" ,1,0,0,0,0,0,0,0,NULL,&atx[26],&atx[161],0,&atx[166]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[162],NULL,0,NULL} ,
+  {424, "Seq-feat" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[206]} ,
+  {0, "delta" ,128,3,0,0,0,0,0,0,NULL,&atx[164],NULL,0,NULL} ,
+  {417, "Delta-ext" ,1,0,0,0,0,1,0,0,NULL,&atx[26],&atx[165],0,&atx[51]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[166],NULL,0,NULL} ,
+  {447, "Delta-seq" ,1,0,0,0,0,0,0,0,NULL,&atx[39],&atx[167],0,&atx[178]} ,
+  {0, "loc" ,128,0,0,0,0,0,0,0,NULL,&atx[62],NULL,0,&atx[168]} ,
+  {0, "literal" ,128,1,0,0,0,0,0,0,NULL,&atx[169],NULL,0,NULL} ,
+  {416, "Seq-literal" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[170],0,&atx[164]} ,
+  {0, "length" ,128,0,0,0,0,0,0,0,NULL,&atx[16],NULL,0,&atx[171]} ,
+  {0, "fuzz" ,128,1,0,1,0,0,0,0,NULL,&atx[122],NULL,0,&atx[172]} ,
+  {0, "seq-data" ,128,2,0,1,0,0,0,0,NULL,&atx[126],NULL,0,NULL} ,
+  {0, "hist" ,128,8,0,1,0,0,0,0,NULL,&atx[174],NULL,0,NULL} ,
+  {414, "Seq-hist" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[175],0,&atx[117]} ,
+  {0, "assembly" ,128,0,0,1,0,0,0,0,NULL,&atx[60],&atx[176],0,&atx[177]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[32],NULL,0,NULL} ,
-  {0, "replaces" ,128,1,0,1,0,0,0,0,NULL,&atx[177],NULL,0,&atx[181]} ,
-  {447, "Seq-hist-rec" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[178],0,&atx[127]} ,
-  {0, "date" ,128,0,0,1,0,0,0,0,NULL,&atx[51],NULL,0,&atx[179]} ,
-  {0, "ids" ,128,1,0,0,0,0,0,0,NULL,&atx[60],&atx[180],0,NULL} ,
+  {0, "replaces" ,128,1,0,1,0,0,0,0,NULL,&atx[178],NULL,0,&atx[182]} ,
+  {448, "Seq-hist-rec" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[179],0,&atx[128]} ,
+  {0, "date" ,128,0,0,1,0,0,0,0,NULL,&atx[51],NULL,0,&atx[180]} ,
+  {0, "ids" ,128,1,0,0,0,0,0,0,NULL,&atx[60],&atx[181],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[54],NULL,0,NULL} ,
-  {0, "replaced-by" ,128,2,0,1,0,0,0,0,NULL,&atx[177],NULL,0,&atx[182]} ,
-  {0, "deleted" ,128,3,0,1,0,0,0,0,NULL,&atx[39],&atx[183],0,NULL} ,
-  {0, "bool" ,128,0,0,0,0,0,0,0,NULL,&atx[18],NULL,0,&atx[184]} ,
+  {0, "replaced-by" ,128,2,0,1,0,0,0,0,NULL,&atx[178],NULL,0,&atx[183]} ,
+  {0, "deleted" ,128,3,0,1,0,0,0,0,NULL,&atx[39],&atx[184],0,NULL} ,
+  {0, "bool" ,128,0,0,0,0,0,0,0,NULL,&atx[18],NULL,0,&atx[185]} ,
   {0, "date" ,128,1,0,0,0,0,0,0,NULL,&atx[51],NULL,0,NULL} ,
-  {0, "annot" ,128,3,0,1,0,0,0,0,NULL,&atx[60],&atx[186],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[187],NULL,0,NULL} ,
-  {409, "Seq-annot" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[188],0,&atx[125]} ,
-  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[60],&atx[189],0,&atx[195]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[190],NULL,0,NULL} ,
-  {459, "Annot-id" ,1,0,0,0,0,0,0,0,NULL,&atx[39],&atx[191],0,&atx[56]} ,
-  {0, "local" ,128,0,0,0,0,0,0,0,NULL,&atx[192],NULL,0,&atx[193]} ,
+  {0, "annot" ,128,3,0,1,0,0,0,0,NULL,&atx[60],&atx[187],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[188],NULL,0,NULL} ,
+  {409, "Seq-annot" ,1,0,0,0,0,1,0,0,NULL,&atx[20],&atx[189],0,&atx[126]} ,
+  {0, "id" ,128,0,0,1,0,0,0,0,NULL,&atx[60],&atx[190],0,&atx[196]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[191],NULL,0,NULL} ,
+  {460, "Annot-id" ,1,0,0,0,0,0,0,0,NULL,&atx[39],&atx[192],0,&atx[56]} ,
+  {0, "local" ,128,0,0,0,0,0,0,0,NULL,&atx[193],NULL,0,&atx[194]} ,
   {421, "Object-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[49]} ,
-  {0, "ncbi" ,128,1,0,0,0,0,0,0,NULL,&atx[16],NULL,0,&atx[194]} ,
+  {0, "ncbi" ,128,1,0,0,0,0,0,0,NULL,&atx[16],NULL,0,&atx[195]} ,
   {0, "general" ,128,2,0,0,0,0,0,0,NULL,&atx[86],NULL,0,NULL} ,
-  {0, "db" ,128,1,0,1,0,0,0,0,NULL,&atx[16],&avnx[153],0,&atx[196]} ,
-  {0, "name" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[197]} ,
-  {0, "desc" ,128,3,0,1,0,0,0,0,NULL,&atx[63],NULL,0,&atx[198]} ,
-  {0, "data" ,128,4,0,0,0,0,0,0,NULL,&atx[39],&atx[199],0,NULL} ,
-  {0, "ftable" ,128,0,0,0,0,0,0,0,NULL,&atx[60],&atx[200],0,&atx[201]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[161],NULL,0,NULL} ,
-  {0, "align" ,128,1,0,0,0,0,0,0,NULL,&atx[60],&atx[202],0,&atx[203]} ,
+  {0, "db" ,128,1,0,1,0,0,0,0,NULL,&atx[16],&avnx[156],0,&atx[197]} ,
+  {0, "name" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[198]} ,
+  {0, "desc" ,128,3,0,1,0,0,0,0,NULL,&atx[63],NULL,0,&atx[199]} ,
+  {0, "data" ,128,4,0,0,0,0,0,0,NULL,&atx[39],&atx[200],0,NULL} ,
+  {0, "ftable" ,128,0,0,0,0,0,0,0,NULL,&atx[60],&atx[201],0,&atx[202]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[162],NULL,0,NULL} ,
+  {0, "align" ,128,1,0,0,0,0,0,0,NULL,&atx[60],&atx[203],0,&atx[204]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[32],NULL,0,NULL} ,
-  {0, "graph" ,128,2,0,0,0,0,0,0,NULL,&atx[60],&atx[204],0,&atx[206]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[205],NULL,0,NULL} ,
+  {0, "graph" ,128,2,0,0,0,0,0,0,NULL,&atx[60],&atx[205],0,&atx[207]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[206],NULL,0,NULL} ,
   {425, "Seq-graph" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[8]} ,
-  {0, "ids" ,128,3,0,0,0,0,0,0,NULL,&atx[60],&atx[207],0,&atx[208]} ,
+  {0, "ids" ,128,3,0,0,0,0,0,0,NULL,&atx[60],&atx[208],0,&atx[209]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[54],NULL,0,NULL} ,
-  {0, "locs" ,128,4,0,0,0,0,0,0,NULL,&atx[60],&atx[209],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} };
+  {0, "locs" ,128,4,0,0,0,0,0,0,NULL,&atx[60],&atx[210],0,&atx[211]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[62],NULL,0,NULL} ,
+  {0, "seq-table" ,128,5,0,0,0,0,0,0,NULL,&atx[212],NULL,0,NULL} ,
+  {437, "Seq-table" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[76]} };
 
 static AsnModule ampx[1] = {
-  { "NCBI-Sequence" , "asnseq.h16",&atx[0],NULL,NULL,0,0} };
+  { "NCBI-Sequence" , "asnseq.h19",&atx[0],NULL,NULL,0,0} };
 
 static AsnValxNodePtr avn = avnx;
 static AsnTypePtr at = atx;
@@ -419,9 +425,9 @@ static AsnModulePtr amp = ampx;
 #define BIOSEQ_id &at[66]
 #define BIOSEQ_id_E &at[67]
 #define BIOSEQ_descr &at[68]
-#define BIOSEQ_inst &at[115]
-#define BIOSEQ_annot &at[185]
-#define BIOSEQ_annot_E &at[186]
+#define BIOSEQ_inst &at[116]
+#define BIOSEQ_annot &at[186]
+#define BIOSEQ_annot_E &at[187]
 
 #define GIBB_MOL &at[73]
 
@@ -432,6 +438,7 @@ static AsnModulePtr amp = ampx;
 #define MOLINFO_tech &at[112]
 #define MOLINFO_techexp &at[113]
 #define MOLINFO_completeness &at[114]
+#define MOLINFO_gbmoltype &at[115]
 
 #define NUMBERING &at[12]
 #define NUMBERING_cont &at[13]
@@ -452,36 +459,37 @@ static AsnModulePtr amp = ampx;
 #define PUBDESC_comment &at[46]
 #define PUBDESC_reftype &at[47]
 
-#define SEQ_ANNOT &at[187]
-#define SEQ_ANNOT_id &at[188]
-#define SEQ_ANNOT_id_E &at[189]
-#define SEQ_ANNOT_db &at[195]
-#define SEQ_ANNOT_name &at[196]
-#define SEQ_ANNOT_desc &at[197]
-#define SEQ_ANNOT_data &at[198]
-#define SEQ_ANNOT_data_ftable &at[199]
-#define SEQ_ANNOT_data_ftable_E &at[200]
-#define SEQ_ANNOT_data_align &at[201]
-#define SEQ_ANNOT_data_align_E &at[202]
-#define SEQ_ANNOT_data_graph &at[203]
-#define SEQ_ANNOT_data_graph_E &at[204]
-#define SEQ_ANNOT_data_ids &at[206]
-#define SEQ_ANNOT_data_ids_E &at[207]
-#define SEQ_ANNOT_data_locs &at[208]
-#define SEQ_ANNOT_data_locs_E &at[209]
-
-#define SEQ_DATA &at[125]
-#define SEQ_DATA_iupacna &at[126]
-#define SEQ_DATA_iupacaa &at[128]
-#define SEQ_DATA_ncbi2na &at[130]
-#define SEQ_DATA_ncbi4na &at[133]
-#define SEQ_DATA_ncbi8na &at[135]
-#define SEQ_DATA_ncbipna &at[137]
-#define SEQ_DATA_ncbi8aa &at[139]
-#define SEQ_DATA_ncbieaa &at[141]
-#define SEQ_DATA_ncbipaa &at[143]
-#define SEQ_DATA_ncbistdaa &at[145]
-#define SEQ_DATA_gap &at[147]
+#define SEQ_ANNOT &at[188]
+#define SEQ_ANNOT_id &at[189]
+#define SEQ_ANNOT_id_E &at[190]
+#define SEQ_ANNOT_db &at[196]
+#define SEQ_ANNOT_name &at[197]
+#define SEQ_ANNOT_desc &at[198]
+#define SEQ_ANNOT_data &at[199]
+#define SEQ_ANNOT_data_ftable &at[200]
+#define SEQ_ANNOT_data_ftable_E &at[201]
+#define SEQ_ANNOT_data_align &at[202]
+#define SEQ_ANNOT_data_align_E &at[203]
+#define SEQ_ANNOT_data_graph &at[204]
+#define SEQ_ANNOT_data_graph_E &at[205]
+#define SEQ_ANNOT_data_ids &at[207]
+#define SEQ_ANNOT_data_ids_E &at[208]
+#define SEQ_ANNOT_data_locs &at[209]
+#define SEQ_ANNOT_data_locs_E &at[210]
+#define SEQ_ANNOT_data_seq_table &at[211]
+
+#define SEQ_DATA &at[126]
+#define SEQ_DATA_iupacna &at[127]
+#define SEQ_DATA_iupacaa &at[129]
+#define SEQ_DATA_ncbi2na &at[131]
+#define SEQ_DATA_ncbi4na &at[134]
+#define SEQ_DATA_ncbi8na &at[136]
+#define SEQ_DATA_ncbipna &at[138]
+#define SEQ_DATA_ncbi8aa &at[140]
+#define SEQ_DATA_ncbieaa &at[142]
+#define SEQ_DATA_ncbipaa &at[144]
+#define SEQ_DATA_ncbistdaa &at[146]
+#define SEQ_DATA_gap &at[148]
 
 #define SEQDESC &at[71]
 #define SEQDESC_mol_type &at[72]
@@ -513,39 +521,39 @@ static AsnModulePtr amp = ampx;
 #define SEQ_DESCR &at[69]
 #define SEQ_DESCR_E &at[70]
 
-#define SEQ_EXT &at[152]
-#define SEQ_EXT_seg &at[153]
-#define SEQ_EXT_ref &at[156]
-#define SEQ_EXT_map &at[158]
-#define SEQ_EXT_delta &at[162]
-
-#define SEQ_HIST &at[173]
-#define SEQ_HIST_assembly &at[174]
-#define SEQ_HIST_assembly_E &at[175]
-#define SEQ_HIST_replaces &at[176]
-#define SEQ_HIST_replaced_by &at[181]
-#define SEQ_HIST_deleted &at[182]
-#define SEQ_HIST_deleted_bool &at[183]
-#define SEQ_HIST_deleted_date &at[184]
-
-#define SEQ_INST &at[116]
-#define SEQ_INST_repr &at[117]
-#define SEQ_INST_mol &at[118]
-#define SEQ_INST_length &at[119]
-#define SEQ_INST_fuzz &at[120]
-#define SEQ_INST_topology &at[122]
-#define SEQ_INST_strand &at[123]
-#define SEQ_INST_seq_data &at[124]
-#define SEQ_INST_ext &at[151]
-#define SEQ_INST_hist &at[172]
-
-#define SEQ_LITERAL &at[168]
-#define SEQ_LITERAL_length &at[169]
-#define SEQ_LITERAL_fuzz &at[170]
-#define SEQ_LITERAL_seq_data &at[171]
-
-#define DELTA_EXT &at[163]
-#define DELTA_EXT_E &at[164]
+#define SEQ_EXT &at[153]
+#define SEQ_EXT_seg &at[154]
+#define SEQ_EXT_ref &at[157]
+#define SEQ_EXT_map &at[159]
+#define SEQ_EXT_delta &at[163]
+
+#define SEQ_HIST &at[174]
+#define SEQ_HIST_assembly &at[175]
+#define SEQ_HIST_assembly_E &at[176]
+#define SEQ_HIST_replaces &at[177]
+#define SEQ_HIST_replaced_by &at[182]
+#define SEQ_HIST_deleted &at[183]
+#define SEQ_HIST_deleted_bool &at[184]
+#define SEQ_HIST_deleted_date &at[185]
+
+#define SEQ_INST &at[117]
+#define SEQ_INST_repr &at[118]
+#define SEQ_INST_mol &at[119]
+#define SEQ_INST_length &at[120]
+#define SEQ_INST_fuzz &at[121]
+#define SEQ_INST_topology &at[123]
+#define SEQ_INST_strand &at[124]
+#define SEQ_INST_seq_data &at[125]
+#define SEQ_INST_ext &at[152]
+#define SEQ_INST_hist &at[173]
+
+#define SEQ_LITERAL &at[169]
+#define SEQ_LITERAL_length &at[170]
+#define SEQ_LITERAL_fuzz &at[171]
+#define SEQ_LITERAL_seq_data &at[172]
+
+#define DELTA_EXT &at[164]
+#define DELTA_EXT_E &at[165]
 
 #define GIBB_MOD &at[76]
 
@@ -570,51 +578,51 @@ static AsnModulePtr amp = ampx;
 #define NUM_REAL_b &at[37]
 #define NUM_REAL_units &at[38]
 
-#define SEG_EXT &at[154]
-#define SEG_EXT_E &at[155]
+#define SEG_EXT &at[155]
+#define SEG_EXT_E &at[156]
 
-#define REF_EXT &at[157]
+#define REF_EXT &at[158]
 
-#define MAP_EXT &at[159]
-#define MAP_EXT_E &at[160]
+#define MAP_EXT &at[160]
+#define MAP_EXT_E &at[161]
 
-#define DELTA_SEQ &at[165]
-#define DELTA_SEQ_loc &at[166]
-#define DELTA_SEQ_literal &at[167]
+#define DELTA_SEQ &at[166]
+#define DELTA_SEQ_loc &at[167]
+#define DELTA_SEQ_literal &at[168]
 
-#define SEQ_HIST_REC &at[177]
-#define SEQ_HIST_REC_date &at[178]
-#define SEQ_HIST_REC_ids &at[179]
-#define SEQ_HIST_REC_ids_E &at[180]
+#define SEQ_HIST_REC &at[178]
+#define SEQ_HIST_REC_date &at[179]
+#define SEQ_HIST_REC_ids &at[180]
+#define SEQ_HIST_REC_ids_E &at[181]
 
-#define IUPACNA &at[127]
+#define IUPACNA &at[128]
 
-#define IUPACAA &at[129]
+#define IUPACAA &at[130]
 
-#define NCBI2NA &at[131]
+#define NCBI2NA &at[132]
 
-#define NCBI4NA &at[134]
+#define NCBI4NA &at[135]
 
-#define NCBI8NA &at[136]
+#define NCBI8NA &at[137]
 
-#define NCBIPNA &at[138]
+#define NCBIPNA &at[139]
 
-#define NCBI8AA &at[140]
+#define NCBI8AA &at[141]
 
-#define NCBIEAA &at[142]
+#define NCBIEAA &at[143]
 
-#define NCBIPAA &at[144]
+#define NCBIPAA &at[145]
 
-#define NCBISTDAA &at[146]
+#define NCBISTDAA &at[147]
 
-#define SEQ_GAP &at[148]
-#define SEQ_GAP_type &at[149]
-#define SEQ_GAP_linkage &at[150]
+#define SEQ_GAP &at[149]
+#define SEQ_GAP_type &at[150]
+#define SEQ_GAP_linkage &at[151]
 
-#define ANNOT_ID &at[190]
-#define ANNOT_ID_local &at[191]
-#define ANNOT_ID_ncbi &at[193]
-#define ANNOT_ID_general &at[194]
+#define ANNOT_ID &at[191]
+#define ANNOT_ID_local &at[192]
+#define ANNOT_ID_ncbi &at[194]
+#define ANNOT_ID_general &at[195]
 
 #define ALIGN_DEF &at[56]
 #define ALIGN_DEF_align_type &at[57]
diff --git a/asnstat/asntable.h b/asnstat/asntable.h
new file mode 100644
index 00000000..92e0b51a
--- /dev/null
+++ b/asnstat/asntable.h
@@ -0,0 +1,195 @@
+/***********************************************************************
+*
+**
+*        Automatic header module from ASNTOOL
+*
+************************************************************************/
+
+#ifndef _ASNTOOL_
+#include <asn.h>
+#endif
+
+static char * asnfilename = "asntable.h15";
+static AsnValxNode avnx[32] = {
+    {20,"location" ,0,0.0,&avnx[1] } ,
+    {20,"location-id" ,1,0.0,&avnx[2] } ,
+    {20,"location-gi" ,2,0.0,&avnx[3] } ,
+    {20,"location-from" ,3,0.0,&avnx[4] } ,
+    {20,"location-to" ,4,0.0,&avnx[5] } ,
+    {20,"location-strand" ,5,0.0,&avnx[6] } ,
+    {20,"location-fuzz-from-lim" ,6,0.0,&avnx[7] } ,
+    {20,"location-fuzz-to-lim" ,7,0.0,&avnx[8] } ,
+    {20,"product" ,10,0.0,&avnx[9] } ,
+    {20,"product-id" ,11,0.0,&avnx[10] } ,
+    {20,"product-gi" ,12,0.0,&avnx[11] } ,
+    {20,"product-from" ,13,0.0,&avnx[12] } ,
+    {20,"product-to" ,14,0.0,&avnx[13] } ,
+    {20,"product-strand" ,15,0.0,&avnx[14] } ,
+    {20,"product-fuzz-from-lim" ,16,0.0,&avnx[15] } ,
+    {20,"product-fuzz-to-lim" ,17,0.0,&avnx[16] } ,
+    {20,"id-local" ,20,0.0,&avnx[17] } ,
+    {20,"xref-id-local" ,21,0.0,&avnx[18] } ,
+    {20,"partial" ,22,0.0,&avnx[19] } ,
+    {20,"comment" ,23,0.0,&avnx[20] } ,
+    {20,"title" ,24,0.0,&avnx[21] } ,
+    {20,"ext" ,25,0.0,&avnx[22] } ,
+    {20,"qual" ,26,0.0,&avnx[23] } ,
+    {20,"dbxref" ,27,0.0,&avnx[24] } ,
+    {20,"data-imp-key" ,30,0.0,&avnx[25] } ,
+    {20,"data-region" ,31,0.0,&avnx[26] } ,
+    {20,"data-cdregion-frame" ,32,0.0,&avnx[27] } ,
+    {20,"ext-type" ,40,0.0,&avnx[28] } ,
+    {20,"qual-qual" ,41,0.0,&avnx[29] } ,
+    {20,"qual-val" ,42,0.0,&avnx[30] } ,
+    {20,"dbxref-db" ,43,0.0,&avnx[31] } ,
+    {20,"dbxref-tag" ,44,0.0,NULL } };
+
+static AsnType atx[68] = {
+  {401, "SeqTable-column-info" ,1,0,0,0,0,1,0,0,NULL,&atx[6],&atx[1],0,&atx[7]} ,
+  {0, "title" ,128,0,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[3]} ,
+  {323, "VisibleString" ,0,26,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "field-id" ,128,1,0,1,0,0,0,0,NULL,&atx[4],&avnx[0],0,&atx[5]} ,
+  {302, "INTEGER" ,0,2,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "field-name" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {311, "SEQUENCE" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {402, "SeqTable-column" ,1,0,0,0,0,1,0,0,NULL,&atx[6],&atx[8],0,&atx[62]} ,
+  {0, "header" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[9]} ,
+  {0, "data" ,128,1,0,1,0,0,0,0,NULL,&atx[10],NULL,0,&atx[45]} ,
+  {409, "SeqTable-multi-data" ,1,0,0,0,0,0,0,0,NULL,&atx[44],&atx[11],0,&atx[51]} ,
+  {0, "int" ,128,0,0,0,0,0,0,0,NULL,&atx[13],&atx[12],0,&atx[14]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[4],NULL,0,NULL} ,
+  {312, "SEQUENCE OF" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "real" ,128,1,0,0,0,0,0,0,NULL,&atx[13],&atx[15],0,&atx[17]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[16],NULL,0,NULL} ,
+  {309, "REAL" ,0,9,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "string" ,128,2,0,0,0,0,0,0,NULL,&atx[13],&atx[18],0,&atx[19]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "bytes" ,128,3,0,0,0,0,0,0,NULL,&atx[13],&atx[20],0,&atx[22]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[21],NULL,0,NULL} ,
+  {304, "OCTET STRING" ,0,4,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "common-string" ,128,4,0,0,0,0,0,0,NULL,&atx[23],NULL,0,&atx[28]} ,
+  {407, "CommonString-table" ,1,0,0,0,0,0,0,0,NULL,&atx[6],&atx[24],0,&atx[29]} ,
+  {0, "strings" ,128,0,0,0,0,0,0,0,NULL,&atx[13],&atx[25],0,&atx[26]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "indexes" ,128,1,0,0,0,0,0,0,NULL,&atx[13],&atx[27],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[4],NULL,0,NULL} ,
+  {0, "common-bytes" ,128,5,0,0,0,0,0,0,NULL,&atx[29],NULL,0,&atx[34]} ,
+  {408, "CommonBytes-table" ,1,0,0,0,0,0,0,0,NULL,&atx[6],&atx[30],0,&atx[10]} ,
+  {0, "bytes" ,128,0,0,0,0,0,0,0,NULL,&atx[13],&atx[31],0,&atx[32]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[21],NULL,0,NULL} ,
+  {0, "indexes" ,128,1,0,0,0,0,0,0,NULL,&atx[13],&atx[33],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[4],NULL,0,NULL} ,
+  {0, "bit" ,128,6,0,0,0,0,0,0,NULL,&atx[21],NULL,0,&atx[35]} ,
+  {0, "loc" ,128,7,0,0,0,0,0,0,NULL,&atx[13],&atx[36],0,&atx[38]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[37],NULL,0,NULL} ,
+  {405, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[43]} ,
+  {0, "id" ,128,8,0,0,0,0,0,0,NULL,&atx[13],&atx[39],0,&atx[41]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[40],NULL,0,NULL} ,
+  {404, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[37]} ,
+  {0, "interval" ,128,9,0,0,0,0,0,0,NULL,&atx[13],&atx[42],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[43],NULL,0,NULL} ,
+  {406, "Seq-interval" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[23]} ,
+  {315, "CHOICE" ,0,-1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "sparse" ,128,2,0,1,0,0,0,0,NULL,&atx[46],NULL,0,&atx[50]} ,
+  {411, "SeqTable-sparse-index" ,1,0,0,0,0,0,0,0,NULL,&atx[44],&atx[47],0,NULL} ,
+  {0, "indexes" ,128,0,0,0,0,0,0,0,NULL,&atx[13],&atx[48],0,&atx[49]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[4],NULL,0,NULL} ,
+  {0, "bit-set" ,128,1,0,0,0,0,0,0,NULL,&atx[21],NULL,0,NULL} ,
+  {0, "default" ,128,3,0,1,0,0,0,0,NULL,&atx[51],NULL,0,&atx[61]} ,
+  {410, "SeqTable-single-data" ,1,0,0,0,0,0,0,0,NULL,&atx[44],&atx[52],0,&atx[46]} ,
+  {0, "int" ,128,0,0,0,0,0,0,0,NULL,&atx[4],NULL,0,&atx[53]} ,
+  {0, "real" ,128,1,0,0,0,0,0,0,NULL,&atx[16],NULL,0,&atx[54]} ,
+  {0, "string" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[55]} ,
+  {0, "bytes" ,128,3,0,0,0,0,0,0,NULL,&atx[21],NULL,0,&atx[56]} ,
+  {0, "bit" ,128,4,0,0,0,0,0,0,NULL,&atx[57],NULL,0,&atx[58]} ,
+  {301, "BOOLEAN" ,0,1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
+  {0, "loc" ,128,5,0,0,0,0,0,0,NULL,&atx[37],NULL,0,&atx[59]} ,
+  {0, "id" ,128,6,0,0,0,0,0,0,NULL,&atx[40],NULL,0,&atx[60]} ,
+  {0, "interval" ,128,7,0,0,0,0,0,0,NULL,&atx[43],NULL,0,NULL} ,
+  {0, "sparse-other" ,128,4,0,1,0,0,0,0,NULL,&atx[51],NULL,0,NULL} ,
+  {403, "Seq-table" ,1,0,0,0,0,1,0,0,NULL,&atx[6],&atx[63],0,&atx[40]} ,
+  {0, "feat-type" ,128,0,0,0,0,0,0,0,NULL,&atx[4],NULL,0,&atx[64]} ,
+  {0, "feat-subtype" ,128,1,0,1,0,0,0,0,NULL,&atx[4],NULL,0,&atx[65]} ,
+  {0, "num-rows" ,128,2,0,0,0,0,0,0,NULL,&atx[4],NULL,0,&atx[66]} ,
+  {0, "columns" ,128,3,0,0,0,0,0,0,NULL,&atx[13],&atx[67],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[7],NULL,0,NULL} };
+
+static AsnModule ampx[1] = {
+  { "NCBI-SeqTable" , "asntable.h15",&atx[0],NULL,NULL,0,0} };
+
+static AsnValxNodePtr avn = avnx;
+static AsnTypePtr at = atx;
+static AsnModulePtr amp = ampx;
+
+
+
+/**************************************************
+*
+*    Defines for Module NCBI-SeqTable
+*
+**************************************************/
+
+#define SEQTABLE_COLUMN_INFO &at[0]
+#define SEQTABLE_COLUMN_INFO_title &at[1]
+#define SEQTABLE_COLUMN_INFO_field_id &at[3]
+#define SEQTABLE_COLUMN_INFO_field_name &at[5]
+
+#define SEQTABLE_COLUMN &at[7]
+#define SEQTABLE_COLUMN_header &at[8]
+#define SEQTABLE_COLUMN_data &at[9]
+#define SEQTABLE_COLUMN_sparse &at[45]
+#define SEQTABLE_COLUMN_default &at[50]
+#define SEQTABLE_COLUMN_sparse_other &at[61]
+
+#define SEQ_TABLE &at[62]
+#define SEQ_TABLE_feat_type &at[63]
+#define SEQ_TABLE_feat_subtype &at[64]
+#define SEQ_TABLE_num_rows &at[65]
+#define SEQ_TABLE_columns &at[66]
+#define SEQ_TABLE_columns_E &at[67]
+
+#define COMMONSTRING_TABLE &at[23]
+#define COMMONSTRING_TABLE_strings &at[24]
+#define COMMONSTRING_TABLE_strings_E &at[25]
+#define COMMONSTRING_TABLE_indexes &at[26]
+#define COMMONSTRING_TABLE_indexes_E &at[27]
+
+#define COMMONBYTES_TABLE &at[29]
+#define COMMONBYTES_TABLE_bytes &at[30]
+#define COMMONBYTES_TABLE_bytes_E &at[31]
+#define COMMONBYTES_TABLE_indexes &at[32]
+#define COMMONBYTES_TABLE_indexes_E &at[33]
+
+#define SEQTABLE_MULTI_DATA &at[10]
+#define SEQTABLE_MULTI_DATA_int &at[11]
+#define SEQTABLE_MULTI_DATA_int_E &at[12]
+#define SEQTABLE_MULTI_DATA_real &at[14]
+#define SEQTABLE_MULTI_DATA_real_E &at[15]
+#define SEQTABLE_MULTI_DATA_string &at[17]
+#define SEQTABLE_MULTI_DATA_string_E &at[18]
+#define SEQTABLE_MULTI_DATA_bytes &at[19]
+#define SEQTABLE_MULTI_DATA_bytes_E &at[20]
+#define MULTI_DATA_common_string &at[22]
+#define MULTI_DATA_common_bytes &at[28]
+#define SEQTABLE_MULTI_DATA_bit &at[34]
+#define SEQTABLE_MULTI_DATA_loc &at[35]
+#define SEQTABLE_MULTI_DATA_loc_E &at[36]
+#define SEQTABLE_MULTI_DATA_id &at[38]
+#define SEQTABLE_MULTI_DATA_id_E &at[39]
+#define SEQTABLE_MULTI_DATA_interval &at[41]
+#define SEQTABLE_MULTI_DATA_interval_E &at[42]
+
+#define SEQTABLE_SINGLE_DATA &at[51]
+#define SEQTABLE_SINGLE_DATA_int &at[52]
+#define SEQTABLE_SINGLE_DATA_real &at[53]
+#define SEQTABLE_SINGLE_DATA_string &at[54]
+#define SEQTABLE_SINGLE_DATA_bytes &at[55]
+#define SEQTABLE_SINGLE_DATA_bit &at[56]
+#define SEQTABLE_SINGLE_DATA_loc &at[58]
+#define SEQTABLE_SINGLE_DATA_id &at[59]
+#define SEQTABLE_SINGLE_DATA_interval &at[60]
+
+#define SEQTABLE_SPARSE_INDEX &at[46]
+#define SEQTABLE_SPARSE_INDEX_indexes &at[47]
+#define SEQTABLE_SPARSE_INDEX_indexes_E &at[48]
+#define SEQTABLE_SPARSE_INDEX_bit_set &at[49]
diff --git a/biostruc/cdd/cdd.asn b/biostruc/cdd/cdd.asn
index 761ecadb..f2bef2b7 100644
--- a/biostruc/cdd/cdd.asn
+++ b/biostruc/cdd/cdd.asn
@@ -1,4 +1,4 @@
---$Revision: 1.25 $
+--$Revision: 1.26 $
 --**********************************************************************
 --
 --  Definitions for CDD's 
@@ -169,8 +169,9 @@ Cdd-descr ::= CHOICE {
   readonly-status INTEGER { unassigned(0),    -- to record read-only status
                             readonly (1),     -- when CD is checked out from
                             readwrite (2),    -- the tracking database, for
-                            other (255) },     -- use within curation software
-  book-ref      Cdd-book-ref
+                            other (255) },    -- use within curation software
+  book-ref      Cdd-book-ref,                 -- links to Entrez/books
+  attribution   Pub                           -- add citations and/or author names
 }
 
 Cdd-descr-set ::= SET OF Cdd-descr
@@ -276,8 +277,9 @@ Align-annot ::= SEQUENCE {
                                         -- "Heme binding site" or "catalytic
                                         -- triad" etc., something that should
                                         -- be used for labels in visualization
-  evidence      SEQUENCE OF Feature-evidence OPTIONAL -- evidence we can
-                                                      -- compute with
+  evidence      SEQUENCE OF Feature-evidence OPTIONAL,  -- evidence we can
+                                                        -- compute with
+  type          INTEGER OPTIONAL        -- for typing annotated features
 }
 
 Align-annot-set ::= SEQUENCE OF Align-annot
@@ -363,7 +365,14 @@ Algorithm-type ::= SEQUENCE {
   gapExtend         INTEGER OPTIONAL,
   gapScaleFactor    INTEGER OPTIONAL,
   nTerminalExt      INTEGER OPTIONAL,
-  cTerminalExt      INTEGER OPTIONAL
+  cTerminalExt      INTEGER OPTIONAL,
+  tree-scope        INTEGER { allDescendants       (0),
+		                  immediateChildrenOnly(1),
+		                  selfOnly             (2),
+		                  other              (255) } OPTIONAL,
+  coloring-scope    INTEGER { allDescendants        (0),
+		                  immediateChildrenOnly (1),
+		                  other               (255) } OPTIONAL
 }
 
 Node-annotation ::= SEQUENCE {
diff --git a/biostruc/cdd/cdd.h b/biostruc/cdd/cdd.h
index 0640300e..9e50ad64 100644
--- a/biostruc/cdd/cdd.h
+++ b/biostruc/cdd/cdd.h
@@ -10,7 +10,7 @@
 #endif
 
 static char * asnfilename = "cdd.h24";
-static AsnValxNode avnx[87] = {
+static AsnValxNode avnx[94] = {
     {20,"unassigned" ,0,0.0,&avnx[1] } ,
     {20,"finished-ok" ,1,0.0,&avnx[2] } ,
     {20,"pending-release" ,2,0.0,&avnx[3] } ,
@@ -79,27 +79,34 @@ static AsnValxNode avnx[87] = {
     {20,"pam70" ,5,0.0,&avnx[66] } ,
     {20,"pam250" ,6,0.0,&avnx[67] } ,
     {20,"other" ,255,0.0,NULL } ,
+    {20,"allDescendants" ,0,0.0,&avnx[69] } ,
+    {20,"immediateChildrenOnly" ,1,0.0,&avnx[70] } ,
+    {20,"selfOnly" ,2,0.0,&avnx[71] } ,
+    {20,"other" ,255,0.0,NULL } ,
+    {20,"allDescendants" ,0,0.0,&avnx[73] } ,
+    {20,"immediateChildrenOnly" ,1,0.0,&avnx[74] } ,
+    {20,"other" ,255,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
     {2,NULL,0,0.0,NULL } ,
     {2,NULL,1,0.0,NULL } ,
-    {20,"unassigned" ,0,0.0,&avnx[72] } ,
-    {20,"cd-info" ,1,0.0,&avnx[73] } ,
-    {20,"align-annot" ,2,0.0,&avnx[74] } ,
-    {20,"seq-list" ,3,0.0,&avnx[75] } ,
-    {20,"seq-tree" ,4,0.0,&avnx[76] } ,
-    {20,"merge-preview" ,5,0.0,&avnx[77] } ,
-    {20,"cross-hits" ,6,0.0,&avnx[78] } ,
-    {20,"notes" ,7,0.0,&avnx[79] } ,
-    {20,"tax-tree" ,8,0.0,&avnx[80] } ,
-    {20,"dart" ,9,0.0,&avnx[81] } ,
-    {20,"dart-selected-rows" ,10,0.0,&avnx[82] } ,
+    {20,"unassigned" ,0,0.0,&avnx[79] } ,
+    {20,"cd-info" ,1,0.0,&avnx[80] } ,
+    {20,"align-annot" ,2,0.0,&avnx[81] } ,
+    {20,"seq-list" ,3,0.0,&avnx[82] } ,
+    {20,"seq-tree" ,4,0.0,&avnx[83] } ,
+    {20,"merge-preview" ,5,0.0,&avnx[84] } ,
+    {20,"cross-hits" ,6,0.0,&avnx[85] } ,
+    {20,"notes" ,7,0.0,&avnx[86] } ,
+    {20,"tax-tree" ,8,0.0,&avnx[87] } ,
+    {20,"dart" ,9,0.0,&avnx[88] } ,
+    {20,"dart-selected-rows" ,10,0.0,&avnx[89] } ,
     {20,"other" ,255,0.0,NULL } ,
-    {20,"unassigned" ,0,0.0,&avnx[84] } ,
-    {20,"user-recorded" ,1,0.0,&avnx[85] } ,
-    {20,"server-generated" ,2,0.0,&avnx[86] } ,
+    {20,"unassigned" ,0,0.0,&avnx[91] } ,
+    {20,"user-recorded" ,1,0.0,&avnx[92] } ,
+    {20,"server-generated" ,2,0.0,&avnx[93] } ,
     {20,"other" ,255,0.0,NULL } };
 
-static AsnType atx[222] = {
+static AsnType atx[226] = {
   {401, "Cdd-id" ,1,0,0,0,0,1,0,0,NULL,&atx[11],&atx[1],0,&atx[12]} ,
   {0, "uid" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[3]} ,
   {302, "INTEGER" ,0,2,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
@@ -115,22 +122,22 @@ static AsnType atx[222] = {
   {402, "Cdd-id-set" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[13],0,&atx[15]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,NULL} ,
   {312, "SEQUENCE OF" ,0,16,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {403, "Cdd" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[16],0,&atx[169]} ,
+  {403, "Cdd" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[16],0,&atx[173]} ,
   {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[17]} ,
   {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[18]} ,
-  {0, "description" ,128,2,0,1,0,0,0,0,NULL,&atx[19],NULL,0,&atx[56]} ,
-  {432, "Cdd-descr-set" ,1,0,0,0,0,0,0,0,NULL,&atx[55],&atx[20],0,&atx[68]} ,
+  {0, "description" ,128,2,0,1,0,0,0,0,NULL,&atx[19],NULL,0,&atx[57]} ,
+  {432, "Cdd-descr-set" ,1,0,0,0,0,0,0,0,NULL,&atx[56],&atx[20],0,&atx[69]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[21],NULL,0,NULL} ,
   {431, "Cdd-descr" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[22],0,&atx[19]} ,
   {0, "othername" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[23]} ,
   {0, "category" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[24]} ,
   {0, "comment" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[25]} ,
   {0, "reference" ,128,3,0,0,0,0,0,0,NULL,&atx[26],NULL,0,&atx[27]} ,
-  {410, "Pub" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[60]} ,
+  {410, "Pub" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[61]} ,
   {0, "create-date" ,128,4,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[29]} ,
   {409, "Date" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[26]} ,
   {0, "tax-source" ,128,5,0,0,0,0,0,0,NULL,&atx[30],NULL,0,&atx[31]} ,
-  {415, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[108]} ,
+  {415, "Org-ref" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[109]} ,
   {0, "source" ,128,6,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[32]} ,
   {0, "status" ,128,7,0,0,0,0,0,0,NULL,&atx[2],&avnx[0],0,&atx[33]} ,
   {0, "update-date" ,128,8,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[34]} ,
@@ -141,12 +148,12 @@ static AsnType atx[222] = {
   {429, "Cdd-repeat" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[39],0,&atx[47]} ,
   {0, "count" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[40]} ,
   {0, "location" ,128,1,0,1,0,0,0,0,NULL,&atx[41],NULL,0,&atx[42]} ,
-  {418, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[124]} ,
+  {418, "Seq-loc" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[125]} ,
   {0, "avglen" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
   {0, "old-root" ,128,12,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[44]} ,
   {0, "curation-status" ,128,13,0,0,0,0,0,0,NULL,&atx[2],&avnx[10],0,&atx[45]} ,
   {0, "readonly-status" ,128,14,0,0,0,0,0,0,NULL,&atx[2],&avnx[20],0,&atx[46]} ,
-  {0, "book-ref" ,128,15,0,0,0,0,0,0,NULL,&atx[47],NULL,0,NULL} ,
+  {0, "book-ref" ,128,15,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[55]} ,
   {430, "Cdd-book-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[48],0,&atx[21]} ,
   {0, "bookname" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[49]} ,
   {0, "textelement" ,128,1,0,0,0,0,0,0,NULL,&atx[50],&avnx[24],0,&atx[51]} ,
@@ -155,172 +162,176 @@ static AsnType atx[222] = {
   {0, "subelementid" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[53]} ,
   {0, "celementid" ,128,4,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[54]} ,
   {0, "csubelementid" ,128,5,0,1,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
+  {0, "attribution" ,128,16,0,0,0,0,0,0,NULL,&atx[26],NULL,0,NULL} ,
   {314, "SET OF" ,0,17,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {0, "seqannot" ,128,3,0,1,0,0,0,0,NULL,&atx[14],&atx[57],0,&atx[59]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
-  {413, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[62]} ,
-  {0, "features" ,128,4,0,1,0,0,0,0,NULL,&atx[60],NULL,0,&atx[61]} ,
-  {411, "Biostruc-annot-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[66]} ,
-  {0, "sequences" ,128,5,0,1,0,0,0,0,NULL,&atx[62],NULL,0,&atx[63]} ,
+  {0, "seqannot" ,128,3,0,1,0,0,0,0,NULL,&atx[14],&atx[58],0,&atx[60]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[59],NULL,0,NULL} ,
+  {413, "Seq-annot" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[63]} ,
+  {0, "features" ,128,4,0,1,0,0,0,0,NULL,&atx[61],NULL,0,&atx[62]} ,
+  {411, "Biostruc-annot-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[67]} ,
+  {0, "sequences" ,128,5,0,1,0,0,0,0,NULL,&atx[63],NULL,0,&atx[64]} ,
   {414, "Seq-entry" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[30]} ,
-  {0, "profile-range" ,128,6,0,1,0,0,0,0,NULL,&atx[64],NULL,0,&atx[65]} ,
+  {0, "profile-range" ,128,6,0,1,0,0,0,0,NULL,&atx[65],NULL,0,&atx[66]} ,
   {417, "Seq-interval" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[41]} ,
-  {0, "trunc-master" ,128,7,0,1,0,0,0,0,NULL,&atx[66],NULL,0,&atx[67]} ,
-  {412, "Bioseq" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[58]} ,
-  {0, "posfreq" ,128,8,0,1,0,0,0,0,NULL,&atx[68],NULL,0,&atx[76]} ,
-  {433, "Matrix" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[69],0,&atx[78]} ,
-  {0, "ncolumns" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[70]} ,
-  {0, "nrows" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[71]} ,
-  {0, "row-labels" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[72],0,&atx[73]} ,
+  {0, "trunc-master" ,128,7,0,1,0,0,0,0,NULL,&atx[67],NULL,0,&atx[68]} ,
+  {412, "Bioseq" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[59]} ,
+  {0, "posfreq" ,128,8,0,1,0,0,0,0,NULL,&atx[69],NULL,0,&atx[77]} ,
+  {433, "Matrix" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[70],0,&atx[79]} ,
+  {0, "ncolumns" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[71]} ,
+  {0, "nrows" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[72]} ,
+  {0, "row-labels" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[73],0,&atx[74]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "scale-factor" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[74]} ,
-  {0, "columns" ,128,4,0,0,0,0,0,0,NULL,&atx[14],&atx[75],0,NULL} ,
+  {0, "scale-factor" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[75]} ,
+  {0, "columns" ,128,4,0,0,0,0,0,0,NULL,&atx[14],&atx[76],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "scoremat" ,128,9,0,1,0,0,0,0,NULL,&atx[68],NULL,0,&atx[77]} ,
-  {0, "distance" ,128,10,0,1,0,0,0,0,NULL,&atx[78],NULL,0,&atx[84]} ,
-  {434, "Triangle" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[79],0,&atx[93]} ,
-  {0, "nelements" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[80]} ,
-  {0, "scores" ,128,1,0,1,0,0,0,0,NULL,&atx[81],NULL,0,&atx[82]} ,
-  {420, "Score-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[127]} ,
-  {0, "div-ranks" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[83],0,NULL} ,
+  {0, "scoremat" ,128,9,0,1,0,0,0,0,NULL,&atx[69],NULL,0,&atx[78]} ,
+  {0, "distance" ,128,10,0,1,0,0,0,0,NULL,&atx[79],NULL,0,&atx[85]} ,
+  {434, "Triangle" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[80],0,&atx[94]} ,
+  {0, "nelements" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[81]} ,
+  {0, "scores" ,128,1,0,1,0,0,0,0,NULL,&atx[82],NULL,0,&atx[83]} ,
+  {420, "Score-set" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[129]} ,
+  {0, "div-ranks" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[84],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "parent" ,128,11,0,1,0,0,0,0,NULL,&atx[0],NULL,0,&atx[85]} ,
-  {0, "children" ,128,12,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[86]} ,
-  {0, "siblings" ,128,13,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[87]} ,
-  {0, "neighbors" ,128,14,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[88]} ,
-  {0, "pending" ,128,15,0,1,0,0,0,0,NULL,&atx[14],&atx[89],0,&atx[101]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[90],NULL,0,NULL} ,
-  {436, "Update-align" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[91],0,&atx[103]} ,
-  {0, "description" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[92],0,&atx[99]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[93],NULL,0,NULL} ,
-  {435, "Update-comment" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[94],0,&atx[90]} ,
-  {0, "comment" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[95]} ,
-  {0, "addthis" ,128,1,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[96]} ,
-  {0, "replaces" ,128,2,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[97]} ,
-  {0, "reject-loc" ,128,3,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[98]} ,
+  {0, "parent" ,128,11,0,1,0,0,0,0,NULL,&atx[0],NULL,0,&atx[86]} ,
+  {0, "children" ,128,12,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[87]} ,
+  {0, "siblings" ,128,13,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[88]} ,
+  {0, "neighbors" ,128,14,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[89]} ,
+  {0, "pending" ,128,15,0,1,0,0,0,0,NULL,&atx[14],&atx[90],0,&atx[102]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[91],NULL,0,NULL} ,
+  {436, "Update-align" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[92],0,&atx[104]} ,
+  {0, "description" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[93],0,&atx[100]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[94],NULL,0,NULL} ,
+  {435, "Update-comment" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[95],0,&atx[91]} ,
+  {0, "comment" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[96]} ,
+  {0, "addthis" ,128,1,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[97]} ,
+  {0, "replaces" ,128,2,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[98]} ,
+  {0, "reject-loc" ,128,3,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[99]} ,
   {0, "reference" ,128,4,0,0,0,0,0,0,NULL,&atx[26],NULL,0,NULL} ,
-  {0, "seqannot" ,128,1,0,1,0,0,0,0,NULL,&atx[58],NULL,0,&atx[100]} ,
+  {0, "seqannot" ,128,1,0,1,0,0,0,0,NULL,&atx[59],NULL,0,&atx[101]} ,
   {0, "type" ,128,2,0,0,0,0,0,0,NULL,&atx[2],&avnx[34],0,NULL} ,
-  {0, "rejects" ,128,16,0,1,0,0,0,0,NULL,&atx[14],&atx[102],0,&atx[109]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[103],NULL,0,NULL} ,
-  {437, "Reject-id" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[104],0,&atx[119]} ,
-  {0, "description" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[105],0,&atx[106]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[93],NULL,0,NULL} ,
-  {0, "ids" ,128,1,0,0,0,0,0,0,NULL,&atx[55],&atx[107],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[108],NULL,0,NULL} ,
-  {416, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[64]} ,
-  {0, "master3d" ,128,17,0,1,0,0,0,0,NULL,&atx[55],&atx[110],0,&atx[111]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[108],NULL,0,NULL} ,
-  {0, "alignannot" ,128,18,0,1,0,0,0,0,NULL,&atx[112],NULL,0,&atx[126]} ,
-  {440, "Align-annot-set" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[113],0,&atx[132]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[114],NULL,0,NULL} ,
-  {439, "Align-annot" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[115],0,&atx[112]} ,
-  {0, "location" ,128,0,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[116]} ,
-  {0, "description" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[117]} ,
-  {0, "evidence" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[118],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[119],NULL,0,NULL} ,
-  {438, "Feature-evidence" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[120],0,&atx[114]} ,
-  {0, "comment" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[121]} ,
-  {0, "reference" ,128,1,0,0,0,0,0,0,NULL,&atx[26],NULL,0,&atx[122]} ,
-  {0, "bsannot" ,128,2,0,0,0,0,0,0,NULL,&atx[60],NULL,0,&atx[123]} ,
-  {0, "seqfeat" ,128,3,0,0,0,0,0,0,NULL,&atx[124],NULL,0,&atx[125]} ,
-  {419, "Seq-feat" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[81]} ,
+  {0, "rejects" ,128,16,0,1,0,0,0,0,NULL,&atx[14],&atx[103],0,&atx[110]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[104],NULL,0,NULL} ,
+  {437, "Reject-id" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[105],0,&atx[120]} ,
+  {0, "description" ,128,0,0,1,0,0,0,0,NULL,&atx[14],&atx[106],0,&atx[107]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[94],NULL,0,NULL} ,
+  {0, "ids" ,128,1,0,0,0,0,0,0,NULL,&atx[56],&atx[108],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[109],NULL,0,NULL} ,
+  {416, "Seq-id" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[65]} ,
+  {0, "master3d" ,128,17,0,1,0,0,0,0,NULL,&atx[56],&atx[111],0,&atx[112]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[109],NULL,0,NULL} ,
+  {0, "alignannot" ,128,18,0,1,0,0,0,0,NULL,&atx[113],NULL,0,&atx[128]} ,
+  {440, "Align-annot-set" ,1,0,0,0,0,0,0,0,NULL,&atx[14],&atx[114],0,&atx[134]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[115],NULL,0,NULL} ,
+  {439, "Align-annot" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[116],0,&atx[113]} ,
+  {0, "location" ,128,0,0,0,0,0,0,0,NULL,&atx[41],NULL,0,&atx[117]} ,
+  {0, "description" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[118]} ,
+  {0, "evidence" ,128,2,0,1,0,0,0,0,NULL,&atx[14],&atx[119],0,&atx[127]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[120],NULL,0,NULL} ,
+  {438, "Feature-evidence" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[121],0,&atx[115]} ,
+  {0, "comment" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[122]} ,
+  {0, "reference" ,128,1,0,0,0,0,0,0,NULL,&atx[26],NULL,0,&atx[123]} ,
+  {0, "bsannot" ,128,2,0,0,0,0,0,0,NULL,&atx[61],NULL,0,&atx[124]} ,
+  {0, "seqfeat" ,128,3,0,0,0,0,0,0,NULL,&atx[125],NULL,0,&atx[126]} ,
+  {419, "Seq-feat" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[82]} ,
   {0, "book-ref" ,128,4,0,0,0,0,0,0,NULL,&atx[47],NULL,0,NULL} ,
-  {0, "style-dictionary" ,128,19,0,1,0,0,0,0,NULL,&atx[127],NULL,0,&atx[128]} ,
-  {421, "Cn3d-style-dictionary" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[129]} ,
-  {0, "user-annotations" ,128,20,0,1,0,0,0,0,NULL,&atx[129],NULL,0,&atx[130]} ,
-  {422, "Cn3d-user-annotations" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[137]} ,
-  {0, "ancestors" ,128,21,0,1,0,0,0,0,NULL,&atx[14],&atx[131],0,&atx[136]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[132],NULL,0,NULL} ,
-  {441, "Domain-parent" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[133],0,&atx[139]} ,
-  {0, "parent-type" ,128,0,0,0,0,0,0,0,NULL,&atx[2],&avnx[40],0,&atx[134]} ,
-  {0, "parentid" ,128,1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[135]} ,
-  {0, "seqannot" ,128,2,0,1,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
-  {0, "scoreparams" ,128,22,0,1,0,0,0,0,NULL,&atx[137],NULL,0,&atx[138]} ,
-  {423, "PssmWithParameters" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[185]} ,
-  {0, "seqtree" ,128,23,0,1,0,0,0,0,NULL,&atx[139],NULL,0,NULL} ,
-  {442, "Sequence-tree" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[140],0,&atx[142]} ,
-  {0, "cdAccession" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[141]} ,
-  {0, "algorithm" ,128,1,0,0,0,0,0,0,NULL,&atx[142],NULL,0,&atx[151]} ,
-  {443, "Algorithm-type" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[143],0,&atx[154]} ,
-  {0, "scoring-Scheme" ,128,0,0,0,0,0,0,0,NULL,&atx[2],&avnx[45],0,&atx[144]} ,
-  {0, "clustering-Method" ,128,1,0,0,0,0,0,0,NULL,&atx[2],&avnx[55],0,&atx[145]} ,
-  {0, "score-Matrix" ,128,2,0,1,0,0,0,0,NULL,&atx[2],&avnx[60],0,&atx[146]} ,
-  {0, "gapOpen" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[147]} ,
-  {0, "gapExtend" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[148]} ,
-  {0, "gapScaleFactor" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[149]} ,
-  {0, "nTerminalExt" ,128,6,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[150]} ,
-  {0, "cTerminalExt" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "isAnnotated" ,128,2,0,0,1,0,0,0,&avnx[68],&atx[152],NULL,0,&atx[153]} ,
+  {0, "type" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
+  {0, "style-dictionary" ,128,19,0,1,0,0,0,0,NULL,&atx[129],NULL,0,&atx[130]} ,
+  {421, "Cn3d-style-dictionary" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[131]} ,
+  {0, "user-annotations" ,128,20,0,1,0,0,0,0,NULL,&atx[131],NULL,0,&atx[132]} ,
+  {422, "Cn3d-user-annotations" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[139]} ,
+  {0, "ancestors" ,128,21,0,1,0,0,0,0,NULL,&atx[14],&atx[133],0,&atx[138]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[134],NULL,0,NULL} ,
+  {441, "Domain-parent" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[135],0,&atx[141]} ,
+  {0, "parent-type" ,128,0,0,0,0,0,0,0,NULL,&atx[2],&avnx[40],0,&atx[136]} ,
+  {0, "parentid" ,128,1,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[137]} ,
+  {0, "seqannot" ,128,2,0,1,0,0,0,0,NULL,&atx[59],NULL,0,NULL} ,
+  {0, "scoreparams" ,128,22,0,1,0,0,0,0,NULL,&atx[139],NULL,0,&atx[140]} ,
+  {423, "PssmWithParameters" ,1,0,0,0,0,0,1,0,NULL,NULL,NULL,0,&atx[189]} ,
+  {0, "seqtree" ,128,23,0,1,0,0,0,0,NULL,&atx[141],NULL,0,NULL} ,
+  {442, "Sequence-tree" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[142],0,&atx[144]} ,
+  {0, "cdAccession" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[143]} ,
+  {0, "algorithm" ,128,1,0,0,0,0,0,0,NULL,&atx[144],NULL,0,&atx[155]} ,
+  {443, "Algorithm-type" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[145],0,&atx[158]} ,
+  {0, "scoring-Scheme" ,128,0,0,0,0,0,0,0,NULL,&atx[2],&avnx[45],0,&atx[146]} ,
+  {0, "clustering-Method" ,128,1,0,0,0,0,0,0,NULL,&atx[2],&avnx[55],0,&atx[147]} ,
+  {0, "score-Matrix" ,128,2,0,1,0,0,0,0,NULL,&atx[2],&avnx[60],0,&atx[148]} ,
+  {0, "gapOpen" ,128,3,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[149]} ,
+  {0, "gapExtend" ,128,4,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[150]} ,
+  {0, "gapScaleFactor" ,128,5,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[151]} ,
+  {0, "nTerminalExt" ,128,6,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[152]} ,
+  {0, "cTerminalExt" ,128,7,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[153]} ,
+  {0, "tree-scope" ,128,8,0,1,0,0,0,0,NULL,&atx[2],&avnx[68],0,&atx[154]} ,
+  {0, "coloring-scope" ,128,9,0,1,0,0,0,0,NULL,&atx[2],&avnx[72],0,NULL} ,
+  {0, "isAnnotated" ,128,2,0,0,1,0,0,0,&avnx[75],&atx[156],NULL,0,&atx[157]} ,
   {301, "BOOLEAN" ,0,1,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {0, "root" ,128,3,0,0,0,0,0,0,NULL,&atx[154],NULL,0,NULL} ,
-  {444, "SeqTree-node" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[155],0,&atx[166]} ,
-  {0, "isAnnotated" ,128,0,0,0,1,0,0,0,&avnx[69],&atx[152],NULL,0,&atx[156]} ,
-  {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[157]} ,
-  {0, "distance" ,128,2,0,1,0,0,0,0,NULL,&atx[158],NULL,0,&atx[159]} ,
+  {0, "root" ,128,3,0,0,0,0,0,0,NULL,&atx[158],NULL,0,NULL} ,
+  {444, "SeqTree-node" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[159],0,&atx[170]} ,
+  {0, "isAnnotated" ,128,0,0,0,1,0,0,0,&avnx[76],&atx[156],NULL,0,&atx[160]} ,
+  {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[161]} ,
+  {0, "distance" ,128,2,0,1,0,0,0,0,NULL,&atx[162],NULL,0,&atx[163]} ,
   {309, "REAL" ,0,9,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
-  {0, "children" ,128,3,0,0,0,0,0,0,NULL,&atx[11],&atx[160],0,&atx[165]} ,
-  {0, "children" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[161],0,&atx[162]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[154],NULL,0,NULL} ,
-  {0, "footprint" ,128,1,0,0,0,0,0,0,NULL,&atx[10],&atx[163],0,NULL} ,
-  {0, "seqRange" ,128,0,0,0,0,0,0,0,NULL,&atx[64],NULL,0,&atx[164]} ,
+  {0, "children" ,128,3,0,0,0,0,0,0,NULL,&atx[11],&atx[164],0,&atx[169]} ,
+  {0, "children" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[165],0,&atx[166]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[158],NULL,0,NULL} ,
+  {0, "footprint" ,128,1,0,0,0,0,0,0,NULL,&atx[10],&atx[167],0,NULL} ,
+  {0, "seqRange" ,128,0,0,0,0,0,0,0,NULL,&atx[65],NULL,0,&atx[168]} ,
   {0, "rowId" ,128,1,0,1,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "annotation" ,128,4,0,1,0,0,0,0,NULL,&atx[166],NULL,0,NULL} ,
-  {445, "Node-annotation" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[167],0,&atx[208]} ,
-  {0, "presentInChildCD" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[168]} ,
+  {0, "annotation" ,128,4,0,1,0,0,0,0,NULL,&atx[170],NULL,0,NULL} ,
+  {445, "Node-annotation" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[171],0,&atx[212]} ,
+  {0, "presentInChildCD" ,128,0,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[172]} ,
   {0, "note" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {404, "Cdd-set" ,1,0,0,0,0,1,0,0,NULL,&atx[55],&atx[170],0,&atx[171]} ,
+  {404, "Cdd-set" ,1,0,0,0,0,1,0,0,NULL,&atx[56],&atx[174],0,&atx[175]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[15],NULL,0,NULL} ,
-  {405, "Cdd-tree" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[172],0,&atx[179]} ,
-  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[173]} ,
-  {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[174]} ,
-  {0, "description" ,128,2,0,1,0,0,0,0,NULL,&atx[19],NULL,0,&atx[175]} ,
-  {0, "parent" ,128,3,0,1,0,0,0,0,NULL,&atx[0],NULL,0,&atx[176]} ,
-  {0, "children" ,128,4,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[177]} ,
-  {0, "siblings" ,128,5,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[178]} ,
+  {405, "Cdd-tree" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[176],0,&atx[183]} ,
+  {0, "name" ,128,0,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[177]} ,
+  {0, "id" ,128,1,0,0,0,0,0,0,NULL,&atx[12],NULL,0,&atx[178]} ,
+  {0, "description" ,128,2,0,1,0,0,0,0,NULL,&atx[19],NULL,0,&atx[179]} ,
+  {0, "parent" ,128,3,0,1,0,0,0,0,NULL,&atx[0],NULL,0,&atx[180]} ,
+  {0, "children" ,128,4,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[181]} ,
+  {0, "siblings" ,128,5,0,1,0,0,0,0,NULL,&atx[12],NULL,0,&atx[182]} ,
   {0, "neighbors" ,128,6,0,1,0,0,0,0,NULL,&atx[12],NULL,0,NULL} ,
-  {406, "Cdd-tree-set" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[180],0,&atx[181]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[171],NULL,0,NULL} ,
-  {407, "Cdd-pref-nodes" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[182],0,&atx[198]} ,
-  {0, "preferred-nodes" ,128,0,0,0,0,0,0,0,NULL,&atx[183],NULL,0,&atx[190]} ,
-  {425, "Cdd-org-ref-set" ,1,0,0,0,0,0,0,0,NULL,&atx[55],&atx[184],0,&atx[195]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[185],NULL,0,NULL} ,
-  {424, "Cdd-org-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[186],0,&atx[183]} ,
-  {0, "reference" ,128,0,0,0,0,0,0,0,NULL,&atx[30],NULL,0,&atx[187]} ,
-  {0, "active" ,128,1,0,0,1,0,0,0,&avnx[70],&atx[152],NULL,0,&atx[188]} ,
-  {0, "parent-tax-id" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[189]} ,
+  {406, "Cdd-tree-set" ,1,0,0,0,0,1,0,0,NULL,&atx[14],&atx[184],0,&atx[185]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[175],NULL,0,NULL} ,
+  {407, "Cdd-pref-nodes" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[186],0,&atx[202]} ,
+  {0, "preferred-nodes" ,128,0,0,0,0,0,0,0,NULL,&atx[187],NULL,0,&atx[194]} ,
+  {425, "Cdd-org-ref-set" ,1,0,0,0,0,0,0,0,NULL,&atx[56],&atx[188],0,&atx[199]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[189],NULL,0,NULL} ,
+  {424, "Cdd-org-ref" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[190],0,&atx[187]} ,
+  {0, "reference" ,128,0,0,0,0,0,0,0,NULL,&atx[30],NULL,0,&atx[191]} ,
+  {0, "active" ,128,1,0,0,1,0,0,0,&avnx[77],&atx[156],NULL,0,&atx[192]} ,
+  {0, "parent-tax-id" ,128,2,0,1,0,0,0,0,NULL,&atx[2],NULL,0,&atx[193]} ,
   {0, "rank" ,128,3,0,1,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "model-organisms" ,128,1,0,1,0,0,0,0,NULL,&atx[183],NULL,0,&atx[191]} ,
-  {0, "optional-nodes" ,128,2,0,1,0,0,0,0,NULL,&atx[183],NULL,0,&atx[192]} ,
-  {0, "description" ,128,3,0,1,0,0,0,0,NULL,&atx[193],NULL,0,NULL} ,
-  {427, "Cdd-pref-node-descr-set" ,1,0,0,0,0,0,0,0,NULL,&atx[55],&atx[194],0,&atx[4]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[195],NULL,0,NULL} ,
-  {426, "Cdd-pref-node-descr" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[196],0,&atx[193]} ,
-  {0, "create-date" ,128,0,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[197]} ,
+  {0, "model-organisms" ,128,1,0,1,0,0,0,0,NULL,&atx[187],NULL,0,&atx[195]} ,
+  {0, "optional-nodes" ,128,2,0,1,0,0,0,0,NULL,&atx[187],NULL,0,&atx[196]} ,
+  {0, "description" ,128,3,0,1,0,0,0,0,NULL,&atx[197],NULL,0,NULL} ,
+  {427, "Cdd-pref-node-descr-set" ,1,0,0,0,0,0,0,0,NULL,&atx[56],&atx[198],0,&atx[4]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[199],NULL,0,NULL} ,
+  {426, "Cdd-pref-node-descr" ,1,0,0,0,0,0,0,0,NULL,&atx[11],&atx[200],0,&atx[197]} ,
+  {0, "create-date" ,128,0,0,0,0,0,0,0,NULL,&atx[28],NULL,0,&atx[201]} ,
   {0, "description" ,128,1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {408, "Cdd-Project" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[199],0,&atx[28]} ,
-  {0, "cds" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[200],0,&atx[201]} ,
+  {408, "Cdd-Project" ,1,0,0,0,0,1,0,0,NULL,&atx[10],&atx[203],0,&atx[28]} ,
+  {0, "cds" ,128,0,0,0,0,0,0,0,NULL,&atx[14],&atx[204],0,&atx[205]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[15],NULL,0,NULL} ,
-  {0, "cdcolor" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[202],0,&atx[203]} ,
+  {0, "cdcolor" ,128,1,0,0,0,0,0,0,NULL,&atx[14],&atx[206],0,&atx[207]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "viewers" ,128,2,0,0,0,0,0,0,NULL,&atx[14],&atx[204],0,&atx[215]} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[205],NULL,0,NULL} ,
-  {447, "Cdd-Viewer" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[206],0,&atx[218]} ,
-  {0, "ctrl" ,128,0,0,0,0,0,0,0,NULL,&atx[2],&avnx[71],0,&atx[207]} ,
-  {0, "rect" ,128,1,0,1,0,0,0,0,NULL,&atx[208],NULL,0,&atx[213]} ,
-  {446, "Cdd-Viewer-Rect" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[209],0,&atx[205]} ,
-  {0, "top" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[210]} ,
-  {0, "left" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[211]} ,
-  {0, "width" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[212]} ,
+  {0, "viewers" ,128,2,0,0,0,0,0,0,NULL,&atx[14],&atx[208],0,&atx[219]} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[209],NULL,0,NULL} ,
+  {447, "Cdd-Viewer" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[210],0,&atx[222]} ,
+  {0, "ctrl" ,128,0,0,0,0,0,0,0,NULL,&atx[2],&avnx[78],0,&atx[211]} ,
+  {0, "rect" ,128,1,0,1,0,0,0,0,NULL,&atx[212],NULL,0,&atx[217]} ,
+  {446, "Cdd-Viewer-Rect" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[213],0,&atx[209]} ,
+  {0, "top" ,128,0,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[214]} ,
+  {0, "left" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[215]} ,
+  {0, "width" ,128,2,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[216]} ,
   {0, "height" ,128,3,0,0,0,0,0,0,NULL,&atx[2],NULL,0,NULL} ,
-  {0, "accessions" ,128,2,0,0,0,0,0,0,NULL,&atx[14],&atx[214],0,NULL} ,
+  {0, "accessions" ,128,2,0,0,0,0,0,0,NULL,&atx[14],&atx[218],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} ,
-  {0, "log" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[216]} ,
-  {0, "scripts" ,128,4,0,1,0,0,0,0,NULL,&atx[14],&atx[217],0,NULL} ,
-  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[218],NULL,0,NULL} ,
-  {448, "Cdd-Script" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[219],0,NULL} ,
-  {0, "type" ,128,0,0,1,0,0,0,0,NULL,&atx[2],&avnx[83],0,&atx[220]} ,
-  {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[221]} ,
+  {0, "log" ,128,3,0,0,0,0,0,0,NULL,&atx[6],NULL,0,&atx[220]} ,
+  {0, "scripts" ,128,4,0,1,0,0,0,0,NULL,&atx[14],&atx[221],0,NULL} ,
+  {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[222],NULL,0,NULL} ,
+  {448, "Cdd-Script" ,1,0,0,0,0,0,0,0,NULL,&atx[10],&atx[223],0,NULL} ,
+  {0, "type" ,128,0,0,1,0,0,0,0,NULL,&atx[2],&avnx[90],0,&atx[224]} ,
+  {0, "name" ,128,1,0,1,0,0,0,0,NULL,&atx[6],NULL,0,&atx[225]} ,
   {0, "commands" ,128,2,0,0,0,0,0,0,NULL,&atx[6],NULL,0,NULL} };
 
 static AsnModule ampx[1] = {
@@ -349,80 +360,80 @@ static AsnModulePtr amp = ampx;
 #define CDD_name &at[16]
 #define CDD_id &at[17]
 #define CDD_description &at[18]
-#define CDD_seqannot &at[56]
-#define CDD_seqannot_E &at[57]
-#define CDD_features &at[59]
-#define CDD_sequences &at[61]
-#define CDD_profile_range &at[63]
-#define CDD_trunc_master &at[65]
-#define CDD_posfreq &at[67]
-#define CDD_scoremat &at[76]
-#define CDD_distance &at[77]
-#define CDD_parent &at[84]
-#define CDD_children &at[85]
-#define CDD_siblings &at[86]
-#define CDD_neighbors &at[87]
-#define CDD_pending &at[88]
-#define CDD_pending_E &at[89]
-#define CDD_rejects &at[101]
-#define CDD_rejects_E &at[102]
-#define CDD_master3d &at[109]
-#define CDD_master3d_E &at[110]
-#define CDD_alignannot &at[111]
-#define CDD_style_dictionary &at[126]
-#define CDD_user_annotations &at[128]
-#define CDD_ancestors &at[130]
-#define CDD_ancestors_E &at[131]
-#define CDD_scoreparams &at[136]
-#define CDD_seqtree &at[138]
-
-#define CDD_SET &at[169]
-#define CDD_SET_E &at[170]
-
-#define CDD_TREE &at[171]
-#define CDD_TREE_name &at[172]
-#define CDD_TREE_id &at[173]
-#define CDD_TREE_description &at[174]
-#define CDD_TREE_parent &at[175]
-#define CDD_TREE_children &at[176]
-#define CDD_TREE_siblings &at[177]
-#define CDD_TREE_neighbors &at[178]
-
-#define CDD_TREE_SET &at[179]
-#define CDD_TREE_SET_E &at[180]
-
-#define CDD_PREF_NODES &at[181]
-#define CDD_PREF_NODES_preferred_nodes &at[182]
-#define CDD_PREF_NODES_model_organisms &at[190]
-#define CDD_PREF_NODES_optional_nodes &at[191]
-#define CDD_PREF_NODES_description &at[192]
-
-#define CDD_PROJECT &at[198]
-#define CDD_PROJECT_cds &at[199]
-#define CDD_PROJECT_cds_E &at[200]
-#define CDD_PROJECT_cdcolor &at[201]
-#define CDD_PROJECT_cdcolor_E &at[202]
-#define CDD_PROJECT_viewers &at[203]
-#define CDD_PROJECT_viewers_E &at[204]
-#define CDD_PROJECT_log &at[215]
-#define CDD_PROJECT_scripts &at[216]
-#define CDD_PROJECT_scripts_E &at[217]
-
-#define CDD_ORG_REF &at[185]
-#define CDD_ORG_REF_reference &at[186]
-#define CDD_ORG_REF_active &at[187]
-#define CDD_ORG_REF_parent_tax_id &at[188]
-#define CDD_ORG_REF_rank &at[189]
-
-#define CDD_ORG_REF_SET &at[183]
-#define CDD_ORG_REF_SET_E &at[184]
-
-#define CDD_PREF_NODE_DESCR &at[195]
-#define CDD_PREF_NODE_DESCR_create_date &at[196]
-#define CDD_PREF_NODE_DESCR_description &at[197]
-
-#define CDD_PREF_NODE_DESCR_SET &at[193]
-#define CDD_PREF_NODE_DESCR_SET_E &at[194]
+#define CDD_seqannot &at[57]
+#define CDD_seqannot_E &at[58]
+#define CDD_features &at[60]
+#define CDD_sequences &at[62]
+#define CDD_profile_range &at[64]
+#define CDD_trunc_master &at[66]
+#define CDD_posfreq &at[68]
+#define CDD_scoremat &at[77]
+#define CDD_distance &at[78]
+#define CDD_parent &at[85]
+#define CDD_children &at[86]
+#define CDD_siblings &at[87]
+#define CDD_neighbors &at[88]
+#define CDD_pending &at[89]
+#define CDD_pending_E &at[90]
+#define CDD_rejects &at[102]
+#define CDD_rejects_E &at[103]
+#define CDD_master3d &at[110]
+#define CDD_master3d_E &at[111]
+#define CDD_alignannot &at[112]
+#define CDD_style_dictionary &at[128]
+#define CDD_user_annotations &at[130]
+#define CDD_ancestors &at[132]
+#define CDD_ancestors_E &at[133]
+#define CDD_scoreparams &at[138]
+#define CDD_seqtree &at[140]
+
+#define CDD_SET &at[173]
+#define CDD_SET_E &at[174]
+
+#define CDD_TREE &at[175]
+#define CDD_TREE_name &at[176]
+#define CDD_TREE_id &at[177]
+#define CDD_TREE_description &at[178]
+#define CDD_TREE_parent &at[179]
+#define CDD_TREE_children &at[180]
+#define CDD_TREE_siblings &at[181]
+#define CDD_TREE_neighbors &at[182]
+
+#define CDD_TREE_SET &at[183]
+#define CDD_TREE_SET_E &at[184]
+
+#define CDD_PREF_NODES &at[185]
+#define CDD_PREF_NODES_preferred_nodes &at[186]
+#define CDD_PREF_NODES_model_organisms &at[194]
+#define CDD_PREF_NODES_optional_nodes &at[195]
+#define CDD_PREF_NODES_description &at[196]
+
+#define CDD_PROJECT &at[202]
+#define CDD_PROJECT_cds &at[203]
+#define CDD_PROJECT_cds_E &at[204]
+#define CDD_PROJECT_cdcolor &at[205]
+#define CDD_PROJECT_cdcolor_E &at[206]
+#define CDD_PROJECT_viewers &at[207]
+#define CDD_PROJECT_viewers_E &at[208]
+#define CDD_PROJECT_log &at[219]
+#define CDD_PROJECT_scripts &at[220]
+#define CDD_PROJECT_scripts_E &at[221]
+
+#define CDD_ORG_REF &at[189]
+#define CDD_ORG_REF_reference &at[190]
+#define CDD_ORG_REF_active &at[191]
+#define CDD_ORG_REF_parent_tax_id &at[192]
+#define CDD_ORG_REF_rank &at[193]
+
+#define CDD_ORG_REF_SET &at[187]
+#define CDD_ORG_REF_SET_E &at[188]
+
+#define CDD_PREF_NODE_DESCR &at[199]
+#define CDD_PREF_NODE_DESCR_create_date &at[200]
+#define CDD_PREF_NODE_DESCR_description &at[201]
+
+#define CDD_PREF_NODE_DESCR_SET &at[197]
+#define CDD_PREF_NODE_DESCR_SET_E &at[198]
 
 #define GLOBAL_ID &at[4]
 #define GLOBAL_ID_accession &at[5]
@@ -461,110 +472,114 @@ static AsnModulePtr amp = ampx;
 #define CDD_DESCR_curation_status &at[44]
 #define CDD_DESCR_readonly_status &at[45]
 #define CDD_DESCR_book_ref &at[46]
+#define CDD_DESCR_attribution &at[55]
 
 #define CDD_DESCR_SET &at[19]
 #define CDD_DESCR_SET_E &at[20]
 
-#define MATRIX &at[68]
-#define MATRIX_ncolumns &at[69]
-#define MATRIX_nrows &at[70]
-#define MATRIX_row_labels &at[71]
-#define MATRIX_row_labels_E &at[72]
-#define MATRIX_scale_factor &at[73]
-#define MATRIX_columns &at[74]
-#define MATRIX_columns_E &at[75]
-
-#define TRIANGLE &at[78]
-#define TRIANGLE_nelements &at[79]
-#define TRIANGLE_scores &at[80]
-#define TRIANGLE_div_ranks &at[82]
-#define TRIANGLE_div_ranks_E &at[83]
-
-#define UPDATE_COMMENT &at[93]
-#define UPDATE_COMMENT_comment &at[94]
-#define UPDATE_COMMENT_addthis &at[95]
-#define UPDATE_COMMENT_replaces &at[96]
-#define UPDATE_COMMENT_reject_loc &at[97]
-#define UPDATE_COMMENT_reference &at[98]
-
-#define UPDATE_ALIGN &at[90]
-#define UPDATE_ALIGN_description &at[91]
-#define UPDATE_ALIGN_description_E &at[92]
-#define UPDATE_ALIGN_seqannot &at[99]
-#define UPDATE_ALIGN_type &at[100]
-
-#define REJECT_ID &at[103]
-#define REJECT_ID_description &at[104]
-#define REJECT_ID_description_E &at[105]
-#define REJECT_ID_ids &at[106]
-#define REJECT_ID_ids_E &at[107]
-
-#define FEATURE_EVIDENCE &at[119]
-#define FEATURE_EVIDENCE_comment &at[120]
-#define FEATURE_EVIDENCE_reference &at[121]
-#define FEATURE_EVIDENCE_bsannot &at[122]
-#define FEATURE_EVIDENCE_seqfeat &at[123]
-#define FEATURE_EVIDENCE_book_ref &at[125]
-
-#define ALIGN_ANNOT &at[114]
-#define ALIGN_ANNOT_location &at[115]
-#define ALIGN_ANNOT_description &at[116]
-#define ALIGN_ANNOT_evidence &at[117]
-#define ALIGN_ANNOT_evidence_E &at[118]
-
-#define ALIGN_ANNOT_SET &at[112]
-#define ALIGN_ANNOT_SET_E &at[113]
-
-#define DOMAIN_PARENT &at[132]
-#define DOMAIN_PARENT_parent_type &at[133]
-#define DOMAIN_PARENT_parentid &at[134]
-#define DOMAIN_PARENT_seqannot &at[135]
-
-#define SEQUENCE_TREE &at[139]
-#define SEQUENCE_TREE_cdAccession &at[140]
-#define SEQUENCE_TREE_algorithm &at[141]
-#define SEQUENCE_TREE_isAnnotated &at[151]
-#define SEQUENCE_TREE_root &at[153]
-
-#define ALGORITHM_TYPE &at[142]
-#define ALGORITHM_TYPE_scoring_Scheme &at[143]
-#define ALGORITHM_TYPE_clustering_Method &at[144]
-#define ALGORITHM_TYPE_score_Matrix &at[145]
-#define ALGORITHM_TYPE_gapOpen &at[146]
-#define ALGORITHM_TYPE_gapExtend &at[147]
-#define ALGORITHM_TYPE_gapScaleFactor &at[148]
-#define ALGORITHM_TYPE_nTerminalExt &at[149]
-#define ALGORITHM_TYPE_cTerminalExt &at[150]
-
-#define SEQTREE_NODE &at[154]
-#define SEQTREE_NODE_isAnnotated &at[155]
-#define SEQTREE_NODE_name &at[156]
-#define SEQTREE_NODE_distance &at[157]
-#define SEQTREE_NODE_children &at[159]
-#define SEQTREE_NODE_children_children &at[160]
-#define SEQTREE_NODE_children_children_E &at[161]
-#define SEQTREE_NODE_children_footprint &at[162]
-#define SEQTREE_NODE_children_footprint_seqRange &at[163]
-#define SEQTREE_NODE_children_footprint_rowId &at[164]
-#define SEQTREE_NODE_annotation &at[165]
-
-#define NODE_ANNOTATION &at[166]
-#define NODE_ANNOTATION_presentInChildCD &at[167]
-#define NODE_ANNOTATION_note &at[168]
-
-#define CDD_VIEWER_RECT &at[208]
-#define CDD_VIEWER_RECT_top &at[209]
-#define CDD_VIEWER_RECT_left &at[210]
-#define CDD_VIEWER_RECT_width &at[211]
-#define CDD_VIEWER_RECT_height &at[212]
-
-#define CDD_VIEWER &at[205]
-#define CDD_VIEWER_ctrl &at[206]
-#define CDD_VIEWER_rect &at[207]
-#define CDD_VIEWER_accessions &at[213]
-#define CDD_VIEWER_accessions_E &at[214]
-
-#define CDD_SCRIPT &at[218]
-#define CDD_SCRIPT_type &at[219]
-#define CDD_SCRIPT_name &at[220]
-#define CDD_SCRIPT_commands &at[221]
+#define MATRIX &at[69]
+#define MATRIX_ncolumns &at[70]
+#define MATRIX_nrows &at[71]
+#define MATRIX_row_labels &at[72]
+#define MATRIX_row_labels_E &at[73]
+#define MATRIX_scale_factor &at[74]
+#define MATRIX_columns &at[75]
+#define MATRIX_columns_E &at[76]
+
+#define TRIANGLE &at[79]
+#define TRIANGLE_nelements &at[80]
+#define TRIANGLE_scores &at[81]
+#define TRIANGLE_div_ranks &at[83]
+#define TRIANGLE_div_ranks_E &at[84]
+
+#define UPDATE_COMMENT &at[94]
+#define UPDATE_COMMENT_comment &at[95]
+#define UPDATE_COMMENT_addthis &at[96]
+#define UPDATE_COMMENT_replaces &at[97]
+#define UPDATE_COMMENT_reject_loc &at[98]
+#define UPDATE_COMMENT_reference &at[99]
+
+#define UPDATE_ALIGN &at[91]
+#define UPDATE_ALIGN_description &at[92]
+#define UPDATE_ALIGN_description_E &at[93]
+#define UPDATE_ALIGN_seqannot &at[100]
+#define UPDATE_ALIGN_type &at[101]
+
+#define REJECT_ID &at[104]
+#define REJECT_ID_description &at[105]
+#define REJECT_ID_description_E &at[106]
+#define REJECT_ID_ids &at[107]
+#define REJECT_ID_ids_E &at[108]
+
+#define FEATURE_EVIDENCE &at[120]
+#define FEATURE_EVIDENCE_comment &at[121]
+#define FEATURE_EVIDENCE_reference &at[122]
+#define FEATURE_EVIDENCE_bsannot &at[123]
+#define FEATURE_EVIDENCE_seqfeat &at[124]
+#define FEATURE_EVIDENCE_book_ref &at[126]
+
+#define ALIGN_ANNOT &at[115]
+#define ALIGN_ANNOT_location &at[116]
+#define ALIGN_ANNOT_description &at[117]
+#define ALIGN_ANNOT_evidence &at[118]
+#define ALIGN_ANNOT_evidence_E &at[119]
+#define ALIGN_ANNOT_type &at[127]
+
+#define ALIGN_ANNOT_SET &at[113]
+#define ALIGN_ANNOT_SET_E &at[114]
+
+#define DOMAIN_PARENT &at[134]
+#define DOMAIN_PARENT_parent_type &at[135]
+#define DOMAIN_PARENT_parentid &at[136]
+#define DOMAIN_PARENT_seqannot &at[137]
+
+#define SEQUENCE_TREE &at[141]
+#define SEQUENCE_TREE_cdAccession &at[142]
+#define SEQUENCE_TREE_algorithm &at[143]
+#define SEQUENCE_TREE_isAnnotated &at[155]
+#define SEQUENCE_TREE_root &at[157]
+
+#define ALGORITHM_TYPE &at[144]
+#define ALGORITHM_TYPE_scoring_Scheme &at[145]
+#define ALGORITHM_TYPE_clustering_Method &at[146]
+#define ALGORITHM_TYPE_score_Matrix &at[147]
+#define ALGORITHM_TYPE_gapOpen &at[148]
+#define ALGORITHM_TYPE_gapExtend &at[149]
+#define ALGORITHM_TYPE_gapScaleFactor &at[150]
+#define ALGORITHM_TYPE_nTerminalExt &at[151]
+#define ALGORITHM_TYPE_cTerminalExt &at[152]
+#define ALGORITHM_TYPE_tree_scope &at[153]
+#define ALGORITHM_TYPE_coloring_scope &at[154]
+
+#define SEQTREE_NODE &at[158]
+#define SEQTREE_NODE_isAnnotated &at[159]
+#define SEQTREE_NODE_name &at[160]
+#define SEQTREE_NODE_distance &at[161]
+#define SEQTREE_NODE_children &at[163]
+#define SEQTREE_NODE_children_children &at[164]
+#define SEQTREE_NODE_children_children_E &at[165]
+#define SEQTREE_NODE_children_footprint &at[166]
+#define SEQTREE_NODE_children_footprint_seqRange &at[167]
+#define SEQTREE_NODE_children_footprint_rowId &at[168]
+#define SEQTREE_NODE_annotation &at[169]
+
+#define NODE_ANNOTATION &at[170]
+#define NODE_ANNOTATION_presentInChildCD &at[171]
+#define NODE_ANNOTATION_note &at[172]
+
+#define CDD_VIEWER_RECT &at[212]
+#define CDD_VIEWER_RECT_top &at[213]
+#define CDD_VIEWER_RECT_left &at[214]
+#define CDD_VIEWER_RECT_width &at[215]
+#define CDD_VIEWER_RECT_height &at[216]
+
+#define CDD_VIEWER &at[209]
+#define CDD_VIEWER_ctrl &at[210]
+#define CDD_VIEWER_rect &at[211]
+#define CDD_VIEWER_accessions &at[217]
+#define CDD_VIEWER_accessions_E &at[218]
+
+#define CDD_SCRIPT &at[222]
+#define CDD_SCRIPT_type &at[223]
+#define CDD_SCRIPT_name &at[224]
+#define CDD_SCRIPT_commands &at[225]
diff --git a/biostruc/cdd/objcdd.c b/biostruc/cdd/objcdd.c
index 6ff74c35..9ecce10a 100644
--- a/biostruc/cdd/objcdd.c
+++ b/biostruc/cdd/objcdd.c
@@ -36,7 +36,7 @@ objcddAsnLoad(void)
 
 /**************************************************
 *    Generated object loaders for Module NCBI-Cdd
-*    Generated using ASNCODE Revision: 6.16 at Feb 8, 2006  1:12 PM
+*    Generated using ASNCODE Revision: 6.16 at Aug 27, 2007  9:39 AM
 *
 **************************************************/
 
@@ -242,6 +242,7 @@ NLM_EXTERN
 CddIdSetPtr LIBCALL
 CddIdSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean isError = FALSE;
    AsnReadFunc func;
@@ -297,6 +298,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 CddIdSetAsnWrite(CddIdSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -788,6 +790,7 @@ NLM_EXTERN
 CddSetPtr LIBCALL
 CddSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean isError = FALSE;
    AsnReadFunc func;
@@ -843,6 +846,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 CddSetAsnWrite(CddSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -1133,6 +1137,7 @@ NLM_EXTERN
 CddTreeSetPtr LIBCALL
 CddTreeSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean isError = FALSE;
    AsnReadFunc func;
@@ -1188,6 +1193,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 CddTreeSetAsnWrite(CddTreeSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -1356,6 +1362,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 CddPrefNodesAsnWrite(CddPrefNodesPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -1817,6 +1824,7 @@ NLM_EXTERN
 CddOrgRefSetPtr LIBCALL
 CddOrgRefSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean isError = FALSE;
    AsnReadFunc func;
@@ -1872,6 +1880,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 CddOrgRefSetAsnWrite(CddOrgRefSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -2106,6 +2115,7 @@ NLM_EXTERN
 CddPrefNodeDescrSetPtr LIBCALL
 CddPrefNodeDescrSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean isError = FALSE;
    AsnReadFunc func;
@@ -2161,6 +2171,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 CddPrefNodeDescrSetAsnWrite(CddPrefNodeDescrSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -2818,6 +2829,9 @@ CddDescrFree(ValNodePtr anp)
    case CddDescr_book_ref:
       CddBookRefFree(anp -> data.ptrvalue);
       break;
+   case CddDescr_attribution:
+      PubFree(anp -> data.ptrvalue);
+      break;
    }
    return MemFree(anp);
 }
@@ -2963,6 +2977,10 @@ CddDescrAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       choice = CddDescr_book_ref;
       func = (AsnReadFunc) CddBookRefAsnRead;
    }
+   else if (atp == CDD_DESCR_attribution) {
+      choice = CddDescr_attribution;
+      func = (AsnReadFunc) PubAsnRead;
+   }
    anp->choice = choice;
    if (func != NULL)
    {
@@ -3086,6 +3104,10 @@ CddDescrAsnWrite(CddDescrPtr anp, AsnIoPtr aip, AsnTypePtr orig)
       writetype = CDD_DESCR_book_ref;
       func = (AsnWriteFunc) CddBookRefAsnWrite;
       break;
+   case CddDescr_attribution:
+      writetype = CDD_DESCR_attribution;
+      func = (AsnWriteFunc) PubAsnWrite;
+      break;
    }
    if (writetype != NULL) {
       retval = (* func)(pnt, aip, writetype);   /* write it out */
@@ -3128,6 +3150,7 @@ NLM_EXTERN
 CddDescrSetPtr LIBCALL
 CddDescrSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean isError = FALSE;
    AsnReadFunc func;
@@ -3183,6 +3206,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 CddDescrSetAsnWrite(CddDescrSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -4081,6 +4105,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 RejectIdAsnWrite(RejectIdPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -4433,6 +4458,13 @@ AlignAnnotAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       }
       atp = AsnReadId(aip,amp, atp);
    }
+   if (atp == ALIGN_ANNOT_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
 
    if (AsnReadVal(aip, atp, &av) <= 0) {
       goto erret;
@@ -4494,6 +4526,8 @@ AlignAnnotAsnWrite(AlignAnnotPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
       retval = AsnWrite(aip, ALIGN_ANNOT_description,  &av);
    }
    AsnGenericChoiceSeqOfAsnWrite(ptr -> evidence, (AsnWriteFunc) FeatureEvidenceAsnWrite, aip, ALIGN_ANNOT_evidence, ALIGN_ANNOT_evidence_E);
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, ALIGN_ANNOT_type,  &av);
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
@@ -4533,6 +4567,7 @@ NLM_EXTERN
 AlignAnnotSetPtr LIBCALL
 AlignAnnotSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean isError = FALSE;
    AsnReadFunc func;
@@ -4588,6 +4623,7 @@ erret:
 NLM_EXTERN Boolean LIBCALL 
 AlignAnnotSetAsnWrite(AlignAnnotSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
 {
+   DataVal av;
    AsnTypePtr atp;
    Boolean retval = FALSE;
 
@@ -5123,6 +5159,20 @@ AlgorithmTypeAsnRead(AsnIoPtr aip, AsnTypePtr orig)
       ptr -> cTerminalExt = av.intvalue;
       atp = AsnReadId(aip,amp, atp);
    }
+   if (atp == ALGORITHM_TYPE_tree_scope) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> tree_scope = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ALGORITHM_TYPE_coloring_scope) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> coloring_scope = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
 
    if (AsnReadVal(aip, atp, &av) <= 0) {
       goto erret;
@@ -5190,6 +5240,10 @@ AlgorithmTypeAsnWrite(AlgorithmTypePtr ptr, AsnIoPtr aip, AsnTypePtr orig)
    retval = AsnWrite(aip, ALGORITHM_TYPE_nTerminalExt,  &av);
    av.intvalue = ptr -> cTerminalExt;
    retval = AsnWrite(aip, ALGORITHM_TYPE_cTerminalExt,  &av);
+   av.intvalue = ptr -> tree_scope;
+   retval = AsnWrite(aip, ALGORITHM_TYPE_tree_scope,  &av);
+   av.intvalue = ptr -> coloring_scope;
+   retval = AsnWrite(aip, ALGORITHM_TYPE_coloring_scope,  &av);
    if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
       goto erret;
    }
diff --git a/biostruc/cdd/objcdd.h b/biostruc/cdd/objcdd.h
index 3eaf9067..f604e296 100644
--- a/biostruc/cdd/objcdd.h
+++ b/biostruc/cdd/objcdd.h
@@ -20,7 +20,7 @@ extern "C" { /* } */
 /**************************************************
 *
 *    Generated objects for Module NCBI-Cdd
-*    Generated using ASNCODE Revision: 6.16 at Feb 8, 2006  1:12 PM
+*    Generated using ASNCODE Revision: 6.16 at Aug 27, 2007  9:39 AM
 *
 **************************************************/
 
@@ -364,6 +364,7 @@ typedef ValNode CddDescr;
 #define CddDescr_curation_status 14
 #define CddDescr_readonly_status 15
 #define CddDescr_book_ref 16
+#define CddDescr_attribution 17
 
 
 NLM_EXTERN CddDescrPtr LIBCALL CddDescrFree PROTO ((CddDescrPtr ));
@@ -507,6 +508,7 @@ typedef struct struct_Align_annot {
    ValNodePtr   location;
    CharPtr   description;
    ValNodePtr   evidence;
+   Int4   type;
 } AlignAnnot, PNTR AlignAnnotPtr;
 
 
@@ -591,6 +593,8 @@ typedef struct struct_Algorithm_type {
    Int4   gapScaleFactor;
    Int4   nTerminalExt;
    Int4   cTerminalExt;
+   Int4   tree_scope;
+   Int4   coloring_scope;
 } AlgorithmType, PNTR AlgorithmTypePtr;
 
 
diff --git a/build.me b/build.me
index 18f10cd5..47fb2af1 100755
--- a/build.me
+++ b/build.me
@@ -1,13 +1,13 @@
 #!/bin/sh
 #
-# $Id: build.me,v 1.9 2004/04/08 17:53:25 lavr Exp $
+# $Id: build.me,v 1.10 2008/01/25 19:57:15 ucko Exp $
 #
 # W A R N I N G ! ! !
 # That script is intended for internal use in NCBI only
 #
 #
 
-#check that we're running withing NCBI
+#check that we're running within NCBI
 MYDOMAIN=`grep '^domain' /etc/resolv.conf |awk '{print $2}'`
 test -z "$MYDOMAIN"  &&  MYDOMAIN="`hostname --fqdn 2>/dev/null`"
 test -z "$MYDOMAIN"  &&  MYDOMAIN="`domainname`"
@@ -16,7 +16,7 @@ if [ `echo "$MYDOMAIN" | grep -c 'nlm[.]nih[.]gov$'` != 1 ] ; then
     exit 1
 fi
 
-SCRIPTDIR=/am/ncbiapdata/scripts
+SCRIPTDIR=/am/ncbiapdata/scripts/build
 CWD=`pwd`
 UPDIR=`dirname $CWD`
 MYDIR=`basename $CWD`
diff --git a/build.me64 b/build.me64
index f4bb17ed..d62dfc65 100755
--- a/build.me64
+++ b/build.me64
@@ -1,6 +1,6 @@
 #!/bin/sh
 #
-# $Id: build.me64,v 6.2 2002/03/01 18:04:07 beloslyu Exp $
+# $Id: build.me64,v 6.3 2008/01/25 19:59:38 ucko Exp $
 #
 # W A R N I N G ! ! !
 # That script is intended for internal use in NCBI only
@@ -10,19 +10,23 @@ NCBI=/netopt/ncbi_tools/ncbi64
 PATH=/usr/bin:/bin:/sbin:/usr/sbin:/usr/ccs/bin:$NCBI/bin:$PATH
 export PATH NCBI
 
-#check that we're running withing NCBI
+#check that we're running within NCBI
 MYDOMAIN=`grep '^domain' /etc/resolv.conf |awk '{print $2}'`
-if [ "$MYDOMAIN" != "nlm.nih.gov" ] ; then
-	echo That script is intended for internal use in NCBI only
-	exit 1
+test -z "$MYDOMAIN"  &&  MYDOMAIN="`hostname --fqdn 2>/dev/null`"
+test -z "$MYDOMAIN"  &&  MYDOMAIN="`domainname`"
+if [ `echo "$MYDOMAIN" | grep -c 'nlm[.]nih[.]gov$'` != 1 ] ; then
+    echo That script is intended for internal use in NCBI only
+    exit 1
 fi
 
+SCRIPTDIR=/am/ncbiapdata/scripts/build
+
 echo "Building ASNs"
 ( cd asn; rm -f asn.all asnpub.all ; chmod +x *.unx; sh all.unx; sh allpub.unx)
 
 if [ ! -d "asnstat" ] ; then
 	mkdir asnstat; ( cd asnstat; sh ../asn/makestat.unx )
-	test -f /am/ncbiapdata/scripts/rebuild_asn && /am/ncbiapdata/scripts/rebuild_asn .
+	test -f $SCRIPTDIR/rebuild_asn && $SCRIPTDIR/rebuild_asn .
 fi
 
 rm -f data/*.val
@@ -50,7 +54,7 @@ fi
 
 echo "building the NCBI C toolkit on Solaris/Sparc in 64-bit mode"
 cd build
-dmake -j 3 -f /am/ncbiapdata/scripts/make.master LCL_TARGET=sol TARGET_INCLUDE=include \
+dmake -j 3 -f $SCRIPTDIR/make.master LCL_TARGET=sol TARGET_INCLUDE=include \
 	DBUGEXTRA=-KPIC DBUGEXTRA2=-g COPYBIN=bin CLLIB=cllib all
 
 exit 0
diff --git a/checkout.date b/checkout.date
index 33c5c5f2..7bb946e7 100644
--- a/checkout.date
+++ b/checkout.date
@@ -1 +1 @@
-Sun Aug 26 12:02:00 EDT 2007
+Sun Mar 2 10:12:54 EST 2008
diff --git a/connect/ncbi_config.h b/connect/ncbi_config.h
index c1032790..6ae394ab 100644
--- a/connect/ncbi_config.h
+++ b/connect/ncbi_config.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_CONFIG__H
 #define CONNECT___NCBI_CONFIG__H
 
-/*  $Id: ncbi_config.h,v 6.13 2006/03/07 17:23:22 lavr Exp $
+/*  $Id: ncbi_config.h,v 6.14 2007/10/12 14:18:31 ucko Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -59,13 +59,13 @@
 #      define HAVE_GETHOSTBYNAME_R 6
 #      define HAVE_GETHOSTBYADDR_R 8
 #    endif
-#    if !defined(HAVE_GETPWUID_R)
-#      define HAVE_GETPWUID_R      5
+#    if !defined(NCBI_HAVE_GETPWUID_R)
+#      define NCBI_HAVE_GETPWUID_R 5
 #    endif
 #  elif defined(OS_UNIX_IRIX)
 #    define NCBI_OS_IRIX 1
-#    if !defined(HAVE_GETPWUID_R)
-#      define HAVE_GETPWUID_R      5
+#    if !defined(NCBI_HAVE_GETPWUID_R)
+#      define NCBI_HAVE_GETPWUID_R 5
 #    endif
 #  elif defined(OS_UNIX_SOL)
 #    define NCBI_OS_SOLARIS 1
diff --git a/connect/ncbi_connection.c b/connect/ncbi_connection.c
index 3fced047..f133a6ad 100644
--- a/connect/ncbi_connection.c
+++ b/connect/ncbi_connection.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_connection.c,v 6.48 2006/02/23 17:43:01 lavr Exp $
+/*  $Id: ncbi_connection.c,v 6.49 2007/10/17 15:25:43 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -42,35 +42,39 @@
  *  INTERNAL
  ***********************************************************************/
 
+#define NCBI_USE_ERRCODE_X   Connect_Connection
+
 
 /* Standard logging message
  */
-#define CONN_LOG_EX(level, descr, status)                  \
-  CORE_LOGF(level,                                         \
+#define CONN_LOG_EX(subcode, level, descr, status)         \
+  CORE_LOGF_X(subcode, level,                                \
             ("%s (connector \"%s\", error \"%s\")", descr, \
              conn->meta.get_type                           \
              ? conn->meta.get_type(conn->meta.c_get_type)  \
              : "Unknown", IO_StatusStr(status)))
 
-#define CONN_LOG(level, descr)  CONN_LOG_EX(level, descr, status)
+#define CONN_LOG(subcode, level, descr)   \
+    CONN_LOG_EX(subcode, level, descr, status)
+
 #ifdef _DEBUG
-#  define CONN_TRACE(descr)  CONN_LOG(eLOG_Trace, descr)
+#  define CONN_TRACE(descr)  CONN_LOG(0, eLOG_Trace, descr)
 #else
 #  define CONN_TRACE(descr)  ((void) 0)
 #endif /*_DEBUG*/
 
 /* Standard macros to verify that the passed connection handle is not NULL
  */
-#define CONN_NOT_NULL_EX(func_name, status)                     \
+#define CONN_NOT_NULL_EX(subcode, func_name, status)            \
   if ( !conn ) {                                                \
-      CORE_LOG(eLOG_Error, "CONN_" #func_name                   \
+      CORE_LOG_X(subcode, eLOG_Error, "CONN_" #func_name          \
                "(conn, ...) -- passed NULL connection handle"); \
       assert(conn);                                             \
       return status;                                            \
   }
 
-#define CONN_NOT_NULL(func_name)              \
-  CONN_NOT_NULL_EX(func_name, eIO_InvalidArg)
+#define CONN_NOT_NULL(subcode, func_name)   \
+  CONN_NOT_NULL_EX(subcode, func_name, eIO_InvalidArg)
 
 
 /* Connection state
@@ -82,10 +86,11 @@ typedef enum ECONN_StateTag {
 } ECONN_State;
 
 
-/* Connection internal data
+/* Connection internal data:  meta *must* come first
  */
 typedef struct SConnectionTag {
     SMetaConnector         meta;       /* VTable of operations and list      */
+
     BUF                    buf;        /* storage for the Peek'd data        */
 #ifdef IMPLEMENTED__CONN_WaitAsync
     SConnectorAsyncHandler async_data; /* info of curr. async event handler  */
@@ -143,13 +148,13 @@ extern EIO_Status CONN_ReInit
     CONNECTOR  x_conn = 0;
     EIO_Status status;
 
-    CONN_NOT_NULL(ReInit);
+    CONN_NOT_NULL(1, ReInit);
 
     /* check arg */
     if (!connector  &&  !conn->meta.list) {
         assert(conn->state == eCONN_Unusable);
         status = eIO_Unknown;
-        CONN_LOG(eLOG_Error,
+        CONN_LOG(2, eLOG_Error,
                  "[CONN_ReInit]  Cannot re-init empty connection with NULL");
         return status;
     }
@@ -177,7 +182,7 @@ extern EIO_Status CONN_ReInit
                                           ? conn->meta.default_timeout
                                           : conn->c_timeout);
                 if (status != eIO_Success) {
-                    CONN_LOG(connector ? eLOG_Error : eLOG_Warning,
+                    CONN_LOG(3, connector ? eLOG_Error : eLOG_Warning,
                              "[CONN_ReInit]  Cannot close current connection");
                     if (connector)
                         return status;
@@ -192,7 +197,7 @@ extern EIO_Status CONN_ReInit
                 if (!x_conn->next  &&  x_conn == conn->meta.list)
                     break;
                 status = eIO_Unknown;
-                CONN_LOG(eLOG_Error,
+                CONN_LOG(4, eLOG_Error,
                          "[CONN_ReInit]  Partial re-init not allowed");
                 return status;
             }
@@ -235,7 +240,7 @@ static EIO_Status s_Open
         : eIO_NotSupported;
 
     if (status != eIO_Success) {
-        CONN_LOG(eLOG_Error, "[CONN_Open]  Cannot open connection");
+        CONN_LOG(5, eLOG_Error, "[CONN_Open]  Cannot open connection");
         return status;
     }
 
@@ -247,7 +252,7 @@ static EIO_Status s_Open
 
 extern const char* CONN_GetType(CONN conn)
 {
-    CONN_NOT_NULL_EX(GetType, 0);
+    CONN_NOT_NULL_EX(6, GetType, 0);
 
     return conn->state == eCONN_Unusable  ||  !conn->meta.list  ||
         !conn->meta.get_type ? 0 : conn->meta.get_type(conn->meta.c_get_type);
@@ -256,7 +261,7 @@ extern const char* CONN_GetType(CONN conn)
 
 extern char* CONN_Description(CONN conn)
 {
-    CONN_NOT_NULL_EX(Description, 0);
+    CONN_NOT_NULL_EX(7, Description, 0);
 
     return conn->state == eCONN_Unusable  ||  !conn->meta.list  ||
         !conn->meta.descr ? 0 : conn->meta.descr(conn->meta.c_descr);
@@ -270,7 +275,7 @@ extern EIO_Status CONN_SetTimeout
 {
     EIO_Status status = eIO_Success;
 
-    CONN_NOT_NULL(SetTimeout);
+    CONN_NOT_NULL(8, SetTimeout);
 
     switch (event) {
     case eIO_Open:
@@ -314,7 +319,7 @@ extern EIO_Status CONN_SetTimeout
         break;
     default:
         status = eIO_InvalidArg;
-        CONN_LOG(eLOG_Error,
+        CONN_LOG(9, eLOG_Error,
                  "[CONN_SetTimeout]  Unknown event to set timeout for");
         assert(0);
         break;
@@ -328,13 +333,13 @@ extern const STimeout* CONN_GetTimeout
 (CONN      conn,
  EIO_Event event)
 {
-    CONN_NOT_NULL_EX(GetTimeout, 0);
+    CONN_NOT_NULL_EX(10, GetTimeout, 0);
 
     switch (event) {
     case eIO_Open:
         return conn->o_timeout;
     case eIO_ReadWrite:
-        CONN_LOG_EX(eLOG_Warning,
+        CONN_LOG_EX(11, eLOG_Warning,
                     "[CONN_GetTimeout]  ReadWrite timeout requested",
                     eIO_InvalidArg);
         /*FALLTHRU*/
@@ -345,7 +350,7 @@ extern const STimeout* CONN_GetTimeout
     case eIO_Close:
         return conn->c_timeout;
     default:
-        CONN_LOG_EX(eLOG_Error,
+        CONN_LOG_EX(12, eLOG_Error,
                     "[CONN_GetTimeout]  Unknown event to get timeout for",
                     eIO_InvalidArg);
         assert(0);
@@ -362,7 +367,7 @@ extern EIO_Status CONN_Wait
 {
     EIO_Status status;
 
-    CONN_NOT_NULL(Wait);
+    CONN_NOT_NULL(13, Wait);
 
     if (conn->state == eCONN_Unusable               ||
         (event != eIO_Read  &&  event != eIO_Write) ||
@@ -385,9 +390,9 @@ extern EIO_Status CONN_Wait
 
     if (status != eIO_Success) {
         if (status != eIO_Timeout)
-            CONN_LOG(eLOG_Error, "[CONN_Wait]  Error waiting on I/O");
+            CONN_LOG(14, eLOG_Error, "[CONN_Wait]  Error waiting on I/O");
         else if (!timeout || timeout->sec || timeout->usec)
-            CONN_LOG(eLOG_Warning, "[CONN_Wait]  I/O timed out");
+            CONN_LOG(15, eLOG_Warning, "[CONN_Wait]  I/O timed out");
     }
 
     return status;
@@ -407,7 +412,7 @@ static EIO_Status s_CONN_Write
     /* check if the write method is specified at all */
     if ( !conn->meta.write ) {
         status = eIO_NotSupported;
-        CONN_LOG(eLOG_Error, "[CONN_Write]  Unable to write data");
+        CONN_LOG(16, eLOG_Error, "[CONN_Write]  Unable to write data");
         return status;
     }
 
@@ -421,7 +426,7 @@ static EIO_Status s_CONN_Write
             CONN_TRACE("[CONN_Write]  Write error");
             status = eIO_Success;
         } else if ( size )
-            CONN_LOG(eLOG_Error, "[CONN_Write]  Cannot write data");
+            CONN_LOG(17, eLOG_Error, "[CONN_Write]  Cannot write data");
     }
     return status;
 }
@@ -464,7 +469,7 @@ extern EIO_Status CONN_Write
     *n_written = 0;
     if (size  &&  !buf)
         return eIO_InvalidArg;
-    CONN_NOT_NULL(Write);
+    CONN_NOT_NULL(18, Write);
 
     if (conn->state == eCONN_Unusable)
         return eIO_InvalidArg;
@@ -491,7 +496,7 @@ extern EIO_Status CONN_PushBack
  const void* buf,
  size_t      size)
 {
-    CONN_NOT_NULL(PushBack);
+    CONN_NOT_NULL(19, PushBack);
 
     if (conn->state != eCONN_Open)
         return eIO_InvalidArg;
@@ -505,7 +510,7 @@ extern EIO_Status CONN_Flush
 {
     EIO_Status status;
 
-    CONN_NOT_NULL(Flush);
+    CONN_NOT_NULL(20, Flush);
 
     if (conn->state == eCONN_Unusable)
         return eIO_InvalidArg;
@@ -522,7 +527,7 @@ extern EIO_Status CONN_Flush
                               conn->w_timeout == kDefaultTimeout ?
                               conn->meta.default_timeout : conn->w_timeout);
     if (status != eIO_Success)
-        CONN_LOG(eLOG_Warning, "[CONN_Flush]  Cannot flush data");
+        CONN_LOG(21, eLOG_Warning, "[CONN_Flush]  Cannot flush data");
     return status;
 }
 
@@ -543,7 +548,7 @@ static EIO_Status s_CONN_Read
     /* check if the read method is specified at all */
     if ( !conn->meta.read ) {
         status = eIO_NotSupported;
-        CONN_LOG(eLOG_Error, "[CONN_Read]  Unable to read data");
+        CONN_LOG(22, eLOG_Error, "[CONN_Read]  Unable to read data");
         return status;
     }
 
@@ -573,7 +578,7 @@ static EIO_Status s_CONN_Read
             CONN_TRACE("[CONN_Read]  Read error");
             status = eIO_Success;
         } else if (size  &&  status != eIO_Closed) {
-            CONN_LOG(status == eIO_Timeout ? eLOG_Warning : eLOG_Error,
+            CONN_LOG(23, status == eIO_Timeout ? eLOG_Warning : eLOG_Error,
                      "[CONN_Read]  Cannot read data");
         }
     }
@@ -627,7 +632,7 @@ extern EIO_Status CONN_Read
     if (size  &&  !buf)
         return eIO_InvalidArg;
 
-    CONN_NOT_NULL(Read);
+    CONN_NOT_NULL(24, Read);
 
     if (conn->state == eCONN_Unusable)
         return eIO_InvalidArg;
@@ -676,7 +681,7 @@ extern EIO_Status CONN_ReadLine
     if (size  &&  !line)
         return eIO_InvalidArg;
 
-    CONN_NOT_NULL(ReadLine);
+    CONN_NOT_NULL(25, ReadLine);
 
     /* perform open, if not opened yet */
     if (conn->state != eCONN_Open)
@@ -728,7 +733,7 @@ extern EIO_Status CONN_ReadLine
 
 extern EIO_Status CONN_Status(CONN conn, EIO_Event dir)
 {
-    CONN_NOT_NULL(Status);
+    CONN_NOT_NULL(26, Status);
 
     if (conn->state == eCONN_Unusable  ||  !conn->meta.list)
         return eIO_Unknown;
@@ -751,7 +756,7 @@ extern EIO_Status CONN_Close(CONN conn)
     FConnCallback func = 0;
     void*         data = 0;
 
-    CONN_NOT_NULL(Close);
+    CONN_NOT_NULL(27, Close);
 
     if (conn->state != eCONN_Unusable) {
         func = conn->cbs[eCONN_OnClose].func;
@@ -782,7 +787,7 @@ extern EIO_Status CONN_SetCallback
     if (i >= CONN_N_CALLBACKS)
         return eIO_InvalidArg;
 
-    CONN_NOT_NULL(SetCallback);
+    CONN_NOT_NULL(28, SetCallback);
 
     if ( old_cb )
         *old_cb = conn->cbs[i];
@@ -819,7 +824,7 @@ extern EIO_Status CONN_WaitAsync
     CONNECTOR  x_connector = conn->connector;
     SConnectorAsyncHandler* x_data = &conn->async_data;
 
-    CONN_NOT_NULL(WaitAsync);
+    CONN_NOT_NULL(29, WaitAsync);
 
     /* perform connect, if not connected yet */
     if (!conn->connected  &&  (status = s_Connect(conn)) != eIO_Success)
@@ -831,7 +836,7 @@ extern EIO_Status CONN_WaitAsync
         x_connector->vtable.wait_async(x_connector->handle, 0, 0) :
         eIO_NotSupported;
     if (status != eIO_Success) {
-        CONN_LOG(eLOG_Error, "[CONN_WaitAsync]  Cannot reset the handler");
+        CONN_LOG(30, eLOG_Error, "[CONN_WaitAsync]  Cannot reset the handler");
         return status;
     }
     if ( x_data->cleanup )
@@ -852,178 +857,8 @@ extern EIO_Status CONN_WaitAsync
     status = x_connector->vtable.wait_async(x_connector->handle,
                                             s_ConnectorAsyncHandler, x_data);
     if (status != eIO_Success) {
-        CONN_LOG(eLOG_Error, "[CONN_WaitAsync]  Cannot set new handler");
+        CONN_LOG(31, eLOG_Error, "[CONN_WaitAsync]  Cannot set new handler");
     }
     return status;
 }
 #endif /* IMPLEMENTED__CONN_WaitAsync */
-
-
-/*
- * --------------------------------------------------------------------------
- * $Log: ncbi_connection.c,v $
- * Revision 6.48  2006/02/23 17:43:01  lavr
- * CONN_Read():  No CLOSED trace on EOF
- *
- * Revision 6.47  2006/02/14 15:49:42  lavr
- * Introduce and use CORE_TRACE macros (NOP in Release mode)
- *
- * Revision 6.46  2006/01/18 03:38:17  lavr
- * Prevent copying STimeout structs into themselves [where can occur]
- *
- * Revision 6.45  2005/05/18 18:15:21  lavr
- * Formatting spot
- *
- * Revision 6.44  2004/11/15 19:33:42  lavr
- * Speed-up CONN_ReadLine()
- *
- * Revision 6.43  2004/11/15 17:39:26  lavr
- * Fix CONN_ReadLine() to always perform connector's read method
- *
- * Revision 6.42  2004/05/26 16:00:06  lavr
- * Minor status fixes in CONN_SetTimeout() and CONN_ReadLine()
- *
- * Revision 6.41  2004/05/24 20:19:19  lavr
- * Fix eIO_InvalidArg conditions (size and no buffer)
- *
- * Revision 6.40  2004/05/24 19:54:59  lavr
- * +CONN_ReadLine()
- *
- * Revision 6.39  2004/03/23 02:27:37  lavr
- * Code formatting
- *
- * Revision 6.38  2004/02/23 15:23:39  lavr
- * New (last) parameter "how" added in CONN_Write() API call
- *
- * Revision 6.37  2003/08/25 14:40:53  lavr
- * Employ new k..Timeout constants
- *
- * Revision 6.36  2003/05/31 05:18:26  lavr
- * Optimize on calling flush; do not require to have flush method
- *
- * Revision 6.35  2003/05/21 17:53:06  lavr
- * Better check for {0,0} timeout in CONN_Read()
- *
- * Revision 6.34  2003/05/20 21:21:45  lavr
- * CONN_Write(): log with different log levels on write errors
- *
- * Revision 6.33  2003/05/19 16:43:40  lavr
- * Bugfix in CONN_SetTimeout();  better close callback sequence
- *
- * Revision 6.32  2003/05/14 03:51:16  lavr
- * +CONN_Description()
- *
- * Revision 6.31  2003/05/12 18:33:21  lavr
- * Names of timeout variables uniformed
- *
- * Revision 6.30  2003/01/28 15:16:37  lavr
- * Fix "NULL" message not to contain double quotes in call names
- *
- * Revision 6.29  2003/01/17 19:44:46  lavr
- * Reduce dependencies
- *
- * Revision 6.28  2003/01/15 19:51:17  lavr
- * +CONN_PushBack()
- *
- * Revision 6.27  2002/09/19 19:43:46  lavr
- * Add more assert()'s and do not rely on CONN_Flush() to open in CONN_Read()
- *
- * Revision 6.26  2002/09/06 15:43:20  lavr
- * Bug fixes of late assignments in Read and Write; Flush changed to open
- * connection if not yet open; more error logging
- *
- * Revision 6.25  2002/08/07 16:32:32  lavr
- * Changed EIO_ReadMethod enums accordingly; log moved to end
- *
- * Revision 6.24  2002/04/26 16:30:26  lavr
- * Checks for kDefaultTimeout and use of default_timeout of meta-connector
- *
- * Revision 6.23  2002/04/24 21:18:04  lavr
- * Beautifying: move open check in front of buffer check in CONN_Wait()
- *
- * Revision 6.22  2002/04/22 19:30:01  lavr
- * Do not put trace message on polling wait (tmo={0,0})
- * More effective CONN_Read w/o repeatitive checkings for eIO_ReadPersist
- *
- * Revision 6.21  2002/03/22 22:17:01  lavr
- * Better check when formally timed out but technically polled in CONN_Wait()
- *
- * Revision 6.20  2002/02/05 22:04:12  lavr
- * Included header files rearranged
- *
- * Revision 6.19  2002/01/30 20:10:56  lavr
- * Remove *n_read = 0 assignment in s_CONN_Read; replace it with assert()
- *
- * Revision 6.18  2001/08/20 20:13:15  vakatov
- * CONN_ReInit() -- Check connection handle for NULL (it was missed in R6.17)
- *
- * Revision 6.17  2001/08/20 20:00:43  vakatov
- * CONN_SetTimeout() to return "EIO_Status".
- * CONN_***() -- Check connection handle for NULL.
- *
- * Revision 6.16  2001/07/10 15:08:35  lavr
- * Edit for style
- *
- * Revision 6.15  2001/06/29 21:06:46  lavr
- * BUGFIX: CONN_LOG now checks for non-NULL get_type virtual function
- *
- * Revision 6.14  2001/06/28 22:00:48  lavr
- * Added function: CONN_SetCallback
- * Added callback: eCONN_OnClose
- *
- * Revision 6.13  2001/06/07 17:54:36  lavr
- * Modified exit branch in s_CONN_Read()
- *
- * Revision 6.12  2001/05/30 19:42:44  vakatov
- * s_CONN_Read() -- do not issue warning if requested zero bytes
- * (by A.Lavrentiev)
- *
- * Revision 6.11  2001/04/24 21:29:04  lavr
- * kDefaultTimeout is used everywhere when timeout is not set explicitly
- *
- * Revision 6.10  2001/02/26 22:52:44  kans
- * Initialize x_read in s_CONN_Read
- *
- * Revision 6.9  2001/02/26 16:32:01  kans
- * Including string.h instead of cstring
- *
- * Revision 6.8  2001/02/25 21:41:50  kans
- * Include <cstring> on Mac to get memset
- *
- * Revision 6.7  2001/02/09 17:34:18  lavr
- * CONN_GetType added; severities of some messages changed
- *
- * Revision 6.6  2001/01/25 16:55:48  lavr
- * CONN_ReInit bugs fixed
- *
- * Revision 6.5  2001/01/23 23:10:53  lavr
- * Typo corrected in description of connection structure
- *
- * Revision 6.4  2001/01/12 23:51:38  lavr
- * Message logging modified for use LOG facility only
- *
- * Revision 6.3  2001/01/03 22:29:59  lavr
- * CONN_Status implemented
- *
- * Revision 6.2  2000/12/29 17:52:59  lavr
- * Adapted to use new connector structure; modified to have
- * an internal tri-state {Unusable | Open | Closed }.
- *
- * Revision 6.1  2000/03/24 22:53:34  vakatov
- * Initial revision
- *
- * Revision 6.4  1999/11/01 16:14:23  vakatov
- * s_CONN_Read() -- milder error levels when hitting EOF
- *
- * Revision 6.3  1999/04/05 15:32:53  vakatov
- * CONN_Wait():  be more mild and discrete about the posted error severity
- *
- * Revision 6.1  1999/04/01 21:48:09  vakatov
- * Fixed for the change in spec:  "n_written/n_read" args in
- * CONN_Write/Read to be non-NULL and "*n_written / *n_read" := 0
- *
- * Revision 6.0  1999/03/25 23:04:57  vakatov
- * Initial revision
- *
- * ==========================================================================
- */
diff --git a/connect/ncbi_connector.c b/connect/ncbi_connector.c
index 9a4f2f62..5b2eda52 100644
--- a/connect/ncbi_connector.c
+++ b/connect/ncbi_connector.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_connector.c,v 6.7 2002/08/13 19:29:49 lavr Exp $
+/* $Id: ncbi_connector.c,v 6.9 2007/10/17 15:25:43 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -35,10 +35,12 @@
 #include <connect/ncbi_connector.h>
 
 
+#define NCBI_USE_ERRCODE_X  Connect_MetaConn
+
 /* Standard logging message
  */
-#define METACONN_LOG(level, descr)                      \
-  CORE_LOGF(level,                                      \
+#define METACONN_LOG(subcode, level, descr)             \
+  CORE_LOGF_X(subcode, level,                             \
             ("%s (connector \"%s\", error \"%s\")",     \
             descr, (*meta->get_type)(meta->c_get_type), \
             IO_StatusStr(status)))
@@ -51,12 +53,13 @@ extern EIO_Status METACONN_Remove
     if (connector) {
         CONNECTOR x_conn;
         
-        for (x_conn = meta->list; x_conn; x_conn = x_conn->next)
+        for (x_conn = meta->list;  x_conn;  x_conn = x_conn->next) {
             if (x_conn == connector)
                 break;
+        }
         if (!x_conn) {
             EIO_Status status = eIO_Unknown;
-            METACONN_LOG(eLOG_Error,
+            METACONN_LOG(1, eLOG_Error,
                          "[METACONN_Remove]  Connector is not in connection");
             return status;
         }
@@ -84,9 +87,9 @@ extern EIO_Status METACONN_Add
 {
     assert(connector && meta);
 
-    if (connector->next || !connector->setup) {
+    if (connector->next  ||  !connector->setup) {
         EIO_Status status = eIO_Unknown;
-        METACONN_LOG(eLOG_Error,
+        METACONN_LOG(2, eLOG_Error,
                      "[METACONN_Add]  Input connector is in use/uninitable");
         return status;
     }
@@ -98,32 +101,3 @@ extern EIO_Status METACONN_Add
 
     return eIO_Success;
 }
-
-
-/*
- * --------------------------------------------------------------------------
- * $Log: ncbi_connector.c,v $
- * Revision 6.7  2002/08/13 19:29:49  lavr
- * Log moved to end
- *
- * Revision 6.6  2002/04/26 16:31:06  lavr
- * Minor style changes in call-by-pointer functions
- *
- * Revision 6.5  2002/03/22 22:17:29  lavr
- * No <stdlib.h> needed in here, removed
- *
- * Revision 6.4  2001/03/02 20:07:56  lavr
- * Typo fixed
- *
- * Revision 6.3  2001/01/25 16:57:08  lavr
- * METACONN_Remove revoked call to free() with connector:
- * connector's DESTROY method is now (back) responsible to call free().
- *
- * Revision 6.2  2001/01/12 23:51:38  lavr
- * Message logging modified for use LOG facility only
- *
- * Revision 6.1  2000/12/29 17:49:29  lavr
- * Initial revision
- *
- * ==========================================================================
- */
diff --git a/connect/ncbi_connector.h b/connect/ncbi_connector.h
index 372f1e6c..7f1a3444 100644
--- a/connect/ncbi_connector.h
+++ b/connect/ncbi_connector.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_CONNECTOR__H
 #define CONNECT___NCBI_CONNECTOR__H
 
-/*  $Id: ncbi_connector.h,v 6.16 2003/08/25 14:47:59 lavr Exp $
+/*  $Id: ncbi_connector.h,v 6.17 2007/09/04 20:25:30 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -247,11 +247,11 @@ typedef void (*FDestroy)
 /* Connector specification.
  */
 typedef struct SConnectorTag {
-    void*                handle;    /* data handle of the connector */
-    CONNECTOR            next;      /* linked list                  */
     SMetaConnector*      meta;      /* back link to CONNECTION      */
     FSetupVTable         setup;     /* used in CONNECTION init      */
     FDestroy             destroy;   /* destroys handle, can be NULL */
+    void*                handle;    /* data handle of the connector */
+    CONNECTOR            next;      /* linked list                  */
 } SConnector;
 
 
@@ -285,63 +285,4 @@ typedef EIO_Status (*FConnectorWaitAsync)
 
 /* @} */
 
-
-/*
- * --------------------------------------------------------------------------
- * $Log: ncbi_connector.h,v $
- * Revision 6.16  2003/08/25 14:47:59  lavr
- * Get rid of old ...TIMEOUT constants [now replaced with k...Timeout]
- *
- * Revision 6.15  2003/05/21 17:52:37  lavr
- * Pre- and post-conditions clarified for read and write virtual methods
- *
- * Revision 6.14  2003/05/14 03:47:53  lavr
- * +(*FConnectorDescr)()
- *
- * Revision 6.13  2003/04/09 17:58:45  siyan
- * Added doxygen support
- *
- * Revision 6.12  2003/01/08 01:59:32  lavr
- * DLL-ize CONNECT library for MSVC (add NCBI_XCONNECT_EXPORT)
- *
- * Revision 6.11  2002/09/19 18:00:11  lavr
- * Header file guard macro changed
- *
- * Revision 6.10  2002/09/06 15:40:54  lavr
- * More comments and notes to the API; log moved to end
- *
- * Revision 6.9  2002/04/26 16:29:32  lavr
- * Add default_timeout member to meta-connector
- *
- * Revision 6.8  2002/03/22 22:18:48  lavr
- * Cosmetic update
- *
- * Revision 6.7  2001/04/24 21:20:01  lavr
- * Introduced CONN_DEFAULT_TIMEOUT and CONN_INFINITE_TIMEOUT
- *
- * Revision 6.6  2001/03/02 20:07:18  lavr
- * Typos fixed
- *
- * Revision 6.5  2001/01/11 16:39:33  lavr
- * FDestroy function is now clearly documented not to destroy
- * the connector itself, only its handle (private internal data).
- *
- * Revision 6.4  2001/01/03 22:29:22  lavr
- * Changed IOStatus -> Status
- *
- * Revision 6.3  2000/12/29 17:45:07  lavr
- * Heavily modified to have a stack of connectors
- * VTable format changed; all virtual function now accept CONNECTOR as a
- * first argument (not void* as in previous versions)
- *
- * Revision 6.2  2000/04/07 19:59:49  vakatov
- * Moved forward-declaration of CONNECTOR from "ncbi_connection.h"
- * to "ncbi_connector.h"
- *
- * Revision 6.1  2000/03/24 22:52:48  vakatov
- * Initial revision
- *
- * ==========================================================================
- */
-
 #endif /* CONNECT___NCBI_CONNECTOR__H */
diff --git a/connect/ncbi_connutil.c b/connect/ncbi_connutil.c
index fe605626..3bb94ac5 100644
--- a/connect/ncbi_connutil.c
+++ b/connect/ncbi_connutil.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_connutil.c,v 6.115 2007/04/05 12:26:02 kazimird Exp $
+/*  $Id: ncbi_connutil.c,v 6.119 2008/02/13 20:25:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -26,7 +26,7 @@
  * Author:  Denis Vakatov, Anton Lavrentiev
  *
  * File Description:
- *   Auxiliary API, mostly CONN-, URL-/BASE64-, and MIME-related
+ *   Auxiliary API, mostly CONN-, URL-, and MIME-related
  *   (see in "ncbi_connutil.h" for more details).
  *
  */
@@ -38,6 +38,8 @@
 #include <errno.h>
 #include <stdlib.h>
 
+#define NCBI_USE_ERRCODE_X   Connect_Util
+
 
 extern const char* ConnNetInfo_GetValue(const char* service, const char* param,
                                         char* value, size_t value_size,
@@ -68,7 +70,7 @@ extern const char* ConnNetInfo_GetValue(const char* service, const char* param,
         s += sizeof(DEF_CONN_REG_SECTION) - 1;
         *s++ = '_';
         memcpy(s, param, plen);
-        if ((val = getenv(strupr(buf))) != 0)
+        if ((val = getenv(buf)) != 0  ||  (val = getenv(strupr(buf))) != 0)
             return strncpy0(value, val, value_size - 1);
 
         /* Next, search for 'CONN_param' in '[service]' registry section */
@@ -268,8 +270,8 @@ extern int/*bool*/ ConnNetInfo_AdjustForHttpProxy(SConnNetInfo* info)
         return 0/*false*/;
 
     if (strlen(info->host) + 16 + strlen(info->path) >= sizeof(info->path)) {
-        CORE_LOG(eLOG_Error,
-                 "[ConnNetInfo_AdjustForHttpProxy]  Adjusted path too long");
+        CORE_LOG_X(1, eLOG_Error,
+                   "[ConnNetInfo_AdjustForHttpProxy]  Adjusted path too long");
         assert(0);
         return 0/*false*/;
     }
@@ -715,15 +717,20 @@ static int/*bool*/ s_IsSufficientAddress(const char* addr)
 }
 
 
-static const char* s_ClientAddress(const char* client_host, int/*bool*/ local)
+static const char* s_ClientAddress(const char* client_host,
+                                   int/*bool*/ local_host)
 {
+    const char* c = client_host;
     unsigned int ip;
-    char addr[64];
+    char addr[80];
     char* s;
 
     assert(client_host);
+    strncpy0(addr, client_host, sizeof(addr) - 1);
+    if (UTIL_NcbiLocalHostName(addr)  &&  (s = strdup(addr)) != 0)
+        client_host = s;
     if (s_IsSufficientAddress(client_host)                          ||
-        !(ip = *client_host  &&  !local
+        !(ip = *client_host  &&  !local_host
           ? SOCK_gethostbyname(client_host)
           : SOCK_GetLocalHostAddress(eDefault))                     ||
         SOCK_ntoa(ip, addr, sizeof(addr)) != 0                      ||
@@ -731,6 +738,8 @@ static const char* s_ClientAddress(const char* client_host, int/*bool*/ local)
         return client_host;
     }
     sprintf(s, "%s(%s)", client_host, addr);
+    if (c != client_host)
+        free((void*) client_host);
     return s;
 }
 
@@ -740,7 +749,7 @@ extern int/*bool*/ ConnNetInfo_SetupStandardArgs(SConnNetInfo* info)
     static const char service[]  = "service";
     static const char address[]  = "address";
     static const char platform[] = "platform";
-    int/*bool*/ local;
+    int/*bool*/ local_host;
     const char* arch;
     const char* addr;
 
@@ -755,12 +764,12 @@ extern int/*bool*/ ConnNetInfo_SetupStandardArgs(SConnNetInfo* info)
         ConnNetInfo_DeleteArg(info, platform);
     else
         ConnNetInfo_PreOverrideArg(info, platform, arch);
-    local = !info->client_host[0];
-    if (local  &&
+    local_host = !info->client_host[0];
+    if (local_host  &&
         !SOCK_gethostbyaddr(0, info->client_host, sizeof(info->client_host))) {
         SOCK_gethostname(info->client_host, sizeof(info->client_host));
     }
-    if (!(addr = s_ClientAddress(info->client_host, local))  ||  !*addr)
+    if (!(addr = s_ClientAddress(info->client_host, local_host))  ||  !*addr)
         ConnNetInfo_DeleteArg(info, address);
     else
         ConnNetInfo_PreOverrideArg(info, address, addr);
@@ -823,7 +832,8 @@ extern void ConnNetInfo_Log(const SConnNetInfo* info, LOG lg)
         return;
 
     if (!info) {
-        LOG_Write(lg, eLOG_Trace, 0, 0, 0, "ConnNetInfo_Log: NULL info");
+        LOG_Write(lg, NCBI_C_ERRCODE_X, 10, eLOG_Trace, 0, 0, 0,
+                  "ConnNetInfo_Log: NULL info");
         return;
     }
 
@@ -833,7 +843,8 @@ extern void ConnNetInfo_Log(const SConnNetInfo* info, LOG lg)
                               ? strlen(info->http_user_header) : 0) +
                              (info->http_referer
                               ? strlen(info->http_referer) : 0)))) {
-        LOG_WRITE(lg, eLOG_Error, "ConnNetInfo_Log: Cannot alloc temp buffer");
+        LOG_WRITE(lg, NCBI_C_ERRCODE_X, 11, eLOG_Error,
+                  "ConnNetInfo_Log: Cannot alloc temp buffer");
         return;
     }
 
@@ -881,7 +892,7 @@ extern void ConnNetInfo_Log(const SConnNetInfo* info, LOG lg)
     s_SaveBool      (s, "proxy_adjusted",  info->http_proxy_adjusted);
     strcat(s, "#################### [END] SConnNetInfo\n");
 
-    LOG_Write(lg, eLOG_Trace, 0, 0, 0, s);
+    LOG_Write(lg, NCBI_C_ERRCODE_X, 12, eLOG_Trace, 0, 0, 0, s);
     free(s);
 }
 
@@ -935,7 +946,7 @@ extern SOCK URL_Connect
     /* check the args */
     if (!host  ||  !*host  ||  !port  ||
         (user_hdr  &&  *user_hdr  &&  user_hdr[user_hdr_len - 1] != '\n')) {
-        CORE_LOG(eLOG_Error, "[URL_Connect]  Bad arguments");
+        CORE_LOG_X(2, eLOG_Error, "[URL_Connect]  Bad arguments");
         assert(0);
         return 0/*error*/;
     }
@@ -944,8 +955,8 @@ extern SOCK URL_Connect
     if (req_method == eReqMethod_Any) {
         req_method = content_length ? eReqMethod_Post : eReqMethod_Get;
     } else if (req_method == eReqMethod_Get  &&  content_length) {
-        CORE_LOG(eLOG_Warning,
-                 "[URL_Connect]  Content length ignored with method GET");
+        CORE_LOG_X(3, eLOG_Warning,
+                   "[URL_Connect]  Content length ignored with method GET");
         content_length = 0;
     }
     switch (req_method) {
@@ -956,8 +967,9 @@ extern SOCK URL_Connect
         x_req_r = "GET ";
         break;
     default:
-        CORE_LOGF(eLOG_Error, ("[URL_Connect]  Unrecognized request method"
-                               " (%d)", (int) req_method));
+        CORE_LOGF_X(4, eLOG_Error,
+                    ("[URL_Connect]  Unrecognized request method (%d)",
+                     (int) req_method));
         assert(0);
         return 0/*error*/;
     }
@@ -1007,9 +1019,10 @@ extern SOCK URL_Connect
               !BUF_Write(&buf, buffer, strlen(buffer))))      ||
 
         !BUF_Write(&buf, "\r\n", 2)) {
-        CORE_LOGF(eLOG_Error, ("[URL_Connect]  Error composing HTTP header for"
-                               " %s:%hu%s%s", host, port, errno ? ": " : "",
-                               errno ? strerror(errno) : ""));
+        CORE_LOGF_X(5, eLOG_Error,
+                    ("[URL_Connect]  Error composing HTTP header for"
+                     " %s:%hu%s%s", host, port, errno ? ": " : "",
+                     errno ? strerror(errno) : ""));
         BUF_Destroy(buf);
         if (x_args  &&  x_args != args)
             free((void*) x_args);
@@ -1020,9 +1033,10 @@ extern SOCK URL_Connect
 
     if (!(header = (char*) malloc(headersize = BUF_Size(buf))) ||
         BUF_Read(buf, header, headersize) != headersize) {
-        CORE_LOGF(eLOG_Error, ("[URL_Connect]  Error storing HTTP header for"
-                               " %s:%hu: %s", host, port,
-                               errno ? strerror(errno) : "Unknown error"));
+        CORE_LOGF_X(6, eLOG_Error,
+                    ("[URL_Connect]  Error storing HTTP header for"
+                     " %s:%hu: %s", host, port,
+                     errno ? strerror(errno) : "Unknown error"));
         if (header)
             free(header);
         BUF_Destroy(buf);
@@ -1034,15 +1048,15 @@ extern SOCK URL_Connect
     st = SOCK_CreateEx(host, port, c_timeout, &sock, header, headersize, log);
     free(header);
     if (st != eIO_Success) {
-        CORE_LOGF(eLOG_Error,
-                  ("[URL_Connect]  Socket connect to %s:%hu failed: %s",
-                   host, port, IO_StatusStr(st)));
+        CORE_LOGF_X(7, eLOG_Error,
+                    ("[URL_Connect]  Socket connect to %s:%hu failed: %s",
+                     host, port, IO_StatusStr(st)));
         return 0/*error*/;
     }
 
     /* setup I/O timeout for the connection */
     if (SOCK_SetTimeout(sock, eIO_ReadWrite, rw_timeout) != eIO_Success) {
-        CORE_LOG(eLOG_Error, "[URL_Connect]  Cannot set connection timeout");
+        CORE_LOG_X(8, eLOG_Error, "[URL_Connect]  Cannot set connection timeout");
         SOCK_Close(sock);
         return 0/*error*/;
     }
@@ -1258,7 +1272,7 @@ extern EIO_Status BUF_StripToPattern
 
 
 /****************************************************************************
- * URL- and BASE64- Encoding/Decoding
+ * URL- Encoding/Decoding
  */
 
 
@@ -1418,178 +1432,6 @@ extern void URL_Encode
 }
 
 
-extern void BASE64_Encode
-(const void* src_buf,
- size_t      src_size,
- size_t*     src_read,
- void*       dst_buf,
- size_t      dst_size,
- size_t*     dst_written,
- size_t*     line_len)
-{
-    static const char syms[] =
-        "ABCDEFGHIJKLMNOPQRSTUVWXYZ" /*26*/
-        "abcdefghijklmnopqrstuvwxyz" /*52*/
-        "0123456789+/";              /*64*/
-    const size_t max_len = line_len ? *line_len : 76;
-    const size_t max_src =
-        ((dst_size - (max_len ? dst_size/(max_len + 1) : 0)) >> 2) * 3;
-    unsigned char* src = (unsigned char*) src_buf;
-    unsigned char* dst = (unsigned char*) dst_buf;
-    size_t len = 0, i = 0, j = 0;
-    unsigned char temp = 0, c;
-    unsigned char shift = 2;
-    if (!max_src  ||  !src_size) {
-        *src_read    = 0;
-        *dst_written = 0;
-        if (dst_size > 0) {
-            *dst = '\0';
-        }
-        return;
-    }
-    if (src_size > max_src) {
-        src_size = max_src;
-    }
-    c = src[0];
-    for (;;) {
-        unsigned char bits = (c >> shift) & 0x3F;
-        if (max_len  &&  len >= max_len) {
-            dst[j++] = '\n';
-            len = 0;
-        }
-        assert((size_t)(temp | bits) < sizeof(syms) - 1);
-        dst[j++] = syms[temp | bits];
-        len++;
-        if (i >= src_size) {
-            break;
-        }
-        shift += 2;
-        shift &= 7;
-        temp = (c << (8 - shift)) & 0x3F;
-        if (shift) {
-            c = ++i < src_size ? src[i] : 0;
-        } else if (i + 1 == src_size) {
-            i++;
-        }
-    }
-    assert(j <= dst_size);
-    *src_read = i;
-    for (i = 0; i < (3 - src_size % 3) % 3; i++) {
-        if (max_len  &&  len >= max_len) {
-            dst[j++] = '\n';
-            len = 0;
-        }
-        dst[j++] = '=';
-        len++;
-    }
-    assert(j <= dst_size);
-    *dst_written = j;
-    if (j < dst_size) {
-        dst[j] = '\0';
-    }
-}
-
-
-extern int/*bool*/ BASE64_Decode
-(const void* src_buf,
- size_t      src_size,
- size_t*     src_read,
- void*       dst_buf,
- size_t      dst_size,
- size_t*     dst_written)
-{
-    unsigned char* src = (unsigned char*) src_buf;
-    unsigned char* dst = (unsigned char*) dst_buf;
-    size_t i = 0, j = 0, k = 0, l;
-    unsigned int temp = 0;
-    if (src_size < 4  ||  dst_size < 3) {
-        *src_read    = 0;
-        *dst_written = 0;
-        return 0/*false*/;
-    }
-    for (;;) {
-        int/*bool*/  ok = i < src_size ? 1/*true*/ : 0/*false*/;
-        unsigned char c = ok ? src[i++] : '=';
-        if (c == '=') {
-            c  = 64; /*end*/
-        } else if (c >= 'A'  &&  c <= 'Z') {
-            c -= 'A';
-        } else if (c >= 'a'  &&  c <= 'z') {
-            c -= 'a' - 26;
-        } else if (c >= '0'  &&  c <= '9') {
-            c -= '0' - 52;
-        } else if (c == '+') {
-            c  = 62;
-        } else if (c == '/') {
-            c  = 63;
-        } else {
-            continue;
-        }
-        temp <<= 6;
-        temp  |= c & 0x3F;
-        if (!(++k & 3)  ||  c == 64) {
-            if (c == 64) {
-                if (k < 2) {
-                    if (ok) {
-                        /* pushback leading '=' */
-                        --i;
-                    }
-                    break;
-                }
-                switch (k) {
-                case 2:
-                    temp >>= 4;
-                    break;
-                case 3:
-                    temp >>= 10;
-                    break;
-                case 4:
-                    temp >>= 8;
-                    break;
-                default:
-                    assert(0);
-                    break;
-                }
-                l = 4 - k;
-                while (l > 0) {
-                    /* eat up '='-padding */
-                    if (i >= src_size)
-                        break;
-                    if (src[i] == '=')
-                        l--;
-                    else if (src[i] != '\r'  &&  src[i] != '\n')
-                        break;
-                    i++;
-                }
-            } else {
-                k = 0;
-            }
-            switch (k) {
-            case 0:
-                dst[j++] = (temp & 0xFF0000) >> 16;
-                /*FALLTHRU*/;
-            case 4:
-                dst[j++] = (temp & 0xFF00) >> 8;
-                /*FALLTHRU*/
-            case 3:
-                dst[j++] = (temp & 0xFF);
-                break;
-            default:
-                break;
-            }
-            if (j + 3 >= dst_size  ||  c == 64) {
-                break;
-            }
-            temp = 0;
-        }
-    }
-    *src_read    = i;
-    *dst_written = j;
-    return i  &&  j ? 1/*true*/ : 0/*false*/;
-}
-
-
-
 /****************************************************************************
  * NCBI-specific MIME content type and sub-types
  */
diff --git a/connect/ncbi_connutil.h b/connect/ncbi_connutil.h
index 9e6fa7e2..fbaa23b2 100644
--- a/connect/ncbi_connutil.h
+++ b/connect/ncbi_connutil.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_CONNUTIL__H
 #define CONNECT___NCBI_CONNUTIL__H
 
-/*  $Id: ncbi_connutil.h,v 6.61 2007/01/24 04:23:08 lavr Exp $
+/*  $Id: ncbi_connutil.h,v 6.62 2007/12/05 19:26:19 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -62,10 +62,6 @@
  *       URL_Decode()
  *       URL_DecodeEx()
  *
- *    4.Perform BASE64 (RFC 1521) encoding/decoding of data:
- *       BASE64_Encode()
- *       BASE64_Decode()
- *
  *    5.Compose or parse NCBI-specific Content-Type's:
  *       EMIME_Type
  *       EMIME_SubType
@@ -548,49 +544,6 @@ extern NCBI_XCONNECT_EXPORT int/*bool*/ URL_DecodeEx
 
 
 
-/* BASE64-encode up to "src_size" symbols(bytes) from buffer "src_buf".
- * Write the encoded data to buffer "dst_buf", but no more than "dst_size"
- * bytes.
- * Assign "*src_read" to the # of bytes successfully encoded from "src_buf".
- * Assign "*dst_written" to the # of bytes written to buffer "dst_buf".
- * Resulting lines will not exceed "*line_len" (or the standard default
- * if "line_len" is NULL) bytes;  *line_len == 0 disables line breaks.
- * To estimate required destination buffer size, you can take into account
- * that BASE64 coding converts every 3 bytes of source into 4 bytes on
- * destination, not including the line breaks ('\n').
- */
-extern NCBI_XCONNECT_EXPORT void BASE64_Encode
-(const void* src_buf,    /* [in]     non-NULL */
- size_t      src_size,   /* [in]              */
- size_t*     src_read,   /* [out]    non-NULL */
- void*       dst_buf,    /* [in/out] non-NULL */
- size_t      dst_size,   /* [in]              */
- size_t*     dst_written,/* [out]    non-NULL */
- size_t*     line_len    /* [in]  may be NULL */
- );
-
-
-/* BASE64-decode up to "src_size" symbols(bytes) from buffer "src_buf".
- * Write the decoded data to buffer "dst_buf", but no more than "dst_size"
- * bytes.
- * Assign "*src_read" to the # of bytes successfully decoded from "src_buf".
- * Assign "*dst_written" to the # of bytes written to buffer "dst_buf".
- * Return FALSE (0) only if cannot decode anything.
- * Destination buffer size, as a worst case, equal to the source size
- * will accomodate the entire input.  As a rule, each 4 bytes of source
- * (line breaks skipped) are converted into 3 bytes on output.
- */
-extern NCBI_XCONNECT_EXPORT int/*bool*/ BASE64_Decode
-(const void* src_buf,    /* [in]     non-NULL */
- size_t      src_size,   /* [in]              */
- size_t*     src_read,   /* [out]    non-NULL */
- void*       dst_buf,    /* [in/out] non-NULL */
- size_t      dst_size,   /* [in]              */
- size_t*     dst_written /* [out]    non-NULL */
- );
-
-
-
 /****************************************************************************
  * NCBI-specific MIME content type and sub-types
  * (the API to compose and parse them)
@@ -731,209 +684,4 @@ size_t HostPortToString
 
 /* @} */
 
-
-/*
- * --------------------------------------------------------------------------
- * $Log: ncbi_connutil.h,v $
- * Revision 6.61  2007/01/24 04:23:08  lavr
- * Synchronized with the C++ Toolkit.
- *
- * Revision 6.60  2006/10/26 18:54:12  jcherry
- * Added export specifier
- *
- * Revision 6.59  2006/08/14 19:08:41  lavr
- * HTTP_REFERER documented as may have added automatically
- *
- * Revision 6.58  2006/06/15 02:43:59  lavr
- * GetUsername, GetVMPageSize, CRC32 moved from here to ncbi_util.h
- *
- * Revision 6.57  2006/06/07 20:03:46  lavr
- * +SConnNetInfo::http_referer
- *
- * Revision 6.56  2006/04/21 14:41:19  lavr
- * REG_CONN_SERVICE_NAME added
- *
- * Revision 6.55  2006/04/21 01:33:22  lavr
- * SConnNetInfo::lb_disable reinstated along with LB_DISABLE reg/env key
- *
- * Revision 6.53  2006/04/20 13:57:51  lavr
- * Registry keys for new switching scheme for service mappers;
- * Registry keys for LOCAL service mappers
- *
- * Revision 6.52  2006/04/19 02:26:05  lavr
- * Document ConnNetInfo_{Pre|Post}OverrideArg in more details
- *
- * Revision 6.51  2006/02/23 15:46:16  lavr
- * Clean ChangeLog
- *
- * Revision 6.50  2006/02/23 15:22:43  lavr
- * +CONNUTIL_GetVMPageSize()
- *
- * Revision 6.49  2006/01/27 19:17:41  lavr
- * Fix NCBI_DEPRECATED placement to satify MSVC compiler
- *
- * Revision 6.48  2006/01/27 17:08:35  lavr
- * Spell CONNUTIL_GetUsername() this way
- *
- * Revision 6.47  2006/01/27 16:57:53  lavr
- * Obsoleted StringHostToPort() and HostPortToString()
- * Added new CONNUTIL_GetUsername()
- *
- * Revision 6.46  2006/01/11 20:19:56  lavr
- * -UTIL_ClientAddress()
- * +ConnNetInfo_DeleteAllArgs()
- * +ConnNetInfo_SetupStandardArgs()
- *
- * Revision 6.45  2006/01/11 16:24:03  lavr
- * +UTIL_ClientAddress()
- *
- * Revision 6.44  2005/11/29 21:32:07  lavr
- * Reserve SConnNetInfo::scheme, user, and pass for future use
- *
- * Revision 6.43  2005/11/29 19:51:51  lavr
- * +CRC32 (pure C interface; not a ZIP version)
- *
- * Revision 6.42  2005/04/20 15:47:24  lavr
- * DEF_CONN_REQ_METHOD changed to ANY
- *
- * Revision 6.41  2005/03/21 17:04:10  lavr
- * BASE64_{En|De}code buffer size estimation hints added
- *
- * Revision 6.40  2005/03/19 02:13:55  lavr
- * +BASE64_{En|De}code
- *
- * Revision 6.39  2005/02/28 17:23:20  lavr
- * Fix HTTP_USER_HEADER env.var. name ("HTTP" was missing)
- *
- * Revision 6.38  2005/02/24 19:51:24  lavr
- * Document CONN_HTTP_USER_HEADER environment
- *
- * Revision 6.37  2005/02/24 19:00:33  lavr
- * +CONN_HTTP_USER_HEADER
- *
- * Revision 6.36  2004/09/16 16:19:16  lavr
- * Mention [in opening comment summary] that EMIME_Type is defined here
- *
- * Revision 6.35  2004/01/14 18:51:41  lavr
- * +eMIME_XmlSoap
- *
- * Revision 6.34  2004/01/07 19:24:40  lavr
- * Added MIME subtype eMIME_Xml
- *
- * Revision 6.33  2003/09/23 21:00:33  lavr
- * Reorder included header files
- *
- * Revision 6.32  2003/08/25 14:48:50  lavr
- * ConnNetInfo_SetUserHeader():  to return completion status
- *
- * Revision 6.31  2003/05/29 17:56:53  lavr
- * More (clarified) comments for URL_Connect()
- *
- * Revision 6.30  2003/05/20 21:24:01  lavr
- * Limit SConnNetInfo::max_try by reasonable "short" value
- *
- * Revision 6.29  2003/04/09 17:58:47  siyan
- * Added doxygen support
- *
- * Revision 6.28  2003/01/17 19:44:20  lavr
- * Reduce dependencies
- *
- * Revision 6.27  2003/01/08 01:59:32  lavr
- * DLL-ize CONNECT library for MSVC (add NCBI_XCONNECT_EXPORT)
- *
- * Revision 6.26  2002/11/19 19:19:24  lavr
- * +ConnNetInfo_ExtendUserHeader()
- *
- * Revision 6.25  2002/11/12 05:49:47  lavr
- * Expand host names to hold 256 chars (instead of 64)
- *
- * Revision 6.24  2002/10/21 18:30:27  lavr
- * +ConnNetInfo_AppendArg()
- * +ConnNetInfo_PrependArg()
- * +ConnNetInfo_DeleteArg()
- * +ConnNetInfo_PreOverrideArg()
- * +ConnNetInfo_PostOverrideArg()
- *
- * Revision 6.23  2002/10/11 19:41:40  lavr
- * +ConnNetInfo_AppendUserHeader()
- * +ConnNetInfo_OverrideUserHeader()
- * +ConnNetInfo_DeleteUserHeader()
- *
- * Revision 6.22  2002/09/19 18:00:21  lavr
- * Header file guard macro changed; log moved to the end
- *
- * Revision 6.21  2002/05/06 19:07:25  lavr
- * -#include <stdlib>; -ConnNetInfo_Print(); +ConnNetInfo_Log()
- *
- * Revision 6.20  2002/02/20 19:12:03  lavr
- * Swapped eENCOD_Url and eENCOD_None; eENCOD_Unknown introduced
- *
- * Revision 6.19  2001/12/30 19:39:36  lavr
- * +ConnNetInfo_ParseURL()
- *
- * Revision 6.18  2001/09/28 20:45:26  lavr
- * SConnNetInfo::max_try equal to 0 is now treated the same way as equal to 1
- *
- * Revision 6.17  2001/09/19 15:58:37  lavr
- * Cut trailing blanks in blank lines
- *
- * Revision 6.16  2001/09/10 21:14:47  lavr
- * Added functions: StringToHostPort()
- *                  HostPortToString()
- *
- * Revision 6.15  2001/06/01 16:01:58  vakatov
- * MIME_ParseContentTypeEx() -- extended description
- *
- * Revision 6.14  2001/05/29 21:15:42  vakatov
- * + eMIME_Plain
- *
- * Revision 6.13  2001/04/24 21:21:38  lavr
- * Special text value "infinite" accepted as infinite timeout from environment
- *
- * Revision 6.12  2001/03/07 23:00:15  lavr
- * Default value for SConnNetInfo::stateless set to empty (FALSE)
- *
- * Revision 6.11  2001/03/02 20:07:07  lavr
- * Typos fixed
- *
- * Revision 6.10  2001/02/26 16:56:41  vakatov
- * Comment SConnNetInfo.
- *
- * Revision 6.9  2001/01/23 23:06:15  lavr
- * SConnNetInfo.debug_printout converted from boolean to enum
- * BUF_StripToPattern() introduced
- *
- * Revision 6.8  2001/01/11 23:05:13  lavr
- * ConnNetInfo_Create() fully documented
- *
- * Revision 6.7  2001/01/08 23:46:10  lavr
- * REQUEST_METHOD -> REQ_METHOD to be consistent with SConnNetInfo
- *
- * Revision 6.6  2001/01/08 22:47:13  lavr
- * ReqMethod constants changed (to conform to coding standard)
- * ClientMode removed; replaced by 2 booleans: stateless and firewall
- * in SConnInfo structure
- *
- * Revision 6.5  2000/12/29 17:47:46  lavr
- * NCBID stuff removed; ClientMode enum added;
- * ConnNetInfo_SetUserHeader added; http_user_header is now
- * included in ConnInfo structure. ConnNetInfo_Destroy parameter
- * changed to be a pointer (was a double pointer).
- *
- * Revision 6.4  2000/11/07 23:23:15  vakatov
- * In-sync with the C Toolkit "connutil.c:R6.15", "connutil.h:R6.13"
- * (with "eMIME_Dispatch" added).
- *
- * Revision 6.3  2000/10/05 22:39:21  lavr
- * SConnNetInfo modified to contain 'client_mode' instead of just 'firewall'
- *
- * Revision 6.2  2000/09/26 22:01:30  lavr
- * Registry entries changed, HTTP request method added
- *
- * Revision 6.1  2000/03/24 22:52:48  vakatov
- * Initial revision
- *
- * ==========================================================================
- */
-
 #endif /* CONNECT___NCBI_CONNUTIL__H */
diff --git a/connect/ncbi_core.c b/connect/ncbi_core.c
index 95d2a4aa..223a573d 100644
--- a/connect/ncbi_core.c
+++ b/connect/ncbi_core.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_core.c,v 6.17 2006/07/13 21:01:04 lavr Exp $
+/*  $Id: ncbi_core.c,v 6.18 2007/10/17 15:25:43 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -264,7 +264,9 @@ extern void LOG_WriteInternal
  int         line,
  const char* message,
  const void* raw_data,
- size_t      raw_size)
+ size_t      raw_size,
+ int         err_code,
+ int         err_subcode)
 {
     if ( lg ) {
         LOG_LOCK_READ;
@@ -274,13 +276,15 @@ extern void LOG_WriteInternal
         if ( lg->handler ) {
             SLOG_Handler call_data;
 
-            call_data.level    = level;
-            call_data.module   = module;
-            call_data.file     = file;
-            call_data.line     = line;
-            call_data.message  = message;
-            call_data.raw_data = raw_data;
-            call_data.raw_size = raw_size;
+            call_data.level       = level;
+            call_data.err_code    = err_code;
+            call_data.err_subcode = err_subcode;
+            call_data.module      = module;
+            call_data.file        = file;
+            call_data.line        = line;
+            call_data.message     = message;
+            call_data.raw_data    = raw_data;
+            call_data.raw_size    = raw_size;
 
             lg->handler(lg->user_data, &call_data);
         }
@@ -457,63 +461,3 @@ extern void REG_Set
         REG_UNLOCK;
     }
 }
-
-
-/*
- * ---------------------------------------------------------------------------
- * $Log: ncbi_core.c,v $
- * Revision 6.17  2006/07/13 21:01:04  lavr
- * Formatting and changing constants to have "k" prefix
- *
- * Revision 6.16  2006/04/20 13:58:46  lavr
- * Wrap registry retrievals
- *
- * Revision 6.15  2005/04/20 18:13:39  lavr
- * +"ncbi_assert.h"
- *
- * Revision 6.14  2003/08/28 18:47:51  ucko
- * Revert previous hack (now handled another way)
- *
- * Revision 6.13  2003/08/27 12:32:30  ucko
- * Yet another attempt to work around the WorkShop lossage with k*Timeout.
- *
- * Revision 6.12  2003/05/05 20:17:17  lavr
- * LOG_WriteInternal() to require data ptr only if data size is not zero
- *
- * Revision 6.11  2003/02/20 17:52:12  lavr
- * Status verbal names changed not to have caps in the middle
- *
- * Revision 6.10  2002/10/28 15:42:48  lavr
- * Use "ncbi_ansi_ext.h" privately and use strncpy0()
- *
- * Revision 6.9  2002/08/13 19:30:13  lavr
- * Verbal representation of eIO_Interrupt; log moved to end
- *
- * Revision 6.8  2001/08/09 16:24:29  lavr
- * Remove last (unneeded) parameter from LOG_Reset()
- *
- * Revision 6.7  2001/04/25 20:52:29  vakatov
- * LOG_WriteInternal() -- abort on "eLOG_Fatal" even if no logging is set
- *
- * Revision 6.6  2001/01/11 16:42:32  lavr
- * Registry Get/Set methods got the 'user_data' argument, forgotten earlier
- *
- * Revision 6.5  2000/10/18 20:29:43  vakatov
- * REG_Get::  pass in the default value (rather than '\0')
- *
- * Revision 6.4  2000/06/23 19:34:43  vakatov
- * Added means to log binary data
- *
- * Revision 6.3  2000/05/30 23:21:36  vakatov
- * LOG_WriteInternal():  exit/abort on "eLOG_Fatal"
- *
- * Revision 6.2  2000/03/24 23:12:07  vakatov
- * Starting the development quasi-branch to implement CONN API.
- * All development is performed in the NCBI C++ tree only, while
- * the NCBI C tree still contains "frozen" (see the last revision) code.
- *
- * Revision 6.1  2000/02/23 22:36:16  vakatov
- * Initial revision
- *
- * ===========================================================================
- */
diff --git a/connect/ncbi_core.h b/connect/ncbi_core.h
index 73d9b547..6a15e108 100644
--- a/connect/ncbi_core.h
+++ b/connect/ncbi_core.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_CORE__H
 #define CONNECT___NCBI_CORE__H
 
-/* $Id: ncbi_core.h,v 6.31 2007/06/25 15:25:32 kazimird Exp $
+/* $Id: ncbi_core.h,v 6.33 2007/10/17 15:25:43 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -313,6 +313,10 @@ extern NCBI_XCONNECT_EXPORT const char* LOG_LevelStr(ELOG_Level level);
  *  Raw data to log (usually NULL)
  * @param raw_size
  *  Size of the raw data (usually zero)
+ * @param err_code
+ *  Error code of the message
+ * @param err_subcode
+ *  Error subcode of the message
  * @sa
  *  FLOG_Handler, LOG_Create, LOG_WriteInternal
  */
@@ -324,6 +328,8 @@ typedef struct {
     int         line;
     const void* raw_data;
     size_t      raw_size;
+    int         err_code;
+    int         err_subcode;
 } SLOG_Handler;
 
 
@@ -441,6 +447,10 @@ extern NCBI_XCONNECT_EXPORT LOG LOG_Delete(LOG lg);
  *  Raw data to log (can be NULL)
  * @param raw_size
  *  Size of the raw data (can be zero)
+ * @param err_code
+ *  Error code of the message
+ * @param err_subcode
+ *  Error subcode of the message
  * @sa
  *  LOG_Create, ELOG_Level, FLOG_Handler, LOG_WRITE, LOG_DATA
  */
@@ -452,8 +462,10 @@ extern NCBI_XCONNECT_EXPORT void LOG_WriteInternal
  int         line,  
  const char* message,
  const void* raw_data,
- size_t      raw_size
- );
+ size_t      raw_size,
+ int         err_code,
+ int         err_subcode
+);
 
 
 
diff --git a/connect/ncbi_core_c.c b/connect/ncbi_core_c.c
index a2de314c..912c8bb0 100644
--- a/connect/ncbi_core_c.c
+++ b/connect/ncbi_core_c.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_core_c.c,v 6.18 2007/06/25 15:33:04 lavr Exp $
+/*  $Id: ncbi_core_c.c,v 6.19 2007/10/18 15:29:26 ivanovp Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -150,7 +150,7 @@ static void s_LOG_Handler(void* user_data/*unused*/, SLOG_Handler* call_data)
     if (!(msg = LOG_ComposeMessage(call_data, fLOG_None)))
         return/*failed*/;
 
-    Nlm_ErrPostStr(sev, 0, 0, msg);
+    Nlm_ErrPostStr(sev, call_data->err_code, call_data->err_subcode, msg);
 
     if (call_data->level == eLOG_Trace)
         Nlm_ErrClear();
@@ -240,6 +240,9 @@ extern void CONNECT_Init(const char* conf_file)
 /*
  * ---------------------------------------------------------------------------
  * $Log: ncbi_core_c.c,v $
+ * Revision 6.19  2007/10/18 15:29:26  ivanovp
+ * Connect and ctools libraries are changed to use new error and log posting system with error codes and subcodes. JIRA: CXX-3
+ *
  * Revision 6.18  2007/06/25 15:33:04  lavr
  * +eMT_TryLock[Read]
  *
diff --git a/connect/ncbi_dispd.c b/connect/ncbi_dispd.c
index 121dbec1..c8bb2ea0 100644
--- a/connect/ncbi_dispd.c
+++ b/connect/ncbi_dispd.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_dispd.c,v 6.84 2007/05/01 20:55:29 kazimird Exp $
+/*  $Id: ncbi_dispd.c,v 6.87 2008/02/14 17:25:50 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -43,6 +43,8 @@
 #include <stdio.h>
 #include <stdlib.h>
 
+#define NCBI_USE_ERRCODE_X   Connect_Dispd
+
 /* Lower bound of up-to-date/out-of-date ratio */
 #define DISPD_STALE_RATIO_OK  0.8
 /* Default rate increase 20% if svc runs locally */
@@ -148,7 +150,7 @@ static int/*bool*/ s_Resolve(SERV_ITER iter)
     assert(!!net_info->stateless == !!iter->stateless);
     /* Obtain additional header information */
     if ((!(s = SERV_Print(iter, 0))
-         || ConnNetInfo_OverrideUserHeader(net_info, s))
+         ||  ConnNetInfo_OverrideUserHeader(net_info, s))
         &&
         ConnNetInfo_OverrideUserHeader(net_info,
                                        iter->ok_down  &&  iter->ok_suppressed
@@ -173,9 +175,9 @@ static int/*bool*/ s_Resolve(SERV_ITER iter)
         ConnNetInfo_DeleteUserHeader(net_info, s);
         free(s);
     }
-    if (!conn || CONN_Create(conn, &c) != eIO_Success) {
-        CORE_LOGF(eLOG_Error, ("[DISPATCHER]  Unable to create aux. %s",
-                               conn ? "connection" : "connector"));
+    if (!conn  ||  CONN_Create(conn, &c) != eIO_Success) {
+        CORE_LOGF_X(1, eLOG_Error, ("[DISPATCHER]  Unable to create aux. %s",
+                                    conn ? "connection" : "connector"));
         assert(0);
         return 0/*failed*/;
     }
@@ -246,8 +248,9 @@ static int/*bool*/ s_Update(SERV_ITER iter, const char* text, int code)
             text += sizeof(HTTP_DISP_FAILURES) - 1;
             while (*text  &&  isspace((unsigned char)(*text)))
                 text++;
-            CORE_LOGF(eLOG_Warning, ("[DISPATCHER %s]  %s",
-                                     failure ? "FAILURE" : "MESSAGE", text));
+            CORE_LOGF_X(2, eLOG_Warning,
+                        ("[DISPATCHER %s]  %s",
+                         failure ? "FAILURE" : "MESSAGE", text));
         }
 #endif /*_DEBUG && !NDEBUG*/
         if (failure)
diff --git a/connect/ncbi_ftp_connector.c b/connect/ncbi_ftp_connector.c
index d912c430..b35f51c5 100644
--- a/connect/ncbi_ftp_connector.c
+++ b/connect/ncbi_ftp_connector.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_ftp_connector.c,v 1.20 2007/01/23 22:31:29 kazimird Exp $
+/*  $Id: ncbi_ftp_connector.c,v 1.21 2007/10/17 15:25:43 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -46,6 +46,9 @@
 #include <stdlib.h>
 
 
+#define NCBI_USE_ERRCODE_X   Connect_FTP
+
+
 /***********************************************************************
  *  INTERNAL -- Auxiliary types and static functions
  ***********************************************************************/
@@ -307,7 +310,7 @@ static EIO_Status s_FTPAbort(SFTPConnector*  xxx,
             status = SOCK_Close(xxx->data);
         else {
             if (status == eIO_Timeout) {
-                CORE_LOG(eLOG_Warning,
+                CORE_LOG_X(1, eLOG_Warning,
                          "[FTP]  Timed out on data connection abort");
             }
             SOCK_Abort(xxx->data);
@@ -740,71 +743,3 @@ extern CONNECTOR FTP_CreateDownloadConnector(const char*    host,
 
     return ccc;
 }
-
-
-/*
- * --------------------------------------------------------------------------
- * $Log: ncbi_ftp_connector.c,v $
- * Revision 1.20  2007/01/23 22:31:29  kazimird
- * Synchronized with the C++ Toolkit.
- *
- * Revision 1.19  2006/12/07 16:21:02  lavr
- * Use minus sign in default password to try to turn off human-readable msgs
- *
- * Revision 1.18  2006/10/23 21:19:07  lavr
- * Empty while() extended with a dummy continue (to avoid misplaced ; warning)
- *
- * Revision 1.17  2006/01/27 17:01:19  lavr
- * Replace obsolete call names with current ones
- *
- * Revision 1.16  2006/01/11 20:21:32  lavr
- * Uniform creation/fill-up of connector structures
- *
- * Revision 1.15  2005/12/14 21:31:04  lavr
- * Two explicit (char*) casts added
- *
- * Revision 1.14  2005/06/08 20:42:05  lavr
- * Use safer memmove() instead of strcpy() in PASV parsing
- *
- * Revision 1.13  2005/06/02 17:52:31  lavr
- * s_VT_Write(): Unused variable "s" removed
- *
- * Revision 1.12  2005/05/20 13:02:13  lavr
- * s_VT_Write() not to cut '\r' -- instead, do this in s_FTPExecute()
- *
- * Revision 1.11  2005/05/20 12:11:00  lavr
- * ABOR sequence reimplemented to work even with buggy FTPDs
- *
- * Revision 1.10  2005/05/18 20:56:45  lavr
- * Use assert() to test flags for validity in constructor
- *
- * Revision 1.9  2005/05/18 18:16:41  lavr
- * Add EFCDC_Flags and TFCDC_Flags to better control underlying SOCK logs
- * Fix s_VT_Write() not to use strchr() -- memchr() must be used there!
- *
- * Revision 1.8  2005/05/11 20:00:25  lavr
- * Empty NLST result list bug fixed
- *
- * Revision 1.7  2005/04/20 18:15:59  lavr
- * +<assert.h>
- *
- * Revision 1.6  2005/01/27 18:59:52  lavr
- * Explicit cast of malloc()ed memory
- *
- * Revision 1.5  2005/01/05 17:40:13  lavr
- * FEAT extensions and fixes for protocol compliance
- *
- * Revision 1.4  2004/12/27 15:31:27  lavr
- * Implement telnet SYNCH and FTP ABORT according to the standard
- *
- * Revision 1.3  2004/12/08 21:03:26  lavr
- * Fixes for default ctor parameters
- *
- * Revision 1.2  2004/12/07 14:21:55  lavr
- * Init wbuf in ctor
- *
- * Revision 1.1  2004/12/06 17:48:38  lavr
- * Initial revision
- *
- * ==========================================================================
- */
diff --git a/connect/ncbi_heapmgr.c b/connect/ncbi_heapmgr.c
index 05d975ea..2596c463 100644
--- a/connect/ncbi_heapmgr.c
+++ b/connect/ncbi_heapmgr.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_heapmgr.c,v 6.39 2007/04/20 01:55:30 kazimird Exp $
+/*  $Id: ncbi_heapmgr.c,v 6.43 2008/02/21 15:26:12 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -116,6 +116,8 @@
 #include <stdlib.h>
 #include <string.h>
 
+#define NCBI_USE_ERRCODE_X   Connect_HeapMgr
+
 #if defined(NCBI_OS_MSWIN)  &&  defined(_WIN64)
 /* Disable ptr->long conversion warning (even on explicit cast!) */
 #  pragma warning (disable : 4311)
@@ -189,9 +191,10 @@ HEAP HEAP_Create(void* base,       TNCBI_Size   size,
     if (!base != !size)
         return 0;
     if (size  &&  size < _HEAP_ALIGNMENT) {
-        CORE_LOGF(eLOG_Error,
-                  ("Heap Create: Storage too small: provided %u, required %u+",
-                   size, _HEAP_ALIGNMENT));
+        CORE_LOGF_X(1, eLOG_Error,
+                    ("Heap Create: Storage too small: "
+                     "provided %u, required %u+",
+                     size, _HEAP_ALIGNMENT));
         return 0;
     }
     if (!(heap = (HEAP) malloc(sizeof(*heap))))
@@ -210,8 +213,9 @@ HEAP HEAP_Create(void* base,       TNCBI_Size   size,
         SHEAP_HeapBlock* b = heap->base;
         /* Reformat the pre-allocated heap */
         if (_HEAP_ALIGN(base, sizeof(SHEAP_Block)) != (unsigned long) base) {
-            CORE_LOGF(eLOG_Warning,
-                     ("Heap Create: Unaligned base (0x%08lX)", (long) base));
+            CORE_LOGF_X(2, eLOG_Warning,
+                        ("Heap Create: Unaligned base (0x%08lX)",
+                         (long) base));
         }
         b->head.flag = HEAP_FREE | HEAP_LAST;
         b->head.size = size;
@@ -230,16 +234,17 @@ HEAP HEAP_AttachFast(const void* base, TNCBI_Size size, int serial)
     if (!base != !size  ||  !(heap = (HEAP) calloc(1, sizeof(*heap))))
         return 0;
     if (_HEAP_ALIGN(base, sizeof(SHEAP_Block)) != (unsigned long) base) {
-        CORE_LOGF(eLOG_Warning,
-                  ("Heap Attach: Unaligned base (0x%08lX)", (long) base));
+        CORE_LOGF_X(3, eLOG_Warning,
+                    ("Heap Attach: Unaligned base (0x%08lX)", (long) base));
     }
     heap->base   = (SHEAP_HeapBlock*) base;
     heap->size   = HEAP_ALIGN(size) >> _HEAP_ALIGNSHIFT;
     heap->serial = serial;
     if (size != heap->size << _HEAP_ALIGNSHIFT) {
-        CORE_LOGF(eLOG_Warning,
-                  ("Heap Attach: Heap size alignment (%u->%u) can result in"
-                   " garbage in data", size, heap->size << _HEAP_ALIGNSHIFT));
+        CORE_LOGF_X(4, eLOG_Warning,
+                    ("Heap Attach: Heap size alignment (%u->%u) "
+                     "can result in garbage in data",
+                     size, heap->size << _HEAP_ALIGNSHIFT));
     }
     return heap;
 }
@@ -253,10 +258,10 @@ HEAP HEAP_Attach(const void* base, int serial)
         const SHEAP_HeapBlock* b = (const SHEAP_HeapBlock*) base;
         for (;;) {
             if (!HEAP_ISUSED(b)  &&  !HEAP_ISFREE(b)) {
-                CORE_LOGF(eLOG_Error,
-                          ("Heap Attach: Heap corrupt @%u (0x%08X, %u)",
-                           HEAP_INDEX(b, (SHEAP_HeapBlock*) base),
-                           b->head.flag, b->head.size));
+                CORE_LOGF_X(5, eLOG_Error,
+                            ("Heap Attach: Heap corrupt @%u (0x%08X, %u)",
+                             HEAP_INDEX(b, (SHEAP_HeapBlock*) base),
+                             b->head.flag, b->head.size));
                 return 0;
             }
             size += b->head.size;
@@ -404,14 +409,14 @@ static SHEAP_Block* s_HEAP_Alloc(HEAP heap, TNCBI_Size size, int/*bool*/ fast)
     char _id[32];
 
     if (!heap) {
-        CORE_LOG(eLOG_Warning, "Heap Alloc: NULL heap");
+        CORE_LOG_X(6, eLOG_Warning, "Heap Alloc: NULL heap");
         return 0;
     }
     assert(!heap->base == !heap->size);
 
     if (!heap->chunk) {
-        CORE_LOGF(eLOG_Error,
-                  ("Heap Alloc%s: Heap read-only", s_HEAP_Id(_id, heap)));
+        CORE_LOGF_X(7, eLOG_Error,
+                    ("Heap Alloc%s: Heap read-only", s_HEAP_Id(_id, heap)));
         return 0;
     }
     if (size < 1)
@@ -425,11 +430,12 @@ static SHEAP_Block* s_HEAP_Alloc(HEAP heap, TNCBI_Size size, int/*bool*/ fast)
         b = f;
         do {
             if (!HEAP_ISFREE(b)) {
-                CORE_LOGF(eLOG_Error,
-                          ("Heap Alloc%s: Heap%s corrupt @%u/%u (0x%08X, %u)",
-                           s_HEAP_Id(_id, heap), b == f ? " header" : "",
-                           HEAP_INDEX(b, heap->base), heap->size,
-                           b->head.flag, b->head.size));
+                CORE_LOGF_X(8, eLOG_Error,
+                            ("Heap Alloc%s: Heap%s corrupt "
+                             "@%u/%u (0x%08X, %u)",
+                             s_HEAP_Id(_id, heap), b == f ? " header" : "",
+                             HEAP_INDEX(b, heap->base), heap->size,
+                             b->head.flag, b->head.size));
                 return 0;
             }
             if (b->head.size >= size)
@@ -445,17 +451,20 @@ static SHEAP_Block* s_HEAP_Alloc(HEAP heap, TNCBI_Size size, int/*bool*/ fast)
     else if (!heap->resize)
         return 0;
     else {
-        TNCBI_Size hsize = ((size + (heap->size << _HEAP_ALIGNSHIFT)
-                             + heap->chunk - 1) / heap->chunk) * heap->chunk;
+        TNCBI_Size dsize = heap->size << _HEAP_ALIGNSHIFT;
+        TNCBI_Size hsize = ((dsize + size + heap->chunk - 1)
+                            / heap->chunk) * heap->chunk;
         SHEAP_HeapBlock* base = (SHEAP_HeapBlock*)
             heap->resize(heap->base, (size_t) hsize, heap->arg);
         if (_HEAP_ALIGN(base, sizeof(SHEAP_Block)) != (unsigned long) base) {
-            CORE_LOGF(eLOG_Warning,
-                      ("Heap Alloc%s: Unaligned base (0x%08lX)",
-                       s_HEAP_Id(_id, heap), (long) base));
+            CORE_LOGF_X(9, eLOG_Warning,
+                        ("Heap Alloc%s: Unaligned base (0x%08lX)",
+                         s_HEAP_Id(_id, heap), (long) base));
         }
         if (!base)
             return 0;
+        dsize = hsize - dsize;
+        memset(base + heap->size, 0, (size_t) dsize); /* security */
 
         b = base + heap->last;
         if (!heap->base) {
@@ -472,7 +481,7 @@ static SHEAP_Block* s_HEAP_Alloc(HEAP heap, TNCBI_Size size, int/*bool*/ fast)
                 /* New block is at the very top on the heap */
                 b = base + heap->size;
                 b->head.flag = HEAP_FREE | HEAP_LAST;
-                b->head.size = hsize - (heap->size << _HEAP_ALIGNSHIFT);
+                b->head.size = dsize;
                 heap->last   = heap->size;
                 if (heap->free < heap->size) {
                     assert(HEAP_ISFREE(base + heap->free));
@@ -484,11 +493,11 @@ static SHEAP_Block* s_HEAP_Alloc(HEAP heap, TNCBI_Size size, int/*bool*/ fast)
                     b->prevfree = heap->size;
                     b->nextfree = heap->size;
                 }
-                heap->free  = heap->size;
+                heap->free = heap->size;
             } else {
                 /* Extend last free block */
                 assert(HEAP_ISFREE(b));
-                b->head.size += hsize - (heap->size << _HEAP_ALIGNSHIFT);
+                b->head.size += dsize;
             }
         }
         heap->base = base;
@@ -586,14 +595,14 @@ void HEAP_Free(HEAP heap, SHEAP_Block* ptr)
     char _id[32];
 
     if (!heap) {
-        CORE_LOG(eLOG_Warning, "Heap Free: NULL heap");
+        CORE_LOG_X(10, eLOG_Warning, "Heap Free: NULL heap");
         return;
     }
     assert(!heap->base == !heap->size);
 
     if (!heap->chunk) {
-        CORE_LOGF(eLOG_Error,
-                  ("Heap Free%s: Heap read-only", s_HEAP_Id(_id, heap)));
+        CORE_LOGF_X(11, eLOG_Error,
+                    ("Heap Free%s: Heap read-only", s_HEAP_Id(_id, heap)));
         return;
     }
     if (!ptr)
@@ -606,14 +615,14 @@ void HEAP_Free(HEAP heap, SHEAP_Block* ptr)
             if (HEAP_ISUSED(b)) {
                 s_HEAP_Free(heap, p, b);
             } else if (HEAP_ISFREE(b)) {
-                CORE_LOGF(eLOG_Warning,
-                          ("Heap Free%s: Freeing free block @%u",
-                           s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base)));
+                CORE_LOGF_X(12, eLOG_Warning,
+                            ("Heap Free%s: Freeing free block @%u",
+                             s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base)));
             } else {
-                CORE_LOGF(eLOG_Error,
-                          ("Heap Free%s: Heap corrupt @%u/%u (0x%08X, %u)",
-                           s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base),
-                           heap->size, b->head.flag, b->head.size));
+                CORE_LOGF_X(13, eLOG_Error,
+                            ("Heap Free%s: Heap corrupt @%u/%u (0x%08X, %u)",
+                             s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base),
+                             heap->size, b->head.flag, b->head.size));
             }
             return;
         }
@@ -621,8 +630,8 @@ void HEAP_Free(HEAP heap, SHEAP_Block* ptr)
         b = HEAP_NEXT(b);
     }
 
-    CORE_LOGF(eLOG_Error,
-              ("Heap Free%s: Block not found", s_HEAP_Id(_id, heap)));
+    CORE_LOGF_X(14, eLOG_Error,
+                ("Heap Free%s: Block not found", s_HEAP_Id(_id, heap)));
 }
 
 
@@ -632,14 +641,14 @@ void HEAP_FreeFast(HEAP heap, SHEAP_Block* ptr, const SHEAP_Block* prev)
     char _id[32];
 
     if (!heap) {
-        CORE_LOG(eLOG_Warning, "Heap Free: NULL heap");
+        CORE_LOG_X(15, eLOG_Warning, "Heap Free: NULL heap");
         return;
     }
     assert(!heap->base == !heap->size);
 
     if (!heap->chunk) {
-        CORE_LOGF(eLOG_Error,
-                  ("Heap Free%s: Heap read-only", s_HEAP_Id(_id, heap)));
+        CORE_LOGF_X(16, eLOG_Error,
+                    ("Heap Free%s: Heap read-only", s_HEAP_Id(_id, heap)));
         return;
     }
     if (!ptr)
@@ -649,19 +658,19 @@ void HEAP_FreeFast(HEAP heap, SHEAP_Block* ptr, const SHEAP_Block* prev)
     b = (SHEAP_HeapBlock*) ptr;
     if (!s_HEAP_fast) {
         if (b < heap->base  ||  b >= heap->base + heap->size) {
-            CORE_LOGF(eLOG_Error,
-                      ("Heap Free%s: Alien block", s_HEAP_Id(_id, heap)));
+            CORE_LOGF_X(17, eLOG_Error,
+                        ("Heap Free%s: Alien block", s_HEAP_Id(_id, heap)));
             return;
         } else if ((!p  &&  b != heap->base)  ||
                    ( p  &&  (p < heap->base  ||  HEAP_NEXT(p) != b))) {
-            CORE_LOGF(eLOG_Warning,
-                      ("Heap Free%s: Invalid hint", s_HEAP_Id(_id, heap)));
+            CORE_LOGF_X(18, eLOG_Warning,
+                        ("Heap Free%s: Invalid hint", s_HEAP_Id(_id, heap)));
             HEAP_Free(heap, ptr);
             return;
         } else if (HEAP_ISFREE(b)) {
-            CORE_LOGF(eLOG_Warning,
-                      ("Heap Free%s: Freeing free block @%u",
-                       s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base)));
+            CORE_LOGF_X(19, eLOG_Warning,
+                        ("Heap Free%s: Freeing free block @%u",
+                         s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base)));
             return;
         }
     }
@@ -685,9 +694,9 @@ static SHEAP_Block* s_HEAP_Walk(const HEAP heap, const SHEAP_Block* ptr)
                 if (s_HEAP_newalk) {
                     if (HEAP_ISUSED(b)  &&  heap->chunk/*RW heap*/  &&
                         heap->base + heap->free == b) {
-                        CORE_LOGF(eLOG_Warning,
-                                  ("Heap Walk%s: Used block @ free ptr %u",
-                                   s_HEAP_Id(_id, heap), heap->free));
+                        CORE_LOGF_X(20, eLOG_Warning,
+                                    ("Heap Walk%s: Used block @ free ptr %u",
+                                     s_HEAP_Id(_id, heap), heap->free));
                     } else if (HEAP_ISFREE(b)  &&
                                (b->prevfree >= heap->size  ||
                                 b->nextfree >= heap->size  ||
@@ -696,26 +705,28 @@ static SHEAP_Block* s_HEAP_Walk(const HEAP heap, const SHEAP_Block* ptr)
                                 (b->prevfree != b->nextfree
                                  && (heap->base + b->prevfree == b  ||
                                      heap->base + b->nextfree == b)))) {
-                        CORE_LOGF(eLOG_Warning,
-                                  ("Heap Walk%s: Free list corrupt @%u/%u"
-                                   " (%u, <-%u, %u->)", s_HEAP_Id(_id,heap),
-                                   HEAP_INDEX(b, heap->base), heap->size,
-                                   b->head.size, b->prevfree, b->nextfree));
+                        CORE_LOGF_X(21, eLOG_Warning,
+                                    ("Heap Walk%s: Free list corrupt @%u/%u"
+                                     " (%u, <-%u, %u->)", s_HEAP_Id(_id,heap),
+                                     HEAP_INDEX(b, heap->base), heap->size,
+                                     b->head.size, b->prevfree, b->nextfree));
                     }
                 }
                 /* Block 'b' seems okay for walking onto, but... */
                 if (!p)
                     return &b->head;
                 if (HEAP_ISLAST(p)) {
-                    CORE_LOGF(eLOG_Error,
-                              ("Heap Walk%s: Misplaced last block @%u",
-                               s_HEAP_Id(_id,heap), HEAP_INDEX(p,heap->base)));
+                    CORE_LOGF_X(22, eLOG_Error,
+                                ("Heap Walk%s: Misplaced last block @%u",
+                                 s_HEAP_Id(_id,heap),
+                                 HEAP_INDEX(p,heap->base)));
                 } else if (s_HEAP_newalk  &&  heap->chunk/*RW heap*/  &&
                            HEAP_ISLAST(b)  &&  heap->base + heap->last != b) {
-                    CORE_LOGF(eLOG_Error,
-                              ("Heap Walk%s: Last block @%u not @ last ptr %u",
-                               s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base),
-                               heap->last));
+                    CORE_LOGF_X(23, eLOG_Error,
+                                ("Heap Walk%s: Last block @%u "
+                                 "not @ last ptr %u",
+                                 s_HEAP_Id(_id, heap),
+                                 HEAP_INDEX(b, heap->base), heap->last));
                 } else if (HEAP_ISFREE(p)  &&  HEAP_ISFREE(b)) {
                     const SHEAP_HeapBlock* c = heap->base;
                     while (c < p) {
@@ -725,28 +736,31 @@ static SHEAP_Block* s_HEAP_Walk(const HEAP heap, const SHEAP_Block* ptr)
                     }
                     if (c < p)
                         return &b->head;
-                    CORE_LOGF(eLOG_Error,
-                              ("Heap Walk%s: Adjacent free blocks @%u and @%u",
-                               s_HEAP_Id(_id, heap), HEAP_INDEX(p, heap->base),
-                               HEAP_INDEX(b, heap->base)));
+                    CORE_LOGF_X(24, eLOG_Error,
+                                ("Heap Walk%s: Adjacent free blocks "
+                                 "@%u and @%u",
+                                 s_HEAP_Id(_id, heap),
+                                 HEAP_INDEX(p, heap->base),
+                                 HEAP_INDEX(b, heap->base)));
                 } else
                     return &b->head;
             } else {
-                CORE_LOGF(eLOG_Error,
-                          ("Heap Walk%s: Heap corrupt @%u/%u (0x%08X, %u)",
-                           s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base),
-                           heap->size, b->head.flag, b->head.size));
+                CORE_LOGF_X(25, eLOG_Error,
+                            ("Heap Walk%s: Heap corrupt @%u/%u (0x%08X, %u)",
+                             s_HEAP_Id(_id, heap), HEAP_INDEX(b, heap->base),
+                             heap->size, b->head.flag, b->head.size));
             }
         } else if (b > heap->base + heap->size) {
-            CORE_LOGF(eLOG_Error,
-                      ("Heap Walk%s: Heap corrupt", s_HEAP_Id(_id, heap)));
+            CORE_LOGF_X(26, eLOG_Error,
+                        ("Heap Walk%s: Heap corrupt", s_HEAP_Id(_id, heap)));
         } else if (b  &&  !HEAP_ISLAST(p)) {
-            CORE_LOGF(eLOG_Error,
-                      ("Heap Walk%s: Last block lost", s_HEAP_Id(_id, heap)));
+            CORE_LOGF_X(27, eLOG_Error,
+                        ("Heap Walk%s: Last block lost",
+                         s_HEAP_Id(_id, heap)));
         }
     } else {
-        CORE_LOGF(eLOG_Error,
-                  ("Heap Walk%s: Alien pointer", s_HEAP_Id(_id, heap)));
+        CORE_LOGF_X(28, eLOG_Error,
+                    ("Heap Walk%s: Alien pointer", s_HEAP_Id(_id, heap)));
     }
     return 0;
 }
@@ -755,7 +769,7 @@ static SHEAP_Block* s_HEAP_Walk(const HEAP heap, const SHEAP_Block* ptr)
 SHEAP_Block* HEAP_Walk(const HEAP heap, const SHEAP_Block* ptr)
 {
     if (!heap) {
-        CORE_LOG(eLOG_Warning, "Heap Walk: NULL heap");
+        CORE_LOG_X(29, eLOG_Warning, "Heap Walk: NULL heap");
         return 0;
     }
     assert(!heap->base == !heap->size);
@@ -782,8 +796,8 @@ HEAP HEAP_Trim(HEAP heap)
     assert(!heap->base == !heap->size);
  
    if (!heap->chunk) {
-        CORE_LOGF(eLOG_Error,
-                  ("Heap Trim%s: Heap read-only", s_HEAP_Id(_id, heap)));
+        CORE_LOGF_X(30, eLOG_Error,
+                    ("Heap Trim%s: Heap read-only", s_HEAP_Id(_id, heap)));
         return 0;
     }
 
@@ -811,9 +825,9 @@ HEAP HEAP_Trim(HEAP heap)
         else if (!base)
             return 0;
         if (_HEAP_ALIGN(base, sizeof(SHEAP_Block)) != (unsigned long) base) {
-            CORE_LOGF(eLOG_Warning,
-                      ("Heap Trim%s: Unaligned base (0x%08lX)",
-                       s_HEAP_Id(_id, heap), (long) base));
+            CORE_LOGF_X(31, eLOG_Warning,
+                        ("Heap Trim%s: Unaligned base (0x%08lX)",
+                         s_HEAP_Id(_id, heap), (long) base));
         }
         prev = HEAP_INDEX(f, heap->base);
         heap->base = base;
@@ -830,8 +844,8 @@ HEAP HEAP_Trim(HEAP heap)
         assert(hsize == heap->size << _HEAP_ALIGNSHIFT);
         assert(hsize % heap->chunk == 0);
     } else if (hsize != heap->size << _HEAP_ALIGNSHIFT) {
-        CORE_LOGF(eLOG_Error,
-                  ("Heap Trim%s: Heap not trimmable", s_HEAP_Id(_id, heap)));
+        CORE_LOGF_X(32, eLOG_Error,
+                    ("Heap Trim%s: Heap not trimmable", s_HEAP_Id(_id, heap)));
     }
 
     assert(!heap->base == !heap->size);
@@ -894,12 +908,15 @@ void HEAP_Detach(HEAP heap)
 
 void HEAP_Destroy(HEAP heap)
 {
+    char _id[32];
+
     if (!heap)
         return;
     assert(!heap->base == !heap->size);
-    if (!heap->chunk  &&  !heap->refc)
-        CORE_LOG(eLOG_Error, "Heap Destroy: Heap read-only");
-    else if (heap->resize/*NB: NULL for heap copies*/)
+    if (!heap->chunk  &&  !heap->refc) {
+        CORE_LOGF_X(33, eLOG_Error,
+                    ("Heap Destroy%s: Heap read-only", s_HEAP_Id(_id, heap)));
+    } else if (heap->resize/*NB: NULL for heap copies*/)
         verify(heap->resize(heap->base, 0, heap->arg) == 0);
     HEAP_Detach(heap);
 }
diff --git a/connect/ncbi_http_connector.c b/connect/ncbi_http_connector.c
index 90787f33..269d0132 100644
--- a/connect/ncbi_http_connector.c
+++ b/connect/ncbi_http_connector.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_http_connector.c,v 6.84 2007/06/15 20:25:29 kazimird Exp $
+/*  $Id: ncbi_http_connector.c,v 6.89 2007/10/22 13:55:30 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -42,6 +42,9 @@
 #include <stdlib.h>
 
 
+#define NCBI_USE_ERRCODE_X   Connect_HTTP
+
+
 /***********************************************************************
  *  INTERNAL -- Auxiliary types and static functions
  ***********************************************************************/
@@ -54,11 +57,17 @@ typedef enum {
     eCC_Unlimited
 } ECanConnect;
 
-
 typedef unsigned EBCanConnect;
 typedef unsigned TBHCC_Flags;
 
 
+typedef enum {
+    eRM_Regular    = 0,
+    eRM_DropUnread = 1,
+    eRM_WaitCalled = 2
+} EReadMode;
+
+
 /* All internal data necessary to perform the (re)connect and I/O
  *
  * The following states are defined:
@@ -108,18 +117,19 @@ static FHTTP_NcbiMessageHook s_MessageHook   = 0;
 /* Try to fix connection parameters (called for an unconnected connector) */
 static int/*bool*/ s_Adjust(SHttpConnector* uuu,
                             char**          redirect,
-                            int/*bool*/     drop_unread)
+                            EReadMode       read_mode)
 {
-    assert(!uuu->sock && uuu->can_connect != eCC_None);
+    assert(!uuu->sock  &&  uuu->can_connect != eCC_None);
     /* we're here because something is going wrong */
     if (++uuu->failure_count >= uuu->net_info->max_try) {
         if (*redirect) {
             free(*redirect);
             *redirect = 0;
         }
-        if (!drop_unread && uuu->failure_count > 1) {
-            CORE_LOGF(eLOG_Error, ("[HTTP]  Too many failed attempts (%d),"
-                                   " giving up", uuu->failure_count));
+        if (read_mode != eRM_DropUnread  &&  uuu->failure_count > 1) {
+            CORE_LOGF_X(1, eLOG_Error,
+                        ("[HTTP]  Too many failed attempts (%d),"
+                         " giving up", uuu->failure_count));
         }
         uuu->can_connect = eCC_None;
         return 0/*failure*/;
@@ -134,8 +144,8 @@ static int/*bool*/ s_Adjust(SHttpConnector* uuu,
         } else
             status = 0/*failed*/;
         if (!status) {
-            CORE_LOGF(eLOG_Error,
-                      ("[HTTP]  Unable to redirect to \"%s\"", *redirect));
+            CORE_LOGF_X(2, eLOG_Error,
+                        ("[HTTP]  Unable to redirect to \"%s\"", *redirect));
         }
         free(*redirect);
         *redirect = 0;
@@ -143,13 +153,14 @@ static int/*bool*/ s_Adjust(SHttpConnector* uuu,
             uuu->can_connect = eCC_None;
             return 0/*failure*/;
         }
-    } else if (!uuu->adjust_net_info ||
-               uuu->adjust_net_info(uuu->net_info,
-                                    uuu->adjust_data,
-                                    uuu->failure_count) == 0) {
-        if (!drop_unread && uuu->failure_count > 1) {
-            CORE_LOGF(eLOG_Error, ("[HTTP]  Retry attempts (%d) exhausted,"
-                                   " giving up", uuu->failure_count));
+    } else if (!uuu->adjust_net_info
+               ||  uuu->adjust_net_info(uuu->net_info,
+                                        uuu->adjust_data,
+                                        uuu->failure_count) == 0) {
+        if (read_mode != eRM_DropUnread  &&  uuu->failure_count > 1) {
+            CORE_LOGF_X(3, eLOG_Error,
+                        ("[HTTP]  Retry attempts (%d) exhausted,"
+                         " giving up", uuu->failure_count));
         }
         uuu->can_connect = eCC_None;
         return 0/*failure*/;
@@ -166,7 +177,7 @@ static void s_DropConnection(SHttpConnector* uuu, const STimeout* timeout)
     size_t http_size = BUF_Size(uuu->http);
     assert(uuu->sock);
     if (http_size  &&  BUF_Read(uuu->http, 0, http_size) != http_size) {
-        CORE_LOG(eLOG_Error, "[HTTP]  Cannot discard HTTP header buffer");
+        CORE_LOG_X(4, eLOG_Error, "[HTTP]  Cannot discard HTTP header buffer");
         assert(0);
     }
     SOCK_SetTimeout(uuu->sock, eIO_Close, timeout);
@@ -180,11 +191,12 @@ static void s_DropConnection(SHttpConnector* uuu, const STimeout* timeout)
  * is non-zero. If unsuccessful, try to adjust uuu->net_info by s_Adjust(),
  * and then re-try the connection attempt.
  */
-static EIO_Status s_Connect(SHttpConnector* uuu, int/*bool*/ drop_unread)
+static EIO_Status s_Connect(SHttpConnector* uuu,
+                            EReadMode       read_mode)
 {
     assert(!uuu->sock);
     if (uuu->can_connect == eCC_None) {
-        CORE_LOG(eLOG_Error, "[HTTP]  Connector is no longer usable");
+        CORE_LOG_X(5, eLOG_Error, "[HTTP]  Connector is no longer usable");
         return eIO_Closed;
     }
 
@@ -233,7 +245,7 @@ static EIO_Status s_Connect(SHttpConnector* uuu, int/*bool*/ drop_unread)
         }
 
         /* connection failed, no socket was created */
-        if (!s_Adjust(uuu, &null, drop_unread))
+        if (!s_Adjust(uuu, &null, read_mode))
             break;
     }
 
@@ -246,7 +258,8 @@ static EIO_Status s_Connect(SHttpConnector* uuu, int/*bool*/ drop_unread)
  * after the HTTP header. If connection/write unsuccessful, retry to reconnect
  * and send the data again until permitted by s_Adjust().
  */
-static EIO_Status s_ConnectAndSend(SHttpConnector* uuu,int/*bool*/ drop_unread)
+static EIO_Status s_ConnectAndSend(SHttpConnector* uuu,
+                                   EReadMode       read_mode)
 {
     EIO_Status status;
 
@@ -254,7 +267,7 @@ static EIO_Status s_ConnectAndSend(SHttpConnector* uuu,int/*bool*/ drop_unread)
         char*  null = 0;
 
         if (!uuu->sock) {
-            if ((status = s_Connect(uuu, drop_unread)) != eIO_Success)
+            if ((status = s_Connect(uuu, read_mode)) != eIO_Success)
                 break;
             assert(uuu->sock);
             uuu->read_header = 1/*true*/;
@@ -302,15 +315,15 @@ static EIO_Status s_ConnectAndSend(SHttpConnector* uuu,int/*bool*/ drop_unread)
             break;
         }
 
-        CORE_LOGF(eLOG_Error,
-                  ("[HTTP]  Error writing body at offset %lu (%s)",
-                   (unsigned long) (BUF_Size(uuu->w_buf) - uuu->w_len),
-                   IO_StatusStr(status)));
+        CORE_LOGF_X(6, eLOG_Error,
+                    ("[HTTP]  Error writing body at offset %lu (%s)",
+                     (unsigned long) (BUF_Size(uuu->w_buf) - uuu->w_len),
+                     IO_StatusStr(status)));
 
         /* write failed; close and try to use another server */
         SOCK_Abort(uuu->sock);
         s_DropConnection(uuu, 0/*no wait*/);
-        if (!s_Adjust(uuu, &null, drop_unread)) {
+        if (!s_Adjust(uuu, &null, read_mode)) {
             uuu->can_connect = eCC_None;
             status = eIO_Closed;
             break;
@@ -322,7 +335,9 @@ static EIO_Status s_ConnectAndSend(SHttpConnector* uuu,int/*bool*/ drop_unread)
 
 
 /* Parse HTTP header */
-static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
+static EIO_Status s_ReadHeader(SHttpConnector* uuu,
+                               char**          redirect,
+                               EReadMode       read_mode)
 {
     EIO_Status  status = eIO_Success;
     int/*bool*/ moved = 0/*false*/;
@@ -339,8 +354,9 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
         /* do we have full header yet? */
         size = BUF_Size(uuu->http);
         if (!(header = (char*) malloc(size + 1))) {
-            CORE_LOGF(eLOG_Error, ("[HTTP]  Cannot allocate header, %lu bytes",
-                                   (unsigned long) size));
+            CORE_LOGF_X(7, eLOG_Error,
+                        ("[HTTP]  Cannot allocate header, %lu bytes",
+                         (unsigned long) size));
             return eIO_Unknown;
         }
         verify(BUF_Peek(uuu->http, header, size) == size);
@@ -358,25 +374,23 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
                     level = eLOG_Error;
                 else if (tmo->sec | tmo->usec)
                     level = eLOG_Warning;
-                else
-#if defined(NCBI_CXX_TOOLKIT)  ||  defined(_DEBUG)
+                else if (read_mode != eRM_WaitCalled)
                     level = eLOG_Trace;
-#else
+                else
                     return status;
-#endif
             } else
                 level = eLOG_Error;
-            CORE_LOGF(level, ("[HTTP]  Error reading header (%s)",
-                              IO_StatusStr(status)));
+            CORE_LOGF_X(8, level, ("[HTTP]  Error reading header (%s)",
+                                   IO_StatusStr(status)));
             return status;
         }
     }
-    assert(header && status == eIO_Success);
+    assert(header  &&  status == eIO_Success);
     /* the entire header has been read */
     uuu->read_header = 0/*false*/;
 
     if (BUF_Read(uuu->http, 0, size) != size) {
-        CORE_LOG(eLOG_Error, "[HTTP]  Cannot discard HTTP header buffer");
+        CORE_LOG_X(9, eLOG_Error, "[HTTP]  Cannot discard HTTP header buffer");
         status = eIO_Unknown;
         assert(0);
     }
@@ -384,16 +398,16 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
     /* HTTP status must come on the first line of the reply */
     if (sscanf(header, " HTTP/%*d.%*d %d ", &http_status) != 1)
         http_status = -1;
-    if (http_status < 200 || 299 < http_status) {
+    if (http_status < 200  ||  299 < http_status) {
         server_error = http_status;
-        if (http_status == 301 || http_status == 302)
+        if (http_status == 301  ||  http_status == 302)
             moved = 1;
-        else if (http_status < 0 || http_status == 403 || http_status == 404)
+        else if (http_status < 0  ||  http_status == 403 || http_status == 404)
             uuu->net_info->max_try = 0;
     }
 
-    if ((server_error || !uuu->error_header) &&
-        uuu->net_info->debug_printout == eDebugPrintout_Some) {
+    if ((server_error  ||  !uuu->error_header)
+        &&  uuu->net_info->debug_printout == eDebugPrintout_Some) {
         /* HTTP header gets printed as part of data logging when
            uuu->net_info->debug_printout == eDebugPrintout_Data. */
         const char* header_header;
@@ -407,7 +421,7 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
             header_header = "HTTP header (unrecoverable error)";
         else
             header_header = "HTTP header (server error, can retry)";
-        CORE_DATA(header, size, header_header);
+        CORE_DATA_X(19, header, size, header_header);
     }
 
     {{
@@ -434,8 +448,9 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
                         }
                     } else {
                         s_MessageIssued = -1;
-                        CORE_LOGF(eLOG_Warning, ("[NCBI-MESSAGE]  %.*s",
-                                                 (int)(s - message), message));
+                        CORE_LOGF_X(10, eLOG_Warning,
+                                    ("[NCBI-MESSAGE]  %.*s",
+                                     (int)(s - message), message));
                     }
                 }
                 break;
@@ -445,7 +460,7 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
 
     if (uuu->flags & fHCC_KeepHeader) {
         if (!BUF_Write(&uuu->r_buf, header, size)) {
-            CORE_LOG(eLOG_Error, "[HTTP]  Cannot keep HTTP header");
+            CORE_LOG_X(11, eLOG_Error, "[HTTP]  Cannot keep HTTP header");
             status = eIO_Unknown;
         }
         free(header);
@@ -453,7 +468,7 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
     }
 
     if (uuu->parse_http_hdr
-        && !(*uuu->parse_http_hdr)(header, uuu->adjust_data, server_error)) {
+        &&  !(*uuu->parse_http_hdr)(header, uuu->adjust_data, server_error)) {
         server_error = 1/*fake, but still boolean true*/;
     }
 
@@ -522,21 +537,22 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
         /* read until EOF */
         SOCK_StripToPattern(uuu->sock, 0, 0, &buf, 0);
         if (!(size = BUF_Size(buf))) {
-            CORE_LOG(eLOG_Trace,
-                     "[HTTP]  No HTTP body received with this error");
+            CORE_LOG_X(12, eLOG_Trace,
+                       "[HTTP]  No HTTP body received with this error");
         } else if ((body = (char*) malloc(size)) != 0) {
             size_t n = BUF_Read(buf, body, size);
             if (n != size) {
-                CORE_LOGF(eLOG_Error, ("[HTTP]  Cannot read server error "
-                                       "body from buffer (%lu out of %lu)",
-                                       (unsigned long) n,
-                                       (unsigned long) size));
+                CORE_LOGF_X(13, eLOG_Error,
+                            ("[HTTP]  Cannot read server error "
+                             "body from buffer (%lu out of %lu)",
+                             (unsigned long) n, (unsigned long) size));
             }
-            CORE_DATA(body, n, "Server error body");
+            CORE_DATA_X(20, body, n, "Server error body");
             free(body);
         } else {
-            CORE_LOGF(eLOG_Error, ("[HTTP]  Cannot allocate server error "
-                                   "body, %lu bytes", (unsigned long) size));
+            CORE_LOGF_X(14, eLOG_Error,
+                        ("[HTTP]  Cannot allocate server error "
+                         "body, %lu bytes", (unsigned long) size));
         }
         BUF_Destroy(buf);
     }
@@ -554,13 +570,13 @@ static EIO_Status s_ReadHeader(SHttpConnector* uuu, char** redirect)
  */
 static EIO_Status s_PreRead(SHttpConnector* uuu,
                             const STimeout* timeout,
-                            int/*bool*/     drop_unread)
+                            EReadMode       read_mode)
 {
     char* redirect = 0;
     EIO_Status status;
 
     for (;;) {
-        status = s_ConnectAndSend(uuu, drop_unread);
+        status = s_ConnectAndSend(uuu, read_mode);
         if (!uuu->sock) {
             assert(status != eIO_Success);
             break;
@@ -577,24 +593,25 @@ static EIO_Status s_PreRead(SHttpConnector* uuu,
         if (!uuu->read_header)
             break;
 
-        if ((status = s_ReadHeader(uuu, &redirect)) == eIO_Success) {
+        if ((status = s_ReadHeader(uuu, &redirect, read_mode)) == eIO_Success){
             size_t w_size = BUF_Size(uuu->w_buf);
             assert(!uuu->read_header);
             /* pending output data no longer needed */
             if (BUF_Read(uuu->w_buf, 0, w_size) != w_size) {
-                CORE_LOG(eLOG_Error, "[HTTP]  Cannot discard output buffer");
+                CORE_LOG_X(15, eLOG_Error,
+                           "[HTTP]  Cannot discard output buffer");
                 assert(0);
             }
             break;
         }
         /* if polling then bail out with eIO_Timeout */
-        if(status == eIO_Timeout && timeout && !timeout->sec && !timeout->usec)
+        if(status == eIO_Timeout && timeout && !(timeout->sec | timeout->usec))
             break;
 
         /* HTTP header read error; disconnect and try to use another server */
         SOCK_Abort(uuu->sock);
         s_DropConnection(uuu, 0/*no wait*/);
-        if (!s_Adjust(uuu, &redirect, drop_unread)) {
+        if (!s_Adjust(uuu, &redirect, read_mode)) {
             uuu->can_connect = eCC_None;
             break;
         }
@@ -639,7 +656,7 @@ static EIO_Status s_Read(SHttpConnector* uuu, void* buf,
                 status = eIO_Unknown;
 
             if (status != eIO_Success)
-                CORE_LOG(eLOG_Error, "[HTTP]  Cannot URL-decode data");
+                CORE_LOG_X(16, eLOG_Error, "[HTTP]  Cannot URL-decode data");
         }
         free(peek_buf);
     } else {
@@ -663,18 +680,18 @@ static EIO_Status s_Read(SHttpConnector* uuu, void* buf,
 
 /* Reset/readout input data and close socket */
 static EIO_Status s_Disconnect(SHttpConnector* uuu,
-                               int/*bool*/     drop_unread,
-                               const STimeout* timeout)
+                               const STimeout* timeout,
+                               EReadMode       read_mode)
 {
     EIO_Status status = eIO_Success;
 
-    if (drop_unread) {
+    if (read_mode == eRM_DropUnread) {
         size_t r_size = BUF_Size(uuu->r_buf);
         if (r_size  &&  BUF_Read(uuu->r_buf, 0, r_size) != r_size) {
-            CORE_LOG(eLOG_Error, "[HTTP]  Cannot drop input buffer");
+            CORE_LOG_X(17, eLOG_Error, "[HTTP]  Cannot drop input buffer");
             assert(0);
         }
-    } else if ((status = s_PreRead(uuu, timeout, 0/*nodrop*/)) == eIO_Success){
+    } else if ((status = s_PreRead(uuu, timeout, read_mode)) == eIO_Success) {
         do {
             char   buf[4096];
             size_t x_read;
@@ -700,8 +717,8 @@ static EIO_Status s_Disconnect(SHttpConnector* uuu,
  * This function is only called to either re-open or close the connector.
  */
 static void s_FlushAndDisconnect(SHttpConnector* uuu,
-                                 const STimeout* timeout,
-                                 int/*bool*/     close)
+                                 int/*bool*/     close,
+                                 const STimeout* timeout)
 {
     size_t w_size;
 
@@ -716,18 +733,18 @@ static void s_FlushAndDisconnect(SHttpConnector* uuu,
         uuu->w_timeout  = timeout;
     }
 
-    if (close  &&  uuu->can_connect != eCC_None  &&  !uuu->sock  &&
-        ((uuu->flags & fHCC_SureFlush)  ||  BUF_Size(uuu->w_buf))) {
+    if (close  &&  uuu->can_connect != eCC_None  &&  !uuu->sock
+        &&  ((uuu->flags & fHCC_SureFlush)  ||  BUF_Size(uuu->w_buf))) {
         /* "WRITE" mode and data (or just flag) pending */
-        s_PreRead(uuu, timeout, 1/*drop_unread*/);
+        s_PreRead(uuu, timeout, eRM_DropUnread);
     }
-    s_Disconnect(uuu, 1/*drop_unread*/, timeout);
+    s_Disconnect(uuu, timeout, eRM_DropUnread);
     assert(!uuu->sock);
 
     /* clear pending output data, if any */
     w_size = BUF_Size(uuu->w_buf);
     if (w_size  &&  BUF_Read(uuu->w_buf, 0, w_size) != w_size) {
-        CORE_LOG(eLOG_Error, "[HTTP]  Cannot drop output buffer");
+        CORE_LOG_X(18, eLOG_Error, "[HTTP]  Cannot drop output buffer");
         assert(0);
     }
 }
@@ -814,7 +831,7 @@ static EIO_Status s_VT_Open
     /* NOTE: the real connect will be performed on the first "READ", or
      * "CLOSE", or on "WAIT" on read -- see in "s_ConnectAndSend()";
      * we just close underlying socket and prepare to open it later */
-    s_FlushAndDisconnect(uuu, timeout, 0/*open*/);
+    s_FlushAndDisconnect(uuu, 0/*open*/, timeout);
 
     /* reset the auto-reconnect feature */
     uuu->can_connect = uuu->flags & fHCC_AutoReconnect
@@ -836,17 +853,17 @@ static EIO_Status s_VT_Wait
     case eIO_Read:
         if (uuu->can_connect == eCC_None)
             return eIO_Closed;
-        if (!uuu->sock || uuu->read_header) {
-            EIO_Status status = s_PreRead(uuu, timeout, 0/*no drop unread*/);
-            if (status != eIO_Success || BUF_Size(uuu->r_buf))
+        if (!uuu->sock  ||  uuu->read_header) {
+            EIO_Status status = s_PreRead(uuu, timeout, eRM_WaitCalled);
+            if (status != eIO_Success  ||  BUF_Size(uuu->r_buf))
                 return status;
             assert(uuu->sock);
         }
         return SOCK_Wait(uuu->sock, eIO_Read, timeout);
     case eIO_Write:
         /* Return 'Closed' if no more writes are allowed (and now - reading) */
-        return uuu->can_connect == eCC_None ||
-            (uuu->sock && uuu->can_connect == eCC_Once)
+        return uuu->can_connect == eCC_None
+            ||  (uuu->sock  &&  uuu->can_connect == eCC_Once)
             ? eIO_Closed : eIO_Success;
     default:
         assert(0);
@@ -867,9 +884,9 @@ static EIO_Status s_VT_Write
     /* if trying to "WRITE" after "READ" then close the socket,
      * and so switch to "WRITE" mode */
     if (uuu->sock) {
-        EIO_Status status = s_Disconnect(uuu,
-                                         uuu->flags & fHCC_DropUnread,
-                                         timeout);
+        EIO_Status status = s_Disconnect(uuu, timeout,
+                                         uuu->flags & fHCC_DropUnread
+                                         ? eRM_DropUnread : eRM_Regular);
         if (status != eIO_Success)
             return status;
     }
@@ -942,7 +959,7 @@ static EIO_Status s_VT_Read
  const STimeout* timeout)
 {
     SHttpConnector* uuu = (SHttpConnector*) connector->handle;
-    EIO_Status status = s_PreRead(uuu, timeout, 0/*no drop unread*/);
+    EIO_Status status = s_PreRead(uuu, timeout, eRM_Regular);
     size_t x_read = BUF_Read(uuu->r_buf, buf, size);
 
     *n_read = x_read;
@@ -973,7 +990,7 @@ static EIO_Status s_VT_Close
  const STimeout* timeout)
 {
     s_FlushAndDisconnect((SHttpConnector*) connector->handle,
-                         timeout, 1/*close*/);
+                         1/*close*/, timeout);
     return eIO_Success;
 }
 
diff --git a/connect/ncbi_lb.c b/connect/ncbi_lb.c
index 983f3a10..f287e375 100644
--- a/connect/ncbi_lb.c
+++ b/connect/ncbi_lb.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_lb.c,v 1.9 2007/06/07 11:25:52 kazimird Exp $
+/*  $Id: ncbi_lb.c,v 1.12 2008/02/14 16:25:55 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -35,6 +35,9 @@
 #include <stdlib.h>
 
 
+#define NCBI_USE_ERRCODE_X   Connect_LB
+
+
 size_t LB_Select(SERV_ITER     iter,          void*  data,
                  FGetCandidate get_candidate, double bonus)
 {
@@ -82,8 +85,9 @@ size_t LB_Select(SERV_ITER     iter,          void*  data,
             const char* name = SERV_NameOfInfo(info);
             SOCK_HostPortToString(info->host, info->port, addr, sizeof(addr));
             CORE_LOGF(eLOG_Note,
-                      ("%d: %s %s\tR=%lf\tS=%lf\tT=%lf\tA=%lf\tP=%lf", (int) n,
-                       name, addr, info->rate, status, total, access, point));
+                      ("%d: %s %s\tR=%lf\tS=%lf\tT=%lf\tA=%lf\tP=%lf",
+                       (int) n, name, addr, info->rate, status, total,
+                       access, point));
         }}
 #endif /*NCBI_LB_DEBUG*/
     }
@@ -99,8 +103,10 @@ size_t LB_Select(SERV_ITER     iter,          void*  data,
                 p = SERV_Preference(iter->pref, access/total, n);
 #ifdef NCBI_LB_DEBUG
                 CORE_LOGF(eLOG_Note,
-                          ("(P=%lf,\tA=%lf,\tT=%lf,\tA/T=%lf,\tN=%d) -> P=%lf",
-                           iter->pref, access, total, access/total,(int)n, p));
+                          ("(P=%lf,\tA=%lf,\tT=%lf,\tA/T=%lf,\tN=%d) "
+                           "-> P=%lf",
+                           iter->pref, access, total, access/total,
+                           (int) n, p));
 #endif /*NCBI_LB_DEBUG*/
                 status = total * p;
                 p = total * (1.0 - p) / (total - access);
@@ -121,9 +127,10 @@ size_t LB_Select(SERV_ITER     iter,          void*  data,
                     status = cand->status;
                     SOCK_HostPortToString(info->host, info->port,
                                           addr, sizeof(addr));
-                    CORE_LOGF(eLOG_Note, ("%d: %s %s\tS=%lf\t%.2lf%%",
-                                          (int) i, SERV_NameOfInfo(info), addr,
-                                          p, p / total * 100.0));
+                    CORE_LOGF(eLOG_Note,
+                              ("%d: %s %s\tS=%lf\t%.2lf%%",
+                               (int) i, SERV_NameOfInfo(info), addr,
+                               p, p / total * 100.0));
                 }
 #endif /*NCBI_LB_DEBUG*/
             }
diff --git a/connect/ncbi_local.c b/connect/ncbi_local.c
index cbd4df70..9b55e8f5 100644
--- a/connect/ncbi_local.c
+++ b/connect/ncbi_local.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_local.c,v 1.13 2007/04/20 01:55:30 kazimird Exp $
+/*  $Id: ncbi_local.c,v 1.14 2008/02/13 20:25:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -108,7 +108,7 @@ static int/*bool*/ s_LoadSingleService(const char* name, SERV_ITER iter)
             info = 0;
         }
         sprintf(buf, "%s_" REG_CONN_LOCAL_SERVER "_%d", name, n);
-        if (!(c = getenv(strupr(buf)))) {
+        if (!(c = getenv(buf))  &&  !(c = getenv(strupr(buf)))) {
             char*  b = buf + strlen(name);
             size_t len;
             *b++ = '\0';
diff --git a/connect/ncbi_priv.h b/connect/ncbi_priv.h
index b57d5507..110fc322 100644
--- a/connect/ncbi_priv.h
+++ b/connect/ncbi_priv.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_PRIV__H
 #define CONNECT___NCBI_PRIV__H
 
-/*  $Id: ncbi_priv.h,v 6.20 2007/06/25 14:25:36 kazimird Exp $
+/*  $Id: ncbi_priv.h,v 6.26 2008/02/28 19:55:44 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -92,21 +92,42 @@ extern NCBI_XCONNECT_EXPORT const char* g_CORE_Sprintf(const char* fmt, ...)
 #endif
 ;
 
-#define CORE_LOG(level, message)  do { \
-    if (g_CORE_Log  ||  (level) == eLOG_Fatal) { \
-        CORE_LOCK_READ; \
-        LOG_WRITE(g_CORE_Log, level, message); \
-        CORE_UNLOCK; \
-    } \
-} while (0)
+#define DO_CORE_LOG_X(macro, level, params)  do {                       \
+        if (g_CORE_Log  ||  (level) == eLOG_Fatal) {                    \
+            CORE_LOCK_READ;                                             \
+            macro params;  /* parentheses already in params */          \
+            CORE_UNLOCK;                                                \
+        }                                                               \
+    } while (0)
 
-#define CORE_LOGF(level, fmt_args)  do { \
-    if (g_CORE_Log  ||  (level) == eLOG_Fatal) { \
-        CORE_LOCK_READ; \
-        LOG_WRITE(g_CORE_Log, level, g_CORE_Sprintf fmt_args); \
-        CORE_UNLOCK; \
-    } \
-} while (0)
+
+#define DO_CORE_LOG_WRITE(code, subcode, level, message)                \
+    DO_CORE_LOG_X( LOG_WRITE, level,                                    \
+                   (g_CORE_Log, code, subcode, level, message) )
+
+#define DO_CORE_LOG_DATA(code, subcode, level, data, size, message)     \
+    DO_CORE_LOG_X( LOG_DATA, level,                                     \
+                   (g_CORE_Log, code, subcode, level, data, size, message) )
+
+#define DO_CORE_LOG_ERRNO(code, subcode, level, x_errno, x_descr, message) \
+    DO_CORE_LOG_X( LOG_WRITE_ERRNO_EX, level,                           \
+                   (g_CORE_Log, code, subcode, level, message,          \
+                    x_errno, x_descr) )
+
+
+#define CORE_LOG_X(subcode, level, message)                             \
+    DO_CORE_LOG_WRITE(NCBI_C_ERRCODE_X, subcode, level, message)
+
+#define CORE_LOGF_X(subcode, level, fmt_args)                           \
+    DO_CORE_LOG_WRITE(NCBI_C_ERRCODE_X, subcode, level,                 \
+                      g_CORE_Sprintf fmt_args)
+
+#define CORE_LOG(level, message)                                        \
+    DO_CORE_LOG_WRITE(0, 0, level, message)
+
+#define CORE_LOGF(level, fmt_args)                                      \
+    DO_CORE_LOG_WRITE(0, 0, level,                                      \
+                      g_CORE_Sprintf fmt_args)
 
 #ifdef _DEBUG
 #  define CORE_TRACE(message)    CORE_LOG(eLOG_Trace, message)
@@ -118,56 +139,88 @@ extern NCBI_XCONNECT_EXPORT const char* g_CORE_Sprintf(const char* fmt, ...)
 #  define CORE_DEBUG_ARG(arg)    /*arg*/
 #endif /*_DEBUG*/
 
-#define CORE_DATA(data, size, message)  do { \
-    if ( g_CORE_Log ) { \
-        CORE_LOCK_READ; \
-        LOG_DATA(g_CORE_Log, data, size, message); \
-        CORE_UNLOCK; \
-    } \
-} while (0)
+#define CORE_DATA_X(subcode, data, size, message)                       \
+    DO_CORE_LOG_DATA(NCBI_C_ERRCODE_X, subcode, eLOG_Trace, data, size, \
+                     message)
 
-#define CORE_DATAF(data, size, fmt_args)  do { \
-    if ( g_CORE_Log ) { \
-        CORE_LOCK_READ; \
-        LOG_DATA(g_CORE_Log, data, size, g_CORE_Sprintf fmt_args); \
-        CORE_UNLOCK; \
-    } \
-} while (0)
+#define CORE_DATAF_X(subcode, data, size, fmt_args)                     \
+    DO_CORE_LOG_DATA(NCBI_C_ERRCODE_X, subcode, eLOG_Trace, data, size, \
+                     g_CORE_Sprintf fmt_args)
 
-#define CORE_LOG_ERRNO(level, x_errno, message)  do { \
-    if (g_CORE_Log  ||  (level) == eLOG_Fatal) { \
-        CORE_LOCK_READ; \
-        LOG_WRITE_ERRNO_EX(g_CORE_Log, level, message, x_errno, 0); \
-        CORE_UNLOCK; \
-    } \
-} while (0)
+#define CORE_DATA_EXX(subcode, level, data, size, message)              \
+    DO_CORE_LOG_DATA(NCBI_C_ERRCODE_X, subcode, level, data, size, message)
+    
+#define CORE_DATAF_EXX(subcode, level, data, size, fmt_args)            \
+    DO_CORE_LOG_DATA(NCBI_C_ERRCODE_X, subcode, level, data, size,      \
+                     g_CORE_Sprintf fmt_args)
 
-#define CORE_LOGF_ERRNO(level, x_errno, fmt_args)  do { \
-    if (g_CORE_Log  ||  (level) == eLOG_Fatal) { \
-        CORE_LOCK_READ; \
-        LOG_WRITE_ERRNO_EX(g_CORE_Log, level, g_CORE_Sprintf fmt_args, \
-                           x_errno, 0); \
-        CORE_UNLOCK; \
-    } \
-} while (0)
+#define CORE_DATA(data, size, message)                                  \
+    DO_CORE_LOG_DATA(0, 0, eLOG_Trace, data, size, message)
+    
+#define CORE_DATAF(data, size, fmt_args)                                \
+    DO_CORE_LOG_DATA(0, 0, eLOG_Trace, data, size,                      \
+                     g_CORE_Sprintf fmt_args)
 
-#define CORE_LOG_ERRNO_EX(level, x_errno, x_descr, message)  do { \
-    if (g_CORE_Log  ||  (level) == eLOG_Fatal) { \
-        CORE_LOCK_READ; \
-        LOG_WRITE_ERRNO_EX(g_CORE_Log, level, message, x_errno, x_descr); \
-        CORE_UNLOCK; \
-    } \
-} while (0)
+#define CORE_DATA_EX(level, data, size, message)                        \
+    DO_CORE_LOG_DATA(0, 0, level, data, size, message)
 
-#define CORE_LOGF_ERRNO_EX(level, x_errno, x_descr, fmt_args)  do { \
-    if (g_CORE_Log  ||  (level) == eLOG_Fatal) { \
-        CORE_LOCK_READ; \
-        LOG_WRITE_ERRNO_EX(g_CORE_Log, level, g_CORE_Sprintf fmt_args, \
-                           x_errno, x_descr); \
-        CORE_UNLOCK; \
-    } \
-} while (0)
+#define CORE_DATAF_EX(level, data, size, fmt_args)                      \
+    DO_CORE_LOG_DATA(0, 0, level, data, size,                           \
+                     g_CORE_Sprintf fmt_args)
+
+#define CORE_LOG_ERRNO_X(subcode, level, x_errno, message)              \
+    DO_CORE_LOG_ERRNO(NCBI_C_ERRCODE_X, subcode, level, x_errno, 0, message)
+
+#define CORE_LOGF_ERRNO_X(subcode, level, x_errno, fmt_args)            \
+    DO_CORE_LOG_ERRNO(NCBI_C_ERRCODE_X, subcode, level, x_errno, 0,     \
+                      g_CORE_Sprintf fmt_args)
+
+#define CORE_LOG_ERRNO_EXX(subcode, level, x_errno, x_descr, message)   \
+    DO_CORE_LOG_ERRNO(NCBI_C_ERRCODE_X, subcode, level,                 \
+                      x_errno, x_descr, message)
+
+#define CORE_LOGF_ERRNO_EXX(subcode, level, x_errno, x_descr, fmt_args)   \
+    DO_CORE_LOG_ERRNO(NCBI_C_ERRCODE_X, subcode, level, x_errno, x_descr, \
+                      g_CORE_Sprintf fmt_args)
+
+#define CORE_LOG_ERRNO(level, x_errno, message)                         \
+    DO_CORE_LOG_ERRNO(0, 0, level, x_errno, 0, message)
+
+#define CORE_LOGF_ERRNO(level, x_errno, fmt_args)                       \
+    DO_CORE_LOG_ERRNO(0, 0, level, x_errno, 0,                          \
+                      g_CORE_Sprintf fmt_args)
 
+#define CORE_LOG_ERRNO_EX(level, x_errno, x_descr, message)             \
+    DO_CORE_LOG_ERRNO(0, 0, level, x_errno, x_descr, message)
+
+#define CORE_LOGF_ERRNO_EX(level, x_errno, x_descr, fmt_args)           \
+    DO_CORE_LOG_ERRNO(0, 0, level, x_errno, x_descr,                    \
+                      g_CORE_Sprintf fmt_args)
+
+
+/******************************************************************************
+ *  Error codes used throughout C-code
+ */
+
+/* Here are only error codes used in C sources. For error codes used in
+ * C++ sources (in C++ Toolkit) see include/connect/error_codes.hpp.
+ */
+NCBI_C_DEFINE_ERRCODE_X(Connect_Connection, 301,  31);
+NCBI_C_DEFINE_ERRCODE_X(Connect_MetaConn,   302,   2);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Util,       303,  12);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Dispd,      304,   2);
+NCBI_C_DEFINE_ERRCODE_X(Connect_FTP,        305,   1);
+NCBI_C_DEFINE_ERRCODE_X(Connect_HeapMgr,    306,  33);
+NCBI_C_DEFINE_ERRCODE_X(Connect_HTTP,       307,  20);
+NCBI_C_DEFINE_ERRCODE_X(Connect_LB,         308,   0);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Sendmail,   309,  31);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Service,    310,   4);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Socket,     311, 110);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Crypt,      312,   6);
+NCBI_C_DEFINE_ERRCODE_X(Connect_LocalNet,   313,  11);
+NCBI_C_DEFINE_ERRCODE_X(Connect_Mghbn,      319,  16);
+NCBI_C_DEFINE_ERRCODE_X(Connect_LBSM,       320,  22);
+NCBI_C_DEFINE_ERRCODE_X(Connect_LBSMD,      321,   8);
 
 
 /******************************************************************************
diff --git a/connect/ncbi_sendmail.c b/connect/ncbi_sendmail.c
index 4ad28370..4952fb9c 100644
--- a/connect/ncbi_sendmail.c
+++ b/connect/ncbi_sendmail.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_sendmail.c,v 6.32 2007/07/18 19:55:28 kazimird Exp $
+/*  $Id: ncbi_sendmail.c,v 6.35 2008/02/14 17:25:50 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -38,6 +38,9 @@
 #include <ctype.h>
 #include <errno.h>
 #include <stdlib.h>
+
+#define NCBI_USE_ERRCODE_X   Connect_Sendmail
+
 #ifdef NCBI_CXX_TOOLKIT
 #define NCBI_SENDMAIL_TOOLKIT "C++"
 #else
@@ -240,20 +243,21 @@ extern const char* CORE_SendMail(const char* to,
  * the Sun compiler much happier, and less wordy :-)
  */
 
-#define SENDMAIL_RETURN(reason)                                            \
+#define SENDMAIL_RETURN(subcode, reason)                                   \
     do {                                                                   \
         if (sock)                                                          \
             SOCK_Close(sock);                                              \
-        CORE_LOGF(eLOG_Error, ("[SendMail]  %s", reason));                 \
+        CORE_LOGF_X(subcode, eLOG_Error, ("[SendMail]  %s", reason));      \
         if (reason/*always true, though, to trick "smart" compiler*/)      \
             return reason;                                                 \
     } while (0)
 
-#define SENDMAIL_RETURN2(reason, explanation)                              \
+#define SENDMAIL_RETURN2(subcode, reason, explanation)                     \
     do {                                                                   \
        if (sock)                                                           \
            SOCK_Close(sock);                                               \
-       CORE_LOGF(eLOG_Error, ("[SendMail]  %s: %s", reason, explanation)); \
+       CORE_LOGF_X( subcode, eLOG_Error,                                   \
+                    ("[SendMail]  %s: %s", reason, explanation) );         \
        if (reason/*always true, though, to trick "smart" compiler*/)       \
            return reason;                                                  \
     } while (0)
@@ -288,20 +292,21 @@ static const char* s_SendRcpt(SOCK sock, const char* to,
             }
         }
         if (k >= buf_size)
-            SENDMAIL_RETURN("Recepient address is too long");
+            SENDMAIL_RETURN(3, "Recepient address is too long");
         buf[k] = '\0'/*just in case*/;
         if (quote) {
-            CORE_LOGF(eLOG_Warning, ("[SendMail]  Unbalanced delimiters in "
-                                     "recepient %s for %s: \"%c\" expected",
-                                     buf, what, quote));
+            CORE_LOGF_X(1, eLOG_Warning,
+                        ("[SendMail]  Unbalanced delimiters in "
+                         "recepient %s for %s: \"%c\" expected",
+                         buf, what, quote));
         }
         if (!s_SockWrite(sock, "RCPT TO: <", 0)  ||
             !s_SockWrite(sock, buf, k)           ||
             !s_SockWrite(sock, ">" MX_CRLF, 1 + 2)) {
-            SENDMAIL_RETURN(write_error);
+            SENDMAIL_RETURN(4, write_error);
         }
         if (!s_SockReadResponse(sock, 250, 251, buf, buf_size))
-            SENDMAIL_RETURN2(proto_error, buf);
+            SENDMAIL_RETURN2(5, proto_error, buf);
         if (!c)
             break;
     }
@@ -351,45 +356,45 @@ const char* CORE_SendMailEx(const char*          to,
 
     info = uinfo ? uinfo : SendMailInfo_Init(&ainfo);
     if (info->magic_number != MX_MAGIC_NUMBER)
-        SENDMAIL_RETURN("Invalid magic number");
+        SENDMAIL_RETURN(6, "Invalid magic number");
 
     if ((!to         ||  !*to)        &&
         (!info->cc   ||  !*info->cc)  &&
         (!info->bcc  ||  !*info->bcc)) {
-        SENDMAIL_RETURN("At least one message recipient must be specified");
+        SENDMAIL_RETURN(7, "At least one message recipient must be specified");
     }
 
     /* Open connection to sendmail */
     if (SOCK_Create(info->mx_host, info->mx_port, &info->mx_timeout, &sock)
         != eIO_Success) {
-        SENDMAIL_RETURN("Cannot connect to sendmail");
+        SENDMAIL_RETURN(8, "Cannot connect to sendmail");
     }
     SOCK_SetTimeout(sock, eIO_ReadWrite, &info->mx_timeout);
 
     /* Follow the protocol conversation, RFC821 */
     if (!SENDMAIL_READ_RESPONSE(220, 0, buffer))
-        SENDMAIL_RETURN2("Protocol error in connection init", buffer);
+        SENDMAIL_RETURN2(9, "Protocol error in connection init", buffer);
 
     if ((!(info->mx_options & fSendMail_StripNonFQDNHost)  ||
          !SOCK_gethostbyaddr(0, buffer, sizeof(buffer)))  &&
         SOCK_gethostname(buffer, sizeof(buffer)) != 0) {
-        SENDMAIL_RETURN("Unable to get local host name");
+        SENDMAIL_RETURN(10, "Unable to get local host name");
     }
     if (!s_SockWrite(sock, "HELO ", 0)  ||
         !s_SockWrite(sock, buffer, 0)   ||
         !s_SockWrite(sock, MX_CRLF, 2)) {
-        SENDMAIL_RETURN("Write error in HELO command");
+        SENDMAIL_RETURN(11, "Write error in HELO command");
     }
     if (!SENDMAIL_READ_RESPONSE(250, 0, buffer))
-        SENDMAIL_RETURN2("Protocol error in HELO command", buffer);
+        SENDMAIL_RETURN2(12, "Protocol error in HELO command", buffer);
 
     if (!s_SockWrite(sock, "MAIL FROM: <", 0)             ||
         !s_SockWrite(sock, info->from, s_FromSize(info))  ||
         !s_SockWrite(sock, ">" MX_CRLF, 1 + 2)) {
-        SENDMAIL_RETURN("Write error in MAIL command");
+        SENDMAIL_RETURN(13, "Write error in MAIL command");
     }
     if (!SENDMAIL_READ_RESPONSE(250, 0, buffer))
-        SENDMAIL_RETURN2("Protocol error in MAIL command", buffer);
+        SENDMAIL_RETURN2(14, "Protocol error in MAIL command", buffer);
 
     if (to && *to) {
         const char* error = SENDMAIL_SENDRCPT("To", to, buffer);
@@ -410,9 +415,9 @@ const char* CORE_SendMailEx(const char*          to,
     }
 
     if (!s_SockWrite(sock, "DATA" MX_CRLF, 0))
-        SENDMAIL_RETURN("Write error in DATA command");
+        SENDMAIL_RETURN(15, "Write error in DATA command");
     if (!SENDMAIL_READ_RESPONSE(354, 0, buffer))
-        SENDMAIL_RETURN2("Protocol error in DATA command", buffer);
+        SENDMAIL_RETURN2(16, "Protocol error in DATA command", buffer);
 
     if (!(info->mx_options & fSendMail_NoMxHeader)) {
         /* Follow RFC822 to compose message headers. Note that
@@ -421,27 +426,28 @@ const char* CORE_SendMailEx(const char*          to,
         if (!s_SockWrite(sock, "Subject: ", 0)             ||
             (subject  &&  !s_SockWrite(sock, subject, 0))  ||
             !s_SockWrite(sock, MX_CRLF, 2))
-            SENDMAIL_RETURN("Write error in sending subject");
+            SENDMAIL_RETURN(17, "Write error in sending subject");
 
         if (to  &&  *to) {
             if (!s_SockWrite(sock, "To: ", 0)              ||
                 !s_SockWrite(sock, to, 0)                  ||
                 !s_SockWrite(sock, MX_CRLF, 2))
-                SENDMAIL_RETURN("Write error in sending To");
+                SENDMAIL_RETURN(18, "Write error in sending To");
         }
 
         if (info->cc  &&  *info->cc) {
             if (!s_SockWrite(sock, "Cc: ", 0)              ||
                 !s_SockWrite(sock, info->cc, 0)            ||
                 !s_SockWrite(sock, MX_CRLF, 2))
-                SENDMAIL_RETURN("Write error in sending Cc");
+                SENDMAIL_RETURN(19, "Write error in sending Cc");
         }
     } else if (subject && *subject)
-        CORE_LOG(eLOG_Warning,"[SendMail]  Subject ignored in as-is messages");
+        CORE_LOG_X(2, eLOG_Warning,
+                   "[SendMail]  Subject ignored in as-is messages");
 
     if (!s_SockWrite(sock, "X-Mailer: CORE_SendMail (NCBI "
                      NCBI_SENDMAIL_TOOLKIT " Toolkit)" MX_CRLF, 0)) {
-        SENDMAIL_RETURN("Write error in sending mailer information");
+        SENDMAIL_RETURN(20, "Write error in sending mailer information");
     }
 
     assert(sizeof(buffer) > sizeof(MX_CRLF) && sizeof(MX_CRLF) >= 3);
@@ -468,12 +474,12 @@ const char* CORE_SendMailEx(const char*          to,
             }
             buffer[k] = '\0'/*just in case*/;
             if (!s_SockWrite(sock, buffer, k))
-                SENDMAIL_RETURN("Write error while sending custom header");
+                SENDMAIL_RETURN(21, "Write error while sending custom header");
         }
         if (n < m)
-            SENDMAIL_RETURN("Header write error");
+            SENDMAIL_RETURN(22, "Header write error");
         if (!newline && !s_SockWrite(sock, MX_CRLF, 2))
-            SENDMAIL_RETURN("Write error while finalizing custom header");
+            SENDMAIL_RETURN(23, "Write error while finalizing custom header");
     }
 
     if (body) {
@@ -481,7 +487,7 @@ const char* CORE_SendMailEx(const char*          to,
         int/*bool*/ newline = 0/*false*/;
         if (!(info->mx_options & fSendMail_NoMxHeader)  &&  m) {
             if (!s_SockWrite(sock, MX_CRLF, 2))
-                SENDMAIL_RETURN("Write error in message body delimiter");
+                SENDMAIL_RETURN(24, "Write error in message body delimiter");
         }
         while (n < m) {
             size_t k = 0;
@@ -507,24 +513,24 @@ const char* CORE_SendMailEx(const char*          to,
             }
             buffer[k] = '\0'/*just in case*/;
             if (!s_SockWrite(sock, buffer, k))
-                SENDMAIL_RETURN("Write error while sending message body");
+                SENDMAIL_RETURN(25, "Write error while sending message body");
         }
         if (n < m)
-            SENDMAIL_RETURN("Body write error");
+            SENDMAIL_RETURN(26, "Body write error");
         if ((!newline  &&  m  &&  !s_SockWrite(sock, MX_CRLF, 2))
             ||  !s_SockWrite(sock, "." MX_CRLF, 1 + 2)) {
-            SENDMAIL_RETURN("Write error while finalizing message body");
+            SENDMAIL_RETURN(27, "Write error while finalizing message body");
         }
     } else if (!s_SockWrite(sock, "." MX_CRLF, 1 + 2))
-        SENDMAIL_RETURN("Write error while finalizing message");
+        SENDMAIL_RETURN(28, "Write error while finalizing message");
 
     if (!SENDMAIL_READ_RESPONSE(250, 0, buffer))
-        SENDMAIL_RETURN2("Protocol error in sending message", buffer);
+        SENDMAIL_RETURN2(29, "Protocol error in sending message", buffer);
 
     if (!s_SockWrite(sock, "QUIT" MX_CRLF, 0))
-        SENDMAIL_RETURN("Write error in QUIT command");
+        SENDMAIL_RETURN(30, "Write error in QUIT command");
     if (!SENDMAIL_READ_RESPONSE(221, 0, buffer))
-        SENDMAIL_RETURN2("Protocol error in QUIT command", buffer);
+        SENDMAIL_RETURN2(31, "Protocol error in QUIT command", buffer);
 
     SOCK_Close(sock);
     return 0;
diff --git a/connect/ncbi_server_info.c b/connect/ncbi_server_info.c
index 21d6399d..34eef8d5 100644
--- a/connect/ncbi_server_info.c
+++ b/connect/ncbi_server_info.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_server_info.c,v 6.65 2007/05/10 14:25:28 kazimird Exp $
+/*  $Id: ncbi_server_info.c,v 6.66 2007/08/28 18:55:29 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -198,6 +198,9 @@ SSERV_Info* SERV_ReadInfoEx(const char* info_str, const char* name)
             return 0;
         while (*str && isspace((unsigned char)(*str)))
             str++;
+    } else {
+        host = 0;
+        port = 0;
     }
     /* read server-specific info according to the detected type */
     info = s_GetAttrByType(type)->vtable.Read(&str, name ? strlen(name)+1 : 0);
diff --git a/connect/ncbi_service.c b/connect/ncbi_service.c
index c3f9e6af..cc5d5fe4 100644
--- a/connect/ncbi_service.c
+++ b/connect/ncbi_service.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_service.c,v 6.91 2007/04/20 01:55:30 kazimird Exp $
+/*  $Id: ncbi_service.c,v 6.94 2007/10/17 15:25:43 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -39,6 +39,8 @@
 #include <stdlib.h>
 #include <time.h>
 
+#define NCBI_USE_ERRCODE_X   Connect_Service
+
 #define CONN_SERVICE_NAME  DEF_CONN_REG_SECTION "_" REG_CONN_SERVICE_NAME
 
 
@@ -244,7 +246,7 @@ static SERV_ITER s_Open(const char*          service,
          !(do_dispd= !s_IsMapperConfigured(service, REG_CONN_DISPD_DISABLE)) ||
          !(op = SERV_DISPD_Open(iter, net_info, info, host_info)))) {
         if (!do_lbsmd  &&  !do_dispd) {
-            CORE_LOGF(eLOG_Warning,
+            CORE_LOGF_X(1, eLOG_Warning,
                       ("[SERV]  No service mappers available for `%s'",
                        service));
         }
@@ -571,11 +573,11 @@ static void s_SetDefaultReferer(SERV_ITER iter, SConnNetInfo* net_info)
         const char* args = net_info->args;
         char        port[8];
 
-        if (net_info->port && net_info->port != DEF_CONN_PORT)
+        if (net_info->port  &&  net_info->port != DEF_CONN_PORT)
             sprintf(port, ":%hu", net_info->port);
         else
             *port = '\0';
-        if (!(referer = (char*) malloc(9 + strlen(host) + strlen(port)
+        if (!(referer = (char*) malloc(7 + 1 + 1 + strlen(host) + strlen(port)
                                        + strlen(path) + strlen(args)))) {
             return;
         }
@@ -584,6 +586,7 @@ static void s_SetDefaultReferer(SERV_ITER iter, SConnNetInfo* net_info)
             strcat(strcat(referer, "?"), args);
     } else if ((str = strdup(iter->op->name)) != 0) {
         const char* host = net_info->client_host;
+        const char* args = net_info->args;
         const char* name = iter->name;
 
         if (!*net_info->client_host  &&
@@ -592,12 +595,18 @@ static void s_SetDefaultReferer(SERV_ITER iter, SConnNetInfo* net_info)
             SOCK_gethostname(net_info->client_host,
                              sizeof(net_info->client_host));
         }
-        if (!(referer = (char*) malloc(3 + 1 + 9 + 1 + 2*strlen(strlwr(str)) +
-                                       strlen(host) + strlen(name)))) {
+        if (!(referer = (char*) malloc(3 + 1 + 1 + 1 + 2*strlen(strlwr(str)) +
+                                       strlen(host) + (args[0]
+                                                       ? strlen(args)
+                                                       : 8 + strlen(name))))) {
             return;
         }
-        strcat(strcat(strcat(strcpy(referer, str), "://"), host), "/");
-        strcat(strcat(strcat(referer, str), "?service="), name);
+        strcat(strcat(strcat(strcat(strcpy
+                                    (referer, str), "://"), host), "/"), str);
+        if (args[0])
+            strcat(strcat(referer, "?"),         args);
+        else
+            strcat(strcat(referer, "?service="), name);
         free(str);
     }
     assert(!net_info->http_referer);
diff --git a/connect/ncbi_service.h b/connect/ncbi_service.h
index 185c96bd..0c66c4af 100644
--- a/connect/ncbi_service.h
+++ b/connect/ncbi_service.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_SERVICE__H
 #define CONNECT___NCBI_SERVICE__H
 
-/*  $Id: ncbi_service.h,v 6.52 2007/05/09 13:55:29 kazimird Exp $
+/*  $Id: ncbi_service.h,v 6.53 2008/02/04 15:56:18 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -37,9 +37,9 @@
 #include <connect/ncbi_host_info.h>
 
 
-/* Revision 6.230 */
+/* Revision 6.240 */
 #define SERV_CLIENT_REVISION_MAJOR  6
-#define SERV_CLIENT_REVISION_MINOR  230
+#define SERV_CLIENT_REVISION_MINOR  240
 
 
 /** @addtogroup ServiceSupport
diff --git a/connect/ncbi_service_connector.c b/connect/ncbi_service_connector.c
index e2588371..6aab851b 100644
--- a/connect/ncbi_service_connector.c
+++ b/connect/ncbi_service_connector.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_service_connector.c,v 6.73 2006/06/07 20:06:48 lavr Exp $
+/*  $Id: ncbi_service_connector.c,v 6.77 2008/02/02 01:55:55 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -41,6 +41,9 @@
 #include <stdlib.h>
 
 
+#define NCBI_USE_ERRCODE_X   Connect_Service
+
+
 typedef struct SServiceConnectorTag {
     const char*     name;               /* Verbal connector type             */
     TSERV_Type      types;              /* Server types, record keeping only */
@@ -141,15 +144,15 @@ static int/*bool*/ s_ParseHeader(const char* header,
             if (uuu->host)
                 break/*failed - duplicate connection info*/;
             header += sizeof(HTTP_CONNECTION_INFO) - 1;
-            while (*header && isspace((unsigned char)(*header)))
+            while (*header  &&  isspace((unsigned char)(*header)))
                 header++;
             if (strncasecmp(header, kStateless, sizeof(kStateless) - 1) == 0) {
                 /* Special keyword for switching into stateless mode */
                 uuu->host = (unsigned int)(-1);
 #if defined(_DEBUG) && !defined(NDEBUG)
                 if (uuu->net_info->debug_printout) {
-                    CORE_LOG(eLOG_Note,
-                             "[SERVICE]  Fallback to stateless requested");
+                    CORE_LOG_X(2, eLOG_Note,
+                               "[SERVICE]  Fallback to stateless requested");
                 }
 #endif
             } else {
@@ -159,7 +162,7 @@ static int/*bool*/ s_ParseHeader(const char* header,
                 }
                 o1 = i1; o2 = i2; o3 = i3; o4 = i4;
                 sprintf(ipaddr, "%u.%u.%u.%u", o1, o2, o3, o4);
-                if (!(uuu->host = SOCK_gethostbyname(ipaddr)) || !uuu->port)
+                if (!(uuu->host = SOCK_gethostbyname(ipaddr))  ||  !uuu->port)
                     break/*failed - bad host:port in connection info*/;
                 uuu->ticket = SOCK_HostToNetLong(ticket);
             }
@@ -167,7 +170,7 @@ static int/*bool*/ s_ParseHeader(const char* header,
         if ((header = strchr(header, '\n')) != 0)
             header++;
     }
-    if (!header || !*header)
+    if (!header  ||  !*header)
         return 1/*success*/;
 
     uuu->host = 0;
@@ -175,15 +178,15 @@ static int/*bool*/ s_ParseHeader(const char* header,
 }
 
 
-static int/*bool*/ s_ContentTypeDefined(const SConnNetInfo* net_info,
-                                        EMIME_Type          mime_t,
-                                        EMIME_SubType       mime_s,
-                                        EMIME_Encoding      mime_e)
+static int/*bool*/ s_IsContentTypeDefined(const SConnNetInfo* net_info,
+                                          EMIME_Type          mime_t,
+                                          EMIME_SubType       mime_s,
+                                          EMIME_Encoding      mime_e)
 {
     const char* s;
 
     assert(net_info);
-    for (s = net_info->http_user_header; s; s = strchr(s, '\n')) {
+    for (s = net_info->http_user_header;  s;  s = strchr(s, '\n')) {
         if (s != net_info->http_user_header)
             s++;
         if (!*s)
@@ -197,13 +200,13 @@ static int/*bool*/ s_ContentTypeDefined(const SConnNetInfo* net_info,
             if (net_info->debug_printout                      &&
                 mime_t != SERV_MIME_TYPE_UNDEFINED            &&
                 mime_t != eMIME_T_Unknown                     &&
-                MIME_ParseContentTypeEx(s, &m_t, &m_s, &m_e)  &&
-                (mime_t != m_t
-                 ||  (mime_s != SERV_MIME_SUBTYPE_UNDEFINED &&
-                      mime_s != eMIME_Unknown &&
-                      m_s != eMIME_Unknown && mime_s != m_s)
-                 ||  (mime_e != eENCOD_None &&
-                      m_e != eENCOD_None && mime_e != m_e))) {
+                (!MIME_ParseContentTypeEx(s, &m_t, &m_s, &m_e)
+                 ||   mime_t != m_t
+                 ||  (mime_s != SERV_MIME_SUBTYPE_UNDEFINED  &&
+                      mime_s != eMIME_Unknown                &&
+                      m_s    != eMIME_Unknown  &&  mime_s != m_s)
+                 ||  (mime_e != eENCOD_None                  &&
+                      m_e    != eENCOD_None    &&  mime_e != m_e))) {
                 const char* c;
                 size_t len;
                 char* t;
@@ -213,7 +216,7 @@ static int/*bool*/ s_ContentTypeDefined(const SConnNetInfo* net_info,
                 }
                 if (!(c = strchr(s, '\n')))
                     c = s + strlen(s);
-                if (c > s && c[-1] == '\r')
+                if (c > s  &&  c[-1] == '\r')
                     c--;
                 len = (size_t)(c - s);
                 if ((t = (char*) malloc(len + 1)) != 0) {
@@ -224,14 +227,16 @@ static int/*bool*/ s_ContentTypeDefined(const SConnNetInfo* net_info,
                                                c_t, sizeof(c_t))) {
                     *c_t = '\0';
                 }
-                CORE_LOGF(eLOG_Warning,
-                          ("[SERVICE]  Content-Type mismatch for \"%s\" "
-                           "%s%s%s%s%s", net_info->service,
-                           t && *t         ? "specified="  : "",
-                           t && *t         ? t             : "",
-                           t && *t && *c_t ? ", "          : "",
-                           *c_t            ? "configured=" : "",
-                           *c_t            ? c_t           : ""));
+                CORE_LOGF_X(3, eLOG_Warning,
+                            ("[SERVICE]  Content-Type mismatch for \"%s\" "
+                             "%s%s%s%s%s%s%s", net_info->service,
+                             t  &&  *t           ? "specified=<"  : "",
+                             t  &&  *t           ? t              : "",
+                             t  &&  *t           ? ">"            : "",
+                             t  &&  *t  &&  *c_t ? ", "           : "",
+                             *c_t                ? "configured=<" : "",
+                             *c_t                ? c_t            : "",
+                             *c_t                ? ">"            : ""));
                 if (t)
                     free(t);
             }
@@ -243,19 +248,18 @@ static int/*bool*/ s_ContentTypeDefined(const SConnNetInfo* net_info,
 }
 
 
-static char* s_AdjustNetParams(SConnNetInfo*  net_info,
-                               EReqMethod     req_method,
-                               const char*    cgi_path,
-                               const char*    cgi_args,
-                               const char*    args,
-                               const char*    static_header,
-                               EMIME_Type     mime_t,
-                               EMIME_SubType  mime_s,
-                               EMIME_Encoding mime_e,
-                               char*          dynamic_header/*will be freed*/)
+static const char* s_AdjustNetParams(SConnNetInfo*  net_info,
+                                     EReqMethod     req_method,
+                                     const char*    cgi_path,
+                                     const char*    cgi_args,
+                                     const char*    args,
+                                     const char*    static_header,
+                                     EMIME_Type     mime_t,
+                                     EMIME_SubType  mime_s,
+                                     EMIME_Encoding mime_e,
+                                     char*          dynamic_header/*freed!*/)
 {
-    char c_t[MAX_CONTENT_TYPE_LEN], *retval;
-    size_t sh_len, dh_len, ct_len;
+    const char *retval = 0;
 
     net_info->req_method = req_method;
 
@@ -265,30 +269,36 @@ static char* s_AdjustNetParams(SConnNetInfo*  net_info,
     if (args)
         strncpy0(net_info->args, args, sizeof(net_info->args) - 1);
     ConnNetInfo_DeleteAllArgs(net_info, cgi_args);
-    if (!ConnNetInfo_PrependArg(net_info, cgi_args, 0)) {
-        if (dynamic_header)
-            free(dynamic_header);
-        return 0/*failed*/;
-    }
 
-    sh_len = static_header  ? strlen(static_header)  : 0;
-    dh_len = dynamic_header ? strlen(dynamic_header) : 0;
-    if (s_ContentTypeDefined(net_info, mime_t, mime_s, mime_e)  ||
-        mime_t == SERV_MIME_TYPE_UNDEFINED                      ||
-        mime_s == SERV_MIME_SUBTYPE_UNDEFINED                   ||
-        !MIME_ComposeContentTypeEx(mime_t, mime_s, mime_e, c_t, sizeof(c_t))) {
-        c_t[0] = '\0';
-        ct_len = 0;
-    } else
-        ct_len = strlen(c_t);
-    if ((retval = (char*) malloc(sh_len + dh_len +ct_len + 1/*EOL*/)) != 0) {
-        strcpy(retval,                   static_header  ? static_header  : "");
-        strcpy(retval + sh_len,          dynamic_header ? dynamic_header : "");
-        strcpy(retval + sh_len + dh_len, c_t);
+    if (ConnNetInfo_PrependArg(net_info, cgi_args, 0)) {
+        size_t sh_len = static_header  ? strlen(static_header)  : 0;
+        size_t dh_len = dynamic_header ? strlen(dynamic_header) : 0;
+        char   c_t[MAX_CONTENT_TYPE_LEN];
+        size_t ct_len, len;
+
+        if (s_IsContentTypeDefined(net_info, mime_t, mime_s, mime_e)  ||
+            mime_t == SERV_MIME_TYPE_UNDEFINED                        ||
+            mime_s == SERV_MIME_SUBTYPE_UNDEFINED                     ||
+            !MIME_ComposeContentTypeEx(mime_t, mime_s, mime_e,
+                                       c_t, sizeof(c_t))) {
+            c_t[0] = '\0';
+            ct_len = 0;
+        } else
+            ct_len = strlen(c_t);
+        if ((len = sh_len + dh_len + ct_len) != 0) {
+            char* temp = (char*) malloc(len + 1/*EOL*/);
+            if (temp) {
+                strcpy(temp,          static_header  ? static_header  : "");
+                strcpy(temp + sh_len, dynamic_header ? dynamic_header : "");
+                strcpy(temp + sh_len + dh_len, c_t);
+                retval = temp;
+            }
+        } else
+            retval = "";
     }
+
     if (dynamic_header)
         free(dynamic_header);
-
     return retval;
 }
 
@@ -326,7 +336,7 @@ static int/*bool*/ s_AdjustNetInfo(SConnNetInfo* net_info,
     const SSERV_Info* info;
 
     assert(n != 0); /* paranoid assertion :-) */
-    if (uuu->net_info->firewall && !uuu->net_info->stateless)
+    if (uuu->net_info->firewall  &&  !uuu->net_info->stateless)
         return 0; /*cannot adjust firewall stateful client*/
 
     for (;;) {
@@ -394,11 +404,11 @@ static int/*bool*/ s_AdjustNetInfo(SConnNetInfo* net_info,
         ConnNetInfo_DeleteUserHeader(net_info, uuu->user_header);
         free((void*) uuu->user_header);
     }
-    uuu->user_header = user_header;
+    uuu->user_header = *user_header ? user_header : 0;
     if (!ConnNetInfo_OverrideUserHeader(net_info, user_header))
         return 0/*false - not adjusted*/;
 
-    if (info->type == fSERV_Ncbid || (info->type & fSERV_Http)) {
+    if (info->type == fSERV_Ncbid  ||  (info->type & fSERV_Http)) {
         SOCK_ntoa(info->host, net_info->host, sizeof(net_info->host));
         net_info->port = info->port;
     } else {
@@ -420,10 +430,10 @@ static CONNECTOR s_Open(SServiceConnector* uuu,
                         int/*bool*/        second_try)
 {
     const char* user_header; /* either "" or non-empty dynamic string */
-    char*       iter_header;
+    char*       iter_header = SERV_Print(uuu->iter, net_info);
     EReqMethod  req_method;
 
-    if (info && info->type != fSERV_Firewall) {
+    if (info  &&  info->type != fSERV_Firewall) {
         /* Not a firewall/relay connection here */
         assert(!second_try);
         /* We know the connection point, let's try to use it! */
@@ -488,8 +498,8 @@ static CONNECTOR s_Open(SServiceConnector* uuu,
         EMIME_Type     mime_t;
         EMIME_SubType  mime_s;
         EMIME_Encoding mime_e;
-        if (net_info->stateless ||
-            (info && (info->u.firewall.type & fSERV_Http))) {
+        if (net_info->stateless  ||
+            (info  &&  (info->u.firewall.type & fSERV_Http))) {
             if (info) {
                 req_method = info->u.firewall.type == fSERV_HttpGet
                     ? eReqMethod_Get : (info->u.firewall.type == fSERV_HttpPost
@@ -516,10 +526,13 @@ static CONNECTOR s_Open(SServiceConnector* uuu,
                                         0, 0, 0, user_header,
                                         mime_t, mime_s, mime_e, 0);
     }
-    if (!user_header)
+    if (!user_header) {
+        if (iter_header)
+            free(iter_header);
         return 0;
+    }
 
-    if ((iter_header = SERV_Print(uuu->iter, net_info)) != 0) {
+    if (iter_header) {
         size_t uh_len;
         if ((uh_len = strlen(user_header)) > 0) {
             char*  ih;
@@ -554,9 +567,9 @@ static CONNECTOR s_Open(SServiceConnector* uuu,
              "\r\n");
     }
 
-    if (!net_info->stateless && (!info                        ||
-                                 info->type == fSERV_Firewall ||
-                                 info->type == fSERV_Ncbid)) {
+    if (!net_info->stateless  &&  (!info                         ||
+                                   info->type == fSERV_Firewall  ||
+                                   info->type == fSERV_Ncbid)) {
         /* HTTP connector is auxiliary only */
         CONNECTOR conn;
         CONN c;
@@ -580,20 +593,20 @@ static CONNECTOR s_Open(SServiceConnector* uuu,
             /* This also triggers parse header callback */
             CONN_Close(c);
         } else {
-            CORE_LOGF(eLOG_Error, ("[SERVICE]  Unable to create aux. %s",
-                                   conn ? "connection" : "connector"));
+            CORE_LOGF_X(4, eLOG_Error, ("[SERVICE]  Unable to create aux. %s",
+                                        conn ? "connection" : "connector"));
             assert(0);
         }
         if (!uuu->host)
             return 0/*failed, no connection info returned*/;
         if (uuu->host == (unsigned int)(-1)) {
             /* Firewall mode only in stateful mode, fallback requested */
-            assert((!info || info->type == fSERV_Firewall) && !second_try);
+            assert((!info  ||  info->type == fSERV_Firewall)  &&  !second_try);
             /* Try to use stateless mode instead */
             net_info->stateless = 1/*true*/;
             return s_Open(uuu, timeout, info, net_info, 1/*second try*/);
         }
-        if (net_info->firewall && *net_info->proxy_host)
+        if (net_info->firewall  &&  *net_info->proxy_host)
             strcpy(net_info->host, net_info->proxy_host);
         else
             SOCK_ntoa(uuu->host, net_info->host, sizeof(net_info->host));
@@ -670,7 +683,7 @@ static EIO_Status s_VT_Open(CONNECTOR connector, const STimeout* timeout)
     CONNECTOR conn;
 
     assert(!uuu->meta.list && !uuu->name);
-    if (!uuu->iter && !s_OpenDispatcher(uuu)) {
+    if (!uuu->iter  &&  !s_OpenDispatcher(uuu)) {
         uuu->status = status;
         return status;
     }
@@ -720,7 +733,7 @@ static EIO_Status s_VT_Open(CONNECTOR connector, const STimeout* timeout)
                 static const char prefix[] = "SERVICE/";
                 char* name = (char*) malloc(sizeof(prefix) + strlen(type));
                 if (name) {
-                    strcpy(&name[0],                prefix);
+                    memcpy(&name[0],                prefix, sizeof(prefix)-1);
                     strcpy(&name[sizeof(prefix)-1], type);
                     uuu->name = name;
                 }
@@ -757,9 +770,9 @@ static void s_Setup(SMetaConnector *meta, CONNECTOR connector)
 {
     SServiceConnector* uuu = (SServiceConnector*) connector->handle;
     /* initialize virtual table */
-    CONN_SET_METHOD(meta, get_type,   s_VT_GetType,   connector);
-    CONN_SET_METHOD(meta, open,       s_VT_Open,      connector);
-    CONN_SET_METHOD(meta, close,      s_VT_Close,     connector);
+    CONN_SET_METHOD(meta, get_type, s_VT_GetType, connector);
+    CONN_SET_METHOD(meta, open,     s_VT_Open,    connector);
+    CONN_SET_METHOD(meta, close,    s_VT_Close,   connector);
     CONN_SET_DEFAULT_TIMEOUT(meta, uuu->net_info->timeout);
     /* all the rest is reset to NULL */
     s_Reset(meta);
@@ -798,7 +811,7 @@ extern CONNECTOR SERVICE_CreateConnectorEx
     CONNECTOR          ccc;
     SServiceConnector* xxx;
 
-    if (!service || !*service)
+    if (!service  ||  !*service)
         return 0;
 
     ccc = (SConnector*)        malloc(sizeof(SConnector));
@@ -843,240 +856,3 @@ extern CONNECTOR SERVICE_CreateConnectorEx
     /* done */
     return ccc;
 }
-
-
-/*
- * --------------------------------------------------------------------------
- * $Log: ncbi_service_connector.c,v $
- * Revision 6.73  2006/06/07 20:06:48  lavr
- * Adjust use of net_infos passed to SERV_Print()
- *
- * Revision 6.72  2006/04/23 18:27:54  lavr
- * BUGFIX:  typo in SServiceConnector allocation caused memory corruption
- *
- * Revision 6.71  2006/04/20 14:00:59  lavr
- * Keep original service name and use it for service mappers
- *
- * Revision 6.70  2006/01/27 17:10:24  lavr
- * Replace obsolete call names with current ones
- *
- * Revision 6.69  2006/01/17 20:28:21  lavr
- * Do not override user-provided Content-Type
- *
- * Revision 6.68  2006/01/12 18:12:46  lavr
- * Fix erroneous use of non-translated service name
- * Stricter checks on uniqueness of returned Connection-Info:
- *
- * Revision 6.67  2006/01/11 20:28:47  lavr
- * Take advantage of ConnNetInfo_SetupStandardArgs();  other changes to
- * allow to pass user-supplied parameters to services (where feasible)
- *
- * Revision 6.66  2006/01/11 16:28:28  lavr
- * Simplify code (mostly, by factoring out)
- *
- * Revision 6.65  2005/12/23 18:12:32  lavr
- * fSERV_StatelessOnly -> fSERV_Stateless
- *
- * Revision 6.64  2005/10/26 14:44:59  lavr
- * Insure service name appears in URLs for HTTP services
- *
- * Revision 6.63  2005/08/12 19:21:52  lavr
- * Take fHCC_Flushable from connector's extra params in case of HTTP
- *
- * Revision 6.62  2005/07/11 18:15:30  lavr
- * SERV_PrintEx() -> SERV_Print()
- *
- * Revision 6.61  2004/07/01 16:28:44  lavr
- * Generate "Referer:" for resolved HTTP service hits
- *
- * Revision 6.60  2003/08/25 14:41:53  lavr
- * Employ new k..Timeout constants  --  log modification only
- *
- * Revision 6.59  2003/05/31 05:16:45  lavr
- * Add ARGSUSED where args are meant to be unused
- *
- * Revision 6.58  2003/05/29 20:13:48  lavr
- * -#include <connect/ncbi_connection.h>
- *
- * Revision 6.57  2003/05/22 20:31:28  lavr
- * Callbacks in the constructor had to be set after successful init only
- *
- * Revision 6.56  2003/05/14 15:43:45  lavr
- * Modify format of host address in dispatcher's CGI query
- *
- * Revision 6.55  2003/05/14 13:55:06  lavr
- * BUGFIX: Buffer overrun in s_GetArgs()
- *
- * Revision 6.54  2003/05/14 04:19:48  lavr
- * BUGFIX: Actually add IP address in "address=" CGI argument
- *
- * Revision 6.53  2003/05/14 03:55:28  lavr
- * Arguments to include host address (for statistics purposes on backends)
- *
- * Revision 6.52  2002/12/19 17:34:58  lavr
- * Do not initiate STATEFUL_CAPABLE challenge with HTTP servers in relay mode
- *
- * Revision 6.51  2002/12/10 22:11:50  lavr
- * Stamp HTTP packets with "User-Agent:" header tag and DISP_PROTOCOL_VERSION
- *
- * Revision 6.50  2002/11/19 19:23:25  lavr
- * Set MIME type whenever possible; introduce status of last op
- *
- * Revision 6.49  2002/11/12 05:52:00  lavr
- * Use client_host from conn.info as value for "address="
- *
- * Revision 6.48  2002/11/01 20:16:05  lavr
- * Expand hostname buffers to hold up to 256 chars
- *
- * Revision 6.47  2002/10/29 22:19:37  lavr
- * Fix proper use of non-transparent proxy if one is specified
- *
- * Revision 6.46  2002/10/28 15:44:00  lavr
- * Use "ncbi_ansi_ext.h" privately and use strncpy0()
- *
- * Revision 6.45  2002/10/22 15:11:24  lavr
- * Zero connector's handle to crash if revisited
- *
- * Revision 6.44  2002/10/21 18:32:28  lavr
- * Append service arguments "address" and "platform" in dispatcher requests
- *
- * Revision 6.43  2002/10/11 19:56:42  lavr
- * Add "myargs" into connector structure (for later use in requests to
- * show address and platform of the dispatcher's requestors)
- *
- * Revision 6.42  2002/09/06 17:45:33  lavr
- * Include <connect/ncbi_priv.h> unconditionally (reported by J.Kans)
- *
- * Revision 6.41  2002/09/06 15:44:02  lavr
- * Use fHCC_SureFlush and CONN_Flush() instead of dummy read
- *
- * Revision 6.40  2002/08/07 16:33:33  lavr
- * Changed EIO_ReadMethod enums accordingly; log moved to end
- *
- * Revision 6.39  2002/06/10 19:51:43  lavr
- * Wrong assertion removed from FIREWALL open case
- *
- * Revision 6.38  2002/05/07 15:31:47  lavr
- * +#include <stdio.h>: noticed by J.Kans
- *
- * Revision 6.37  2002/05/06 19:17:33  lavr
- * Take advantage of SERV_ServiceName()
- *
- * Revision 6.36  2002/04/26 16:28:51  lavr
- * SSERVICE_Params: reset added for use in open/close pairs
- * No checks for kDefaultTimeout: now real timeouts always go from CONN
- *
- * Revision 6.35  2002/03/30 03:34:32  lavr
- * BUGFIX: Memory leak from SERV_ITER in usused connector
- *
- * Revision 6.34  2002/03/22 22:18:28  lavr
- * Remove uuu->conn (contained in uuu->meta.list); honor timeout on open
- *
- * Revision 6.33  2002/03/22 19:52:18  lavr
- * Do not include <stdio.h>: included from ncbi_util.h or ncbi_priv.h
- *
- * Revision 6.32  2002/03/19 22:14:53  lavr
- * Proper indentation of nested preprocessor directives
- *
- * Revision 6.31  2002/03/11 22:00:22  lavr
- * Support encoding in MIME content type for server data
- *
- * Revision 6.30  2001/12/04 15:56:47  lavr
- * Use strdup() instead of explicit strcpy(malloc(...), ...)
- *
- * Revision 6.29  2001/10/26 21:17:59  lavr
- * 'service=name' now always precedes other params in connects to DISPD/NCBID
- *
- * Revision 6.28  2001/09/28 20:51:31  lavr
- * Comments revised; parameter (and SHttpConnector's) names adjusted
- * Retry logic moved entirely into s_Adjust()
- *
- * Revision 6.27  2001/09/24 20:29:36  lavr
- * +SSERVICE_Extra* parameter in constructor; store and use of this parameter
- *
- * Revision 6.26  2001/09/10 21:21:20  lavr
- * Support for temporary switching into firewall mode as per dispatcher request
- *
- * Revision 6.25  2001/07/26 15:12:17  lavr
- * while(1) -> for(;;)
- *
- * Revision 6.24  2001/06/05 14:11:29  lavr
- * SERV_MIME_UNDEFINED split into 2 (typed) constants:
- * SERV_MIME_TYPE_UNDEFINED and SERV_MIME_SUBTYPE_UNDEFINED
- *
- * Revision 6.23  2001/06/04 17:02:17  lavr
- * Insert MIME type/subtype in Content-Type for servers,
- * which have this feature configured
- *
- * Revision 6.22  2001/05/30 18:46:38  lavr
- * Always call dispatcher in header-parsing callback (to see err.msg. if any)
- *
- * Revision 6.21  2001/05/23 21:53:19  lavr
- * Do not close dispatcher in Open; leave it as it is
- *
- * Revision 6.20  2001/05/17 15:03:07  lavr
- * Typos corrected
- *
- * Revision 6.19  2001/05/11 15:32:05  lavr
- * Minor patch in code of 'fallback to STATELESS'
- *
- * Revision 6.18  2001/05/08 20:27:05  lavr
- * Patches in re-try code
- *
- * Revision 6.17  2001/05/03 16:37:09  lavr
- * Flow control fixed in s_Open for firewall connection
- *
- * Revision 6.16  2001/04/26 20:20:57  lavr
- * Default tags are explicitly used to differ from a Web browser
- *
- * Revision 6.15  2001/04/25 15:49:54  lavr
- * Memory leaks in Open (when unsuccessful) fixed
- *
- * Revision 6.14  2001/04/24 21:36:50  lavr
- * More structured code to re-try abrupted connection/mapping attempts
- *
- * Revision 6.13  2001/03/07 23:01:07  lavr
- * fSERV_Any used instead of 0 in SERVICE_CreateConnector
- *
- * Revision 6.12  2001/03/06 23:55:37  lavr
- * SOCK_gethostaddr -> SOCK_gethostbyname
- *
- * Revision 6.11  2001/03/02 20:10:07  lavr
- * Typo fixed
- *
- * Revision 6.10  2001/03/01 00:32:15  lavr
- * FIX: Empty update does not generate parse error
- *
- * Revision 6.9  2001/02/09 17:35:45  lavr
- * Modified: fSERV_StatelessOnly overrides info->stateless
- * Bug fixed: free(type) -> free(name)
- *
- * Revision 6.8  2001/01/25 17:04:43  lavr
- * Reversed:: DESTROY method calls free() to delete connector structure
- *
- * Revision 6.7  2001/01/23 23:09:19  lavr
- * Flags added to 'Ex' constructor
- *
- * Revision 6.6  2001/01/11 16:38:18  lavr
- * free(connector) removed from s_Destroy function
- * (now always called from outside, in METACONN_Remove)
- *
- * Revision 6.5  2001/01/08 22:39:40  lavr
- * Further development of service-mapping protocol: stateless/stateful
- * is now separated from firewall/direct mode (see also in few more files)
- *
- * Revision 6.4  2001/01/03 22:35:53  lavr
- * Next working revision (bugfixes and protocol changes)
- *
- * Revision 6.3  2000/12/29 18:05:12  lavr
- * First working revision.
- *
- * Revision 6.2  2000/10/20 17:34:39  lavr
- * Partially working service connector (service mapping works)
- * Checkin for backup purposes
- *
- * Revision 6.1  2000/10/07 22:14:07  lavr
- * Initial revision, placeholder mostly
- *
- * ==========================================================================
- */
diff --git a/connect/ncbi_socket.c b/connect/ncbi_socket.c
index 3eb2cc54..411e619c 100644
--- a/connect/ncbi_socket.c
+++ b/connect/ncbi_socket.c
@@ -1,4 +1,4 @@
-/*  $Id: ncbi_socket.c,v 6.210 2007/08/21 16:55:29 kazimird Exp $
+/*  $Id: ncbi_socket.c,v 6.224 2008/02/18 14:55:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -40,6 +40,8 @@
 #include <connect/ncbi_buffer.h>
 #include <connect/ncbi_socket_unix.h>
 
+#define NCBI_USE_ERRCODE_X   Connect_Socket
+
 /* OS must be specified in the command-line ("-D....") or in the conf. header
  */
 #if !defined(NCBI_OS_UNIX) && !defined(NCBI_OS_MSWIN) && !defined(NCBI_OS_MAC)
@@ -57,7 +59,6 @@
 /* #define HAVE_GETADDRINFO 1 */
 /* #define HAVE_GETNAMEINFO 1 */
 
-
 /* Uncomment this (or specify "-DHAVE_GETHOSTBY***_R=") only if:
  * 0) you are compiling this outside of the NCBI C or C++ Toolkits
  *    (USE_NCBICONF is not #define'd), and
@@ -74,7 +75,6 @@
 /* #define HAVE_GETHOSTBYNAME_R 6 */
 /* #define HAVE_GETHOSTBYADDR_R 8 */
 
-
 /* Uncomment this (or specify "-DHAVE_SIN_LEN") only if:
  * 0) you are compiling this outside of the NCBI C or C++ Toolkits
  *    (USE_NCBICONF is not #define'd), and
@@ -83,7 +83,6 @@
 
 /* #define HAVE_SIN_LEN 1 */
 
-
 /* Platform-specific system headers
  */
 
@@ -100,6 +99,9 @@
 #  include <netinet/in.h>
 #  ifndef NCBI_COMPILER_METROWERKS
 #    include <netinet/tcp.h>
+#    if defined(NCBI_OS_LINUX)  &&  !defined(IP_MTU)
+#      define IP_MTU 14
+#    endif
 #  endif
 #  if !defined(NCBI_OS_BEOS) && !defined(NCBI_COMPILER_MW_MSL)
 #    include <arpa/inet.h>
@@ -148,7 +150,6 @@
 #include <stdlib.h>
 
 
-
 /******************************************************************************
  *  TYPEDEFS & MACROS
  */
@@ -642,9 +643,8 @@ static const char* s_StrError(int error)
     };
     size_t i, n = sizeof(errmap) / sizeof(errmap[0]) - 1/*dummy entry*/;
 
-    /* always called on error so get error number here if not having already */
-    if ( !error )
-        error = errno;
+    if (!error)
+        return "";
     for (i = 0;  i < n;  i++) {
         if (errmap[i].errnum == error)
             return errmap[i].errtxt;
@@ -744,11 +744,12 @@ static void s_DoLog
         }
         CORE_TRACEF(("%s%s%s", s_ID(sock, _id), head, tail));
         break;
+
     case eIO_Read:
     case eIO_Write:
         if (sock->stype == eSOCK_Datagram) {
             const struct sockaddr_in* sin = (const struct sockaddr_in*) sa;
-            assert(sa && sa->sa_family == AF_INET);
+            assert(sa  &&  sa->sa_family == AF_INET);
             SOCK_HostPortToString(sin->sin_addr.s_addr,
                                   ntohs(sin->sin_port),
                                   tail, sizeof(tail));
@@ -772,8 +773,9 @@ static void s_DoLog
                 sock->stype == eSOCK_Datagram
                 ? (event == eIO_Read ? " from " : " to ")
                 : "", tail);
-        CORE_DATA(data, size, head);
+        CORE_DATA_X(109, data, size, head);
         break;
+
     case eIO_Close:
         {{
             int n = sprintf(head, "%lu byte%s",
@@ -803,9 +805,11 @@ static void s_DoLog
                      sock->stype == eSOCK_ServerSideKeep
                      ? "Leaving" : "Closing", head,tail));
         break;
+
     default:
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::s_DoLog]  Invalid event %u",
-                               s_ID(sock, _id), (unsigned int) event));
+        CORE_LOGF_X(1, eLOG_Error,
+                    ("%s[SOCK::s_DoLog]  Invalid event %u",
+                     s_ID(sock, _id), (unsigned int) event));
         assert(0);
         break;
     }
@@ -861,59 +865,60 @@ extern void SOCK_AllowSigPipeAPI(void)
 
 static void s_ShowDataLayout(void)
 {
-    CORE_LOGF(eLOG_Note, ("SOCK data layout:\n"
-                          "    Sizeof(SOCK_struct) = %u, offsets follow\n"
-                          "\tsock:      %u\n"
-                          "\tid:        %u\n"
-                          "\thost:      %u\n"
-                          "\tport:      %u\n"
-                          "\tbitfield:  16 bits\n"
-                          "\tr_timeout: %u\n"
-                          "\tr_tv:      %u\n"
-                          "\tr_to:      %u\n"
-                          "\tw_timeout: %u\n"
-                          "\tw_tv:      %u\n"
-                          "\tw_to:      %u\n"
-                          "\tc_timeout: %u\n"
-                          "\tc_tv:      %u\n"
-                          "\tc_to:      %u\n"
-                          "\tr_buf:     %u\n"
-                          "\tw_buf:     %u\n"
-                          "\tw_len:     %u\n"
-                          "\tn_read:    %u\n"
-                          "\tn_written: %u\n"
-                          "\tn_in:      %u\n"
-                          "\tn_out:     %u\n"
-                          "\tmyport:    %u"
+    CORE_LOGF_X(2, eLOG_Note,
+                ("SOCK data layout:\n"
+                 "    Sizeof(SOCK_struct) = %u, offsets follow\n"
+                 "\tsock:      %u\n"
+                 "\tid:        %u\n"
+                 "\thost:      %u\n"
+                 "\tport:      %u\n"
+                 "\tbitfield:  16 bits\n"
+                 "\tr_timeout: %u\n"
+                 "\tr_tv:      %u\n"
+                 "\tr_to:      %u\n"
+                 "\tw_timeout: %u\n"
+                 "\tw_tv:      %u\n"
+                 "\tw_to:      %u\n"
+                 "\tc_timeout: %u\n"
+                 "\tc_tv:      %u\n"
+                 "\tc_to:      %u\n"
+                 "\tr_buf:     %u\n"
+                 "\tw_buf:     %u\n"
+                 "\tw_len:     %u\n"
+                 "\tn_read:    %u\n"
+                 "\tn_written: %u\n"
+                 "\tn_in:      %u\n"
+                 "\tn_out:     %u\n"
+                 "\tmyport:    %u"
 #  ifdef NCBI_OS_UNIX
-                          "\n\tpath:      %u"
+                 "\n\tpath:      %u"
 #  endif /*NCBI_OS_UNIX*/
-                          , (unsigned int) sizeof(SOCK_struct),
-                          (unsigned int) offsetof(SOCK_struct, sock),
-                          (unsigned int) offsetof(SOCK_struct, id),
-                          (unsigned int) offsetof(SOCK_struct, host),
-                          (unsigned int) offsetof(SOCK_struct, port),
-                          (unsigned int) offsetof(SOCK_struct, r_timeout),
-                          (unsigned int) offsetof(SOCK_struct, r_tv),
-                          (unsigned int) offsetof(SOCK_struct, r_to),
-                          (unsigned int) offsetof(SOCK_struct, w_timeout),
-                          (unsigned int) offsetof(SOCK_struct, w_tv),
-                          (unsigned int) offsetof(SOCK_struct, w_to),
-                          (unsigned int) offsetof(SOCK_struct, c_timeout),
-                          (unsigned int) offsetof(SOCK_struct, c_tv),
-                          (unsigned int) offsetof(SOCK_struct, c_to),
-                          (unsigned int) offsetof(SOCK_struct, r_buf),
-                          (unsigned int) offsetof(SOCK_struct, w_buf),
-                          (unsigned int) offsetof(SOCK_struct, w_len),
-                          (unsigned int) offsetof(SOCK_struct, n_read),
-                          (unsigned int) offsetof(SOCK_struct, n_written),
-                          (unsigned int) offsetof(SOCK_struct, n_in),
-                          (unsigned int) offsetof(SOCK_struct, n_out),
-                          (unsigned int) offsetof(SOCK_struct, myport)
+                 , (unsigned int) sizeof(SOCK_struct),
+                 (unsigned int) offsetof(SOCK_struct, sock),
+                 (unsigned int) offsetof(SOCK_struct, id),
+                 (unsigned int) offsetof(SOCK_struct, host),
+                 (unsigned int) offsetof(SOCK_struct, port),
+                 (unsigned int) offsetof(SOCK_struct, r_timeout),
+                 (unsigned int) offsetof(SOCK_struct, r_tv),
+                 (unsigned int) offsetof(SOCK_struct, r_to),
+                 (unsigned int) offsetof(SOCK_struct, w_timeout),
+                 (unsigned int) offsetof(SOCK_struct, w_tv),
+                 (unsigned int) offsetof(SOCK_struct, w_to),
+                 (unsigned int) offsetof(SOCK_struct, c_timeout),
+                 (unsigned int) offsetof(SOCK_struct, c_tv),
+                 (unsigned int) offsetof(SOCK_struct, c_to),
+                 (unsigned int) offsetof(SOCK_struct, r_buf),
+                 (unsigned int) offsetof(SOCK_struct, w_buf),
+                 (unsigned int) offsetof(SOCK_struct, w_len),
+                 (unsigned int) offsetof(SOCK_struct, n_read),
+                 (unsigned int) offsetof(SOCK_struct, n_written),
+                 (unsigned int) offsetof(SOCK_struct, n_in),
+                 (unsigned int) offsetof(SOCK_struct, n_out),
+                 (unsigned int) offsetof(SOCK_struct, myport)
 #  ifdef NCBI_OS_UNIX
-                          , (unsigned int) offsetof(SOCK_struct, path)
+                 , (unsigned int) offsetof(SOCK_struct, path)
 #  endif /*NCBI_OS_UNIX*/
-                          ));
+                 ));
 }
 
 #endif /*SOCK_HAVE_SHOWDATALAYOUT*/
@@ -935,10 +940,11 @@ extern EIO_Status SOCK_InitializeAPI(void)
     {{
         WSADATA wsadata;
         int x_errno = WSAStartup(MAKEWORD(1,1), &wsadata);
-        if (x_errno != 0) {
+        if (x_errno) {
             CORE_UNLOCK;
-            CORE_LOG_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                              "[SOCK::InitializeAPI]  Failed WSAStartup()");
+            CORE_LOG_ERRNO_EXX(3, eLOG_Error,
+                               x_errno, SOCK_STRERROR(x_errno),
+                               "[SOCK::InitializeAPI]  Failed WSAStartup()");
             return eIO_Unknown;
         }
     }}
@@ -983,8 +989,9 @@ extern EIO_Status SOCK_ShutdownAPI(void)
         int x_errno = WSACleanup() ? SOCK_ERRNO : 0;
         CORE_UNLOCK;
         if ( x_errno ) {
-            CORE_LOG_ERRNO_EX(eLOG_Warning, x_errno, SOCK_STRERROR(x_errno),
-                              "[SOCK::ShutdownAPI]  Failed WSACleanup()");
+            CORE_LOG_ERRNO_EXX(4, eLOG_Warning,
+                               x_errno, SOCK_STRERROR(x_errno),
+                               "[SOCK::ShutdownAPI]  Failed WSACleanup()");
             return eIO_Unknown;
         }
     }}
@@ -1152,6 +1159,7 @@ static EIO_Status s_Select(size_t                n,
 
     for (;;) { /* (optionally) auto-resume if interrupted by a signal */
         struct timeval xx_tv;
+        int x_errno;
 
         n_fds = 0;
         FD_ZERO(&r_fds);
@@ -1289,12 +1297,12 @@ static EIO_Status s_Select(size_t                n,
             break;
 
         /* n_fds < 0 */
-        if (SOCK_ERRNO != SOCK_EINTR) {
-            int  x_errno = SOCK_ERRNO;
+        if ((x_errno = SOCK_ERRNO) != SOCK_EINTR) {
             char _id[32];
-            CORE_LOGF_ERRNO_EX(eLOG_Trace, x_errno, SOCK_STRERROR(x_errno),
-                               ("%s[SOCK::s_Select]  Failed select()",
-                                n == 1 ? s_ID(polls[0].sock, _id) : ""));
+            CORE_LOGF_ERRNO_EXX(5, eLOG_Trace,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("%s[SOCK::s_Select]  Failed select()",
+                                 n == 1 ? s_ID(polls[0].sock, _id) : ""));
             return eIO_Unknown;
         }
 
@@ -1367,7 +1375,7 @@ static EIO_Status s_IsConnected(SOCK                  sock,
         status = eIO_Unknown;
     }
 #endif /*NCBI_OS_UNIX || NCBI_OS_MSWIN*/
-#if defined(_DEBUG) && !defined(NDEBUG)
+#if defined(_DEBUG)  &&  !defined(NDEBUG)
     if (status == eIO_Success) {
 #  ifdef NCBI_OS_UNIX
         if (!sock->path[0])
@@ -1401,10 +1409,26 @@ static EIO_Status s_IsConnected(SOCK                  sock,
                !s_SetReuseAddress(sock->sock, 1/*true*/)) {
         int x_errno = SOCK_ERRNO;
         char _id[32];
-        CORE_LOGF_ERRNO_EX(eLOG_Note, x_errno, SOCK_STRERROR(x_errno),
-                           ("%s[SOCK::s_IsConnected]  Failed "
-                            "setsockopt(REUSEADDR)", s_ID(sock, _id)));
+        CORE_LOGF_ERRNO_EXX(6, eLOG_Note,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("%s[SOCK::s_IsConnected]  Failed "
+                             "setsockopt(REUSEADDR)", s_ID(sock, _id)));
     }
+#if defined(_DEBUG)  &&  !defined(NDEBUG)
+    else {
+        int    mtu;
+        char   _id[32];
+#  ifdef IP_MTU
+        size_t mtulen = sizeof(mtu);
+        if (getsockopt(sock->sock, SOL_IP, IP_MTU, &mtu, &mtulen) != 0)
+#  endif
+            mtu = -1;
+        if (sock->log == eOn  ||  (sock->log == eDefault  &&  s_Log == eOn)) {
+            CORE_TRACEF(("%sConnection established, MTU = %d",
+                         s_ID(sock, _id), mtu));
+        }
+    }
+#endif /*_DEBUG && !NDEBUG*/
     return status;
 }
 
@@ -1490,9 +1514,10 @@ static int s_Recv(SOCK        sock,
                 x_errno                != SOCK_EINTR) {
                 /* catch unknown ERROR */
                 sock->r_status = eIO_Unknown;
-                CORE_LOGF_ERRNO_EX(eLOG_Trace, x_errno, SOCK_STRERROR(x_errno),
-                                   ("%s[SOCK::s_Recv] "
-                                    " Failed recv()", s_ID(sock, xx_buffer)));
+                CORE_LOGF_ERRNO_EXX(7, eLOG_Trace,
+                                    x_errno, SOCK_STRERROR(x_errno),
+                                    ("%s[SOCK::s_Recv]  Failed recv()",
+                                     s_ID(sock, xx_buffer)));
             }
             return n_read ? (int) n_read : -1;
         }
@@ -1516,9 +1541,9 @@ static int s_Recv(SOCK        sock,
             if ((size_t) x_read > n_todo)
                 x_read = n_todo;
             if (error) {
-                CORE_LOGF_ERRNO(eLOG_Error, errno,
-                                ("%s[SOCK::s_Recv]  Cannot store data in "
-                                 "peek buffer", s_ID(sock, xx_buffer)));
+                CORE_LOGF_ERRNO_X(8, eLOG_Error, errno,
+                                  ("%s[SOCK::s_Recv]  Cannot store data in "
+                                   "peek buffer", s_ID(sock, xx_buffer)));
                 sock->eof      = 1/*failure*/;
                 sock->r_status = eIO_Closed;
                 if ( peek )
@@ -1640,8 +1665,9 @@ static EIO_Status s_WipeRBuf(SOCK sock)
 
     if (size  &&  BUF_Read(sock->r_buf, 0, size) != size) {
         char _id[32];
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::s_WipeRBuf] "
-                               " Cannot drop aux. data buf", s_ID(sock, _id)));
+        CORE_LOGF_X(9, eLOG_Error,
+                    ("%s[SOCK::s_WipeRBuf]  Cannot drop aux. data buf",
+                     s_ID(sock, _id)));
         assert(0);
         status = eIO_Unknown;
     } else
@@ -1659,8 +1685,9 @@ static EIO_Status s_WipeWBuf(SOCK sock)
     assert(sock->stype == eSOCK_Datagram);
     if (size  &&  BUF_Read(sock->w_buf, 0, size) != size) {
         char _id[32];
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::s_WipeWBuf] "
-                               " Cannot drop aux. data buf", s_ID(sock, _id)));
+        CORE_LOGF_X(10, eLOG_Error,
+                    ("%s[SOCK::s_WipeWBuf]  Cannot drop aux. data buf",
+                     s_ID(sock, _id)));
         assert(0);
         status = eIO_Unknown;
     } else
@@ -1766,9 +1793,10 @@ static EIO_Status s_Send(SOCK        sock,
             if (x_errno != SOCK_EPIPE      &&  x_errno != SOCK_ENOTCONN     &&
                 x_errno != SOCK_ECONNRESET &&  x_errno != SOCK_ECONNABORTED &&
                 x_errno != SOCK_ENETRESET  &&  x_errno != SOCK_ETIMEDOUT) {
-                CORE_LOGF_ERRNO_EX(eLOG_Trace, x_errno, SOCK_STRERROR(x_errno),
-                                   ("%s[SOCK::s_Send] "
-                                    " Failed send()", s_ID(sock, _id)));
+                CORE_LOGF_ERRNO_EXX(11, eLOG_Trace,
+                                    x_errno, SOCK_STRERROR(x_errno),
+                                    ("%s[SOCK::s_Send]  Failed send()",
+                                     s_ID(sock, _id)));
                 break;
             }
             sock->w_status = eIO_Closed;
@@ -1834,11 +1862,11 @@ static EIO_Status s_WritePending(SOCK                  sock,
 {
     const struct timeval* x_tv;
     EIO_Status status;
-    int x_errno;
     size_t off;
 
     assert(sock->stype != eSOCK_Datagram  &&  sock->sock != SOCK_INVALID);
     if ( sock->pending ) {
+        int x_errno;
         status = s_IsConnected(sock, tv, &x_errno, writeable);
         if (status != eIO_Success) {
             if (status != eIO_Timeout) {
@@ -1855,9 +1883,10 @@ static EIO_Status s_WritePending(SOCK                  sock,
 #endif /*NCBI_OS_UNIX*/
                     SOCK_HostPortToString(sock->host, ntohs(sock->port),
                                           addr, sizeof(addr));
-                CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                                   ("%s[SOCK::s_WritePending]  Failed pending "
-                                    "connect() to %s", s_ID(sock, _id), addr));
+                CORE_LOGF_ERRNO_EXX(12, eLOG_Error,
+                                    x_errno, SOCK_STRERROR(x_errno),
+                                    ("%s[SOCK::s_WritePending]  Failed pending"
+                                     " connect() to %s",s_ID(sock, _id),addr));
                 sock->w_status = status;
             }
             return status;
@@ -2050,11 +2079,11 @@ static EIO_Status s_Shutdown(SOCK                  sock,
         if (sock->w_status == eIO_Closed)
             return eIO_Success;  /* has been shut down already */
         if ((status = s_WritePending(sock, tv, 0, 0)) != eIO_Success) {
-            CORE_LOGF(!tv  ||  (tv->tv_sec | tv->tv_usec)
-                      ? eLOG_Warning : eLOG_Trace,
-                      ("%s[SOCK::s_Shutdown]  Shutting down for "
-                       "write with some output pending (%s)",
-                       s_ID(sock, _id), IO_StatusStr(status)));
+            CORE_LOGF_X(13, !tv  ||  (tv->tv_sec | tv->tv_usec)
+                        ? eLOG_Warning : eLOG_Trace,
+                        ("%s[SOCK::s_Shutdown]  Shutting down for "
+                         "write with some output pending (%s)",
+                         s_ID(sock, _id), IO_StatusStr(status)));
         }
         x_how = SOCK_SHUTDOWN_WR;
         sock->w_status = eIO_Closed;
@@ -2070,11 +2099,11 @@ static EIO_Status s_Shutdown(SOCK                  sock,
             return eIO_Success;
         if (sock->w_status != eIO_Closed
             &&  (status = s_WritePending(sock, tv, 0, 0)) != eIO_Success) {
-            CORE_LOGF(!tv  ||  (tv->tv_sec | tv->tv_usec)
-                      ? eLOG_Warning : eLOG_Trace,
-                      ("%s[SOCK::s_Shutdown]  Shutting down for "
-                       "R/W with some output pending (%s)",
-                       s_ID(sock, _id), IO_StatusStr(status)));
+            CORE_LOGF_X(14, !tv  ||  (tv->tv_sec | tv->tv_usec)
+                        ? eLOG_Warning : eLOG_Trace,
+                        ("%s[SOCK::s_Shutdown]  Shutting down for "
+                         "R/W with some output pending (%s)",
+                         s_ID(sock, _id), IO_StatusStr(status)));
         }
         x_how = SOCK_SHUTDOWN_RDWR;
         sock->eof = 0/*false*/;
@@ -2091,26 +2120,33 @@ static EIO_Status s_Shutdown(SOCK                  sock,
         return eIO_Success;
 #endif /*NCBI_OS_MSWIN*/
     default:
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::s_Shutdown]  Invalid direction %u",
-                               s_ID(sock, _id), (unsigned int) how));
+        CORE_LOGF_X(15, eLOG_Error,
+                    ("%s[SOCK::s_Shutdown]  Invalid direction %u",
+                     s_ID(sock, _id), (unsigned int) how));
         return eIO_InvalidArg;
     }
 
     if (s_Initialized  &&  SOCK_SHUTDOWN(sock->sock, x_how) != 0) {
         int x_errno = SOCK_ERRNO;
+#ifdef NCBI_OS_MSWIN
+        if (x_errno == WSANOTINITIALISED)
+            s_Initialized = 0/*false*/;
+        else
+#endif /*NCBI_OS_MSWIN*/
         if (
-#if defined(NCBI_OS_LINUX)/*bug in the Linux kernel to report*/  || \
-    defined(NCBI_OS_IRIX)                                        || \
-    defined(NCBI_OS_OSF1)
+#if   defined(NCBI_OS_LINUX)/*bug in the Linux kernel to report*/  || \
+      defined(NCBI_OS_IRIX)                                        || \
+      defined(NCBI_OS_OSF1)
             x_errno != SOCK_ENOTCONN
 #else
             x_errno != SOCK_ENOTCONN  ||  sock->pending
 #endif /*UNIX flavors*/
             )
-            CORE_LOGF_ERRNO_EX(eLOG_Warning, x_errno, SOCK_STRERROR(x_errno),
-                               ("%s[SOCK::s_Shutdown]  Failed shutdown(%s)",
-                                s_ID(sock, _id), how == eIO_Read ? "READ" :
-                                how == eIO_Write ? "WRITE" : "READ/WRITE"));
+            CORE_LOGF_ERRNO_EXX(16, eLOG_Warning,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("%s[SOCK::s_Shutdown]  Failed shutdown(%s)",
+                                 s_ID(sock, _id), how == eIO_Read ? "READ" :
+                                 how == eIO_Write ? "WRITE" : "READ/WRITE"));
     }
     return eIO_Success;
 }
@@ -2153,21 +2189,23 @@ static EIO_Status s_Close(SOCK sock, int/*bool*/ abort)
                 &&  setsockopt(sock->sock, SOL_SOCKET, SO_LINGER,
                                (char*) &lgr, sizeof(lgr)) != 0) {
                 int x_errno = SOCK_ERRNO;
-                CORE_LOGF_ERRNO_EX(eLOG_Trace, x_errno, SOCK_STRERROR(x_errno),
-                                   ("%s[SOCK::s_%s]  Failed setsockopt"
-                                    "(SO_LINGER)", s_ID(sock, _id),
-                                    abort ? "Abort" : "Close"));
+                CORE_LOGF_ERRNO_EXX(17, eLOG_Trace,
+                                    x_errno, SOCK_STRERROR(x_errno),
+                                    ("%s[SOCK::s_%s]  Failed setsockopt"
+                                     "(SO_LINGER)", s_ID(sock, _id),
+                                     abort ? "Abort" : "Close"));
             }
 #  ifdef TCP_LINGER2
             if (abort  ||  (tv  &&  !(tv->tv_sec | tv->tv_usec))) {
                 int no = -1;
                 if (setsockopt(sock->sock, IPPROTO_TCP, TCP_LINGER2,
                                (char*) &no, sizeof(no)) != 0  &&  !abort) {
-                    int x_err = SOCK_ERRNO;
-                    CORE_LOGF_ERRNO_EX(eLOG_Trace, x_err, SOCK_STRERROR(x_err),
-                                       ("%s[SOCK::s_%s]  Failed setsockopt"
-                                        "(TCP_LINGER2)", s_ID(sock, _id),
-                                        abort ? "Abort" : "Close"));
+                    int x_errno = SOCK_ERRNO;
+                    CORE_LOGF_ERRNO_EXX(18, eLOG_Trace,
+                                        x_errno, SOCK_STRERROR(x_errno),
+                                        ("%s[SOCK::s_%s]  Failed setsockopt"
+                                         "(TCP_LINGER2)", s_ID(sock, _id),
+                                         abort ? "Abort" : "Close"));
                 }
             }
 #  endif /*TCP_LINGER2*/
@@ -2180,16 +2218,20 @@ static EIO_Status s_Close(SOCK sock, int/*bool*/ abort)
         } else
             sock->r_status = sock->w_status = eIO_Closed;
         /* set the socket back to blocking mode */
-        if (!s_SetNonblock(sock->sock, 0/*false*/)  &&  !abort) {
-            CORE_LOGF(eLOG_Trace, ("%s[SOCK::s_Close]  Cannot set socket "
-                                   "back to blocking mode", s_ID(sock, _id)));
+        if (s_Initialized && !s_SetNonblock(sock->sock, 0/*false*/) && !abort){
+            int x_errno = SOCK_ERRNO;
+            CORE_LOGF_ERRNO_EXX(19, eLOG_Trace,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("%s[SOCK::s_Close]  Cannot set socket "
+                                 "back to blocking mode", s_ID(sock, _id)));
         }
     } else {
         status = s_WritePending(sock, sock->c_timeout, 0, 0);
         if (status != eIO_Success) {
-            CORE_LOGF(eLOG_Warning, ("%s[SOCK::s_Close]  Leaving with some "
-                                     "output data pending (%s)",
-                                     s_ID(sock, _id), IO_StatusStr(status)));
+            CORE_LOGF_X(20, eLOG_Warning,
+                        ("%s[SOCK::s_Close]  Leaving with some "
+                         "output data pending (%s)",
+                         s_ID(sock, _id), IO_StatusStr(status)));
         }
     }
     sock->w_len = 0;
@@ -2213,12 +2255,18 @@ static EIO_Status s_Close(SOCK sock, int/*bool*/ abort)
             if (!s_Initialized)
                 break;
             x_errno = SOCK_ERRNO;
+#ifdef NCBI_OS_MSWIN
+            if (x_errno == WSANOTINITIALISED) {
+                s_Initialized = 0/*false*/;
+                break;
+            }
+#endif /*NCBI_OS_MSWIN*/
             if (abort  ||  x_errno != SOCK_EINTR) {
-                CORE_LOGF_ERRNO_EX(abort > 1 ? eLOG_Error : eLOG_Warning,
-                                   x_errno, SOCK_STRERROR(x_errno),
-                                   ("%s[SOCK::s_%s]  Failed close()",
-                                    s_ID(sock, _id),
-                                    abort ? "Abort" : "Close"));
+                CORE_LOGF_ERRNO_EXX(21, abort > 1 ? eLOG_Error : eLOG_Warning,
+                                    x_errno, SOCK_STRERROR(x_errno),
+                                    ("%s[SOCK::s_%s]  Failed close()",
+                                     s_ID(sock, _id),
+                                     abort ? "Abort" : "Close"));
                 if (abort++ > 1  ||  x_errno != SOCK_EINTR) {
                     status = eIO_Unknown;
                     break;
@@ -2229,6 +2277,7 @@ static EIO_Status s_Close(SOCK sock, int/*bool*/ abort)
 
     /* return */
     sock->sock = SOCK_INVALID;
+    sock->myport = 0;
     return status;
 }
 
@@ -2280,9 +2329,10 @@ static EIO_Status s_Connect(SOCK            sock,
             /* get address of the remote host (assume the same host if NULL) */
             x_host = host  &&  *host ? SOCK_gethostbyname(host) : sock->host;
             if ( !x_host ) {
-                CORE_LOGF(eLOG_Error, ("%s[SOCK::s_Connect]  Failed "
-                                       "SOCK_gethostbyname(\"%.64s\")",
-                                       s_ID(sock, _id), host));
+                CORE_LOGF_X(22, eLOG_Error,
+                            ("%s[SOCK::s_Connect]  Failed"
+                             " SOCK_gethostbyname(\"%.64s\")",
+                             s_ID(sock, _id), host));
                 return eIO_Unknown;
             }
             addr.sin.sin_addr.s_addr = x_host;
@@ -2294,16 +2344,17 @@ static EIO_Status s_Connect(SOCK            sock,
 #endif /*HAVE_SIN_LEN*/
             sock->host = x_host;
             sock->port = x_port;
-            c = SOCK_HostPortToString(x_host, ntohs(x_port), s, sizeof(s))
-                ? s : "???";
+            SOCK_HostPortToString(x_host, ntohs(x_port), s, sizeof(s));
+            c = s;
         }
 
     /* check the new socket */
     if ((x_sock = socket(addr.sa.sa_family, SOCK_STREAM, 0)) == SOCK_INVALID) {
         int x_errno = SOCK_ERRNO;
-        CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                           ("%s[SOCK::s_Connect]  Cannot create socket",
-                            s_ID(sock, _id)));
+        CORE_LOGF_ERRNO_EXX(23, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("%s[SOCK::s_Connect]  Cannot create socket",
+                             s_ID(sock, _id)));
         return eIO_Unknown;
     }
     sock->sock     = x_sock;
@@ -2314,8 +2365,11 @@ static EIO_Status s_Connect(SOCK            sock,
 
     /* set the socket I/O to non-blocking mode */
     if ( !s_SetNonblock(x_sock, 1/*true*/) ) {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::s_Connect]  Cannot set socket to "
-                               "non-blocking mode", s_ID(sock, _id)));
+        int x_errno = SOCK_ERRNO;
+        CORE_LOGF_ERRNO_EXX(24, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("%s[SOCK::s_Connect]  Cannot set socket to"
+                             " non-blocking mode", s_ID(sock, _id)));
         s_Close(sock, 1/*abort*/);
         return eIO_Unknown;
     }
@@ -2339,9 +2393,10 @@ static EIO_Status s_Connect(SOCK            sock,
             (n == 0  ||  x_errno != SOCK_EALREADY)     &&
             x_errno != SOCK_EWOULDBLOCK) {
             if (x_errno != SOCK_EINTR) {
-                CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                                   ("%s[SOCK::s_Connect]  Failed connect() "
-                                    "to %s", s_ID(sock, _id), c));
+                CORE_LOGF_ERRNO_EXX(25, eLOG_Error,
+                                    x_errno, SOCK_STRERROR(x_errno),
+                                    ("%s[SOCK::s_Connect]  Failed connect() "
+                                     "to %s", s_ID(sock, _id), c));
             }
             s_Close(sock, 1/*abort*/);
             /* unrecoverable error */
@@ -2354,10 +2409,11 @@ static EIO_Status s_Connect(SOCK            sock,
 
             status = s_IsConnected(sock, s_to2tv(timeout, &tv), &x_errno, 0);
             if (status != eIO_Success) {
-                CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                                   ("%s[SOCK::s_Connect]  Failed pending "
-                                    "connect() to %s (%s)",
-                                    s_ID(sock, _id), c, IO_StatusStr(status)));
+                CORE_LOGF_ERRNO_EXX(26, eLOG_Error,
+                                    x_errno, SOCK_STRERROR(x_errno),
+                                    ("%s[SOCK::s_Connect]  Failed pending "
+                                     "connect() to %s (%s)", s_ID(sock, _id),
+                                     c, IO_StatusStr(status)));
                 s_Close(sock, 1/*abort*/);
                 return status;
             }
@@ -2406,9 +2462,9 @@ static EIO_Status s_Create(const char*     host,
         if (!BUF_SetChunkSize(&x_sock->w_buf, datalen) ||
             !BUF_Write(&x_sock->w_buf, data, datalen)) {
             char _id[32];
-            CORE_LOGF_ERRNO(eLOG_Error, errno,
-                            ("%s[SOCK::CreateEx] "
-                             " Cannot store initial data", s_ID(x_sock, _id)));
+            CORE_LOGF_ERRNO_X(27, eLOG_Error, errno,
+                              ("%s[SOCK::CreateEx]  Cannot store initial data",
+                               s_ID(x_sock, _id)));
             SOCK_Close(x_sock);
             return eIO_Unknown;
         }
@@ -2469,27 +2525,24 @@ extern EIO_Status TRIGGER_Create(TRIGGER* trigger, ESwitch log)
         int fd[2];
 
         if (pipe(fd) < 0) {
-            int x_errno = errno;
-            CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                               ("TRIGGER#%u[?]: [TRIGGER::Create] "
-                                " Cannot create pipe", x_id));
+            CORE_LOGF_ERRNO_X(28, eLOG_Error, errno,
+                              ("TRIGGER#%u[?]: [TRIGGER::Create] "
+                               " Cannot create pipe", x_id));
             return eIO_Closed;
         }
 
         if (!s_SetNonblock(fd[0], 1/*true*/)  ||
-            !s_SetNonblock(fd[0], 1/*true*/)) {
-            int x_errno = errno;
-            CORE_LOGF_ERRNO_EX(eLOG_Warning, x_errno, SOCK_STRERROR(x_errno),
-                               ("TRIGGER#%u[?]: [TRIGGER::Create] "
-                                " Failed to set non-blocking mode", x_id));
+            !s_SetNonblock(fd[1], 1/*true*/)) {
+            CORE_LOGF_ERRNO_X(29, eLOG_Warning, errno,
+                              ("TRIGGER#%u[?]: [TRIGGER::Create] "
+                               " Failed to set non-blocking mode", x_id));
         }
 
         if (!s_SetCloexec(fd[0], 1/*true*/)  ||
             !s_SetCloexec(fd[1], 1/*true*/)) {
-            int x_errno = errno;
-            CORE_LOGF_ERRNO_EX(eLOG_Warning, x_errno, SOCK_STRERROR(x_errno),
-                               ("TRIGGER#%u[?]: [TRIGGER::Create] "
-                                " Failed to set close-on-exec", x_id));
+            CORE_LOGF_ERRNO_X(30, eLOG_Warning, errno,
+                              ("TRIGGER#%u[?]: [TRIGGER::Create] "
+                               " Failed to set close-on-exec", x_id));
         }
 
         if (!(*trigger = (TRIGGER) calloc(1, sizeof(*trigger)))) {
@@ -2513,8 +2566,8 @@ extern EIO_Status TRIGGER_Create(TRIGGER* trigger, ESwitch log)
 
 #  else
 
-    CORE_LOGF(eLOG_Error, ("TRIGGER#%u[?]: [TRIGGER::Create] "
-                           " Not yet supported on this platform", x_id));
+    CORE_LOGF_X(31, eLOG_Error, ("TRIGGER#%u[?]: [TRIGGER::Create] "
+                                 " Not yet supported on this platform", x_id));
     return eIO_NotSupported;
 
 #  endif /*NCBI_OS_UNIX*/
@@ -2572,8 +2625,8 @@ extern EIO_Status TRIGGER_Set(TRIGGER trigger)
 
 #  else
 
-    CORE_LOG(eLOG_Error,
-             "[TRIGGER::Set]  Not yet supported on this platform");
+    CORE_LOG_X(32, eLOG_Error,
+               "[TRIGGER::Set]  Not yet supported on this platform");
     return eIO_NotSupported;
 
 #  endif /*NCBI_OS_UNIX*/
@@ -2615,8 +2668,8 @@ extern EIO_Status TRIGGER_IsSet(TRIGGER trigger)
 
 #  else
 
-    CORE_LOG(eLOG_Error,
-             "[TRIGGER::IsSet]  Not yet supported on this platform");
+    CORE_LOG_X(33, eLOG_Error,
+               "[TRIGGER::IsSet]  Not yet supported on this platform");
     return eIO_NotSupported;
 
 #  endif /*NCBI_OS_UNIX*/
@@ -2680,9 +2733,10 @@ static EIO_Status s_CreateListening(const char*    path,
     /* create new(listening) socket */
     if ((x_lsock = socket(addr.sa.sa_family, SOCK_STREAM, 0)) == SOCK_INVALID){
         int x_errno = SOCK_ERRNO;
-        CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                           ("LSOCK#%u[?]: [LSOCK::Create] "
-                            " Cannot create socket", x_id));
+        CORE_LOGF_ERRNO_EXX(34, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("LSOCK#%u[?]: [LSOCK::Create] "
+                             " Cannot create socket", x_id));
         return eIO_Unknown;
     }
 
@@ -2696,10 +2750,11 @@ static EIO_Status s_CreateListening(const char*    path,
          */
         if ( !s_SetReuseAddress(x_lsock, 1/*true*/) ) {
             int x_errno = SOCK_ERRNO;
-            CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                               ("LSOCK#%u[%u]: [LSOCK::Create] "
-                                " Failed setsockopt(REUSEADDR)",
-                                x_id, (unsigned int) x_lsock));
+            CORE_LOGF_ERRNO_EXX(35, eLOG_Error,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("LSOCK#%u[%u]: [LSOCK::Create] "
+                                 " Failed setsockopt(REUSEADDR)",
+                                 x_id, (unsigned int) x_lsock));
             SOCK_CLOSE(x_lsock);
             return eIO_Unknown;
         }
@@ -2725,16 +2780,17 @@ static EIO_Status s_CreateListening(const char*    path,
 #ifdef HAVE_SIN_LEN
             addr.sin.sin_len         = addrlen;
 #endif /*HAVE_SIN_LEN*/
-            c = SOCK_HostPortToString(htonl(ip), port, s, sizeof(s))
-                ? s : "?:?";
+            SOCK_HostPortToString(htonl(ip), port, s, sizeof(s));
+            c = s;
         }
     if (bind(x_lsock, &addr.sa, addrlen) != 0) {
         int x_errno = SOCK_ERRNO;
-        CORE_LOGF_ERRNO_EX(x_errno == SOCK_EADDRINUSE ? eLOG_Trace : eLOG_Error,
-                           x_errno, SOCK_STRERROR(x_errno),
-                           ("LSOCK#%u[%u]: [LSOCK::Create] "
-                            " Failed bind(%s)", x_id,
-                            (unsigned int) x_lsock, c));
+        CORE_LOGF_ERRNO_EXX(36, x_errno == SOCK_EADDRINUSE
+                            ? eLOG_Trace : eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("LSOCK#%u[%u]: [LSOCK::Create] "
+                             " Failed bind(%s)", x_id,
+                             (unsigned int) x_lsock, c));
         SOCK_CLOSE(x_lsock);
         return x_errno == SOCK_EADDRINUSE ? eIO_Closed : eIO_Unknown;
     }
@@ -2742,23 +2798,38 @@ static EIO_Status s_CreateListening(const char*    path,
     /* listen */
     if (listen(x_lsock, backlog) != 0) {
         int x_errno = SOCK_ERRNO;
-        CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                           ("LSOCK#%u[%u]: [LSOCK::Create]  Failed "
-                            "listen(%hu) at %s", x_id, (unsigned int) x_lsock,
-                            backlog, s));
+        CORE_LOGF_ERRNO_EXX(37, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("LSOCK#%u[%u]: [LSOCK::Create]  Failed "
+                             "listen(%hu) at %s", x_id, (unsigned int) x_lsock,
+                             backlog, c));
         SOCK_CLOSE(x_lsock);
         return eIO_Unknown;
     }
 
     /* set to non-blocking mode */
     if ( !s_SetNonblock(x_lsock, 1/*true*/) ) {
-        CORE_LOGF(eLOG_Error, ("LSOCK#%u[%u]: [LSOCK::Create] "
-                               " Cannot set socket to non-blocking mode",
-                               x_id, (unsigned int) x_lsock));
+        int x_errno = SOCK_ERRNO;
+        CORE_LOGF_ERRNO_EXX(38, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("LSOCK#%u[%u]: [LSOCK::Create] "
+                             " Cannot set socket to non-blocking mode",
+                             x_id, (unsigned int) x_lsock));
         SOCK_CLOSE(x_lsock);
         return eIO_Unknown;
     }
 
+#ifdef NCBI_OS_UNIX
+    if ((flags & fLSCE_CloseOnExec)  &&  !s_SetCloexec(x_lsock, 1/*true*/)) {
+        int x_errno = SOCK_ERRNO;
+        CORE_LOGF_ERRNO_EXX(110, eLOG_Warning,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("LSOCK#%u[%u]: [LSOCK::Create] "
+                             " Cannot set socket close-on-exec mode",
+                             x_id, (unsigned int) x_lsock));
+    }
+#endif /*NCBI_OS_UNIX*/
+
     /* allocate memory for the internal socket structure */
     if (!(*lsock = (LSOCK)calloc(1, sizeof(**lsock) + (path?strlen(path):0)))){
         return eIO_Unknown;
@@ -2827,8 +2898,9 @@ extern EIO_Status LSOCK_Accept(LSOCK           lsock,
     struct SOCK_tag temp;
 
     if (lsock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("LSOCK#%u[?]: [LSOCK::Accept] "
-                               " Invalid socket", lsock->id));
+        CORE_LOGF_X(39, eLOG_Error,
+                    ("LSOCK#%u[?]: [LSOCK::Accept]  Invalid socket",
+                     lsock->id));
         assert(0);
         return eIO_Unknown;
     }
@@ -2865,18 +2937,22 @@ extern EIO_Status LSOCK_Accept(LSOCK           lsock,
         }
     if ((x_sock = accept(lsock->sock, &addr.sa, &addrlen)) == SOCK_INVALID) {
         int x_errno = SOCK_ERRNO;
-        CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                           ("LSOCK#%u[%u]: [LSOCK::Accept] "
-                            " Failed accept()", lsock->id,
-                            (unsigned int) lsock->sock));
+        CORE_LOGF_ERRNO_EXX(40, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("LSOCK#%u[%u]: [LSOCK::Accept] "
+                             " Failed accept()", lsock->id,
+                             (unsigned int) lsock->sock));
         return eIO_Unknown;
     }
     lsock->n_accept++;
     /* man accept(2) notes that non-blocking state may not be inherited */
     if ( !s_SetNonblock(x_sock, 1/*true*/) ) {
-        CORE_LOGF(eLOG_Error, ("SOCK#%u[%u]: [LSOCK::Accept]  Cannot"
-                               " set accepted socket to non-blocking mode",
-                               x_id, (unsigned int) x_sock));
+        int x_errno = SOCK_ERRNO;
+        CORE_LOGF_ERRNO_EXX(41, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("SOCK#%u[%u]: [LSOCK::Accept]  Cannot"
+                             " set accepted socket to non-blocking mode",
+                             x_id, (unsigned int) x_sock));
         memset(&temp, 0, sizeof(temp));
         temp.stype = eSOCK_ServerSideKeep;
         temp.type  = eSocket;
@@ -2891,10 +2967,11 @@ extern EIO_Status LSOCK_Accept(LSOCK           lsock,
 #endif /*NCBI_OS_UNIX*/
         !s_SetReuseAddress(x_sock, 1/*true*/)) {
         int x_errno = SOCK_ERRNO;
-        CORE_LOGF_ERRNO_EX(eLOG_Warning, x_errno, SOCK_STRERROR(x_errno),
-                           ("SOCK#%u[%u]: [LSOCK::Accept] "
-                            " Failed setsockopt(REUSEADDR)",
-                            x_id, (unsigned int) x_sock));
+        CORE_LOGF_ERRNO_EXX(42, eLOG_Warning,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("SOCK#%u[%u]: [LSOCK::Accept] "
+                             " Failed setsockopt(REUSEADDR)",
+                             x_id, (unsigned int) x_sock));
     }
 
     /* create new SOCK structure */
@@ -2949,32 +3026,38 @@ extern EIO_Status LSOCK_Accept(LSOCK           lsock,
 extern EIO_Status LSOCK_Close(LSOCK lsock)
 {
     EIO_Status status;
-    const char* c;
     char s[80];
 
     if (lsock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("LSOCK#%u[?]: [LSOCK::Close] "
-                               " Invalid socket", lsock->id));
+        CORE_LOGF_X(43, eLOG_Error,
+                    ("LSOCK#%u[?]: [LSOCK::Close]  Invalid socket",
+                     lsock->id));
         assert(0);
         return eIO_Unknown;
     }
 
     /* set the socket back to blocking mode */
     if (s_Initialized  &&  !s_SetNonblock(lsock->sock, 0/*false*/)) {
-        CORE_LOGF(eLOG_Trace, ("LSOCK#%u[%u]: [LSOCK::Close] "
-                               " Cannot set socket back to blocking mode",
-                               lsock->id, (unsigned int) lsock->sock));
+        int x_errno = SOCK_ERRNO;
+        CORE_LOGF_ERRNO_EXX(44, eLOG_Trace,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("LSOCK#%u[%u]: [LSOCK::Close] "
+                             " Cannot set socket back to blocking mode",
+                             lsock->id, (unsigned int) lsock->sock));
     }
 
-#ifdef NCBI_OS_UNIX
-    if ( lsock->path[0] )
-        c = lsock->path;
-    else
-#endif /*NCBI_OS_UNIX*/
-        c = SOCK_HostPortToString(0, lsock->port, s, sizeof(s)) ? s : ":?";
-
     /* statistics & logging */
     if (lsock->log == eOn  ||  (lsock->log == eDefault  &&  s_Log == eOn)) {
+        const char* c;
+#ifdef NCBI_OS_UNIX
+        if ( lsock->path[0] )
+            c = lsock->path;
+        else
+#endif /*NCBI_OS_UNIX*/ 
+            {
+                SOCK_HostPortToString(0, lsock->port, s, sizeof(s));
+                c = s;
+            }
         CORE_TRACEF(("LSOCK#%u[%u]: Closing at %s "
                      "(%u accept%s total)", lsock->id,
                      (unsigned int) lsock->sock, c,
@@ -2990,9 +3073,11 @@ extern EIO_Status LSOCK_Close(LSOCK lsock)
         /* error */
         if (SOCK_ERRNO != SOCK_EINTR) {
             int x_errno = SOCK_ERRNO;
-            CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                               ("LSOCK#%u[%u]: [LSOCK::Close]  Failed close()",
-                                lsock->id, (unsigned int) lsock->sock));
+            CORE_LOGF_ERRNO_EXX(45, eLOG_Error,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("LSOCK#%u[%u]: [LSOCK::Close] "
+                                 " Failed close()", lsock->id,
+                                 (unsigned int) lsock->sock));
             status = eIO_Unknown;
             break;
         }
@@ -3015,10 +3100,11 @@ extern EIO_Status LSOCK_GetOSHandle(LSOCK  lsock,
                                     size_t handle_size)
 {
     if (!handle  ||  handle_size != sizeof(lsock->sock)) {
-        CORE_LOGF(eLOG_Error, ("LSOCK#%u[%u]: [LSOCK::GetOSHandle] "
-                               " Invalid handle %s%lu", lsock->id,
-                               (unsigned int) lsock->sock, handle? "size ": "",
-                               handle ? (unsigned long) handle_size : 0));
+        CORE_LOGF_X(46, eLOG_Error,
+                    ("LSOCK#%u[%u]: [LSOCK::GetOSHandle] "
+                     " Invalid handle %s%lu", lsock->id,
+                     (unsigned int) lsock->sock, handle? "size ": "",
+                     handle ? (unsigned long) handle_size : 0));
         assert(0);
         return eIO_InvalidArg;
     }
@@ -3111,10 +3197,11 @@ extern EIO_Status SOCK_CreateOnTopEx(const void*   handle,
     assert(!datalen  ||  data);
 
     if (!handle  ||  handle_size != sizeof(xx_sock)) {
-        CORE_LOGF(eLOG_Error, ("SOCK#%u[?]: [SOCK::CreateOnTopEx] "
-                               " Invalid handle %s%lu", x_id,
-                               handle ? "size " : "",
-                               handle ? (unsigned long) handle_size : 0));
+        CORE_LOGF_X(47, eLOG_Error,
+                    ("SOCK#%u[?]: [SOCK::CreateOnTopEx] "
+                     " Invalid handle %s%lu", x_id,
+                     handle ? "size " : "",
+                     handle ? (unsigned long) handle_size : 0));
         assert(0);
         return eIO_InvalidArg;
     }
@@ -3162,9 +3249,10 @@ extern EIO_Status SOCK_CreateOnTopEx(const void*   handle,
                 return eIO_Closed;
             assert(peer.sa.sa_family == AF_UNIX);
             if (!peer.un.sun_path[0]) {
-                CORE_LOGF(eLOG_Error, ("SOCK#%u[%u]: [SOCK::CreateOnTopEx] "
-                                       " Unbound UNIX socket",
-                                       x_id, (unsigned int) xx_sock));
+                CORE_LOGF_X(48, eLOG_Error,
+                            ("SOCK#%u[%u]: [SOCK::CreateOnTopEx] "
+                             " Unbound UNIX socket",
+                             x_id, (unsigned int) xx_sock));
                 assert(0);
                 return eIO_InvalidArg;
             }
@@ -3177,9 +3265,9 @@ extern EIO_Status SOCK_CreateOnTopEx(const void*   handle,
     /* store initial data */
     if (datalen  &&  (!BUF_SetChunkSize(&w_buf, datalen)  ||
                       !BUF_Write(&w_buf, data, datalen))) {
-        CORE_LOGF_ERRNO(eLOG_Error, errno,
-                        ("SOCK#%u[%u]: [SOCK::CreateOnTopEx]  Cannot store "
-                         "initial data", x_id, (unsigned int) xx_sock));
+        CORE_LOGF_ERRNO_X(49, eLOG_Error, errno,
+                          ("SOCK#%u[%u]: [SOCK::CreateOnTopEx]  Cannot store "
+                           "initial data", x_id, (unsigned int) xx_sock));
         BUF_Destroy(w_buf);
         return eIO_Unknown;
     }
@@ -3219,9 +3307,12 @@ extern EIO_Status SOCK_CreateOnTopEx(const void*   handle,
 
     /* set to non-blocking mode */
     if ( !s_SetNonblock(xx_sock, 1/*true*/) ) {
+        int x_errno = SOCK_ERRNO;
         char _id[32];
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::CreateOnTopEx]  Cannot set socket "
-                               "to non-blocking mode", s_ID(x_sock, _id)));
+        CORE_LOGF_ERRNO_EXX(50, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("%s[SOCK::CreateOnTopEx]  Cannot set socket "
+                             "to non-blocking mode", s_ID(x_sock, _id)));
         x_sock->sock = SOCK_INVALID;
         SOCK_Close(x_sock);
         return eIO_Unknown;
@@ -3250,9 +3341,10 @@ static EIO_Status s_Reconnect(SOCK            sock,
     if (sock->stype & eSOCK_ServerSide) {
         char _id[32];
         if (!host  ||  !*host  ||  !port) {
-            CORE_LOGF(eLOG_Error, ("%s[SOCK::Reconnect]  Attempt to reconnect "
-                                   "server-side socket as the client one to "
-                                   "its peer address", s_ID(sock, _id)));
+            CORE_LOGF_X(51, eLOG_Error,
+                        ("%s[SOCK::Reconnect]  Attempt to reconnect "
+                         "server-side socket as the client one to "
+                         "its peer address", s_ID(sock, _id)));
             return eIO_InvalidArg;
         }
         sock->stype = eSOCK_ClientSide;
@@ -3274,8 +3366,8 @@ extern EIO_Status SOCK_Reconnect(SOCK            sock,
     char _id[32];
 
     if (sock->sock == eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Reconnect] "
-                               " Datagram socket", s_ID(sock, _id)));
+        CORE_LOGF_X(52, eLOG_Error,
+                    ("%s[SOCK::Reconnect]  Datagram socket", s_ID(sock, _id)));
         assert(0);
         return eIO_InvalidArg;
     }
@@ -3284,9 +3376,10 @@ extern EIO_Status SOCK_Reconnect(SOCK            sock,
 
 #ifdef NCBI_OS_UNIX
     if (sock->path[0] && (host || port)) {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Reconnect] "
-                               " Cannot reconnect UNIX socket \"%s\" as INET",
-                               s_ID(sock, _id), sock->path));
+        CORE_LOGF_X(53, eLOG_Error,
+                    ("%s[SOCK::Reconnect] "
+                     " Cannot reconnect UNIX socket \"%s\" as INET",
+                     s_ID(sock, _id), sock->path));
         assert(0);
         return eIO_InvalidArg;
     }
@@ -3301,13 +3394,13 @@ extern EIO_Status SOCK_Shutdown(SOCK      sock,
     char _id[32];
 
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Shutdown] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(54, eLOG_Error,
+                    ("%s[SOCK::Shutdown]  Invalid socket", s_ID(sock, _id)));
         return eIO_Closed;
     }
     if (sock->stype == eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Shutdown] "
-                               " Datagram socket", s_ID(sock, _id)));
+        CORE_LOGF_X(55, eLOG_Error,
+                    ("%s[SOCK::Shutdown]  Datagram socket", s_ID(sock, _id)));
         assert(0);
         return eIO_InvalidArg;
     }
@@ -3322,8 +3415,10 @@ extern EIO_Status SOCK_CloseEx(SOCK sock, int/*bool*/ destroy)
     if (!s_Initialized) {
         sock->sock = SOCK_INVALID;
         status = eIO_Success;
+    } else if (sock->sock == SOCK_INVALID) {
+        status = eIO_Closed;
     } else
-        status = sock->sock == SOCK_INVALID ? eIO_Success : s_Close(sock, 0);
+        status = s_Close(sock, 0/*orderly*/);
 
     if (destroy) {
         BUF_Destroy(sock->r_buf);
@@ -3347,22 +3442,35 @@ extern EIO_Status SOCK_Wait(SOCK            sock,
     char _id[32];
 
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Wait] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(56, eLOG_Error,
+                    ("%s[SOCK::Wait]  Invalid socket", s_ID(sock, _id)));
         return eIO_Closed;
     }
 
     /* check against already shutdown socket there */
     switch ( event ) {
+    case eIO_Open:
+        if (sock->stype == eSOCK_Datagram)
+            return eIO_Success/*always connected*/;
+        if (sock->pending) {
+            struct timeval tv;
+            int x_errno/*unused*/;
+            return s_IsConnected(sock, s_to2tv(timeout, &tv), &x_errno, 0);
+        }
+        if (sock->r_status == eIO_Success  &&  sock->w_status == eIO_Success)
+            return eIO_Success;
+        if (sock->r_status == eIO_Closed   &&  sock->w_status == eIO_Closed)
+            return eIO_Closed;
+        return eIO_Unknown;
     case eIO_Read:
         if (BUF_Size(sock->r_buf) != 0)
             return eIO_Success;
         if (sock->stype == eSOCK_Datagram)
             return eIO_Closed;
         if (sock->r_status == eIO_Closed) {
-            CORE_LOGF(eLOG_Warning, ("%s[SOCK::Wait(R)]  Socket has already "
-                                     "been %s", s_ID(sock, _id),
-                                     sock->eof ? "closed" : "shut down"));
+            CORE_LOGF_X(57, eLOG_Warning,
+                        ("%s[SOCK::Wait(R)]  Socket has already been %s",
+                         s_ID(sock, _id), sock->eof ? "closed" : "shut down"));
             return eIO_Closed;
         }
         if ( sock->eof )
@@ -3372,8 +3480,9 @@ extern EIO_Status SOCK_Wait(SOCK            sock,
         if (sock->stype == eSOCK_Datagram)
             return eIO_Success;
         if (sock->w_status == eIO_Closed) {
-            CORE_LOGF(eLOG_Warning, ("%s[SOCK::Wait(W)]  Socket has already "
-                                     "been shut down", s_ID(sock, _id)));
+            CORE_LOGF_X(58, eLOG_Warning,
+                        ("%s[SOCK::Wait(W)]  Socket has already "
+                         "been shut down", s_ID(sock, _id)));
             return eIO_Closed;
         }
         break;
@@ -3383,31 +3492,34 @@ extern EIO_Status SOCK_Wait(SOCK            sock,
         if ((sock->r_status == eIO_Closed  ||  sock->eof)  &&
             (sock->w_status == eIO_Closed)) {
             if (sock->r_status == eIO_Closed) {
-                CORE_LOGF(eLOG_Warning, ("%s[SOCK::Wait(RW)]  Socket has "
-                                         "already been shut down",
-                                         s_ID(sock, _id)));
+                CORE_LOGF_X(59, eLOG_Warning,
+                            ("%s[SOCK::Wait(RW)]  Socket has "
+                             "already been shut down", s_ID(sock, _id)));
             }
             return eIO_Closed;
         }
         if (sock->r_status == eIO_Closed  ||  sock->eof) {
             if (sock->r_status == eIO_Closed) {
-                CORE_LOGF(eLOG_Note, ("%s[SOCK::Wait(RW)]  Socket has already "
-                                      "been %s", s_ID(sock, _id), sock->eof
-                                      ? "closed" : "shut down for reading"));
+                CORE_LOGF_X(60, eLOG_Note,
+                            ("%s[SOCK::Wait(RW)]  Socket has already "
+                             "been %s", s_ID(sock, _id), sock->eof
+                             ? "closed" : "shut down for reading"));
             }
             event = eIO_Write;
             break;
         }
         if (sock->w_status == eIO_Closed) {
-            CORE_LOGF(eLOG_Note,("%s[SOCK::Wait(RW)]  Socket has already been "
-                                 "shut down for writing", s_ID(sock, _id)));
+            CORE_LOGF_X(61, eLOG_Note,
+                        ("%s[SOCK::Wait(RW)]  Socket has already been "
+                         "shut down for writing", s_ID(sock, _id)));
             event = eIO_Read;
             break;
         }
         break;
     default:
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Wait]  Invalid event %u",
-                               s_ID(sock, _id), (unsigned int) event));
+        CORE_LOGF_X(62, eLOG_Error,
+                    ("%s[SOCK::Wait]  Invalid event %u",
+                     s_ID(sock, _id), (unsigned int) event));
         return eIO_InvalidArg;
     }
 
@@ -3556,8 +3668,9 @@ extern EIO_Status SOCK_SetTimeout(SOCK            sock,
         sock->c_timeout = s_to2tv(timeout, &sock->c_tv);
         break;
     default:
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::SetTimeout]  Invalid event %u",
-                               s_ID(sock, _id), (unsigned int) event));
+        CORE_LOGF_X(63, eLOG_Error,
+                    ("%s[SOCK::SetTimeout]  Invalid event %u",
+                     s_ID(sock, _id), (unsigned int) event));
         assert(0);
         return eIO_InvalidArg;
     }
@@ -3593,8 +3706,9 @@ extern const STimeout* SOCK_GetTimeout(SOCK      sock,
     case eIO_Close:
         return s_tv2to(sock->c_timeout, &sock->c_to);
     default:
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::GetTimeout]  Invalid event %u",
-                               s_ID(sock, _id), (unsigned int) event));
+        CORE_LOGF_X(64, eLOG_Error,
+                    ("%s[SOCK::GetTimeout]  Invalid event %u",
+                     s_ID(sock, _id), (unsigned int) event));
         assert(0);
     }
     return 0;
@@ -3633,16 +3747,17 @@ extern EIO_Status SOCK_Read(SOCK           sock,
             break;
 
         default:
-            CORE_LOGF(eLOG_Error, ("%s[SOCK::Read]  Invalid read method %u",
-                                   s_ID(sock, _id), (unsigned int) how));
+            CORE_LOGF_X(65, eLOG_Error,
+                        ("%s[SOCK::Read]  Invalid read method %u",
+                         s_ID(sock, _id), (unsigned int) how));
             assert(0);
             x_read = 0;
             status = eIO_InvalidArg;
             break;
         }
     } else {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Read] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(66, eLOG_Error,
+                    ("%s[SOCK::Read]  Invalid socket", s_ID(sock, _id)));
         x_read = 0;
         status = eIO_Closed;
     }
@@ -3731,8 +3846,8 @@ extern EIO_Status SOCK_PushBack(SOCK        sock,
 {
     if (sock->sock == SOCK_INVALID) {
         char _id[32];
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::PushBack] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(67, eLOG_Error,
+                    ("%s[SOCK::PushBack]  Invalid socket", s_ID(sock, _id)));
         return eIO_Closed;
     }
 
@@ -3754,9 +3869,10 @@ extern EIO_Status SOCK_Write(SOCK            sock,
         switch ( how ) {
         case eIO_WriteOutOfBand:
             if (sock->stype == eSOCK_Datagram) {
-                CORE_LOGF(eLOG_Error, ("%s[SOCK::Write] "
-                                       " OOB not supported for datagrams",
-                                       s_ID(sock, _id)));
+                CORE_LOGF_X(68, eLOG_Error,
+                            ("%s[SOCK::Write] "
+                             " OOB not supported for datagrams",
+                             s_ID(sock, _id)));
                 status = eIO_NotSupported;
                 x_written = 0;
                 break;
@@ -3780,16 +3896,17 @@ extern EIO_Status SOCK_Write(SOCK            sock,
             break;
 
         default:
-            CORE_LOGF(eLOG_Error, ("%s[SOCK::Write]  Invalid write method %u",
-                                   s_ID(sock, _id), (unsigned int) how));
+            CORE_LOGF_X(69, eLOG_Error,
+                        ("%s[SOCK::Write]  Invalid write method %u",
+                         s_ID(sock, _id), (unsigned int) how));
             assert(0);
             x_written = 0;
             status = eIO_InvalidArg;
             break;
         }
     } else {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Write] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(70, eLOG_Error,
+                    ("%s[SOCK::Write]  Invalid socket", s_ID(sock, _id)));
         x_written = 0;
         status = eIO_Closed;
     }
@@ -3805,13 +3922,13 @@ extern EIO_Status SOCK_Abort(SOCK sock)
     char _id[32];
 
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Warning, ("%s[SOCK::Abort] "
-                                 " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(71, eLOG_Warning,
+                    ("%s[SOCK::Abort]  Invalid socket", s_ID(sock, _id)));
         return eIO_Closed;
     }
     if (sock->stype == eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[SOCK::Abort] "
-                               " Datagram socket", s_ID(sock, _id)));
+        CORE_LOGF_X(72, eLOG_Error,
+                    ("%s[SOCK::Abort]  Datagram socket", s_ID(sock, _id)));
         assert(0);
         return eIO_InvalidArg;
     }
@@ -3826,14 +3943,44 @@ extern EIO_Status SOCK_Abort(SOCK sock)
 extern EIO_Status SOCK_Status(SOCK      sock,
                               EIO_Event direction)
 {
-    if (direction != eIO_Read  &&  direction != eIO_Write) {
+    switch (direction) {
+    case eIO_Open:
+    case eIO_Read:
+    case eIO_Write:
+        if (sock->sock == SOCK_INVALID)
+            return eIO_Closed;
+        if (sock->pending)
+            return eIO_Timeout;
         if (direction == eIO_Open)
-            return sock->sock == SOCK_INVALID ? eIO_Closed : eIO_Success;
+            return eIO_Success;
+        break;
+    default:
         return eIO_InvalidArg;
     }
+    return s_Status(sock, direction);
+}
+
 
-    return (sock->sock == SOCK_INVALID ? eIO_Closed :
-            sock->pending ? eIO_Timeout : s_Status(sock, direction));
+extern unsigned short SOCK_GetLocalPort(SOCK          sock,
+                                        ENH_ByteOrder byte_order)
+{
+    if (sock->sock == SOCK_INVALID)
+        return 0;
+
+    if (!sock->myport) {
+        struct sockaddr_in addr;
+        SOCK_socklen_t addrlen = sizeof(addr);
+        memset(&addr, 0, addrlen);
+#  ifdef HAVE_SIN_LEN
+        addr.sin_len = addrlen;
+#  endif /*HAVE_SIN_LEN*/
+        if (getsockname(sock->sock,
+                        (struct sockaddr*) &addr, &addrlen) == 0) {
+            assert(addr.sin_family == AF_INET);
+            sock->myport = ntohs(addr.sin_port);
+        }
+    }
+    return byte_order != eNH_HostByteOrder? htons(sock->myport) : sock->myport;
 }
 
 
@@ -3875,9 +4022,10 @@ extern EIO_Status SOCK_GetOSHandle(SOCK   sock,
 {
     if (!handle  ||  handle_size != sizeof(sock->sock)) {
         char _id[32];
-        CORE_LOGF(eLOG_Error,("%s[SOCK::GetOSHandle]  Invalid handle %s%lu",
-                              s_ID(sock, _id), handle ? "size " : "",
-                              handle ? (unsigned long) handle_size : 0));
+        CORE_LOGF_X(73, eLOG_Error,
+                    ("%s[SOCK::GetOSHandle]  Invalid handle %s%lu",
+                     s_ID(sock, _id), handle ? "size " : "",
+                     handle ? (unsigned long) handle_size : 0));
         assert(0);
         return eIO_InvalidArg;
     }
@@ -3939,10 +4087,11 @@ extern void SOCK_SetReuseAddress(SOCK sock, int/*bool*/ on_off)
     if (sock->sock != SOCK_INVALID && !s_SetReuseAddress(sock->sock, on_off)) {
         int x_errno = SOCK_ERRNO;
         char _id[32];
-        CORE_LOGF_ERRNO_EX(eLOG_Warning, x_errno, SOCK_STRERROR(x_errno),
-                           ("%s[SOCK::SetReuseAddress] "
-                            " Failed setsockopt(%sREUSEADDR)",
-                            s_ID(sock, _id), on_off ? "" : "NO"));
+        CORE_LOGF_ERRNO_EXX(74, eLOG_Warning,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("%s[SOCK::SetReuseAddress] "
+                             " Failed setsockopt(%sREUSEADDR)",
+                             s_ID(sock, _id), on_off ? "" : "NO"));
     }
 }
 
@@ -3956,10 +4105,11 @@ extern void SOCK_DisableOSSendDelay(SOCK sock, int/*bool*/ on_off)
                        (void*)&n, sizeof(n)) != 0) {
             int x_errno = SOCK_ERRNO;
             char _id[32];
-            CORE_LOGF_ERRNO_EX(eLOG_Warning, x_errno, SOCK_STRERROR(x_errno),
-                               ("%s[SOCK::DisableOSSendDelay] "
-                                " Failed setsockopt(%sTCP_NODELAY)",
-                               s_ID(sock, _id), on_off ? "" : "!"));
+            CORE_LOGF_ERRNO_EXX(75, eLOG_Warning,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("%s[SOCK::DisableOSSendDelay] "
+                                 " Failed setsockopt(%sTCP_NODELAY)",
+                                 s_ID(sock, _id), on_off ? "" : "!"));
         }
     }
 #endif /*TCP_NODELAY*/
@@ -3984,16 +4134,20 @@ extern EIO_Status DSOCK_CreateEx(SOCK* sock, ESwitch log)
     /* create new datagram socket */
     if ((x_sock = socket(AF_INET, SOCK_DGRAM, 0)) == SOCK_INVALID) {
         int x_errno = SOCK_ERRNO;
-        CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                           ("SOCK#%u[?]: [DSOCK::Create] "
-                            " Cannot create socket", x_id));
+        CORE_LOGF_ERRNO_EXX(76, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("SOCK#%u[?]: [DSOCK::Create] "
+                             " Cannot create socket", x_id));
         return eIO_Unknown;
     }
 
     /* set to non-blocking mode */
     if ( !s_SetNonblock(x_sock, 1/*true*/) ) {
-        CORE_LOGF(eLOG_Error, ("SOCK#%u[%u]: [DSOCK::Create]  Cannot set "
-                               "socket to non-blocking mode", x_id, x_sock));
+        int x_errno = SOCK_ERRNO;
+        CORE_LOGF_ERRNO_EXX(77, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("SOCK#%u[%u]: [DSOCK::Create]  Cannot set "
+                             "socket to non-blocking mode", x_id, x_sock));
         SOCK_CLOSE(x_sock);
         return eIO_Unknown;
     }
@@ -4033,14 +4187,15 @@ extern EIO_Status DSOCK_Bind(SOCK sock, unsigned short port)
     char _id[32];
 
     if (sock->stype != eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Bind] "
-                               " Not a datagram socket", s_ID(sock, _id)));
+        CORE_LOGF_X(78, eLOG_Error,
+                    ("%s[DSOCK::Bind] "
+                     " Not a datagram socket", s_ID(sock, _id)));
         assert(0);
         return eIO_InvalidArg;
     }
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Bind] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(79, eLOG_Error,
+                    ("%s[DSOCK::Bind]  Invalid socket", s_ID(sock, _id)));
         return eIO_Closed;
     }
 
@@ -4054,7 +4209,8 @@ extern EIO_Status DSOCK_Bind(SOCK sock, unsigned short port)
 #endif /*HAVE_SIN_LEN*/
     if (bind(sock->sock, (struct sockaddr*) &addr, sizeof(addr)) != 0) {
         int x_errno = SOCK_ERRNO;
-        CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
+        CORE_LOGF_ERRNO_EXX(80, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
                            ("%s[DSOCK::Bind]  Failed bind()", s_ID(sock,_id)));
         return x_errno == SOCK_EADDRINUSE ? eIO_Closed : eIO_Unknown;
     }
@@ -4073,14 +4229,15 @@ extern EIO_Status DSOCK_Connect(SOCK sock,
     char _id[32];
 
     if (sock->stype != eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Connect] "
-                               " Not a datagram socket", s_ID(sock, _id)));
+        CORE_LOGF_X(81, eLOG_Error,
+                    ("%s[DSOCK::Connect] "
+                     " Not a datagram socket", s_ID(sock, _id)));
         assert(0);
         return eIO_InvalidArg;
     }
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Connect] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(82, eLOG_Error,
+                    ("%s[DSOCK::Connect]  Invalid socket", s_ID(sock, _id)));
         return eIO_Closed;
     }
 
@@ -4094,15 +4251,17 @@ extern EIO_Status DSOCK_Connect(SOCK sock,
         sock->port = htons(port);
     if (host  &&  *host) {
         if ((sock->host = SOCK_gethostbyname(host)) == 0) {
-            CORE_LOGF(eLOG_Error, ("%s[DSOCK::Connect]  Failed "
-                                   "SOCK_gethostbyname(\"%.64s\")",
-                                   s_ID(sock, _id), host));
+            CORE_LOGF_X(83, eLOG_Error,
+                        ("%s[DSOCK::Connect]  Failed "
+                         "SOCK_gethostbyname(\"%.64s\")",
+                         s_ID(sock, _id), host));
             return eIO_Unknown;
         }
     }
-    if (!sock->host || !sock->port) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::Connect] "
-                               " Address incomplete", s_ID(sock, _id)));
+    if (!sock->host  ||  !sock->port) {
+        CORE_LOGF_X(84, eLOG_Error,
+                    ("%s[DSOCK::Connect] "
+                     " Address incomplete", s_ID(sock, _id)));
         return eIO_InvalidArg;
     }
 
@@ -4118,9 +4277,10 @@ extern EIO_Status DSOCK_Connect(SOCK sock,
         char addr[80];
         int x_errno = SOCK_ERRNO;
         SOCK_HostPortToString(sock->host, ntohs(sock->port),addr,sizeof(addr));
-        CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                           ("%s[DSOCK::Connect]  Failed connect() to %s",
-                            s_ID(sock, _id), addr));
+        CORE_LOGF_ERRNO_EXX(85, eLOG_Error,
+                            x_errno, SOCK_STRERROR(x_errno),
+                            ("%s[DSOCK::Connect]  Failed connect() to %s",
+                             s_ID(sock, _id), addr));
         return eIO_Unknown;
     }
 
@@ -4146,14 +4306,15 @@ extern EIO_Status DSOCK_SendMsg(SOCK            sock,
     struct sockaddr_in addr;
 
     if (sock->stype != eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::SendMsg] "
-                               " Not a datagram socket", s_ID(sock, w)));
+        CORE_LOGF_X(86, eLOG_Error,
+                    ("%s[DSOCK::SendMsg] "
+                     " Not a datagram socket", s_ID(sock, w)));
         assert(0);
         return eIO_InvalidArg;
     }
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::SendMsg] "
-                               " Invalid socket", s_ID(sock, w)));
+        CORE_LOGF_X(87, eLOG_Error,
+                    ("%s[DSOCK::SendMsg]  Invalid socket", s_ID(sock, w)));
         return eIO_Closed;
     }
 
@@ -4166,17 +4327,19 @@ extern EIO_Status DSOCK_SendMsg(SOCK            sock,
     x_port = port ? htons(port) : sock->port;
     if (host  &&  *host) {
         if ( !(x_host = SOCK_gethostbyname(host)) ) {
-            CORE_LOGF(eLOG_Error, ("%s[DSOCK::SendMsg]  Failed "
-                                   "SOCK_gethostbyname(\"%.64s\")",
-                                   s_ID(sock, w), host));
+            CORE_LOGF_X(88, eLOG_Error,
+                        ("%s[DSOCK::SendMsg]  Failed "
+                         "SOCK_gethostbyname(\"%.64s\")",
+                         s_ID(sock, w), host));
             return eIO_Unknown;
         }
     } else
         x_host = sock->host;
 
     if (!x_host  ||  !x_port) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::SendMsg] "
-                               " Address incomplete", s_ID(sock, w)));
+        CORE_LOGF_X(89, eLOG_Error,
+                    ("%s[DSOCK::SendMsg] "
+                     " Address incomplete", s_ID(sock, w)));
         return eIO_Unknown;
     }
 
@@ -4211,8 +4374,9 @@ extern EIO_Status DSOCK_SendMsg(SOCK            sock,
             sock->n_out++;
             if ((size_t) x_written != x_msgsize) {
                 sock->w_status = status = eIO_Closed;
-                CORE_LOGF(eLOG_Error, ("%s[DSOCK::SendMsg] "
-                                       " Partial datagram sent",s_ID(sock,w)));
+                CORE_LOGF_X(90, eLOG_Error,
+                            ("%s[DSOCK::SendMsg] "
+                             " Partial datagram sent",s_ID(sock,w)));
                 break;
             }
             sock->w_status = status = eIO_Success;
@@ -4242,9 +4406,10 @@ extern EIO_Status DSOCK_SendMsg(SOCK            sock,
         }
 
         if (x_errno != SOCK_EINTR) {
-            CORE_LOGF_ERRNO_EX(eLOG_Trace, x_errno, SOCK_STRERROR(x_errno),
-                               ("%s[DSOCK::SendMsg] "
-                                " Failed sendto()", s_ID(sock, w)));
+            CORE_LOGF_ERRNO_EXX(91, eLOG_Trace,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("%s[DSOCK::SendMsg] "
+                                 " Failed sendto()", s_ID(sock, w)));
             break;
         }
 
@@ -4277,14 +4442,15 @@ extern EIO_Status DSOCK_RecvMsg(SOCK            sock,
     void*      x_msg;
 
     if (sock->stype != eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::RecvMsg] "
-                               " Not a datagram socket", s_ID(sock, w)));
+        CORE_LOGF_X(92, eLOG_Error,
+                    ("%s[DSOCK::RecvMsg] "
+                     " Not a datagram socket", s_ID(sock, w)));
         assert(0);
         return eIO_InvalidArg;
     }
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::RecvMsg] "
-                               " Invalid socket", s_ID(sock, w)));
+        CORE_LOGF_X(93, eLOG_Error,
+                    ("%s[DSOCK::RecvMsg]  Invalid socket", s_ID(sock, w)));
         return eIO_Closed;
     }
 
@@ -4350,9 +4516,10 @@ extern EIO_Status DSOCK_RecvMsg(SOCK            sock,
             x_errno != SOCK_EAGAIN       &&
             x_errno != SOCK_EINTR) {
             /* catch unknown ERROR */
-            CORE_LOGF_ERRNO_EX(eLOG_Trace, x_errno, SOCK_STRERROR(x_errno),
-                               ("%s[DSOCK::RecvMsg] "
-                                " Failed recvfrom()", s_ID(sock, w)));
+            CORE_LOGF_ERRNO_EXX(94, eLOG_Trace,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("%s[DSOCK::RecvMsg] "
+                                 " Failed recvfrom()", s_ID(sock, w)));
             break;
         }
 
@@ -4395,14 +4562,15 @@ extern EIO_Status DSOCK_WaitMsg(SOCK sock, const STimeout* timeout)
     struct timeval tv;
 
     if (sock->stype != eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::WaitMsg] "
-                               " Not a datagram socket", s_ID(sock, _id)));
+        CORE_LOGF_X(95, eLOG_Error,
+                    ("%s[DSOCK::WaitMsg] "
+                     " Not a datagram socket", s_ID(sock, _id)));
         assert(0);
         return eIO_InvalidArg;
     }
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::WaitMsg] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(96, eLOG_Error,
+                    ("%s[DSOCK::WaitMsg]  Invalid socket", s_ID(sock, _id)));
         return eIO_Closed;
     }
 
@@ -4424,14 +4592,15 @@ extern EIO_Status DSOCK_WipeMsg(SOCK sock, EIO_Event direction)
     EIO_Status status;
 
     if (sock->stype != eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::WipeMsg] "
-                               " Not a datagram socket", s_ID(sock, _id)));
+        CORE_LOGF_X(97, eLOG_Error,
+                    ("%s[DSOCK::WipeMsg] "
+                     " Not a datagram socket", s_ID(sock, _id)));
         assert(0);
         return eIO_InvalidArg;
     }
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::WipeMsg] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(98, eLOG_Error,
+                    ("%s[DSOCK::WipeMsg]  Invalid socket", s_ID(sock, _id)));
         return eIO_Closed;
     }
 
@@ -4443,8 +4612,9 @@ extern EIO_Status DSOCK_WipeMsg(SOCK sock, EIO_Event direction)
         sock->w_status = status = s_WipeWBuf(sock);
         break;
     default:
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::WipeMsg]  Invalid direction %u",
-                               s_ID(sock, _id), (unsigned int) direction));
+        CORE_LOGF_X(99, eLOG_Error,
+                    ("%s[DSOCK::WipeMsg]  Invalid direction %u",
+                     s_ID(sock, _id), (unsigned int) direction));
         assert(0);
         status = eIO_InvalidArg;
         break;
@@ -4459,14 +4629,16 @@ extern EIO_Status DSOCK_SetBroadcast(SOCK sock, int/*bool*/ broadcast)
     char _id[32];
 
     if (sock->stype != eSOCK_Datagram) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::SetBroadcast] "
-                               " Not a datagram socket", s_ID(sock, _id)));
+        CORE_LOGF_X(100, eLOG_Error,
+                    ("%s[DSOCK::SetBroadcast] "
+                     " Not a datagram socket", s_ID(sock, _id)));
         assert(0);
         return eIO_InvalidArg;
     }
     if (sock->sock == SOCK_INVALID) {
-        CORE_LOGF(eLOG_Error, ("%s[DSOCK::SetBroadcast] "
-                               " Invalid socket", s_ID(sock, _id)));
+        CORE_LOGF_X(101, eLOG_Error,
+                    ("%s[DSOCK::SetBroadcast]  Invalid socket",
+                     s_ID(sock, _id)));
         return eIO_Closed;
     }
 
@@ -4481,10 +4653,11 @@ extern EIO_Status DSOCK_SetBroadcast(SOCK sock, int/*bool*/ broadcast)
         if (setsockopt(sock->sock, SOL_SOCKET, SO_BROADCAST,
                        (const char*) &bcast, sizeof(bcast)) != 0) {
             int x_errno = SOCK_ERRNO;
-            CORE_LOGF_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                               ("%s[DSOCK::SetBroadcast] "
-                                " Failed setsockopt(%sBROADCAST)",
-                                s_ID(sock, _id), bcast ? "" : "NO"));
+            CORE_LOGF_ERRNO_EXX(102, eLOG_Error,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("%s[DSOCK::SetBroadcast] "
+                                 " Failed setsockopt(%sBROADCAST)",
+                                 s_ID(sock, _id), bcast ? "" : "NO"));
             return eIO_Unknown;
         }
     }}
@@ -4535,11 +4708,13 @@ extern int SOCK_gethostname(char*  name,
     name[0] = name[namelen - 1] = '\0';
     if (gethostname(name, (int) namelen) != 0) {
         int x_errno = SOCK_ERRNO;
-        CORE_LOG_ERRNO_EX(eLOG_Error, x_errno, SOCK_STRERROR(x_errno),
-                          "[SOCK_gethostname]  Failed gethostname()");
+        CORE_LOG_ERRNO_EXX(103, eLOG_Error,
+                           x_errno, SOCK_STRERROR(x_errno),
+                           "[SOCK_gethostname]  Failed gethostname()");
         error = 1;
     } else if ( name[namelen - 1] ) {
-        CORE_LOG(eLOG_Error, "[SOCK_gethostname]  Buffer too small");
+        CORE_LOG_X(104, eLOG_Error,
+                   "[SOCK_gethostname]  Buffer too small");
         error = 1;
     }
 
@@ -4557,54 +4732,54 @@ extern int SOCK_ntoa(unsigned int host,
 {
     const unsigned char* b = (const unsigned char*) &host;
     char str[16/*sizeof("255.255.255.255")*/];
+    int len;
 
-    assert(buf && buflen > 0);
-    verify(sprintf(str, "%u.%u.%u.%u", b[0], b[1], b[2], b[3]) > 0);
-    assert(strlen(str) < sizeof(str));
+    assert(buf  &&  buflen > 0);
+    verify((len = sprintf(str, "%u.%u.%u.%u", b[0], b[1], b[2], b[3])) > 0);
+    assert((size_t) len < sizeof(str));
 
-    if (strlen(str) >= buflen) {
-        buf[0] = '\0';
-        return -1/*failed*/;
+    if ((size_t) len < buflen) {
+        memcpy(buf, str, len + 1);
+        return 0/*success*/;
     }
 
-    strcpy(buf, str);
-    return 0/*success*/;
+    buf[0] = '\0';
+    return -1/*failed*/;
 }
 
 
 extern int/*bool*/ SOCK_isip(const char* host)
 {
-    return SOCK_isipEx(host, strlen(host));
+    return SOCK_isipEx(host, 0/*nofullquad*/);
 }
 
 
-extern int/*bool*/ SOCK_isipEx(const char* host, size_t len)
+extern int/*bool*/ SOCK_isipEx(const char* host, int/*bool*/ fullquad)
 {
-    const char* dot = 0;
+    const char* c = host;
+    unsigned long val;
     int dots = 0;
-    size_t i;
-
-    if (len > 15)
-        return 0/*longer than the longest 255.255.255.255*/;
-    for (i = 0;  i < len;  i++) {
-        if (host[i] == '.') {
-            size_t n;
-            char* e;
-            long v;
-            if (i == 0  ||  ++dots > 3)
-                return 0/*false*/;
-            n = (size_t)(&host[i] - (dot ? dot : host - 1));
-            if (n <= 1  ||  n > 4)
-                return 0/*false*/;
-            errno = 0;
-            v = strtol(dot ? dot + 1 : host, &e, 0);
-            if (errno  ||  e != &host[i]  ||  v < 0  ||  v > 255)
-                return 0/*false*/;
-            dot = &host[i];
-        } else if (!isdigit((unsigned char) host[i]))
+
+    for (;;) {
+        char* e;
+        if (!isdigit((unsigned char)(*c)))
+            return 0/*false*/;
+        errno = 0;
+        val = strtoul(c, &e, fullquad ? 10 : 0);
+        if (c == e  ||  errno)
+            return 0/*false*/;
+        c = e;
+        if (*c != '.')
+            break;
+        if (++dots > 3)
+            return 0/*false*/;
+        if (val > 255)
             return 0/*false*/;
+        c++;
     }
-    return !(dots < 3);
+
+    return !*c  &&
+        (!fullquad  ||  dots == 3)  &&  val <= (0xFFFFFFFFUL >> (dots << 3));
 }
 
 
@@ -4663,9 +4838,10 @@ extern unsigned int SOCK_gethostbyname(const char* hostname)
                     x_errno = SOCK_ERRNO;
                 else
                     x_errno += EAI_BASE;
-                CORE_LOGF_ERRNO_EX(eLOG_Warning,x_errno,SOCK_STRERROR(x_errno),
-                                   ("[SOCK_gethostbyname]  Failed "
-                                    "getaddrinfo(\"%.64s\")", hostname));
+                CORE_LOGF_ERRNO_EXX(105, eLOG_Warning,
+                                    x_errno, SOCK_STRERROR(x_errno),
+                                    ("[SOCK_gethostbyname]  Failed "
+                                     "getaddrinfo(\"%.64s\")", hostname));
             }
             host = 0;
         }
@@ -4720,9 +4896,11 @@ extern unsigned int SOCK_gethostbyname(const char* hostname)
             if (x_errno == NETDB_INTERNAL + DNS_BASE)
                 x_errno = SOCK_ERRNO;
 #  endif /*NETDB_INTERNAL*/
-            CORE_LOGF_ERRNO_EX(eLOG_Warning, x_errno, SOCK_STRERROR(x_errno),
-                               ("[SOCK_gethostbyname]  Failed "
-                                "gethostbyname%s(\"%.64s\")",suffix,hostname));
+            CORE_LOGF_ERRNO_EXX(106, eLOG_Warning,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("[SOCK_gethostbyname]  Failed "
+                                 "gethostbyname%s(\"%.64s\")",
+                                 suffix, hostname));
         }
 
 #endif /*HAVE_GETADDR_INFO*/
@@ -4756,22 +4934,29 @@ extern char* SOCK_gethostbyaddr(unsigned int host,
         addr.sin_len = sizeof(addr);
 #  endif /*HAVE_SIN_LEN*/
         if ((x_errno = getnameinfo((struct sockaddr*) &addr, sizeof(addr),
-                                   name, namelen, 0, 0, 0)) != 0) {
+                                   name, namelen, 0, 0, 0)) != 0  ||  !*name) {
             if (SOCK_ntoa(host, name, namelen) != 0) {
+                if (!x_errno) {
+#ifdef ENOSPC
+                    x_errno = ENOSPC;
+#else
+                    x_errno = ERANGE;
+#endif /*ENOSPC*/
+                }
                 name[0] = '\0';
                 name = 0;
             }
             if (!name  &&  s_Log == eOn) {
                 char addr[16];
-                if (SOCK_ntoa(host, addr, sizeof(addr)) != 0)
-                    strcpy(addr, "<unknown>");
+                SOCK_ntoa(host, addr, sizeof(addr));
                 if (x_errno == EAI_SYSTEM)
                     x_errno = SOCK_ERRNO;
                 else
                     x_errno += EAI_BASE;
-                CORE_LOGF_ERRNO_EX(eLOG_Warning,x_errno,SOCK_STRERROR(x_errno),
-                                   ("[SOCK_gethostbyaddr]  Failed "
-                                    "getnameinfo(%s)", addr));
+                CORE_LOGF_ERRNO_EXX(107, eLOG_Warning,
+                                    x_errno, SOCK_STRERROR(x_errno),
+                                    ("[SOCK_gethostbyaddr]  Failed "
+                                     "getnameinfo(%s)", addr));
             }
         }
         return name;
@@ -4810,7 +4995,11 @@ extern char* SOCK_gethostbyaddr(unsigned int host,
 
         if (!he  ||  strlen(he->h_name) >= namelen) {
             if (he  ||  SOCK_ntoa(host, name, namelen) != 0) {
+#ifdef ENOSPC
+                x_errno = ENOSPC;
+#else
                 x_errno = ERANGE;
+#endif /*ENOSPC*/
                 name[0] = '\0';
                 name = 0;
             }
@@ -4828,11 +5017,11 @@ extern char* SOCK_gethostbyaddr(unsigned int host,
             if (x_errno == NETDB_INTERNAL + DNS_BASE)
                 x_errno = SOCK_ERRNO;
 #  endif /*NETDB_INTERNAL*/
-            if (SOCK_ntoa(host, addr, sizeof(addr)) != 0)
-                strcpy(addr, "<unknown>");
-            CORE_LOGF_ERRNO_EX(eLOG_Warning, x_errno, SOCK_STRERROR(x_errno),
-                               ("[SOCK_gethostbyaddr]  Failed "
-                                "gethostbyaddr%s(%s)", suffix, addr));
+            SOCK_ntoa(host, addr, sizeof(addr));
+            CORE_LOGF_ERRNO_EXX(108, eLOG_Warning,
+                                x_errno, SOCK_STRERROR(x_errno),
+                                ("[SOCK_gethostbyaddr]  Failed "
+                                 "gethostbyaddr%s(%s)", suffix, addr));
         }
 
         return name;
@@ -4905,24 +5094,24 @@ extern size_t SOCK_HostPortToString(unsigned int   host,
                                     char*          buf,
                                     size_t         buflen)
 {
-    char   x_buf[16/*sizeof("255.255.255.255")*/ + 8/*:port*/];
+    char   x_buf[16/*sizeof("255.255.255.255")*/ + 6/*:port#*/];
     size_t n;
 
-    if (!buf || !buflen)
+    if (!buf  ||  !buflen)
         return 0;
     if (!host)
-        *x_buf = 0;
+        *x_buf = '\0';
     else if (SOCK_ntoa(host, x_buf, sizeof(x_buf)) != 0) {
-        *buf = 0;
+        *buf = '\0';
         return 0;
     }
     n = strlen(x_buf);
-    if (port || !host)
+    if (port  ||  !host)
         n += sprintf(x_buf + n, ":%hu", port);
     assert(n < sizeof(x_buf));
     if (n >= buflen)
-        n = buflen - 1;
+        n  = buflen - 1;
     memcpy(buf, x_buf, n);
-    buf[n] = 0;
+    buf[n] = '\0';
     return n;
 }
diff --git a/connect/ncbi_socket.h b/connect/ncbi_socket.h
index e93b7c05..998ac966 100644
--- a/connect/ncbi_socket.h
+++ b/connect/ncbi_socket.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_SOCKET__H
 #define CONNECT___NCBI_SOCKET__H
 
-/*  $Id: ncbi_socket.h,v 6.65 2007/04/09 15:25:44 kazimird Exp $
+/*  $Id: ncbi_socket.h,v 6.68 2007/11/05 15:25:52 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -38,8 +38,6 @@
  *********************************
  * Generic:
  *
- *  SOCK, LSOCK
- *
  *  SOCK_AllowSigPipeAPI
  *
  *  SOCK_InitializeAPI
@@ -77,6 +75,7 @@
  *  SOCK_Status
  *  SOCK_Write
  *  SOCK_Abort
+ *  SOCK_GetLocalPort
  *  SOCK_GetPeerAddress
  *  SOCK_GetPeerAddressString
  *
@@ -1084,6 +1083,21 @@ extern NCBI_XCONNECT_EXPORT EIO_Status SOCK_Abort
  );
 
 
+/** Get local port of the socket.
+ * @param sock
+ *  [in] socket handle 
+ * @param byte_order
+ *  [in] port byte order
+ * @return
+ *  If "network_byte_order" is true(non-zero) then return the port in the
+ *  network byte order; otherwise return it in the local host byte order.
+ */
+extern NCBI_XCONNECT_EXPORT unsigned short SOCK_GetLocalPort
+(SOCK            sock,
+ ENH_ByteOrder   byte_order          
+ );
+
+
 /** Get host and port of the socket's peer.
  * @param sock
  *  [in]  socket handle 
@@ -1442,25 +1456,28 @@ extern NCBI_XCONNECT_EXPORT int SOCK_ntoa
  );
 
 
-/** Equivalent to SOCK_isipEx(host, strlen(host)).
- * @sa SOCK_isipEx
+/**
+ * @param host
+ *  [in] '\0'-terminated string to check against being a plain IP address
+ * @param fullquad
+ *  [in] non-zero to only accept "host" if it is a full-quad IP notation
+ * @return
+ *  Non-zero (true) if given string is an IP address, zero (false) otherwise.
  */
-extern NCBI_XCONNECT_EXPORT int/*bool*/ SOCK_isip
-(const char* host
+extern NCBI_XCONNECT_EXPORT int/*bool*/ SOCK_isipEx
+(const char* host,
+ int/*bool*/ fullquad
  );
 
 
-/**
+/** Equivalent of SOCK_isip(host, 0)
  * @param host
- *  [in] host name to check against being a plain IP address
- * @param len
- *  [in] length of "host" to check for
+ *  [in] '\0'-terminated string to check against being a plain IP address
  * @return
  *  Non-zero (true) if given string is an IP address, zero (false) otherwise.
  */
-extern NCBI_XCONNECT_EXPORT int/*bool*/ SOCK_isipEx
-(const char* host,
- size_t      len
+extern NCBI_XCONNECT_EXPORT int/*bool*/ SOCK_isip
+(const char* host
  );
 
 
diff --git a/connect/ncbi_util.c b/connect/ncbi_util.c
index 02a74379..245545c8 100644
--- a/connect/ncbi_util.c
+++ b/connect/ncbi_util.c
@@ -1,4 +1,4 @@
-/* $Id: ncbi_util.c,v 6.42 2007/07/31 16:25:29 kazimird Exp $
+/* $Id: ncbi_util.c,v 6.49 2008/02/29 00:25:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -47,7 +47,7 @@
 #  ifndef NCBI_OS_SOLARIS
 #    include <limits.h>
 #  endif
-#  if defined(HAVE_GETPWUID)  ||  defined(HAVE_GETPWUID_R)
+#  if defined(HAVE_GETPWUID)  ||  defined(NCBI_HAVE_GETPWUID_R)
 #    include <pwd.h>
 #  endif
 #  include <unistd.h>
@@ -58,6 +58,8 @@
 #  include <windows.h>
 #endif
 
+#define NCBI_USE_ERRCODE_X   Connect_Util
+
 #define NCBI_USE_PRECOMPILED_CRC32_TABLES 1
 
 
@@ -139,7 +141,8 @@ extern int/*bool*/ CORE_SetLOGFILE_NAME_Ex
 {
     FILE* fp = fopen(filename, "a");
     if ( !fp ) {
-        CORE_LOGF_ERRNO(eLOG_Error, errno, ("Cannot open \"%s\"", filename));
+        CORE_LOGF_ERRNO_X(9, eLOG_Error, errno,
+                          ("Cannot open \"%s\"", filename));
         return 0/*false*/;
     }
 
@@ -172,9 +175,9 @@ inline
 #endif /*__GNUC__*/
 static int/*bool*/ s_IsQuoted(unsigned char c)
 {
-    return (c == '\t'  ||   c == '\v'  ||  c == '\b'  ||
-            c == '\r'  ||   c == '\f'  ||  c == '\a'  ||
-            c == '\n'  ||   c == '\\'  ||  c == '\''  ||
+    return (c == '\t'  ||  c == '\v'  ||  c == '\b'  ||
+            c == '\r'  ||  c == '\f'  ||  c == '\a'  ||
+            c == '\n'  ||  c == '\\'  ||  c == '\''  ||
             c == '"' ? 1/*true*/ : 0/*false*/);
 }
 
@@ -356,8 +359,12 @@ extern char* LOG_ComposeMessage
                 if (!isprint(*d)) {
                     int/*bool*/ reduce;
                     unsigned char v;
-                    reduce = (i == 1          ||  s_IsQuoted(d[1])  ||
-                              !isprint(d[1])  ||  d[1] < '0'  ||  d[1] > '7');
+                    if (format_flags & fLOG_FullOctal)
+                        reduce = 0/*false*/;
+                    else {
+                        reduce = (i == 1         || s_IsQuoted(d[1]) ||
+                                  !isprint(d[1]) || d[1] < '0' || d[1] > '7');
+                    }
                     *s++ = '\\';
                     v =  *d >> 6;
                     if (v  ||  !reduce) {
@@ -468,7 +475,7 @@ static int/*bool*/ s_SafeCopy(const char* src, char** beg, const char* end)
 }
 
 
-extern char* MessagePlusErrno
+extern const char* MessagePlusErrno
 (const char*  message,
  int          x_errno,
  const char*  descr,
@@ -478,9 +485,14 @@ extern char* MessagePlusErrno
     char* beg;
     char* end;
 
+    /* Check for an empty result */
+    if (!x_errno  &&  (!descr  ||  !*descr))
+        return !message  ||  !*message ? "" : message;
+
     /* Check and init */
     if (!buf  ||  !buf_size)
         return 0;
+
     buf[0] = '\0';
     if (buf_size < 2)
         return buf;  /* empty */
@@ -494,10 +506,6 @@ extern char* MessagePlusErrno
         }
     }
 
-    /* Check for an empty result, calculate string lengths */
-    if ((!message  ||  !*message)  &&  !x_errno  &&  (!descr  ||  !*descr))
-        return buf;  /* empty */
-
     /* Compose:   <message> {errno=<x_errno>,<descr>} */
     beg = buf;
     end = buf + buf_size - 1;
@@ -625,7 +633,7 @@ extern const char* CORE_GetUsername(char* buf, size_t bufsize)
     char loginbuf[LOGIN_NAME_MAX + 1];
 #  endif
     struct passwd* pw;
-#  if !defined(NCBI_OS_SOLARIS)  &&  defined(HAVE_GETPWUID_R)
+#  if !defined(NCBI_OS_SOLARIS)  &&  defined(NCBI_HAVE_GETPWUID_R)
     struct passwd pwd;
     char pwdbuf[256];
 #  endif
@@ -677,7 +685,7 @@ extern const char* CORE_GetUsername(char* buf, size_t bufsize)
 #  endif
 
 #  if defined(NCBI_OS_SOLARIS)  ||  \
-    (!defined(HAVE_GETPWUID_R)  &&  defined(HAVE_GETPWUID))
+    (!defined(NCBI_HAVE_GETPWUID_R)  &&  defined(HAVE_GETPWUID))
     /* NB:  getpwuid() is MT-safe on Solaris, so use it here, if available */
 #  ifndef NCBI_OS_SOLARIS
     CORE_LOCK_WRITE;
@@ -689,23 +697,23 @@ extern const char* CORE_GetUsername(char* buf, size_t bufsize)
 #  endif
     if (pw  &&  pw->pw_name)
         return buf;
-#  elif defined(HAVE_GETPWUID_R)
-#    if   HAVE_GETPWUID_R == 4
+#  elif defined(NCBI_HAVE_GETPWUID_R)
+#    if   NCBI_HAVE_GETPWUID_R == 4
     /* obsolete but still existent */
     pw = getpwuid_r(getuid(), &pwd, pwdbuf, sizeof(pwdbuf));
-#    elif HAVE_GETPWUID_R == 5
+#    elif NCBI_HAVE_GETPWUID_R == 5
     /* POSIX-conforming */
     if (getpwuid_r(getuid(), &pwd, pwdbuf, sizeof(pwdbuf), &pw) != 0)
         pw = 0;
 #    else
-#      error "Unknown value of HAVE_GETPWUID_R, 4 or 5 expected."
+#      error "Unknown value of NCBI_HAVE_GETPWUID_R, 4 or 5 expected."
 #    endif
     if (pw  &&  pw->pw_name) {
         assert(pw == &pwd);
         strncpy0(buf, pw->pw_name, bufsize - 1);
         return buf;
     }
-#  endif /*HAVE_GETPWUID_R*/
+#  endif /*NCBI_HAVE_GETPWUID_R*/
 
 #endif /*!NCBI_OS_UNIX*/
 
@@ -935,3 +943,31 @@ extern int/*bool*/ UTIL_MatchesMask(const char* name, const char* mask)
 {
     return UTIL_MatchesMaskEx(name, mask, 1/*ignore case*/);
 }
+
+
+extern char* UTIL_NcbiLocalHostName(char* hostname)
+{
+    static const struct {
+        const char* text;
+        size_t      len;
+    } kEndings[] = {
+        { ".ncbi.nlm.nih.gov", 17},
+        { ".ncbi.nih.gov", 13}
+    };
+    size_t len = hostname ? strlen(hostname) : 0;
+
+    if (len) {
+        size_t i;
+        for (i = 0;  i < sizeof(kEndings) / sizeof(kEndings[0]);  i++) {
+            assert(strlen(kEndings[i].text) == kEndings[i].len);
+            if (len > kEndings[i].len) {
+                size_t prefix = len - kEndings[i].len;
+                if (strcasecmp(hostname + prefix, kEndings[i].text) == 0) {
+                    hostname[prefix] = '\0';
+                    return hostname;
+                }
+            }
+        }
+    }
+    return 0;
+}
diff --git a/connect/ncbi_util.h b/connect/ncbi_util.h
index 11c4228f..a87c88ef 100644
--- a/connect/ncbi_util.h
+++ b/connect/ncbi_util.h
@@ -1,7 +1,7 @@
 #ifndef CONNECT___NCBI_UTIL__H
 #define CONNECT___NCBI_UTIL__H
 
-/*  $Id: ncbi_util.h,v 6.28 2007/07/31 16:25:29 kazimird Exp $
+/*  $Id: ncbi_util.h,v 6.33 2008/02/29 00:25:42 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -54,6 +54,7 @@
  *
  * 4. Miscellaneous:
  *       UTIL_MatchesMask[Ex]()
+ *       UTIL_NcbiLocalHostName()
  *
  */
 
@@ -105,28 +106,31 @@ extern NCBI_XCONNECT_EXPORT MT_LOCK CORE_GetLOCK(void);
  * @sa
  *  LOG_WriteInternal
  */
-#define LOG_Write(lg,level,module,file,line,message) \
-  (void) (((lg)  ||  (level) == eLOG_Fatal) ?                         \
-  (LOG_WriteInternal(lg,level,module,file,line,message,0,0), 0) : 1)
-#define LOG_Data(lg,level,module,file,line,data,size,message) \
-  (void) (((lg)  ||  (level) == eLOG_Fatal) ?                         \
-  (LOG_WriteInternal(lg,level,module,file,line,message,data,size), 0) : 1)
+#define LOG_Write(lg,code,subcode,level,module,file,line,message) \
+  (void) (((lg)  ||  (level) == eLOG_Fatal) ?                     \
+  (LOG_WriteInternal(lg,level,module,file,line,message,0,0,       \
+                     code,subcode), 0) : 1)
+#define LOG_Data(lg,code,subcode,level,module,file,line,data,size,message) \
+  (void) (((lg)  ||  (level) == eLOG_Fatal) ?                              \
+  (LOG_WriteInternal(lg,level,module,file,line,message,data,size,          \
+                     code,subcode), 0) : 1)
 
 
 /** Auxiliary plain macros to write message (maybe, with raw data) to the log.
  * @sa
  *   LOG_Write, LOG_Data
  */
-#define  LOG_WRITE(lg, level, message) \
-  LOG_Write(lg, level, THIS_MODULE, THIS_FILE, __LINE__, message)
+#define  LOG_WRITE(lg, code, subcode, level, message)   \
+  LOG_Write(lg, code, subcode, level,                   \
+            THIS_MODULE, THIS_FILE, __LINE__, message)
 
 #ifdef   LOG_DATA
 /* AIX's <pthread.h> defines LOG_DATA to be an integer constant;
    we must explicitly drop such definitions to avoid trouble */
 #  undef LOG_DATA
 #endif
-#define  LOG_DATA(lg, data, size, message) \
-  LOG_Data(lg, eLOG_Trace, THIS_MODULE, THIS_FILE, __LINE__, \
+#define  LOG_DATA(lg, code, subcode, level, data, size, message)       \
+  LOG_Data(lg, code, subcode, level, THIS_MODULE, THIS_FILE, __LINE__, \
            data, size, message)
 
 
@@ -229,11 +233,12 @@ typedef enum {
     fLOG_Module        = 0x2,
     fLOG_FileLine      = 0x4,    /**< always here for eLOG_Trace level       */
     fLOG_DateTime      = 0x8,
+    fLOG_FullOctal     = 0x2000, /**< do not do reduction in octal data bytes*/
     fLOG_OmitNoteLevel = 0x4000, /**< do not add NOTE if eLOG_Note is level  */
     fLOG_None          = 0x8000  /**< nothing but spec'd parts, msg and data */
 } ELOG_Format;
 typedef unsigned int TLOG_FormatFlags; /**< binary OR of "ELOG_FormatFlags"  */
-#define fLOG_Short  (fLOG_Level)
+#define fLOG_Short   fLOG_Level
 #define fLOG_Full   (fLOG_Level | fLOG_Module | fLOG_FileLine)
 
 extern NCBI_XCONNECT_EXPORT TLOG_FormatFlags CORE_SetLOGFormatFlags
@@ -295,7 +300,7 @@ extern NCBI_XCONNECT_EXPORT void LOG_ToFILE
 
 
 /** Add current "errno" (and maybe its description) to the message:
- * <message> {errno=<errno>,<descr>}
+ * <message>[ {errno=[<errno>][,][<descr>]}]
  * @param message
  *  [in]  message text (can be NULL)
  * @param x_errno
@@ -305,13 +310,13 @@ extern NCBI_XCONNECT_EXPORT void LOG_ToFILE
  * @param buf
  *  [out] buffer to put the composed message to
  * @param buf_size
- *  [in]  maximal buffer size
+ *  [in]  buffer size available for use
  * @return
- *  Return "buf"
+ *  Return "buf" if composition occurred, else "message" (if non-empty) or ""
  * @sa
  *  LOG_ComposeMessage
  */
-extern NCBI_XCONNECT_EXPORT char* MessagePlusErrno
+extern NCBI_XCONNECT_EXPORT const char* MessagePlusErrno
 (const char*  message,
  int          x_errno,
  const char*  descr,
@@ -325,11 +330,14 @@ extern NCBI_XCONNECT_EXPORT char* MessagePlusErrno
  * @sa
  *  LOG_WRITE_ERRNO
  */
-#define LOG_WRITE_ERRNO_EX(lg, level, message, x_errno, x_descr)  do {   \
+#define LOG_WRITE_ERRNO_EX(lg, code, subcode, level, message,            \
+                           x_errno, x_descr)                             \
+do {                                                                     \
     if ((lg)  ||  (level) == eLOG_Fatal) {                               \
         char _buf[1024];                                                 \
-        LOG_WRITE(lg, level, MessagePlusErrno(message, x_errno, x_descr, \
-                                              _buf, sizeof(_buf)));      \
+        LOG_WRITE(lg, code, subcode, level,                              \
+                  MessagePlusErrno(message, x_errno, x_descr,            \
+                                   _buf, sizeof(_buf)));                 \
     }                                                                    \
 } while (0)
 
@@ -338,8 +346,41 @@ extern NCBI_XCONNECT_EXPORT char* MessagePlusErrno
  * @sa
  *   LOG_WRITE_ERRNO_EX
  */
-#define LOG_WRITE_ERRNO(lg, level, message)                              \
-     LOG_WRITE_ERRNO_EX(lg, level, message, errno, 0)
+#define LOG_WRITE_ERRNO(lg, code, subcode, level, message)               \
+     LOG_WRITE_ERRNO_EX(lg, code, subcode, level, message, errno, 0)
+
+
+/* Several defines brought here from ncbidiag.hpp. Names of macros slightly
+ * changed (added _C) because some sources include this header and
+ * ncbidiag.hpp simultaneously
+ */
+
+/** Defines global error code name with given value (err_code)
+ */
+#define NCBI_C_DEFINE_ERRCODE_X(name, err_code, max_err_subcode)        \
+    enum enum##name {                                                   \
+        eErrCodeX_##name = err_code                                     \
+        /* automatic subcode checking is not implemented in C code */   \
+    }
+
+/** Makes one identifier from 2 parts
+ */
+#define NCBI_C_CONCAT_IDENTIFIER(prefix, postfix) prefix##postfix
+
+/** Returns value of error code by its name defined by NCBI_DEFINE_ERRCODE_X
+ *
+ * @sa NCBI_C_DEFINE_ERRCODE_X
+ */
+#define NCBI_C_ERRCODE_X_NAME(name)   \
+    NCBI_C_CONCAT_IDENTIFIER(eErrCodeX_, name)
+
+/** Returns currently set default error code. Default error code is set by
+ *  definition of NCBI_USE_ERRCODE_X with name of error code as its value.
+ *
+ * @sa NCBI_DEFINE_ERRCODE_X
+ */
+#define NCBI_C_ERRCODE_X   NCBI_C_ERRCODE_X_NAME(NCBI_USE_ERRCODE_X)
+
 
 
 
@@ -452,13 +493,23 @@ extern NCBI_XCONNECT_EXPORT int/*bool*/ UTIL_MatchesMaskEx
  *  TODO!
  * @param mask
  *  TODO!
-*/
+ */
 extern NCBI_XCONNECT_EXPORT int/*bool*/ UTIL_MatchesMask
 (const char* name,
  const char* mask
 );
 
 
+/** Cut off well-known NCBI domain suffix out of the passed "hostname".
+ * @param hostname
+ *  Hostname to shorten (if possible)
+ * @return 0 if the hostname wasn't modified, otherwise return "hostname".
+ */
+extern char* UTIL_NcbiLocalHostName
+(char*       hostname
+ );
+
+
 #ifdef __cplusplus
 }  /* extern "C" */
 #endif
diff --git a/connect/test/test_ncbi_connutil_misc.c b/connect/test/test_ncbi_connutil_misc.c
index 0269fe32..e0a1c4a4 100644
--- a/connect/test/test_ncbi_connutil_misc.c
+++ b/connect/test/test_ncbi_connutil_misc.c
@@ -1,4 +1,4 @@
-/*  $Id: test_ncbi_connutil_misc.c,v 6.25 2006/06/15 03:02:52 lavr Exp $
+/*  $Id: test_ncbi_connutil_misc.c,v 6.26 2007/12/05 19:26:19 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -147,60 +147,6 @@ static void TEST_URL_Encoding(void)
 
 
 /***********************************************************************
- *  TEST:  BASE64_Encode(), BAS64_Decode()
- */
-
-static void TEST_BASE64_Encoding(void)
-{
-    const char test_string[] = "Quick brown fox jumps over the lazy dog";
-    char buf1[1024], buf2[1024], buf3[1024];
-    size_t read, written, len = 16, i, j;
-
-    BASE64_Encode(test_string, strlen(test_string) + 1, &read,
-                  buf1, sizeof(buf1), &written, &len);
-    assert(read == strlen(test_string) + 1);
-    assert(written < sizeof(buf1));
-    assert(buf1[written] == '\0');
-
-    assert(BASE64_Decode(buf1, written, &read,
-                         buf2, sizeof(buf2), &written));
-    assert(strlen(buf1) == read);
-    assert(written == strlen(test_string) + 1);
-    assert(buf2[written - 1] == '\0');
-    assert(strcmp(buf2, test_string) == 0);
-
-    for (i = 0; i < 100; i++) {
-        len = rand() % 250;
-        memset(buf1, '\0', sizeof(buf1));
-        memset(buf2, '\0', sizeof(buf2));
-        memset(buf3, '\0', sizeof(buf3));
-        for (j = 0; j < len; j++) {
-            buf1[j] = rand() & 0xFF;
-        }
-
-        j = rand() % 100;
-        BASE64_Encode(buf1, len, &read, buf2, sizeof(buf2), &written, &j);
-        if (len != read)
-            fprintf(stderr, "len = %d, read = %d\n", (int)len, (int)read);
-        assert(len == read);
-        assert (written < sizeof(buf2));
-        assert(buf2[written] == '\0');
-
-        if (rand() & 1) {
-            buf2[written] = '=';
-        }
-        j = written;
-        BASE64_Decode(buf2, j, &read, buf3, sizeof(buf3), &written);
-        if (j != read)
-            fprintf(stderr, "j = %d, read = %d\n", (int)j, (int)read);
-        assert(j == read);
-        assert(len == written);
-        assert(memcmp(buf1, buf3, len) == 0);
-    }
-}
-
-
-/***********************************************************************
  *  TEST:  Miscellaneous
  */
 
@@ -382,92 +328,9 @@ int main(void)
     CORE_SetLOGFILE(stderr, 0/*false*/);
 
     TEST_URL_Encoding();
-    TEST_BASE64_Encoding();
     TEST_MIME();
     TEST_ConnNetInfo();
 
     CORE_SetLOG(0);
     return 0;
 }
-
-
-/*
- * ---------------------------------------------------------------------------
- * $Log: test_ncbi_connutil_misc.c,v $
- * Revision 6.25  2006/06/15 03:02:52  lavr
- * GetUsername test moved from here to test_ncbi_core.c
- *
- * Revision 6.24  2006/04/19 02:22:57  lavr
- * Modify test for Pre/Post overrides of SConnNetInfo::args
- *
- * Revision 6.23  2006/04/19 01:39:16  lavr
- * ConnNetInfo_*Arg tests added
- *
- * Revision 6.22  2006/01/31 17:12:07  lavr
- * CONNUTIL_GetUsername() test added
- *
- * Revision 6.21  2005/08/18 19:00:48  lavr
- * More thorough BASE64_{En|De}code() tests
- *
- * Revision 6.20  2005/07/11 18:24:28  lavr
- * Spell ADDEND
- *
- * Revision 6.19  2005/05/02 16:12:16  lavr
- * Use global random seed
- *
- * Revision 6.18  2005/04/20 18:23:26  lavr
- * +<stdlib.h>
- *
- * Revision 6.17  2005/03/21 17:04:51  lavr
- * BASE64_{En|De}code tests extended
- *
- * Revision 6.16  2005/03/19 02:17:08  lavr
- * Fix change log entry
- *
- * Revision 6.15  2005/03/19 02:14:10  lavr
- * +Test for BASE64_{En|De}code
- *
- * Revision 6.14  2004/04/01 14:14:02  lavr
- * Spell "occurred", "occurrence", and "occurring"
- *
- * Revision 6.13  2004/01/14 18:53:09  lavr
- * Use "application/xml+soap" in the test case
- *
- * Revision 6.12  2004/01/07 19:24:03  lavr
- * Added test for MIME content-type "application/xml"
- *
- * Revision 6.11  2002/12/13 21:20:55  lavr
- * Move log to end
- *
- * Revision 6.10  2002/11/22 15:09:40  lavr
- * Replace all occurrences of "ray" with "yar"
- *
- * Revision 6.9  2002/10/11 19:57:17  lavr
- * Add tests for ConnNetInfo_*UserHeader() routines
- *
- * Revision 6.8  2002/03/22 19:46:51  lavr
- * Test_assert.h made last among the include files
- *
- * Revision 6.7  2002/02/20 19:12:39  lavr
- * Swapped eENCOD_Url and eENCOD_None; eENCOD_Unknown introduced; test cleaned
- *
- * Revision 6.6  2002/02/05 21:45:55  lavr
- * Included header files rearranged
- *
- * Revision 6.5  2002/01/16 21:23:15  vakatov
- * Utilize header "test_assert.h" to switch on ASSERTs in the Release mode too
- *
- * Revision 6.4  2000/11/07 23:24:43  vakatov
- * [MIME]  In-sync with the C Toolkit "connutil.c:R6.15"
- *
- * Revision 6.3  2000/04/12 15:22:07  vakatov
- * Always #undef NDEBUG
- *
- * Revision 6.2  2000/03/29 17:21:48  vakatov
- * + CORE_SetLOG(0) at the program end.
- *
- * Revision 6.1  2000/03/24 22:53:38  vakatov
- * Initial revision
- *
- * ===========================================================================
- */
diff --git a/connect/test/test_ncbi_core.c b/connect/test/test_ncbi_core.c
index 36bdd195..3e58f85c 100644
--- a/connect/test/test_ncbi_core.c
+++ b/connect/test/test_ncbi_core.c
@@ -1,4 +1,4 @@
-/*  $Id: test_ncbi_core.c,v 6.13 2007/06/25 16:55:29 kazimird Exp $
+/*  $Id: test_ncbi_core.c,v 6.15 2008/02/28 20:25:52 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -258,10 +258,10 @@ static void TEST_CORE_Log(void)
   verify(LOG_Delete(x_log) == x_log);
   assert(TEST_CORE_LogUserData == 1);
 
-  LOG_WRITE(0, eLOG_Trace, 0);
-  LOG_Write(0, eLOG_Trace, 0, 0, 0, 0);
-  LOG_WRITE(x_log, eLOG_Trace, 0);
-  LOG_Write(x_log, eLOG_Trace, 0, 0, 0, 0);
+  LOG_WRITE(0, 0, 0, eLOG_Trace, 0);
+  LOG_Write(0, 0, 0, eLOG_Trace, 0, 0, 0, 0);
+  LOG_WRITE(x_log, 0, 0, eLOG_Trace, 0);
+  LOG_Write(x_log, 0, 0, eLOG_Trace, 0, 0, 0, 0);
 
   verify(LOG_Delete(x_log) == x_log);
   assert(TEST_CORE_LogUserData == 1);
@@ -273,16 +273,16 @@ static void TEST_CORE_Log(void)
   TEST_CORE_LogUserData = 2;
 
   /* do the test logging */
-  LOG_WRITE(x_log, eLOG_Trace, 0);
-  LOG_Write(x_log, eLOG_Trace, 0, 0, 0, 0);
-  LOG_WRITE(x_log, eLOG_Warning, "");
+  LOG_WRITE(x_log, 0, 0, eLOG_Trace, 0);
+  LOG_Write(x_log, 0, 0, eLOG_Trace, 0, 0, 0, 0);
+  LOG_WRITE(x_log, 0, 0, eLOG_Warning, "");
   /* LOG_WRITE(x_log, eLOG_Fatal, "Something fatal"); */
 #undef  THIS_MODULE
 #define THIS_MODULE "FooModuleName"
-  LOG_WRITE(x_log, eLOG_Error, "With changed module name");
+  LOG_WRITE(x_log, 0, 0, eLOG_Error, "With changed module name");
 #undef  THIS_FILE
 #define THIS_FILE "BarFileName"
-  LOG_WRITE(x_log, eLOG_Critical, "With changed module and file name");
+  LOG_WRITE(x_log, 0, 0, eLOG_Critical, "With changed module and file name");
 #undef  THIS_FILE
 #define THIS_FILE __FILE__
 #undef  THIS_MODULE
@@ -316,16 +316,16 @@ static void TEST_UTIL_Log(void)
   LOG_ToFILE(x_log, stdout, 0/*false*/);
 
   /* simple logging */
-  LOG_WRITE(x_log, eLOG_Trace, 0);
-  LOG_Write(x_log, eLOG_Trace, 0, 0, 0, 0);
-  LOG_WRITE(x_log, eLOG_Warning, "");
+  LOG_WRITE(x_log, 0, 0, eLOG_Trace, 0);
+  LOG_Write(x_log, 0, 0, eLOG_Trace, 0, 0, 0, 0);
+  LOG_WRITE(x_log, 0, 0, eLOG_Warning, "");
   /* LOG_WRITE(x_log, eLOG_Fatal, "Something fatal"); */
 #undef  THIS_MODULE
 #define THIS_MODULE "FooModuleName"
-  LOG_WRITE(x_log, eLOG_Error, "With changed module name");
+  LOG_WRITE(x_log, 0, 0, eLOG_Error, "With changed module name");
 #undef  THIS_FILE
 #define THIS_FILE "BarFileName"
-  LOG_WRITE(x_log, eLOG_Critical, "With changed module and file name");
+  LOG_WRITE(x_log, 0, 0, eLOG_Critical, "With changed module and file name");
 #undef  THIS_FILE
 #define THIS_FILE __FILE__
 #undef  THIS_MODULE
@@ -338,20 +338,20 @@ static void TEST_UTIL_Log(void)
     for (i = 0;  i < sizeof(data);  i++) {
         data[i] = (unsigned char) (i % 256);
     }
-    LOG_DATA(x_log, data, sizeof(data), "Data logging test");
+    LOG_DATA(x_log, 0, 0, eLOG_Note, data, sizeof(data), "Data logging test");
   }}
 
   /* logging with errno */
   errno = 0;
-  LOG_WRITE_ERRNO(x_log, eLOG_Warning, 0);  
-  LOG_WRITE_ERRNO(x_log, eLOG_Error, "");
-  LOG_WRITE_ERRNO(x_log, eLOG_Critical, "OKAY");
+  LOG_WRITE_ERRNO(x_log, 0, 0, eLOG_Warning, 0);  
+  LOG_WRITE_ERRNO(x_log, 0, 0, eLOG_Error, "");
+  LOG_WRITE_ERRNO(x_log, 0, 0, eLOG_Critical, "OKAY");
 
 #undef  THIS_FILE
 #define THIS_FILE 0
-  (void)strtod("1e-999999", 0);  LOG_WRITE_ERRNO(x_log, eLOG_Warning, 0);  
-  (void)strtod("1e-999999", 0);  LOG_WRITE_ERRNO(x_log, eLOG_Error, "");
-  (void)strtod("1e-999999", 0);  LOG_WRITE_ERRNO(x_log, eLOG_Critical, "FAIL");
+  (void)strtod("1e-999999", 0);  LOG_WRITE_ERRNO(x_log, 0, 0, eLOG_Warning, 0);  
+  (void)strtod("1e-999999", 0);  LOG_WRITE_ERRNO(x_log, 0, 0, eLOG_Error, "");
+  (void)strtod("1e-999999", 0);  LOG_WRITE_ERRNO(x_log, 0, 0, eLOG_Critical, "FAIL");
 
   /* delete */
   verify(LOG_Delete(x_log) == 0);
diff --git a/connect/test/test_ncbi_http_get.c b/connect/test/test_ncbi_http_get.c
index 7876f201..d5df86be 100644
--- a/connect/test/test_ncbi_http_get.c
+++ b/connect/test/test_ncbi_http_get.c
@@ -1,4 +1,4 @@
-/*  $Id: test_ncbi_http_get.c,v 6.14 2005/04/20 15:51:19 lavr Exp $
+/*  $Id: test_ncbi_http_get.c,v 6.15 2007/09/26 14:55:37 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -115,7 +115,7 @@ int main(int argc, char* argv[])
         fclose(fp);
 
     t = time(0);
-    for (;;) {
+    do {
         status = CONN_Wait(conn, eIO_Read, net_info->timeout);
         if (status != eIO_Success) {
             if (status == eIO_Closed)
@@ -124,21 +124,20 @@ int main(int argc, char* argv[])
                 CORE_LOG(eLOG_Fatal, "Timed out");
 #ifdef NCBI_OS_UNIX
             usleep(500);
-#endif
+#endif /*NCBI_OS_UNIX*/
             continue;
         }
 
-        status = CONN_Read(conn, blk, sizeof(blk), &n, eIO_ReadPlain);
-        if (status != eIO_Success && status != eIO_Closed)
+        status = CONN_ReadLine(conn, blk, sizeof(blk), &n);
+        if (status != eIO_Success  &&  status != eIO_Closed)
             CORE_LOGF(eLOG_Fatal, ("Read error: %s", IO_StatusStr(status)));
-        if (n) {
+        if (n == sizeof(blk))
+            CORE_LOGF(eLOG_Warning, ("Line too long, continuing..."));
+        if (n)
             fwrite(blk, 1, n, stdout);
-            fflush(stdout);
-        } else if (status == eIO_Closed) {
-            break;
-        } else
-            CORE_LOG(eLOG_Fatal, "Empty read");
-    }
+        fputc('\n', stdout);
+        fflush(stdout);
+    } while (status == eIO_Success);
 
     ConnNetInfo_Destroy(net_info);
     CORE_LOG(eLOG_Note, "Closing connection");
@@ -148,52 +147,3 @@ int main(int argc, char* argv[])
     CORE_SetLOG(0);
     return 0;
 }
-
-
-/*
- * --------------------------------------------------------------------------
- * $Log: test_ncbi_http_get.c,v $
- * Revision 6.14  2005/04/20 15:51:19  lavr
- * Allow addtl file argument to attach as a body ('-' for stdin)
- *
- * Revision 6.13  2005/04/19 16:37:52  lavr
- * Allow HTTP method to be overridden from the environment
- *
- * Revision 6.12  2003/09/30 20:59:39  lavr
- * Fix typo in previous log message
- *
- * Revision 6.11  2003/09/30 20:57:15  lavr
- * Allow to set zero timeout via environment
- *
- * Revision 6.10  2003/05/20 23:52:01  lavr
- * Explicit cast "time_t"->"unsigned" to avoid GCC warning
- *
- * Revision 6.9  2003/05/19 16:58:37  lavr
- * Modified to use {0,0} timeouts in CONN_Wait() and use app timeout handling
- *
- * Revision 6.8  2003/05/14 03:58:43  lavr
- * Match changes in respective APIs of the tests
- *
- * Revision 6.7  2002/10/28 15:47:06  lavr
- * Use "ncbi_ansi_ext.h" privately
- *
- * Revision 6.6  2002/08/14 14:42:46  lavr
- * Use fwrite() instead of printf() when printing out the data fetched
- *
- * Revision 6.5  2002/08/07 16:38:08  lavr
- * EIO_ReadMethod enums changed accordingly; log moved to end
- *
- * Revision 6.4  2002/03/22 19:47:23  lavr
- * Test_assert.h made last among the include files
- *
- * Revision 6.3  2002/02/05 21:45:55  lavr
- * Included header files rearranged
- *
- * Revision 6.2  2002/01/16 21:23:15  vakatov
- * Utilize header "test_assert.h" to switch on ASSERTs in the Release mode too
- *
- * Revision 6.1  2001/12/30 19:42:06  lavr
- * Initial revision
- *
- * ==========================================================================
- */
diff --git a/connect/test/test_ncbi_socket.c b/connect/test/test_ncbi_socket.c
index fbb0dc28..197a1cfe 100644
--- a/connect/test/test_ncbi_socket.c
+++ b/connect/test/test_ncbi_socket.c
@@ -1,4 +1,4 @@
-/*  $Id: test_ncbi_socket.c,v 6.25 2007/07/06 16:55:28 kazimird Exp $
+/*  $Id: test_ncbi_socket.c,v 6.26 2007/10/19 11:25:50 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -736,7 +736,7 @@ static const char* s_ntoa(unsigned int host)
 }
 
 
-static int/*bool*/ TEST_gethostbyname(const char* name)
+static unsigned int TEST_gethostbyname(const char* name)
 {
     char         buf[256];
     unsigned int host;
@@ -745,23 +745,21 @@ static int/*bool*/ TEST_gethostbyname(const char* name)
 
     host = SOCK_gethostbyname(name);
     fprintf(log_fp, "SOCK_gethostbyname(\"%s\"):  0x%08X [%s]\n",
-            name, (unsigned int) host, s_ntoa(host));
-    if ( !host ) {
-        return 0/*false*/;
-    }
-      
-    name = SOCK_gethostbyaddr(host, buf, sizeof(buf));
-    if ( name ) {
-        assert(name == buf);
-        assert(0 < strlen(buf)  &&  strlen(buf) < sizeof(buf));
-        fprintf(log_fp, "SOCK_gethostbyaddr(0x%08X [%s]):  \"%s\"\n",
-                (unsigned int) host, s_ntoa(host), name);
-    } else {
-        fprintf(log_fp, "SOCK_gethostbyaddr(0x%08X [%s]):  <not found>\n",
-                (unsigned int) host, s_ntoa(host));
+            name, (unsigned int) SOCK_NetToHostLong(host), s_ntoa(host));
+    if ( host ) {
+        name = SOCK_gethostbyaddr(host, buf, sizeof(buf));
+        if ( name ) {
+            assert(name == buf);
+            assert(0 < strlen(buf)  &&  strlen(buf) < sizeof(buf));
+            fprintf(log_fp, "SOCK_gethostbyaddr(0x%08X [%s]):  \"%s\"\n",
+                    (unsigned int) SOCK_NetToHostLong(host), s_ntoa(host),
+                    name);
+        } else {
+            fprintf(log_fp, "SOCK_gethostbyaddr(0x%08X [%s]):  <not found>\n",
+                    (unsigned int) SOCK_NetToHostLong(host), s_ntoa(host));
+        }
     }
-
-    return 1/*true*/;
+    return host;
 }
 
 
@@ -770,23 +768,23 @@ static int/*bool*/ TEST_gethostbyaddr(unsigned int host)
     const char*  name;
     char         buf[1024];
 
-    fprintf(log_fp, "- - - - - - -\n");
+    fprintf(log_fp, "------------\n");
 
     name = SOCK_gethostbyaddr(host, buf, sizeof(buf));
     if ( name ) {
         assert(name == buf);
         assert(0 < strlen(buf)  &&  strlen(buf) < sizeof(buf));
         fprintf(log_fp, "SOCK_gethostbyaddr(0x%08X [%s]):  \"%s\"\n",
-                (unsigned int) host, s_ntoa(host), name);
+                (unsigned int) SOCK_NetToHostLong(host), s_ntoa(host), name);
     } else {
         fprintf(log_fp, "SOCK_gethostbyaddr(0x%08X [%s]):  <not found>\n",
-                (unsigned int) host, s_ntoa(host));
+                (unsigned int) SOCK_NetToHostLong(host), s_ntoa(host));
         return 0/*false*/;
     }
 
     host = SOCK_gethostbyname(name);
     fprintf(log_fp, "SOCK_gethostbyname(\"%s\"):  0x%08X [%s]\n",
-            name, (unsigned int) host, s_ntoa(host));
+            name, (unsigned int) SOCK_NetToHostLong(host), s_ntoa(host));
       
     return 1/*true*/;
 }
@@ -805,8 +803,6 @@ static void TEST_gethostby(void)
     assert( !TEST_gethostbyname("a1....b1") );
     assert( !TEST_gethostbyname("boo.foo.bar.doo") );
 
-    fprintf(log_fp, "\n++++++++++++++++++++++\n");
-
     (void) TEST_gethostbyname("localhost");
     (void) TEST_gethostbyname("ncbi.nlm.nih.gov");
 
@@ -823,6 +819,72 @@ static void TEST_gethostby(void)
 }
 
 
+static int/*bool*/ TEST_isip(const char* ip)
+{
+    int retval = SOCK_isip(ip);
+
+    fprintf(log_fp, "------------\n");
+    
+    fprintf(log_fp, "SOCK_isip(\"%s\"):  %s\n", ip, retval ? "True" : "False");
+
+    return retval;
+}
+
+
+
+/* Try SOCK_isip()
+ */
+static void TEST_SOCK_isip(void)
+{
+    fprintf(log_fp, "\n===============================\n");
+
+    assert(TEST_isip("0")  &&  TEST_isip("0.0.0.0"));
+    assert(TEST_gethostbyname("0") == 0);
+    assert(TEST_isip("1"));
+    assert(TEST_gethostbyname("1") == SOCK_HostToNetLong(1));
+    assert(TEST_isip("0x7F000002"));
+    assert(TEST_gethostbyname("0x7F000002") ==
+           TEST_gethostbyname("127.0.0.2"));
+
+    assert(TEST_isip("127.234"));
+    assert(TEST_gethostbyname("127.234") ==
+           TEST_gethostbyname("127.0.0.234"));
+    assert(TEST_isip("127.16777215"));
+    assert(TEST_gethostbyname("127.16777215") ==
+           TEST_gethostbyname("127.255.255.255"));
+
+    assert(TEST_isip("127.234.0x345"));
+    assert(TEST_gethostbyname("127.234.3.69") ==
+           TEST_gethostbyname("127.234.3.69"));
+    assert(TEST_isip("127.234.0xFFFF"));
+    assert(TEST_gethostbyname("127.234.0xFFFF") ==
+           TEST_gethostbyname("127.234.255.255"));
+
+    assert(TEST_isip("127.012344321"));
+    assert(TEST_gethostbyname("127.012344321") ==
+           TEST_gethostbyname("127.41.200.209"));
+    assert(TEST_isip("127.077777777"));
+    assert(TEST_gethostbyname("127.077777777") ==
+           TEST_gethostbyname("127.255.255.255"));
+
+    assert(TEST_isip("0.0321.0xAB.123"));
+    assert(TEST_isip("255.255.255.255"));
+
+    assert(!TEST_isip("a"));
+    assert(!TEST_isip("-1"));
+    assert(!TEST_isip("1.2.3a"));
+    assert(!TEST_isip("1.0xDEATH"));
+    assert(!TEST_isip("1.2.3.256"));
+    assert(!TEST_isip("1.2.0200000"));
+    assert(!TEST_isip("1.1.1.1."));
+    assert(!TEST_isip("1.1.-1.1"));
+    assert(!TEST_isip("1.0x100.1.1"));
+    assert(!TEST_isip("1.0100000000"));
+    assert(!TEST_isip("0x100000000"));
+
+    fprintf(log_fp, "\n===============================\n");
+}
+
 
 /* Main function
  * Parse command-line options, initialize and cleanup API internals;
@@ -920,6 +982,8 @@ extern int main(int argc, char** argv)
 
         TEST_gethostby();
 
+        TEST_SOCK_isip();
+
         TEST__client(server_host, (unsigned short)server_port, timeout);
         assert(SOCK_ShutdownAPI() == eIO_Success);
         CORE_SetLOG(0);
diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c
index 302b56b4..0cd5f295 100644
--- a/corelib/ncbierr.c
+++ b/corelib/ncbierr.c
@@ -23,9 +23,9 @@
 *
 * ===========================================================================
 *
-* $Id: ncbierr.c,v 6.24 2006/11/09 17:46:58 kans Exp $
+* $Id: ncbierr.c,v 6.25 2008/01/18 17:09:13 lavr Exp $
 *
-* $Revision: 6.24 $
+* $Revision: 6.25 $
 *
 * Authors:  Schuler, Sirotkin (UserErr stuff)
 *
@@ -71,6 +71,9 @@
 * 03-06-95 Schuler     Fixed problem with ErrMsgRoot_fopen
 *
 * $Log: ncbierr.c,v $
+* Revision 6.25  2008/01/18 17:09:13  lavr
+* Use SEV_MIN (instead of explicit SEV_INFO) in level setting routines
+*
 * Revision 6.24  2006/11/09 17:46:58  kans
 * added cast to quiet CodeWarrior complaint
 *
@@ -1542,7 +1545,7 @@ NLM_EXTERN ErrSev LIBCALL ErrSetLogLevel (ErrSev level)
 {
 	AppErrInfoPtr info = GetAppErrInfo();
 	ErrSev prev = (ErrSev) info->opts.log_level;
-	info->opts.log_level = (short) MAX(SEV_INFO,MIN(level,SEV_MAX));
+	info->opts.log_level = (short) MAX(SEV_MIN,MIN(level,SEV_MAX));
 	return prev;
 }
 
@@ -1561,7 +1564,7 @@ NLM_EXTERN ErrSev LIBCALL ErrSetMessageLevel (ErrSev level)
 {
 	AppErrInfoPtr info = GetAppErrInfo();
 	ErrSev prev = (ErrSev) info->opts.msg_level;
-	info->opts.msg_level = (short) MAX(SEV_INFO,MIN(level,SEV_MAX));
+	info->opts.msg_level = (short) MAX(SEV_MIN,MIN(level,SEV_MAX));
 	return prev;
 }
 
@@ -1580,7 +1583,7 @@ NLM_EXTERN ErrSev LIBCALL ErrSetFatalLevel (ErrSev level)
 {
 	AppErrInfoPtr info = GetAppErrInfo();
 	ErrSev prev = (ErrSev) info->opts.die_level;
-	info->opts.die_level = (short) MAX(SEV_INFO,MIN(level,SEV_MAX));
+	info->opts.die_level = (short) MAX(SEV_MIN,MIN(level,SEV_MAX));
 	return prev;
 }
 
diff --git a/ctools/asn_connection.c b/ctools/asn_connection.c
index 9676e31c..9579123d 100644
--- a/ctools/asn_connection.c
+++ b/ctools/asn_connection.c
@@ -1,4 +1,4 @@
-/*  $Id: asn_connection.c,v 1.8 2004/11/23 16:15:29 lavr Exp $
+/*  $Id: asn_connection.c,v 1.9 2007/10/17 15:25:44 kazimird Exp $
  * ===========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -32,6 +32,10 @@
 
 #include <ctools/asn_connection.h>
 #include "../connect/ncbi_priv.h"
+#include "error_codes.h"
+
+
+#define NCBI_USE_ERRCODE_X   Ctools_ASN
 
 
 #ifdef __cplusplus
@@ -70,7 +74,7 @@ static void s_CloseAsnConn(CONN conn, ECONN_Callback type, void* data)
     struct SAsnConn_Cbdata* cbdata = (struct SAsnConn_Cbdata*) data;
 
     assert(type == eCONN_OnClose && cbdata && cbdata->ptr);
-    CONN_SetCallback(conn, type, &cbdata->cb, 0); 
+    CONN_SetCallback(conn, type, &cbdata->cb, 0);
     AsnIoFree(cbdata->ptr, 0/*not a file - don't close*/);
     if ( cbdata->cb.func )
         (*cbdata->cb.func)(conn, type, cbdata->cb.data);
@@ -91,8 +95,8 @@ static void s_SetAsnConn_CloseCb(CONN conn, AsnIoPtr ptr)
         cb.data = cbdata;
         CONN_SetCallback(conn, eCONN_OnClose, &cb, &cbdata->cb);
     } else
-        CORE_LOG(eLOG_Error,
-                 "Cannot create cleanup callback for ASN conn-based stream");
+        CORE_LOG_X(1, eLOG_Error,
+                   "Cannot create cleanup callback for ASN conn-based stream");
 }
 
 
@@ -165,35 +169,3 @@ CONN CreateAsnConn_Service(const char*     service,
     return CreateAsnConn_ServiceEx(service, input_fmt, input,
                                    output_fmt, output, fSERV_Any, 0, 0);
 }
-
-
-/*
- * --------------------------------------------------------------------------
- * $Log: asn_connection.c,v $
- * Revision 1.8  2004/11/23 16:15:29  lavr
- * -<connect/ncbi_service_connector.h> now included from <ctools/asn_connectionh>
- *
- * Revision 1.7  2004/03/23 02:29:19  lavr
- * Remove redundant inits in I/O callbacks
- *
- * Revision 1.6  2004/02/23 15:23:50  lavr
- * New (last) parameter "how" added in CONN_Write() API call
- *
- * Revision 1.5  2003/11/13 16:01:31  lavr
- * Included headers revised
- *
- * Revision 1.4  2002/08/07 16:38:18  lavr
- * EIO_ReadMethod enums changed accordingly; log moved to end
- *
- * Revision 1.3  2001/09/24 20:32:44  lavr
- * +SSERVICE_Extra* parameter in CreateAsnConn_ServiceEx()
- *
- * Revision 1.2  2001/06/29 14:04:17  lavr
- * Close callback removes itself when called; fixes not to add callbacks
- * in CreateAsnConn_ServiceEx, because they are already there!
- *
- * Revision 1.1  2001/06/28 21:58:23  lavr
- * Initial revision
- *
- * ==========================================================================
- */
diff --git a/ctools/error_codes.h b/ctools/error_codes.h
new file mode 100644
index 00000000..79ad1ed8
--- /dev/null
+++ b/ctools/error_codes.h
@@ -0,0 +1,45 @@
+#ifndef CTOOLS___ERROR_CODES__H
+#define CTOOLS___ERROR_CODES__H
+
+/*  $Id: error_codes.h,v 1.1 2007/10/17 17:49:03 lavr Exp $
+ * ===========================================================================
+ *
+ *                            PUBLIC DOMAIN NOTICE
+ *               National Center for Biotechnology Information
+ *
+ *  This software/database is a "United States Government Work" under the
+ *  terms of the United States Copyright Act.  It was written as part of
+ *  the author's official duties as a United States Government employee and
+ *  thus cannot be copyrighted.  This software/database is freely available
+ *  to the public for use. The National Library of Medicine and the U.S.
+ *  Government have not placed any restriction on its use or reproduction.
+ *
+ *  Although all reasonable efforts have been taken to ensure the accuracy
+ *  and reliability of the software and data, the NLM and the U.S.
+ *  Government do not and cannot warrant the performance or results that
+ *  may be obtained by using this software or data. The NLM and the U.S.
+ *  Government disclaim all warranties, express or implied, including
+ *  warranties of performance, merchantability or fitness for any particular
+ *  purpose.
+ *
+ *  Please cite the author in any work or product based on this material.
+ *
+ * ===========================================================================
+ *
+ * Authors:  Pavel Ivanov
+ *
+ */
+
+/// @file error_codes.hpp
+/// Definition of all error codes used in C code of ctools library
+/// (xctools.lib).
+///
+
+
+#include "../connect/ncbi_priv.h"
+
+
+NCBI_C_DEFINE_ERRCODE_X(Ctools_ASN,  901,  1);
+
+
+#endif  /* CTOOLS___ERROR_CODES__H */
diff --git a/data/country_lat_lon.txt b/data/country_lat_lon.txt
index 2814ddc6..96ea9631 100644
--- a/data/country_lat_lon.txt
+++ b/data/country_lat_lon.txt
@@ -68,7 +68,8 @@ Cayman Islands	CJ	-81.5	19.2	-81.1	19.4	-80.2	19.6	-79.7	19.8
 Central African Republic	CT	14.4	2.2	27.5	11.0
 Chad	CD	13.4	7.4	24.0	23.5
 Chile	CI	-75.8	-56.0	-66.4	-17.5
-China	CH	73.5	20.2	134.8	53.6
+China	CH	73.5	20.2	134.8	53.6	108.6	18.1	111.1	20.2
+China: Hainan	XX	108.6	18.1	111.1	20.2
 Christmas Island	KT	105.5	-10.6	105.7	-10.4
 Clipperton Island	IP	-109.3	10.2	-109.2	10.3
 Cocos Islands	CK	96.8	-12.2	96.9	-11.8
@@ -238,7 +239,6 @@ Sao Tome and Principe	TP	6.4	0.0	1.7	7.5
 Saudi Arabia	SA	34.4	15.6	55.7	32.2
 Senegal	SG	-17.6	12.3	-11.4	16.7
 Serbia	RB	18.8	41.8	23.1	46.2
-Serbia and Montenegro	YI	
 Seychelles	SE	50.7	-9.6	51.1	-9.2	52.7	-7.2	52.8	-7.0	53.0	-6.3	53.7	-5.1	55.2	-5.9	56.0	-3.7	56.2	-7.2	56.3	-7.1
 Sierra Leone	SL	-13.4	6.9	-10.3	10.0
 Singapore	SN	103.6	1.1	104.1	1.5
@@ -341,6 +341,5 @@ Wallis and Futuna	WF	-178.3	-14.4	-178.0	-14.2	-176.3	-13.4	-176.1	-13.2
 West Bank	WE	34.8	31.3	35.6	32.6
 Western Sahara	WI	-17.2	20.7	-8.7	27.7
 Yemen	YM	41.8	11.7	54.5	19.0
-Yugoslavia	XX	13.3	40.8	23.0	46.9
 Zambia	ZA	21.9	-18.1	33.7	-8.2
 Zimbabwe	ZI	25.2	-22.5	33.1	-15.6
diff --git a/data/featdef.prt b/data/featdef.prt
index 0d869e73..3af3f9fc 100644
--- a/data/featdef.prt
+++ b/data/featdef.prt
@@ -121,7 +121,7 @@ FeatDefGroupSet ::= {
     menulabel "Small Nuclear RNA" ,
     featdef-key 9 ,
     seqfeat-key 5 ,
-    entrygroup 3 ,
+    entrygroup 0 ,
     displaygroup 3 ,
     molgroup na
   } ,
@@ -130,7 +130,7 @@ FeatDefGroupSet ::= {
     menulabel "Small Cytoplasmic RNA" ,
     featdef-key 10 ,
     seqfeat-key 5 ,
-    entrygroup 3 ,
+    entrygroup 0 ,
     displaygroup 3 ,
     molgroup na
   } ,
@@ -850,7 +850,7 @@ FeatDefGroupSet ::= {
     menulabel "Small Nucleolar RNA" ,
     featdef-key 90 ,
     seqfeat-key 5 ,
-    entrygroup 3 ,
+    entrygroup 0 ,
     displaygroup 3 ,
     molgroup na
   } ,
@@ -881,6 +881,24 @@ FeatDefGroupSet ::= {
     displaygroup 5 ,
     molgroup na
   } ,
+  {                   -- ncRNA
+    typelabel "ncRNA" ,
+    menulabel "Non-coding RNA" ,
+    featdef-key 94 ,
+    seqfeat-key 5 ,
+    entrygroup 3 ,
+    displaygroup 3 ,
+    molgroup na
+  } ,
+  {                   -- tmRNA
+    typelabel "tmRNA" ,
+    menulabel "Transfer-messenger RNA" ,
+    featdef-key 95 ,
+    seqfeat-key 5 ,
+    entrygroup 3 ,
+    displaygroup 3 ,
+    molgroup na
+  } ,
 
 }
 }
diff --git a/data/featdef.val b/data/featdef.val
index 9c57282d..18127853 100644
--- a/data/featdef.val
+++ b/data/featdef.val
diff --git a/data/lineages.txt b/data/lineages.txt
index 172f1475..0e86f362 100644
--- a/data/lineages.txt
+++ b/data/lineages.txt
@@ -1,58 +1,32 @@
-14
+15
 139	Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae; Borrelia; Borrelia burgdorferi group
-197	Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae; Campylobacter
 210	Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae; Helicobacter
 235	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Brucellaceae; Brucella
-274	Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus
 287	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
-294	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
-303	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
-305	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Ralstonia
-358	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium
 375	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae; Bradyrhizobium
-394	Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium
-446	Bacteria; Proteobacteria; Gammaproteobacteria; Legionellales; Legionellaceae; Legionella
 485	Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria
 487	Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria
-550	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Enterobacter; Enterobacter cloacae complex
 562	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia
-573	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Klebsiella
-602	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella
-621	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Shigella
-622	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Shigella
-623	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Shigella
-666	Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio
 727	Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Haemophilus
-777	Bacteria; Proteobacteria; Gammaproteobacteria; Legionellales; Coxiellaceae; Coxiella
 813	Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; Chlamydia
 1280	Bacteria; Firmicutes; Bacillales; Staphylococcus
 1282	Bacteria; Firmicutes; Bacillales; Staphylococcus
-1307	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1311	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1313	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
 1314	Bacteria; Firmicutes; Lactobacillales; Streptococcaceae; Streptococcus
-1351	Bacteria; Firmicutes; Lactobacillales; Enterococcaceae; Enterococcus
-1352	Bacteria; Firmicutes; Lactobacillales; Enterococcaceae; Enterococcus
 1396	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group
 1402	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
 1423	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
-1428	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group
-1496	Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
-1502	Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Clostridium
-1598	Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus
 1639	Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria
-1642	Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria
 1718	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae; Corynebacterium
 1773	Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae; Mycobacterium; Mycobacterium tuberculosis complex
-2247	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halorubrum
-2371	Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xylella
 2711	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
 2762	Eukaryota; Glaucocystophyceae; Cyanophoraceae; Cyanophora
 2769	Eukaryota; Rhodophyta; Florideophyceae; Gigartinales; Gigartinaceae; Chondrus
 2788	Eukaryota; Rhodophyta; Bangiophyceae; Bangiales; Bangiaceae; Porphyra
-2832	Eukaryota; Haptophyceae; Pavlovales; Pavlova
+2832	Eukaryota; Haptophyceae; Pavlovales; Pavlovaceae; Pavlova
 2850	Eukaryota; stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Naviculales; Phaeodactylaceae; Phaeodactylum
-2903	Eukaryota; Haptophyceae; Isochrysidales; Emiliania
+2903	Eukaryota; Haptophyceae; Isochrysidales; Noelaerhabdaceae; Emiliania
 2926	Eukaryota; Alveolata; Dinophyceae; Gonyaulacales; Gonyaulacaceae; Alexandrium
 2961	Eukaryota; Alveolata; Dinophyceae; Gymnodiniales; Gymnodiniaceae; Amphidinium
 3037	Eukaryota; Euglenozoa; Euglenida; Euglenales; Euglena
@@ -61,7 +35,6 @@
 3055	Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Chlamydomonadales; Chlamydomonadaceae; Chlamydomonas
 3088	Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Sphaeropleales; Scenedesmaceae; Scenedesmus
 3111	Eukaryota; Viridiplantae; Chlorophyta; Trebouxiophyceae; Chlorellales; Chlorellaceae; Prototheca
-3190	Eukaryota; Viridiplantae; Chlorophyta; Prasinophyceae; Chlorodendrales; Chlorodendraceae; Scherffelia
 3197	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Marchantiophyta; Superclass II; Marchantiopsida; Marchantiidae; Marchantiales; Marchantiaceae; Marchantia
 3218	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta; Moss Superclass V; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella
 3225	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta; Moss Superclass V; Bryopsida; Dicranidae; Dicranales; Ditrichaceae; Ceratodon
@@ -69,42 +42,38 @@
 3329	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Picea
 3330	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Picea
 3332	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Picea
-3347	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
 3352	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
+3357	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pseudotsuga
 3369	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Cupressaceae; Cryptomeria
 3377	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Gnetophyta; Gnetopsida; Welwitschiales; Welwitschiaceae; Welwitschia
 3382	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Gnetophyta; Gnetopsida; Gnetales; Gnetaceae; Gnetum
 3415	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; magnoliids; Magnoliales; Magnoliaceae; Liriodendron
 3435	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; magnoliids; Laurales; Lauraceae; Persea
 3467	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Ranunculales; Papaveraceae; Eschscholzioideae; Eschscholzia
+3483	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Cannabaceae; Cannabis
 3486	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Cannabaceae; Humulus
 3505	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fagales; Betulaceae; Betula
-3522	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fagales; Casuarinaceae; Casuarina
 3544	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Aizoaceae; Mesembryanthemum
-3605	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Vitales; Vitaceae; Vitis
 3635	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
 3641	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Malvales; Malvaceae; Byttnerioideae; Theobroma
 3649	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Caricaceae; Carica
 3656	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
 3659	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
-3690	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 3691	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 3693	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 3694	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
-3695	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 3696	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 3702	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
 3708	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
 3711	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
 3712	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
-3747	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Fragaria
-3750	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus
+3714	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+3726	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Raphanus
 3755	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
 3760	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
-3802	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Saxifragales; Grossulariaceae; Ribes
 3818	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Aeschynomeneae; Arachis
-3821	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Cajanus
 3827	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Cicereae; Cicer
+3832	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Indigofereae; Cyamopsis
 3847	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
 3848	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
 3870	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Genisteae; Lupinus
@@ -113,34 +82,35 @@
 3885	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
 3886	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
 3888	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Vicieae; Pisum
+3899	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
+3917	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
 3933	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; Myrtales; Myrtaceae; Eucalyptus
 3981	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Euphorbiaceae; Crotonoideae; Micrandreae; Hevea
 3983	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Euphorbiaceae; Crotonoideae; Manihoteae; Manihot
 3988	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
 3993	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Euphorbiaceae; Euphorbioideae; Euphorbieae; Euphorbia
 4006	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Linaceae; Linum
-4045	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Apiales; Apiaceae; Apioideae; apioid superclade; Apium clade; Apium
 4054	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Apiales; Araliaceae; Panax
 4058	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Gentianales; Apocynaceae; Rauvolfioideae; Vinceae; Catharanthus
-4072	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Capsicum
-4081	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
-4096	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Nicotiana
-4097	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Nicotiana
-4100	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Nicotiana
-4102	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Petunia
-4108	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanum
-4113	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanum
+4072	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Capsiceae; Capsicum
+4081	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
+4096	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
+4097	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
+4100	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
+4108	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
+4113	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
 4120	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea
 4151	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Plantaginaceae; Antirrhineae; Antirrhinum
 4155	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Phrymaceae; Mimulus
 4182	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Pedaliaceae; Sesamum
+4222	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Carduoideae; Cardueae; Carthamus
 4232	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
+4233	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
 4234	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
 4236	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactuca
 4432	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Proteales; Nelumbonaceae; Nelumbo
 4442	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; Ericales; Theaceae; Camellia
 4498	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Aveneae; Avena
-4511	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Chloridoideae; Eragrostideae; Eleusine
 4513	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Hordeum
 4521	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Poeae; Lolium
 4529	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza
@@ -155,10 +125,9 @@
 4547	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Saccharum; Saccharum officinarum complex
 4550	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Secale
 4558	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
-4560	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
 4565	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Triticum
+4567	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Triticum
 4568	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Triticum
-4571	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Triticum
 4573	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Aegilops
 4577	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Zea
 4606	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Poeae; Festuca
@@ -166,62 +135,55 @@
 4641	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Zingiberales; Musaceae; Musa
 4679	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Alliaceae; Allium
 4686	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Asparagaceae; Asparagus
-4690	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Lilium
-4754	Eukaryota; Fungi; Ascomycota; Pneumocystidomycetes; Pneumocystidaceae; Pneumocystis
+4754	Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Pneumocystidomycetes; Pneumocystidaceae; Pneumocystis
 4787	Eukaryota; stramenopiles; Oomycetes; Peronosporales; Phytophthora
 4792	Eukaryota; stramenopiles; Oomycetes; Peronosporales; Phytophthora
-4808	Eukaryota; Fungi; Chytridiomycota; Blastocladiales; Blastocladiaceae; Blastocladiella
-4853	Eukaryota; Fungi; Zygomycota; Zygomycetes; Mucorales; Cunninghamellaceae; Cunninghamella
+4808	Eukaryota; Fungi; Blastocladiomycota; Blastocladiomycetes; Blastocladiales; Blastocladiaceae; Blastocladiella
+4853	Eukaryota; Fungi; Fungi incertae sedis; Basal fungal lineages; Mucoromycotina; Mucorales; Cunninghamellaceae; Cunninghamella
 4876	Eukaryota; Fungi; Glomeromycota; Glomeromycetes; Glomerales; Glomeraceae; Glomus
 4881	Eukaryota; Ichthyosporea; Ichthyophonida; Amoebidiaceae; Amoebidium
-4896	Eukaryota; Fungi; Ascomycota; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces
-4905	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Pichia
-4911	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
-4916	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
-4920	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Pichia
-4931	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
-4932	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
-4934	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Lachancea
-4952	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Dipodascaceae; Yarrowia
-4956	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Zygosaccharomyces
-5011	Eukaryota; Fungi; Ascomycota; Taphrinomycetes; Taphrinales; Taphrinaceae; Taphrina
-5022	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes; Pleosporales; Leptosphaeriaceae; Leptosphaeria; Leptosphaeria maculans complex
-5037	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; Ajellomycetaceae; Ajellomyces
-5059	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
-5061	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
-5062	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
-5085	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
-5101	Eukaryota; Fungi; Ascomycota; Ascomycota incertae sedis; Amorphothecaceae; Amorphotheca
-5116	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Diaporthales; Cryphonectriaceae; Cryphonectria-Endothia complex; Cryphonectria
-5141	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Sordariaceae; Neurospora
-5180	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Sclerotinia
-5270	Eukaryota; Fungi; Basidiomycota; Ustilaginomycetes; Ustilaginomycetidae; Ustilaginales; Ustilaginaceae; Ustilago
-5272	Eukaryota; Fungi; Basidiomycota; Urediniomycetes; Microbotryomycetidae; Microbotryales; Microbotryaceae; Microbotryum
-5278	Eukaryota; Fungi; Basidiomycota; Urediniomycetes; Microbotryomycetidae; Leucosporidiales; Leucosporidium
-5306	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Aphyllophorales; Corticiaceae; Phanerochaete
-5322	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Pleurotaceae; Pleurotus
-5325	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Aphyllophorales; Trametes
-5334	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Schizophyllaceae; Schizophyllum
-5346	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Psathyrellaceae; Coprinopsis
-5353	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Tricholomataceae; Lentinula
-5418	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Heterobasidiomycetes; Tremellomycetidae; Tremellales; mitosporic Tremellales; Cryptococcus
-5466	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Phyllachorales; Phyllachoraceae; mitosporic Phyllachoraceae; Colletotrichum
-5476	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
-5478	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
-5480	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
-5482	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
-5507	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium; Fusarium oxysporum complex
-5514	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium
-5518	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella
-5530	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Clavicipitaceae; mitosporic Clavicipitaceae; Metarhizium
-5541	Eukaryota; Fungi; Ascomycota; mitosporic Ascomycota; Thermomyces
-5544	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
-5551	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; Arthrodermataceae; mitosporic Arthrodermataceae; Trichophyton
-5580	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes et Chaetothyriomycetes incertae sedis; Dothioraceae; mitosporic Dothioraceae; Aureobasidium
-5599	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes; Pleosporales; Pleosporaceae; mitosporic Pleosporaceae; Alternaria; Alternaria alternata group
-5606	Eukaryota; Fungi; Ascomycota; mitosporic Ascomycota; Saitoella
+4896	Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces
+4905	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Pichia
+4911	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
+4916	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
+4920	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Pichia
+4932	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+4934	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Lachancea
+4952	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Dipodascaceae; Yarrowia
+4956	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Zygosaccharomyces
+5007	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Dekkera
+5011	Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Taphrinomycetes; Taphrinales; Taphrinaceae; Taphrina
+5037	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; Ajellomycetaceae; Ajellomyces
+5059	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+5061	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+5062	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+5101	Eukaryota; Fungi; Dikarya; Ascomycota; Ascomycota incertae sedis; Amorphothecaceae; Amorphotheca
+5116	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Diaporthales; Cryphonectriaceae; Cryphonectria-Endothia complex; Cryphonectria
+5141	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Sordariaceae; Neurospora
+5180	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Sclerotinia
+5264	Eukaryota; Fungi; Dikarya; Basidiomycota; Pucciniomycotina; Pucciniomycetes; Pucciniales; Pucciniaceae; Uromyces
+5270	Eukaryota; Fungi; Dikarya; Basidiomycota; Ustilaginomycotina; Ustilaginomycetes; Ustilaginales; Ustilaginaceae; Ustilago
+5272	Eukaryota; Fungi; Dikarya; Basidiomycota; Pucciniomycotina; Microbotryomycetes; Microbotryales; Microbotryaceae; Microbotryum
+5278	Eukaryota; Fungi; Dikarya; Basidiomycota; Pucciniomycotina; Microbotryomycetes; Leucosporidiales; Leucosporidium
+5306	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Corticiales; Corticiaceae; Phanerochaete
+5325	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Polyporales; Trametes
+5346	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetidae; Agaricales; Psathyrellaceae; Coprinopsis
+5353	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetidae; Agaricales; Tricholomataceae; Lentinula
+5418	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Tremellomycetes; Tremellales; mitosporic Tremellales; Cryptococcus
+5476	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
+5478	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
+5480	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
+5482	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
+5508	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium; Fusarium oxysporum species complex
+5514	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium
+5518	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella
+5530	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Clavicipitaceae; mitosporic Clavicipitaceae; Metarhizium
+5541	Eukaryota; Fungi; Dikarya; Ascomycota; mitosporic Ascomycota; Thermomyces
+5544	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
+5551	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; Arthrodermataceae; mitosporic Arthrodermataceae; Trichophyton
+5580	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Dothideomycetes et Chaetothyriomycetes incertae sedis; Dothioraceae; mitosporic Dothioraceae; Aureobasidium
+5606	Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Taphrinomycotina incertae sedis; Saitoella
 5660	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania; Leishmania braziliensis species complex
-5661	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
 5664	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
 5691	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma
 5693	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma; Schizotrypanum
@@ -232,32 +194,34 @@
 5759	Eukaryota; Entamoebidae; Entamoeba
 5778	Eukaryota; Lobosea; Euamoebida; Hartmannellidae; Hartmannella
 5791	Eukaryota; Mycetozoa; Myxogastria; Myxogastromycetidae; Physariida; Physarum
-5802	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Eimeriidae; Eimeria
-5807	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Cryptosporidiidae; Cryptosporidium
-5811	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Toxoplasma
-5821	Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
-5825	Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
-5833	Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
-5855	Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
-5861	Eukaryota; Alveolata; Apicomplexa; Haemosporida; Plasmodium
-5874	Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae; Theileria
-5875	Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae; Theileria
-5888	Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Peniculida; Parameciidae; Paramecium
-5911	Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Hymenostomatida; Tetrahymenina; Tetrahymenidae; Tetrahymena
+5802	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; Eimeriorina; Eimeriidae; Eimeria
+5807	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; Eimeriorina; Cryptosporidiidae; Cryptosporidium
+5811	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; Eimeriorina; Sarcocystidae; Toxoplasma
+5821	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Vinckeia)
+5823	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Vinckeia)
+5825	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Vinckeia)
+5833	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Laverania)
+5855	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Plasmodium)
+5861	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Vinckeia)
+5865	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Piroplasmida; Babesiidae; Babesia
+5874	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Piroplasmida; Theileriidae; Theileria
+5875	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Piroplasmida; Theileriidae; Theileria
+5888	Eukaryota; Alveolata; Ciliophora; Intramacronucleata; Oligohymenophorea; Peniculida; Parameciidae; Paramecium
+5911	Eukaryota; Alveolata; Ciliophora; Intramacronucleata; Oligohymenophorea; Hymenostomatida; Tetrahymenina; Tetrahymenidae; Tetrahymena
+5932	Eukaryota; Alveolata; Ciliophora; Intramacronucleata; Oligohymenophorea; Hymenostomatida; Ophryoglenina; Ichthyophthirius
 6085	Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Anthomedusae; Hydridae; Hydra
 6087	Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Anthomedusae; Hydridae; Hydra
-6088	Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Anthomedusae; Hydridae; Hydra
 6096	Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Anthomedusae; Hydractiniidae; Podocoryne
 6131	Eukaryota; Metazoa; Cnidaria; Anthozoa; Hexacorallia; Scleractinia; Astrocoeniina; Acroporidae; Acropora
 6161	Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Seriata; Tricladida; Paludicola; Dugesiidae; Dugesia
 6182	Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Strigeidida; Schistosomatoidea; Schistosomatidae; Schistosoma
 6183	Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Strigeidida; Schistosomatoidea; Schistosomatidae; Schistosoma
+6198	Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Opisthorchiida; Opisthorchiata; Opisthorchioidea; Opisthorchiidae; Opisthorchis
+6204	Eukaryota; Metazoa; Platyhelminthes; Cestoda; Eucestoda; Cyclophyllidea; Taeniidae; Taenia
 6210	Eukaryota; Metazoa; Platyhelminthes; Cestoda; Eucestoda; Cyclophyllidea; Taeniidae; Echinococcus
-6211	Eukaryota; Metazoa; Platyhelminthes; Cestoda; Eucestoda; Cyclophyllidea; Taeniidae; Echinococcus
 6238	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
 6239	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
 6248	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Panagrolaimoidea; Strongyloididae; Strongyloides
-6252	Eukaryota; Metazoa; Nematoda; Chromadorea; Ascaridida; Ascaridoidea; Ascarididae; Ascaris
 6253	Eukaryota; Metazoa; Nematoda; Chromadorea; Ascaridida; Ascaridoidea; Ascarididae; Ascaris
 6265	Eukaryota; Metazoa; Nematoda; Chromadorea; Ascaridida; Ascaridoidea; Toxocaridae; Toxocara
 6279	Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Brugia
@@ -269,48 +233,45 @@
 6304	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Meloidogynidae; Meloidogyninae; Meloidogyne
 6305	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Meloidogynidae; Meloidogyninae; Meloidogyne
 6306	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Meloidogynidae; Meloidogyninae; Meloidogyne
-6313	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Metastrongyloidea; Angiostrongylidae; Angiostrongylus
 6317	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Haemonchidae; Ostertagiinae; Ostertagia
 6325	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Aphelenchoidoidea; Aphelenchoididae; Bursaphelenchus
 6326	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Aphelenchoidoidea; Aphelenchoididae; Bursaphelenchus
 6334	Eukaryota; Metazoa; Nematoda; Enoplea; Trichocephalida; Trichinellidae; Trichinella
-6359	Eukaryota; Metazoa; Annelida; Polychaeta; Palpata; Aciculata; Phyllodocida; Nereididae; Platynereis
+6396	Eukaryota; Metazoa; Annelida; Clitellata; Oligochaeta; Haplotaxida; Lumbricina; Lumbricidae; Eisenia
 6500	Eukaryota; Metazoa; Mollusca; Gastropoda; Orthogastropoda; Apogastropoda; Heterobranchia; Euthyneura; Opisthobranchia; Anaspidea; Aplysioidea; Aplysiidae; Aplysia
-6523	Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Basommatophora; Lymnaeoidea; Lymnaeidae; Lymnaea
 6526	Eukaryota; Metazoa; Mollusca; Gastropoda; Pulmonata; Basommatophora; Lymnaeoidea; Planorbidae; Biomphalaria
-6550	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Mytiloida; Mytiloidea; Mytilidae; Mytilinae; Mytilus
+6549	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Mytiloida; Mytiloidea; Mytilidae; Mytilinae; Mytilus
 6565	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Ostreoida; Ostreoidea; Ostreidae; Crassostrea
-6579	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Pectinoida; Pectinoidea; Pectinidae; Pecten
 6613	Eukaryota; Metazoa; Mollusca; Cephalopoda; Coleoidea; Neocoleoidea; Decapodiformes; Sepioidea; Sepiolidae; Euprymna
-6669	Eukaryota; Metazoa; Arthropoda; Crustacea; Branchiopoda; Diplostraca; Cladocera; Anomopoda; Daphniidae; Daphnia
 6687	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Penaeus
 6689	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Litopenaeus
 6706	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Pleocyemata; Astacidea; Nephropoidea; Nephropidae; Homarus
 6759	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Pleocyemata; Brachyura; Eubrachyura; Portunoidea; Portunidae; Carcinus
 6763	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Pleocyemata; Brachyura; Eubrachyura; Portunoidea; Portunidae; Callinectes
 6772	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Pleocyemata; Brachyura; Eubrachyura; Ocypodoidea; Ocypodidae; Ocypodinae; Uca complex; Celuca
-6941	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Boophilus
-6943	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Amblyomma
-6945	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Ixodes
-6954	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Psoroptidia; Analgoidea; Pyroglyphidae; Dermatophagoides
-6984	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Dictyoptera; Blattaria; Blaberoidea; Blaberidae; Diplopterinae; Diploptera
+6837	Eukaryota; Metazoa; Arthropoda; Crustacea; Maxillopoda; Copepoda; Calanoida; Calanidae; Calanus
+6941	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Rhipicephalinae; Rhipicephalus; Boophilus
+6943	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Amblyomminae; Amblyomma
+6945	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Ixodinae; Ixodes
+6999	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Orthoptera; Ensifera; Grylloidea; Gryllidae; Gryllinae; Gryllus
 7004	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Orthoptera; Caelifera; Acridomorpha; Acridoidea; Acrididae; Oedipodinae; Locusta
 7029	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Macrosiphini; Acyrthosiphon
 7038	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aleyrodiformes; Aleyrodoidea; Aleyrodidae; Aleyrodinae; Bemisia
 7070	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Tenebrionidae; Tribolium
-7091	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Bombycidae; Bombyx
+7091	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Bombycidae; Bombycinae; Bombyx
 7108	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Amphipyrinae; Spodoptera
 7130	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Sphingoidea; Sphingidae; Sphinginae; Manduca
 7153	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Chironomoidea; Chironomidae; Chironominae; Chironomus
 7159	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Culicinae; Culicini; Aedes; Stegomyia
 7165	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Anophelinae; Anopheles
+7167	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Anophelinae; Anopheles
+7176	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Culicinae; Culicini; Culex; Culex
 7186	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Sciaroidea; Sciaridae; Rhynchosciara
 7200	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Psychodoidea; Psychodidae; Lutzomyia; Lutzomyia
 7217	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7220	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7222	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7227	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
-7229	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7230	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7234	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7237	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
@@ -320,10 +281,11 @@
 7245	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7260	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
 7425	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Chalcidoidea; Pteromalidae; Pteromalinae; Nasonia
+7426	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Chalcidoidea; Pteromalidae; Pteromalinae; Nasonia
 7460	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Apis
-7515	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Siphonaptera; Pulicidae; Pulicinae; Ctenocephalides
+7515	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Siphonaptera; Pulicidae; Archaeopsyllinae; Ctenocephalides
 7539	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Doryphorini; Leptinotarsa
-7594	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Asterozoa; Asteroidea; Valvatacea; Valvatida; Asterinidae; Asterina
+7594	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Asterozoa; Asteroidea; Valvatacea; Valvatida; Asterinidae; Patiria
 7650	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Strongylocentrotidae; Hemicentrotus
 7656	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Echinidae; Paracentrotus
 7668	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Strongylocentrotidae; Strongylocentrotus
@@ -334,42 +296,39 @@
 7764	Eukaryota; Metazoa; Chordata; Craniata; Hyperotreti; Myxiniformes; Myxinidae; Eptatretinae; Eptatretus
 7782	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Squalea; Hypnosqualea; Pristiorajea; Batoidea; Rajiformes; Rajidae; Leucoraja
 7797	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Squalea; Hypnosqualea; Squaliformes; Squaloidei; Squalidae; Squalus
-7801	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Elasmobranchii; Galeomorphii; Galeoidea; Orectolobiformes; Ginglymostomatidae; Ginglymostoma
 7868	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes; Holocephali; Chimaeriformes; Callorhinchidae; Callorhinchus
 7904	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Chondrostei; Acipenseriformes; Acipenseridae; Acipenser
 7955	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio
-7957	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Carassius
 7962	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Cyprinus
 7998	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Siluriformes; Ictaluridae; Ictalurus
+8010	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Esociformes; Esocidae; Esox
 8014	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Osmeridae; Osmerus
 8022	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
 8023	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
 8030	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmo
-8032	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmo
+8038	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salvelinus
 8049	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Paracanthopterygii; Gadiformes; Gadidae; Gadus
 8078	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Cyprinodontiformes; Fundulidae; Fundulus
-8083	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Cyprinodontiformes; Poeciliidae; Xiphophorus
+8081	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Cyprinodontiformes; Poeciliidae; Poecilia
 8090	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Atherinomorpha; Beloniformes; Adrianichthyidae; Oryziinae; Oryzias
 8128	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei; Cichlidae; African cichlids; Pseudocrenilabrinae; Tilapiini; Oreochromis
 8153	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei; Cichlidae; African cichlids; Pseudocrenilabrinae; Haplochromini; Astatotilapia
-8168	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Percidae; Perca
 8175	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Sparidae; Sparus
 8222	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Gobioidei; Gobiidae; Gillichthys
 8237	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Scombroidei; Scombridae; Thunnus
-8245	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Scombroidei; Xiphiidae; Xiphias
 8255	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Paralichthyidae; Paralichthys
 8260	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Platichthys
-8265	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Pseudopleuronectes
 8267	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Pleuronectiformes; Pleuronectoidei; Pleuronectidae; Hippoglossus
 8296	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Caudata; Salamandroidea; Ambystomatidae; Ambystoma
 8355	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Mesobatrachia; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus
 8364	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Mesobatrachia; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana
-8724	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; Colubroidea; Viperidae; Crotalinae; Bothrops
-8752	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; Colubroidea; Viperidae; Crotalinae; Lachesis
-8839	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Anseriformes; Anatidae; Anas
-9031	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Gallus
-9103	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Galliformes; Phasianidae; Meleagris
+8479	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Testudines; Cryptodira; Testudinoidea; Emydidae; Chrysemys
+8496	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Crocodylidae; Alligatorinae; Alligator
+8839	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Anseriformes; Anatidae; Anas
+9031	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Gallus
+9103	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galliformes; Phasianidae; Meleagridinae; Meleagris
 9258	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Monotremata; Ornithorhynchidae; Ornithorhynchus
+9315	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Diprotodontia; Macropodidae; Macropus
 9337	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Diprotodontia; Phalangeridae; Trichosurus
 9361	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Xenarthra; Dasypodidae; Dasypus
 9365	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Insectivora; Erinaceidae; Erinaceinae; Erinaceus
@@ -379,7 +338,6 @@
 9541	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
 9544	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
 9545	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca
-9555	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Cercopithecidae; Cercopithecinae; Papio
 9593	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Gorilla
 9597	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Pan
 9598	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Pan
@@ -388,7 +346,6 @@
 9612	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia; Canidae; Canis
 9614	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia; Canidae; Canis
 9615	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia; Canidae; Canis
-9667	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia; Mustelidae; Mustelinae; Mustela
 9685	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Felinae; Felis
 9739	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Cetacea; Odontoceti; Delphinidae; Tursiops
 9785	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Afrotheria; Proboscidea; Elephantidae; Loxodonta
@@ -398,383 +355,353 @@
 9915	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bos
 9925	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Caprinae; Capra
 9940	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Caprinae; Ovis
+9978	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Lagomorpha; Ochotonidae; Ochotona
 9986	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Lagomorpha; Leporidae; Oryctolagus
 10029	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Cricetidae; Cricetinae; Cricetulus
 10036	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Cricetidae; Cricetinae; Mesocricetus
-10041	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Cricetidae; Neotominae; Peromyscus
 10090	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus
+10092	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus
 10116	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Rattus
 10141	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Hystricognathi; Caviidae; Cavia
-10298	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Alphaherpesvirinae; Simplexvirus
+10195	Eukaryota; Metazoa; Rotifera; Monogononta; Ploimida; Brachionidae; Brachionus
+10224	Eukaryota; Metazoa; Hemichordata; Enteropneusta; Harrimaniidae; Saccoglossus
 10359	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae; Cytomegalovirus
 10407	Viruses; Retro-transcribing viruses; Hepadnaviridae; Orthohepadnavirus
-10566	Viruses; dsDNA viruses, no RNA stage; Papillomaviridae; unclassified Papillomaviridae
-10632	Viruses; dsDNA viruses, no RNA stage; Polyomaviridae; Polyomavirus
-10995	Viruses; dsRNA viruses; Birnaviridae; Avibirnavirus
-11082	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus; Japanese encephalitis virus group
-11099	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Pestivirus
 11103	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Hepacivirus
-11120	Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Coronaviridae; Coronavirus; Group 3 species
 11176	Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Paramyxovirinae; Avulavirus
 11234	Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Paramyxovirinae; Morbillivirus
-11250	Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Pneumovirinae; Pneumovirus
 11292	Viruses; ssRNA negative-strand viruses; Mononegavirales; Rhabdoviridae; Lyssavirus
-11665	Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Equine lentivirus group
-11673	Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Feline lentivirus group
 11676	Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group
 11709	Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group
 11723	Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group
-11786	Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Gammaretrovirus
-11966	Viruses; Retro-transcribing viruses; Retroviridae
-12092	Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae; Hepatovirus
-12162	Viruses; ssRNA positive-strand viruses, no DNA stage; Closteroviridae; Closterovirus
-12461	Viruses; ssRNA positive-strand viruses, no DNA stage; Hepeviridae; Hepevirus
-12721	Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group
+11908	Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Deltaretrovirus
+12092	Viruses; ssRNA positive-strand viruses, no DNA stage; Picornavirales; Picornaviridae; Hepatovirus
 12968	Eukaryota; stramenopiles; Blastocystis
 13040	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Curculionidae; Entiminae; Entimini; Diaprepes
 13164	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Macrosiphini; Myzus
-13230	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Mimosoideae; Mimoseae; Prosopis
+13249	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Euhemiptera; Heteroptera; Panheteroptera; Cimicomorpha; Reduviidae; Triatominae; Rhodnius
 13258	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; magnoliids; Piperales; Aristolochiaceae; Saruma
 13333	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella
 13415	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Cupressaceae; Chamaecyparis
 13427	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Cichorium
 13443	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
 13489	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Moronidae; Dicentrarchus
-13563	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Schizophyllaceae; Heterobasidion; Heterobasidion annosum species complex
 13616	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Metatheria; Didelphimorphia; Didelphidae; Monodelphis
 13642	Eukaryota; Mycetozoa; Dictyosteliida; Polysphondylium
-13684	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes; Pleosporales; Phaeosphaeriaceae; Phaeosphaeria
+13686	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Vespoidea; Formicidae; Myrmicinae; Solenopsis
 13818	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Moniliformopses; Filicophyta; Filicopsida; Filicales; Pteridaceae; Adiantum
 15368	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Brachypodieae; Brachypodium
-27288	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
-27291	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
-27293	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
-27294	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
-27337	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Phyllachorales; mitosporic Phyllachorales; Verticillium
+27288	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+27292	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+27293	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+27294	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kazachstania
+27337	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Phyllachorales; mitosporic Phyllachorales; Verticillium
 27405	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Marsupenaeus
-27828	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Cooperiidae; Cooperia
+27606	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Cetacea; Mysticeti; Balaenidae; Eubalaena
 27835	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Heligmonellidae; Nippostrongylinae; Nippostrongylus
-27923	Eukaryota; Metazoa; Ctenophora; Cyclocoela; Lobata; Bolinopsidae; Mnemiopsis
 28344	Viruses; ssRNA positive-strand viruses, no DNA stage; Nidovirales; Arteriviridae; Arterivirus
-28526	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
+28377	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Iguania; Iguanidae; Polychrotinae; Anolis
+28526	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
 28532	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Cleomaceae; Cleome
-28583	Eukaryota; Fungi; Chytridiomycota; Blastocladiales; Blastocladiaceae; Allomyces
-28610	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Tephritoidea; Tephritidae; Rhagoletis
-28901	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella
+28583	Eukaryota; Fungi; Blastocladiomycota; Blastocladiomycetes; Blastocladiales; Blastocladiaceae; Allomyces
 28909	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Chloridoideae; Cynodonteae; Cynodon
-28985	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
-29001	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes; Pleosporales; Pleosporaceae; mitosporic Pleosporaceae; Alternaria
-29058	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Noctuoidea; Noctuidae; Heliothinae; Helicoverpa
+28985	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
+29001	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Dothideomycetes; Pleosporomycetidae; Pleosporales; Pleosporaceae; mitosporic Pleosporaceae; Alternaria
+29031	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Psychodoidea; Psychodidae; Phlebotomus; Phlebotomus
 29158	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Mytiloida; Mytiloidea; Mytilidae; Mytilinae; Mytilus
 29159	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Ostreoida; Ostreoidea; Ostreidae; Crassostrea
 29170	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Ancylostomatoidea; Ancylostomatidae; Ancylostomatinae; Ancylostoma
-29176	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Neospora
+29172	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Dictyocaulidae; Dictyocaulinae; Dictyocaulus
+29176	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; Eimeriorina; Sarcocystidae; Neospora
 29488	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Photorhabdus
 29546	Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Lawsonia
+29655	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Zosteraceae; Zostera
 29729	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
 29730	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
 29760	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Vitales; Vitaceae; Vitis
-29875	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
-29883	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Tricholomataceae; Laccaria
+29875	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
+29883	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetidae; Agaricales; Tricholomataceae; Laccaria
 30286	Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Stolidobranchia; Molgulidae; Molgula
-30522	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bos
+30538	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Tylopoda; Camelidae; Lama
 30608	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Strepsirrhini; Lemuriformes; Cheirogaleidae; Microcebus
 30611	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Strepsirrhini; Lorisiformes; Galagidae; Otolemur
 31033	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes; Tetradontoidea; Tetraodontidae; Takifugu
+31192	Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Holothuroidea; Aspidochirotacea; Aspidochirotida; Holothuriidae; Holothuria
 31199	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Pectinoida; Pectinoidea; Pectinidae; Argopecten
 31234	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
 31243	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Globodera
-32593	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Sarcocystis
-33069	Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas
+31271	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Vinckeia)
+31286	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma
+31646	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Hepacivirus
+31647	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Hepacivirus
+32593	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; Eimeriorina; Sarcocystidae; Sarcocystis
 33085	Eukaryota; Entamoebidae; Entamoeba
-33129	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
-33169	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Eremothecium
-33178	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
 33431	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Heliconiinae; Heliconiini; Heliconius
-33616	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Ciconiiformes; Cathartidae; Gymnogyps
 34146	Eukaryota; Viridiplantae; Streptophyta; Zygnemophyceae; Desmidiales; Closteriaceae; Closterium
 34176	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Poeae; Lolium
 34245	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Zinnia
-34256	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Nepeteae; Mentha
 34274	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
 34305	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
 34316	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; Myrtales; Myrtaceae; Eucalyptus
-34317	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; Myrtales; Myrtaceae; Eucalyptus
 34342	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Cycadophyta; Cycadales; Zamiaceae; Zamia
-34358	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kazachstania
-34488	Eukaryota; Fungi; Zygomycota; Zygomycetes; Entomophthorales; Ancylistaceae; Conidiobolus
+34358	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kazachstania
 34506	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Panagrolaimoidea; Strongyloididae; Strongyloides
 34602	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Argasidae; Argasinae; Argas
-34607	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Amblyomma
-34610	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Amblyomma
-34631	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Rhipicephalus
+34610	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Amblyomminae; Amblyomma
+34631	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Rhipicephalinae; Rhipicephalus; Rhipicephalus
 34739	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Saturniidae; Saturniinae; Saturniini; Antheraea
 34740	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Heliconiinae; Heliconiini; Heliconius
-34816	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Moronidae; Morone
-35520	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Paniceae; Pennisetum
 35525	Eukaryota; Metazoa; Arthropoda; Crustacea; Branchiopoda; Diplostraca; Cladocera; Anomopoda; Daphniidae; Daphnia
-35570	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Muscoidea; Muscidae; Stomoxys
 35630	Eukaryota; Metazoa; Cnidaria; Hydrozoa; Hydroida; Anthomedusae; Hydractiniidae; Hydractinia
 35632	Eukaryota; Metazoa; Annelida; Clitellata; Oligochaeta; Haplotaxida; Lumbricina; Lumbricidae; Lumbricus
 35845	Eukaryota; Viridiplantae; Chlorophyta; Ulvophyceae; Dasycladales; Polyphysaceae; Acetabularia
 35872	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Paniceae; Cenchrus
 35883	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea
-35884	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea
 35938	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Robinieae; Robinia
 36090	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Globodera
-36094	Eukaryota; Metazoa; Mollusca; Gastropoda; Orthogastropoda; Vetigastropoda; Haliotoidea; Haliotidae; Haliotis
+36148	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Euhemiptera; Membracoidea; Cicadellidae; Cicadellinae; Graphocephala
 36307	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; Colubroidea; Viperidae; Crotalinae; Deinagkistrodon
+36329	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Laverania)
 36596	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
-37099	Eukaryota; Haptophyceae; Isochrysidales; Isochrysis
-37296	Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Gammaherpesvirinae; Rhadinovirus
+36774	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+37011	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Pan
+37012	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Pan
+37099	Eukaryota; Haptophyceae; Isochrysidales; Isochrysidaceae; Isochrysis
 37347	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Scandentia; Tupaiidae; Tupaia
-37656	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
+37546	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Hippoboscoidea; Glossinidae; Glossina
 37682	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Aegilops
 37690	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Poncirus
-37727	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Penicillium
+37727	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Penicillium
 37862	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Heterorhabditidae; Heterorhabditis
-38032	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Ophiostomatales; Ophiostomataceae; Ophiostoma
-38033	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Chaetomiaceae; Chaetomium
-38249	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma
+38032	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Ophiostomatales; Ophiostomataceae; Ophiostoma
 38271	Eukaryota; Glaucocystophyceae; Glaucocystales; Glaucocystaceae; Glaucocystis
 38588	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta; Moss Superclass V; Bryopsida; Dicranidae; Pottiales; Pottiaceae; Tortula
-38705	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Bambusoideae; Bambuseae; Phyllostachys
 38727	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Paniceae; Panicum
-38865	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fagales; Fagaceae; Quercus
 38937	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Iguania; Iguanidae; Polychrotinae; Anolis
-38942	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fagales; Fagaceae; Quercus
 39350	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Ocimeae; Ocimum
+39946	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza
+39947	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza
 39984	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Rhizophoraceae; Bruguiera
-40366	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
-40559	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Botryotinia
-40697	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Glycyphagoidea; Echimyopodidae; Blomia
+40410	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Tremellomycetes; Tremellales; Tremellaceae; Filobasidiella
+40559	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Botryotinia
 41882	Eukaryota; Viridiplantae; Streptophyta; Mesostigmatophyceae; Mesostigmatales; Mesostigmataceae; Mesostigma
 42156	Eukaryota; Metazoa; Nematoda; Chromadorea; Spirurida; Filarioidea; Onchocercidae; Litomosoides
-42251	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Pezizomycetes; Pezizales; Tuberaceae; Tuber
+42251	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Pezizomycetes; Pezizales; Tuberaceae; Tuber
 42254	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Insectivora; Soricidae; Soricinae; Sorex
-42329	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Cycadophyta; Cycadales; Zamiaceae; Zamia
-42890	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Sarcocystis
+42890	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; Eimeriorina; Sarcocystidae; Sarcocystis
+43116	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Caudata; Salamandroidea; Ambystomatidae; Ambystoma
 43166	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
 43179	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Sciuridae; Xerinae; Marmotini; Spermophilus
 43195	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactuca
-43425	Eukaryota; Fungi; Glomeromycota; Glomeromycetes; Glomerales; Glomeraceae; Glomus
-43925	Eukaryota; stramenopiles; Eustigmatophyceae; Nannochloropsis
-43928	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobaculum
+44271	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
 44689	Eukaryota; Mycetozoa; Dictyosteliida; Dictyostelium
-44745	Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Chlamydomonadales; Haematococcaceae; Haematococcus
 45264	Eukaryota; Metazoa; Cnidaria; Anthozoa; Hexacorallia; Scleractinia; Astrocoeniina; Acroporidae; Acropora
 45351	Eukaryota; Metazoa; Cnidaria; Anthozoa; Hexacorallia; Actiniaria; Edwardsiidae; Nematostella
 45464	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Trichostrongyloidea; Haemonchidae; Ostertagiinae; Teladorsagia
-45687	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine
-45929	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Pratylenchidae; Pratylenchinae; Pratylenchus
 45931	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Pratylenchidae; Pratylenchinae; Pratylenchus
 46003	Eukaryota; Metazoa; Nematoda; Enoplea; Dorylaimida; Dorylaimina; Longidoroidea; Longidoridae; Xiphinema
-46012	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Pratylenchidae; Radopholinae; Radopholus
-46208	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Toxorhynchitinae; Toxorhynchites
-46433	Eukaryota; Granuloreticulosea; Athalamea; Reticulomyxidae; Reticulomyxa
+46681	Eukaryota; Entamoebidae; Entamoeba
 47315	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
-47615	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypioides
 47626	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Gossypium
-47664	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 48483	Eukaryota; Jakobidae; Reclinomonas
-48498	Eukaryota; Metazoa; Cnidaria; Anthozoa; Hexacorallia; Scleractinia; Faviina; Faviidae; Montastraea
+48668	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Rutilus
 49390	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
 49495	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Moniliformopses; Filicophyta; Filicopsida; Filicales; Pteridaceae; Ceratopteris
 50187	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Cupressaceae; Taiwania
 50225	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Taraxacum
+50390	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Chrysomeloidea; Chrysomelidae; Galerucinae; Diabroticina; Diabroticites; Diabrotica
+50591	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Sparidae; Lithognathus
 51029	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Heterodera
 51031	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Ancylostomatoidea; Ancylostomatidae; Bunostominae; Necator
-51074	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Orthoptera; Ensifera; Gryllidae; Gryllinae; Gryllus
 51240	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fagales; Juglandaceae; Juglans
 51329	Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Chlamydomonadales; Chlamydomonadaceae; Polytomella
-51453	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
+51351	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
+51453	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
 51511	Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona; Phlebobranchia; Cionidae; Ciona
-51655	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Yponomeutoidea; Plutellidae; Plutella
-51657	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Nakaseomyces
+51657	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Nakaseomyces
 51695	Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Chlamydomonadales; Chlamydomonadaceae; Chlamydomonas
-51953	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Arecaceae; Arecoideae; Cocoeae; Elaeidinae; Elaeis
-52283	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Psoroptidia; Sarcoptoidea; Sarcoptidae; Sarcoptes
+51953	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis
 52545	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza
-52714	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Leymus
+52641	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Peracarida; Amphipoda; Gammaridea; Gammaroidea; Gammaridae; Gammarus
+52824	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Brassica
 53326	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Strongylida; Ancylostomatoidea; Ancylostomatidae; Ancylostomatinae; Ancylostoma
-53468	Eukaryota; Metazoa; Platyhelminthes; Cestoda; Eucestoda; Cyclophyllidea; Mesocestoididae; Mesocestoides
 54126	Eukaryota; Metazoa; Nematoda; Chromadorea; Diplogasterida; Neodiplogasteridae; Pristionchus
 54290	Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; GBV-C/HGV group
-54734	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Dothideomycetes et Chaetothyriomycetes incertae sedis; Mycosphaerellaceae; Mycosphaerella
+54734	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Dothideomycetes; Dothideomycetidae; Capnodiales; Mycosphaerellaceae; Mycosphaerella
 55188	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
+55529	Eukaryota; Cryptophyta; Cryptomonadaceae; Guillardia
 55670	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Eupatorieae; Stevia
-55960	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Agavaceae; Yucca
+57267	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Laverania)
+57486	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus
 57577	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
 57918	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Fragaria
 58031	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Cycadophyta; Cycadales; Cycadaceae; Cycas
+58641	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Debaryomyces
 58824	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Pyraloidea; Pyralidae; Phycitinae; Plodia
 59463	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Microchiroptera; Vespertilionidae; Myotis
-59479	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Microchiroptera; Rhinolophidae; Rhinolophinae; Rhinolophus
-59689	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
-59729	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae; Estrildinae; Taeniopygia
+59691	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
+59729	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae; Estrildinae; Taeniopygia
 59747	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Meloidogynidae; Meloidogyninae; Meloidogyne
 59777	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Lycopodiophyta; Isoetopsida; Selaginellales; Selaginellaceae; Selaginella
 59861	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Coregonus
+61369	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium; Fusarium oxysporum species complex
+61970	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Chondrostei; Acipenseriformes; Acipenseridae; Acipenser
 62324	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Anophelinae; Anopheles
-62890	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
-63409	Eukaryota; Viridiplantae; Chlorophyta; Ulvophyceae; Ulvales; Ulvaceae; Ulva
+62688	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Leotiomycetes; Erysiphales; Erysiphaceae; Blumeria
+62890	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
 63629	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza
 63632	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Aveneae; Agrostis
 64093	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Orobanchaceae; Rhinantheae; Triphysaria
-64468	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Litopenaeus
-64495	Eukaryota; Fungi; Zygomycota; Zygomycetes; Mucorales; Mucoraceae; Rhizopus
-64602	Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Natrialba
-64884	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
-65344	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Euhemiptera; Heteroptera; Panheteroptera; Cimicomorpha; Reduviidae; Triatominae; Triatoma
-66189	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Testudines; Cryptodira; Testudinoidea; Testudinidae; Geochelone
+64495	Eukaryota; Fungi; Fungi incertae sedis; Basal fungal lineages; Mucoromycotina; Mucorales; Mucoraceae; Rhizopus
+65032	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Tortricoidea; Tortricidae; Tortricinae; Epiphyas
 66468	Eukaryota; Alveolata; Dinophyceae; Peridiniales; Heterocapsaceae; Heterocapsa
 66913	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Siluriformes; Ictaluridae; Ictalurus
 67593	Eukaryota; stramenopiles; Oomycetes; Peronosporales; Phytophthora
 68887	Viruses; ssDNA viruses; Anellovirus
 69266	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; Ericales; Ericaceae; Vaccinioideae; Vaccinieae; Vaccinium
 69293	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Gasterosteiformes; Gasterosteidae; Gasterosteus
-69721	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Araceae; Aroideae; Zantedeschieae; Zantedeschia
+69721	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Araceae; Philodendroideae; Zantedeschieae; Zantedeschia
+69919	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Phrymaceae; Mimulus
+70285	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Thymallus
 70415	Eukaryota; Metazoa; Nematoda; Enoplea; Trichocephalida; Trichuridae; Trichuris
-70448	Eukaryota; Viridiplantae; Chlorophyta; Prasinophyceae; Mamiellales; Mamiellaceae; Ostreococcus
 71139	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; Myrtales; Myrtaceae; Eucalyptus
-71150	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Boletales; Paxilineae; Paxillaceae; Paxillus
+71150	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetidae; Boletales; Paxilineae; Paxillaceae; Paxillus
+71272	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; Myrtales; Myrtaceae; Eucalyptus
 71647	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pinus; Pinus
 72019	Eukaryota; Ichthyosporea; Ichthyophonida; Sphaeroforma
 72036	Eukaryota; Metazoa; Arthropoda; Crustacea; Maxillopoda; Copepoda; Siphonostomatoida; Caligidae; Lepeophtheirus
+72095	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Scorpaeniformes; Scorpaenoidei; Sebastidae; Sebastinae; Sebastes
 72658	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Boechera
 72664	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Thellungiella
+73239	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Vinckeia)
 73275	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
+73280	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
 73304	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
-74495	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Orbiliomycetes; Orbiliales; Orbiliaceae; mitosporic Orbiliaceae; Monacrosporium
-74648	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Rosa
-74649	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Rosa
+74495	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Orbiliomycetes; Orbiliales; Orbiliaceae; mitosporic Orbiliaceae; Monacrosporium
 74940	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Oncorhynchus
 75329	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cobitidae; Cobitinae; Misgurnus
 75702	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
 75943	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactuca
 75947	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactuca
 75948	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactuca
-76149	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Plumbaginaceae; Plumbago
 76159	Eukaryota; Rhodophyta; Bangiophyceae; Bangiales; Bangiaceae; Porphyra
 76772	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Sciuridae; Xerinae; Marmotini; Spermophilus
-76867	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Agaricales; Cortinariaceae; Hebeloma
-77038	Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Wolbachieae; Wolbachia
+76867	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetidae; Agaricales; Cortinariaceae; Hebeloma
+76912	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Zea
+77009	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Hordeum
 77108	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Nymphaeales; Nymphaeaceae; Nuphar
+77133	Bacteria; environmental samples
 77306	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei; Cichlidae; African cichlids; Pseudocrenilabrinae; Haplochromini; Paralabidochromis
+77504	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Ichneumonoidea; Braconidae; Aphidiinae; Lysiphlebus
 77588	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza
-78579	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Chaetomiaceae; Corynascus
+78579	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Chaetomiaceae; Corynascus
 78828	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae; Epidendroideae; higher Epidendroideae; Vandeae; Aeridinae; Phalaenopsis
 79327	Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Seriata; Tricladida; Paludicola; Dugesiidae; Schmidtea
 79738	Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Seriata; Tricladida; Paludicola; Dugesiidae; Dugesia
-79858	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; mitosporic Onygenales; Geomyces
+79858	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; mitosporic Onygenales; Geomyces
 79880	Bacteria; Firmicutes; Bacillales; Bacillaceae; Bacillus
 79923	Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea; Opisthorchiida; Opisthorchiata; Opisthorchioidea; Opisthorchiidae; Clonorchis
+80265	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis
 80365	Eukaryota; stramenopiles; Phaeophyceae; Laminariales; Laminariaceae; Laminaria
-80765	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Aphidini; Aphis
-80863	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
+80765	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Aphidini; Aphis; Aphis
 81526	Eukaryota; Choanoflagellida; Codonosigidae; Monosiga
-82927	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Acanthaceae; Acanthaceae incertae sedis; Avicennia
+82528	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Iridaceae; Crocus
 83308	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza
-83558	Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; Chlamydophila
-83675	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Sarcocystidae; Neospora
-84072	Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Acoelomorpha; Acoela; Sagittiferidae; Symsagittifera
 85571	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
 85681	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
 86005	Bacteria; Firmicutes; Bacillales; Alicyclobacillaceae; Pasteuria
 86509	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae; Epidendroideae; higher Epidendroideae; Vandeae; Aeridinae; Phalaenopsis
-87530	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; Ericales; Myrsinaceae; Cyclamen
-88036	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Lycopodiophyta; Isoetopsida; Selaginellales; Selaginellaceae; Selaginella
-89411	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Descurainia
 89462	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bubalus
 90988	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Pimephales
 91374	Eukaryota; Euglenozoa; Diplonemida; Diplonema
-93883	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Tineoidea; Tineidae; Tineinae; Tineola
-94232	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Percoidei; Serranidae; Epinephelinae; Epinephelus
-94289	Eukaryota; Alveolata; Ciliophora; Spirotrichea; Stichotrichia; Stichotrichida; Oxytrichidae; Sterkiella
+94289	Eukaryota; Alveolata; Ciliophora; Intramacronucleata; Spirotrichea; Stichotrichia; Stichotrichida; Oxytrichidae; Sterkiella
 94328	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Zingiberales; Zingiberaceae; Zingiber
-96480	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Malvales; Malvaceae; Malvoideae; Malva
-96939	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Vitales; Vitaceae; Vitis
 97005	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Heteroderidae; Heteroderinae; Heterodera
-97485	Eukaryota; Haptophyceae; Prymnesiales; Prymnesium
+97485	Eukaryota; Haptophyceae; Prymnesiales; Prymnesiaceae; Prymnesium
 98038	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Thellungiella
-99586	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; Colubroidea; Viperidae; Viperinae; Echis
 99883	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes; Tetradontoidea; Tetraodontidae; Tetraodon
-101203	Eukaryota; stramenopiles; Oomycetes; Saprolegniales; Saprolegniaceae; Saprolegnia
-102803	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Curculionidae; Scolytinae; Ips
-103999	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Campanulaceae; Codonopsis
-104355	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Aphyllophorales; Polyporaceae; Gloeophyllum
-105581	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus x Poncirus
-106566	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus
+100272	Eukaryota; environmental samples
+100933	Eukaryota; Cercozoa; Cercomonadida; Cercomonadidae; Cercomonas
+101020	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Fragaria
+103874	Eukaryota; Diplomonadida; Hexamitidae; Hexamitinae; Spironucleus
+104355	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Gloeophyllales; Gloeophyllaceae; Gloeophyllum
+105145	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Glycyphagoidea; Glycyphagidae; Glycyphagus
 107243	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Thlaspi
 108210	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Aeschynomeneae; Arachis
 108607	Eukaryota; Pelobiontida; Mastigamoebidae; Mastigamoeba
-109760	Eukaryota; Fungi; Chytridiomycota; Spizellomycetales; Spizellomycetaceae; Spizellomyces
-110365	Eukaryota; Alveolata; Apicomplexa; Gregarinia; Eugregarinida; Gregarinidae; Gregarina
-110368	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Satyrinae; Elymniini; Mycalesina; Bicyclus
+109027	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Orthopteroidea; Orthoptera; Ensifera; Grylloidea; Gryllidae; Trigonidiinae; Laupala
+109760	Eukaryota; Fungi; Chytridiomycota; Chytridiomycetes; Spizellomycetales; Spizellomycetaceae; Spizellomyces
+109997	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Raphanus
+110368	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Papilionoidea; Nymphalidae; Satyrinae; Satyrini; Mycalesina; Bicyclus
 110450	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza
-110520	Eukaryota; Metazoa; Arthropoda; Crustacea; Maxillopoda; Cirripedia; Thoracica; Sessilia; Balanidae; Balanus
-110835	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Chloridoideae; Eragrostideae; Eragrostis
+110771	Eukaryota; Entamoebidae; Entamoeba
+110835	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Chloridoideae; Cynodonteae; Eragrostis
+112091	Eukaryota; stramenopiles; Oomycetes; Saprolegniales; Saprolegniaceae; Aphanomyces
+112509	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Triticeae; Hordeum
 113636	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
-114525	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
-114526	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+114280	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Cichorium
 115339	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Araneae; Mygalomorphae; Theraphosidae; Acanthoscurria
-117187	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella
-120305	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Serpentes; Colubroidea; Colubridae; Xenodontinae; Philodryas
-121225	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Phthiraptera; Anoplura; Pediculidae; Pediculus
-121540	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Senecioneae; Senecio
-121541	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Senecioneae; Senecio
-121759	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; mitosporic Onygenales; Paracoccidioides
+115547	Archaea; environmental samples
+117187	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella
+121224	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Phthiraptera; Anoplura; Pediculidae; Pediculus
+121226	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Phthiraptera; Anoplura; Pediculidae; Pediculus
+121759	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; mitosporic Onygenales; Paracoccidioides
 121845	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Psylliformes; Psylloidea; Psyllidae; Diaphorina
-123226	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Scorpiones; Buthida; Buthoidea; Buthidae; Mesobuthus
-124917	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Culicinae; Culicini; Armigeres; Armigeres
-126914	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Amaranthaceae; Suaeda
 128735	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Rosoideae; Rosa
 128810	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Saccharum; Saccharum officinarum complex
 130453	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Aeschynomeneae; Arachis
 131310	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Panagrolaimoidea; Strongyloididae; Parastrongyloides
 132711	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
+135651	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
 136089	Eukaryota; Malawimonadidae; Malawimonas
 136217	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Zingiberales; Zingiberaceae; Curcuma
-138072	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; aphid secondary symbionts
+137071	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Laverania)
 139456	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Dendrobranchiata; Penaeoidea; Penaeidae; Fenneropenaeus
-140311	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus
 142860	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Euphorbiaceae; Euphorbioideae; Euphorbieae; Euphorbia
 143017	Eukaryota; Jakobidae; Jakoba
-145475	Eukaryota; Viridiplantae; Chlorophyta; Trebouxiophyceae; Helicosporidium
+143606	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Gobiocypris
+145481	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Bryophyta; Moss Superclass V; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella
 146911	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Scleroglossa; Gekkota; Gekkonidae; Gekkoninae; Gekko
-148305	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Magnaporthaceae; Magnaporthe
-153471	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
-155694	Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Peracarida; Isopoda; Cirolanidae; Eurydice
-155874	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Chaetomiaceae; Chaetomium
+148305	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Magnaporthaceae; Magnaporthe
+155874	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Chaetomiaceae; Chaetomium
+155900	unclassified sequences; environmental samples
 156230	Eukaryota; Alveolata; Dinophyceae; Gymnodiniales; Gymnodiniaceae; Karenia
+158441	Eukaryota; Metazoa; Arthropoda; Hexapoda; Collembola; Arthropleona; Entomobryoidea; Isotomidae; Proisotominae; Folsomia
 160621	Eukaryota; Alveolata; Dinophyceae; Gonyaulacales; Lingulodinium
 161934	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Amaranthaceae; Beta
 162145	Viruses; ssRNA negative-strand viruses; Mononegavirales; Paramyxoviridae; Pneumovirinae; Metapneumovirus
-162425	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiales; Trichocomaceae; Emericella
-164110	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Nicotiana
+162425	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; Emericella
 164328	Eukaryota; stramenopiles; Oomycetes; Peronosporales; Phytophthora
-168635	Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona; Aplousobranchia; Didemnidae; Diplosoma
-168636	Eukaryota; Metazoa; Annelida; Clitellata; Oligochaeta; Haplotaxida; Lumbricina; Lumbricidae; Eisenia
-169388	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Nectria
-170000	Eukaryota; Fungi; Basidiomycota; Urediniomycetes; Urediniomycetidae; Uredinales; Phakopsoraceae; Phakopsora
+169388	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium; Fusarium solani species complex
+170000	Eukaryota; Fungi; Dikarya; Basidiomycota; Pucciniomycotina; Pucciniomycetes; Pucciniales; Phakopsoraceae; Phakopsora
 171252	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
-172665	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Lepidosauria; Squamata; Iguania; Iguanidae; Polychrotinae; Anolis
-176275	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Clavicipitaceae; Cordyceps
-178872	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Boletales; Sclerodermatineae; Pisolithaceae; Pisolithus
-179119	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Amaranthaceae; Salicornia
+172969	Eukaryota; Rhodophyta; Florideophyceae; Gracilariales; Gracilariaceae; Gracilaria
+175245	Eukaryota; Fungi; environmental samples
+176275	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Cordycipitaceae; Cordyceps
+177089	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Coccoidea; Pseudococcidae; Maconellicoccus
 179676	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Chironomoidea; Ceratopogonidae; Ceratopogoninae; Culicoides; Monoculicoides
+180454	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Anophelinae; Anopheles
 181200	Eukaryota; Mycetozoa; Hyperamoeba
-183855	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; Myrtales; Myrtaceae; Eucalyptus
+184922	Eukaryota; Diplomonadida; Hexamitidae; Giardiinae; Giardia
+185431	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma
 186039	Eukaryota; stramenopiles; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Bacillariales; Bacillariaceae; Fragilariopsis
-188904	Eukaryota; Alveolata; Dinophyceae; Gymnodiniales; Gymnodiniaceae; Karlodinium
+186617	Viruses; environmental samples
+187813	Eukaryota; stramenopiles; Oomycetes; Peronosporales; Phytophthora
 189293	Eukaryota; Metazoa; Nematoda; Chromadorea; Tylenchida; Tylenchina; Tylenchoidea; Meloidogynidae; Meloidogyninae; Meloidogyne
 189785	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Tamaricaceae; Tamarix
+189793	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Tamaricaceae; Tamarix
 192875	Eukaryota; Ichthyosporea; Capsaspora
 194530	Eukaryota; Heterolobosea; Schizopyrenida; Vahlkampfiidae; Sawyeria
 197043	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Euhemiptera; Membracoidea; Cicadellidae; Cicadellinae; Homalodisca
-199306	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Eurotiomycetes; Onygenales; mitosporic Onygenales; Coccidioides
+198431	unclassified sequences; environmental samples
+199306	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; mitosporic Onygenales; Coccidioides
+202578	Eukaryota; Metazoa; Mollusca; Bivalvia; Pteriomorphia; Pectinoida; Pectinoidea; Pectinidae; Chlamys
 204232	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Aveneae; Agrostis
-208273	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Chloridoideae; Eragrostideae; Eragrostis
+208348	Eukaryota; Fungi; Dikarya; Basidiomycota; Pucciniomycotina; Pucciniomycetes; Pucciniales; Pucciniaceae; Puccinia
+214684	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Tremellomycetes; Tremellales; Tremellaceae; Filobasidiella
+215693	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Carduoideae; Cardueae; Centaurea
+217475	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Aeschynomeneae; Arachis
+217619	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
 219666	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Gentianales; Rubiaceae; Rubioideae; Spermacoceae; Hedyotis
 219667	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Gentianales; Rubiaceae; Rubioideae; Spermacoceae; Hedyotis
 219738	Eukaryota; Metazoa; Nematoda; Enoplea; Trichocephalida; Trichuridae; Trichuris
@@ -782,58 +709,123 @@
 221722	Eukaryota; Malawimonadidae; Malawimonas
 221724	Eukaryota; Jakobidae; Seculamonas
 222440	Eukaryota; Oxymonadida; Streblomastigidae; Streblomastix
+223430	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Ranunculales; Ranunculaceae; Aquilegia
+223625	Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Sarcoptiformes; Astigmata; Acaroidea; Suidasiidae; Suidasia
 223852	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Aphidini; Toxoptera
-226208	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Nepeteae; Salvia
-226899	Eukaryota; Fungi; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Ophiostomatales; Ophiostomataceae; Ophiostoma
+226126	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+226208	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Mentheae; Salvia
+226891	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Mutisioideae; Mutisieae; Gerbera
+226899	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Ophiostomatales; Ophiostomataceae; Grosmannia
 227086	Eukaryota; Cercozoa; Chlorarachniophyceae; Bigelowiella
-230603	Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+227321	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; Emericella
+229533	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Nectriaceae; Gibberella
+230603	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
+230844	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Cricetidae; Neotominae; Peromyscus
+232082	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; mitosporic Hypocreales; Fusarium; Fusarium solani species complex
 232323	Eukaryota; Metazoa; Tardigrada; Eutardigrada; Apochela; Hypsibiidae; Hypsibius
-237895	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eimeriida; Cryptosporidiidae; Cryptosporidium
+237561	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
+237631	Eukaryota; Fungi; Dikarya; Basidiomycota; Ustilaginomycotina; Ustilaginomycetes; Ustilaginales; Ustilaginaceae; Ustilago
 240906	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Pooideae; Poeae; Puccinellia
 241073	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Vitales; Vitaceae; Vitis
-245552	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Alstroemeriaceae; Alstroemeria
+242507	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetes incertae sedis; Magnaporthaceae; Magnaporthe
+246410	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; mitosporic Onygenales; Coccidioides
 246827	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Vitales; Vitaceae; Vitis
-255244	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
-256318	unclassified sequences; environmental samples
-257784	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; Ericales; Ericaceae; Ericoideae; Rhodoreae; Rhododendron
-257976	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei; Cichlidae; African cichlids; Pseudocrenilabrinae; Haplochromini; Ptyochromis
-261158	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Buprestoidea; Buprestidae; Julodinae; Julodis
-262489	Bacteria; Proteobacteria; Deltaproteobacteria
+256318	unclassified sequences; metagenomes
+261423	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Ruscaceae; Polygonatum
 263995	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Acoraceae; Acorus
 266772	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Euhemiptera; Membracoidea; Cicadellidae; Tettigellinae; Oncometopia
-271171	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Macrotyloma
 272140	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Amaryllidaceae; Lycoris
+272627	Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales; Rhodospirillaceae; Magnetospirillum
 278021	Eukaryota; Fungi; Microsporidia; Antonospora
-279009	Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Homobasidiomycetes; Aphyllophorales; Antrodia
-279580	Eukaryota; Alveolata; Ciliophora; Oligohymenophorea; Scuticociliatia; Philasterida; Philasteridae; Miamiensis
-279730	Eukaryota; Metazoa; Annelida; Clitellata; Hirudinida; Hirudinea; Rhynchobdellida; Glossiphoniidae; Haementeria
-285720	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Senecioneae; Senecio
-286530	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanum; Lycopersicon
+278161	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Pseudotsuga
+279009	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Polyporales; Antrodia
+280699	Eukaryota; Rhodophyta; Bangiophyceae; Cyanidiales; Cyanidiaceae; Cyanidioschyzon
+282301	Eukaryota; Metazoa; Platyhelminthes; Turbellaria; Macrostomorpha; Macrostomida; Macrostomidae; Macrostomum
+283643	Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Tremellomycetes; Tremellales; Tremellaceae; Filobasidiella
+284590	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Kluyveromyces
+284591	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Dipodascaceae; Yarrowia
+284592	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Debaryomyces
+284593	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; mitosporic Saccharomycetales; Candida
+284811	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Eremothecium
+284812	Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces
 288796	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Caudata; Salamandroidea; Ambystomatidae; Ambystoma
-292446	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Scirtoidea; Eucinetidae; Eucinetus
-292453	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Staphyliniformia; Georissidae; Georissus
-292455	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Staphyliniformia; Histeridae; Histerinae; Hister
-292456	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Scarabaeiformia; Scarabaeidae; Scarabaeinae; Scarabaeus
-292458	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Elateroidea; Elateridae; Elaterinae; Agriotes
 293754	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; Caryophyllales; Plumbaginaceae; Limonium
-293756	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
-304329	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea; Saturniidae; Hemileucinae; Lonomia
-307502	Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Wolbachieae; Wolbachia
-307630	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
-307631	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
-309804	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus x Poncirus
-322160	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Sapindales; Rutaceae; Citrus
+294381	Eukaryota; Entamoebidae; Entamoeba
+294707	Eukaryota; Metazoa; Mollusca; Cephalopoda; Coleoidea; Neocoleoidea; Decapodiformes; Sepioidea; Idiosepiidae; Idiosepius
+294746	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Pichia
+296543	Eukaryota; stramenopiles; Bacillariophyta; Coscinodiscophyceae; Thalassiosirophycidae; Thalassiosirales; Thalassiosiraceae; Thalassiosira
+306901	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Chaetomiaceae; Chaetomium
+312017	Eukaryota; Alveolata; Ciliophora; Intramacronucleata; Oligohymenophorea; Hymenostomatida; Tetrahymenina; Tetrahymenidae; Tetrahymena
+313595	Bacteria; Bacteroidetes; Flavobacteria; Flavobacteriales; Flavobacteriaceae; Psychroflexus
+321614	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Dothideomycetes; Pleosporomycetidae; Pleosporales; Phaeosphaeriaceae; Phaeosphaeria
+322104	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Pichia
+325569	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Sclerotinia
+328428	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Raphanus
+330879	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+331117	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; Neosartorya
+332648	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Leotiomycetes; Helotiales; Sclerotiniaceae; Botryotinia
+332952	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+333668	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Piroplasmida; Theileriidae; Theileria
 333970	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Taraxacum
-338618	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Ranunculales; Ranunculaceae; Aquilegia
-339852	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus
+339724	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; Ajellomycetaceae; Ajellomyces
+341663	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+342587	Eukaryota; Alveolata; Dinophyceae; Gymnodiniales; Gymnodiniaceae; Karlodinium
 342808	Eukaryota; Trimastix
-352374	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus
-358432	Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Scarabaeiformia; Trogidae; Trox
-373101	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Coniferopsida; Coniferales; Pinaceae; Picea
-378006	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis
+344612	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+347515	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
+347529	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Carduoideae; Cardueae; Centaurea
+352472	Eukaryota; Mycetozoa; Dictyosteliida; Dictyostelium
+352914	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Vinckeia)
+353151	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; Eimeriorina; Cryptosporidiidae; Cryptosporidium
+353152	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; Eimeriorina; Cryptosporidiidae; Cryptosporidium
+353153	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Trypanosoma; Schizotrypanum
+353154	Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Piroplasmida; Theileriidae; Theileria
+367110	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Sordariomycetidae; Sordariales; Sordariaceae; Neurospora
+370354	Eukaryota; Entamoebidae; Entamoeba
+370355	Eukaryota; Entamoebidae; Entamoeba
+377281	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Limnanthaceae; Limnanthes
+379508	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Lodderomyces
+381124	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Zea
+383379	Eukaryota; Alveolata; Apicomplexa; Coccidia; Eucoccidiorida; Eimeriorina; Sarcocystidae; Toxoplasma
 386100	Eukaryota; Metazoa; Porifera; Demospongiae; Homoscleromorpha; Homosclerophorida; Plakinidae; Oscarella
 392300	Eukaryota; Jakobidae; Histiona
-392814	Eukaryota; Viridiplantae; Chlorophyta; Prasinophyceae; Mamiellales; Mamiellaceae; Micromonas
-400101	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Perciformes; Labroidei; Cichlidae; African cichlids; Pseudocrenilabrinae; Haplochromini; Lipochromis
+392613	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; Ascosphaeraceae; Ascosphaera
+393116	Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria
+393119	Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria
+394104	Bacteria; Proteobacteria; Gammaproteobacteria; sulfur-oxidizing symbionts; Endoriftia
+396776	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; mitosporic Onygenales; Coccidioides
 400408	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; campanulids; Asterales; Asteraceae; Asteroideae; Heliantheae; Helianthus
-404567	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; PACCAD clade; Panicoideae; Paniceae; Pennisetum
+403677	Eukaryota; stramenopiles; Oomycetes; Peronosporales; Phytophthora
+408172	unclassified sequences; metagenomes; ecological metagenomes
+410661	unclassified sequences; metagenomes; organismal metagenomes
+412133	Eukaryota; Parabasalidea; Trichomonada; Trichomonadida; Trichomonadidae; Trichomonadinae; Trichomonas
+412675	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Cucurbitales; Cucurbitaceae; Cucumis
+418459	Eukaryota; Fungi; Dikarya; Basidiomycota; Pucciniomycotina; Pucciniomycetes; Pucciniales; Pucciniaceae; Puccinia
+419109	Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio
+423536	Eukaryota; Alveolata; Perkinsea; Perkinsida; Perkinsidae; Perkinsus
+425011	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Eurotiales; Trichocomaceae; mitosporic Trichocomaceae; Aspergillus
+431241	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes; Hypocreomycetidae; Hypocreales; Hypocreaceae; Hypocrea
+431595	Eukaryota; stramenopiles; Oomycetes; Pythiales; Pythiaceae; Pythium
+434306	Eukaryota; Entamoebidae; Entamoeba
+435258	Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania
+436017	Eukaryota; Viridiplantae; Chlorophyta; Prasinophyceae; Mamiellales; Mamiellaceae; Ostreococcus
+436907	Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Vanderwaltozyma
+441154	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+441155	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+441156	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+441157	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+441158	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+441159	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+441160	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+441161	Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Burkholderia; pseudomallei group
+443226	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; mitosporic Onygenales; Coccidioides
+444079	unclassified sequences; metagenomes; organismal metagenomes
+447454	Bacteria; candidate division TM7
+447634	other sequences; artificial sequences; vectors
+447635	other sequences; artificial sequences; vectors
+452646	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia; Mustelidae; Mustelinae; Neovison
+454286	Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Eurotiomycetes; Eurotiomycetidae; Onygenales; mitosporic Onygenales; Coccidioides
+457179	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Raphanus
+463046	Eukaryota; Heterolobosea; Schizopyrenida; Gruberellidae; Stachyamoeba
+463157	Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Raphanus
+473542	Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
diff --git a/data/sequin.hlp b/data/sequin.hlp
index e69cde04..5400f541 100644
--- a/data/sequin.hlp
+++ b/data/sequin.hlp
@@ -82,6 +82,11 @@ pop-up menus and spreadsheets.
 #You may also use tables to import annotation of source information. 
 The formatting of these tables will be discussed below.
 
+#When entering information, you must use ASCII characters.  Non-ASCII
+characters, such as those with an accent or umlaut, can not be displayed
+properly.  If you enter a non-ASCII character, you will be prompted to select
+an alternative in a pop-up box.
+ 
 *Overview of Sequin
 
 #If you are using Sequin for the first time, you will be prompted to
@@ -205,7 +210,8 @@ it to the database. If you select "Release Date", fields will appear in
 which you can indicate the date on which the sequences should be
 released to the public.  The submission will then be held back until
 formal publication of the sequence or GenBank Accession number, or
-until the release date, whichever comes first.
+until the release date, whichever comes first.  The maximum hold 
+time is five years.
 
 **Tentative Title for Manuscript
 
@@ -1404,12 +1410,13 @@ the database selected for entry.
 #If Sequin detects problems with the format of your record, you will see a
 screen listing the validation errors as well as suggestions for how to fix the
 discrepancies.  Single clicking on an error message scrolls the record viewer
-to the feature that is causing the error.  Double clicking on the error message
-launches a new form on which you can enter information to correct the problem. 
-If you are annotating a set of multiple sequences, shift-click to scroll to the
-target sequence and feature.  You can also dismiss the suggestion and proceed
-on your own. When you think you have corrected all the problems, click on
-"Revalidate".
+to the feature that is causing the error.  Double clicking on the error
+message launches the relevant feature editor on which you can correct the
+problem.  If you are annotating a set of multiple sequences, shift-click to
+scroll to the target sequence and feature.  When you think you have corrected
+all the problems, click on "Revalidate".  You can submit files with errors,
+but it is strongly recommended that you correct as many errors as possible
+prior to submission.
 
 #Message:  Select Verbose, Normal, Terse, or Table. Verbose gives a more
 detailed explanation of the problem.
@@ -2318,7 +2325,7 @@ protein_bind).
 
 #Feature sequence is different from that presented in the entry and
 cannot be described by any other Difference key (conflict, unsure,
-old_sequence, mutation, variation, allele, or modified_base).
+ mutation, variation, allele, or modified_base).
 
 *misc_feature
 
@@ -2335,8 +2342,8 @@ source key (/proviral).
 *misc_RNA
 
 #Any transcript or RNA product that cannot be defined by other RNA keys
-(prim_transcript, precursor_RNA, mRNA, 5'clip, 3'clip, 5'UTR, 3'UTR,
-exon, intron, polyA_site, rRNA, tRNA, scRNA, snoRNA, and snRNA).
+(prim_transcript, precursor_RNA, mRNA, 5'UTR, 3'UTR,
+exon, transit_peptide, polyA_site, rRNA, tRNA, and ncRNA).
 
 *misc_signal
 
@@ -2361,14 +2368,16 @@ qualifier value).
 #messenger RNA; includes 5' untranslated region (5' UTR), coding sequences
 (CDS, exon) and 3' untranslated region (3' UTR).
 
-*N_region
+*ncRNA
 
-#Extra nucleotides inserted between rearranged immunoglobulin segments.
+#non-coding RNA; a non-protein-coding transcript other than ribosomal RNA and
+transfer RNA, including antisense RNA, guide RNA, scRNA, siRNA, miRNA, piRNA,
+snoRNA, and snRNA.  The specific type of ncRNA must be specified in the
+/ncRNA_class qualifier.
 
-*old_sequence
+*N_region
 
-#The presented sequence revises a previous version of the sequence at
-this location.
+#Extra nucleotides inserted between rearranged immunoglobulin segments.
 
 *operon
 
@@ -2430,10 +2439,6 @@ rpt_type and mobile_element have controlled vocabularies.  These
 qualifiers have check boxes or pull-down menus to ensure that the
 correct format is used.
 
-*repeat_unit
-
-#Single repeat element.
-
 *rep_origin
 
 #Origin of replication; starting site for duplication of nucleic acid to
@@ -2457,27 +2462,12 @@ unit; many have a base composition or other property different from the
 genome average that allows them to be separated from the bulk (main
 band) genomic DNA.
 
-*scRNA
-
-#Small cytoplasmic RNA; any one of several small cytoplasmic RNA
-molecules present in the cytoplasm and (sometimes) nucleus of a
-eukaryote.
-
 *sig_peptide
 
 #Signal peptide coding sequence; coding sequence for an N-terminal
 domain of a secreted protein; this domain is involved in attaching
 nascent polypeptide to the membrane; leader sequence.
 
-*snRNA
-
-#Small nuclear RNA involved in pre-mRNA splicing and processing. 
-
-*snoRNA
-
-#Small nucleolar RNA molecules generally involved in rRNA modification
-and processing.
-
 *source
 
 #Identifies the biological source of the specified span of the sequence.
@@ -2511,6 +2501,11 @@ correct initiation; consensus=TATA(A or T)A(A or T).
 to a promoter region that causes RNA polymerase to terminate
 transcription; may also be site of binding of repressor protein.
 
+*tmRNA
+
+#Transfer messenger RNA; acts as a tRNA first, then an mRNA that encodes a
+peptide tag.
+
 *transit_peptide
 
 #Transit peptide coding sequence; coding sequence for an N-terminal
@@ -2546,21 +2541,11 @@ region (V_region) and the last few amino acids of the leader peptide.
 RFLPs, polymorphisms, etc.) that differ from the presented sequence at
 this location (and possibly others).
 
-*3'clip
-
-#3'-most region of a precursor transcript that is clipped off during
-processing.
-
 *3'UTR
 
 #Region near or at the 3' end of a mature transcript (usually following
 the stop codon) that is not translated into a protein; trailer.
 
-*5'clip
-
-#5'-most region of a precursor transcript that is clipped off during
-processing.
-
 *5'UTR
 
 #Region near or at the 5' end of a mature transcript (usually preceding
@@ -2596,11 +2581,10 @@ Biological Source Features, like other features, provide organism
 information about a specific interval on a given sequence.
 
 #In most cases, you will want to use a Biological Source Descriptor, because
-all the sequences in the entry will derive from the same source. 
-However, if you have sequenced a transgenic molecule, for example, one
-that is part plant and part bacterial, you would use Biological Source
-Features to annotate which sequence was derived from plant and which from
-bacteria.
+all the sequences in the entry will derive from the same source.  However, if
+you have sequenced a transgenic molecule, for example, one that is part plant
+and part bacterial, you would use Biological Source Features to annotate which
+sequence was derived from plant and which from bacteria.
 
 #To add a Biological Source Descriptor, select Biological Source under
 the Descriptor section of the Annotate menu.  To add a Biological
@@ -2734,7 +2718,8 @@ transmission.
 
 #-Environmental-sample: Identifies sequence derived by direct molecular
 isolation from an unidentified organism.  You cannot include extra text when
-using this modifier; the text box will change to TRUE upon selection of this modifier from the pull-down list 
+using this modifier; the text box will change to TRUE upon selection of this
+modifier from the pull-down list
 
 #-Frequency:  Frequency of occurrence of a feature.
 
@@ -2770,14 +2755,12 @@ information in the mandatory format.
 #-Map:  Map location of the gene.
 
 #-Metagenomic:  Identifies sequence from a culture-independent genomic
-#analysis of an environmental sample submitted as part of a whole genome
-#shotgun project.  You may not include extra text when using this modifier,
-#instead the text box will change to TRUE upon selection.
+analysis of an environmental sample submitted as part of a whole genome
+shotgun project.  You may not include extra text when using this modifier,
+instead the text box will change to TRUE upon selection.
 
 #-Plasmid-name:  Name of plasmid from which the sequence was obtained.
 
-#-Plastid-name:  Name of plastid from which the sequence was obtained.
-
 #-Pop-variant:  Name of the population variant from which the sequence was
 obtained.
 
@@ -2816,7 +2799,7 @@ additional organism information as text in the field at the bottom of
 the page. You may add multiple modifiers to describe the source organism. 
 
 #Clicking on the X button to the right of the text box will remove the text
-#and clear the modifier from the pull-down in that line.
+and clear the modifier from the pull-down in that line.
 
 #The following is a description of the available modifiers:
 
@@ -2828,6 +2811,14 @@ of the formal name.  An example is HIV-1.
 #-Authority: The author or authors of the organism name from which sequence
 was obtained.
 
+#-Bio-material:  An identifier of the stored biological material from which
+the sequence was obtained.  This qualifier should be used to cite collections
+that are not appropriate in specimen-voucher or culture-collection.  Examples
+include stock centers and seed banks.  Mandatory format is "institution
+code:collection code:material_id".  However, only material_id is required.
+Selecting this modifier in the pull-down list will generate separate boxes for
+entering the information in the correct format.
+
 #-Biotype:  See biovar.
 
 #-Biovar:  Variety of a species (usually a fungus, bacteria, or virus)
@@ -2844,6 +2835,16 @@ characterized by its biochemical properties.
 
 #-Cultivar:  Cultivated variety of plant from which sequence was obtained.
 
+#-Culture-collection:  Identifier and institution code of the microbial or
+viral culture or stored cell-line from which the sequence was obtained.  This
+qualifier should be used to cite the collection where the author has deposited
+the culture or from which the culture was obtained.  Personal library
+collections should be annotated in strain and not in culture-collection.
+Mandatory format is "institution code:collection code:culture_id".  However,
+collection code is not required.  Selecting this modifier in the pull-down
+list will generate separate boxes for entering the information in the correct
+format.
+
 #-Ecotype: The named ecotype (population adapted to a local habitat) from
 which sequence was obtained (customarily applied to populations of
 Arabidopsis thaliana).
@@ -2860,7 +2861,7 @@ was obtained (usually restricted to certain parasitic fungi).
 #-Isolate:  Identification or description of the specific individual
 from which this sequence was obtained.  An example is Patient X14.
 
-#-Old name:  Do not select this item.
+#-Metagenome-source: Used only for genome projects.  Do not select this item.
 
 #-Pathovar:  Variety of a species (usually a fungus, bacteria or virus)
 characterized by the biological target of the pathogen.  Examples
@@ -2880,9 +2881,13 @@ exists in a symbiotic, parasititc, or other special relationship with
 some second organism, use this modifier to identify the name of the
 host species.
 
-#-Specimen-voucher: An identifier of the individual or collection of the
-source organism and the place where it is currently stored, usually an
-institution.
+#-Specimen-voucher: Identifier of the physical specimen from which the
+sequence was obtained.  The qualifier is intended for use where the sample is
+still available in a curated museum, herbarium, frozen tissue collection, or
+personal collection.  Mandatory format is "institution code:collection
+code:specimen_id".  However, only specimen_id is required.  Selecting this
+modifier in the pull-down list will generate separate boxes for entering the
+information in the correct format.
 
 #-Strain:  Strain of organism from which sequence was obtained.
 
@@ -3099,7 +3104,7 @@ because it does not have the appropriate annotations.
 
 #Close this entry.
 
-*Export 
+*Export GenBank 
 
 #Exports the currently displayed format to a file.  Do not use export
 ASN1 for submission of sequences to the database.
@@ -3691,8 +3696,14 @@ Nucleotide Definition Line (Title)
 </A>
 , above.
 
+#Sort Unique Count by Group opens a new window which displays your record(s)
+the number of times an individual line appears in the flatfile(s).  This is
+particularly useful when checking that all records in a large set contain the
+required source or feature information.
+ 
 >Options Menu
 
+#This menu is only available when using Sequin in its network-aware mode.
 *Font
 
 #Use this item to change the display font.  From the pop-up menus,
@@ -4084,7 +4095,7 @@ be entered as the location relative to the alignment coordinates.
 <P CLASS=medium1><B>Questions or Comments?</B>
 <BR>Write to the <A HREF="mailto:info@ncbi.nlm.nih.gov">NCBI Service
 Desk</A></P>
-<P CLASS=medium1>Revised July 20, 2007
+<P CLASS=medium1>Revised October 31, 2007
 
 </CENTER>
 
diff --git a/data/taxlist.txt b/data/taxlist.txt
index 7ff408d6..f3a47eec 100644
--- a/data/taxlist.txt
+++ b/data/taxlist.txt
@@ -1,7 +1,8 @@
-14
+15
 Acanthamoeba castellanii		1	4	INV	5755
 Acanthoscurria gomesiana		1	5	INV	115339
 Acetabularia acetabulum		6	1	PLN	35845
+Acipenser sinensis	Chinese sturgeon	1	2	VRT	61970
 Acipenser transmontanus	white sturgeon	1	2	VRT	7904
 Acorus americanus		1	1	PLN	263995
 Acropora millepora		1	4	INV	45264
@@ -11,24 +12,21 @@ Adiantum capillus-veneris		1	1	PLN	13818
 Aedes aegypti	yellow fever mosquito	1	5	INV	7159
 Aegilops speltoides		1	1	PLN	4573
 Aegilops tauschii		1	1	PLN	37682
-Agriotes lineatus		1	5	INV	292458
-Agrobacterium tumefaciens		11	0	BCT	358
 Agrostis capillaris		1	1	PLN	204232
 Agrostis stolonifera		1	1	PLN	63632
-Aids-associated retrovirus		1	0	VRL	11966
 Ajellomyces capsulatus		1	4	PLN	5037
+Ajellomyces capsulatus NAm1		1	4	PLN	339724
 Alexandrium tamarense		1	4	PLN	2926
+Alligator mississippiensis	American alligator	1	2	VRT	8496
 Allium cepa	onion	1	1	PLN	4679
 Allomyces macrogynus		1	4	PLN	28583
-Alstroemeria peruviana		1	1	PLN	245552
-Alternaria alternata		1	4	PLN	5599
 Alternaria brassicicola		1	4	PLN	29001
 Amblyomma americanum	lone star tick	1	5	INV	6943
-Amblyomma cajennense		1	5	INV	34607
 Amblyomma variegatum		1	5	INV	34610
 Amborella trichopoda		1	1	PLN	13333
 Ambystoma mexicanum	axolotl	1	2	VRT	8296
 Ambystoma ordinarium	Puerto Hondo stream salamander	1	2	VRT	288796
+Ambystoma tigrinum tigrinum	Eastern tiger salamander	1	2	VRT	43116
 Amoebidium parasiticum		1	4	INV	4881
 Amorphotheca resinae	creosote fungus	1	4	PLN	5101
 Amphidinium carterae		1	4	PLN	2961
@@ -36,48 +34,50 @@ Ananas comosus	pineapple	1	1	PLN	4615
 Anas platyrhynchos		1	2	VRT	8839
 Ancylostoma caninum	dog hookworm	1	5	INV	29170
 Ancylostoma ceylanicum		1	5	INV	53326
-Angiostrongylus cantonensis		1	5	INV	6313
+Anolis carolinensis	green anole	1	2	VRT	28377
 Anolis sagrei	brown anole	1	2	VRT	38937
-Anolis smaragdinus		1	2	VRT	172665
-Anopheles funestus		1	5	INV	62324
+Anopheles albimanus		1	5	INV	7167
+Anopheles funestus	African malaria mosquito	1	5	INV	62324
 Anopheles gambiae	African malaria mosquito	1	5	INV	7165
+Anopheles gambiae str. PEST		1	5	INV	180454
 Antheraea mylitta		1	5	INV	34739
 Antirrhinum majus	snapdragon	1	1	PLN	4151
 Antonospora locustae		1	1	INV	278021
 Antrodia cinnamomea		1	4	PLN	279009
+Aphanomyces cochlioides		1	1	PLN	112091
 Aphis gossypii	cotton aphid	1	5	INV	80765
 Apis mellifera	honey bee	1	5	INV	7460
-Apium graveolens		1	1	PLN	4045
 Aplysia californica	California sea hare	1	5	INV	6500
-Aquilegia formosa x Aquilegia pubescens		1	1	PLN	338618
-Arabidopsis arenosa x Arabidopsis thaliana		1	1	PLN	378006
-Arabidopsis lyrata		1	1	PLN	59689
+Aquilegia formosa		1	1	PLN	223430
+Arabidopsis lyrata subsp. petraea		1	1	PLN	59691
 Arabidopsis thaliana	thale cress	1	1	PLN	3702
 Arachis batizocoi		1	1	PLN	108210
 Arachis duranensis		1	1	PLN	130453
 Arachis hypogaea	peanut	1	1	PLN	3818
+Arachis stenosperma		1	1	PLN	217475
 Argas monolakensis		1	5	INV	34602
 Argopecten irradians		1	5	INV	31199
-Armigeres subalbatus		1	5	INV	124917
-Ascaris lumbricoides	common roundworm	1	5	INV	6252
 Ascaris suum	pig roundworm	1	5	INV	6253
+Ascosphaera apis USDA-ARSEF 7405		1	4	PLN	392613
+Ashbya gossypii ATCC 10895		1	3	PLN	284811
 Asparagus officinalis	garden asparagus	1	1	PLN	4686
+Aspergillus clavatus NRRL 1		1	4	PLN	344612
 Aspergillus flavus		1	4	PLN	5059
-Aspergillus fumigatus		1	4	PLN	5085
+Aspergillus flavus NRRL3357		1	4	PLN	332952
+Aspergillus fumigatus Af293		1	4	PLN	330879
+Aspergillus nidulans FGSC A4		1	4	PLN	227321
 Aspergillus niger		1	4	PLN	5061
+Aspergillus niger CBS 513.88		1	4	PLN	425011
 Aspergillus oryzae		1	4	PLN	5062
-Aspergillus terreus		1	4	PLN	33178
+Aspergillus terreus NIH2624		1	4	PLN	341663
 Astatotilapia burtoni		1	2	VRT	8153
-Asterina pectinifera		1	9	INV	7594
 Aureobasidium pullulans		1	4	PLN	5580
 Avena sativa	oat	1	1	PLN	4498
-Avicennia marina		1	1	PLN	82927
+Babesia bovis		1	4	INV	5865
 Bacillus cereus		11	0	BCT	1396
 Bacillus clausii		11	0	BCT	79880
 Bacillus licheniformis		11	0	BCT	1402
 Bacillus subtilis		11	0	BCT	1423
-Bacillus thuringiensis		11	0	BCT	1428
-Balanus glandula		1	5	INV	110520
 Bemisia tabaci		1	5	INV	7038
 Beta vulgaris		1	1	PLN	161934
 Betula pendula	European white birch	1	1	PLN	3505
@@ -86,147 +86,161 @@ Bigelowiella natans		1	1	INV	227086
 Biomphalaria glabrata		1	5	INV	6526
 Blastocladiella emersonii		1	4	PLN	4808
 Blastocystis hominis		1	1	PLN	12968
-Blomia tropicalis		1	5	INV	40697
+Blumeria graminis f. sp. hordei		1	4	PLN	62688
 Boechera stricta		1	1	PLN	72658
 Bombyx mori	domestic silkworm	1	5	INV	7091
-Boophilus microplus	southern cattle tick	1	5	INV	6941
 Borrelia burgdorferi	Lyme disease spirochete	11	0	BCT	139
 Bos indicus		1	2	MAM	9915
-Bos indicus x Bos taurus	hybrid cattle	1	2	MAM	30522
 Bos taurus	cattle	1	2	MAM	9913
-Bothrops jararaca	jararaca	1	2	VRT	8724
 Botryotinia fuckeliana		1	4	PLN	40559
-Bovine viral diarrhea virus 1		1	0	VRL	11099
+Botryotinia fuckeliana B05.10		1	4	PLN	332648
+Brachionus plicatilis		1	5	INV	10195
 Brachypodium distachyon		1	1	PLN	15368
 Bradyrhizobium japonicum		11	0	BCT	375
 Branchiostoma floridae	Florida lancelet	1	5	INV	7739
+Brassica carinata		1	1	PLN	52824
 Brassica napus	rape	1	1	PLN	3708
 Brassica oleracea		1	1	PLN	3712
+Brassica oleracea var. alboglabra	Chinese kale	1	1	PLN	3714
+Brassica oleracea var. italica	asparagus broccoli	1	1	PLN	36774
 Brassica rapa		1	1	PLN	3711
+Brassica rapa subsp. pekinensis		1	1	PLN	51351
 Brucella abortus		11	0	BCT	235
 Brugia malayi		1	5	INV	6279
 Bruguiera gymnorhiza		1	1	PLN	39984
 Bubalus bubalis	water buffalo	1	2	MAM	89462
+Burkholderia pseudomallei 112		11	0	BCT	441154
+Burkholderia pseudomallei 14		11	0	BCT	441160
+Burkholderia pseudomallei 381		11	0	BCT	441157
+Burkholderia pseudomallei 7894		11	0	BCT	441156
+Burkholderia pseudomallei 9		11	0	BCT	441158
+Burkholderia pseudomallei 91		11	0	BCT	441159
+Burkholderia pseudomallei B7210		11	0	BCT	441155
+Burkholderia pseudomallei DM98		11	0	BCT	441161
 Bursaphelenchus mucronatus		1	5	INV	6325
 Bursaphelenchus xylophilus		1	5	INV	6326
+Caenorhabditis brenneri		1	5	INV	135651
 Caenorhabditis briggsae		1	5	INV	6238
+Caenorhabditis briggsae AF16		1	5	INV	473542
 Caenorhabditis elegans		1	5	INV	6239
 Caenorhabditis remanei		1	5	INV	31234
-Cajanus cajan	pigeon pea	1	1	PLN	3821
+Calanus finmarchicus		1	5	INV	6837
 Callinectes sapidus	blue crab	1	5	INV	6763
 Callithrix jacchus	white-tufted-ear marmoset	1	2	PRI	9483
 Callorhinchus milii	elephantfish	1	2	VRT	7868
 Camellia sinensis		1	1	PLN	4442
-Campylobacter jejuni		11	0	BCT	197
 Candida albicans		12	4	PLN	5476
+Candida albicans SC5314		12	4	PLN	237561
 Candida glabrata		1	3	PLN	5478
+Candida glabrata CBS 138		1	3	PLN	284593
 Candida parapsilosis		12	4	PLN	5480
 Candida tropicalis		12	3	PLN	5482
-Candidatus Hamiltonella defensa		11	0	BCT	138072
-Canis familiaris	dog	1	2	MAM	9615
+candidate division TM7 single-cell isolate TM7a		11	0	BCT	447454
 Canis latrans	coyote	1	2	MAM	9614
 Canis lupus	gray wolf	1	2	MAM	9612
+Canis lupus familiaris	dog	1	2	MAM	9615
+Cannabis sativa	hemp	1	1	PLN	3483
 Capra hircus	goat	1	2	MAM	9925
 Capsaspora owczarzaki		1	1	INV	192875
 Capsicum annuum		1	1	PLN	4072
-Carassius auratus	goldfish	1	2	VRT	7957
 Carcinus maenas	green crab	1	5	INV	6759
 Carica papaya	papaya	1	1	PLN	3649
-Casuarina glauca	swamp oak	1	1	PLN	3522
+Carthamus tinctorius	safflower	1	1	PLN	4222
 Catharanthus roseus	Madagascar periwinkle	1	1	PLN	4058
 Cavia porcellus	domestic guinea pig	1	2	ROD	10141
 Celuca pugilator	Atlantic sand fiddler crab	1	5	INV	6772
 Cenchrus ciliaris		1	1	PLN	35872
+Centaurea maculosa		1	1	PLN	215693
+Centaurea solstitialis		1	1	PLN	347529
 Ceratodon purpureus		1	1	PLN	3225
 Ceratopteris richardii		1	1	PLN	49495
+Cercomonas longicauda		1	1	INV	100933
 Chaetomium cupreum		1	4	PLN	155874
-Chaetomium globosum		1	4	PLN	38033
+Chaetomium globosum CBS 148.51		1	4	PLN	306901
 Chamaecyparis obtusa		1	1	PLN	13415
 Chironomus tentans		1	5	INV	7153
 Chlamydia trachomatis		11	0	BCT	813
 Chlamydomonas incerta		1	1	PLN	51695
 Chlamydomonas reinhardtii		1	1	PLN	3055
-Chlamydophila pneumoniae		11	0	BCT	83558
+Chlamys farreri		1	5	INV	202578
 Chlorocebus aethiops	African green monkey	1	2	PRI	9534
 Chondrus crispus	carragheen	1	4	PLN	2769
+Chrysemys picta		1	2	VRT	8479
 Cicer arietinum	chickpea	1	1	PLN	3827
+Cichorium endivia		1	1	PLN	114280
 Cichorium intybus	chicory	1	1	PLN	13427
 Ciona intestinalis		1	13	INV	7719
 Ciona savignyi		1	13	INV	51511
 Citrus aurantium		1	1	PLN	43166
 Citrus clementina		1	1	PLN	85681
-Citrus clementina x Citrus tangerina		1	1	PLN	307631
-Citrus jambhiri	rough lemon	1	1	PLN	64884
-Citrus macrophylla		1	1	PLN	307630
 Citrus reshni		1	1	PLN	171252
 Citrus reticulata		1	1	PLN	85571
-Citrus reticulata x Citrus temple		1	1	PLN	322160
 Citrus sinensis		1	1	PLN	2711
-Citrus sinensis x Poncirus trifoliata		1	1	PLN	105581
-Citrus tristeza virus		1	0	VRL	12162
 Citrus unshiu		1	1	PLN	55188
-Citrus x paradisi		1	1	PLN	37656
-Citrus x paradisi x Poncirus trifoliata		1	1	PLN	309804
 Cleome hassleriana		1	1	PLN	28532
 Clonorchis sinensis		1	9	INV	79923
 Closterium peracerosum-strigosum-littorale complex		1	1	PLN	34146
-Clostridium difficile		11	0	BCT	1496
-Clostridium perfringens		11	0	BCT	1502
+Coccidioides immitis H538.4		1	4	PLN	396776
+Coccidioides immitis RMSCC 3703		1	4	PLN	454286
+Coccidioides immitis RS		1	4	PLN	246410
 Coccidioides posadasii		1	4	PLN	199306
-Codonopsis lanceolata		1	1	PLN	103999
+Coccidioides posadasii str. Silveira		1	4	PLN	443226
 Coffea arabica	coffee	1	1	PLN	13443
 Coffea canephora		1	1	PLN	49390
-Colletotrichum trifolii		1	4	PLN	5466
-Conidiobolus coronatus		1	4	PLN	34488
-Cooperia oncophora		1	5	INV	27828
 Coprinopsis cinerea		1	4	PLN	5346
 Cordyceps bassiana		1	4	PLN	176275
-Coregonus clupeaformis		1	2	VRT	59861
+Coregonus clupeaformis	lake whitefish	1	2	VRT	59861
 Corynascus heterothallicus		1	4	PLN	78579
 Corynebacterium glutamicum		11	0	BCT	1718
-Coxiella burnetii		11	0	BCT	777
 Crassostrea gigas	Pacific oyster	1	5	INV	29159
 Crassostrea virginica	eastern oyster	1	5	INV	6565
 Cricetulus griseus	Chinese hamster	1	2	ROD	10029
+Crocus sativus		1	1	PLN	82528
 Cryphonectria parasitica		1	4	PLN	5116
 Cryptococcus laurentii		1	4	PLN	5418
+Cryptococcus neoformans var. neoformans		1	4	PLN	40410
+Cryptococcus neoformans var. neoformans B-3501A		1	4	PLN	283643
+Cryptococcus neoformans var. neoformans JEC21		1	4	PLN	214684
 Cryptomeria japonica	Japanese cedar	1	1	PLN	3369
-Cryptosporidium hominis		1	4	INV	237895
+Cryptosporidium hominis TU502		1	4	INV	353151
 Cryptosporidium parvum		1	4	INV	5807
+Cryptosporidium parvum Iowa II		1	4	INV	353152
 Ctenocephalides felis	cat flea	1	5	INV	7515
 Cucumis melo	muskmelon	1	1	PLN	3656
+Cucumis melo subsp. agrestis		1	1	PLN	217619
+Cucumis melo subsp. melo		1	1	PLN	412675
 Cucumis sativus	cucumber	1	1	PLN	3659
+Culex pipiens quinquefasciatus	southern house mosquito	1	5	INV	7176
 Culicoides sonorensis		1	5	INV	179676
 Cunninghamella elegans		1	4	PLN	4853
 Curcuma longa		1	1	PLN	136217
+Cyamopsis tetragonoloba	guar	1	1	PLN	3832
+Cyanidioschyzon merolae strain 10D		1	1	PLN	280699
 Cyanophora paradoxa		1	1	PLN	2762
 Cycas rumphii		1	1	PLN	58031
-Cyclamen persicum		1	1	PLN	87530
 Cynodon dactylon	Bermuda grass	1	1	PLN	28909
 Cyprinus carpio	common carp	1	2	VRT	7962
 Danio rerio	zebrafish	1	2	VRT	7955
 Daphnia magna		1	5	INV	35525
-Daphnia pulex		1	5	INV	6669
 Dasypus novemcinctus	nine-banded armadillo	1	2	MAM	9361
+Debaryomyces hansenii CBS767		1	3	PLN	284592
+Debaryomyces hansenii var. hansenii		1	3	PLN	58641
 Deinagkistrodon acutus		1	2	VRT	36307
-delta proteobacterium MLMS-1		11	0	BCT	262489
-Dermatophagoides farinae	American house dust mite	1	5	INV	6954
-Descurainia sophia		1	1	PLN	89411
-Diaphorina citri		1	5	INV	121845
+Dekkera bruxellensis		1	4	PLN	5007
+Diabrotica virgifera virgifera	western corn rootworm	1	5	INV	50390
+Diaphorina citri	Asian citrus psyllid	1	5	INV	121845
 Diaprepes abbreviatus	Diaprepes root weevil	1	5	INV	13040
 Dicentrarchus labrax	European sea bass	1	2	VRT	13489
+Dictyocaulus viviparus	bovine lungworm	1	5	INV	29172
 Dictyostelium discoideum		1	1	INV	44689
+Dictyostelium discoideum AX4		1	1	INV	352472
 Diplonema papillatum		1	4	INV	91374
-Diploptera punctata	Pacific beetle cockroach	1	5	INV	6984
-Diplosoma listerianum		1	13	INV	168635
 Dirofilaria immitis	dog heartworm nematode	1	5	INV	6287
-Drosophila americana		1	5	INV	40366
 Drosophila ananassae		1	5	INV	7217
 Drosophila auraria		1	5	INV	47315
 Drosophila erecta		1	5	INV	7220
 Drosophila grimshawi		1	5	INV	7222
 Drosophila melanogaster	fruit fly	1	5	INV	7227
-Drosophila miranda		1	5	INV	7229
 Drosophila mojavensis		1	5	INV	7230
 Drosophila persimilis		1	5	INV	7234
 Drosophila pseudoobscura		1	5	INV	7237
@@ -239,140 +253,137 @@ Dugesia japonica		1	9	INV	6161
 Dugesia ryukyuensis		1	9	INV	79738
 Dunaliella salina		1	1	PLN	3046
 Echinococcus granulosus		1	9	INV	6210
-Echinococcus multilocularis		1	9	INV	6211
 Echinops telfairi	small Madagascar hedgehog	1	2	MAM	9371
-Echis ocellatus		1	2	VRT	99586
 Eimeria tenella		1	4	INV	5802
-Eisenia andrei		1	5	INV	168636
+Eisenia fetida	common brandling worm	1	5	INV	6396
 Elaeis guineensis	African oil palm	1	1	PLN	51953
-Eleusine coracana	finger millet	1	1	PLN	4511
+Elaeis oleifera		1	1	PLN	80265
 Emericella nidulans		1	4	PLN	162425
 Emiliania huxleyi		1	4	PLN	2903
+Endoriftia persephone 'Hot96_1+Hot96_2'		11	0	BCT	394104
+Entamoeba dispar		1	1	INV	46681
+Entamoeba dispar SAW760		1	1	INV	370354
 Entamoeba histolytica		1	1	INV	5759
+Entamoeba histolytica HM-1:IMSS		1	1	INV	294381
 Entamoeba invadens		1	1	INV	33085
-Enterobacter cloacae		11	0	BCT	550
-Enterococcus faecalis		11	0	BCT	1351
-Enterococcus faecium		11	0	BCT	1352
-environmental sequence		1	2	ENV	256318
-Epinephelus coioides	orange-spotted grouper	1	2	VRT	94232
+Entamoeba invadens IP1		1	1	INV	370355
+Entamoeba moshkovskii FIC		1	1	INV	434306
+Entamoeba terrapinae		1	1	INV	110771
+Epiphyas postvittana		1	5	INV	65032
 Eptatretus burgeri	inshore hagfish	1	2	VRT	7764
-Equine infectious anemia virus		1	0	VRL	11665
 Equus caballus	horse	1	2	MAM	9796
-Eragrostis pilosa		1	1	PLN	208273
 Eragrostis tef		1	1	PLN	110835
-Eremothecium gossypii		1	3	PLN	33169
 Erinaceus europaeus	western European hedgehog	1	2	MAM	9365
 Escherichia coli		11	0	BCT	562
 Eschscholzia californica	California poppy	1	1	PLN	3467
+Esox lucius	northern pike	1	2	VRT	8010
+Eubalaena glacialis	North Atlantic right whale	1	2	MAM	27606
 Eucalyptus camaldulensis	Murray red gum	1	1	PLN	34316
-Eucalyptus globulus		1	1	PLN	34317
+Eucalyptus globulus subsp. bicostata		1	1	PLN	71272
 Eucalyptus grandis		1	1	PLN	71139
 Eucalyptus gunnii	cider tree	1	1	PLN	3933
-Eucalyptus tereticornis		1	1	PLN	183855
-Eucinetus sp. APV-2005		1	5	INV	292446
 Euglena gracilis		1	4	PLN	3039
 Euglena longa		1	4	PLN	3037
 Euphorbia esula	leafy spurge	1	1	PLN	3993
 Euphorbia tirucalli		1	1	PLN	142860
 Euprymna scolopes		1	5	INV	6613
-Eurydice pulchra		1	5	INV	155694
-Feline immunodeficiency virus		1	0	VRL	11673
-Felis catus	cat	1	2	MAM	9685
+Felis catus	domestic cat	1	2	MAM	9685
 Fenneropenaeus chinensis		1	5	INV	139456
 Festuca arundinacea		1	1	PLN	4606
+Folsomia candida		1	5	INV	158441
+fossil metagenome		11	2	ENV	444079
 Fragaria vesca		1	1	PLN	57918
-Fragaria x ananassa		1	1	PLN	3747
+Fragaria vesca subsp. vesca		1	1	PLN	101020
 Fragilariopsis cylindrus		1	1	PLN	186039
 Fundulus heteroclitus	killifish	1	2	VRT	8078
-Fusarium oxysporum		1	4	PLN	5507
+Fusarium oxysporum f. sp. cucumerinum		1	4	PLN	5508
+Fusarium oxysporum f. sp. melonis		1	4	PLN	61369
 Fusarium solani		1	4	PLN	169388
 Fusarium sporotrichioides		1	4	PLN	5514
+Fusarium virguliforme		1	4	PLN	232082
 Gadus morhua	Atlantic cod	1	2	VRT	8049
 Gallus gallus	chicken	1	2	VRT	9031
-Gasterosteus aculeatus	three spined stickleback	1	2	VRT	69293
+Gammarus pulex		1	5	INV	52641
+Gasterosteus aculeatus	three-spined stickleback	1	2	VRT	69293
 GB virus C		1	0	VRL	54290
 Gekko japonicus		1	2	VRT	146911
-Geochelone nigra		1	2	VRT	66189
+Gene trapping vector VICTR75		11	0	SYN	447634
+Gene trapping vector VICTR76		11	0	SYN	447635
 Geomyces pannorum		1	4	PLN	79858
-Georissus sp. APV-2005		1	5	INV	292453
+Gerbera hybrid cv. 'Terra Regina'		1	1	PLN	226891
 Giardia intestinalis		1	0	INV	5741
+Giardia lamblia ATCC 50803		1	0	INV	184922
 Gibberella moniliformis		1	4	PLN	117187
 Gibberella zeae		1	4	PLN	5518
+Gibberella zeae PH-1		1	4	PLN	229533
 Gillichthys mirabilis	long-jawed mudsucker	1	2	VRT	8222
-Ginglymostoma cirratum	nurse shark	1	2	VRT	7801
 Ginkgo biloba	maidenhair tree	1	1	PLN	3311
 Glaucocystis nostochinearum		1	1	PLN	38271
 Globodera pallida		1	5	INV	36090
 Globodera rostochiensis		1	5	INV	31243
 Gloeophyllum trabeum		1	4	PLN	104355
 Glomus intraradices		1	4	PLN	4876
-Glomus versiforme		1	4	PLN	43425
-Glycine clandestina		1	1	PLN	45687
+Glossina morsitans morsitans		1	5	INV	37546
 Glycine max	soybean	1	1	PLN	3847
 Glycine soja		1	1	PLN	3848
+Glycyphagus domesticus		1	5	INV	105145
 Gnetum gnemon		1	1	PLN	3382
+Gobiocypris rarus		1	2	VRT	143606
 Gorilla gorilla	gorilla	1	2	PRI	9593
-Gossypioides kirkii		1	1	PLN	47615
 Gossypium arboreum		1	1	PLN	29729
 Gossypium exiguum		1	1	PLN	47626
 Gossypium herbaceum		1	1	PLN	34274
 Gossypium hirsutum	upland cotton	1	1	PLN	3635
 Gossypium raimondii		1	1	PLN	29730
-Gregarina niphandrodes		1	4	INV	110365
-Gryllus pennsylvanicus		1	5	INV	51074
-Gymnogyps californianus	California condor	1	2	VRT	33616
-Haematococcus pluvialis		1	1	PLN	44745
-Haementeria depressa		1	5	INV	279730
+Gracilaria changii		1	4	PLN	172969
+Graphocephala atropunctata		1	5	INV	36148
+Grosmannia clavigera		1	4	PLN	226899
+Gryllus bimaculatus	two-spotted cricket	1	5	INV	6999
+Guillardia theta		1	1	PLN	55529
 Haemonchus contortus		1	5	INV	6289
 Haemophilus influenzae		11	0	BCT	727
-Haliotis discus		1	5	INV	36094
-Halobaculum gomorrense		11	0	BCT	43928
 Halocynthia roretzi		1	13	INV	7729
-Halorubrum lacusprofundi		11	0	BCT	2247
 Hartmannella vermiformis		1	1	INV	5778
 Hebeloma cylindrosporum		1	4	PLN	76867
 Hedyotis centranthoides		1	1	PLN	219666
 Hedyotis terminalis		1	1	PLN	219667
 Helianthus annuus	common sunflower	1	1	PLN	4232
 Helianthus argophyllus		1	1	PLN	73275
+Helianthus ciliaris		1	1	PLN	73280
 Helianthus exilis		1	1	PLN	400408
 Helianthus paradoxus		1	1	PLN	73304
 Helianthus petiolaris		1	1	PLN	4234
+Helianthus tuberosus		1	1	PLN	4233
 Helicobacter pylori		11	0	BCT	210
 Heliconius erato	crimson-patched longwing	1	5	INV	33431
 Heliconius melpomene		1	5	INV	34740
-Helicosporidium sp. ex Simulium jonesii		1	1	PLN	145475
-Helicoverpa armigera	cotton bollworm	1	5	INV	29058
 Hemicentrotus pulcherrimus		1	9	INV	7650
 Hepatitis A virus		1	0	VRL	12092
 Hepatitis B virus		1	0	VRL	10407
 Hepatitis C virus		1	0	VRL	11103
-Hepatitis E virus		1	0	VRL	12461
-Heterobasidion annosum		1	4	PLN	13563
+Hepatitis C virus subtype 1a		1	0	VRL	31646
+Hepatitis C virus subtype 1b		1	0	VRL	31647
 Heterocapsa triquetra		1	4	PLN	66468
 Heterodera glycines		1	5	INV	51029
 Heterodera schachtii		1	5	INV	97005
 Heterorhabditis bacteriophora		1	5	INV	37862
 Hevea brasiliensis		1	1	PLN	3981
 Hippoglossus hippoglossus	Atlantic halibut	1	2	VRT	8267
-Hister sp. APV-2005		1	5	INV	292455
 Histiona aroides		1	1	INV	392300
+Holothuria glaberrima		1	9	INV	31192
 Homalodisca coagulata	glassy-winged sharpshooter	1	5	INV	197043
 Homarus americanus	American lobster	1	5	INV	6706
 Homo sapiens	human	1	2	PRI	9606
 Hordeum vulgare		1	1	PLN	4513
-Human herpesvirus 1	Herpes simplex virus type 1	1	0	VRL	10298
+Hordeum vulgare subsp. spontaneum		1	1	PLN	77009
+Hordeum vulgare subsp. vulgare	domesticated barley	1	1	PLN	112509
 Human herpesvirus 5	Human cytomegalovirus	1	0	VRL	10359
-Human herpesvirus 8	Kaposi's sarcoma-associated herpesvirus - Human herpesvirus 8	1	0	VRL	37296
-Human immunodeficiency virus		1	0	VRL	12721
 Human immunodeficiency virus 1		1	0	VRL	11676
 Human immunodeficiency virus 2		1	0	VRL	11709
 Human metapneumovirus		1	0	VRL	162145
-Human papillomavirus		1	0	VRL	10566
-Human respiratory syncytial virus		1	0	VRL	11250
+Human T-lymphotropic virus 1		1	0	VRL	11908
 Humulus lupulus	European hop	1	1	PLN	3486
 Hydra magnipapillata		1	4	INV	6085
-Hydra oligactis		1	4	INV	6088
 Hydra vulgaris		1	4	INV	6087
 Hydractinia echinata		1	4	INV	35630
 Hyperamoeba dachnaya		1	1	INV	181200
@@ -380,90 +391,83 @@ Hypocrea jecorina		1	4	PLN	51453
 Hypocrea lixii		1	4	PLN	5544
 Hypocrea virens		1	4	PLN	29875
 Hypsibius dujardini		1	5	INV	232323
-Ictalurus furcatus		1	2	VRT	66913
+Ichthyophthirius multifiliis		6	4	INV	5932
+Ictalurus furcatus	blue catfish	1	2	VRT	66913
 Ictalurus punctatus	channel catfish	1	2	VRT	7998
-Infectious bronchitis virus		1	0	VRL	11120
-Infectious bursal disease virus	Gumboro virus	1	0	VRL	10995
+Idiosepius paradoxus		1	5	INV	294707
 Ipomoea batatas	sweet potato	1	1	PLN	4120
 Ipomoea nil	Japanese morning glory	1	1	PLN	35883
-Ipomoea trifida		1	1	PLN	35884
-Ips pini	North American pine engraver	1	5	INV	102803
 Isochrysis galbana		1	1	PLN	37099
 Ixodes scapularis	black-legged tick	1	5	INV	6945
 Jakoba bahamiensis		1	1	INV	221721
 Jakoba libera		1	1	INV	143017
-JC polyomavirus		1	0	VRL	10632
 Juglans regia	English walnut	1	1	PLN	51240
-Julodis onopordi		1	5	INV	261158
 Karenia brevis		1	4	PLN	156230
-Karlodinium micrum		1	4	PLN	188904
+Karlodinium micrum		1	4	PLN	342587
 Kazachstania exigua		1	3	PLN	34358
-Klebsiella pneumoniae		11	0	BCT	573
+Kazachstania unispora		1	3	PLN	27294
 Kluyveromyces lactis		1	4	PLN	28985
+Kluyveromyces lactis NRRL Y-1140		1	4	PLN	284590
 Kluyveromyces marxianus		1	3	PLN	4911
 Kluyveromyces thermotolerans		1	3	PLN	4916
 Laccaria bicolor		1	4	PLN	29883
 Lachancea kluyveri		1	3	PLN	4934
-Lachesis muta	bushmaster	1	2	VRT	8752
-Lactobacillus reuteri		11	0	BCT	1598
 Lactuca perennis		1	1	PLN	43195
 Lactuca saligna		1	1	PLN	75948
 Lactuca sativa		1	1	PLN	4236
 Lactuca serriola		1	1	PLN	75943
 Lactuca virosa		1	1	PLN	75947
+Lama pacos	alpaca	1	2	MAM	30538
 Laminaria digitata		1	1	PLN	80365
+Laupala kohalensis		1	5	INV	109027
 Lawsonia intracellularis		11	0	BCT	29546
-Legionella pneumophila		11	0	BCT	446
 Leishmania braziliensis		1	4	INV	5660
-Leishmania donovani		1	4	INV	5661
+Leishmania donovani chagasi		1	4	INV	44271
+Leishmania infantum JPCM5		1	4	INV	435258
 Leishmania major		1	4	INV	5664
+Leishmania major strain Friedlin		1	4	INV	347515
 Lentinula edodes	shiitake mushroom	1	4	PLN	5353
 Lepeophtheirus salmonis	salmon louse	1	5	INV	72036
 Leptinotarsa decemlineata	Colorado potato beetle	1	5	INV	7539
-Leptosphaeria maculans	blackleg of rapeseed fungus	1	4	PLN	5022
 Leucoraja erinacea	little skate	1	2	VRT	7782
 Leucosporidium scottii		1	4	PLN	5278
-Leymus chinensis		1	1	PLN	52714
-Lilium longiflorum	trumpet lily	1	1	PLN	4690
+Limnanthes alba subsp. versicolor		1	1	PLN	377281
 Limonium bicolor		1	1	PLN	293754
 Lingulodinium polyedrum		1	4	PLN	160621
 Linum usitatissimum	flax	1	1	PLN	4006
-Lipochromis sp. 'matumbi hunter'		1	2	VRT	400101
 Liriodendron tulipifera		1	1	PLN	3415
-Listeria innocua		11	0	BCT	1642
 Listeria monocytogenes		11	0	BCT	1639
+Listeria monocytogenes FSL F2-515		11	0	BCT	393116
+Listeria monocytogenes FSL J1-208		11	0	BCT	393119
+Lithognathus mormyrus		1	2	VRT	50591
 Litomosoides sigmodontis		1	5	INV	42156
-Litopenaeus setiferus	white shrimp	1	5	INV	64468
 Litopenaeus vannamei	Pacific white shrimp	1	5	INV	6689
 Locusta migratoria	migratory locust	1	5	INV	7004
+Lodderomyces elongisporus NRRL YB-4239		1	3	PLN	379508
 Lolium multiflorum	Italian ryegrass	1	1	PLN	4521
 Lolium temulentum		1	1	PLN	34176
-Lonomia obliqua		1	5	INV	304329
 Lotus japonicus		1	1	PLN	34305
 Loxodonta africana	African savanna elephant	1	2	MAM	9785
 Lumbricus rubellus	humus earthworm	1	5	INV	35632
 Lupinus albus	white lupine	1	1	PLN	3870
 Lutzomyia longipalpis		1	5	INV	7200
-Lycopersicon esculentum		1	1	PLN	4081
-Lycopersicon esculentum x Lycopersicon pimpinellifolium		1	1	PLN	286530
-Lycopersicon hirsutum		1	1	PLN	62890
-Lycopersicon pennellii		1	1	PLN	28526
 Lycoris longituba		1	1	PLN	272140
-Lymnaea stagnalis	great pond snail	1	5	INV	6523
+Lysiphlebus testaceipes		1	5	INV	77504
 Macaca fascicularis	crab-eating macaque	1	2	PRI	9541
 Macaca mulatta	rhesus monkey	1	2	PRI	9544
 Macaca nemestrina	pig-tailed macaque	1	2	PRI	9545
-Macrotyloma uniflorum		1	1	PLN	271171
+Maconellicoccus hirsutus	hibiscus mealybug	1	5	INV	177089
+Macropus eugenii	tammar wallaby	1	2	MAM	9315
+Macrostomum lignano		1	9	INV	282301
 Magnaporthe grisea		1	4	PLN	148305
+Magnaporthe grisea 70-15		1	4	PLN	242507
+Magnetospirillum magnetotacticum MS-1		11	0	BCT	272627
 Malawimonas californiana		1	1	INV	221722
 Malawimonas jakobiformis		1	1	INV	136089
-Malus sieboldii		1	1	PLN	106566
-Malus x domestica		1	1	PLN	3750
-Malus x domestica x Malus sieversii		1	1	PLN	339852
-Malva pusilla		1	1	PLN	96480
 Manduca sexta	tobacco hornworm	1	5	INV	7130
 Manihot esculenta	cassava	1	1	PLN	3983
 Marchantia polymorpha	liverwort	1	1	PLN	3197
+marine metagenome		11	2	ENV	408172
 Marsupenaeus japonicus		1	5	INV	27405
 Mastigamoeba balamuthi		1	1	INV	108607
 Measles virus		1	0	VRL	11234
@@ -476,63 +480,59 @@ Meloidogyne hapla		1	5	INV	6305
 Meloidogyne incognita	southern root-knot nematode	1	5	INV	6306
 Meloidogyne javanica	root-knot nematode	1	5	INV	6303
 Meloidogyne paranaensis		1	5	INV	189293
-Mentha x piperita	peppermint	1	1	PLN	34256
 Mesembryanthemum crystallinum	common iceplant	1	1	PLN	3544
-Mesobuthus gibbosus	Mediterranean checkered scorpion	1	5	INV	123226
-Mesocestoides corti		1	9	INV	53468
 Mesocricetus auratus	golden hamster	1	2	ROD	10036
 Mesostigma viride		1	1	PLN	41882
+metagenome sequence		11	2	ENV	256318
 Metarhizium anisopliae		1	4	PLN	5530
-Miamiensis avidus		6	4	INV	279580
 Microbotryum violaceum		1	4	PLN	5272
 Microcebus murinus	gray mouse lemur	1	2	PRI	30608
-Micromonas sp. CCMP490		1	1	PLN	392814
 Mimulus guttatus	spotted monkey flower	1	1	PLN	4155
-Misgurnus anguillicaudatus		1	2	VRT	75329
-Mnemiopsis leidyi		1	4	INV	27923
+Mimulus lewisii		1	1	PLN	69919
+Misgurnus anguillicaudatus	oriental weatherfish	1	2	VRT	75329
 Molgula tectiformis		1	13	INV	30286
 Monacrosporium haptotylum		1	4	PLN	74495
 Monodelphis domestica	gray short-tailed opossum	1	2	MAM	13616
 Monosiga ovata		1	1	INV	81526
-Montastraea faveolata		1	4	INV	48498
-Morone saxatilis	striped sea-bass	1	2	VRT	34816
-Murine leukemia virus		1	0	VRL	11786
+mouse gut metagenome		11	2	ENV	410661
 Mus musculus	house mouse	1	2	ROD	10090
-Musa acuminata		1	1	PLN	4641
-Mustela vison	American mink	1	2	MAM	9667
+Mus musculus domesticus	western European house mouse	1	2	ROD	10092
+Mus musculus molossinus	Japanese wild mouse	1	2	ROD	57486
+Musa acuminata	dessert banana	1	1	PLN	4641
 Mycobacterium tuberculosis		11	0	BCT	1773
 Mycosphaerella graminicola		1	4	PLN	54734
 Myotis lucifugus	little brown bat	1	2	MAM	59463
-Mytilus edulis		1	5	INV	6550
+Mytilus californianus	California mussel	1	5	INV	6549
 Mytilus galloprovincialis	Mediterranean mussel	1	5	INV	29158
 Myzus persicae	green peach aphid	1	5	INV	13164
 Nakaseomyces delphensis		1	3	PLN	51657
-Nannochloropsis oculata		1	1	PLN	43925
-Nasonia vitripennis		1	5	INV	7425
-Natrialba asiatica		11	0	BCT	64602
+Nasonia giraulti		1	5	INV	7426
+Nasonia vitripennis	jewel wasp	1	5	INV	7425
 Necator americanus		1	5	INV	51031
 Neisseria gonorrhoeae		11	0	BCT	485
 Neisseria meningitidis		11	0	BCT	487
 Nelumbo nucifera		1	1	PLN	4432
-Nematostella vectensis		1	4	INV	45351
+Nematostella vectensis	starlet sea anemone	1	4	INV	45351
+Neosartorya fischeri NRRL 181		1	4	PLN	331117
 Neospora caninum		1	4	INV	29176
-Neospora hughesi		1	4	INV	83675
+Neovison vison		1	2	MAM	452646
 Neurospora crassa		1	4	PLN	5141
+Neurospora crassa OR74A		1	4	PLN	367110
 Newcastle disease virus		1	0	VRL	11176
 Nicotiana benthamiana		1	1	PLN	4100
-Nicotiana langsdorffii x Nicotiana sanderae		1	1	PLN	164110
 Nicotiana sylvestris	wood tobacco	1	1	PLN	4096
 Nicotiana tabacum	common tobacco	1	1	PLN	4097
 Nippostrongylus brasiliensis		1	5	INV	27835
 Nuphar advena		1	1	PLN	77108
+Ochotona princeps	American pika	1	2	MAM	9978
 Ocimum basilicum	sweet basil	1	1	PLN	39350
 Onchocerca volvulus		1	5	INV	6282
 Oncometopia nigricans		1	5	INV	266772
 Oncorhynchus mykiss	rainbow trout	1	2	VRT	8022
 Oncorhynchus nerka	sockeye salmon	1	2	VRT	8023
 Oncorhynchus tshawytscha	Chinook salmon	1	2	VRT	74940
-Ophiostoma clavigerum		1	4	PLN	226899
 Ophiostoma piliferum		1	4	PLN	38032
+Opisthorchis viverrini		1	9	INV	6198
 Oreochromis niloticus	Nile tilapia	1	2	VRT	8128
 Ornithorhynchus anatinus	platypus	1	2	MAM	9258
 Oryctolagus cuniculus	rabbit	1	2	MAM	9986
@@ -548,19 +548,22 @@ Oryza officinalis		1	1	PLN	4535
 Oryza punctata		1	1	PLN	4537
 Oryza ridleyi		1	1	PLN	83308
 Oryza rufipogon		1	1	PLN	4529
-Oryza sativa		1	1	PLN	4530
+Oryza sativa	rice	1	1	PLN	4530
+Oryza sativa Indica Group		1	1	PLN	39946
+Oryza sativa Japonica Group		1	1	PLN	39947
 Oryzias latipes	Japanese medaka	1	2	VRT	8090
 Oscarella carmela		1	4	INV	386100
 Osmerus mordax	rainbow smelt	1	2	VRT	8014
 Ostertagia ostertagi		1	5	INV	6317
-Ostreococcus tauri		1	1	PLN	70448
+Ostreococcus lucimarinus CCE9901		1	1	PLN	436017
 Otolemur garnettii	small-eared galago	1	2	PRI	30611
 Ovis aries	sheep	1	2	MAM	9940
 Pan paniscus	pygmy chimpanzee	1	2	PRI	9597
 Pan troglodytes	chimpanzee	1	2	PRI	9598
+Pan troglodytes troglodytes		1	2	PRI	37011
+Pan troglodytes verus		1	2	PRI	37012
 Panax ginseng		1	1	PLN	4054
 Panicum virgatum	switchgrass	1	1	PLN	38727
-Papio anubis	olive baboon	1	2	PRI	9555
 Paracentrotus lividus	common urchin	1	9	INV	7656
 Paracoccidioides brasiliensis		1	4	PLN	121759
 Paralabidochromis chilotes		1	2	VRT	77306
@@ -568,272 +571,261 @@ Paralichthys olivaceus	bastard halibut	1	2	VRT	8255
 Paramecium tetraurelia		6	4	INV	5888
 Parastrongyloides trichosuri		1	5	INV	131310
 Pasteuria penetrans		11	0	BCT	86005
+Patiria pectinifera		1	9	INV	7594
 Pavlova lutheri		1	1	PLN	2832
 Paxillus involutus		1	4	PLN	71150
-Pecten maximus		1	5	INV	6579
-Pediculus humanus	human lice	1	5	INV	121225
+Pediculus humanus capitis	human head louse	1	5	INV	121226
+Pediculus humanus corporis	human body louse	1	5	INV	121224
 Penaeus monodon	black tiger shrimp	1	5	INV	6687
 Penicillium marneffei		1	4	PLN	37727
-Pennisetum ciliare	buffelgrass	1	1	PLN	35520
 Pennisetum glaucum		1	1	PLN	4543
-Pennisetum glaucum x Pennisetum squamulatum		1	1	PLN	404567
-Perca fluviatilis	perch	1	2	VRT	8168
-Peromyscus leucopus	white-footed mouse	1	2	ROD	10041
+Perkinsus marinus ATCC 50983		1	4	INV	423536
+Peromyscus maniculatus bairdii	prairie deer mouse	1	2	ROD	230844
 Persea americana	avocado	1	1	PLN	3435
 Petromyzon marinus	sea lamprey	1	2	VRT	7757
-Petunia x hybrida		1	1	PLN	4102
 Phaeodactylum tricornutum		1	1	PLN	2850
-Phaeosphaeria nodorum		1	4	PLN	13684
+Phaeosphaeria nodorum SN15		1	4	PLN	321614
 Phakopsora pachyrhizi		1	4	PLN	170000
 Phalaenopsis equestris		1	1	PLN	78828
 Phalaenopsis violacea		1	1	PLN	86509
 Phanerochaete chrysosporium		1	4	PLN	5306
-Phaseolus acutifolius	tepary bean	1	1	PLN	33129
 Phaseolus coccineus		1	1	PLN	3886
 Phaseolus vulgaris		1	1	PLN	3885
-Philodryas olfersii		1	2	VRT	120305
+Phlebotomus papatasi		1	5	INV	29031
 Photorhabdus luminescens		11	0	BCT	29488
-Phyllostachys pubescens		1	1	PLN	38705
 Physarum polycephalum	slime mold	1	1	INV	5791
 Physcomitrella patens		1	1	PLN	3218
+Physcomitrella patens subsp. patens		1	1	PLN	145481
+Phytophthora brassicae		1	1	PLN	187813
 Phytophthora infestans	potato late blight agent	1	1	PLN	4787
+Phytophthora infestans T30-4		1	1	PLN	403677
 Phytophthora parasitica		1	1	PLN	4792
 Phytophthora ramorum	Sudden oak death agent	1	1	PLN	164328
 Phytophthora sojae		1	1	PLN	67593
 Picea abies	Norway spruce	1	1	PLN	3329
-Picea engelmannii x Picea glauca		1	1	PLN	373101
 Picea glauca	white spruce	1	1	PLN	3330
 Picea sitchensis	Sitka spruce	1	1	PLN	3332
 Pichia angusta		1	3	PLN	4905
 Pichia farinosa		1	3	PLN	4920
+Pichia guilliermondii ATCC 6260		1	3	PLN	294746
+Pichia stipitis CBS 6054		12	3	PLN	322104
 Pimephales promelas		1	2	VRT	90988
 Pinus pinaster		1	1	PLN	71647
-Pinus radiata	Monterey pine	1	1	PLN	3347
 Pinus taeda	loblolly pine	1	1	PLN	3352
-Pisolithus microcarpus		1	4	PLN	178872
 Pisum sativum	pea	1	1	PLN	3888
 Plasmodium berghei		1	4	INV	5821
+Plasmodium berghei strain ANKA		1	4	INV	5823
 Plasmodium chabaudi		1	4	INV	5825
+Plasmodium chabaudi chabaudi		1	4	INV	31271
 Plasmodium falciparum	malaria parasite P. falciparum	1	4	INV	5833
+Plasmodium falciparum 3D7		1	4	INV	36329
+Plasmodium falciparum Dd2		1	4	INV	57267
+Plasmodium falciparum HB3		1	4	INV	137071
 Plasmodium vivax	malaria parasite P. vivax	1	4	INV	5855
 Plasmodium yoelii		1	4	INV	5861
+Plasmodium yoelii yoelii		1	4	INV	73239
+Plasmodium yoelii yoelii str. 17XNL		1	4	INV	352914
 Platichthys flesus	European flounder	1	2	VRT	8260
-Platynereis dumerilii	Dumeril's clam worm	1	5	INV	6359
-Pleurotus ostreatus	oyster mushroom	1	4	PLN	5322
 Plodia interpunctella	Indianmeal moth	1	5	INV	58824
-Plumbago zeylanica		1	1	PLN	76149
-Plutella xylostella	diamondback moth	1	5	INV	51655
 Pneumocystis carinii		1	4	PLN	4754
 Podocoryne carnea		1	4	INV	6096
-Polysphondylium pallidum		1	4	INV	13642
+Poecilia reticulata	guppy	1	2	VRT	8081
+Polygonatum sibiricum		1	1	PLN	261423
+Polysphondylium pallidum		1	1	INV	13642
 Polytomella parva		1	1	PLN	51329
 Poncirus trifoliata		1	1	PLN	37690
 Pongo pygmaeus	orangutan	1	2	PRI	9600
-Populus alba x Populus tremula		1	1	PLN	80863
-Populus alba x Populus tremula var. glandulosa		1	1	PLN	153471
 Populus deltoides		1	1	PLN	3696
 Populus euphratica		1	1	PLN	75702
-Populus fremontii x Populus angustifolia		1	1	PLN	352374
 Populus nigra		1	1	PLN	3691
-Populus tomentiglandulosa		1	1	PLN	255244
 Populus tremula		1	1	PLN	113636
-Populus tremula x Populus tremuloides		1	1	PLN	47664
 Populus tremuloides	quaking aspen	1	1	PLN	3693
 Populus trichocarpa		1	1	PLN	3694
-Populus trichocarpa x Populus deltoides		1	1	PLN	3695
-Populus trichocarpa x Populus nigra		1	1	PLN	293756
-Populus x canadensis		1	1	PLN	3690
 Porcine respiratory and reproductive syndrome virus		1	0	VRL	28344
 Porphyra haitanensis		1	4	PLN	76159
 Porphyra yezoensis		1	4	PLN	2788
-Pratylenchus penetrans		1	5	INV	45929
 Pratylenchus vulnus		1	5	INV	45931
 Pristionchus pacificus		1	5	INV	54126
-Prosopis juliflora		1	1	PLN	13230
 Prototheca wickerhamii		1	1	PLN	3111
 Prunus armeniaca	apricot	1	1	PLN	36596
-Prunus cerasus		1	1	PLN	140311
 Prunus dulcis	almond	1	1	PLN	3755
 Prunus persica	peach	1	1	PLN	3760
 Prymnesium parvum		1	1	PLN	97485
 Pseudomonas aeruginosa		11	0	BCT	287
-Pseudomonas fluorescens		11	0	BCT	294
-Pseudomonas putida		11	0	BCT	303
-Pseudomonas viridiflava		11	0	BCT	33069
-Pseudopleuronectes americanus	winter flounder	1	2	VRT	8265
-Ptyochromis sp. 'redtail sheller'		1	2	VRT	257976
+Pseudotsuga menziesii	Douglas-fir	1	1	PLN	3357
+Pseudotsuga menziesii var. menziesii		1	1	PLN	278161
+Psychroflexus torquis ATCC 700755		11	0	BCT	313595
 Puccinellia tenuiflora		1	1	PLN	240906
-Quercus petraea	sessile oak	1	1	PLN	38865
-Quercus robur		1	1	PLN	38942
+Puccinia graminis f. sp. tritici CRL 75-36-700-3		1	4	PLN	418459
+Puccinia triticina		1	4	PLN	208348
+Pythium ultimum DAOM BR144		1	1	PLN	431595
 Rabies virus		1	0	VRL	11292
-Radopholus similis		1	5	INV	46012
-Ralstonia solanacearum		11	0	BCT	305
+Raphanus raphanistrum subsp. landra		1	1	PLN	328428
+Raphanus raphanistrum subsp. maritimus		1	1	PLN	457179
+Raphanus raphanistrum subsp. raphanistrum		1	1	PLN	109997
+Raphanus sativus	radish	1	1	PLN	3726
+Raphanus sativus var. oleiformis		1	1	PLN	463157
 Rattus norvegicus	Norway rat	1	2	ROD	10116
 Reclinomonas americana		1	1	INV	48483
-Reticulomyxa filosa		1	1	INV	46433
-Rhagoletis pomonella	apple maggot	1	5	INV	28610
-Rhinolophus ferrumequinum	greater horseshoe bat	1	2	MAM	59479
 Rhipicephalus appendiculatus		1	5	INV	34631
-Rhizobium sp. NGR234		11	0	BCT	394
+Rhipicephalus microplus	southern cattle tick	1	5	INV	6941
 Rhizopus oryzae		1	1	PLN	64495
-Rhododendron catawbiense		1	1	PLN	257784
+Rhodnius prolixus		1	5	INV	13249
 Rhynchosciara americana		1	5	INV	7186
-Ribes americanum		1	1	PLN	3802
 Ricinus communis	castor bean	1	1	PLN	3988
 Robinia pseudoacacia		1	1	PLN	35938
-Rosa chinensis		1	1	PLN	74649
 Rosa hybrid cultivar		1	1	PLN	128735
-Rosa wichurana		1	1	PLN	74648
-Saccharomyces bayanus		1	3	PLN	4931
-Saccharomyces cariocanus		1	3	PLN	114526
+Rutilus rutilus	roach minnow	1	2	VRT	48668
 Saccharomyces castellii		1	3	PLN	27288
 Saccharomyces cerevisiae	baker's yeast	1	3	PLN	4932
-Saccharomyces mikatae		1	3	PLN	114525
-Saccharomyces paradoxus		1	3	PLN	27291
+Saccharomyces mikatae IFO 1815		1	3	PLN	226126
+Saccharomyces pastorianus		1	3	PLN	27292
 Saccharomyces servazzii		1	3	PLN	27293
-Saccharomyces unisporus		1	3	PLN	27294
 Saccharomyces uvarum		1	3	PLN	230603
 Saccharum hybrid cultivar		1	1	PLN	128810
 Saccharum officinarum		1	1	PLN	4547
+Saccoglossus kowalevskii		1	9	INV	10224
 Saitoella complicata		1	4	PLN	5606
-Salicornia brachiata		1	1	PLN	179119
 Salmo salar	Atlantic salmon	1	2	VRT	8030
-Salmo trutta	brown trout	1	2	VRT	8032
-Salmonella enterica		11	0	BCT	28901
-Salmonella typhimurium		11	0	BCT	602
+Salvelinus fontinalis	brook trout	1	2	VRT	8038
 Salvia miltiorrhiza		1	1	PLN	226208
-Saprolegnia parasitica		1	1	PLN	101203
 Sarcocystis falcatula		1	4	INV	32593
 Sarcocystis neurona		1	4	INV	42890
-Sarcoptes scabiei		1	5	INV	52283
 Saruma henryi		1	1	PLN	13258
 Sawyeria marylandensis		1	1	INV	194530
-Scarabaeus laticollis		1	5	INV	292456
 Scenedesmus obliquus		1	22	PLN	3088
-Scherffelia dubia		1	1	PLN	3190
 Schistosoma japonicum		1	9	INV	6182
 Schistosoma mansoni		1	9	INV	6183
-Schizophyllum commune		1	4	PLN	5334
 Schizosaccharomyces pombe	fission yeast	1	4	PLN	4896
+Schizosaccharomyces pombe 972h-		1	4	PLN	284812
 Schmidtea mediterranea		1	9	INV	79327
 Sclerotinia sclerotiorum		1	4	PLN	5180
+Sclerotinia sclerotiorum 1980		1	4	PLN	325569
+Sebastes rastrelliger	grass rockfish	1	2	VRT	72095
 Secale cereale	rye	1	1	PLN	4550
 Seculamonas ecuadoriensis		1	1	INV	221724
 Selaginella lepidophylla		1	1	PLN	59777
-Selaginella moellendorffii		1	1	PLN	88036
-Senecio aethnensis		1	1	PLN	121540
-Senecio cambrensis		1	1	PLN	285720
-Senecio chrysanthemifolius		1	1	PLN	121541
 Sesamum indicum	sesame	1	1	PLN	4182
-Shigella boydii		11	0	BCT	621
-Shigella dysenteriae		11	0	BCT	622
-Shigella flexneri		11	0	BCT	623
 Simian immunodeficiency virus		1	0	VRL	11723
 Solanum chacoense	Chaco potato	1	1	PLN	4108
+Solanum habrochaites		1	1	PLN	62890
+Solanum lycopersicum		1	1	PLN	4081
+Solanum pennellii		1	1	PLN	28526
 Solanum tuberosum	potato	1	1	PLN	4113
+Solenopsis invicta	red fire ant	1	5	INV	13686
 Sorex araneus	European shrew	1	2	MAM	42254
 Sorghum bicolor	sorghum	1	1	PLN	4558
-Sorghum halepense		1	1	PLN	4560
 Sorghum propinquum		1	1	PLN	132711
 Sparus aurata	gilthead seabream	1	2	VRT	8175
 Spermophilus lateralis	golden-mantled ground squirrel	1	2	ROD	76772
 Spermophilus tridecemlineatus	thirteen-lined ground squirrel	1	2	ROD	43179
 Sphaeroforma arctica		1	1	INV	72019
+Spironucleus barkhanus		6	0	INV	103874
 Spizellomyces punctatus		1	16	PLN	109760
 Spodoptera frugiperda	fall armyworm	1	5	INV	7108
 Squalus acanthias	spiny dogfish	1	2	VRT	7797
+Stachyamoeba lipophora		1	1	INV	463046
 Staphylococcus aureus		11	0	BCT	1280
 Staphylococcus epidermidis		11	0	BCT	1282
 Sterkiella histriomuscorum		6	4	INV	94289
 Stevia rebaudiana		1	1	PLN	55670
-Stomoxys calcitrans	stable fly	1	5	INV	35570
 Streblomastix strix		6	1	INV	222440
 Streptococcus agalactiae		11	0	BCT	1311
 Streptococcus pneumoniae		11	0	BCT	1313
 Streptococcus pyogenes		11	0	BCT	1314
-Streptococcus suis		11	0	BCT	1307
 Strongylocentrotus purpuratus		1	9	INV	7668
 Strongyloides ratti		1	5	INV	34506
 Strongyloides stercoralis		1	5	INV	6248
-Suaeda salsa		1	1	PLN	126914
+Suidasia medanensis		1	5	INV	223625
 Sus scrofa	pig	1	2	MAM	9823
-Symsagittifera roscoffensis		1	5	INV	84072
+Taenia solium	pork tapeworm	1	9	INV	6204
 Taeniopygia guttata		1	2	VRT	59729
 Taiwania cryptomerioides		1	1	PLN	50187
-Takifugu rubripes		1	2	VRT	31033
+Takifugu rubripes	torafugu	1	2	VRT	31033
 Tamarix androssowii		1	1	PLN	189785
+Tamarix hispida		1	1	PLN	189793
 Taphrina deformans	peach leaf curl fungus	1	4	PLN	5011
 Taraxacum kok-saghyz		1	1	PLN	333970
 Taraxacum officinale		1	1	PLN	50225
 Teladorsagia circumcincta		1	5	INV	45464
 Tetrahymena thermophila		6	4	INV	5911
+Tetrahymena thermophila SB210		6	4	INV	312017
 Tetraodon nigroviridis		1	2	VRT	99883
+Thalassiosira pseudonana CCMP1335		1	4	PLN	296543
 Theileria annulata		1	4	INV	5874
+Theileria annulata strain Ankara		1	4	INV	353154
 Theileria parva		1	4	INV	5875
+Theileria parva strain Muguga		1	4	INV	333668
 Thellungiella halophila		1	1	PLN	98038
 Thellungiella salsuginea		1	1	PLN	72664
 Theobroma cacao	cacao	1	1	PLN	3641
 Thermomyces lanuginosus		1	4	PLN	5541
-Thermus thermophilus		11	0	BCT	274
 Thlaspi caerulescens		1	1	PLN	107243
 Thunnus thynnus	bluefin tuna	1	2	VRT	8237
-Tineola bisselliella		1	5	INV	93883
+Thymallus arcticus	Arctic grayling	1	2	VRT	70285
 Torque teno virus		1	0	VRL	68887
 Tortula ruralis		1	1	PLN	38588
 Toxocara canis		1	5	INV	6265
 Toxoplasma gondii		1	4	INV	5811
+Toxoplasma gondii RH		1	4	INV	383379
 Toxoptera citricida	brown citrus aphid	1	5	INV	223852
-Toxorhynchites amboinensis		1	5	INV	46208
 Trametes versicolor		1	4	PLN	5325
-Triatoma brasiliensis		1	5	INV	65344
 Tribolium castaneum	red flour beetle	1	5	INV	7070
 Trichinella spiralis		1	5	INV	6334
+Trichoderma reesei QM6a		1	4	PLN	431241
 Trichomonas vaginalis		1	0	INV	5722
+Trichomonas vaginalis G3		1	0	INV	412133
 Trichophyton rubrum		1	4	PLN	5551
 Trichosurus vulpecula	silver-gray brushtail possum	1	2	MAM	9337
 Trichuris muris		1	5	INV	70415
 Trichuris vulpis		1	5	INV	219738
 Trifolium pratense		1	1	PLN	57577
+Trifolium repens	white clover	1	1	PLN	3899
 Trimastix pyriformis		1	1	INV	342808
 Triphysaria versicolor		1	1	PLN	64093
 Triticum aestivum	bread wheat	1	1	PLN	4565
 Triticum monococcum		1	1	PLN	4568
-Triticum turgidum		1	1	PLN	4571
+Triticum turgidum subsp. durum	durum wheat	1	1	PLN	4567
 Tritrichomonas foetus		1	0	INV	5724
-Trox sp. JH-2005		1	5	INV	358432
 Trypanosoma brucei		1	4	INV	5691
-Trypanosoma carassii		1	4	INV	38249
+Trypanosoma brucei rhodesiense		1	4	INV	31286
+Trypanosoma brucei TREU927		1	4	INV	185431
 Trypanosoma cruzi		1	4	INV	5693
+Trypanosoma cruzi strain CL Brener		1	4	INV	353153
 Tuber borchii	whitish truffle	1	4	PLN	42251
 Tupaia belangeri	northern tree shrew	1	2	MAM	37347
 Tursiops truncatus	bottlenosed dolphin	1	2	MAM	9739
-Ulva linza		1	1	PLN	63409
+uncultured archaeon		11	0	ENV	115547
+uncultured bacterium		11	0	ENV	77133
+uncultured eukaryote		1	1	ENV	100272
+uncultured fungus		1	4	ENV	175245
+uncultured marine virus		1	0	ENV	186617
+uncultured organism		11	2	ENV	155900
+uncultured prokaryote		11	0	ENV	198431
+Uromyces appendiculatus		1	4	PLN	5264
 Ustilago maydis		1	4	PLN	5270
+Ustilago maydis 521		1	4	PLN	237631
 Vaccinium corymbosum		1	1	PLN	69266
+Vanderwaltozyma polyspora DSM 70294		1	3	PLN	436907
 Verticillium dahliae		1	4	PLN	27337
-Vibrio cholerae		11	0	BCT	666
-Vitis aestivalis		1	1	PLN	3605
+Vibrio parahaemolyticus AQ3810		11	0	BCT	419109
+Vigna unguiculata	cowpea	1	1	PLN	3917
 Vitis hybrid cultivar		1	1	PLN	241073
-Vitis riparia		1	1	PLN	96939
 Vitis shuttleworthii		1	1	PLN	246827
 Vitis vinifera		1	1	PLN	29760
 Welwitschia mirabilis		1	1	PLN	3377
-West Nile virus		1	0	VRL	11082
-Wolbachia endosymbiont of Drosophila ananassae		11	0	BCT	307502
-Wolbachia endosymbiont of Drosophila simulans		11	0	BCT	77038
 Wuchereria bancrofti		1	5	INV	6293
 Xenopus laevis	African clawed frog	1	2	VRT	8355
 Xenopus tropicalis	western clawed frog	1	2	VRT	8364
-Xiphias gladius	swordfish	1	2	VRT	8245
 Xiphinema index		1	5	INV	46003
-Xiphophorus maculatus	southern platyfish	1	2	VRT	8083
-Xylella fastidiosa		11	0	BCT	2371
 Yarrowia lipolytica		1	3	PLN	4952
-Yucca filamentosa		1	1	PLN	55960
+Yarrowia lipolytica CLIB122		1	3	PLN	284591
 Zamia fischeri		1	1	PLN	34342
-Zamia furfuracea		1	1	PLN	42329
 Zantedeschia aethiopica		1	1	PLN	69721
 Zea mays		1	1	PLN	4577
+Zea mays subsp. mays	maize	1	1	PLN	381124
+Zea mays subsp. parviglumis		1	1	PLN	76912
 Zingiber officinale		1	1	PLN	94328
 Zinnia elegans		1	1	PLN	34245
+Zostera marina		1	1	PLN	29655
 Zygosaccharomyces rouxii		1	3	PLN	4956
diff --git a/demo/.BLAST_VERSION b/demo/.BLAST_VERSION
index c36c6482..8c57128f 100644
--- a/demo/.BLAST_VERSION
+++ b/demo/.BLAST_VERSION
@@ -1 +1 @@
-2.2.17
+2.2.18
diff --git a/demo/asn2all.c b/demo/asn2all.c
index e00e1c7d..9af408e9 100644
--- a/demo/asn2all.c
+++ b/demo/asn2all.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/26/04
 *
-* $Revision: 1.36 $
+* $Revision: 1.37 $
 *
 * File Description:
 *
@@ -53,7 +53,7 @@
 #include <pmfapi.h>
 #include <lsqfetch.h>
 
-#define ASN2ALL_APP_VER "2.3"
+#define ASN2ALL_APP_VER "2.4"
 
 CharPtr ASN2ALL_APPLICATION = ASN2ALL_APP_VER;
 
diff --git a/demo/asn2gb.c b/demo/asn2gb.c
index 03e52ec4..ffb209b8 100644
--- a/demo/asn2gb.c
+++ b/demo/asn2gb.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 6.102 $
+* $Revision: 6.103 $
 *
 * File Description:  New GenBank flatfile generator application
 *
@@ -50,7 +50,7 @@
 #include <explore.h>
 #include <asn2gnbp.h>
 
-#define ASN2GB_APP_VER "4.3"
+#define ASN2GB_APP_VER "4.4"
 
 CharPtr ASN2GB_APPLICATION = ASN2GB_APP_VER;
 
diff --git a/demo/asnbarval.c b/demo/asnbarval.c
index 2218bf9a..7e925556 100644
--- a/demo/asnbarval.c
+++ b/demo/asnbarval.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/23/07
 *
-* $Revision: 1.2 $
+* $Revision: 1.3 $
 *
 * File Description:
 *
@@ -492,21 +492,6 @@ static ValNodePtr DoLockFarComponents (
   return rsult;
 }
 
-static ValNodePtr FreeFilenameList (ValNodePtr filename_list)
-{
-  ValNodePtr vnp_next;
-  if (filename_list == NULL) return NULL;
-  vnp_next = filename_list->next;
-  filename_list->next = NULL;
-  if (filename_list->choice == 2) {
-    filename_list = ValNodeFreeData (filename_list);
-  } else {
-    filename_list = ValNodeFree (filename_list);
-  }
-  vnp_next = FreeFilenameList (vnp_next);
-  return NULL;
-}
-
 static void ProcessSeqEntryList (BRFlagPtr drfp, CharPtr filename)
 {
   ValNodePtr  pass_fail_list, vnp;
diff --git a/demo/asndisc.c b/demo/asndisc.c
index 467e44aa..a5da7aef 100644
--- a/demo/asndisc.c
+++ b/demo/asndisc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/23/07
 *
-* $Revision: 1.11 $
+* $Revision: 1.20 $
 *
 * File Description:
 *
@@ -80,10 +80,10 @@ typedef struct drflags {
   CharPtr  output_dir;
   FILE     *outfp;
   Int4     numrecords;
+  DiscReportOutputConfigData ocd;
   DiscrepancyConfigData dcd;
   ValNodePtr            sep_list;
   ValNodePtr            bsplist;
-  ValNodePtr            filename_list;
 } DRFlagData, PNTR DRFlagPtr;
 
 #ifdef INTERNAL_NCBI_ASNDISC
@@ -493,31 +493,15 @@ static ValNodePtr DoLockFarComponents (
   return rsult;
 }
 
-static ValNodePtr FreeFilenameList (ValNodePtr filename_list)
-{
-  ValNodePtr vnp_next;
-  if (filename_list == NULL) return NULL;
-  vnp_next = filename_list->next;
-  filename_list->next = NULL;
-  if (filename_list->choice == 2) {
-    filename_list = ValNodeFreeData (filename_list);
-  } else {
-    filename_list = ValNodeFree (filename_list);
-  }
-  vnp_next = FreeFilenameList (vnp_next);
-  return NULL;
-}
-
 static void ProcessSeqEntryList (DRFlagPtr drfp, CharPtr filename)
 {
-  ValNodePtr  discrepancy_list, vnp, subcat;
+  ValNodePtr  discrepancy_list, vnp;
   ObjMgrPtr   omp;
   SeqEntryPtr sep;
   FILE        *ofp = NULL;
   Boolean     need_ofp_close = FALSE;
   Char        path [PATH_MAX];
   CharPtr     ptr;
-  ClickableItemPtr cip;
 
   if (drfp == NULL || drfp->sep_list == NULL) return;
 
@@ -568,17 +552,7 @@ static void ProcessSeqEntryList (DRFlagPtr drfp, CharPtr filename)
   }
 
   discrepancy_list = CollectDiscrepancies (&(drfp->dcd), drfp->sep_list, taxlookup);
-  for (vnp = discrepancy_list; vnp != NULL; vnp = vnp->next) {
-    cip = (ClickableItemPtr) vnp->data.ptrvalue;
-    if (cip != NULL) {
-      WriteDiscrepancyEx (ofp, vnp->data.ptrvalue, drfp->dcd.use_feature_table_format, drfp->filename_list, "DiscRep");
-      if (cip->item_list == NULL && cip->subcategories != NULL) {
-        for (subcat = cip->subcategories; subcat != NULL; subcat = subcat->next) {
-          WriteDiscrepancyEx (ofp, subcat->data.ptrvalue, drfp->dcd.use_feature_table_format, drfp->filename_list, "DiscRep");
-        }
-      }
-    }
-  }
+  WriteAsnDiscReport (discrepancy_list, ofp, &(drfp->ocd), TRUE);
   discrepancy_list = FreeClickableList (discrepancy_list);
   for (vnp = drfp->sep_list; vnp != NULL; vnp = vnp->next) {
     sep = vnp->data.ptrvalue;
@@ -592,7 +566,7 @@ static void ProcessSeqEntryList (DRFlagPtr drfp, CharPtr filename)
   SeqEntrySetScope (NULL);
   drfp->sep_list = ValNodeFree (drfp->sep_list);
   
-  drfp->filename_list = FreeFilenameList (drfp->filename_list);
+  drfp->ocd.filename_list = FreeFilenameList (drfp->ocd.filename_list);
 
   drfp->bsplist = UnlockFarComponents (drfp->bsplist);
 
@@ -707,8 +681,8 @@ static void ProcessSingleRecord (
 
     if (sep != NULL) {
       ValNodeAddPointer (&(drfp->sep_list), 0, sep);
-      ValNodeAddInt (&(drfp->filename_list), FILENAME_LIST_ENTITY_ID_ITEM, (Int4) entityID);
-      ValNodeAddPointer (&(drfp->filename_list), FILENAME_LIST_FILENAME_ITEM, StringSave (filename));
+      ValNodeAddInt (&(drfp->ocd.filename_list), FILENAME_LIST_ENTITY_ID_ITEM, (Int4) entityID);
+      ValNodeAddPointer (&(drfp->ocd.filename_list), FILENAME_LIST_FILENAME_ITEM, StringSave (filename));
 
       if (drfp->lock) {
         bsplist_next = DoLockFarComponents (sep, drfp);
@@ -942,16 +916,18 @@ typedef enum {
   e_argEnableTests,
   d_argDisableTests,
   s_argOutputSuffix,
-  q_argOutputDir,
+  r_argOutputDir,
   Z_argRemoteCDS,
   a_argType,
   b_argBinary,
   c_argCompressed,
-  r_argRemote,
+  R_argRemote,
   k_argLocalFetch,
   I_argAsnIdx,
   l_argLockFar,
   T_argThreads,
+  X_argExpandCategories,
+  S_argSummaryReport,
   C_argMaxCount
 } DRFlagNum;
 
@@ -985,7 +961,7 @@ Args myargs [] = {
   {"Output File Suffix", ".dr", NULL, NULL,
     TRUE, 's', ARG_STRING, 0.0, 0, NULL},
   {"Output Directory", NULL, NULL, NULL,
-    TRUE, 'q', ARG_STRING, 0.0, 0, NULL},
+    TRUE, 'r', ARG_STRING, 0.0, 0, NULL},
   {"Remote CDS Product Fetch", "F", NULL, NULL,
     TRUE, 'Z', ARG_BOOLEAN, 0.0, 0, NULL},
   {"ASN.1 Type (a Any, e Seq-entry, b Bioseq, s Bioseq-set, m Seq-submit, t Batch Bioseq-set, u Batch Seq-submit)", "a", NULL, NULL,
@@ -995,7 +971,7 @@ Args myargs [] = {
   {"Batch File is Compressed", "F", NULL, NULL,
     TRUE, 'c', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Remote Fetching from ID", "F", NULL, NULL,
-    TRUE, 'r', ARG_BOOLEAN, 0.0, 0, NULL},
+    TRUE, 'R', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Local Fetching", "F", NULL, NULL,
     TRUE, 'k', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Path to Indexed Binary ASN.1 Data", NULL, NULL, NULL,
@@ -1004,49 +980,20 @@ Args myargs [] = {
     TRUE, 'l', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Use Threads", "F", NULL, NULL,
     TRUE, 'T', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Expand Report Categories (comma-delimited list of test names or ALL)\n\tALL\n\tMISSING_GENES\n\tEXTRA_GENES\n\tMISSING_LOCUS_TAGS\n\tDUPLICATE_LOCUS_TAGS\n\tBAD_LOCUS_TAG_FORMAT\n"
+   "\tINCONSISTENT_LOCUS_TAG_PREFIX\n\tNON_GENE_LOCUS_TAG\n\tMISSING_PROTEIN_ID\n\tINCONSISTENT_PROTEIN_ID\n"
+   "\tFEATURE_LOCATION_CONFLICT\n\tGENE_PRODUCT_CONFLICT\n\tDUPLICATE_GENE_LOCUS\n\tEC_NUMBER_NOTE\n\tPSEUDO_MISMATCH\n"
+   "\tJOINED_FEATURES\n\tOVERLAPPING_GENES\n\tOVERLAPPING_CDS\n\tSHORT_CONTIG\n\tINCONSISTENT_BIOSOURCE\n\tSUSPECT_PRODUCT_NAMES\n"
+   "\tINCONSISTENT_SOURCE_DEFLINE\n\tPARTIAL_CDS_COMPLETE_SEQUENCE\n\tEC_NUMBER_ON_UNKNOWN_PROTEIN\n\tTAX_LOOKUP_MISSING\n"
+   "\tTAX_LOOKUP_MISMATCH\n\tSHORT_SEQUENCES\n\tSUSPECT_PHRASES\n", "", NULL, NULL,
+    TRUE, 'X', ARG_STRING, 0.0, 0, NULL},
+  {"Summary Report", "F", NULL, NULL,
+    TRUE, 'S', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Max Count", "0", NULL, NULL,
     TRUE, 'C', ARG_INT, 0.0, 0, NULL},
 };
 
 
-static CharPtr SetTestsFromString (CharPtr list, Boolean enable, DiscrepancyConfigPtr dcp)
-{
-  CharPtr         ptr, tmp, name_start, err_msg;
-  DiscrepancyType test_type;
-  CharPtr         err_fmt = "%s is an unrecognized test name";
-  
-  if (dcp == NULL) return StringSave ("Unable to configure");
-
-  if (!StringDoesHaveText (list)) {
-      return StringSave ("No tests specified!");
-  }
-
-  tmp = StringSave (list);
-  name_start = tmp;
-  while (name_start != NULL && StringDoesHaveText (name_start)) {
-    ptr = StringChr (name_start, ',');
-    if (ptr != NULL) {
-      *ptr = 0;
-    }
-    TrimSpacesAroundString (name_start);
-    test_type = GetDiscrepancyTypeFromSettingName (name_start);
-    if (test_type == MAX_DISC_TYPE) {
-      err_msg = (CharPtr) MemNew (StringLen (err_fmt) + StringLen (name_start));
-      sprintf (err_msg, err_fmt, name_start);
-      tmp = MemFree (tmp);
-      return err_msg;
-    }
-    dcp->conf_list[test_type] = enable;
-    if (ptr == NULL) {
-      name_start = NULL;
-    } else {
-      name_start = ptr + 1;
-    }
-  }
-  tmp = MemFree (tmp);
-  return NULL;  
-}
-
 static CharPtr GetTestNameList (CharPtr intro)
 {
   Int4 i, len;
@@ -1115,7 +1062,7 @@ Int2 Main (void)
   /* set up help descriptions for enable and disable */
   myargs[e_argEnableTests].prompt = GetTestNameList("Enable Tests (comma-delimited list of test names)\n");
   myargs[d_argDisableTests].prompt = GetTestNameList("Disable Tests (comma-delimited list of test names)\n");
-
+  myargs[X_argExpandCategories].prompt = GetTestNameList("Expand Report Categories (comma-delimited list of test names or ALL)\n");
   /* process command line arguments */
 
   sprintf (app, "asndisc %s", ASNDISC_APPLICATION);
@@ -1131,7 +1078,7 @@ Int2 Main (void)
   dfd.output_suffix = (CharPtr) myargs [s_argOutputSuffix].strvalue;
   infile = (CharPtr) myargs [i_argInputFile].strvalue;
   outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
-  output_dir = (CharPtr) myargs [q_argOutputDir].strvalue;
+  output_dir = (CharPtr) myargs [r_argOutputDir].strvalue;
   if (StringDoesHaveText (outfile) && StringDoesHaveText (output_dir)) {
     Message (MSG_FATAL, "-o and -q are incompatible: specify the output file name with the full path.");
     return 1;
@@ -1144,7 +1091,7 @@ Int2 Main (void)
   }
 
   dorecurse = (Boolean) myargs [u_argRecurse].intvalue;
-  remote = (Boolean ) myargs [r_argRemote].intvalue;
+  remote = (Boolean ) myargs [R_argRemote].intvalue;
   local = (Boolean) myargs [k_argLocalFetch].intvalue;
 
   asnidx = (CharPtr) myargs [I_argAsnIdx].strvalue;
@@ -1152,6 +1099,8 @@ Int2 Main (void)
   lock = (Boolean) myargs [l_argLockFar].intvalue;
   usethreads = (Boolean) myargs [T_argThreads].intvalue;
   dfd.farFetchCDSproducts = (Boolean) myargs [Z_argRemoteCDS].intvalue;
+  ExpandDiscrepancyReportTestsFromString ((CharPtr) myargs [X_argExpandCategories].strvalue, TRUE, &dfd.ocd);
+  dfd.ocd.summary_report = (Boolean) myargs [S_argSummaryReport].intvalue;
 
   /* set up Discrepancy Report Configuration */
   enabled_list = (CharPtr) myargs [e_argEnableTests].strvalue;
@@ -1167,13 +1116,13 @@ Int2 Main (void)
     DisableTRNATests (&(dfd.dcd));
 
     /* now disable tests from string */
-    err_msg = SetTestsFromString (disabled_list, FALSE, &(dfd.dcd));
+    err_msg = SetDiscrepancyReportTestsFromString (disabled_list, FALSE, &(dfd.dcd));
   } else if (StringDoesHaveText (enabled_list)) {
     for (k = 0; k < MAX_DISC_TYPE; k++) {
       dfd.dcd.conf_list[k] = FALSE;
     }
     /* now enable tests from string */
-    err_msg = SetTestsFromString (enabled_list, TRUE, &(dfd.dcd));
+    err_msg = SetDiscrepancyReportTestsFromString (enabled_list, TRUE, &(dfd.dcd));
   } else {
     /* enable all tests by default */
     for (k = 0; k < MAX_DISC_TYPE; k++) {
@@ -1189,6 +1138,7 @@ Int2 Main (void)
 
   if ((Boolean) myargs[f_argUseFT].intvalue) {
     dfd.dcd.use_feature_table_format = TRUE;
+    dfd.ocd.use_feature_table_format = TRUE;
   }
 
   dfd.maxcount = (Int4) myargs [C_argMaxCount].intvalue;
diff --git a/demo/asnmacro.c b/demo/asnmacro.c
new file mode 100755
index 00000000..7e980c28
--- /dev/null
+++ b/demo/asnmacro.c
@@ -0,0 +1,708 @@
+/*   asnmacro.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  asnmacro.c
+*
+* Author:  Colleen Bollin
+*
+* Version Creation Date:   4/12/07
+*
+* $Revision: 1.3 $
+*
+* File Description: 
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* Date     Name        Description of modification
+* -------  ----------  -----------------------------------------------------
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <objall.h>
+#include <objsset.h>
+#include <objsub.h>
+#include <objfdef.h>
+#include <sequtil.h>
+#include <gather.h>
+#include <sqnutils.h>
+#include <explore.h>
+#include <actutils.h>
+#include <algo/blast/api/twoseq_api.h>
+#define NLM_GENERATED_CODE_PROTO
+#include <asnmacro.h>
+#include <objmacro.h>
+#include <macroapi.h>
+
+#define ASNMACRO_APP_VER "1.0"
+
+CharPtr ASNMACRO_APPLICATION = ASNMACRO_APP_VER;
+
+/* for alignments */
+static SeqAlignPtr LIBCALLBACK GetSeqAlign (BioseqPtr bsp1, BioseqPtr bsp2)
+{
+   BLAST_SummaryOptions *options = NULL;
+   SeqAlignPtr           salp = NULL;
+   
+   if (bsp1 == NULL || bsp2 == NULL) return NULL;
+
+   BLAST_SummaryOptionsInit(&options);
+   if (bsp1->length > 10000 || bsp2->length > 10000)
+   {
+      options->filter_string = StringSave ("m L");
+      options->word_size = 20;
+      options->cutoff_evalue = act_get_eval (60);
+      options->hint = eNone;
+   }
+   else
+   {
+    options->filter_string = StringSave ("m F");
+   }
+   if (ISA_na (bsp1->mol))
+   {
+     options->program = eBlastn;
+   }
+   else
+   {
+     options->program = eBlastp;
+   }
+
+   BLAST_TwoSequencesSearch(options, bsp1, bsp2, &salp);
+   BLAST_SummaryOptionsFree(options);
+   return salp;
+}
+
+static SeqAlignPtr LIBCALLBACK GetSeqAlignPiece (SeqLocPtr slp1, SeqLocPtr slp2)
+{
+   BLAST_SummaryOptions *options = NULL;
+   SBlastSeqalignArray * seqalign_arr=NULL;
+   SeqAlignPtr           salp = NULL;
+   BioseqPtr             bsp;
+   
+   if (slp1 == NULL || slp2 == NULL) return NULL;
+
+
+   bsp = BioseqFindFromSeqLoc (slp1);
+   if (bsp == NULL)
+   {
+     return NULL;
+   }
+   
+   BLAST_SummaryOptionsInit(&options);
+   
+   if (ISA_na (bsp->mol))
+   {
+     options->program = eBlastn;
+   }
+   else
+   {
+     options->program = eBlastp;
+   }
+
+   options->gapped_calculation = TRUE;
+   options->cutoff_evalue = 10;
+   options->gap_x_dropoff = 100;
+   options->gap_open = 4;
+   options->gap_extend = 1;
+   options->nucleotide_mismatch = -1; 
+   options->word_size = 7;
+
+   BLAST_TwoSeqLocSets(options, slp1, slp2, NULL, &seqalign_arr, NULL, NULL, NULL);
+   
+   if (seqalign_arr != NULL)
+   {
+     salp = seqalign_arr->array[0];
+     seqalign_arr->array[0] = NULL;
+     seqalign_arr = SBlastSeqalignArrayFree(seqalign_arr);
+   }
+    
+   BLAST_SummaryOptionsFree(options);
+   return salp;
+}
+
+static SeqAlignPtr GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp)
+{
+   return Sqn_GlobalAlign2SeqEx (bsp1, bsp2, revcomp, GetSeqAlign, GetSeqAlignPiece);
+}
+
+
+
+typedef struct outputstream {
+  CharPtr  results_dir;
+  CharPtr  base;
+  CharPtr  suffix;
+  CharPtr  outfile;
+  CharPtr  outsuffix;
+  AsnIoPtr aip;
+  Boolean  is_binary;
+} OutputStreamData, PNTR OutputStreamPtr;
+
+typedef struct inputstream {
+  CharPtr directory;
+  CharPtr base;
+  CharPtr suffix;
+  Boolean is_binary;
+  Boolean is_seqentry;
+} InputStreamData, PNTR InputStreamPtr;
+
+typedef struct asnstream {
+  AsnModulePtr amp;
+  AsnTypePtr   atp_se;
+  AsnTypePtr   atp_bss;
+  AsnTypePtr   atp_bss_se;
+} AsnStreamData, PNTR AsnStreamPtr;
+
+static FILE* OpenOneFile (
+  CharPtr directory,
+  CharPtr base,
+  CharPtr suffix
+)
+
+{
+  Char  file [FILENAME_MAX], path [PATH_MAX];
+
+  if (base == NULL) {
+    base = "";
+  }
+  if (suffix == NULL) {
+    suffix = "";
+  }
+
+  StringNCpy_0 (path, directory, sizeof (path));
+  sprintf (file, "%s%s", base, suffix);
+  FileBuildPath (path, NULL, file);
+
+  return FileOpen (path, "r");
+}
+
+static AsnIoPtr AsnIoFromInputStream (
+  InputStreamPtr isp
+)
+
+{
+  AsnIoPtr aip;
+  Char     file [FILENAME_MAX], path [PATH_MAX];
+  CharPtr  read_flag;
+
+  if (isp == NULL) return NULL;
+
+  if (isp->is_binary) {
+    read_flag = "rb";
+  } else {
+    read_flag = "r";
+  }
+
+  if (isp->base == NULL) {
+    aip = AsnIoOpen ("stdin", read_flag);
+  } else {
+    StringNCpy_0 (path, isp->directory, sizeof (path));
+    sprintf (file, "%s%s", isp->base, isp->suffix);
+    FileBuildPath (path, NULL, file);
+    aip = AsnIoOpen (path, read_flag);
+  }
+  return aip;
+}
+
+
+static AsnIoPtr AsnIoFromOutputStream (OutputStreamPtr osp)
+{
+  AsnIoPtr   aip;
+  Char       file [FILENAME_MAX], path [PATH_MAX];
+  CharPtr    write_flag;
+
+  if (osp == NULL) return NULL;
+  if (osp->aip == NULL) {
+    write_flag = osp->is_binary ? "wb" : "w";
+    if (StringDoesHaveText (osp->outfile)) {
+      StringNCpy_0 (path, osp->outfile, sizeof (path));
+    } else {
+      if (osp->base == NULL) {
+        aip = AsnIoOpen ("stdout", write_flag);
+      } else {
+        if (osp->outsuffix == NULL) {
+          osp->outsuffix = "";
+        }
+        StringNCpy_0 (path, osp->results_dir, sizeof (path));
+        sprintf (file, "%s%s%s", osp->base, osp->suffix, osp->outsuffix);
+        FileBuildPath (path, NULL, file);
+        aip = AsnIoOpen (path, write_flag);
+        if (aip == NULL) {
+          Message (MSG_POSTERR, "Unable to write to %s.", path);
+        }
+      }
+    }
+  } else {
+    aip = osp->aip;
+  }
+  return aip;
+}
+
+static void WriteOneFile (
+  OutputStreamPtr osp,
+  SeqEntryPtr sep
+)
+
+{
+  AsnIoPtr   aip;
+
+  aip = AsnIoFromOutputStream (osp);
+  if (aip != NULL) {
+    SeqEntryAsnWrite (sep, aip, NULL);
+    AsnIoFlush (aip);
+  }
+  if (aip != osp->aip) {
+    AsnIoClose (aip);
+  }
+}
+
+
+static Uint2 ProcessOneAsn (
+  FILE* fp,
+  CharPtr path,
+  ValNodePtr macro
+)
+
+{
+  Pointer        dataptr;
+  Uint2          datatype, entityID = 0;
+  SeqEntryPtr    sep;
+  Int4           num_fields = 0, num_features = 0;
+
+  if (fp == NULL) return 0;
+
+  dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, TRUE, FALSE, TRUE, FALSE);
+  if (dataptr == NULL) {
+    Message (MSG_POSTERR, "Unable to read data from %s.", path);
+    return 0;
+  }
+
+  SeqMgrIndexFeatures (entityID, NULL);
+  sep = GetTopSeqEntryForEntityID (entityID);
+  ApplyMacroToSeqEntry (sep, macro, &num_fields, &num_features);
+  Message (MSG_POST, "For file %s, macro script affected %d fields and created %d features", path, num_fields, num_features);
+
+  return entityID;
+}
+
+/* return -1 if failure, 0 if success */
+static Int4 ProcessOneRecord (
+  CharPtr directory,
+  OutputStreamPtr osp,
+  ValNodePtr macro
+)
+
+{
+  Uint2              entityID;
+  FILE               *fp;
+  SeqEntryPtr        sep;
+
+  if (osp == NULL) return -1;
+  fp = OpenOneFile (directory, osp->base, osp->suffix);
+  if (fp == NULL) return -1;
+
+  entityID = ProcessOneAsn (fp, osp->base == NULL ? "input stream" : osp->base, macro);
+  
+  FileClose (fp);
+
+  if (entityID == 0) return -1;
+
+  /* finish processing */
+
+  sep = GetTopSeqEntryForEntityID (entityID);
+  if (sep != NULL) {
+    WriteOneFile (osp, sep);
+  }
+
+  ObjMgrFreeByEntityID (entityID);
+  return 0;
+}
+
+static Int4 ProcessStream (InputStreamPtr isp, OutputStreamPtr osp, AsnStreamPtr asp, ValNodePtr macro)
+{
+  AsnTypePtr   atp, atp_srch;
+  AsnIoPtr asn_in, asn_out;
+  Int4         rval = 0;
+  SeqEntryPtr  sep;
+  Uint2        entityID;
+  DataVal av;
+  Int4         num_fields = 0, num_features = 0;
+  Int4         tmp_fields, tmp_features;
+  
+  if (isp == NULL || osp == NULL || asp == NULL) return 1;
+
+  asn_in = AsnIoFromInputStream (isp);
+  asn_out = AsnIoFromOutputStream (osp);
+
+  if (isp->is_seqentry) {
+    atp = asp->atp_se;
+    atp_srch = asp->atp_se;
+  }
+  else {
+    atp = asp->atp_bss;
+    atp_srch = asp->atp_bss_se;
+  }
+
+  while ((atp = AsnReadId(asn_in, asp->amp, atp)) != NULL && rval == 0) {
+    if (atp != atp_srch) {
+      AsnReadVal(asn_in, atp, &av);
+      AsnWrite(asn_out, atp, &av);
+      AsnKillValue(atp, &av);
+      continue;
+    }
+    if ((sep = SeqEntryAsnRead(asn_in, atp)) == NULL) {
+      Message (MSG_POSTERR, "SeqEntryAsnRead failure");
+      rval = 1;
+    }
+    if (rval == 0) {
+      entityID = ObjMgrRegister (OBJ_SEQENTRY, sep);
+      tmp_fields = 0;
+      tmp_features = 0;
+      ApplyMacroToSeqEntry (sep, macro, &tmp_fields, &tmp_features);
+      num_fields += tmp_fields;
+      num_features += tmp_features;
+      DeleteMarkedObjects (entityID, 0, NULL);
+      RenormalizeNucProtSets (sep, TRUE);
+      if (! SeqEntryAsnWrite(sep, asn_out, atp)) {
+       Message (MSG_POSTERR, "SeqEntryAsnWrite failure");
+       rval = 1;
+      }
+      AsnIoFlush(asn_out);
+      ObjMgrFreeByEntityID (entityID);
+    }
+  }                             /* Endwhile, AsnReadId */
+
+  AsnIoClose(asn_in);
+  if (asn_out != osp->aip) {
+    AsnIoClose(asn_out);
+  }
+  Message (MSG_POST, "Macro script affected %d fields and created %d features", num_fields, num_features);
+  return rval;
+}
+
+/* return -1 on failure, 0 on success */
+static Int4 FileRecurse (
+  CharPtr         directory,
+  InputStreamPtr  isp,
+  OutputStreamPtr osp,
+  AsnStreamPtr    asp,
+  ValNodePtr      macro
+)
+
+{
+  Char        path [PATH_MAX];
+  CharPtr     ptr;
+  CharPtr     str;
+  ValNodePtr  head, vnp;
+  CharPtr     orig_dir, orig_base;
+  Int4        rval = 0;
+
+  /* get list of all files in source directory */
+
+  head = DirCatalog (directory);
+
+  for (vnp = head; vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == 0) {
+      str = (CharPtr) vnp->data.ptrvalue;
+      if (StringDoesHaveText (str)) {
+
+        /* does filename have desired substring? */
+
+        ptr = StringStr (str, osp->suffix);
+
+        if (ptr != NULL) {
+
+          /* make sure detected suffix is really at end of filename */
+
+          if (StringCmp (ptr, osp->suffix) == 0) {
+            *ptr = '\0';
+
+            /* process file that has desired suffix (usually .fsa) */
+            osp->base = str;
+            orig_dir = isp->directory;
+            isp->directory = directory;
+            orig_base = isp->base;
+            isp->base = str;
+            if (isp->is_binary) {
+              rval |= ProcessStream (isp, osp, asp, macro);
+            } else {
+              rval |= ProcessOneRecord (directory, osp, macro);
+            }
+            isp->directory = orig_dir;
+            isp->base = orig_base;
+            osp->base = NULL;
+          }
+        }
+      }
+    } else if (vnp->choice == 1) {
+
+      /* recurse into subdirectory */
+
+      StringNCpy_0 (path, directory, sizeof (path));
+      str = (CharPtr) vnp->data.ptrvalue;
+      FileBuildPath (path, str, NULL);
+      rval |= FileRecurse (path, isp, osp, asp, macro);
+    }
+  }
+
+  /* clean up file list */
+
+  ValNodeFreeData (head);
+  return rval;
+}
+
+static Boolean SetUpAsnStreamData (AsnStreamPtr asp)
+
+{
+  if (asp == NULL) return FALSE;
+
+  if (! SeqSetAsnLoad()) {
+    Message (MSG_POSTERR, "Unable to load SeqSet parse tree");
+    return FALSE;
+  }
+  asp->amp = AsnAllModPtr();
+  if (asp->amp == NULL) {
+    Message (MSG_POSTERR, "Unable to obtain ASN.1 module pointer");
+    return FALSE;
+  }
+
+  /* Get pointers to ASN.1 types that must be dealt with in asn_in */
+
+  if ( (asp->atp_bss = AsnFind("Bioseq-set")) == NULL) {
+    Message (MSG_POSTERR, "could not find type Bioseq-set");
+    return FALSE;
+  }
+  if ( (asp->atp_bss_se = AsnFind("Bioseq-set.seq-set.E")) == NULL) {
+    Message (MSG_POSTERR, "AsnFind failure: Bioseq-set.seq-set.E");
+    return FALSE;
+  }
+  if ( (asp->atp_se = AsnFind("Seq-entry")) == NULL) {
+    Message (MSG_POSTERR, "AsnFind failure: Seq-entry");
+    return FALSE;
+  }
+  return TRUE;
+}
+
+
+static ValNodePtr ReadMacroFile (CharPtr macro_file)
+{
+
+  AsnIoPtr       aip;
+  ValNodePtr     action_list;
+
+  aip = AsnIoOpen (macro_file, "r");
+  if (aip == NULL) {
+    Message (MSG_POSTERR, "Unable to open %s", macro_file);
+    return NULL;
+  }
+  action_list = MacroActionListAsnRead (aip, NULL);
+  if (action_list == NULL) {
+    Message (MSG_POSTERR, "Unable to read action list from %s.", macro_file);
+  }
+  AsnIoClose (aip);
+  return action_list;
+}
+
+
+/* Args structure contains command-line arguments */
+
+#define p_argInputPath         0
+#define r_argOutputPath        1
+#define i_argInputFile         2
+#define o_argOutputFile        3
+#define x_argSuffix            4
+#define s_argOutSuffix         5
+#define b_argInputBinary       6
+#define e_argInputSeqEntry     7
+#define d_argOutputBinary      8
+#define m_argMacroFile         9
+
+Args myargs [] = {
+  {"Path to Files", NULL, NULL, NULL,
+    TRUE, 'p', ARG_STRING, 0.0, 0, NULL},
+  {"Path for Results", NULL, NULL, NULL,
+    TRUE, 'r', ARG_STRING, 0.0, 0, NULL},
+  {"Single Input File", NULL, NULL, NULL,
+    TRUE, 'i', ARG_FILE_IN, 0.0, 0, NULL},
+  {"Single Output File", NULL, NULL, NULL,
+    TRUE, 'o', ARG_FILE_OUT, 0.0, 0, NULL},
+  {"Suffix", ".sqn", NULL, NULL,
+    TRUE, 'x', ARG_STRING, 0.0, 0, NULL},
+  {"Suffix for stripped files", "", NULL, NULL,
+    TRUE, 's', ARG_STRING, 0.0, 0, NULL},
+  {"Input is binary", "F", NULL, NULL,
+    TRUE, 'b', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Input is Seq-entry", "F", NULL, NULL,
+    TRUE, 'e', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Output is binary", "F", NULL, NULL,
+    TRUE, 'b', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Macro file", "NULL", NULL, NULL,
+    TRUE, 'm', ARG_FILE_IN, 0.0, 0, NULL}
+};
+
+Int2 Main(void)
+{
+  Char             app [64];
+  CharPtr          directory;
+  CharPtr          ptr;
+  Char             sfx [32];
+  OutputStreamData osd;
+  InputStreamData  isd;
+  AsnStreamData    asd;
+  Int4             rval = 0;
+  CharPtr          macro_file;
+  ValNodePtr       action_list;
+
+  /* standard setup */
+
+  ErrSetFatalLevel (SEV_MAX);
+  ErrClearOptFlags (EO_SHOW_USERSTR);
+  UseLocalAsnloadDataAndErrMsg ();
+  ErrPathReset ();
+
+  /* finish resolving internal connections in ASN.1 parse tables */
+
+  if (! AllObjLoad ()) {
+    Message (MSG_FATAL, "AllObjLoad failed");
+    return 1;
+  }
+  if (! SubmitAsnLoad ()) {
+    Message (MSG_FATAL, "SubmitAsnLoad failed");
+    return 1;
+  }
+  if (! FeatDefSetLoad ()) {
+    Message (MSG_FATAL, "FeatDefSetLoad failed");
+    return 1;
+  }
+  if (! SeqCodeSetLoad ()) {
+    Message (MSG_FATAL, "SeqCodeSetLoad failed");
+    return 1;
+  }
+  if (! GeneticCodeTableLoad ()) {
+    Message (MSG_FATAL, "GeneticCodeTableLoad failed");
+    return 1;
+  }
+
+  SetUpAsnStreamData (&asd);
+
+  /* initialize OuputStreamData */
+  MemSet (&osd, 0, sizeof (osd));
+
+  /* initialize InputStreamData */
+  MemSet (&isd, 0, sizeof (isd));
+
+  /* process command line arguments */
+
+  sprintf (app, "asnmacro %s", ASNMACRO_APPLICATION);
+  if (! GetArgs (app, sizeof (myargs) / sizeof (Args), myargs)) {
+    return 0;
+  }
+
+  macro_file = (CharPtr) myargs [m_argMacroFile].strvalue;
+  action_list = ReadMacroFile (macro_file);
+
+  directory = (CharPtr) myargs [p_argInputPath].strvalue;
+  osd.results_dir = (CharPtr) myargs [r_argOutputPath].strvalue;
+  if (StringHasNoText (osd.results_dir)) {
+    osd.results_dir = NULL;
+  }
+  osd.suffix = (CharPtr) myargs [x_argSuffix].strvalue;
+  osd.outsuffix = (CharPtr) myargs [s_argOutSuffix].strvalue;
+  osd.base = (CharPtr) myargs [i_argInputFile].strvalue;
+  osd.outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
+  if (StringHasNoText (osd.outfile)) {
+    osd.outfile = NULL;
+  }
+  osd.is_binary = (Boolean) myargs [d_argOutputBinary].intvalue;
+
+  if (osd.base == "stdin") {
+    osd.base = NULL;
+  }
+
+  /* if we don't have an output directory or an output file, and the user hasn't provided an
+   * output suffix, add a default.
+   */
+  if (osd.results_dir == NULL && osd.outfile == NULL && StringHasNoText (osd.outsuffix)) {
+    osd.outsuffix = ".processed";
+  } 
+
+  isd.is_binary = (Boolean) myargs [b_argInputBinary].intvalue;
+  isd.is_seqentry = (Boolean) myargs [e_argInputSeqEntry].intvalue;
+  isd.directory = directory;
+  isd.base = osd.base;
+  isd.suffix = osd.suffix;
+
+  if (StringDoesHaveText (osd.outfile)) {
+    osd.aip = AsnIoOpen (osd.outfile, "w");
+    if (osd.aip == NULL) {
+      Message (MSG_FATAL, "Unable to open output file");
+      return 1;
+    }
+  } else {
+    if (StringHasNoText (osd.results_dir)) {
+      osd.results_dir = directory;
+    }
+    /* if we're putting the results in a separate directory, strip the directory name from the output base */
+    if (!StringHasNoText (osd.results_dir) && !StringHasNoText (osd.base)) {
+#ifdef OS_MSWIN
+      ptr = StringRChr (osd.base, '\\');
+#else
+      ptr = StringRChr (osd.base, '/');
+#endif
+      if (ptr != NULL) {
+        osd.base = ptr + 1;
+      }
+    }
+  }
+
+
+  if (StringHasNoText(directory) && StringHasNoText(osd.base)) {
+    rval = ProcessStream (&isd, &osd, &asd, action_list);
+  } else if (StringDoesHaveText (osd.base)) {
+    ptr = StringRChr (osd.base, '.');
+    sfx[0] = '\0';
+    if (ptr != NULL) {
+      StringNCpy_0 (sfx, ptr, sizeof (sfx));
+      *ptr = '\0';
+    }
+    osd.suffix = sfx;
+    isd.suffix = sfx;
+    if (isd.is_binary) {
+      rval = ProcessStream (&isd, &osd, &asd, action_list);
+    } else {
+      rval = ProcessOneRecord (directory, &osd, action_list);
+    }
+  } else {
+
+    rval = FileRecurse (directory, &isd, &osd, &asd, action_list);
+  }
+
+  if (osd.aip != NULL) {
+    AsnIoFlush (osd.aip);
+    AsnIoClose (osd.aip);
+  }
+  return rval;
+}
diff --git a/demo/asnval.c b/demo/asnval.c
index 41251a62..4a676193 100644
--- a/demo/asnval.c
+++ b/demo/asnval.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   11/3/04
 *
-* $Revision: 1.55 $
+* $Revision: 1.56 $
 *
 * File Description:
 *
@@ -60,7 +60,7 @@
 #include <accpubseq.h>
 #endif
 
-#define ASNVAL_APP_VER "4.7"
+#define ASNVAL_APP_VER "4.8"
 
 CharPtr ASNVAL_APPLICATION = ASNVAL_APP_VER;
 
diff --git a/demo/blast_driver.c b/demo/blast_driver.c
index 01950658..59ee9e63 100644
--- a/demo/blast_driver.c
+++ b/demo/blast_driver.c
@@ -1,4 +1,4 @@
-/* $Id: blast_driver.c,v 1.128 2007/05/04 15:37:10 papadopo Exp $
+/* $Id: blast_driver.c,v 1.129 2007/10/23 16:03:23 madden Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -32,10 +32,10 @@ Author: Ilya Dondoshansky
 Contents: Main function for running BLAST
 
 ******************************************************************************
- * $Revision: 1.128 $
+ * $Revision: 1.129 $
  * */
 
-static char const rcsid[] = "$Id: blast_driver.c,v 1.128 2007/05/04 15:37:10 papadopo Exp $";
+static char const rcsid[] = "$Id: blast_driver.c,v 1.129 2007/10/23 16:03:23 madden Exp $";
 
 #include <ncbi.h>
 #include <sqnutils.h>
@@ -315,11 +315,6 @@ s_FillOptions(SBlastOptions* options)
       word_options->window_size = 40;
    }
 
-   if (lookup_options->mb_template_length > 0) {
-      if (word_options->window_size > 0)
-          word_options->ungapped_extension = FALSE;
-   }
-
    BLAST_FillExtensionOptions(ext_options, program_number, greedy_extension, 
       myargs[ARG_XDROP].intvalue, myargs[ARG_XDROP_FINAL].intvalue);
 
diff --git a/demo/blastall.c b/demo/blastall.c
index 17b1bd6e..18f6dd4d 100644
--- a/demo/blastall.c
+++ b/demo/blastall.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: blastall.c,v 6.198 2007/05/07 13:29:11 kans Exp $";
+static char const rcsid[] = "$Id: blastall.c,v 6.201 2008/01/02 14:02:06 madden Exp $";
 
-/* $Id: blastall.c,v 6.198 2007/05/07 13:29:11 kans Exp $
+/* $Id: blastall.c,v 6.201 2008/01/02 14:02:06 madden Exp $
 **************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -28,6 +28,15 @@ static char const rcsid[] = "$Id: blastall.c,v 6.198 2007/05/07 13:29:11 kans Ex
 ************************************************************************** 
  * 
  * $Log: blastall.c,v $
+ * Revision 6.201  2008/01/02 14:02:06  madden
+ * Make composition-based score adjustments the default for blastp and tblastn
+ *
+ * Revision 6.200  2007/11/13 20:31:51  madden
+ * Enable ARG_BESTHITS arg (culling)
+ *
+ * Revision 6.199  2007/10/10 13:16:46  madden
+ * Fix composition-based command-lines for blastall_old (from Alejandro Schaffer)
+ *
  * Revision 6.198  2007/05/07 13:29:11  kans
  * added casts for Seq-data.gap (SeqDataPtr, SeqGapPtr, ByteStorePtr)
  *
@@ -1024,7 +1033,7 @@ static Args myargs[] = {
       "0", NULL, NULL, FALSE, 'W', ARG_INT, 0.0, 0, NULL},            /* ARG_WORDSIZE */
     { "Effective length of the database (use zero for the real size)", 
       "0", NULL, NULL, FALSE, 'z', ARG_FLOAT, 0.0, 0, NULL},          /* ARG_DBSIZE */
-    { "Number of best hits from a region to keep (off by default, if used a value of 100 is recommended)", 
+    { "Number of best hits from a region to keep. Off by default.\nIf used a value of 100 is recommended.  Very high values of -v or -b is also suggested", 
       "0", NULL, NULL, FALSE, 'K', ARG_INT, 0.0, 0, NULL},            /* ARG_BESTHITS */
     { "0 for multiple hit, 1 for single hit (does not apply to blastn)",
        "0",  NULL, NULL, FALSE, 'P', ARG_INT, 0.0, 0, NULL},           /* ARG_MULTIPLEHITS */
@@ -1085,14 +1094,14 @@ static Args myargs[] = {
       "F", NULL, NULL, TRUE, 'V', ARG_BOOLEAN, 0.0, 0, NULL},              /* ARG_FORCE_OLD */
 #endif  /* BLASTALL_TOOLS_ONLY */
 #endif
-    { "Use composition-based statistics for blastp or tblastn:\n"                /* ARG_COMP_BASED_STATS */
+    { "Use composition-based score adjustments for blastp or tblastn:\n"                /* ARG_COMP_BASED_STATS */
       "      As first character:\n"
       "      D or d: default (equivalent to T)\n"
       "      0 or F or f: no composition-based statistics\n"
-      "      1 or T or t: Composition-based statistics as in "
-      "NAR 29:2994-3005, 2001\n"
-      "      2: Composition-based score adjustment as in "
+      "      2 or T or t: Composition-based score adjustments as in "
       "Bioinformatics 21:902-911,\n"
+      "      1: Composition-based statistics as in "
+      "NAR 29:2994-3005, 2001\n"
       "          2005, conditioned on sequence properties\n"
       "      3: Composition-based score adjustment as in "
       "Bioinformatics 21:902-911,\n"
@@ -1250,7 +1259,7 @@ s_FillOptions(SBlastOptions* options)
       MAX(myargs[ARG_DESCRIPTIONS].intvalue, 
           myargs[ARG_ALIGNMENTS].intvalue),
           is_gapped, 
-      0,                /* culling limit */
+      myargs[ARG_BESTHITS].intvalue,  /* culling limit */
       0);               /* min diag separation */
  
    hit_options->longest_intron = MIN(myargs[ARG_INTRON].intvalue, MAX_INTRON_LENGTH);
@@ -1274,13 +1283,11 @@ s_FillOptions(SBlastOptions* options)
        case '0': case 'F': case 'f':
            ext_options->compositionBasedStats = eNoCompositionBasedStats;
            break;
-       case 'D': case 'd':
-       case '1': case 'T': case 't':
+       case '1':
            ext_options->compositionBasedStats = eCompositionBasedStats;
            break;
-       case '2':
-           ErrPostEx(SEV_WARNING, 1, 0, "the -C 2 argument "
-                     "is currently experimental\n");
+       case 'D': case 'd':
+       case '2': case 'T': case 't':
            ext_options->compositionBasedStats = eCompositionMatrixAdjust;
            break;
        case '3':
@@ -1976,10 +1983,10 @@ Int2 Main_old (void)
     } else {
         /* Set options specific to gapped tblastn and blastp */
         switch (myargs[ARG_COMP_BASED_STATS].strvalue[0]) {
-        case 'D': case 'd':
         case '0': case 'F': case 'f':
             options->tweak_parameters = eNoCompositionBasedStats;
             break;
+        case 'D': case 'd':
         case '1': case 'T': case 't':
             options->tweak_parameters = eCompositionBasedStats;
             break;
diff --git a/demo/blastclust.c b/demo/blastclust.c
index fa195867..159c0958 100644
--- a/demo/blastclust.c
+++ b/demo/blastclust.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: blastclust.c,v 6.48 2005/08/19 20:12:32 dondosha Exp $";
+static char const rcsid[] = "$Id: blastclust.c,v 6.49 2007/12/21 14:00:47 madden Exp $";
 
-/*  $RCSfile: blastclust.c,v $  $Revision: 6.48 $  $Date: 2005/08/19 20:12:32 $
+/*  $RCSfile: blastclust.c,v $  $Revision: 6.49 $  $Date: 2007/12/21 14:00:47 $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -33,6 +33,9 @@ static char const rcsid[] = "$Id: blastclust.c,v 6.48 2005/08/19 20:12:32 dondos
 *
 * ---------------------------------------------------------------------------
 * $Log: blastclust.c,v $
+* Revision 6.49  2007/12/21 14:00:47  madden
+* Exit if query cannot be processed, JIRA SB-32
+*
 * Revision 6.48  2005/08/19 20:12:32  dondosha
 * Added extensive doxygen-style comments
 *
@@ -1316,6 +1319,8 @@ Int2 Main (void)
              do_the_blast_run(search);
           } else if (search) {
              BlastErrorPrint(search->error_return);
+             ErrPostEx(SEV_ERROR, 1, 0, "Failed to process query number %ld", (long) index);
+             return 1;
           }
           search = BlastSearchBlkDestruct(search);
           query_bsp = BioseqFree(query_bsp);
diff --git a/demo/blastpgp.c b/demo/blastpgp.c
index d2bfc9b7..31ac2210 100644
--- a/demo/blastpgp.c
+++ b/demo/blastpgp.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: blastpgp.c,v 6.137 2007/03/14 17:55:27 madden Exp $";
+static char const rcsid[] = "$Id: blastpgp.c,v 6.139 2008/01/02 20:16:11 madden Exp $";
 
-/* $Id: blastpgp.c,v 6.137 2007/03/14 17:55:27 madden Exp $ */
+/* $Id: blastpgp.c,v 6.139 2008/01/02 20:16:11 madden Exp $ */
 /**************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -26,8 +26,14 @@ static char const rcsid[] = "$Id: blastpgp.c,v 6.137 2007/03/14 17:55:27 madden
 * appreciated.                                                            *
 *                                                                         *
 **************************************************************************
- * $Revision: 6.137 $ 
+ * $Revision: 6.139 $ 
  * $Log: blastpgp.c,v $
+ * Revision 6.139  2008/01/02 20:16:11  madden
+ * XML output respects -v and -b option, JIRA SB-30
+ *
+ * Revision 6.138  2008/01/02 14:02:06  madden
+ * Make composition-based score adjustments the default for blastp and tblastn
+ *
  * Revision 6.137  2007/03/14 17:55:27  madden
  *   - #include string.h to get a prototype for strcasecmp In
  *   - In tick_callback, suppress unused parameter warnings in tick_callback
@@ -712,17 +718,17 @@ static Args myargs[] = {
       NULL, NULL, NULL, TRUE, 'l', ARG_STRING, 0.0, 0, NULL},
     {"Use lower case filtering of FASTA sequence",                     /* ARG_LCASE */
      "F", NULL,NULL,TRUE,'U',ARG_BOOLEAN, 0.0,0,NULL},
-    { "Use composition based statistics\n"                             /* ARG_COMP_BASED_STATS */
+    { "Use composition based score adjustment\n"                             /* ARG_COMP_BASED_STATS */
       "As first character:\n"
       "0 or F or f: no composition-based statistics\n"
-      "1 or T or t: Composition-based statistics as in NAR  29:2994--3005, 2001\n"
-      "2: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties in round 1\n"
+      "2 or T or t: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties in round 1\n"
+      "1: Composition-based statistics as in NAR  29:2994--3005, 2001\n"
       "3: Composition-based score adjustment as in Bioinformatics 21:902-911, "
       "2005, unconditionally in round 1\n"
       "As second character, if first character is equivalent to 1, 2, or 3:\n"
       "U or u: unified p-value combining alignment p-value and "
       "compositional p-value in round 1 only\n",
-      "1", NULL, NULL, FALSE, 't', ARG_STRING, 0.0, 0, NULL},
+      "2", NULL, NULL, FALSE, 't', ARG_STRING, 0.0, 0, NULL},
     { "ASN.1 Scoremat input of checkpoint data:\n"
       "0: no scoremat input\n"
       "1: Restart is from ASCII scoremat checkpoint file,\n"
@@ -1126,14 +1132,12 @@ PGPBlastOptionsPtr PGPReadBlastOptions(void)
         break;
     case 'T':
     case 't':
-    case '1':
-        options->tweak_parameters = eCompositionBasedStats;
-        break;
     case '2':
-        ErrPostEx(SEV_WARNING, 1, 0, "the -t 2 argument "
-                  "is currently experimental\n");
         options->tweak_parameters = eCompositionMatrixAdjust;
         break;
+    case '1':
+        options->tweak_parameters = eCompositionBasedStats;
+        break;
     case '3':
         ErrPostEx(SEV_WARNING, 1, 0, "the -t 3 argument "
                   "is currently experimental\n");
@@ -1919,11 +1923,14 @@ Int2 Main (void)
                                !bop->options->gapped_calculation, thisPassNum,
                                "No hits found", search->mask);
                 } else {
-                    iterp = BXMLBuildOneIteration(head, other_returns,
+                    BlastPruneSapStructPtr prune =
+                        BlastPruneHitsFromSeqAlign(head, bop->number_of_alignments, NULL);
+                    iterp = BXMLBuildOneIteration(prune->sap, other_returns,
                                bop->options->is_ooframe,
                                !bop->options->gapped_calculation, thisPassNum,
                                (search->posConverged ? "CONVERGED" : NULL), 
                                search->mask);
+                    prune = BlastPruneSapStructDestruct(prune);
                 }
                 
                 IterationAsnWrite(iterp, psixp->aip, psixp->atp);
diff --git a/demo/cleanasn.c b/demo/cleanasn.c
index 0916a557..297ad432 100644
--- a/demo/cleanasn.c
+++ b/demo/cleanasn.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/19/99
 *
-* $Revision: 6.10 $
+* $Revision: 6.15 $
 *
 * File Description: 
 *
@@ -50,6 +50,7 @@
 #include <sequtil.h>
 #include <sqnutils.h>
 #include <explore.h>
+#include <tofasta.h>
 #include <toasn3.h>
 #include <pmfapi.h>
 #include <tax3api.h>
@@ -57,7 +58,7 @@
 #include <accpubseq.h>
 #endif
 
-#define CLEANASN_APP_VER "1.4"
+#define CLEANASN_APP_VER "1.6"
 
 CharPtr CLEANASN_APPLICATION = CLEANASN_APP_VER;
 
@@ -71,7 +72,9 @@ typedef struct cleanflags {
   CharPtr       clean;
   CharPtr       link;
   CharPtr       feat;
+  CharPtr       mods;
   Boolean       taxon;
+  Boolean       pub;
   AsnModulePtr  amp;
   AsnTypePtr    atp_bss;
   AsnTypePtr    atp_bsss;
@@ -204,7 +207,156 @@ static void RemoveUnnecGeneXref (
   }
 }
 
-static void DoCleeanup (
+static void AddSpTaxnameToList (SeqDescrPtr sdp, Pointer userdata)
+{
+  BioSourcePtr biop;
+
+  if (sdp == NULL || sdp->choice != Seq_descr_source || userdata == NULL) return;
+
+  biop = (BioSourcePtr) sdp->data.ptrvalue;
+  if (biop == NULL || biop->org == NULL || !IsSpName (biop->org->taxname)) return;
+
+  ValNodeAddPointer ((ValNodePtr PNTR) userdata, 0, biop->org->taxname);
+}
+
+
+static Boolean ShouldExcludeSp (SeqEntryPtr sep)
+{
+  ValNodePtr name_list = NULL, vnp1, vnp2;
+  Boolean    all_diff = TRUE;
+
+  if (sep == NULL) return TRUE;
+  VisitDescriptorsInSep (sep, &name_list, AddSpTaxnameToList);
+
+  name_list = ValNodeSort (name_list, SortVnpByString);
+
+  if (name_list != NULL && name_list->next != NULL) {
+    for (vnp1 = name_list; vnp1 != NULL && vnp1->next != NULL && all_diff; vnp1 = vnp1->next) {
+      for (vnp2 = vnp1->next; vnp2 != NULL && all_diff; vnp2 = vnp2->next) {
+        if (StringCmp (vnp1->data.ptrvalue, vnp2->data.ptrvalue) == 0) {
+          all_diff = FALSE;
+        }
+      }
+    }
+  }
+
+  name_list = ValNodeFree (name_list);
+
+  return all_diff;
+}
+
+static void DoAutoDef (
+  SeqEntryPtr sep,
+  Uint2 entityID
+)
+
+{
+  ValNodePtr                    defline_clauses = NULL;
+  DeflineFeatureRequestList     feature_requests;
+  Int4                          index;
+  ValNodePtr                    modifier_indices = NULL;
+  ModifierItemLocalPtr          modList;
+  OrganismDescriptionModifiers  odmp;
+  SeqEntryPtr                   oldscope;
+
+  if (sep == NULL) return;
+  if (entityID < 1) return;
+
+  modList = MemNew (NumDefLineModifiers () * sizeof (ModifierItemLocalData));
+  if (modList == NULL) return;
+
+  InitFeatureRequests (&feature_requests);
+
+  SetRequiredModifiers (modList);
+  CountModifiers (modList, sep);
+
+  odmp.use_labels = TRUE;
+  odmp.max_mods = -99;
+  odmp.keep_paren = TRUE;
+  odmp.exclude_sp = ShouldExcludeSp (sep);
+  odmp.exclude_cf = FALSE;
+  odmp.exclude_aff = FALSE;
+  odmp.exclude_nr = FALSE;
+  odmp.include_country_extra = FALSE;
+  odmp.clone_isolate_HIV_rule_num = clone_isolate_HIV_rule_want_both;
+  odmp.use_modifiers = FALSE;
+  odmp.allow_semicolon_in_modifier = FALSE;
+
+
+  RemoveNucProtSetTitles (sep);  
+  oldscope = SeqEntrySetScope (sep);
+
+  BuildDefLineFeatClauseList (sep, entityID, &feature_requests,
+                              DEFAULT_ORGANELLE_CLAUSE, FALSE, FALSE,
+                              &defline_clauses);
+  if (AreFeatureClausesUnique (defline_clauses)) {
+    modifier_indices = GetModifierIndicesFromModList (modList);
+  } else {
+    modifier_indices = FindBestModifiers (sep, modList);
+  }
+
+  BuildDefinitionLinesFromFeatureClauseLists (defline_clauses, modList,
+                                              modifier_indices, &odmp);
+  DefLineFeatClauseListFree (defline_clauses);
+  if (modList != NULL) {
+    for (index = 0; index < NumDefLineModifiers (); index++) {
+      ValNodeFree (modList [index].values_seen);
+    }
+    MemFree (modList);
+  }
+  modifier_indices = ValNodeFree (modifier_indices);
+
+  ClearProteinTitlesInNucProts (entityID, NULL);
+  InstantiateProteinTitles (entityID, NULL);
+
+  SeqEntrySetScope (oldscope);
+}
+
+static void LookupPubdesc (
+  PubdescPtr pdp,
+  Pointer userdata
+)
+
+{
+  CitArtPtr        cap;
+  MedlineEntryPtr  mep;
+  PubmedEntryPtr   pep;
+  Int4             pmid = 0;
+  ValNodePtr       vnp;
+
+  if (pdp == NULL) return;
+
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    switch (vnp->choice) {
+      case PUB_Muid :
+        /* ignore obsolete muids */
+        break;
+      case PUB_PMid :
+        pmid = vnp->data.intvalue;
+        break;
+      default :
+        /* return on real pub */
+        return;
+        break;
+    }
+  }
+
+  if (pmid == 0) return;
+
+  pep = GetPubMedForUid (pmid);
+  if (pep == NULL) return;
+  mep = (MedlineEntryPtr) pep->medent;
+  if (mep != NULL && mep->cit != NULL) {
+    cap = AsnIoMemCopy ((Pointer) mep->cit,
+                        (AsnReadFunc) CitArtAsnRead,
+                        (AsnWriteFunc) CitArtAsnWrite);
+    ValNodeAddPointer (&(pdp->pub), PUB_Article, (Pointer) cap);
+  }
+
+  PubmedEntryFree (pep);
+}
+
+static void DoCleanup (
   SeqEntryPtr sep,
   Uint2 entityID,
   CleanFlagPtr cfp
@@ -214,41 +366,50 @@ static void DoCleeanup (
   if (sep == NULL || cfp == NULL) return;
 
   if (StringChr (cfp->clean, 'b') != NULL) {
-	BasicSeqEntryCleanup (sep);
+    BasicSeqEntryCleanup (sep);
   }
   if (StringChr (cfp->clean, 's') != NULL) {
-	SeriousSeqEntryCleanup (sep, NULL, NULL);
+    SeriousSeqEntryCleanup (sep, NULL, NULL);
   }
 
   if (cfp->taxon) {
-	Taxon3ReplaceOrgInSeqEntry (sep, FALSE);
+    Taxon3ReplaceOrgInSeqEntry (sep, FALSE);
+  }
+
+  if (cfp->pub) {
+    VisitPubdescsInSep (sep, NULL, LookupPubdesc);
   }
 
   if (StringChr (cfp->link, 'o') != NULL) {
-	SeqMgrIndexFeatures (entityID, 0);
-	LinkCDSmRNAbyOverlap (sep);
+    SeqMgrIndexFeatures (entityID, 0);
+    LinkCDSmRNAbyOverlap (sep);
   }
   if (StringChr (cfp->link, 'p') != NULL) {
-	SeqMgrIndexFeatures (entityID, 0);
-	LinkCDSmRNAbyProduct (sep);
+    SeqMgrIndexFeatures (entityID, 0);
+    LinkCDSmRNAbyProduct (sep);
   }
   if (StringChr (cfp->link, 'r') != NULL) {
-	SeqMgrIndexFeatures (entityID, 0);
-	ReassignFeatureIDs (sep);
+    SeqMgrIndexFeatures (entityID, 0);
+    ReassignFeatureIDs (sep);
   }
   if (StringChr (cfp->link, 'c') != NULL) {
-	ClearFeatureIDs (sep);
+    ClearFeatureIDs (sep);
   }
 
   if (StringChr (cfp->feat, 'u') != NULL) {
-	VisitFeaturesInSep (sep, NULL, RemoveFeatUser);
+    VisitFeaturesInSep (sep, NULL, RemoveFeatUser);
   }
   if (StringChr (cfp->feat, 'd') != NULL) {
-	VisitFeaturesInSep (sep, NULL, RemoveFeatDbxref);
+    VisitFeaturesInSep (sep, NULL, RemoveFeatDbxref);
   }
   if (StringChr (cfp->feat, 'r') != NULL) {
-	SeqMgrIndexFeatures (entityID, 0);
-	VisitFeaturesInSep (sep, NULL, RemoveUnnecGeneXref);
+    SeqMgrIndexFeatures (entityID, 0);
+    VisitFeaturesInSep (sep, NULL, RemoveUnnecGeneXref);
+  }
+
+  if (StringChr (cfp->mods, 'd') != NULL) {
+    SeqMgrIndexFeatures (entityID, 0);
+    DoAutoDef (sep, entityID);
   }
 }
 
@@ -373,7 +534,7 @@ static void CleanupSingleRecord (
       sep = GetTopSeqEntryForEntityID (entityID);
       if (sep != NULL && StringDoesHaveText (path)) {
 
-        DoCleeanup (sep, entityID, cfp);
+        DoCleanup (sep, entityID, cfp);
 
         aop = AsnIoOpen (path, "w");
         if (aop != NULL) {
@@ -407,7 +568,6 @@ static void CleanupMultipleRecord (
   DataVal      av;
   BioseqPtr    bsp;
   Char         buf [41];
-  Char         cmmd [256];
   Uint2        entityID;
   FILE         *fp;
   SeqEntryPtr  fsep;
@@ -419,6 +579,7 @@ static void CleanupMultipleRecord (
   SeqEntryPtr  sep;
   time_t       starttime, stoptime, worsttime;
 #ifdef OS_UNIX
+  Char         cmmd [256];
   CharPtr      gzcatprog;
   int          ret;
   Boolean      usedPopen = FALSE;
@@ -541,7 +702,7 @@ static void CleanupMultipleRecord (
           }
 
           starttime = GetSecs ();
-          DoCleeanup (sep, entityID, cfp);
+          DoCleanup (sep, entityID, cfp);
           stoptime = GetSecs ();
 
           if (stoptime - starttime > worsttime) {
@@ -615,12 +776,14 @@ static void CleanupOneRecord (
 #define a_argType          6
 #define b_argBinary        7
 #define c_argCompressed    8
-#define l_argLogFile       9
+#define L_argLogFile       9
 #define R_argRemote       10
 #define K_argClean        11
 #define N_argLink         12
 #define F_argFeat         13
-#define T_argTaxonLookup  14
+#define M_argMods         14
+#define T_argTaxonLookup  15
+#define P_argPubLookup    16
 
 Args myargs [] = {
   {"Path to Files", NULL, NULL, NULL,
@@ -647,8 +810,8 @@ Args myargs [] = {
     TRUE, 'b', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Bioseq-set is Compressed", "F", NULL, NULL,
     TRUE, 'c', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Log fFile", NULL, NULL, NULL,
-    TRUE, 'l', ARG_FILE_OUT, 0.0, 0, NULL},
+  {"Log File", NULL, NULL, NULL,
+    TRUE, 'L', ARG_FILE_OUT, 0.0, 0, NULL},
   {"Remote Fetching from ID", "F", NULL, NULL,
     TRUE, 'R', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Cleanup\n"
@@ -666,8 +829,13 @@ Args myargs [] = {
    "      d Remove db_xref\n"
    "      r Remove Redundant Gene xref", NULL, NULL, NULL,
     TRUE, 'F', ARG_STRING, 0.0, 0, NULL},
+  {"Miscellaneous\n"
+   "      d Automatic Definition Line", NULL, NULL, NULL,
+    TRUE, 'M', ARG_STRING, 0.0, 0, NULL},
   {"Taxonomy Lookup", "F", NULL, NULL,
     TRUE, 'T', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Publication Lookup", "F", NULL, NULL,
+    TRUE, 'P', ARG_BOOLEAN, 0.0, 0, NULL},
 };
 
 Int2 Main (void)
@@ -772,7 +940,9 @@ Int2 Main (void)
   cfd.clean = myargs [K_argClean].strvalue;
   cfd.link = myargs [N_argLink].strvalue;
   cfd.feat = myargs [F_argFeat].strvalue;
+  cfd.mods = myargs [M_argMods].strvalue;
   cfd.taxon = (Boolean) myargs [T_argTaxonLookup].intvalue;
+  cfd.pub = (Boolean) myargs [P_argPubLookup].intvalue;
 
   cfd.amp = AsnAllModPtr ();
   cfd.atp_bss = AsnFind ("Bioseq-set");
@@ -781,7 +951,7 @@ Int2 Main (void)
   cfd.atp_bsc = AsnFind ("Bioseq-set.class");
   cfd.bssp_atp = AsnLinkType (NULL, cfd.atp_bss);
 
-  logfile = (CharPtr) myargs [l_argLogFile].strvalue;
+  logfile = (CharPtr) myargs [L_argLogFile].strvalue;
   if (StringDoesHaveText (logfile)) {
     cfd.logfp = FileOpen (logfile, "w");
   }
@@ -797,6 +967,10 @@ Int2 Main (void)
 #endif
   }
 
+  if (remote || cfd.pub) {
+    PubMedFetchEnable ();
+  }
+
   starttime = GetSecs ();
 
   if (StringDoesHaveText (directory)) {
@@ -819,6 +993,10 @@ Int2 Main (void)
     FileClose (cfd.logfp);
   }
 
+  if (remote || cfd.pub) {
+    PubMedFetchDisable ();
+  }
+
   if (remote) {
 #ifdef INTERNAL_NCBI_CLEANASN
     PUBSEQBioseqFetchDisable ();
diff --git a/demo/copymat.c b/demo/copymat.c
index 71ad592b..cc09a1f7 100644
--- a/demo/copymat.c
+++ b/demo/copymat.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: copymat.c,v 6.47 2006/11/24 19:06:15 kans Exp $";
+static char const rcsid[] = "$Id: copymat.c,v 6.48 2008/02/01 14:04:25 madden Exp $";
 
 /*
 * ===========================================================================
@@ -36,6 +36,9 @@ Contents: main routines for copymatrices program to convert
 score matrices output by makematrices into a single byte-encoded file.
    
 $Log: copymat.c,v $
+Revision 6.48  2008/02/01 14:04:25  madden
+LookupTableWrapInit prototype change
+
 Revision 6.47  2006/11/24 19:06:15  kans
 added include of blast_filter.h
 
@@ -637,7 +640,7 @@ Boolean RPSCreateLookupFile(ScoreRow *combinedMatrix, Int4 numProfiles,
     BlastSeqLocNew(&lookup_segment, 0, all_length);
 
     /* Need query for psi-blast??  where to put the PSSM? */
-    LookupTableWrapInit(NULL, lookup_options, lookup_segment, sbp, &lookup_wrap_ptr, NULL, NULL);
+    LookupTableWrapInit(NULL, lookup_options, NULL, lookup_segment, sbp, &lookup_wrap_ptr, NULL, NULL);
    
     RPSPsiMatrixDetach(sbp);
     sbp = BlastScoreBlkFree(sbp);
diff --git a/demo/cspeedtest.c b/demo/cspeedtest.c
new file mode 100644
index 00000000..6157d0c3
--- /dev/null
+++ b/demo/cspeedtest.c
@@ -0,0 +1,1099 @@
+/*   cspeedtest.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  cspeedtest.c
+*
+* Author:  Jonathan Kans
+*
+* Version Creation Date:   12/17/07
+*
+* $Revision: 1.10 $
+*
+* File Description: 
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* Date     Name        Description of modification
+* -------  ----------  -----------------------------------------------------
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <objall.h>
+#include <objsset.h>
+#include <objfdef.h>
+#include <objsub.h>
+#include <sequtil.h>
+#include <sqnutils.h>
+#include <explore.h>
+#include <toasn3.h>
+#include <pmfapi.h>
+#include <tofasta.h>
+#include <asn2gnbk.h>
+#include <valid.h>
+
+#define CSPEEDTEST_APP_VER "1.3"
+
+CharPtr CSPEEDTEST_APPLICATION = CSPEEDTEST_APP_VER;
+
+typedef struct cspeedflags {
+  Boolean       batch;
+  Boolean       binary;
+  Boolean       compressed;
+  Boolean       lock;
+  Int2          type;
+  Int4          maxcount;
+  CharPtr       io;
+  CharPtr       clean;
+  CharPtr       index;
+  CharPtr       seq;
+  CharPtr       feat;
+  CharPtr       desc;
+  CharPtr       verify;
+  AsnModulePtr  amp;
+  AsnTypePtr    atp_bss;
+  AsnTypePtr    atp_bsss;
+  AsnTypePtr    atp_se;
+  AsnTypePtr    atp_bsc;
+  AsnTypePtr    bssp_atp;
+  BioseqSet     bss;
+  FILE          *ofp;
+  FILE          *logfp;
+} CSpeedFlagData, PNTR CSpeedFlagPtr;
+
+static void DoVisitFeaturesTest (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  /* empty visit callback */
+}
+
+static void DoGeneOverlapPrintTest (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  CSpeedFlagPtr      cfp;
+  SeqMgrFeatContext  gcontext;
+  SeqFeatPtr         gene;
+  CharPtr            str1, str2;
+
+  if (sfp == NULL) return;
+  cfp = (CSpeedFlagPtr) userdata;
+  if (cfp == NULL || cfp->ofp == NULL) return;
+
+  if (sfp->data.choice == SEQFEAT_GENE) return;
+  gene = SeqMgrGetOverlappingGene (sfp->location, &gcontext);
+  if (gene == NULL) return;
+
+  str1 = SeqLocPrint (sfp->location);
+  str2 = SeqLocPrint (gene->location);
+  if (str1 != NULL && str2 != NULL) {
+    fprintf (cfp->ofp, "[%s] -> [%s]\n", str1, str2);
+  } else {
+    fprintf (cfp->ofp, "? -> ?\n");
+  }
+  MemFree (str1);
+  MemFree (str2);
+}
+
+static void DoGeneOverlapSpeedTest (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  CSpeedFlagPtr      cfp;
+  SeqMgrFeatContext  gcontext;
+  SeqFeatPtr         gene;
+
+  if (sfp == NULL) return;
+  cfp = (CSpeedFlagPtr) userdata;
+  if (cfp == NULL || cfp->ofp == NULL) return;
+
+  if (sfp->data.choice == SEQFEAT_GENE) return;
+  gene = SeqMgrGetOverlappingGene (sfp->location, &gcontext);
+  if (gene == NULL) return;
+}
+
+static void LIBCALLBACK EmptyStreamProc (
+  CharPtr sequence,
+  Pointer userdata
+)
+
+{
+  /* empty stream callback */
+}
+
+static void DoFastaSeq (
+  BioseqPtr bsp,
+  Pointer userdata
+)
+
+{
+  CSpeedFlagPtr  cfp;
+
+  if (bsp == NULL) return;
+  cfp = (CSpeedFlagPtr) userdata;
+  if (cfp == NULL) return;
+
+  if (cfp->ofp != NULL) {
+    BioseqFastaStream (bsp, cfp->ofp, STREAM_EXPAND_GAPS, 70, 0, 0, TRUE);
+  } else {
+    SeqPortStream (bsp, STREAM_EXPAND_GAPS, NULL, EmptyStreamProc);
+  }
+}
+
+static void DoFastaRaw (
+  BioseqPtr bsp,
+  Pointer userdata
+)
+
+{
+  CSpeedFlagPtr  cfp;
+
+  if (bsp == NULL) return;
+  cfp = (CSpeedFlagPtr) userdata;
+  if (cfp == NULL) return;
+
+  if (cfp->ofp != NULL) {
+    fprintf (cfp->ofp, ">\n");
+    BioseqFastaStream (bsp, cfp->ofp, STREAM_EXPAND_GAPS, 70, 0, 0, FALSE);
+  } else {
+    SeqPortStream (bsp, STREAM_EXPAND_GAPS, NULL, EmptyStreamProc);
+  }
+}
+
+static void DoFastaDefline (
+  BioseqPtr bsp,
+  Pointer userdata
+)
+
+{
+  Char           buf [4096];
+  CSpeedFlagPtr  cfp;
+  Char           id [128];
+
+  if (bsp == NULL) return;
+  cfp = (CSpeedFlagPtr) userdata;
+  if (cfp == NULL) return;
+
+  id [0] = '\0';
+  SeqIdWrite (bsp->id, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
+  buf [0] = '\0';
+  CreateDefLine (NULL, bsp, buf, sizeof (buf) - 1, 0, NULL, NULL);
+
+  if (cfp->ofp != NULL) {
+    fprintf (cfp->ofp, ">%s %s\n", id, buf);
+  }
+}
+
+static void DoFastaFeat (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  CSpeedFlagPtr  cfp;
+  CharPtr        str;
+
+  if (sfp == NULL) return;
+  cfp = (CSpeedFlagPtr) userdata;
+  if (cfp == NULL) return;
+
+  if (cfp->ofp != NULL) {
+    str = SeqLocPrint (sfp->location);
+    if (str != NULL) {
+      fprintf (cfp->ofp, "> [%s]\n", str);
+      MemFree (str);
+    }
+    SeqLocFastaStream (sfp->location, cfp->ofp, STREAM_EXPAND_GAPS, 70, 0, 0);
+  } else {
+    SeqPortStreamLoc (sfp->location, STREAM_EXPAND_GAPS, NULL, EmptyStreamProc);
+  }
+}
+
+static void DoFastaTrans (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  ByteStorePtr   bs;
+  CSpeedFlagPtr  cfp;
+  CharPtr        seq, str;
+
+  if (sfp == NULL) return;
+  cfp = (CSpeedFlagPtr) userdata;
+  if (cfp == NULL) return;
+
+  if (sfp->data.choice != SEQFEAT_CDREGION) return;
+  bs = ProteinFromCdRegion (sfp, FALSE);
+  if (bs == NULL) return;
+
+  seq = (CharPtr) BSMerge (bs, NULL);
+  BSFree (bs);
+  if (seq == NULL) return;
+
+  if (cfp->ofp != NULL) {
+    str = SeqLocPrint (sfp->location);
+    if (str != NULL) {
+      fprintf (cfp->ofp, "> (%s)\n", str);
+      MemFree (str);
+    }
+    fprintf (cfp->ofp, "%s\n", seq);
+  }
+
+  MemFree (seq);
+}
+
+static CharPtr compatSeverityLabel [] = {
+  "NONE", "NOTE: valid", "WARNING: valid", "ERROR: valid", "REJECT: valid", "FATAL: valid", "MAX", NULL
+};
+
+static void LIBCALLBACK ValidCallback (
+  ErrSev severity,
+  int errcode,
+  int subcode,
+  Uint2 entityID,
+  Uint2 itemtype,
+  Uint4 itemID,
+  CharPtr accession,
+  CharPtr message,
+  CharPtr objtype,
+  CharPtr label,
+  CharPtr context,
+  CharPtr location,
+  CharPtr product,
+  Pointer userdata
+)
+
+{
+  CharPtr  catname, errname;
+  FILE     *fp;
+
+  fp = (FILE *) userdata;
+  if (fp == NULL) return;
+
+  if (severity < SEV_NONE || severity > SEV_MAX) {
+    severity = SEV_MAX;
+  }
+
+  catname = GetValidCategoryName (errcode);
+  errname = GetValidErrorName (errcode, subcode);
+
+  if (catname == NULL) {
+    catname = "?";
+  }
+  if (errname == NULL) {
+    errname = "?";
+  }
+
+  if (accession == NULL) {
+    accession = "";
+  }
+  if (message == NULL) {
+    message = "";
+  }
+  if (objtype == NULL) {
+    objtype = "";
+  }
+  if (label == NULL) {
+    label = "";
+  }
+
+  fprintf (fp, "%s [%s.%s] %s %s: %s",
+           compatSeverityLabel [severity],
+           catname, errname, message, objtype, label);
+  if (location != NULL) {
+    fprintf (fp, " %s", location);
+  }
+  if (context != NULL) {
+    fprintf (fp, " %s", context);
+  }
+  if (product != NULL) {
+    fprintf (fp, " -> %s", product);
+  }
+  fprintf (fp, "\n");
+}
+
+static void DoProcess (
+  SeqEntryPtr sep,
+  Uint2 entityID,
+  CSpeedFlagPtr cfp
+)
+
+{
+  ErrSev          oldErrSev;
+  ValidStructPtr  vsp;
+
+  if (sep == NULL || cfp == NULL) return;
+
+  if (StringChr (cfp->clean, 'b') != NULL) {
+    BasicSeqEntryCleanup (sep);
+  }
+  if (StringChr (cfp->clean, 's') != NULL) {
+    SeriousSeqEntryCleanup (sep, NULL, NULL);
+  }
+
+  if (StringChr (cfp->index, 'f') != NULL) {
+    SeqMgrIndexFeatures (entityID, 0);
+  }
+
+  if (StringChr (cfp->seq, 's') != NULL) {
+    VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaSeq);
+  }
+  if (StringChr (cfp->seq, 'r') != NULL) {
+    VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaRaw);
+  }
+  if (StringChr (cfp->seq, 'd') != NULL) {
+    VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaDefline);
+  }
+  if (StringChr (cfp->seq, 'f') != NULL) {
+    VisitFeaturesInSep (sep, (Pointer) cfp, DoFastaFeat);
+  }
+  if (StringChr (cfp->seq, 't') != NULL) {
+    VisitFeaturesInSep (sep, (Pointer) cfp, DoFastaTrans);
+  }
+
+  if (StringChr (cfp->feat, 'v') != NULL) {
+    VisitFeaturesInSep (sep, NULL, DoVisitFeaturesTest);
+  }
+  if (StringChr (cfp->feat, 'g') != NULL) {
+    if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
+      SeqMgrIndexFeatures (entityID, 0);
+    }
+    VisitFeaturesInSep (sep, (Pointer) cfp, DoGeneOverlapPrintTest);
+  }
+  if (StringChr (cfp->feat, 'h') != NULL) {
+    if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
+      SeqMgrIndexFeatures (entityID, 0);
+    }
+    VisitFeaturesInSep (sep, (Pointer) cfp, DoGeneOverlapSpeedTest);
+  }
+  if (StringChr (cfp->feat, 'x') != NULL) {
+  }
+  if (StringChr (cfp->feat, 'o') != NULL) {
+  }
+  if (StringChr (cfp->feat, 'd') != NULL) {
+  }
+  if (StringChr (cfp->feat, 't') != NULL) {
+    SeqEntryToGnbk (sep, NULL, FTABLE_FMT, SEQUIN_MODE, NORMAL_STYLE,
+                    0, 0, SHOW_PROT_FTABLE, NULL, cfp->ofp);
+  }
+
+  if (StringChr (cfp->desc, 'b') != NULL) {
+  }
+  if (StringChr (cfp->desc, 't') != NULL) {
+  }
+
+  if (StringChr (cfp->verify, 'v') != NULL) {
+    if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
+      SeqMgrIndexFeatures (entityID, 0);
+    }
+    vsp = ValidStructNew ();
+    if (vsp != NULL) {
+      vsp->useSeqMgrIndexes = TRUE;
+      vsp->suppressContext = TRUE;
+      vsp->seqSubmitParent = TRUE;
+      vsp->testLatLonSubregion = TRUE;
+      oldErrSev = ErrSetMessageLevel (SEV_NONE);
+      vsp->errfunc = ValidCallback;
+      vsp->userdata = (Pointer) cfp->ofp;
+      /* vsp->convertGiToAccn = FALSE; */
+      ValidateSeqEntry (sep, vsp);
+      ValidStructFree (vsp);
+      ErrSetMessageLevel (oldErrSev);
+    }
+  }
+  if (StringChr (cfp->verify, 'b') != NULL) {
+    if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
+      SeqMgrIndexFeatures (entityID, 0);
+    }
+    SeqEntryToGnbk (sep, NULL, GENBANK_FMT, SEQUIN_MODE, NORMAL_STYLE,
+                    0, 0, 0, NULL, cfp->ofp);
+  }
+
+  if (cfp->ofp != NULL) {
+    fflush (cfp->ofp);
+  }
+}
+
+static void ProcessSingleRecord (
+  CharPtr filename,
+  CSpeedFlagPtr cfp
+)
+
+{
+  AsnIoPtr      aip;
+  BioseqPtr     bsp;
+  ValNodePtr    bsplist = NULL;
+  BioseqSetPtr  bssp;
+  Pointer       dataptr = NULL;
+  Uint2         datatype, entityID = 0;
+  FileCache     fc;
+  FILE          *fp;
+  Int1          iotype;
+  Char          line [512];
+  Int4          maxio = 1;
+  SeqEntryPtr   sep;
+  time_t        starttime, stoptime, worsttime;
+  CharPtr       str;
+  Int4          x;
+
+  if (cfp == NULL) return;
+
+  if (StringHasNoText (filename)) return;
+
+  if (StringChr (cfp->io, 'r') != NULL) {
+    maxio = cfp->maxcount;
+  }
+
+  starttime = GetSecs ();
+
+  for (x = 0; x < maxio; x++) {
+    if (entityID != 0) {
+      ObjMgrFreeByEntityID (entityID);
+      entityID = 0;
+      dataptr = NULL;
+    }
+
+    if (cfp->type == 1) {
+
+      fp = FileOpen (filename, "r");
+      if (fp == NULL) {
+        Message (MSG_POSTERR, "Failed to open '%s'", filename);
+        return;
+      }
+
+      dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, FALSE, FALSE, FALSE);
+
+      FileClose (fp);
+
+      entityID = ObjMgrRegister (datatype, dataptr);
+
+    } else if (cfp->type >= 2 && cfp->type <= 5) {
+
+      aip = AsnIoOpen (filename, cfp->binary? "rb" : "r");
+      if (aip == NULL) {
+        Message (MSG_POSTERR, "AsnIoOpen failed for input file '%s'", filename);
+        return;
+      }
+
+      switch (cfp->type) {
+        case 2 :
+          dataptr = (Pointer) SeqEntryAsnRead (aip, NULL);
+          datatype = OBJ_SEQENTRY;
+          break;
+        case 3 :
+          dataptr = (Pointer) BioseqAsnRead (aip, NULL);
+          datatype = OBJ_BIOSEQ;
+          break;
+        case 4 :
+          dataptr = (Pointer) BioseqSetAsnRead (aip, NULL);
+          datatype = OBJ_BIOSEQSET;
+          break;
+        case 5 :
+          dataptr = (Pointer) SeqSubmitAsnRead (aip, NULL);
+          datatype = OBJ_SEQSUB;
+          break;
+        default :
+          break;
+      }
+
+      AsnIoClose (aip);
+
+      entityID = ObjMgrRegister (datatype, dataptr);
+
+    } else if (cfp->type == 6) {
+
+      fp = FileOpen (filename, "r");
+      if (fp == NULL) {
+        Message (MSG_POSTERR, "Failed to open '%s'", filename);
+        return;
+      }
+
+      dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, FALSE, FALSE, FALSE);
+
+      FileClose (fp);
+
+      entityID = ObjMgrRegister (datatype, dataptr);
+
+    } else if (cfp->type == 7) {
+
+      fp = FileOpen (filename, "r");
+      if (fp == NULL) {
+        Message (MSG_POSTERR, "Failed to open '%s'", filename);
+        return;
+      }
+
+      FileCacheSetup (&fc, fp);
+
+      str = FileCacheReadLine (&fc, line, sizeof (line), NULL);
+      while (str != NULL) {
+        str = FileCacheReadLine (&fc, line, sizeof (line), NULL);
+      }
+
+      FileClose (fp);
+
+      return;
+
+    } else {
+      Message (MSG_POSTERR, "Input format type '%d' unrecognized", (int) cfp->type);
+      return;
+    }
+  }
+
+  if (entityID < 1 || dataptr == NULL) {
+    Message (MSG_POSTERR, "Data read failed for input file '%s'", filename);
+    return;
+  }
+
+  if (datatype == OBJ_SEQSUB || datatype == OBJ_SEQENTRY ||
+        datatype == OBJ_BIOSEQ || datatype == OBJ_BIOSEQSET) {
+
+    stoptime = GetSecs ();
+    worsttime = stoptime - starttime;
+    if (cfp->logfp != NULL) {
+      fprintf (cfp->logfp, "ASN reading time %ld seconds\n", (long) worsttime);
+      fflush (cfp->logfp);
+    }
+
+    sep = GetTopSeqEntryForEntityID (entityID);
+
+    if (sep == NULL) {
+      sep = SeqEntryNew ();
+      if (sep != NULL) {
+        if (datatype == OBJ_BIOSEQ) {
+          bsp = (BioseqPtr) dataptr;
+          sep->choice = 1;
+          sep->data.ptrvalue = bsp;
+          SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep);
+        } else if (datatype == OBJ_BIOSEQSET) {
+          bssp = (BioseqSetPtr) dataptr;
+          sep->choice = 2;
+          sep->data.ptrvalue = bssp;
+          SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) bssp, sep);
+        } else {
+          sep = SeqEntryFree (sep);
+        }
+      }
+      sep = GetTopSeqEntryForEntityID (entityID);
+    }
+
+    if (sep != NULL) {
+
+      if (cfp->lock) {
+        starttime = GetSecs ();
+
+        bsplist = LockFarComponents (sep);
+
+        stoptime = GetSecs ();
+        worsttime = stoptime - starttime;
+        if (cfp->logfp != NULL) {
+          fprintf (cfp->logfp, "Far component locking time %ld seconds\n", (long) worsttime);
+          fflush (cfp->logfp);
+        }
+      }
+
+      if (StringChr (cfp->io, 'w') != NULL) {
+        starttime = GetSecs ();
+
+        iotype = ASNIO_TEXT_OUT;
+        if (StringChr (cfp->io, 'b') != NULL) {
+          iotype = ASNIO_BIN_OUT;
+        }
+
+        for (x = 0; x < cfp->maxcount; x++) {
+          aip = AsnIoNew (iotype, cfp->ofp, NULL, NULL, NULL);
+          if (aip != NULL) {
+            SeqEntryAsnWrite (sep, aip, NULL);
+            AsnIoFree (aip, FALSE);
+          }
+        }
+
+        stoptime = GetSecs ();
+        worsttime = stoptime - starttime;
+        if (cfp->logfp != NULL) {
+          fprintf (cfp->logfp, "ASN writing time %ld seconds\n", (long) worsttime);
+          fflush (cfp->logfp);
+        }
+      }
+
+      starttime = GetSecs ();
+
+      for (x = 0; x < cfp->maxcount; x++) {
+        DoProcess (sep, entityID, cfp);
+      }
+
+      stoptime = GetSecs ();
+      worsttime = stoptime - starttime;
+      if (cfp->logfp != NULL) {
+        fprintf (cfp->logfp, "Internal processing time %ld seconds\n", (long) worsttime);
+        fflush (cfp->logfp);
+      }
+
+      ObjMgrFreeByEntityID (entityID);
+
+      bsplist = UnlockFarComponents (bsplist);
+    }
+
+  } else {
+
+    Message (MSG_POSTERR, "Datatype %d not recognized", (int) datatype);
+  }
+}
+
+static void ProcessMultipleRecord (
+  CharPtr filename,
+  CSpeedFlagPtr cfp
+)
+
+{
+  AsnIoPtr     aip;
+  AsnTypePtr   atp;
+  BioseqPtr    bsp;
+  Char         buf [41];
+  Uint2        entityID;
+  FILE         *fp;
+  SeqEntryPtr  fsep;
+  Char         longest [41];
+  Int4         numrecords, x;
+  SeqEntryPtr  sep;
+  time_t       starttime, stoptime, worsttime;
+#ifdef OS_UNIX
+  Char         cmmd [256];
+  CharPtr      gzcatprog;
+  int          ret;
+  Boolean      usedPopen = FALSE;
+#endif
+
+  if (cfp == NULL) return;
+
+  if (StringHasNoText (filename)) return;
+
+#ifndef OS_UNIX
+  if (cfp->compressed) {
+    Message (MSG_POSTERR, "Can only decompress on-the-fly on UNIX machines");
+    return;
+  }
+#endif
+
+#ifdef OS_UNIX
+  if (cfp->compressed) {
+    gzcatprog = getenv ("NCBI_UNCOMPRESS_BINARY");
+    if (gzcatprog != NULL) {
+      sprintf (cmmd, "%s %s", gzcatprog, filename);
+    } else {
+      ret = system ("gzcat -h >/dev/null 2>&1");
+      if (ret == 0) {
+        sprintf (cmmd, "gzcat %s", filename);
+      } else if (ret == -1) {
+        Message (MSG_POSTERR, "Unable to fork or exec gzcat in ScanBioseqSetRelease");
+        return;
+      } else {
+        ret = system ("zcat -h >/dev/null 2>&1");
+        if (ret == 0) {
+          sprintf (cmmd, "zcat %s", filename);
+        } else if (ret == -1) {
+          Message (MSG_POSTERR, "Unable to fork or exec zcat in ScanBioseqSetRelease");
+          return;
+        } else {
+          Message (MSG_POSTERR, "Unable to find zcat or gzcat in ScanBioseqSetRelease - please edit your PATH environment variable");
+          return;
+        }
+      }
+    }
+    fp = popen (cmmd, /* cfp->binary? "rb" : */ "r");
+    usedPopen = TRUE;
+  } else {
+    fp = FileOpen (filename, cfp->binary? "rb" : "r");
+  }
+#else
+  fp = FileOpen (filename, cfp->binary? "rb" : "r");
+#endif
+  if (fp == NULL) {
+    Message (MSG_POSTERR, "FileOpen failed for input file '%s'", filename);
+    return;
+  }
+
+  aip = AsnIoNew (cfp->binary? ASNIO_BIN_IN : ASNIO_TEXT_IN, fp, NULL, NULL, NULL);
+  if (aip == NULL) {
+    Message (MSG_ERROR, "AsnIoNew failed for input file '%s'", filename);
+    return;
+  }
+
+  if (cfp->logfp != NULL) {
+    fprintf (cfp->logfp, "%s\n\n", filename);
+    fflush (cfp->logfp);
+  }
+
+  longest [0] = '\0';
+  worsttime = 0;
+  numrecords = 0;
+
+  atp = cfp->atp_bss;
+
+  while ((atp = AsnReadId (aip, cfp->amp, atp)) != NULL) {
+    if (atp == cfp->atp_se) {
+
+      sep = SeqEntryAsnRead (aip, atp);
+      if (sep != NULL) {
+
+        entityID = ObjMgrGetEntityIDForChoice (sep);
+
+        fsep = FindNthBioseq (sep, 1);
+        if (fsep != NULL && fsep->choice == 1) {
+          bsp = (BioseqPtr) fsep->data.ptrvalue;
+          if (bsp != NULL) {
+            SeqIdWrite (bsp->id, buf, PRINTID_FASTA_LONG, sizeof (buf));
+            if (cfp->logfp != NULL) {
+              fprintf (cfp->logfp, "%s\n", buf);
+              fflush (cfp->logfp);
+            }
+          }
+        }
+
+        starttime = GetSecs ();
+        for (x = 0; x < cfp->maxcount; x++) {
+          DoProcess (sep, entityID, cfp);
+        }
+        stoptime = GetSecs ();
+
+        if (stoptime - starttime > worsttime) {
+          worsttime = stoptime - starttime;
+          StringCpy (longest, buf);
+        }
+        numrecords++;
+
+        ObjMgrFreeByEntityID (entityID);
+      }
+
+    } else {
+
+      AsnReadVal (aip, atp, NULL);
+    }
+  }
+
+  AsnIoFree (aip, FALSE);
+
+#ifdef OS_UNIX
+  if (usedPopen) {
+    pclose (fp);
+  } else {
+    FileClose (fp);
+  }
+#else
+  FileClose (fp);
+#endif
+  if (cfp->logfp != NULL && (! StringHasNoText (longest))) {
+    fprintf (cfp->logfp, "Longest processing time %ld seconds on %s\n",
+             (long) worsttime, longest);
+    fprintf (cfp->logfp, "Total number of records %ld\n", (long) numrecords);
+    fflush (cfp->logfp);
+  }
+}
+
+static void ProcessOneRecord (
+  CharPtr filename,
+  Pointer userdata
+)
+
+{
+  CSpeedFlagPtr  cfp;
+
+  if (StringHasNoText (filename)) return;
+  cfp = (CSpeedFlagPtr) userdata;
+  if (cfp == NULL) return;
+
+  if (cfp->batch) {
+    ProcessMultipleRecord (filename, cfp);
+  } else {
+    ProcessSingleRecord (filename, cfp);
+  }
+}
+
+/* Args structure contains command-line arguments */
+
+#define p_argInputPath     0
+#define i_argInputFile     1
+#define o_argOutputFile    2
+#define f_argFilter        3
+#define x_argSuffix        4
+#define a_argType          5
+#define b_argBinary        6
+#define c_argCompressed    7
+#define l_argLockFar       8
+#define L_argLogFile       9
+#define R_argRemote       10
+#define X_argMaxCount     11
+#define O_argInOut        12
+#define K_argClean        13
+#define I_argIndex        14
+#define S_argSeq          15
+#define F_argFeat         16
+#define D_argDesc         17
+#define V_argVerify       18
+
+Args myargs [] = {
+  {"Path to Files", NULL, NULL, NULL,
+    TRUE, 'p', ARG_STRING, 0.0, 0, NULL},
+  {"Single Input File", "stdin", NULL, NULL,
+    TRUE, 'i', ARG_FILE_IN, 0.0, 0, NULL},
+  {"Output File", "stdout", NULL, NULL,
+    TRUE, 'o', ARG_FILE_OUT, 0.0, 0, NULL},
+  {"Substring Filter", NULL, NULL, NULL,
+    TRUE, 'f', ARG_STRING, 0.0, 0, NULL},
+  {"File Selection Suffix", ".ent", NULL, NULL,
+    TRUE, 'x', ARG_STRING, 0.0, 0, NULL},
+  {"ASN.1 Type\n"
+   "      a Any\n"
+   "      e Seq-entry\n"
+   "      b Bioseq\n"
+   "      s Bioseq-set\n"
+   "      m Seq-submit\n"
+   "      t Batch Processing\n"
+   "      f FASTA\n"
+   "      l Read by Lines", "a", NULL, NULL,
+    TRUE, 'a', ARG_STRING, 0.0, 0, NULL},
+  {"Bioseq-set is Binary", "F", NULL, NULL,
+    TRUE, 'b', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Bioseq-set is Compressed", "F", NULL, NULL,
+    TRUE, 'c', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Lock Components in Advance", "F", NULL, NULL,
+    TRUE, 'l', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Log File", NULL, NULL, NULL,
+    TRUE, 'L', ARG_FILE_OUT, 0.0, 0, NULL},
+  {"Remote Fetching from ID", "F", NULL, NULL,
+    TRUE, 'R', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Max Repeat Count", "1", NULL, NULL,
+    TRUE, 'X', ARG_INT, 0.0, 0, NULL},
+  {"Input Output\n"
+   "      r Read ASN.1\n"
+   "      w Write Text ASN.1\n"
+   "      wb Write Binary ASN.1", NULL, NULL, NULL,
+    TRUE, 'O', ARG_STRING, 0.0, 0, NULL},
+  {"Cleanup\n"
+   "      b BasicSeqEntryCleanup\n"
+   "      s SeriousSeqEntryCleanup", NULL, NULL, NULL,
+    TRUE, 'K', ARG_STRING, 0.0, 0, NULL},
+  {"Index\n"
+   "      f Feature Indexing", NULL, NULL, NULL,
+    TRUE, 'I', ARG_STRING, 0.0, 0, NULL},
+  {"Sequence\n"
+   "      s FASTA of Sequence\n"
+   "      r Raw FASTA no Defline\n"
+   "      d Just FASTA Defline\n"
+   "      f FASTA by Feature\n"
+   "      t FASTA of Translation", NULL, NULL, NULL,
+    TRUE, 'S', ARG_STRING, 0.0, 0, NULL},
+  {"Feature\n"
+   "      v Visit Features\n"
+   "      g Gene Overlap Print\n"
+   "      h Gene Overlap Speed\n"
+   "      x Gene by Xref\n"
+   "      o Operon by Overlap\n"
+   "      d Feature by ID\n"
+   "      t Feature Table", NULL, NULL, NULL,
+    TRUE, 'F', ARG_STRING, 0.0, 0, NULL},
+  {"Descriptor\n"
+   "      b BioSource\n"
+   "      t Title", NULL, NULL, NULL,
+    TRUE, 'D', ARG_STRING, 0.0, 0, NULL},
+  {"Verification\n"
+   "      v Validate with Normal Stringency\n"
+   "      b Generate GenBank Flatfile\n", NULL, NULL, NULL,
+    TRUE, 'V', ARG_STRING, 0.0, 0, NULL},
+};
+
+Int2 Main (void)
+
+{
+  Char            app [64], type;
+  CSpeedFlagData  cfd;
+  CharPtr         directory, filter, infile, logfile, outfile, str, suffix;
+  Boolean         remote;
+  time_t          runtime, starttime, stoptime;
+
+  /* standard setup */
+
+  ErrSetFatalLevel (SEV_MAX);
+  ErrClearOptFlags (EO_SHOW_USERSTR);
+  UseLocalAsnloadDataAndErrMsg ();
+  ErrPathReset ();
+
+  /* finish resolving internal connections in ASN.1 parse tables */
+
+  if (! AllObjLoad ()) {
+    Message (MSG_FATAL, "AllObjLoad failed");
+    return 1;
+  }
+  if (! SubmitAsnLoad ()) {
+    Message (MSG_FATAL, "SubmitAsnLoad failed");
+    return 1;
+  }
+  if (! FeatDefSetLoad ()) {
+    Message (MSG_FATAL, "FeatDefSetLoad failed");
+    return 1;
+  }
+  if (! SeqCodeSetLoad ()) {
+    Message (MSG_FATAL, "SeqCodeSetLoad failed");
+    return 1;
+  }
+  if (! GeneticCodeTableLoad ()) {
+    Message (MSG_FATAL, "GeneticCodeTableLoad failed");
+    return 1;
+  }
+
+  /* process command line arguments */
+
+  sprintf (app, "cspeedtest %s", CSPEEDTEST_APPLICATION);
+  if (! GetArgs (app, sizeof (myargs) / sizeof (Args), myargs)) {
+    return 0;
+  }
+
+  MemSet ((Pointer) &cfd, 0, sizeof (CSpeedFlagData));
+
+  directory = (CharPtr) myargs [p_argInputPath].strvalue;
+  infile = (CharPtr) myargs [i_argInputFile].strvalue;
+  outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
+  filter = (CharPtr) myargs [f_argFilter].strvalue;
+  suffix = (CharPtr) myargs [x_argSuffix].strvalue;
+
+  cfd.batch = FALSE;
+  cfd.binary = (Boolean) myargs [b_argBinary].intvalue;
+  cfd.compressed = (Boolean) myargs [c_argCompressed].intvalue;
+  cfd.lock = (Boolean) myargs [l_argLockFar].intvalue;
+  cfd.type = 1;
+
+  str = myargs [a_argType].strvalue;
+  TrimSpacesAroundString (str);
+  if (StringDoesHaveText (str)) {
+    type = str [0];
+  } else {
+    type = 'a';
+  }
+
+  type = TO_LOWER (type);
+  switch (type) {
+    case 'a' :
+      cfd.type = 1;
+      break;
+    case 'e' :
+      cfd.type = 2;
+      break;
+    case 'b' :
+      cfd.type = 3;
+      break;
+    case 's' :
+      cfd.type = 4;
+      break;
+    case 'm' :
+      cfd.type = 5;
+      break;
+    case 't' :
+      cfd.type = 1;
+      cfd.batch = TRUE;
+      break;
+    case 'f' :
+      cfd.type = 6;
+      break;
+    case 'l' :
+      cfd.type = 7;
+      break;
+    default :
+      cfd.type = 1;
+      break;
+  }
+
+  remote = (Boolean) myargs [R_argRemote].intvalue;
+
+  cfd.maxcount = myargs [X_argMaxCount].intvalue;
+  if (cfd.maxcount < 1) {
+    cfd.maxcount = 1;
+  }
+
+  cfd.io = myargs [O_argInOut].strvalue;
+  cfd.clean = myargs [K_argClean].strvalue;
+  cfd.index = myargs [I_argIndex].strvalue;
+  cfd.seq = myargs [S_argSeq].strvalue;
+  cfd.feat = myargs [F_argFeat].strvalue;
+  cfd.desc = myargs [D_argDesc].strvalue;
+  cfd.verify = myargs [V_argVerify].strvalue;
+
+  cfd.amp = AsnAllModPtr ();
+  cfd.atp_bss = AsnFind ("Bioseq-set");
+  cfd.atp_bsss = AsnFind ("Bioseq-set.seq-set");
+  cfd.atp_se = AsnFind ("Bioseq-set.seq-set.E");
+  cfd.atp_bsc = AsnFind ("Bioseq-set.class");
+  cfd.bssp_atp = AsnLinkType (NULL, cfd.atp_bss);
+
+  logfile = (CharPtr) myargs [L_argLogFile].strvalue;
+  if (StringDoesHaveText (logfile)) {
+    cfd.logfp = FileOpen (logfile, "w");
+  }
+
+  if (remote) {
+    PubSeqFetchEnable ();
+  }
+
+  if (StringDoesHaveText (outfile)) {
+    cfd.ofp = FileOpen (outfile, "w");
+  }
+
+  starttime = GetSecs ();
+
+  if (StringDoesHaveText (directory)) {
+
+    DirExplore (directory, NULL, suffix, FALSE, ProcessOneRecord, (Pointer) &cfd);
+
+  } else if (StringDoesHaveText (infile)) {
+
+    ProcessOneRecord (infile, (Pointer) &cfd);
+  }
+
+  if (cfd.ofp != NULL) {
+    FileClose (cfd.ofp);
+  }
+
+  stoptime = GetSecs ();
+  runtime = stoptime - starttime;
+  if (cfd.logfp != NULL) {
+    fprintf (cfd.logfp, "Finished in %ld seconds\n", (long) runtime);
+    FileClose (cfd.logfp);
+  }
+
+  if (remote) {
+    PubSeqFetchDisable ();
+  }
+
+  return 0;
+}
+
diff --git a/demo/megablast.c b/demo/megablast.c
index 1682d8a6..c012083d 100644
--- a/demo/megablast.c
+++ b/demo/megablast.c
@@ -1,5 +1,5 @@
-static char const rcsid[] = "$Id: megablast.c,v 6.199 2007/03/20 14:56:58 camacho Exp $";
-/* $Id: megablast.c,v 6.199 2007/03/20 14:56:58 camacho Exp $
+static char const rcsid[] = "$Id: megablast.c,v 6.201 2007/10/23 16:03:23 madden Exp $";
+/* $Id: megablast.c,v 6.201 2007/10/23 16:03:23 madden Exp $
 **************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -26,6 +26,12 @@ static char const rcsid[] = "$Id: megablast.c,v 6.199 2007/03/20 14:56:58 camach
 *                                                                         *
 ************************************************************************** 
  * $Log: megablast.c,v $
+ * Revision 6.201  2007/10/23 16:03:23  madden
+ * No longer set ungapped_extension as an initial word option
+ *
+ * Revision 6.200  2007/10/03 17:12:36  papadopo
+ * do not ignore the value of -H when configuring the current blast engine
+ *
  * Revision 6.199  2007/03/20 14:56:58  camacho
  * Call GeneticCodeSingletonInit/GeneticCodeSingletonFini
  *
@@ -1948,14 +1954,6 @@ BLAST_FillOptions(SBlastOptions* options, Blast_SummaryReturn* sum_returns)
       lambda*myargs[ARG_XDROP].intvalue/NCBIMATH_LN2, 
       lambda*myargs[ARG_XDROP_FINAL].intvalue/NCBIMATH_LN2);
 
-   /* For discontiguous megablast we skip ungapped extensions
-      when using the 2-hit wordfinder */
-   if (lookup_options->mb_template_length > 0)
-   {
-      if (word_options->window_size > 0)
-          word_options->ungapped_extension = FALSE;
-   }
-
    BLAST_FillHitSavingOptions(hit_options, 
       myargs[ARG_EVALUE].floatvalue, 
       MAX(myargs[ARG_DESCRIPTIONS].intvalue, 
@@ -1963,6 +1961,7 @@ BLAST_FillOptions(SBlastOptions* options, Blast_SummaryReturn* sum_returns)
       score_options->gapped_calculation, 
       0,                /* turn off culling */
       diag_separation);
+   hit_options->hsp_num_max = myargs[ARG_MAXHSP].intvalue;
 
    if (myargs[ARG_MINSCORE].intvalue)
         hit_options->cutoff_score = myargs[ARG_MINSCORE].intvalue;
diff --git a/demo/nps2gps.c b/demo/nps2gps.c
index 0468f47f..d926a85b 100644
--- a/demo/nps2gps.c
+++ b/demo/nps2gps.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   5/12/05
 *
-* $Revision: 1.11 $
+* $Revision: 1.13 $
 *
 * File Description:
 *
@@ -50,7 +50,7 @@
 #include <toasn3.h>
 #include <pmfapi.h>
 
-#define NPS2GPSAPP_VER "1.9"
+#define NPS2GPSAPP_VER "2.1"
 
 CharPtr NPS2GPSAPPLICATION = NPS2GPSAPP_VER;
 
@@ -60,6 +60,7 @@ typedef struct n2gdata {
   Boolean  failure;
   Boolean  lock;
   Boolean  byFeatID;
+  Boolean  useProtID;
 } N2GData, PNTR N2GPtr;
 
 typedef struct npsseqs {
@@ -381,10 +382,30 @@ static SeqIdPtr MakeIdFromLocusTag (
   return NULL;
 }
 
+static SeqIdPtr MakeIdFromProtein (
+  BioseqPtr pbsp
+)
+
+{
+  Char      buf [64], tmp [64];
+  SeqIdPtr  sip;
+
+  if (pbsp == NULL) return NULL;
+  sip = SeqIdFindBestAccession (pbsp->id);
+  if (sip == NULL) return NULL;
+  SeqIdWrite (sip, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1);
+  if (StringHasNoText (buf)) return NULL;
+  StringCpy (tmp, "gnl|MTRACK|");
+  StringCat (tmp, buf);
+  StringCat (tmp, "_mrna");
+  return MakeSeqID (tmp);
+}
+
 static void InstantiateMrnaIntoProt (
   SeqFeatPtr cds,
   SeqFeatPtr mrna,
-  Int2Ptr ctrp
+  Int2Ptr ctrp,
+  N2GPtr ngp
 )
 
 {
@@ -397,11 +418,11 @@ static void InstantiateMrnaIntoProt (
   CharPtr       rnaseq;
   ValNodePtr    vnp;
 
-  if (cds == NULL || mrna == NULL) return;
+  if (cds == NULL || mrna == NULL || ngp == NULL) return;
   if (cds->product == NULL || mrna->product != NULL) return;
 
   pbsp = BioseqFindFromSeqLoc (cds->product);
-  if (pbsp  == NULL) return;
+  if (pbsp == NULL) return;
   psep = SeqMgrGetSeqEntryForData (pbsp);
   if (psep == NULL) return;
 
@@ -423,8 +444,13 @@ static void InstantiateMrnaIntoProt (
   mbsp->length = BSLen (bs);
   BioseqPack (mbsp);
 
-  /* now adds _# suffix to general Seq-id if ambiguous */
+  /* now adds _# suffix to general Seq-id if ambiguous - but messed up Drosophila record, so only use feature ID */
+  /*
   mbsp->id = MakeIdFromLocusTag (mrna);
+  */
+  if (ngp->useProtID) {
+    mbsp->id = MakeIdFromProtein (pbsp);
+  }
   if (mbsp->id == NULL) {
     mbsp->id = MakeNewProteinSeqIdEx (mrna->location, NULL, NULL, ctrp);
   }
@@ -544,7 +570,7 @@ static void LoopThroughCDSs (
         count = SeqMgrGetAllOverlappingFeatures (sfp->location, FEATDEF_mRNA, NULL, 0,
                                                  CHECK_INTERVALS, (Pointer) &ld, FindSingleMrnaProc);
         if (ld.count == 1 && ld.mrna != NULL) {
-          InstantiateMrnaIntoProt (sfp, ld.mrna, ctrp);
+          InstantiateMrnaIntoProt (sfp, ld.mrna, ctrp, ngp);
           sfp->idx.scratch = (Pointer) MemNew (sizeof (Int4));
           ld.mrna->idx.scratch = (Pointer) MemNew (sizeof (Int4));
           goOn = TRUE;
@@ -736,7 +762,7 @@ static void NPStoGPS (
     while (sfp != NULL) {
       mrna = GetmRNAByFeatureID (sfp);
       if (mrna != NULL) {
-        InstantiateMrnaIntoProt (sfp, mrna, &ctr);
+        InstantiateMrnaIntoProt (sfp, mrna, &ctr, ngp);
       }
       sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_CDREGION, 0, &fcontext);
     }
@@ -959,6 +985,7 @@ static void ProcessOneRecord (
 #define R_argRemote      6
 #define L_argLockFar     7
 #define F_argUseFeatID   8
+#define P_argUseProtID   9
 
 
 Args myargs [] = {
@@ -980,6 +1007,8 @@ Args myargs [] = {
     TRUE, 'L', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Map by Feature ID", "F", NULL, NULL,
     TRUE, 'F', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"mRNA ID from Protein", "F", NULL, NULL,
+    TRUE, 'P', ARG_BOOLEAN, 0.0, 0, NULL},
 };
 
 Int2 Main (void)
@@ -1032,6 +1061,7 @@ Int2 Main (void)
   ngd.failure = FALSE;
   ngd.lock = (Boolean) myargs [L_argLockFar].intvalue;
   ngd.byFeatID = (Boolean) myargs [F_argUseFeatID].intvalue;
+  ngd.useProtID = (Boolean) myargs [P_argUseProtID].intvalue;
 
   directory = (CharPtr) myargs [p_argInputPath].strvalue;
   results = (CharPtr) myargs [r_argOutputPath].strvalue;
diff --git a/demo/raw2delt.c b/demo/raw2delt.c
new file mode 100644
index 00000000..cdb74ec5
--- /dev/null
+++ b/demo/raw2delt.c
@@ -0,0 +1,657 @@
+/*   raw2delt.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  raw2delt.c
+*
+* Author:  Colleen Bollin
+*
+* Version Creation Date:   4/12/07
+*
+* $Revision: 1.2 $
+*
+* File Description: 
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* Date     Name        Description of modification
+* -------  ----------  -----------------------------------------------------
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <objall.h>
+#include <objsset.h>
+#include <objsub.h>
+#include <objfdef.h>
+#include <sequtil.h>
+#include <gather.h>
+#include <sqnutils.h>
+#include <explore.h>
+#include <seqport.h>
+
+#define RAW2DELT_APP_VER "1.0"
+
+CharPtr RAW2DELT_APPLICATION = RAW2DELT_APP_VER;
+
+typedef struct outputstream {
+  CharPtr  results_dir;
+  CharPtr  base;
+  CharPtr  suffix;
+  CharPtr  outfile;
+  CharPtr  outsuffix;
+  AsnIoPtr aip;
+  Boolean  is_binary;
+} OutputStreamData, PNTR OutputStreamPtr;
+
+typedef struct inputstream {
+  CharPtr directory;
+  CharPtr base;
+  CharPtr suffix;
+  Boolean is_binary;
+  Boolean is_seqentry;
+} InputStreamData, PNTR InputStreamPtr;
+
+typedef struct asnstream {
+  AsnModulePtr amp;
+  AsnTypePtr   atp_se;
+  AsnTypePtr   atp_bss;
+  AsnTypePtr   atp_bss_se;
+} AsnStreamData, PNTR AsnStreamPtr;
+
+static FILE* OpenOneFile (
+  CharPtr directory,
+  CharPtr base,
+  CharPtr suffix
+)
+
+{
+  Char  file [FILENAME_MAX], path [PATH_MAX];
+
+  if (base == NULL) {
+    base = "";
+  }
+  if (suffix == NULL) {
+    suffix = "";
+  }
+
+  StringNCpy_0 (path, directory, sizeof (path));
+  sprintf (file, "%s%s", base, suffix);
+  FileBuildPath (path, NULL, file);
+
+  return FileOpen (path, "r");
+}
+
+static AsnIoPtr AsnIoFromInputStream (
+  InputStreamPtr isp
+)
+
+{
+  AsnIoPtr aip;
+  Char     file [FILENAME_MAX], path [PATH_MAX];
+  CharPtr  read_flag;
+
+  if (isp == NULL) return NULL;
+
+  if (isp->is_binary) {
+    read_flag = "rb";
+  } else {
+    read_flag = "r";
+  }
+
+  if (isp->base == NULL) {
+    aip = AsnIoOpen ("stdin", read_flag);
+  } else {
+    StringNCpy_0 (path, isp->directory, sizeof (path));
+    sprintf (file, "%s%s", isp->base, isp->suffix);
+    FileBuildPath (path, NULL, file);
+    aip = AsnIoOpen (path, read_flag);
+  }
+  return aip;
+}
+
+
+static AsnIoPtr AsnIoFromOutputStream (OutputStreamPtr osp)
+{
+  AsnIoPtr   aip;
+  Char       file [FILENAME_MAX], path [PATH_MAX];
+  CharPtr    write_flag;
+
+  if (osp == NULL) return NULL;
+  if (osp->aip == NULL) {
+    write_flag = osp->is_binary ? "wb" : "w";
+    if (StringDoesHaveText (osp->outfile)) {
+      StringNCpy_0 (path, osp->outfile, sizeof (path));
+    } else {
+      if (osp->base == NULL) {
+        aip = AsnIoOpen ("stdout", write_flag);
+      } else {
+        if (osp->outsuffix == NULL) {
+          osp->outsuffix = "";
+        }
+        StringNCpy_0 (path, osp->results_dir, sizeof (path));
+        sprintf (file, "%s%s%s", osp->base, osp->suffix, osp->outsuffix);
+        FileBuildPath (path, NULL, file);
+        aip = AsnIoOpen (path, write_flag);
+        if (aip == NULL) {
+          Message (MSG_POSTERR, "Unable to write to %s.", path);
+        }
+      }
+    }
+  } else {
+    aip = osp->aip;
+  }
+  return aip;
+}
+
+static void WriteOneFile (
+  OutputStreamPtr osp,
+  SeqEntryPtr sep
+)
+
+{
+  AsnIoPtr   aip;
+
+  aip = AsnIoFromOutputStream (osp);
+  if (aip != NULL) {
+    SeqEntryAsnWrite (sep, aip, NULL);
+    AsnIoFlush (aip);
+  }
+  if (aip != osp->aip) {
+    AsnIoClose (aip);
+  }
+}
+
+
+static void CollectBioseqsForConversion (BioseqPtr bsp, Pointer userdata)
+{
+  ValNodePtr PNTR list;
+  
+  if (bsp == NULL || bsp->repr != Seq_repr_raw || ISA_aa (bsp->mol)) return;
+  if (userdata == NULL)
+  {
+    return;
+  }
+  list = (ValNodePtr PNTR) userdata;
+  
+  ValNodeAddPointer (list, 0, bsp);
+}
+
+
+static void ProcessSeqEntry (SeqEntryPtr sep, Int4Ptr gap_sizes)
+{
+  ValNodePtr     bsp_list = NULL, vnp;
+  BioseqPtr      bsp;
+
+  if (sep == NULL || gap_sizes == NULL) return;
+
+  VisitBioseqsInSep (sep, &bsp_list, CollectBioseqsForConversion);
+
+  for (vnp = bsp_list; vnp != NULL; vnp = vnp->next) {
+    bsp = (BioseqPtr) vnp->data.ptrvalue;
+    ConvertNsToGaps (bsp, gap_sizes);
+  }
+  bsp_list = ValNodeFree (bsp_list);
+}
+
+static Uint2 ProcessOneAsn (
+  FILE* fp,
+  CharPtr path,
+  Int4Ptr gap_sizes
+)
+
+{
+  Pointer        dataptr;
+  Uint2          datatype, entityID = 0;
+  SeqEntryPtr    sep;
+
+  if (fp == NULL || gap_sizes == NULL) return 0;
+
+  dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, TRUE, FALSE, TRUE, FALSE);
+  if (dataptr == NULL) {
+    Message (MSG_POSTERR, "Unable to read data from %s.", path);
+    return 0;
+  }
+
+  sep = GetTopSeqEntryForEntityID (entityID);
+  ProcessSeqEntry (sep, gap_sizes);
+
+  return entityID;
+}
+
+/* return -1 if failure, 0 if success */
+static Int4 ProcessOneRecord (
+  CharPtr directory,
+  OutputStreamPtr osp,
+  Int4Ptr   gap_sizes
+)
+
+{
+  Uint2              entityID;
+  FILE               *fp;
+  SeqEntryPtr        sep;
+
+  if (osp == NULL || gap_sizes == NULL) return -1;
+  fp = OpenOneFile (directory, osp->base, osp->suffix);
+  if (fp == NULL) return -1;
+
+  entityID = ProcessOneAsn (fp, osp->base == NULL ? "input stream" : osp->base, gap_sizes);
+  
+  FileClose (fp);
+
+  if (entityID == 0) return -1;
+
+  /* finish processing */
+
+  sep = GetTopSeqEntryForEntityID (entityID);
+  if (sep != NULL) {
+    WriteOneFile (osp, sep);
+  }
+
+  ObjMgrFreeByEntityID (entityID);
+  return 0;
+}
+
+static Int4 ProcessStream (InputStreamPtr isp, OutputStreamPtr osp, AsnStreamPtr asp, Int4Ptr gap_sizes)
+{
+  AsnTypePtr   atp, atp_srch;
+  AsnIoPtr asn_in, asn_out;
+  Int4         rval = 0;
+  SeqEntryPtr  sep;
+  Uint2        entityID;
+  DataVal av;
+  
+  if (isp == NULL || osp == NULL || asp == NULL || gap_sizes == NULL) return 1;
+
+  asn_in = AsnIoFromInputStream (isp);
+  asn_out = AsnIoFromOutputStream (osp);
+
+  if (isp->is_seqentry) {
+    atp = asp->atp_se;
+    atp_srch = asp->atp_se;
+  }
+  else {
+    atp = asp->atp_bss;
+    atp_srch = asp->atp_bss_se;
+  }
+
+  while ((atp = AsnReadId(asn_in, asp->amp, atp)) != NULL && rval == 0) {
+    if (atp != atp_srch) {
+      AsnReadVal(asn_in, atp, &av);
+      AsnWrite(asn_out, atp, &av);
+      AsnKillValue(atp, &av);
+      continue;
+    }
+    if ((sep = SeqEntryAsnRead(asn_in, atp)) == NULL) {
+      Message (MSG_POSTERR, "SeqEntryAsnRead failure");
+      rval = 1;
+    } else  {
+      entityID = ObjMgrRegister (OBJ_SEQENTRY, sep);
+      ProcessSeqEntry (sep, gap_sizes);
+
+      if (! SeqEntryAsnWrite(sep, asn_out, atp)) {
+       Message (MSG_POSTERR, "SeqEntryAsnWrite failure");
+       rval = 1;
+      }
+      AsnIoFlush(asn_out);
+      ObjMgrFreeByEntityID (entityID);
+    }
+  }                             /* Endwhile, AsnReadId */
+
+  AsnIoClose(asn_in);
+  if (asn_out != osp->aip) {
+    AsnIoClose(asn_out);
+  }
+  
+  return rval;
+}
+
+/* return -1 on failure, 0 on success */
+static Int4 FileRecurse (
+  CharPtr         directory,
+  InputStreamPtr  isp,
+  OutputStreamPtr osp,
+  AsnStreamPtr    asp,
+  Int4Ptr         gap_sizes
+)
+
+{
+  Char        path [PATH_MAX];
+  CharPtr     ptr;
+  CharPtr     str;
+  ValNodePtr  head, vnp;
+  CharPtr     orig_dir, orig_base;
+  Int4        rval = 0;
+
+  /* get list of all files in source directory */
+
+  head = DirCatalog (directory);
+
+  for (vnp = head; vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == 0) {
+      str = (CharPtr) vnp->data.ptrvalue;
+      if (StringDoesHaveText (str)) {
+
+        /* does filename have desired substring? */
+
+        ptr = StringStr (str, osp->suffix);
+
+        if (ptr != NULL) {
+
+          /* make sure detected suffix is really at end of filename */
+
+          if (StringCmp (ptr, osp->suffix) == 0) {
+            *ptr = '\0';
+
+            /* process file that has desired suffix (usually .fsa) */
+            osp->base = str;
+            orig_dir = isp->directory;
+            isp->directory = directory;
+            orig_base = isp->base;
+            isp->base = str;
+            if (isp->is_binary) {
+              rval |= ProcessStream (isp, osp, asp, gap_sizes);
+            } else {
+              rval |= ProcessOneRecord (directory, osp, gap_sizes);
+            }
+            isp->directory = orig_dir;
+            isp->base = orig_base;
+            osp->base = NULL;
+          }
+        }
+      }
+    } else if (vnp->choice == 1) {
+
+      /* recurse into subdirectory */
+
+      StringNCpy_0 (path, directory, sizeof (path));
+      str = (CharPtr) vnp->data.ptrvalue;
+      FileBuildPath (path, str, NULL);
+      rval |= FileRecurse (path, isp, osp, asp, gap_sizes);
+    }
+  }
+
+  /* clean up file list */
+
+  ValNodeFreeData (head);
+  return rval;
+}
+
+static Boolean SetUpAsnStreamData (AsnStreamPtr asp)
+
+{
+  if (asp == NULL) return FALSE;
+
+  if (! SeqSetAsnLoad()) {
+    Message (MSG_POSTERR, "Unable to load SeqSet parse tree");
+    return FALSE;
+  }
+  asp->amp = AsnAllModPtr();
+  if (asp->amp == NULL) {
+    Message (MSG_POSTERR, "Unable to obtain ASN.1 module pointer");
+    return FALSE;
+  }
+
+  /* Get pointers to ASN.1 types that must be dealt with in asn_in */
+
+  if ( (asp->atp_bss = AsnFind("Bioseq-set")) == NULL) {
+    Message (MSG_POSTERR, "could not find type Bioseq-set");
+    return FALSE;
+  }
+  if ( (asp->atp_bss_se = AsnFind("Bioseq-set.seq-set.E")) == NULL) {
+    Message (MSG_POSTERR, "AsnFind failure: Bioseq-set.seq-set.E");
+    return FALSE;
+  }
+  if ( (asp->atp_se = AsnFind("Seq-entry")) == NULL) {
+    Message (MSG_POSTERR, "AsnFind failure: Seq-entry");
+    return FALSE;
+  }
+  return TRUE;
+}
+
+/* Args structure contains command-line arguments */
+
+#define p_argInputPath         0
+#define r_argOutputPath        1
+#define i_argInputFile         2
+#define o_argOutputFile        3
+#define x_argSuffix            4
+#define s_argOutSuffix         5
+#define b_argInputBinary       6
+#define e_argInputSeqEntry     7
+#define d_argOutputBinary      8
+#define u_argEqUnknownGap      9
+#define U_argGTEqUnknownGap   10
+#define k_argEqUnknownGap     11
+#define K_argGtEqUnknownGap   12
+
+
+Args myargs [] = {
+  {"Path to Files", NULL, NULL, NULL,
+    TRUE, 'p', ARG_STRING, 0.0, 0, NULL},
+  {"Path for Results", NULL, NULL, NULL,
+    TRUE, 'r', ARG_STRING, 0.0, 0, NULL},
+  {"Single Input File", NULL, NULL, NULL,
+    TRUE, 'i', ARG_FILE_IN, 0.0, 0, NULL},
+  {"Single Output File", NULL, NULL, NULL,
+    TRUE, 'o', ARG_FILE_OUT, 0.0, 0, NULL},
+  {"Suffix", ".sqn", NULL, NULL,
+    TRUE, 'x', ARG_STRING, 0.0, 0, NULL},
+  {"Suffix for converted files", "", NULL, NULL,
+    TRUE, 's', ARG_STRING, 0.0, 0, NULL},
+  {"Input is binary", "F", NULL, NULL,
+    TRUE, 'b', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Input is Seq-entry", "F", NULL, NULL,
+    TRUE, 'e', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Output is binary", "F", NULL, NULL,
+    TRUE, 'b', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Exact size to convert to unknown length gap", "-1", NULL, NULL,
+    TRUE, 'u', ARG_INT, 0.0, 0, NULL},
+  {"Size greater than/equal to to convert to unknown length gap", "-1", NULL, NULL,
+    TRUE, 'U', ARG_INT, 0.0, 0, NULL},
+  {"Exact size to convert to known length gap", "-1", NULL, NULL,
+    TRUE, 'k', ARG_INT, 0.0, 0, NULL},
+  {"Size greater than/equal to to convert to known length gap", "-1", NULL, NULL,
+    TRUE, 'K', ARG_INT, 0.0, 0, NULL},
+};
+
+Int2 Main(void)
+{
+  Char             app [64];
+  CharPtr          directory;
+  CharPtr          ptr;
+  Char             sfx [32];
+  OutputStreamData osd;
+  InputStreamData  isd;
+  AsnStreamData    asd;
+  Int4             gap_sizes[2];
+  Int4             rval = 0;
+  Int4             u_eq = 0, u_gteq = -1, k_eq = 0, k_gteq = -1;
+
+  /* standard setup */
+
+  ErrSetFatalLevel (SEV_MAX);
+  ErrClearOptFlags (EO_SHOW_USERSTR);
+  UseLocalAsnloadDataAndErrMsg ();
+  ErrPathReset ();
+
+  /* finish resolving internal connections in ASN.1 parse tables */
+
+  if (! AllObjLoad ()) {
+    Message (MSG_FATAL, "AllObjLoad failed");
+    return 1;
+  }
+  if (! SubmitAsnLoad ()) {
+    Message (MSG_FATAL, "SubmitAsnLoad failed");
+    return 1;
+  }
+  if (! FeatDefSetLoad ()) {
+    Message (MSG_FATAL, "FeatDefSetLoad failed");
+    return 1;
+  }
+  if (! SeqCodeSetLoad ()) {
+    Message (MSG_FATAL, "SeqCodeSetLoad failed");
+    return 1;
+  }
+  if (! GeneticCodeTableLoad ()) {
+    Message (MSG_FATAL, "GeneticCodeTableLoad failed");
+    return 1;
+  }
+
+  SetUpAsnStreamData (&asd);
+
+  /* initialize OuputStreamData */
+  MemSet (&osd, 0, sizeof (osd));
+
+  /* initialize InputStreamData */
+  MemSet (&isd, 0, sizeof (isd));
+
+  /* initialize gap_sizes */
+  gap_sizes[0] = 0;
+  gap_sizes[1] = 0;
+
+  /* process command line arguments */
+
+  sprintf (app, "raw2delt %s", RAW2DELT_APPLICATION);
+  if (! GetArgs (app, sizeof (myargs) / sizeof (Args), myargs)) {
+    return 0;
+  }
+
+  u_eq = (Int4) myargs [u_argEqUnknownGap].intvalue;
+  u_gteq = (Int4) myargs [U_argGTEqUnknownGap].intvalue;
+  k_eq = (Int4) myargs [k_argEqUnknownGap].intvalue;
+  k_gteq = (Int4) myargs [K_argGtEqUnknownGap].intvalue;
+
+  if (u_eq < 1 && u_gteq < 1 && k_eq < 1 && k_gteq < 1) {
+    Message (MSG_FATAL, "Must specify values for at least one of -u, -U, -k, -K");
+    return 1;
+  } else if (u_eq > -1 && u_gteq > -1) {
+    Message (MSG_FATAL, "May only specify value for -u or -U, not both");
+    return 1;
+  } else if (k_eq > -1 && k_gteq > -1) {
+    Message (MSG_FATAL, "May only specify value for -k or -K, not both");
+    return 1;
+  }
+    
+  if (u_eq > 0) {
+    gap_sizes[0] = u_eq;
+  } else if (u_gteq > 0) {
+    gap_sizes[0] = 0 - u_gteq;
+  }
+
+  if (k_eq > 0) {
+    gap_sizes[1] = k_eq;
+  } else if (k_gteq > 0) {
+    gap_sizes[1] = 0 - k_gteq;
+  }
+
+  if (gap_sizes[0] == gap_sizes[1]) {
+    Message (MSG_FATAL, "Cannot specify the same size for known and unknown length gaps");
+    return 1;
+  }
+
+  directory = (CharPtr) myargs [p_argInputPath].strvalue;
+  osd.results_dir = (CharPtr) myargs [r_argOutputPath].strvalue;
+  if (StringHasNoText (osd.results_dir)) {
+    osd.results_dir = NULL;
+  }
+  osd.suffix = (CharPtr) myargs [x_argSuffix].strvalue;
+  osd.outsuffix = (CharPtr) myargs [s_argOutSuffix].strvalue;
+  osd.base = (CharPtr) myargs [i_argInputFile].strvalue;
+  osd.outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
+  if (StringHasNoText (osd.outfile)) {
+    osd.outfile = NULL;
+  }
+  osd.is_binary = (Boolean) myargs [d_argOutputBinary].intvalue;
+
+  if (osd.base == "stdin") {
+    osd.base = NULL;
+  }
+
+  /* if we don't have an output directory or an output file, and the user hasn't provided an
+   * output suffix, add a default.
+   */
+  if (osd.results_dir == NULL && osd.outfile == NULL && StringHasNoText (osd.outsuffix)) {
+    osd.outsuffix = ".delta";
+  } 
+
+  isd.is_binary = (Boolean) myargs [b_argInputBinary].intvalue;
+  isd.is_seqentry = (Boolean) myargs [e_argInputSeqEntry].intvalue;
+  isd.directory = directory;
+  isd.base = osd.base;
+  isd.suffix = osd.suffix;
+
+  if (StringDoesHaveText (osd.outfile)) {
+    osd.aip = AsnIoOpen (osd.outfile, "w");
+    if (osd.aip == NULL) {
+      Message (MSG_FATAL, "Unable to open output file");
+      return 1;
+    }
+  } else {
+    if (StringHasNoText (osd.results_dir)) {
+      osd.results_dir = directory;
+    }
+    /* if we're putting the results in a separate directory, strip the directory name from the output base */
+    if (!StringHasNoText (osd.results_dir) && !StringHasNoText (osd.base)) {
+#ifdef OS_MSWIN
+      ptr = StringRChr (osd.base, '\\');
+#else
+      ptr = StringRChr (osd.base, '/');
+#endif;
+      if (ptr != NULL) {
+        osd.base = ptr + 1;
+      }
+    }
+  }
+
+
+  if (StringHasNoText(directory) && StringHasNoText(osd.base)) {
+    rval = ProcessStream (&isd, &osd, &asd, gap_sizes);
+  } else if (StringDoesHaveText (osd.base)) {
+    ptr = StringRChr (osd.base, '.');
+    sfx[0] = '\0';
+    if (ptr != NULL) {
+      StringNCpy_0 (sfx, ptr, sizeof (sfx));
+      *ptr = '\0';
+    }
+    osd.suffix = sfx;
+    isd.suffix = sfx;
+    if (isd.is_binary) {
+      rval = ProcessStream (&isd, &osd, &asd, gap_sizes);
+    } else {
+      rval = ProcessOneRecord (directory, &osd, gap_sizes);
+    }
+  } else {
+
+    rval = FileRecurse (directory, &isd, &osd, &asd, gap_sizes);
+  }
+
+  if (osd.aip != NULL) {
+    AsnIoFlush (osd.aip);
+    AsnIoClose (osd.aip);
+  }
+  return rval;
+}
diff --git a/demo/seedtop.c b/demo/seedtop.c
index a6650d6e..556c857f 100644
--- a/demo/seedtop.c
+++ b/demo/seedtop.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: seedtop.c,v 6.18 2006/08/04 20:40:15 papadopo Exp $";
+static char const rcsid[] = "$Id: seedtop.c,v 6.19 2008/01/09 19:17:49 merezhuk Exp $";
 
-/* $Id: seedtop.c,v 6.18 2006/08/04 20:40:15 papadopo Exp $ */
+/* $Id: seedtop.c,v 6.19 2008/01/09 19:17:49 merezhuk Exp $ */
 /**************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -35,9 +35,12 @@ Maintainer: Alejandro Schaffer
  
 Contents: main routine for pseed3, stand-alone counterpart to PHI-BLAST.
  
-$Revision: 6.18 $
+$Revision: 6.19 $
 
 $Log: seedtop.c,v $
+Revision 6.19  2008/01/09 19:17:49  merezhuk
+-K option, extra hitArraySz parameter to get_a_pat call; print error if array size is not enough
+
 Revision 6.18  2006/08/04 20:40:15  papadopo
 allow filtering of query sequences
 
@@ -103,7 +106,7 @@ extern "C" {
 #endif
 
 
-#define NUMARG 20
+#define NUMARG 21
 
 static Args myargs [NUMARG] = {
   { "Database", 
@@ -145,7 +148,10 @@ static Args myargs [NUMARG] = {
   { "Filter query sequence with SEG",
 	"F", NULL, NULL, FALSE, 'F', ARG_BOOLEAN, 0.0, 0, NULL},
   { "Force searching for patterns even if they are too likely",
-	"F", NULL, NULL, FALSE, 'f', ARG_BOOLEAN, 0.0, 0, NULL}     
+    "F", NULL, NULL, FALSE, 'f', ARG_BOOLEAN, 0.0, 0, NULL},
+  { "internal hit buffer size multiplier (default: 2 /query_length/ )", 
+	"2", NULL, NULL, FALSE, 'K', ARG_INT, 0.0, 0, NULL},
+     
 };
 
 
@@ -200,6 +206,7 @@ Int2 Main(void)
         BLAST_OptionsBlkPtr options; /*used as placeholder for fillCandLambda*/
         ValNodePtr error_returns=NULL; /*store error messages*/
         ValNodePtr info_vnp = NULL;    /* store information messages */
+	Int4  hitArraySz = 0;
 
         seedSearch = (seedSearchItems *) ckalloc(sizeof(seedSearchItems));
         seedResults = (seedResultItems *) ckalloc(sizeof(seedResultItems));
@@ -343,9 +350,9 @@ Int2 Main(void)
 	  num_seq = readdb_get_num_entries(rdpt);
 	  dbLength = (Nlm_FloatHi) readdb_get_dblen(rdpt);              
         }
-
-	occurArray = (Int4 *) ckalloc(sizeof(Int4)*queryLength*2);
-	hitArray = (Int4 *) MemNew(sizeof(Int4)*queryLength*2);
+	hitArraySz = (Int4)(queryLength* myargs[20].intvalue);
+	occurArray = (Int4 *) ckalloc(sizeof(Int4)*hitArraySz);
+	hitArray = (Int4 *) MemNew(sizeof(Int4)*hitArraySz);
 
 	/* perform the search one pattern at a time */
 	while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, 
@@ -353,7 +360,7 @@ Int2 Main(void)
 				   program_flag, unfilter_query, query, 
                                    queryLength, is_dna,
                                    patternSearch, seedSearch, TRUE, 
-                                   &error_returns, &info_vnp)) {
+                                   &error_returns, &info_vnp,hitArraySz)) {
 
           PGPOutTextMessages(info_vnp, outfp);
           info_vnp = ValNodeFreeData(info_vnp);
@@ -443,18 +450,25 @@ Int2 Main(void)
             }
           }
 	}
+	if( error_returns )   BlastErrorPrint(error_returns);	
 
         BLAST_ScoreBlkDestruct(sbp);
         GapAlignBlkDelete(gap_align);
         BLASTOptionDelete(options);
 	rdpt = readdb_destruct(rdpt);
+	/* */
         MemFree(occurArray);
+	
         MemFree(hitArray);
+	
         MemFree(query);
         MemFree(unfilter_query);
+	
         MemFree(seedSearch);
-        MemFree(seedResults);
+	
+        MemFree(seedResults);	
         MemFree(patternSearch);
+	
         FileClose(patfp);
         FileClose(infp);
         FreeArgs(NUMARG, myargs);
diff --git a/demo/tbl2asn.c b/demo/tbl2asn.c
index b2362ba9..2aae8664 100644
--- a/demo/tbl2asn.c
+++ b/demo/tbl2asn.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   5/5/00
 *
-* $Revision: 6.199 $
+* $Revision: 6.223 $
 *
 * File Description:
 *
@@ -68,50 +68,67 @@
 #include <accpubseq.h>
 #endif
 
-#define TBL2ASN_APP_VER "9.0"
+#define TBL2ASN_APP_VER "10.3"
 
 CharPtr TBL2ASN_APPLICATION = TBL2ASN_APP_VER;
 
 typedef struct tblargs {
-  Boolean  fastaset;
-  Int2     whichclass;
-  Boolean  deltaset;
-  Boolean  alignset;
-  Boolean  gapped;
-  Boolean  phrapace;
-  Boolean  genprodset;
-  Boolean  linkbyoverlap;
-  Boolean  linkbyproduct;
-  Boolean  implicitgaps;
-  Boolean  forcelocalid;
-  Boolean  gpstonps;
-  Boolean  gnltonote;
-  Boolean  removeunnecxref;
-  Boolean  dotaxlookup;
-  CharPtr  accn;
-  CharPtr  center;
-  CharPtr  organism;
-  CharPtr  srcquals;
-  CharPtr  comment;
-  CharPtr  commentFile;
-  CharPtr  tableFile;
-  Boolean  findorf;
-  Boolean  runonorf;
-  Boolean  altstart;
-  Boolean  conflict;
-  Boolean  validate;
-  Boolean  flatfile;
-  Boolean  seqidfromfile;
-  Boolean  smartfeats;
-  Boolean  smarttitle;
-  Boolean  logtoterminal;
-  CharPtr  aln_beginning_gap;
-  CharPtr  aln_end_gap;
-  CharPtr  aln_middle_gap;
-  CharPtr  aln_missing;
-  CharPtr  aln_match;
-  Boolean  aln_is_protein;
-  Boolean  save_bioseq_set;
+  Boolean     raw2delt;
+  Int2        r2dmin;
+  Boolean     r2dunk100;
+  Boolean     fastaset;
+  Int2        whichclass;
+  Boolean     deltaset;
+  Boolean     alignset;
+  Boolean     gapped;
+  Boolean     phrapace;
+  Boolean     genprodset;
+  Boolean     linkbyoverlap;
+  Boolean     linkbyproduct;
+  Boolean     implicitgaps;
+  Boolean     forcelocalid;
+  Boolean     gpstonps;
+  Boolean     gnltonote;
+  Boolean     removeunnecxref;
+  Boolean     dotaxlookup;
+  Boolean     dopublookup;
+  CharPtr     accn;
+  CharPtr     center;
+  CharPtr     organism;
+  CharPtr     srcquals;
+  CharPtr     comment;
+  CharPtr     commentFile;
+  CharPtr     tableFile;
+  Boolean     findorf;
+  Boolean     runonorf;
+  Boolean     altstart;
+  Boolean     conflict;
+  Boolean     validate;
+  Boolean     relaxed;
+  Boolean     discrepancy;
+  Boolean     flatfile;
+  Boolean     seqidfromfile;
+  Boolean     smartfeats;
+  Boolean     smarttitle;
+  Boolean     logtoterminal;
+  CharPtr     aln_beginning_gap;
+  CharPtr     aln_end_gap;
+  CharPtr     aln_middle_gap;
+  CharPtr     aln_missing;
+  CharPtr     aln_match;
+  Boolean     aln_is_protein;
+  Boolean     save_bioseq_set;
+  ValNodePtr  locus_tag_list;
+  ValNodePtr  missing_locus_tag;
+  ValNodePtr  cds_product_list;
+  ValNodePtr  missing_cds_product;
+  ValNodePtr  mrna_product_list;
+  ValNodePtr  missing_mrna_product;
+  ValNodePtr  adjacent_locus_tag_disc_list;
+  ValNodePtr  missing_gnl_list;
+  ValNodePtr  gnl_list;
+  ValNodePtr  discrepancy_list;
+  DiscReportOutputConfigData disc_rep_config;
 } TblArgs, PNTR TblArgsPtr;
 
 static FILE* OpenOneFile (
@@ -184,15 +201,87 @@ static void WriteOneFile (
   AsnIoClose (aip);
 }
 
+static CharPtr compatSeverityLabel [] = {
+  "NONE", "NOTE: valid", "WARNING: valid", "ERROR: valid", "REJECT: valid", "FATAL: valid", "MAX", NULL
+};
+
+static void LIBCALLBACK ValidCallback (
+  ErrSev severity,
+  int errcode,
+  int subcode,
+  Uint2 entityID,
+  Uint2 itemtype,
+  Uint4 itemID,
+  CharPtr accession,
+  CharPtr message,
+  CharPtr objtype,
+  CharPtr label,
+  CharPtr context,
+  CharPtr location,
+  CharPtr product,
+  Pointer userdata
+)
+
+{
+  CharPtr  catname, errname;
+  FILE     *fp;
+
+  fp = (FILE *) userdata;
+  if (fp == NULL) return;
+
+  if (severity < SEV_NONE || severity > SEV_MAX) {
+    severity = SEV_MAX;
+  }
+
+  catname = GetValidCategoryName (errcode);
+  errname = GetValidErrorName (errcode, subcode);
+
+  if (catname == NULL) {
+    catname = "?";
+  }
+  if (errname == NULL) {
+    errname = "?";
+  }
+
+  if (accession == NULL) {
+    accession = "";
+  }
+  if (message == NULL) {
+    message = "";
+  }
+  if (objtype == NULL) {
+    objtype = "";
+  }
+  if (label == NULL) {
+    label = "";
+  }
+
+  fprintf (fp, "%s [%s.%s] %s %s: %s",
+           compatSeverityLabel [severity],
+           catname, errname, message, objtype, label);
+  if (location != NULL) {
+    fprintf (fp, " %s", location);
+  }
+  if (context != NULL) {
+    fprintf (fp, " %s", context);
+  }
+  if (product != NULL) {
+    fprintf (fp, " -> %s", product);
+  }
+  fprintf (fp, "\n");
+}
+
 static void ValidateOneFile (
   CharPtr results,
   CharPtr base,
   CharPtr suffix,
-  SeqEntryPtr sep
+  SeqEntryPtr sep,
+  Boolean relaxed
 )
 
 {
   Char            file [FILENAME_MAX], path [PATH_MAX];
+  FILE            *ofp;
   ErrSev          oldErrSev;
   ValidStructPtr  vsp;
 
@@ -200,22 +289,24 @@ static void ValidateOneFile (
   sprintf (file, "%s%s", base, suffix);
   FileBuildPath (path, NULL, file);
 
-  ErrSetOptFlags (EO_LOGTO_USRFILE);
-  ErrSetLogfile (path, ELOG_APPEND | ELOG_NOCREATE);
-
   vsp = ValidStructNew ();
   if (vsp != NULL) {
     vsp->useSeqMgrIndexes = TRUE;
     vsp->suppressContext = TRUE;
     vsp->seqSubmitParent = TRUE;
+    if (! relaxed) {
+      vsp->testLatLonSubregion = TRUE;
+    }
     oldErrSev = ErrSetMessageLevel (SEV_NONE);
+    ofp = FileOpen (path, "w");
+    vsp->errfunc = ValidCallback;
+    vsp->userdata = (Pointer) ofp;
+    /* vsp->convertGiToAccn = FALSE; */
     ValidateSeqEntry (sep, vsp);
     ValidStructFree (vsp);
+    FileClose (ofp);
     ErrSetMessageLevel (oldErrSev);
   }
-
-  ErrSetLogfile (NULL, ELOG_APPEND | ELOG_NOCREATE);
-  ErrClearOptFlags  (EO_LOGTO_USRFILE);
 }
 
 static void FlatfileOneFile (
@@ -873,6 +964,7 @@ static Int2 GetGenCodeForBsp (
 typedef struct gcmdata {
   SeqFeatPtr  gene;
   SeqFeatPtr  feat;
+  CharPtr     label;
 } GmcData, PNTR GmcDataPtr;
 
 static int LIBCALLBACK SortByGenePtr (
@@ -907,15 +999,20 @@ static void EnhanceOneCDS (
   GBQualPtr       gbq;
   Char            id [64];
   SeqIdPtr        ids, sip;
+  size_t          len;
+  CharPtr         name, nwstr, ptr, str;
   ObjectIdPtr     oip;
   ProtRefPtr      prp;
-  CharPtr         ptr, str;
   Char            tmp [256];
+  ValNodePtr      vnp;
   SeqFeatXrefPtr  xref;
 
   if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return;
 
+  name = NULL;
+  vnp = NULL;
   prp = NULL;
+
   for (xref = sfp->xref; xref != NULL; xref = xref->next) {
     if (xref->data.choice == SEQFEAT_PROT) {
       prp = (ProtRefPtr) xref->data.value.ptrvalue;
@@ -943,10 +1040,44 @@ static void EnhanceOneCDS (
 
     if (StringDoesHaveText (str)) {
       if (prp != NULL && prp->name != NULL) {
+        vnp = prp->name;
+        name = (CharPtr) vnp->data.ptrvalue;
+      }
+      if (StringDoesHaveText (name) && vnp != NULL) {
         if (alt_splice) {
-          AddQualifierToFeature (sfp, "product", str);
+          ptr = StringChr (str, '-');
+          if (ptr != NULL && StringLen (ptr) == 3) {
+            ptr++;
+            ptr++;
+            sprintf (tmp, "%s, isoform %s", str, ptr);
+            len = StringLen (name) + StringLen (", ") + StringLen (tmp);
+            nwstr = (CharPtr) MemNew (sizeof (Char) * (len + 2));
+            if (nwstr != NULL) {
+              StringCpy (nwstr, name);
+              /*
+              StringCat (nwstr, ", ");
+              */
+              StringCat (nwstr, " ");
+              StringCat (nwstr, tmp);
+              vnp->data.ptrvalue = (Pointer) nwstr;
+              MemFree (name);
+            }
+          } else {
+            AddQualifierToFeature (sfp, "product", str);
+          }
         } else {
-          AddQualifierToFeature (sfp, "product", str);
+          len = StringLen (name) + StringLen (", ") + StringLen (str);
+          nwstr = (CharPtr) MemNew (sizeof (Char) * (len + 2));
+          if (nwstr != NULL) {
+            StringCpy (nwstr, name);
+            /*
+            StringCat (nwstr, ", ");
+            */
+            StringCat (nwstr, " ");
+            StringCat (nwstr, str);
+            vnp->data.ptrvalue = (Pointer) nwstr;
+            MemFree (name);
+          }
         }
       } else {
         if (alt_splice) {
@@ -956,9 +1087,6 @@ static void EnhanceOneCDS (
             ptr++;
             sprintf (tmp, "%s, isoform %s", str, ptr);
             AddQualifierToFeature (sfp, "product", tmp);
-            /*
-            AddQualifierToFeature (sfp, "product", str);
-            */
           } else {
             AddQualifierToFeature (sfp, "product", str);
           }
@@ -982,7 +1110,8 @@ static void EnhanceOneMrna (
   GBQualPtr    gbq;
   Char         id [64];
   SeqIdPtr     ids, sip;
-  CharPtr      name, ptr, str;
+  size_t       len;
+  CharPtr      name, nwstr, ptr, str;
   ObjectIdPtr  oip;
   RnaRefPtr    rrp;
   Char         tmp [256];
@@ -990,6 +1119,7 @@ static void EnhanceOneMrna (
   if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return;
 
   name = NULL;
+
   rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
   if (rrp != NULL && rrp->type == 2 && rrp->ext.choice == 1) {
     name = rrp->ext.value.ptrvalue;
@@ -1015,11 +1145,41 @@ static void EnhanceOneMrna (
     }
 
     if (StringDoesHaveText (str)) {
-      if (StringDoesHaveText (name)) {
+      if (StringDoesHaveText (name) && StringCmp (str, name) != 0) {
         if (alt_splice) {
-          AddQualifierToFeature (sfp, "note", str);
+          ptr = StringChr (str, '-');
+          if (ptr != NULL && StringLen (ptr) == 3) {
+            ptr++;
+            ptr++;
+            sprintf (tmp, "%s, transcript variant %s", str, ptr);
+            len = StringLen (name) + StringLen (", ") + StringLen (tmp);
+            nwstr = (CharPtr) MemNew (sizeof (Char) * (len + 2));
+            if (nwstr != NULL) {
+              StringCpy (nwstr, name);
+              /*
+              StringCat (nwstr, ", ");
+              */
+              StringCat (nwstr, " ");
+              StringCat (nwstr, tmp);
+              rrp->ext.value.ptrvalue = (Pointer) nwstr;
+              MemFree (name);
+            }
+          } else {
+            AddQualifierToFeature (sfp, "product", str);
+          }
         } else {
-          AddQualifierToFeature (sfp, "note", str);
+          len = StringLen (name) + StringLen (", ") + StringLen (str);
+          nwstr = (CharPtr) MemNew (sizeof (Char) * (len + 2));
+          if (nwstr != NULL) {
+            StringCpy (nwstr, name);
+            /*
+            StringCat (nwstr, ", ");
+            */
+            StringCat (nwstr, " ");
+            StringCat (nwstr, str);
+            rrp->ext.value.ptrvalue = (Pointer) nwstr;
+            MemFree (name);
+          }
         }
       } else {
         if (alt_splice) {
@@ -1029,9 +1189,6 @@ static void EnhanceOneMrna (
             ptr++;
             sprintf (tmp, "%s, transcript variant %s", str, ptr);
             AddQualifierToFeature (sfp, "product", tmp);
-            /*
-            AddQualifierToFeature (sfp, "note", str);
-            */
           } else {
             AddQualifierToFeature (sfp, "product", str);
           }
@@ -1200,6 +1357,7 @@ static BioseqPtr AttachSeqAnnotEntity (
       }
 
       PromoteXrefsExEx (sfp, bsp, entityID, TRUE, FALSE, tbl->genprodset, tbl->forcelocalid);
+      sep = GetTopSeqEntryForEntityID (entityID);
     }
   } else {
     buf [0] = '\0';
@@ -1217,6 +1375,7 @@ static BioseqPtr AttachSeqAnnotEntity (
     }
     Message (MSG_POSTERR, "Feature table identifiers %s do not match record", buf);
   }
+  sep = GetTopSeqEntryForEntityID (entityID);
   return bsp;
 }
 
@@ -1391,15 +1550,17 @@ static void ProcessOneNuc (
 
 {
   Boolean        addNewBiop = TRUE;
+  Boolean        addNewMip = TRUE;
   BioSourcePtr   biop = NULL;
   SeqFeatPtr     cds;
   GBBlockPtr     gbp;
   Int2           genCode;
   size_t         len;
-  MolInfoPtr     mip;
+  MolInfoPtr     mip = NULL;
   Boolean        mito;
   OrgNamePtr     onp;
   OrgRefPtr      orp;
+  SeqDescrPtr    sdp;
   SeqHistPtr     shp;
   SqnTagPtr      stp = NULL;
   CharPtr        str;
@@ -1463,44 +1624,52 @@ static void ProcessOneNuc (
     AddMissingSourceInfo (biop);
   }
 
-  if (BioseqGetSeqDescr (bsp, Seq_descr_molinfo, NULL) == NULL) {
+  sdp = BioseqGetSeqDescr (bsp, Seq_descr_molinfo, NULL);
+  if (sdp != NULL && sdp->choice == Seq_descr_molinfo) {
+    mip = (MolInfoPtr) sdp->data.ptrvalue;
+    addNewMip = FALSE;
+  } else {
     mip = MolInfoNew ();
-    if (mip != NULL) {
-      if (stp != NULL) {
-        mip = ParseTitleIntoMolInfo (stp, mip);
-      }
-      if (mip->biomol == 0 && template_molinfo != NULL)
-      {
-        mip->biomol = template_molinfo->biomol;
-      }
-      if (mip->biomol == 0) {
-        mip->biomol = MOLECULE_TYPE_GENOMIC;
-      }
+  }
+  if (mip != NULL) {
+    if (stp != NULL) {
+      mip = ParseTitleIntoMolInfo (stp, mip);
+    }
+    if (mip->biomol == 0 && template_molinfo != NULL)
+    {
+      mip->biomol = template_molinfo->biomol;
+    }
+    if (mip->biomol == 0) {
+      mip->biomol = MOLECULE_TYPE_GENOMIC;
+    }
+    if (addNewMip) {
       SeqDescrAddPointer (&(bsp->descr), Seq_descr_molinfo, (Pointer) mip);
-      switch (mip->biomol) {
-        case MOLECULE_TYPE_PRE_MRNA :
-        case MOLECULE_TYPE_MRNA :
-        case MOLECULE_TYPE_RRNA :
-        case MOLECULE_TYPE_TRNA :
-        case MOLECULE_TYPE_SNRNA :
-        case MOLECULE_TYPE_SCRNA :
-        case MOLECULE_TYPE_CRNA :
-        case MOLECULE_TYPE_SNORNA :
-        case MOLECULE_TYPE_TRANSCRIBED_RNA :
-          if (bsp->mol == Seq_mol_dna) {
-            str = SqnTagFind (stp, "molecule");
-            if (str == NULL) {
-              str = SqnTagFind (stp, "mol");
-            }
-            if (str != NULL) {
-              if (StringICmp (str, "dna") == 0) break;
-            }
-            bsp->mol = Seq_mol_rna;
+    }
+    switch (mip->biomol) {
+      case MOLECULE_TYPE_PRE_MRNA :
+      case MOLECULE_TYPE_MRNA :
+      case MOLECULE_TYPE_RRNA :
+      case MOLECULE_TYPE_TRNA :
+      case MOLECULE_TYPE_SNRNA :
+      case MOLECULE_TYPE_SCRNA :
+      case MOLECULE_TYPE_CRNA :
+      case MOLECULE_TYPE_SNORNA :
+      case MOLECULE_TYPE_TRANSCRIBED_RNA :
+      case MOLECULE_TYPE_NCRNA :
+      case MOLECULE_TYPE_TMRNA :
+        if (bsp->mol == Seq_mol_dna) {
+          str = SqnTagFind (stp, "molecule");
+          if (str == NULL) {
+            str = SqnTagFind (stp, "mol");
           }
-          break;
-        default :
-          break;
-      }
+          if (str != NULL) {
+            if (StringICmp (str, "dna") == 0) break;
+          }
+          bsp->mol = Seq_mol_rna;
+        }
+        break;
+      default :
+        break;
     }
   }
 
@@ -1598,12 +1767,15 @@ static void ProcessOneAnnot (
   BioseqPtr   bsp;
   Int2        genCode;
   SeqFeatPtr  sfp;
+  SeqEntryPtr sep;
 
   if (sap == NULL || tbl == NULL) return;
 
   bsp = AttachSeqAnnotEntity (entityID, sap, tbl);
   if (bsp == NULL) return;
 
+    sep = GetTopSeqEntryForEntityID (entityID);
+
   /* correct all idx parent pointers */
 
   AssignIDsInEntity (entityID, 0, NULL);
@@ -1621,6 +1793,7 @@ static void ProcessOneAnnot (
       PromoteXrefsExEx (sfp, bsp, entityID, TRUE, FALSE, tbl->genprodset, tbl->forcelocalid);
     }
   }
+  sep = GetTopSeqEntryForEntityID (entityID);
 }
 
 static void UpdateException (
@@ -2039,6 +2212,96 @@ static Uint2 ProcessOneAsn (
   return entityID;
 }
 
+static Uint2 ProcessRaw2Delt (
+  FILE* fp,
+  BioSourcePtr src,
+  TblArgsPtr tbl,
+  CharPtr localname,
+  SeqEntryPtr gsep,
+  MolInfoPtr template_molinfo
+)
+
+{
+  BioseqPtr      bsp = NULL;
+  BioseqSetPtr   bssp;
+  Pointer        dataptr;
+  Uint2          datatype, entityID;
+  Int4           gap_sizes [2];
+  ObjMgrDataPtr  omdptop;
+  ObjMgrData     omdata;
+  Uint2          parenttype;
+  Pointer        parentptr;
+  SeqEntryPtr    sep;
+  SeqIdPtr       sip;
+
+  if (fp == NULL) return 0;
+
+  if (gsep != NULL) {
+    bssp = (BioseqSetPtr) gsep->data.ptrvalue;
+    if (bssp == NULL) return 0;
+
+    SaveSeqEntryObjMgrData (gsep, &omdptop, &omdata);
+    GetSeqEntryParent (gsep, &parentptr, &parenttype);
+
+    dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, TRUE, FALSE, TRUE, FALSE);
+    if (datatype == OBJ_BIOSEQ) {
+      bssp->seq_set = SeqMgrGetSeqEntryForData (dataptr);
+      SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) dataptr, gsep);
+    } else if (datatype == OBJ_BIOSEQSET) {
+      bssp->seq_set = SeqMgrGetSeqEntryForData (dataptr);
+      SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) dataptr, gsep);
+    } else if (datatype == OBJ_SEQENTRY) {
+      sep = (SeqEntryPtr) dataptr;
+      bssp->seq_set = sep;
+      if (IS_Bioseq (sep)) {
+        SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) sep->data.ptrvalue, gsep);
+      } else if (IS_Bioseq_set (sep)) {
+        SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) sep->data.ptrvalue, gsep);
+      } else return 0;
+    } else return 0;
+
+    SeqMgrLinkSeqEntry (gsep, parenttype, parentptr);
+    RestoreSeqEntryObjMgrData (gsep, omdptop, &omdata);
+
+    entityID = ObjMgrRegister (OBJ_BIOSEQSET, (Pointer) bssp);
+  } else {
+    dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, TRUE, FALSE, TRUE, FALSE);
+  }
+  if (dataptr == NULL) return 0;
+
+  sep = GetTopSeqEntryForEntityID (entityID);
+  bsp = FindNucBioseq (sep);
+  if (bsp == NULL) {
+    ObjMgrFreeByEntityID (entityID);
+    return 0;
+  }
+
+  if (StringDoesHaveText (localname)) {
+    sip = MakeSeqID (localname);
+    if (sip != NULL) {
+      bsp->id = SeqIdSetFree (bsp->id);
+      bsp->id = sip;
+      SeqMgrReplaceInBioseqIndex (bsp);
+      VisitFeaturesOnBsp (bsp, (Pointer) bsp->id, CorrectFeatureSeqIds);
+    }
+  }
+
+  if (bsp->repr == Seq_repr_raw) {
+    if (tbl->r2dunk100) {
+      gap_sizes [0] = 100;
+    } else {
+      gap_sizes [0] = 0;
+    }
+    gap_sizes [1] = -(tbl->r2dmin);
+
+    ConvertNsToGaps (bsp, gap_sizes);
+  }
+
+  ProcessOneNuc (entityID, bsp, src, tbl, template_molinfo);
+
+  return entityID;
+}
+
 static Uint2 ProcessGappedSet (
   FILE* fp,
   BioSourcePtr src,
@@ -3789,8 +4052,41 @@ static void RemoveUnnecGeneXref (
   }
 }
 
+static CharPtr RnaTypeLabel (
+  SeqFeatPtr rna
+)
+
+{
+  if (rna == NULL) return "RNA";
+  switch (rna->idx.subtype) {
+    case FEATDEF_preRNA :
+      return "preRNA";
+    case FEATDEF_mRNA :
+      return "mRNA";
+    case FEATDEF_tRNA :
+      return "tRNA";
+    case FEATDEF_rRNA :
+      return "rRNA";
+    case FEATDEF_snRNA :
+      return "snRNA";
+    case FEATDEF_scRNA :
+      return "scRNA";
+    case FEATDEF_otherRNA :
+      return "otherRNA";
+    case FEATDEF_snoRNA :
+      return "snoRNA";
+    case FEATDEF_ncRNA :
+      return "ncRNA";
+    case FEATDEF_tmRNA :
+      return "tmRNA";
+    default :
+      break;
+  }
+  return "RNA";
+}
+
 static void AddMrnaTitles (
-  SeqLocPtr slp,
+  SeqFeatPtr rna,
   CharPtr organism
 )
 
@@ -3803,9 +4099,10 @@ static void AddMrnaTitles (
   size_t             len;
   SeqFeatPtr         sfp;
   CharPtr            str;
+  CharPtr            typ = NULL;
 
-  if (slp == NULL) return;
-  bsp = BioseqFindFromSeqLoc (slp);
+  if (rna == NULL || rna->product == NULL) return;
+  bsp = BioseqFindFromSeqLoc (rna->product);
   if (bsp == NULL) return;
   if (! ISA_na (bsp->mol)) return;
   if (BioseqGetTitle (bsp) != NULL) return;
@@ -3823,8 +4120,9 @@ static void AddMrnaTitles (
       cdslabel = NULL;
     }
   }
+  typ = RnaTypeLabel (rna); 
   len = StringLen (organism) + StringLen (genelabel) + StringLen (cdslabel) +
-        StringLen (" mRNA, complete cds.") + 10;
+        StringLen (" mRNA, complete cds.") + StringLen (typ) + 10;
   str = (CharPtr) MemNew (len * sizeof (Char));
   if (str == NULL) return;
   str [0] = '\0';
@@ -3842,20 +4140,25 @@ static void AddMrnaTitles (
       StringCat (str, ")");
   }
   if (cdslabel != NULL && genelabel != NULL) {
+    StringCat (str, " ");
+    StringCat (str, typ);
     if (ccontext.partialL || ccontext.partialR) {
-      StringCat (str, " mRNA, partial cds.");
+      StringCat (str, ", partial cds.");
     } else {
-      StringCat (str, " mRNA, complete cds.");
+      StringCat (str, ", complete cds.");
     }
   } else if (genelabel != NULL) {
-    StringCat (str, " mRNA.");
+    StringCat (str, " ");
+    StringCat (str, typ);
+    StringCat (str, ".");
   }
   SeqDescrAddPointer (&(bsp->descr), Seq_descr_title, (Pointer) str);
 }
 
 static void MakeOneMrnaTitle (
-  SeqFeatPtr mrna,
+  SeqFeatPtr rna,
   SeqFeatPtr gene,
+  CharPtr label,
   CharPtr organism,
   Boolean alt_splice
 )
@@ -3864,36 +4167,35 @@ static void MakeOneMrnaTitle (
   BioseqPtr          bsp;
   SeqMgrFeatContext  ccontext;
   SeqFeatPtr         cds;
-  CharPtr            cdslabel = NULL;
   GeneRefPtr         grp;
   Char               id [64];
+  CharPtr            lbl = NULL;
   size_t             len;
+  CharPtr            ptr;
   CharPtr            str;
+  CharPtr            typ = NULL;
 
-  if (mrna == NULL || mrna->product == NULL) return;
+  if (rna == NULL || rna->product == NULL) return;
 
-  grp = SeqMgrGetGeneXref (mrna);
+  grp = SeqMgrGetGeneXref (rna);
   if (SeqMgrGeneIsSuppressed (grp)) return;
   if (grp == NULL && gene != NULL) {
     grp = (GeneRefPtr) gene->data.value.ptrvalue;
   }
   if (grp == NULL) return;
 
-  bsp = BioseqFindFromSeqLoc (mrna->product);
+  bsp = BioseqFindFromSeqLoc (rna->product);
   if (bsp == NULL) return;
   SeqIdWrite (bsp->id, id, PRINTID_TEXTID_ACC_VER, sizeof (id) - 1);
 
+  typ = RnaTypeLabel (rna); 
+  lbl = StringSaveNoNull (label);
+
   cds = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &ccontext);
-  if (cds != NULL) {
-    cdslabel = ccontext.label;
-    if (StringHasNoText (cdslabel)) {
-      cdslabel = NULL;
-    }
-  }
 
   len = StringLen (organism) + StringLen (grp->locus_tag) + StringLen (grp->locus) +
-        StringLen (id) + StringLen (" transcript variant") + StringLen (cdslabel) +
-        StringLen (" mRNA, complete cds.") + 20;
+        StringLen (id) + StringLen (" transcript variant") + StringLen (lbl) +
+        StringLen (" mRNA, complete cds.") + StringLen (typ) + 20;
   str = (CharPtr) MemNew (len * sizeof (Char));
   if (str == NULL) return;
   str [0] = '\0';
@@ -3901,33 +4203,44 @@ static void MakeOneMrnaTitle (
   if (StringDoesHaveText (organism)) {
     StringCat (str, organism);
   }
-  if (cdslabel != NULL) {
+  if (lbl != NULL) {
     StringCat (str, " ");
-    StringCat (str, cdslabel);
+    ptr = StringStr (lbl, ", transcript variant ");
+    if (ptr != NULL) {
+      *ptr = '\0';
+      ptr += 2;
+      StringCat (str, lbl);
+      if (StringDoesHaveText (grp->locus)) {
+          StringCat (str, " (");
+          StringCat (str, grp->locus);
+          StringCat (str, ")");
+      }
+      StringCat (str, " ");
+      StringCat (str, ptr);
+    } else {
+      StringCat (str, lbl);
+      if (StringDoesHaveText (grp->locus)) {
+          StringCat (str, " (");
+          StringCat (str, grp->locus);
+          StringCat (str, ")");
+      }
+    }
   }
-  if (StringDoesHaveText (grp->locus_tag)) {
+  if (cds != NULL) {
     StringCat (str, " ");
-    StringCat (str, grp->locus_tag);
-  }
-  if (StringDoesHaveText (grp->locus)) {
-      StringCat (str, " (");
-      StringCat (str, grp->locus);
-      StringCat (str, ")");
-  }
-  if (alt_splice && StringDoesHaveText (id)) {
-      StringCat (str, " transcript variant ");
-      StringCat (str, id);
-  }
-  if (cdslabel != NULL) {
+    StringCat (str, typ);
     if (ccontext.partialL || ccontext.partialR) {
-      StringCat (str, " mRNA, partial cds.");
+      StringCat (str, ", partial cds.");
     } else {
-      StringCat (str, " mRNA, complete cds.");
+      StringCat (str, ", complete cds.");
     }
   } else {
-    StringCat (str, " mRNA.");
+    StringCat (str, " ");
+    StringCat (str, typ);
+    StringCat (str, ".");
   }
   SeqDescrAddPointer (&(bsp->descr), Seq_descr_title, (Pointer) str);
+  MemFree (lbl);
 }
 
 static void MakeSmartMrnaTitles (
@@ -3937,10 +4250,10 @@ static void MakeSmartMrnaTitles (
 
 {
   SeqMgrFeatContext  context;
-  GmcDataPtr  gdp, head;
-  GeneRefPtr  grp;
-  Int2        i, j, k, numgene, nummrna;
-  SeqFeatPtr  sfp;
+  GmcDataPtr         gdp, head;
+  GeneRefPtr         grp;
+  Int2               i, j, k, numgene, nummrna;
+  SeqFeatPtr         sfp;
 
   if (bsp == NULL) return;
 
@@ -3949,11 +4262,11 @@ static void MakeSmartMrnaTitles (
 
   sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &context);
   while (sfp != NULL) {
-    switch (sfp->idx.subtype) {
-      case FEATDEF_GENE :
+    switch (sfp->data.choice) {
+      case SEQFEAT_GENE :
         numgene++;
         break;
-      case FEATDEF_mRNA :
+      case SEQFEAT_RNA :
         nummrna++;
         break;
       default :
@@ -3968,17 +4281,18 @@ static void MakeSmartMrnaTitles (
     head = (GmcDataPtr) MemNew (sizeof (GmcData) * (size_t) (nummrna + 1));
     if (head != NULL) {
       gdp = head;
-      sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_mRNA, &context);
+      sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_RNA, 0, &context);
       while (sfp != NULL) {
-        if (sfp->idx.subtype == FEATDEF_mRNA) {
+        if (sfp->product != NULL) {
           gdp->feat = sfp;
+          gdp->label = context.label;
           grp = SeqMgrGetGeneXref (sfp);
           if (grp == NULL || (! SeqMgrGeneIsSuppressed (grp))) {
             gdp->gene = SeqMgrGetOverlappingGene (sfp->location, NULL);
           }
           gdp++;
         }
-        sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_mRNA, &context);
+        sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_RNA, 0, &context);
       }
       HeapSort (head, (size_t) nummrna, sizeof (GmcData), SortByGenePtr);
       for (i = 0; i < nummrna; i += j) {
@@ -3986,11 +4300,11 @@ static void MakeSmartMrnaTitles (
         for (j = 1; i + j < nummrna && sfp == head [i + j].gene; j++) continue;
         if (j == 1) {
           /* no alt splicing */
-          MakeOneMrnaTitle (head [i].feat, head [i].gene, organism, FALSE);
+          MakeOneMrnaTitle (head [i].feat, head [i].gene, head [i].label, organism, FALSE);
         } else {
           /* is alt splicing */
           for (k = 0; k < j; k++) {
-            MakeOneMrnaTitle (head [i + k].feat, head [i].gene, organism, TRUE);
+            MakeOneMrnaTitle (head [i + k].feat, head [i + k].gene, head [i + k].label, organism, TRUE);
           }
         }
       }
@@ -4605,6 +4919,245 @@ static void ConvertStructuredComment (
   sdp->data.ptrvalue = uop;
 }
 
+static void CleanUpLatLonAndCountry (
+  BioSourcePtr biop,
+  Pointer userdata
+)
+
+{
+  CharPtr       fix_lat_lon;
+  Boolean       format_ok = FALSE;
+  CharPtr       lat_lon = NULL;
+  Boolean       lat_in_range = FALSE;
+  Boolean       lon_in_range = FALSE;
+  CharPtr PNTR  list;
+  CharPtr       new_country;
+  SubSourcePtr  ssp;
+
+  if (biop == NULL) return;
+  list = (CharPtr PNTR) userdata;
+  if (list == NULL) return;
+
+  for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
+    if (ssp->subtype == SUBSRC_country && StringDoesHaveText (ssp->name)) {
+      new_country = GetCountryFix (ssp->name, list);
+      if (new_country != NULL) {
+        ssp->name = MemFree (ssp->name);
+        ssp->name = new_country;
+      }
+    } else if (ssp->subtype == SUBSRC_lat_lon && StringDoesHaveText (ssp->name)) {
+      lat_lon = ssp->name;
+      IsCorrectLatLonFormat (lat_lon, &format_ok, &lat_in_range, &lon_in_range);
+      if (! format_ok) {
+        fix_lat_lon = FixLatLonFormat (lat_lon);
+        if (fix_lat_lon != NULL) {
+          ssp->name = MemFree (ssp->name);
+          ssp->name = fix_lat_lon;
+        }
+      }
+    }
+  }
+}
+
+static void LookupPubdesc (
+  PubdescPtr pdp,
+  Pointer userdata
+)
+
+{
+  CitArtPtr        cap;
+  MedlineEntryPtr  mep;
+  PubmedEntryPtr   pep;
+  Int4             pmid = 0;
+  ValNodePtr       vnp;
+
+  if (pdp == NULL) return;
+
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    switch (vnp->choice) {
+      case PUB_Muid :
+        /* ignore obsolete muids */
+        break;
+      case PUB_PMid :
+        pmid = vnp->data.intvalue;
+        break;
+      default :
+        /* return on real pub */
+        return;
+        break;
+    }
+  }
+
+  if (pmid == 0) return;
+
+  pep = GetPubMedForUid (pmid);
+  if (pep == NULL) return;
+  mep = (MedlineEntryPtr) pep->medent;
+  if (mep != NULL && mep->cit != NULL) {
+    cap = AsnIoMemCopy ((Pointer) mep->cit,
+                        (AsnReadFunc) CitArtAsnRead,
+                        (AsnWriteFunc) CitArtAsnWrite);
+    ValNodeAddPointer (&(pdp->pub), PUB_Article, (Pointer) cap);
+  }
+
+  PubmedEntryFree (pep);
+}
+
+
+typedef struct globaldiscrepancylists {
+  ValNodePtr locus_tag_list;
+  ValNodePtr missing_locus_tag;
+} GlobalDiscrepancyListsData, PNTR GlobalDiscrepancyListPtr;
+
+static void CollectGlobalDiscrepancyData (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  GeneRefPtr         grp;
+  GlobalDiscrepancyListPtr tbl;
+
+  if (sfp == NULL || sfp->idx.subtype != FEATDEF_GENE) return;
+  tbl = (GlobalDiscrepancyListPtr) userdata;
+  if (tbl == NULL) return;
+
+  grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+  if (grp != NULL) {
+    if (grp->pseudo) return;
+    if (StringDoesHaveText (grp->locus_tag)) {
+      ValNodeAddPointer (&(tbl->locus_tag_list), 0, 
+                          GlobalDiscrepancyNew (grp->locus_tag, OBJ_SEQFEAT, sfp));
+    } else {
+      ValNodeAddPointer (&(tbl->missing_locus_tag), 0,
+                          GlobalDiscrepancyNew (NULL, OBJ_SEQFEAT, sfp));
+    }
+  }
+}
+
+
+static void SaveStringsForDiscrepancyItemList (ValNodePtr list, Boolean use_feature_fmt);
+
+static void SaveStringsForDiscrepancyItems (ClickableItemPtr cip, Boolean use_feature_fmt)
+{
+  ValNodePtr vnp, list_copy;
+  CharPtr    str;
+
+  if (cip == NULL) return;
+  if (use_feature_fmt) {
+    list_copy = ReplaceDiscrepancyItemWithFeatureTableStrings (cip->item_list);
+    cip->item_list = ValNodeFree (cip->item_list);
+    cip->item_list = list_copy;
+  } else {
+    for (vnp = cip->item_list; vnp != NULL; vnp = vnp->next) {
+      str = GetDiscrepancyItemText (vnp);
+      vnp->choice = 0;
+      vnp->data.ptrvalue = str;
+    }
+  }
+  SaveStringsForDiscrepancyItemList (cip->subcategories, use_feature_fmt);
+}
+
+
+static void SaveStringsForDiscrepancyItemList (ValNodePtr list, Boolean use_feature_fmt)
+{
+  while (list != NULL) {
+    SaveStringsForDiscrepancyItems (list->data.ptrvalue, use_feature_fmt);
+    list = list->next;
+  }
+}
+
+
+#ifdef INTERNAL_NCBI_ASNDISC
+const PerformDiscrepancyTest taxlookup = CheckTaxNamesAgainstTaxDatabase;
+#else
+const PerformDiscrepancyTest taxlookup = NULL;
+#endif
+
+
+static void DiscrepancyReportOneRecord (TblArgsPtr tbl, SeqEntryPtr sep)
+{
+  ClickableItemPtr adjacent_cip = NULL;
+  ValNode          sep_list;
+  ValNodePtr       local_discrepancy_list = NULL;
+  Uint2            entityID;
+  DiscrepancyConfigData dcd;
+  GlobalDiscrepancyListsData lists;
+  GenProdSetDiscrepancyListsData gps_lists;
+  ProtIdListsData                prot_lists;
+  Int4                  k;
+
+  if (tbl == NULL || sep == NULL) return;
+
+  entityID = SeqMgrGetEntityIDForSeqEntry (sep);
+  if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
+    SeqMgrIndexFeatures (entityID, NULL);
+  }
+
+  MemSet (&lists, 0, sizeof (GlobalDiscrepancyListsData));
+  VisitGenProdSetFeatures (sep, &lists, CollectGlobalDiscrepancyData);
+  MemSet (&gps_lists, 0, sizeof (GenProdSetDiscrepancyListsData));
+  CheckGenProdSetsInSeqEntry (sep, &gps_lists);
+  MemSet (&prot_lists, 0, sizeof (ProtIdListsData));
+  VisitBioseqsInSep (sep, &prot_lists, FindProteinIDCallback);
+
+  if (lists.locus_tag_list != NULL) {
+    /* collect adjacent genes */
+    lists.locus_tag_list = ValNodeSort (lists.locus_tag_list, SortVnpByGlobalDiscrepancyString);
+    adjacent_cip = FindAdjacentDuplicateLocusTagGenes (lists.locus_tag_list);
+    if (adjacent_cip != NULL) {
+      SaveStringsForDiscrepancyItems (adjacent_cip, tbl->disc_rep_config.use_feature_table_format);
+      ValNodeAddPointer (&(tbl->adjacent_locus_tag_disc_list), 0, adjacent_cip);
+    }
+  }
+
+  /* convert lists to strings and add to global lists */
+  ConvertGlobalDiscrepancyListToText (lists.locus_tag_list, tbl->disc_rep_config.use_feature_table_format);
+  ValNodeLink (&(tbl->locus_tag_list), lists.locus_tag_list);
+  ConvertGlobalDiscrepancyListToText (lists.missing_locus_tag, tbl->disc_rep_config.use_feature_table_format);
+  ValNodeLink (&(tbl->missing_locus_tag), lists.missing_locus_tag);
+  ConvertGlobalDiscrepancyListToText (gps_lists.cds_product_list, tbl->disc_rep_config.use_feature_table_format);
+  ValNodeLink (&(tbl->cds_product_list), gps_lists.cds_product_list);
+  ConvertGlobalDiscrepancyListToText (gps_lists.missing_protein_id, tbl->disc_rep_config.use_feature_table_format);
+  ValNodeLink (&(tbl->missing_cds_product), gps_lists.missing_protein_id);
+  ConvertGlobalDiscrepancyListToText (gps_lists.mrna_product_list, tbl->disc_rep_config.use_feature_table_format);
+  ValNodeLink (&(tbl->mrna_product_list), gps_lists.mrna_product_list);
+  ConvertGlobalDiscrepancyListToText (gps_lists.missing_mrna_product, tbl->disc_rep_config.use_feature_table_format);
+  ValNodeLink (&(tbl->missing_mrna_product), gps_lists.missing_mrna_product);
+  ConvertGlobalDiscrepancyListToText (prot_lists.gnl_list, tbl->disc_rep_config.use_feature_table_format);
+  ValNodeLink (&tbl->gnl_list, prot_lists.gnl_list);
+  ConvertGlobalDiscrepancyListToText (prot_lists.missing_gnl_list, tbl->disc_rep_config.use_feature_table_format);
+  ValNodeLink (&tbl->missing_gnl_list, prot_lists.missing_gnl_list);
+
+  /* setup discrepancy report config */
+  MemSet (&dcd, 0, sizeof (DiscrepancyConfigData));
+  /* enable all tests except tRNA */
+  for (k = 0; k < MAX_DISC_TYPE; k++) {
+    dcd.conf_list[k] = TRUE;
+  }
+  DisableTRNATests (&(dcd));
+  /* disable tests that are global */
+  dcd.conf_list[DISC_GENE_MISSING_LOCUS_TAG] = FALSE;
+  dcd.conf_list[DISC_GENE_DUPLICATE_LOCUS_TAG] = FALSE;
+  dcd.conf_list[DISC_GENE_LOCUS_TAG_BAD_FORMAT] = FALSE;
+  dcd.conf_list[DISC_GENE_LOCUS_TAG_INCONSISTENT_PREFIX] = FALSE;
+  dcd.conf_list[DISC_MISSING_GENPRODSET_PROTEIN] = FALSE;
+  dcd.conf_list[DISC_DUP_GENPRODSET_PROTEIN] = FALSE;
+  dcd.conf_list[DISC_MISSING_GENPRODSET_TRANSCRIPT_ID] = FALSE;
+  dcd.conf_list[DISC_DUP_GENPRODSET_TRANSCRIPT_ID] = FALSE;
+  dcd.conf_list[DISC_MISSING_PROTEIN_ID] = FALSE;
+  dcd.conf_list[DISC_INCONSISTENT_PROTEIN_ID_PREFIX] = FALSE;
+
+  sep_list.data.ptrvalue = sep;
+  sep_list.next = NULL;
+  local_discrepancy_list = CollectDiscrepancies (&dcd, &sep_list, taxlookup);
+
+  SaveStringsForDiscrepancyItemList (local_discrepancy_list, tbl->disc_rep_config.use_feature_table_format);
+  ValNodeLink (&(tbl->discrepancy_list), local_discrepancy_list);
+
+}
+
+
 static void ProcessOneRecord (
   SubmitBlockPtr sbp,
   PubdescPtr pdp,
@@ -4641,6 +5194,7 @@ static void ProcessOneRecord (
   Boolean            has_create_date;
   SeqGraphPtr        lastsgp;
   Int4               linenum = 0;
+  CharPtr PNTR       list;
   CharPtr            localname = NULL;
   MolInfoPtr         mip;
   ErrSev             msev;
@@ -4712,6 +5266,8 @@ static void ProcessOneRecord (
     entityID = ProcessGappedSet (fp, src, tbl, gsep, template_molinfo);
   } else if (tbl->phrapace) {
     entityID = ProcessPhrapAce (fp, src, tbl, localname, gsep, template_molinfo, directory, base);
+  } else if (tbl->raw2delt) {
+    entityID = ProcessRaw2Delt (fp, src, tbl, localname, gsep, template_molinfo);
   } else {
     entityID = ProcessOneAsn (fp, src, tbl, localname, gsep, template_molinfo);
   }
@@ -4719,6 +5275,26 @@ static void ProcessOneRecord (
 
   if (entityID == 0) return;
 
+  if (tbl->dotaxlookup) {
+    sep = GetTopSeqEntryForEntityID (entityID);
+    if (sep != NULL) {
+
+      /* optionally do network taxonomy lookup - prior to instantiating mRNA and protein titles */
+
+      Taxon3ReplaceOrgInSeqEntry (sep, FALSE);
+    }
+  }
+
+  if (tbl->dopublookup) {
+    sep = GetTopSeqEntryForEntityID (entityID);
+    if (sep != NULL) {
+
+      /* optionally do network publication lookup of just PMID references */
+
+      VisitPubdescsInSep (sep, NULL, LookupPubdesc);
+    }
+  }
+
   organism = NULL;
   if (tbl->genprodset) {
     descr = ExtractBioSourceAndPubs (bssp->seq_set);
@@ -4749,6 +5325,8 @@ static void ProcessOneRecord (
 
     /* indexing needed to find segmented bsp if location is on part */
 
+    sep = GetTopSeqEntryForEntityID (entityID);
+
     SeqMgrIndexFeatures (entityID, NULL);
 
     while ((! failure) && (dataptr = ReadFeatureTableFile (fp, &datatype, NULL, &linenum, &failure)) != NULL) {
@@ -4762,6 +5340,8 @@ static void ProcessOneRecord (
       }
     }
     FileClose (fp);
+    sep = GetTopSeqEntryForEntityID (entityID);
+
 
     if (failure) {
       if (StringHasNoText (tblfile)) {
@@ -5053,6 +5633,11 @@ static void ProcessOneRecord (
       VisitFeaturesInSep (sep, NULL, RemoveUnnecGeneXref);
     }
 
+    if (! tbl->relaxed) {
+      list = GetValidCountryList ();
+      VisitBioSourcesInSep (sep, (Pointer) list, CleanUpLatLonAndCountry);
+    }
+
     /* need to reindex so hypothetical protein titles pick up locus_tag */
     SeqMgrIndexFeatures (entityID, NULL);
     InstantiateProteinTitles (entityID, NULL);
@@ -5065,10 +5650,10 @@ static void ProcessOneRecord (
       if (tbl->smarttitle) {
         MakeSmartMrnaTitles (bsp, organism);
       } else {
-        sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_mRNA, &context);
+        sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_RNA, 0, &context);
         while (sfp != NULL) {
-          AddMrnaTitles (sfp->product, organism);
-          sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_mRNA, &context);
+          AddMrnaTitles (sfp, organism);
+          sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_RNA, 0, &context);
         }
       }
     }
@@ -5078,7 +5663,8 @@ static void ProcessOneRecord (
     }
 
     if (StringDoesHaveText (tbl->accn)) {
-      VisitBioseqsInSep (sep, tbl->accn, MakeAccessionID);
+      bsp = FindNucBioseq (sep);
+      MakeAccessionID (bsp, tbl->accn);
     }
 
     VisitDescriptorsInSep (sep, NULL, ConvertStructuredComment);
@@ -5097,13 +5683,6 @@ static void ProcessOneRecord (
       LinkCDSmRNAbyProduct (sep);
     }
 
-    /* optionally do network taxonomy lookup */
-
-    if (tbl->dotaxlookup) {
-      sep = GetTopSeqEntryForEntityID (entityID);
-      Taxon3ReplaceOrgInSeqEntry (sep, FALSE);
-    }
-
     if (StringHasNoText (results)) {
       results = directory;
     }
@@ -5133,6 +5712,10 @@ static void ProcessOneRecord (
       Message (MSG_OK, "Illegal GO term format detected in note - contact database for instructions");
     }
 
+    if (tbl->discrepancy) {
+      DiscrepancyReportOneRecord (tbl, sep);
+    }
+
     if (tbl->validate || tbl->flatfile) {
       if (pdp != NULL) {
 
@@ -5152,7 +5735,7 @@ static void ProcessOneRecord (
       }
       if (tbl->validate) {
         Message (MSG_POST, "Validating %s\n", base);
-        ValidateOneFile (results, base, ".val", sep);
+        ValidateOneFile (results, base, ".val", sep, tbl->relaxed);
       }
     }
   }
@@ -5160,6 +5743,128 @@ static void ProcessOneRecord (
   ObjMgrFreeByEntityID (entityID);
 }
 
+
+static void DoDiscrepancySummary (
+  TblArgsPtr tbl,
+  FILE *fp
+)
+
+{
+  ValNodePtr  local_list = NULL;
+  ClickableItemPtr cip;
+
+  if (tbl == NULL) return;
+
+  tbl->locus_tag_list = ValNodeSort (tbl->locus_tag_list, SortVnpByGlobalDiscrepancyString);
+  tbl->missing_locus_tag = ValNodeSort (tbl->missing_locus_tag, SortVnpByGlobalDiscrepancyString);
+  tbl->cds_product_list = ValNodeSort (tbl->cds_product_list, SortVnpByGlobalDiscrepancyString);
+  tbl->missing_cds_product = ValNodeSort (tbl->missing_cds_product, SortVnpByGlobalDiscrepancyString);
+  tbl->mrna_product_list = ValNodeSort (tbl->mrna_product_list, SortVnpByGlobalDiscrepancyString);
+  tbl->missing_mrna_product = ValNodeSort (tbl->missing_mrna_product, SortVnpByGlobalDiscrepancyString);
+
+  if (tbl->locus_tag_list != NULL) {    
+    if (tbl->missing_locus_tag != NULL) {
+      cip = ReportMissingFields (tbl->missing_locus_tag, discReportMissingLocusTags, DISC_GENE_MISSING_LOCUS_TAG);
+      if (cip != NULL) {
+        ValNodeAddPointer (&local_list, 0, cip);
+      }
+    }
+    CollateDiscrepancyReports (&(tbl->adjacent_locus_tag_disc_list));
+    cip = ReportNonUniqueGlobalDiscrepancy (tbl->locus_tag_list, 
+                                            discReportDuplicateLocusTagFmt, 
+                                            discReportOneDuplicateLocusTagFmt,
+                                            DISC_GENE_DUPLICATE_LOCUS_TAG,
+                                            TRUE);
+    if (cip != NULL) {
+      ValNodeAddPointer (&local_list, 0, cip);
+      if (tbl->adjacent_locus_tag_disc_list != NULL) {
+        ValNodeLink (&(cip->subcategories), tbl->adjacent_locus_tag_disc_list);
+      }
+    } else if (tbl->adjacent_locus_tag_disc_list != NULL) {
+      ValNodeLink (&local_list, tbl->adjacent_locus_tag_disc_list);
+    }
+    tbl->adjacent_locus_tag_disc_list = NULL;
+
+    /* inconsistent locus tags */
+    ValNodeLink (&local_list,
+                 ReportInconsistentGlobalDiscrepancyPrefixes (tbl->locus_tag_list,
+                                                              discReportInconsistentLocusTagPrefixFmt,
+                                                              DISC_GENE_LOCUS_TAG_INCONSISTENT_PREFIX));
+    /* bad formats */
+    cip = ReportBadLocusTagFormat (tbl->locus_tag_list);
+    if (cip != NULL) {
+      ValNodeAddPointer (&local_list, 0, cip);
+    }
+  }
+
+  if (tbl->cds_product_list != NULL) {
+    /* report duplicates */
+    cip = ReportNonUniqueGlobalDiscrepancy (tbl->cds_product_list, 
+                                            discReportDuplicateProteinIDFmt,
+                                            discReportOneDuplicateProteinIDFmt,
+                                            DISC_DUP_GENPRODSET_PROTEIN,
+                                            TRUE);
+    if (cip != NULL) {
+      ValNodeAddPointer (&local_list, 0, cip);
+    }
+
+    /* report inconsistent IDs */
+    ValNodeLink (&local_list,
+                 ReportInconsistentGlobalDiscrepancyPrefixes (tbl->cds_product_list,
+                                                              discReportInconsistentProteinIDPrefixFmt,
+                                                              DISC_INCONSISTENT_PROTEIN_ID_PREFIX));
+  }
+
+  if (tbl->mrna_product_list != NULL) {
+    if (tbl->missing_locus_tag != NULL) {
+      cip = ReportMissingFields (tbl->mrna_product_list, discReportMissingTranscriptIDFmt, DISC_MISSING_GENPRODSET_TRANSCRIPT_ID);
+      if (cip != NULL) {
+        ValNodeAddPointer (&local_list, 0, cip);
+      }
+    }
+
+    cip = ReportNonUniqueGlobalDiscrepancy (tbl->mrna_product_list,
+                                            discReportDuplicateTranscriptIdFmt,
+                                            discReportOneDuplicateTranscriptIdFmt,
+                                            DISC_DUP_GENPRODSET_TRANSCRIPT_ID,
+                                            TRUE);
+    if (cip != NULL) {
+      ValNodeAddPointer (&local_list, 0, cip);
+    }
+  }
+
+  /* missing gnl protein IDs */
+  cip = ReportMissingFields (tbl->missing_gnl_list, discReportBadProteinIdFmt, DISC_MISSING_PROTEIN_ID);
+  if (cip != NULL) {
+    ValNodeAddPointer (&local_list, 0, cip);
+  }
+  tbl->gnl_list = ValNodeSort (tbl->gnl_list, SortVnpByGlobalDiscrepancyString);
+  ValNodeLink (&local_list, 
+                ReportInconsistentGlobalDiscrepancyStrings (tbl->gnl_list,
+                                                            discReportInconsistentProteinIDPrefixFmt,
+                                                            DISC_INCONSISTENT_PROTEIN_ID_PREFIX));
+
+
+  tbl->locus_tag_list = FreeGlobalDiscrepancyList (tbl->locus_tag_list);
+  tbl->missing_locus_tag = FreeGlobalDiscrepancyList (tbl->missing_locus_tag);
+  tbl->cds_product_list = FreeGlobalDiscrepancyList (tbl->cds_product_list);
+  tbl->missing_cds_product = FreeGlobalDiscrepancyList (tbl->missing_cds_product);
+  tbl->mrna_product_list = FreeGlobalDiscrepancyList (tbl->mrna_product_list);
+  tbl->missing_mrna_product = FreeGlobalDiscrepancyList (tbl->missing_mrna_product);
+  tbl->missing_gnl_list = FreeGlobalDiscrepancyList (tbl->missing_gnl_list);
+  tbl->gnl_list = FreeGlobalDiscrepancyList (tbl->gnl_list);
+
+
+  /* group discrepany reports from separate files */
+  CollateDiscrepancyReports (&(tbl->discrepancy_list));
+  
+    
+  WriteAsnDiscReport (local_list, fp, &(tbl->disc_rep_config), TRUE);
+  local_list = FreeClickableList (local_list);
+
+  WriteAsnDiscReport (tbl->discrepancy_list, fp, &(tbl->disc_rep_config), TRUE);
+}
+
 static CharPtr overwriteMsg = "Your template with a .sqn suffix will be overwritten.  Do you wish to continue?";
 
 static Boolean TemplateOverwriteRisk (
@@ -5535,6 +6240,41 @@ static CharPtr ReadCommentFile (
   return tmp;
 }
 
+static CharPtr ParseCommaField (
+  CharPtr PNTR strP
+)
+
+{
+  CharPtr  ptr;
+  CharPtr  str;
+
+  if (strP == NULL) return NULL;
+
+  str = *strP;
+  if (StringHasNoText (str)) {
+    *strP = NULL;
+    return NULL;
+  }
+
+  ptr = StringChr (str, ',');
+  if (ptr == NULL) {
+    *strP = NULL;
+    return str;
+  }
+
+  *ptr = '\0';
+  ptr++;
+  if (StringHasNoText (ptr)) {
+    ptr = NULL;
+  }
+  *strP = ptr;
+
+  if (StringHasNoText (str)) {
+    str = NULL;
+  }
+  return str;
+}
+
 /* Args structure contains command-line arguments */
 
 #define p_argInputPath         0
@@ -5543,46 +6283,43 @@ static CharPtr ReadCommentFile (
 #define o_argOutputFile        3
 #define x_argSuffix            4
 #define t_argTemplate          5
-#define s_argFastaSet          6
-#define w_argWhichClass        7
-#define d_argDeltaSet          8
-#define l_argAlignment         9
-#define z_argGapped           10
-#define e_argPhrapAce         11
-#define g_argGenProdSet       12
-#define F_argFeatIdLinks      13
-#define H_argImplicitGaps     14
-#define a_argAccession        15
-#define C_argCenter           16
-#define n_argOrgName          17
-#define j_argSrcQuals         18
-#define y_argComment          19
-#define Y_argCommentFile      20
-#define D_argDescrsFile       21
-#define f_argTableFile        22
-#define c_argFindOrf          23
-#define m_argAltStart         24
-#define k_argConflict         25
-#define v_argValidate         26
-#define b_argGenBank          27
-#define q_argFileID           28
-#define u_argUndoGPS          29
-#define h_argGnlToNote        30
-#define B_argBegGap           31
-#define E_argEndGap           32
-#define G_argMidGap           33
-#define X_argMissing          34
-#define M_argMatch            35
-#define P_argIsProt           36
-#define R_argRemote           37
-#define S_argSmartFeats       38
-#define Q_argSmartTitle       39
-#define U_argUnnecXref        40
-#define L_argLocalID          41
-#define T_argTaxLookup        42
-#define W_argLogProgress      43
-#define O_argRunonOrf         44
-#define K_argBioseqSet        45
+#define a_argType              6
+#define s_argFastaSet          7
+#define w_argWhichClass        8
+#define d_argDeltaSet          9
+#define l_argAlignment        10
+#define z_argGapped           11
+#define e_argPhrapAce         12
+#define g_argGenProdSet       13
+#define F_argFeatIdLinks      14
+#define H_argImplicitGaps     15
+#define A_argAccession        16
+#define C_argCenter           17
+#define n_argOrgName          18
+#define j_argSrcQuals         19
+#define y_argComment          20
+#define Y_argCommentFile      21
+#define D_argDescrsFile       22
+#define f_argTableFile        23
+#define k_argCdsFlags         24
+#define c_argFindOrf          25
+#define V_argVerify           26
+#define v_argValidate         27
+#define b_argGenBank          28
+#define q_argFileID           29
+#define u_argUndoGPS          30
+#define h_argGnlToNote        31
+#define G_argGapFields        32
+#define R_argRemote           33
+#define S_argSmartFeats       34
+#define Q_argSmartTitle       35
+#define U_argUnnecXref        36
+#define L_argLocalID          37
+#define T_argTaxLookup        38
+#define P_argPubLookup        39
+#define W_argLogProgress      40
+#define K_argBioseqSet        41
+#define Z_argDiscRepFile      42
 
 Args myargs [] = {
   {"Path to Files", NULL, NULL, NULL,
@@ -5597,26 +6334,36 @@ Args myargs [] = {
     TRUE, 'x', ARG_STRING, 0.0, 0, NULL},
   {"Template File", NULL, NULL, NULL,
     TRUE, 't', ARG_FILE_IN, 0.0, 0, NULL},
+  {"File Type\n"
+   "      a Any\n"
+   "      r20u Runs of 20+ Ns are gaps, 100 Ns are unknown length\n"
+   "      r20k Runs of 20+ Ns are gaps, 100 Ns are known length\n"
+   "      s FASTA Set (s Batch, s1 Pop, s2 Phy, s3 Mut, s4 Eco)\n"
+   "      d FASTA Delta, di FASTA Delta with Implicit Gaps\n"
+   "      l FASTA+Gap Alignment\n"
+   "      z FASTA with Gap Lines\n"
+   "      e PHRAP/ACE\n", "a", NULL, NULL,
+    TRUE, 'a', ARG_STRING, 0.0, 0, NULL},
   {"Read FASTAs as Set", "F", NULL, NULL,
     TRUE, 's', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Fasta Set Class (1 Pop, 2 Phy, 3 Mut, 4 Eco)", "0", "0", "4",
+  {"Fasta Set Class (1 Pop, 2 Phy, 3 Mut, 4 Eco) (obsolete: use -a s1-4)", "0", "0", "4",
     FALSE, 'w', ARG_INT, 0.0, 0, NULL},
-  {"Read FASTAs as Delta", "F", NULL, NULL,
+  {"Read FASTAs as Delta (obsolete: use -a d)", "F", NULL, NULL,
     TRUE, 'd', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Read FASTA+Gap Alignment", "F", NULL, NULL,
+  {"Read FASTA+Gap Alignment (obsolete: use -a l)", "F", NULL, NULL,
     TRUE, 'l', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Read FASTAs with Gap Lines", "F", NULL, NULL,
+  {"Read FASTAs with Gap Lines (obsolete: use -a z)", "F", NULL, NULL,
     TRUE, 'z', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Read PHRAP/ACE Format", "F", NULL, NULL,
+  {"Read PHRAP/ACE Format (obsolete: use -a e)", "F", NULL, NULL,
     TRUE, 'e', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Genomic Product Set", "F", NULL, NULL,
     TRUE, 'g', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Feature ID Links (o by Overlap, p by Product)", NULL, NULL, NULL,
     TRUE, 'F', ARG_STRING, 0.0, 0, NULL},
-  {"Implicit Gaps", "F", NULL, NULL,
+  {"Implicit Gaps (obsolete: use -a di)", "F", NULL, NULL,
     TRUE, 'H', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Accession", NULL, NULL, NULL,
-    TRUE, 'a', ARG_STRING, 0.0, 0, NULL},
+    TRUE, 'A', ARG_STRING, 0.0, 0, NULL},
   {"Genome Center Tag", NULL, NULL, NULL,
     TRUE, 'C', ARG_STRING, 0.0, 0, NULL},
   {"Organism Name", NULL, NULL, NULL,
@@ -5631,15 +6378,22 @@ Args myargs [] = {
     TRUE, 'D', ARG_FILE_IN, 0.0, 0, NULL},
   {"Single Table File", NULL, NULL, NULL,
     TRUE, 'f', ARG_FILE_IN, 0.0, 0, NULL},
-  {"Annotate Longest ORF", "F", NULL, NULL,
+  {"CDS Flags (combine any of the following letters)\n"
+   "      c Annotate Longest ORF\n"
+   "      r Allow Runon ORFs\n"
+   "      m Allow Alternative Starts\n"
+   "      k Set Conflict on Mismatch\n", NULL, NULL, NULL,
+    TRUE, 'k', ARG_STRING, 0.0, 0, NULL},
+  {"Annotate Longest ORF (obsolete: use -k c)", "F", NULL, NULL,
     TRUE, 'c', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Allow Alternative Starts", "F", NULL, NULL,
-    TRUE, 'm', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Set Conflict on Mismatch", "F", NULL, NULL,
-    TRUE, 'k', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Validate", "F", NULL, NULL,
+  {"Verification (combine any of the following letters)\n"
+   "      v Validate with Normal Stringency\n"
+   "      r Validate without Country Check\n"
+   "      b Generate GenBank Flatfile\n", NULL, NULL, NULL,
+    TRUE, 'V', ARG_STRING, 0.0, 0, NULL},
+  {"Validate (obsolete: use -V v)", "F", NULL, NULL,
     TRUE, 'v', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Generate GenBank File", "F", NULL, NULL,
+  {"Generate GenBank File (obsolete: use -V b)", "F", NULL, NULL,
     TRUE, 'b', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Seq ID from File Name", "F", NULL, NULL,
     TRUE, 'q', ARG_BOOLEAN, 0.0, 0, NULL},
@@ -5647,19 +6401,12 @@ Args myargs [] = {
     TRUE, 'u', ARG_BOOLEAN, 0.0, 0, NULL},
   {"General ID to Note", "F", NULL, NULL,
     TRUE, 'h', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Alignment Beginning Gap Characters",  NULL, NULL, NULL,
-    TRUE, 'B', ARG_STRING, 0.0, 0, NULL},
-  {"Alignment End Gap Characters",  NULL, NULL, NULL,
-    TRUE, 'E', ARG_STRING, 0.0, 0, NULL},
-  {"Alignment Middle Gap Characters",  NULL, NULL, NULL,
+  {"Alignment Gap Flags (comma separated fields, e.g., p,-,-,-,?,. )\n"
+   "      n Nucleotide or p Protein,\n"
+   "      Begin, Middle, End Gap Characters,\n"
+   "      Missing Characters, Match Characters\n",  NULL, NULL, NULL,
     TRUE, 'G', ARG_STRING, 0.0, 0, NULL},
-  {"Alignment Missing Characters",  NULL, NULL, NULL,
-    TRUE, 'X', ARG_STRING, 0.0, 0, NULL},
-  {"Alignment Match Characters",  NULL, NULL, NULL,
-    TRUE, 'M', ARG_STRING, 0.0, 0, NULL},
-  {"Alignment Is Proteins", "F", NULL, NULL,
-    TRUE, 'P', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Remote Fetching from ID", "F", NULL, NULL,
+  {"Remote Sequence Record Fetching from ID", "F", NULL, NULL,
     TRUE, 'R', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Smart Feature Annotation", "F", NULL, NULL,
     TRUE, 'S', ARG_BOOLEAN, 0.0, 0, NULL},
@@ -5671,12 +6418,14 @@ Args myargs [] = {
     TRUE, 'L', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Remote Taxonomy Lookup", "F", NULL, NULL,
     TRUE, 'T', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Remote Publication Lookup", "F", NULL, NULL,
+    TRUE, 'P', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Log Progress", "F", NULL, NULL,
     TRUE, 'W', ARG_BOOLEAN, 0.0, 0, NULL},
-  {"Allow Runon ORFs", "F", NULL, NULL,
-    TRUE, 'O', ARG_BOOLEAN, 0.0, 0, NULL},
   {"Save Bioseq-set", "F", NULL, NULL,
     TRUE, 'K', ARG_BOOLEAN, 0.0, 0, NULL},
+  {"Discrepancy Report Output File", NULL, NULL, NULL,
+    TRUE, 'Z', ARG_FILE_OUT, 0.0, 0, NULL},
 };
 
 Int2 Main (void)
@@ -5692,6 +6441,7 @@ Int2 Main (void)
   CharPtr         descrs;
   CharPtr         directory;
   FILE            *fp;
+  Char            gapstring [128];
   TextFsaPtr      gotags;
   CharPtr         os;
   CharPtr         outfile;
@@ -5711,11 +6461,14 @@ Int2 Main (void)
   Char            str [64];
   CharPtr         suffix;
   TblArgs         tbl;
+  CharPtr         tmp;
   CharPtr         tmplate;
+  CharPtr         disc_rep_file = NULL;
 
   /* standard setup */
 
   ErrSetFatalLevel (SEV_MAX);
+  ErrSetMessageLevel (SEV_MAX);
   ErrClearOptFlags (EO_SHOW_USERSTR);
   UseLocalAsnloadDataAndErrMsg ();
   ErrPathReset ();
@@ -5772,12 +6525,75 @@ Int2 Main (void)
 
   MemSet ((Pointer) &tbl, 0, sizeof (TblArgs));
 
-  tbl.fastaset = (Boolean) myargs [s_argFastaSet].intvalue;
+  /* process obsolete format arguments first, warn if used */
+
   tbl.whichclass = (Boolean) myargs [w_argWhichClass].intvalue;
+  if (tbl.whichclass) {
+    Message (MSG_POST, "-w is obsolete, use -a s1-4 instead");
+  }
   tbl.deltaset = (Boolean) myargs [d_argDeltaSet].intvalue;
+  if (tbl.deltaset) {
+    Message (MSG_POST, "-d is obsolete, use -a d instead");
+  }
   tbl.alignset = (Boolean) myargs [l_argAlignment].intvalue;
+  if (tbl.alignset) {
+    Message (MSG_POST, "-l is obsolete, use -a l instead");
+  }
   tbl.gapped = (Boolean) myargs [z_argGapped].intvalue;
+  if (tbl.gapped) {
+    Message (MSG_POST, "-z is obsolete, use -a z instead");
+  }
   tbl.phrapace = (Boolean) myargs [e_argPhrapAce].intvalue;
+  if (tbl.phrapace) {
+    Message (MSG_POST, "-e is obsolete, use -a e instead");
+  }
+  tbl.implicitgaps = (Boolean) myargs [H_argImplicitGaps].intvalue;
+  if (tbl.implicitgaps) {
+    Message (MSG_POST, "-H is obsolete, use -a di instead");
+  }
+
+  /* -s is heavily used and will remain as an alternative to -a s */
+
+  tbl.fastaset = (Boolean) myargs [s_argFastaSet].intvalue;
+
+  /* process new -a type argument */
+
+  ptr = myargs [a_argType].strvalue;
+  if (StringICmp (ptr, "r20u") == 0) {
+    tbl.raw2delt = TRUE;
+    tbl.r2dmin = 20;
+    tbl.r2dunk100 = TRUE;
+  } else if (StringICmp (ptr, "r20k") == 0) {
+    tbl.raw2delt = TRUE;
+    tbl.r2dmin = 20;
+    tbl.r2dunk100 = FALSE;
+  } else if (StringICmp (ptr, "s") == 0) {
+    tbl.fastaset = TRUE;
+  } else if (StringICmp (ptr, "w1") == 0 || StringICmp (ptr, "s1") == 0) {
+    tbl.fastaset = TRUE;
+    tbl.whichclass = 1;
+  } else if (StringICmp (ptr, "w2") == 0 || StringICmp (ptr, "s2") == 0) {
+    tbl.fastaset = TRUE;
+    tbl.whichclass = 2;
+  } else if (StringICmp (ptr, "w3") == 0 || StringICmp (ptr, "s3") == 0) {
+    tbl.fastaset = TRUE;
+    tbl.whichclass = 3;
+  } else if (StringICmp (ptr, "w4") == 0 || StringICmp (ptr, "s4") == 0) {
+    tbl.fastaset = TRUE;
+    tbl.whichclass = 4;
+  } else if (StringICmp (ptr, "d") == 0) {
+    tbl.deltaset = TRUE;
+  } else if (StringICmp (ptr, "di") == 0) {
+    tbl.deltaset = TRUE;
+    tbl.implicitgaps = TRUE;
+  } else if (StringICmp (ptr, "l") == 0) {
+    tbl.alignset = TRUE;
+  } else if (StringICmp (ptr, "z") == 0) {
+    tbl.gapped = TRUE;
+  } else if (StringICmp (ptr, "e") == 0) {
+    tbl.phrapace = TRUE;
+  }
+
   tbl.genprodset = (Boolean) myargs [g_argGenProdSet].intvalue;
   ptr = myargs [F_argFeatIdLinks].strvalue;
   if (StringICmp (ptr, "o") == 0) {
@@ -5785,42 +6601,106 @@ Int2 Main (void)
   } else if (StringICmp (ptr, "p") == 0) {
     tbl.linkbyproduct = TRUE;
   }
-  tbl.implicitgaps = (Boolean) myargs [H_argImplicitGaps].intvalue;
   tbl.forcelocalid = (Boolean) myargs [L_argLocalID].intvalue;
   tbl.gpstonps = (Boolean) myargs [u_argUndoGPS].intvalue;
   tbl.gnltonote = (Boolean) myargs [h_argGnlToNote].intvalue;
-  tbl.accn = (CharPtr) myargs [a_argAccession].strvalue;
+  tbl.accn = (CharPtr) myargs [A_argAccession].strvalue;
   tbl.center = (CharPtr) myargs [C_argCenter].strvalue;
   tbl.organism = (CharPtr) myargs [n_argOrgName].strvalue;
   tbl.srcquals = (CharPtr) myargs [j_argSrcQuals].strvalue;
   tbl.comment = (CharPtr) myargs [y_argComment].strvalue;
   tbl.commentFile = ReadCommentFile ((CharPtr) myargs [Y_argCommentFile].strvalue);
+
+  /* process obsolete findorf argument first, warn if used */
+
   tbl.findorf = (Boolean) myargs [c_argFindOrf].intvalue;
-  tbl.runonorf = (Boolean) myargs [O_argRunonOrf].intvalue;
+  if (tbl.findorf) {
+    Message (MSG_POST, "-c is obsolete, use -k c instead");
+  }
+
+  ptr = myargs [k_argCdsFlags].strvalue;
+  if (StringChr (ptr, 'c') != NULL) {
+    tbl.findorf = TRUE;
+  }
+  if (StringChr (ptr, 'r') != NULL) {
+    tbl.runonorf = TRUE;
+    tbl.findorf = TRUE;
+  }
+  if (StringChr (ptr, 'm') != NULL) {
+    tbl.altstart = TRUE;
+  }
+  if (StringChr (ptr, 'k') != NULL) {
+    tbl.conflict = TRUE;
+  }
+  /*
   if (!tbl.findorf && tbl.runonorf) {
-    Message (MSG_FATAL, "-O cannot be used without -c");
+    Message (MSG_FATAL, "-k r cannot be used without -k c");
     return 1;
   }
-  tbl.altstart = (Boolean) myargs [m_argAltStart].intvalue;
-  tbl.conflict = (Boolean) myargs [k_argConflict].intvalue;
+  */
+
+  /* process obsolete validate/flatfile arguments first, warn if used */
+
   tbl.validate = (Boolean) myargs [v_argValidate].intvalue;
+  if (tbl.validate) {
+    Message (MSG_POST, "-v is obsolete, use -V v instead");
+  }
   tbl.flatfile = (Boolean) myargs [b_argGenBank].intvalue;
+  if (tbl.flatfile) {
+    Message (MSG_POST, "-b is obsolete, use -V b instead");
+  }
+
+  ptr = myargs [V_argVerify].strvalue;
+  if (StringChr (ptr, 'v') != NULL) {
+    tbl.validate = TRUE;
+  }
+  if (StringChr (ptr, 'r') != NULL) {
+    tbl.validate = TRUE;
+    tbl.relaxed = TRUE;
+  }
+  if (StringChr (ptr, 'b') != NULL) {
+    tbl.flatfile = TRUE;
+  }
+
+  
+
   tbl.seqidfromfile = (Boolean) myargs [q_argFileID].intvalue;
   tbl.smartfeats = (Boolean) myargs [S_argSmartFeats].intvalue;
   tbl.smarttitle = (Boolean) myargs [Q_argSmartTitle].intvalue;
   tbl.removeunnecxref = (Boolean) myargs [U_argUnnecXref].intvalue;
   tbl.dotaxlookup = (Boolean) myargs [T_argTaxLookup].intvalue;
+  tbl.dopublookup = (Boolean) myargs [P_argPubLookup].intvalue;
   tbl.logtoterminal = (Boolean) myargs [W_argLogProgress].intvalue;
 
-  /* arguments for alignment reading */
-  tbl.aln_beginning_gap = (CharPtr) myargs [B_argBegGap].strvalue;
-  tbl.aln_end_gap = (CharPtr) myargs [E_argEndGap].strvalue;
-  tbl.aln_middle_gap = (CharPtr) myargs [G_argMidGap].strvalue;
-  tbl.aln_missing = (CharPtr) myargs [X_argMissing].strvalue;
-  tbl.aln_match = (CharPtr) myargs [M_argMatch].strvalue;
-  tbl.aln_is_protein = (Boolean) myargs [P_argIsProt].intvalue;
   tbl.save_bioseq_set = (Boolean) myargs [K_argBioseqSet].intvalue;
 
+  disc_rep_file = (CharPtr) myargs [Z_argDiscRepFile].strvalue;
+  if (!StringHasNoText (disc_rep_file)) {
+    tbl.discrepancy = TRUE;
+  }
+
+
+  /* arguments for alignment reading, e.g., "p,-,-,-,?,." */
+
+  gapstring [0] = '\0';
+  ptr = (CharPtr) myargs [G_argGapFields].strvalue;
+  StringNCpy_0 (gapstring, ptr, sizeof (gapstring));
+
+  ptr = gapstring;
+  tmp = ParseCommaField (&ptr);
+  if (tmp != NULL) {
+    if (StringChr (tmp, 'p') != NULL) {
+      tbl.aln_is_protein = TRUE;
+    } else if (StringChr (tmp, 'n') == NULL) {
+      Message (MSG_FATAL, "-G must start with p for Protein or n for Nucleotide");
+      return 1;
+    }
+  }
+  tbl.aln_beginning_gap = ParseCommaField (&ptr);
+  tbl.aln_middle_gap = ParseCommaField (&ptr);
+  tbl.aln_end_gap = ParseCommaField (&ptr);
+  tbl.aln_missing = ParseCommaField (&ptr);
+  tbl.aln_match = ParseCommaField (&ptr);
 
   if (StringHasNoText (tbl.accn)) {
     tbl.accn = NULL;
@@ -5851,7 +6731,7 @@ Int2 Main (void)
       || StringDoesHaveText (tbl.aln_missing)
       || StringDoesHaveText (tbl.aln_match)
       || tbl.aln_is_protein)) {
-    Message (MSG_FATAL, "Alignment options (-B, -E, -G, -X, -M, -P) can only be used with -l");
+    Message (MSG_FATAL, "-G can only be used with -a l");
     return 1;
   }
 
@@ -5964,7 +6844,7 @@ Int2 Main (void)
   TextFsaAdd (gotags, "go_function");
   TextFsaAdd (gotags, "go_process");
 
-  /* register fetch function */
+  /* register fetch functions */
 
   if (remote) {
 #ifdef INTERNAL_NCBI_TBL2ASN
@@ -5977,6 +6857,10 @@ Int2 Main (void)
 #endif
   }
 
+  if (remote || tbl.dopublookup) {
+    PubMedFetchEnable ();
+  }
+
   /* process one or more records */
 
   if (StringDoesHaveText (outfile) && StringHasNoText (base)) {
@@ -6010,6 +6894,16 @@ Int2 Main (void)
     AsnIoClose (aip);
   }
 
+  if (tbl.discrepancy) {
+    tbl.disc_rep_config.summary_report = FALSE;
+    tbl.disc_rep_config.expand_report_categories[DISC_SUPERFLUOUS_GENE] = TRUE;
+    tbl.disc_rep_config.expand_report_categories[DISC_RNA_CDS_OVERLAP] = TRUE;
+    tbl.disc_rep_config.expand_report_categories[DISC_SUSPECT_PRODUCT_NAME] = TRUE;
+    fp = FileOpen (disc_rep_file, "w");
+    DoDiscrepancySummary (&tbl, fp);
+    FileClose (fp);
+  }
+
   if (sbp != NULL) {
     SubmitBlockFree (sbp);
   }
@@ -6025,7 +6919,11 @@ Int2 Main (void)
 
   TextFsaFree (gotags);
 
-  /* close fetch function */
+  /* close fetch functions */
+
+  if (remote || tbl.dopublookup) {
+    PubMedFetchDisable ();
+  }
 
   if (remote) {
 #ifdef INTERNAL_NCBI_TBL2ASN
diff --git a/desktop/biosrc.c b/desktop/biosrc.c
index 8ecc6d81..a2dd561b 100644
--- a/desktop/biosrc.c
+++ b/desktop/biosrc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.85 $
+* $Revision: 6.87 $
 *
 * File Description: 
 *
@@ -72,6 +72,8 @@ static ENUM_ALIST(biosource_genome_alist)
   {"Proplastid",          18},
   {"Endogenous-virus",    19},
   {"Hydrogenosome",       20},
+  {"Chromosome",          21},
+  {"Chromatophore",       22},
 END_ENUM_ALIST
 
 extern EnumFieldAssoc  biosource_genome_simple_alist [];
@@ -98,6 +100,8 @@ ENUM_ALIST(biosource_genome_simple_alist)
   {"Proplastid",          18},
   {"Endogenous-virus",    19},
   {"Hydrogenosome",       20},
+  {"Chromosome",          21},
+  {"Chromatophore",       22},
 END_ENUM_ALIST
 
 extern EnumFieldAssoc  biosource_origin_alist [];
@@ -900,55 +904,6 @@ static CharPtr AllButFirstLinePrtProc (DoC d, Int2 item, Pointer ptr)
   }
 }
 
-static CharPtr MergeValNodeStrings (ValNodePtr list)
-
-{
-  size_t      len;
-  CharPtr     ptr;
-  CharPtr     str;
-  CharPtr     tmp;
-  ValNodePtr  vnp;
-
-
-  ptr = NULL;
-  if (list != NULL) {
-    vnp = list;
-    len = 0;
-    while (vnp != NULL) {
-      if (vnp->data.ptrvalue != NULL) {
-        len += StringLen ((CharPtr) vnp->data.ptrvalue) + 1;
-      }
-      vnp = vnp->next;
-    }
-    if (len > 0) {
-      ptr = MemNew (sizeof (Char) * (len + 2));
-      if (ptr != NULL) {
-        vnp = list;
-        tmp = NULL;
-        while (vnp != NULL) {
-          if (vnp->data.ptrvalue != NULL) {
-            if (tmp == NULL) {
-              tmp = ptr;
-            } else {
-              tmp = StringMove (tmp, "; ");
-            }
-            str = StringSave ((CharPtr) vnp->data.ptrvalue);
-            TrimSpacesAroundString (str);
-            len = StringLen (str);
-            if (len > 0 && str [len - 1] == ';') {
-              str [len - 1] = '\0';
-            }
-            tmp = StringMove (tmp, str);
-            MemFree (str);
-          }
-          vnp = vnp->next;
-        }
-      }
-    }
-  }
-  return ptr;
-}
-
 
 static Char useGenomicText [] = "\
 (Use 'Genomic' for a sequence encoded by a nuclear gene.)\n";
diff --git a/desktop/bspview.c b/desktop/bspview.c
index 6e7e96dc..670bca13 100644
--- a/desktop/bspview.c
+++ b/desktop/bspview.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   4/30/95
 *
-* $Revision: 6.141 $
+* $Revision: 6.142 $
 *
 * File Description: 
 *
@@ -84,7 +84,7 @@
 extern ForM smartBioseqViewForm;
 ForM smartBioseqViewForm = NULL;
 
-#define MAX_VIEWABLE_TARGET_SEQUENCES 60000
+#define MAX_VIEWABLE_TARGET_SEQUENCES 32768
 
 static void LookForGenomeTag (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent)
 
diff --git a/desktop/cdrgn.c b/desktop/cdrgn.c
index 83057a92..888e9ff9 100644
--- a/desktop/cdrgn.c
+++ b/desktop/cdrgn.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.99 $
+* $Revision: 6.114 $
 *
 * File Description: 
 *
@@ -136,7 +136,6 @@ typedef struct rnaform {
   GrouP         pages [NUM_PAGES];
   DialoG        foldertabs;
   Int2          currentPage;
-  TexT          prodSeqIdTxt;
   Boolean       empty_feat;
 } RnaForm, PNTR RnaFormPtr;
 
@@ -154,6 +153,19 @@ typedef struct rnapage {
   DialoG        anticodon;
   GrouP         trnaPages [3];
   RnaFormPtr    rfp;
+
+  /* for ncRNA page */
+  GrouP         ncrnaGrp;
+  DialoG        ncrnaClass;
+  TexT          ncrnaProduct;
+
+  /* for tmRNA page */
+  GrouP         tmrnaGrp;
+  TexT          tmrnaProduct;
+  DialoG        tmrnaTagPeptide;
+  
+  /* for switching between types */
+  Int4          prev_rna_type;
 } RnaPage, PNTR RnaPagePtr;
 
 
@@ -1313,7 +1325,10 @@ static Pointer ProductToSeqLocPtr (DialoG d)
       return NULL;
     }
   }
-  if (ppp != NULL && ppp->bsptr != NULL) {
+
+  if (ppp == NULL) return NULL;  
+
+  if (ppp->bsptr != NULL) {
     if (ppp->nucProducts) {
       if (! Visible (d)) return NULL; /* not an mRNA, do not make product */
     }
@@ -1366,18 +1381,6 @@ static Pointer ProductToSeqLocPtr (DialoG d)
           }
         }
       }
-    } else if (rfp != NULL && rfp->prodSeqIdTxt != NULL) {
-      GetTitle (rfp->prodSeqIdTxt, id, sizeof (id) - 1);
-      if ((! StringHasNoText (id)) && StringChr (id, '|') != NULL) {
-        sip = MakeSeqID (id);
-        if (sip != NULL) {
-          slp = ValNodeNew (NULL);
-          if (slp != NULL) {
-            slp->choice = 3;
-            slp->data.ptrvalue = SeqIdStripLocus (sip);
-          }
-        }
-      }
     }
   }
   return (Pointer) slp;
@@ -1512,6 +1515,171 @@ static DialoG CreateProteinOrMRNAProductDialog (GrouP h, CharPtr title,
   return (DialoG) p;
 }
 
+
+typedef struct rnatranscriptiddlg {
+  DIALOG_MESSAGE_BLOCK
+  DialoG               product;
+  Boolean              usePopupForProduct;
+  GrouP                far_id_grp;
+  TexT                 far_id;
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer              change_userdata;
+} RnaTranscriptIDDlgData, PNTR RnaTranscriptIdDlgPtr;
+
+static void ChangeTranscriptIDSequenceSelection (Pointer userdata)
+{
+  RnaTranscriptIdDlgPtr  dlg;
+  ValNodePtr             vnp;
+
+  dlg = (RnaTranscriptIdDlgPtr) userdata;
+  if (dlg == NULL) return;
+
+  if (dlg->far_id_grp != NULL)
+  {
+    vnp = DialogToPointer (dlg->product);
+    if (vnp == NULL || vnp->data.ptrvalue == NULL) 
+    {
+      Enable (dlg->far_id_grp);
+    }
+    else 
+    {
+      Disable (dlg->far_id_grp);
+    }
+    vnp = ValNodeFree (vnp);
+  }
+
+  if (dlg->change_notify != NULL)
+  {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+static void ChangeTranscriptIDText (TexT t)
+{
+  RnaTranscriptIdDlgPtr  dlg;
+
+  dlg = (RnaTranscriptIdDlgPtr) GetObjectExtra (t);
+  if (dlg == NULL) return;
+
+  if (dlg->change_notify != NULL)
+  {
+    (dlg->change_notify) (dlg->change_userdata);
+  }  
+}
+
+
+static void LocToTranscriptIDDialog (DialoG d, Pointer data)
+{
+  RnaTranscriptIdDlgPtr  dlg;
+  SeqLocPtr              slp;
+  BioseqPtr              bsp;
+  ValNode                vn;
+  SeqIdPtr               sip;
+  Char                   str [128];
+
+  dlg = (RnaTranscriptIdDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+  slp = (SeqLocPtr) data;
+
+  if (slp == NULL)
+  {
+    PointerToDialog (dlg->product, NULL);
+    SafeSetTitle (dlg->far_id, "");
+  }
+  else
+  {
+    sip = SeqLocId (slp);
+    bsp = BioseqFind (sip);
+    if (bsp == NULL)
+    {
+      PointerToDialog (dlg->product, NULL);
+      SeqIdWrite (sip, str, PRINTID_FASTA_LONG, sizeof (str));
+      SafeSetTitle (dlg->far_id, str);
+    }
+    else
+    {
+      vn.choice = 0;
+      vn.data.ptrvalue = sip;
+      vn.next = NULL;
+      PointerToDialog (dlg->product, &vn);
+      SafeSetTitle (dlg->far_id, "");
+    }    
+  }
+}
+
+
+static Pointer TranscriptIDDialogToLoc (DialoG d)
+{
+  RnaTranscriptIdDlgPtr  dlg;
+  SeqLocPtr              slp = NULL;
+  ValNodePtr             vnp;
+  SeqIdPtr               sip = NULL;
+  CharPtr                str;
+
+  dlg = (RnaTranscriptIdDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  vnp = DialogToPointer (dlg->product);
+  if (vnp == NULL || vnp->data.ptrvalue == NULL)
+  {
+    if (!TextHasNoText (dlg->far_id))
+    {
+      str = SaveStringFromText (dlg->far_id);
+      sip = MakeSeqID (str);
+      str = MemFree (str);
+    }
+  }
+  else
+  {
+    sip = SeqIdDup (vnp->data.ptrvalue);
+  }
+  vnp = ValNodeFree (vnp);
+  
+  if (sip != NULL)
+  {
+    slp = ValNodeNew (NULL);
+    slp->choice = SEQLOC_WHOLE;
+    slp->data.ptrvalue = SeqIdStripLocus (sip);
+  }
+
+  return slp;
+}
+
+
+static DialoG CreateRNATranscriptIDDialog (GrouP h, Uint2 entityID, Boolean allow_far_id, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  GrouP                  p;
+  RnaTranscriptIdDlgPtr  dlg;
+  ValNodePtr             bsp_list = NULL;
+
+  p = HiddenGroup (h, 3, 0, NULL);
+  SetGroupSpacing (p, 10, 10);
+
+  dlg = (RnaTranscriptIdDlgPtr) MemNew (sizeof (RnaTranscriptIDDlgData));
+  if (dlg == NULL) return NULL;
+
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = LocToTranscriptIDDialog;
+  dlg->fromdialog = TranscriptIDDialogToLoc;
+
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  StaticPrompt (p, "Transcript Sequence ID", 0, popupMenuHeight, programFont, 'l');
+  dlg->product = SequenceSelectionDialogEx (p, ChangeTranscriptIDSequenceSelection, dlg, FALSE, TRUE, TRUE, FALSE, entityID, SHORT_SELECTION_LIST);
+  if (allow_far_id) 
+  {
+    dlg->far_id_grp = HiddenGroup (p, 2, 0, NULL);
+    StaticPrompt (dlg->far_id_grp, "Far ID", 0, dialogTextHeight, programFont, 'l');
+    dlg->far_id = DialogText (dlg->far_id_grp, "", 5, ChangeTranscriptIDText);
+    SetObjectExtra (dlg->far_id, dlg, NULL);
+  }
+
+  return (DialoG) p;
+}
+
+
 extern SeqLocPtr PredictCodingRegion (BioseqPtr nuc, BioseqPtr prot, Int2 genCode)
 
 {
@@ -3090,7 +3258,7 @@ static Boolean FixCdRegionFormProteinFeatures (CdRgnFormPtr cfp, BioseqPtr newpr
   sip = SeqLocId (slp);
   target = BioseqFind (sip);
   if (target != NULL) {
-    if (!SeqEdFixProteinFeatures (target, newprot, FALSE))
+    if (!SeqEdFixProteinFeatures (target, newprot, FALSE, Sequin_GlobalAlign2Seq))
     {
       if (ANS_CANCEL == Message (MSG_OKC, "Unable to construct alignment between old and new proteins.\nYou will need to adjust the protein features manually if you continue."))
       {
@@ -5777,16 +5945,15 @@ static ENUM_ALIST(rna_type_alist)
   {"mRNA",         2},
   {"tRNA",         3},
   {"rRNA",         4},
-  {"snRNA",        5},
-  {"scRNA",        6},
-  {"snoRNA",       7},
+  {"ncRNA",        8},
+  {"tmRNA",        9},
   {"misc_RNA",   255},
 END_ENUM_ALIST
 
 static Uint1 check_rna_type (Uint1 type)
 
 {
-  if (type > 7 && type != 255) return 0;
+  if (type > 9 && type != 255) return 0;
   return type;
 }
 
@@ -5882,7 +6049,76 @@ static DialoG CreateMrnaUserObjectDialog (GrouP h, CharPtr label, SeqEntryPtr se
   return (DialoG) p;
 }
 
-/* trna aa conversion modified from Tatiana Tatusov's code */
+
+static Uint1 RnaFeatDefFromRnaRef (RnaRefPtr rrp)
+{
+  if (rrp == NULL) {
+    return FEATDEF_otherRNA;
+  }
+
+  switch (rrp->type) 
+  {
+    case 1:
+      return FEATDEF_preRNA;
+      break;
+    case 2:
+      return FEATDEF_mRNA;
+      break;
+    case 3:
+      return FEATDEF_tRNA;
+      break;
+    case 4:
+      return FEATDEF_rRNA;
+      break;
+    case 5:
+      return FEATDEF_snRNA;
+      break;
+    case 6:
+      return FEATDEF_scRNA;
+      break;
+    case 7:
+      return FEATDEF_snoRNA;
+      break;
+    case 255:
+      if (rrp->ext.choice != 1 || StringHasNoText (rrp->ext.value.ptrvalue)) {
+        return FEATDEF_otherRNA;
+      } else if (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
+                 || IsStringInNcRNAClassList(rrp->ext.value.ptrvalue)) {
+        return FEATDEF_ncRNA;
+      } else if (StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0) {
+        return FEATDEF_tmRNA;
+      } else {
+        return FEATDEF_otherRNA;
+      }
+    default:
+      return FEATDEF_otherRNA;
+      break;
+  }
+}
+
+
+static Uint1 RnaSubtypeFromRnaRef (RnaRefPtr rrp)
+{
+  if (rrp == NULL) {
+    return 0;
+  }
+
+  if (rrp->type == 255) {
+    if (rrp->ext.choice == 1 && StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0) {
+      return 9;
+    } else if (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
+               || IsStringInNcRNAClassList (rrp->ext.value.ptrvalue)) {
+      return 8;
+    } else {
+      return 255;
+    }
+  } else if (rrp->type == 5 || rrp->type == 6 || rrp->type == 7) {
+    return 8;
+  } else {
+    return rrp->type;
+  }
+}
+
 
 static void RnaRefPtrToRnaPage (DialoG d, Pointer data)
 
@@ -5905,8 +6141,9 @@ static void RnaRefPtrToRnaPage (DialoG d, Pointer data)
   rrp = (RnaRefPtr) data;
 
   if (rrp != NULL) {
+
     SetEnumPopup (rpp->type, rna_type_alist,
-                  (UIEnum) check_rna_type (rrp->type));
+                  RnaSubtypeFromRnaRef(rrp));
     SafeSetStatus (rpp->pseudo, rrp->pseudo);
     switch (rrp->type) {
       case 0 :
@@ -5914,12 +6151,16 @@ static void RnaRefPtrToRnaPage (DialoG d, Pointer data)
         SafeHide (rpp->nameGrp);
         SafeHide (rpp->rrnaPrompt);
         SafeHide (rpp->ornaPrompt);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
         break;
       case 3 :
         SafeSetTitle (rpp->name, "");
         SafeHide (rpp->nameGrp);
         SafeHide (rpp->rrnaPrompt);
         SafeHide (rpp->ornaPrompt);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
         SafeSetValue (rpp->AAitem, 1);
         if (rrp->ext.choice == 2) {
           trna = rrp->ext.value.ptrvalue;
@@ -6024,17 +6265,63 @@ static void RnaRefPtrToRnaPage (DialoG d, Pointer data)
         SafeHide (rpp->ornaPrompt);
         SafeShow (rpp->rrnaPrompt);
         SafeShow (rpp->nameGrp);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
         break;
+      case 5:
+      case 6:
+      case 7:
+      case 8:
       case 255 :
         SafeHide (rpp->trnaGrp);
-        if (rrp->ext.choice == 1 && rrp->ext.value.ptrvalue != NULL) {
-          SafeSetTitle (rpp->name, (CharPtr) rrp->ext.value.ptrvalue);
-        } else {
-          SafeSetTitle (rpp->name, "");
-        }
+        SafeHide (rpp->nameGrp);
         SafeHide (rpp->rrnaPrompt);
-        SafeShow (rpp->ornaPrompt);
-        SafeShow (rpp->nameGrp);
+        SafeHide (rpp->ornaPrompt);
+        if (rrp->type == 5) {
+          PointerToDialog (rpp->ncrnaClass, "snRNA");
+          SafeHide (rpp->tmrnaGrp);
+          SafeShow (rpp->ncrnaGrp); 
+        } else if (rrp->type == 6) {
+          PointerToDialog (rpp->ncrnaClass, "scRNA");
+          SafeHide (rpp->tmrnaGrp);
+          SafeShow (rpp->ncrnaGrp); 
+        } else if (rrp->type == 7) {
+          PointerToDialog (rpp->ncrnaClass, "snoRNA");
+          SafeHide (rpp->tmrnaGrp);
+          SafeShow (rpp->ncrnaGrp); 
+        } else if (rrp->type == 255) {
+          if (rrp->ext.choice == 1) {
+            if (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0) {
+              SafeHide (rpp->tmrnaGrp);
+              SafeShow (rpp->ncrnaGrp);
+              /* get class from qual */
+            } else if (IsStringInNcRNAClassList (rrp->ext.value.ptrvalue)) {
+              SafeHide (rpp->tmrnaGrp);
+              SafeShow (rpp->ncrnaGrp);
+              /* get class from rrp */
+              PointerToDialog (rpp->ncrnaClass, rrp->ext.value.ptrvalue);
+            } else if (StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0) {
+              SafeHide (rpp->ncrnaGrp);
+              SafeShow (rpp->tmrnaGrp);
+            } else {
+              if (StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") != 0) {
+                SafeSetTitle (rpp->name, (CharPtr) rrp->ext.value.ptrvalue);
+              }
+              SafeHide (rpp->ornaPrompt);
+              SafeShow (rpp->rrnaPrompt);
+              SafeShow (rpp->nameGrp);
+              SafeHide (rpp->ncrnaGrp);
+              SafeHide (rpp->tmrnaGrp);
+            }
+          } else {
+            SafeSetTitle (rpp->name, "");
+            SafeHide (rpp->ornaPrompt);
+            SafeShow (rpp->rrnaPrompt);
+            SafeShow (rpp->nameGrp);
+            SafeHide (rpp->ncrnaGrp);
+            SafeHide (rpp->tmrnaGrp);
+          }
+        }
         break;
       default :
         SafeHide (rpp->trnaGrp);
@@ -6046,6 +6333,8 @@ static void RnaRefPtrToRnaPage (DialoG d, Pointer data)
         SafeHide (rpp->rrnaPrompt);
         SafeHide (rpp->ornaPrompt);
         SafeShow (rpp->nameGrp);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
         break;
     }
   } else {
@@ -6057,6 +6346,8 @@ static void RnaRefPtrToRnaPage (DialoG d, Pointer data)
     SafeHide (rpp->ornaPrompt);
     SafeSetValue (rpp->AAitem, 0);
     SafeHide (rpp->trnaGrp);
+    SafeHide (rpp->ncrnaGrp);
+    SafeHide (rpp->tmrnaGrp);
   }
 }
 
@@ -6086,10 +6377,14 @@ static Pointer RnaPageToRnaRefPtr (DialoG d)
     rrp = RnaRefNew ();
     if (rrp != NULL) {
       if (GetEnumPopup (rpp->type, rna_type_alist, &val)) {
-        rrp->type = (Uint1) val;
+        if (val == 8 || val == 9) {
+          rrp->type = 255;
+        } else {
+          rrp->type = (Uint1) val;
+        }
       }
       rrp->pseudo = GetStatus (rpp->pseudo);
-      switch (rrp->type) {
+      switch (val) {
         case 3 :
           rrp->ext.choice = 2;
           trna = (tRNAPtr) MemNew (sizeof (tRNA));
@@ -6158,6 +6453,18 @@ static Pointer RnaPageToRnaRefPtr (DialoG d)
             trna->anticodon = DialogToPointer (rpp->anticodon);
           }
           break;
+        case 5:
+        case 6:
+        case 7:
+        case 8: /* ncRNA */
+          rrp->ext.choice = 1;
+          rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+          break;
+        case 9: /* tmRNA */
+          rrp->ext.choice = 1;
+          rrp->ext.value.ptrvalue = StringSave ("tmRNA");
+          break;
+        case 255:
         default :
           if (! TextHasNoText (rpp->name)) {
             rrp->ext.choice = 1;
@@ -6170,6 +6477,369 @@ static Pointer RnaPageToRnaRefPtr (DialoG d)
   return (Pointer) rrp;
 }
 
+
+static GBQualPtr FindOrAddQual (SeqFeatPtr sfp, CharPtr qual_name)
+{
+  GBQualPtr gbq;
+
+  if (sfp == NULL) return NULL;
+  gbq = sfp->qual;
+  while (gbq != NULL && StringCmp (gbq->qual, qual_name) != 0) {
+    gbq = gbq->next;
+  }
+  if (gbq == NULL) {
+    gbq = GBQualNew ();
+    gbq->qual = StringSave (qual_name);
+    gbq->next = sfp->qual;
+    sfp->qual = gbq;
+  }
+  return gbq;
+}
+
+
+static void RemoveQualByName (SeqFeatPtr sfp, CharPtr qual_name)
+{
+  GBQualPtr gbq, gbq_next, gbq_prev = NULL;
+
+  if (sfp == NULL || StringHasNoText (qual_name))
+  {
+    return;
+  }
+  gbq = sfp->qual;
+  while (gbq != NULL)
+  {
+    gbq_next = gbq->next;
+    if (StringCmp (gbq->qual, qual_name) == 0)
+    {
+      if (gbq_prev == NULL)
+      {
+        sfp->qual = gbq->next;
+      }
+      else
+      {
+        gbq_prev->next = gbq->next;
+      }
+      gbq->next = NULL;
+      gbq = GBQualFree (gbq);
+    }
+    else
+    {
+      gbq_prev = gbq;
+    }
+    gbq = gbq_next;
+  }
+}
+
+static void SetRNAMiscNameForType (SeqFeatPtr sfp, UIEnum val)
+{
+  RnaRefPtr  rrp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return;
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  
+  if (rrp == NULL) { 
+    rrp = RnaRefNew ();
+    sfp->data.value.ptrvalue = rrp;
+  }
+
+  if (val == 8) {
+    rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+    rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+    rrp->ext.choice = 1;
+  } else if (val == 9) {
+    rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+    rrp->ext.value.ptrvalue = StringSave ("tmRNA");
+    rrp->ext.choice = 1;
+  } else if (val == 255) {
+    rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+    rrp->ext.value.ptrvalue = StringSave ("misc_RNA");
+    rrp->ext.choice = 1;
+  }
+
+}
+
+
+extern void ConvertProductQualToRnaRefName (SeqFeatPtr sfp)
+{
+  RnaRefPtr rrp;
+  GBQualPtr gbq, gbq_prev = NULL;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL) return;
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+
+  gbq = sfp->qual;
+  while (gbq != NULL && StringCmp (gbq->qual, "product") != 0) {
+    gbq_prev = gbq;
+    gbq = gbq->next;
+  }
+  if (gbq != NULL) {
+    rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+    rrp->ext.choice = 1;
+    rrp->ext.value.ptrvalue = gbq->val;
+    gbq->val = NULL;
+    if (gbq_prev == NULL) {
+      sfp->qual = gbq->next;
+    } else {
+      gbq_prev->next = gbq->next;
+    }
+    gbq->next = NULL;
+    gbq = GBQualFree (gbq);
+  }
+}
+
+
+static void ConvertRnaRefNameToProductQual (SeqFeatPtr sfp)
+{
+  RnaRefPtr rrp;
+  GBQualPtr gbq, gbq_prev = NULL;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL) return;
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (rrp->ext.choice != 1) return;
+  
+  gbq = GBQualNew ();
+  gbq->next = sfp->qual;
+  sfp->qual = gbq;
+  gbq->qual = StringSave ("product");
+  gbq->val = StringSave (rrp->ext.value.ptrvalue);
+}
+
+
+static void AddRnaSpecificQualsForType (SeqFeatPtr sfp, RnaPagePtr rpp, UIEnum val)
+{
+  CharPtr    str;
+  GBQualPtr  gbq;
+  RnaRefPtr  rrp;
+
+  if (rpp == NULL || sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return;
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+
+  if (val == 8) {
+    str = DialogToPointer (rpp->ncrnaClass);
+    if (StringHasNoText (str)) {
+      str = MemFree (str);
+      RemoveQualByName (sfp, "ncRNA_class"); 
+    } else {
+      gbq = FindOrAddQual (sfp, "ncRNA_class");
+      gbq->val = MemFree (gbq->val);
+      gbq->val = str;
+    }
+    if (TextHasNoText (rpp->ncrnaProduct)) {
+      RemoveQualByName (sfp, "product");
+    } else {
+      gbq = FindOrAddQual (sfp, "product");
+      gbq->val = MemFree (gbq->val);
+      gbq->val = SaveStringFromText (rpp->ncrnaProduct);
+    }
+  } else if (val == 9) {
+    str = DialogToPointer (rpp->tmrnaTagPeptide);
+    if (StringHasNoText (str)) {
+      str = MemFree (str);
+      RemoveQualByName (sfp, "tag_peptide");
+    } else {
+      gbq = FindOrAddQual (sfp, "tag_peptide");
+      gbq->val = MemFree (gbq->val);
+      gbq->val = str;
+    }
+    if (TextHasNoText (rpp->tmrnaProduct)) {
+      RemoveQualByName (sfp, "product");
+    } else {
+      gbq = FindOrAddQual (sfp, "product");
+      gbq->val = MemFree (gbq->val);
+      gbq->val = SaveStringFromText (rpp->tmrnaProduct);
+    }
+  } else if (val == 255) {
+    if (TextHasNoText (rpp->name)) {
+      RemoveQualByName (sfp, "product");
+    } else {
+      str = SaveStringFromText (rpp->name);
+      if (StringCmp (str, "misc_RNA") == 0) {
+        str = MemFree (str);
+      } else {
+        gbq = FindOrAddQual (sfp, "product");
+        gbq->val = MemFree (gbq->val);
+        gbq->val = str;
+      }
+    }
+  }
+}
+
+
+extern void AddRnaSpecificQuals (SeqFeatPtr sfp, DialoG d)
+{
+  RnaPagePtr rpp;
+  UIEnum     val;
+
+  rpp = (RnaPagePtr) GetObjectExtra (d);
+  if (rpp == NULL || sfp == NULL) return;
+
+  if (GetEnumPopup (rpp->type, rna_type_alist, &val)) {
+    AddRnaSpecificQualsForType (sfp, rpp, val);
+    SetRNAMiscNameForType (sfp, val);
+    if (val != 8) {
+      RemoveQualByName (sfp, "ncRNA_class");
+    }
+    if (val != 8 && val != 9 && val != 255) {
+      ConvertProductQualToRnaRefName (sfp);
+    }
+  }
+}
+
+
+extern void SetRnaSpecificQuals (SeqFeatPtr sfp, DialoG d)
+{
+  RnaPagePtr rpp;
+  RnaRefPtr  rrp;
+  GBQualPtr  gbq;
+
+  rpp = (RnaPagePtr) GetObjectExtra (d);
+  if (rpp == NULL || sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL) return;
+
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if ((rrp->type == 5 || rrp->type == 6 || rrp->type == 7)
+      && rrp->ext.choice == 1
+      && StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0) {
+    SetTitle (rpp->ncrnaProduct, rrp->ext.value.ptrvalue);
+  }
+  else if (rrp->type != 255 || rrp->ext.choice != 1) return;
+
+  if (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0) {
+    gbq = sfp->qual;
+    while (gbq != NULL) {
+      if (StringCmp (gbq->qual, "ncRNA_class") == 0) {
+        PointerToDialog (rpp->ncrnaClass, gbq->val);
+      } else if (StringCmp (gbq->qual, "product") == 0) {
+        SetTitle (rpp->ncrnaProduct, gbq->val);
+      }
+      gbq = gbq->next;
+    }
+  } else if (StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0) {
+    gbq = sfp->qual;
+    while (gbq != NULL) {
+      if (StringCmp (gbq->qual, "tag_peptide") == 0) {
+        PointerToDialog (rpp->tmrnaTagPeptide, gbq->val);
+      } else if (StringCmp (gbq->qual, "product") == 0) {
+        SetTitle (rpp->tmrnaProduct, gbq->val);
+      }
+      gbq = gbq->next;
+    }
+  } else if (IsStringInNcRNAClassList (rrp->ext.value.ptrvalue)) {
+    gbq = sfp->qual;
+    while (gbq != NULL) {
+      if (StringCmp (gbq->qual, "product") == 0) {
+        SetTitle (rpp->ncrnaProduct, gbq->val);
+      }
+      gbq = gbq->next;
+    }
+  } else if (StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0) {
+    gbq = sfp->qual;
+    while (gbq != NULL) {
+      if (StringCmp (gbq->qual, "product") == 0) {
+        SetTitle (rpp->name, gbq->val);
+      }
+      gbq = gbq->next;
+    }
+  }
+}
+
+
+extern void ConvertToOldRNAFormat (SeqFeatPtr sfp)
+{
+  RnaRefPtr rrp;
+  GBQualPtr gbq, gbq_prod = NULL, gbq_class = NULL, gbq_prev = NULL, gbq_next;
+  Boolean   do_convert = TRUE;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA)
+  {
+    return;
+  }
+
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (rrp == NULL || rrp->type != 255 || rrp->ext.choice != 1
+      || StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0)
+  {
+    return;
+  }
+  for (gbq = sfp->qual; gbq != NULL && (gbq_prod == NULL || gbq_class == NULL); gbq = gbq->next)
+  {
+    if (StringCmp (gbq->qual, "ncRNA_class") == 0)
+    {
+      gbq_class = gbq;
+    }
+    else if (StringCmp (gbq->qual, "product") == 0)
+    {
+      gbq_prod = gbq;
+    }
+  }
+
+  if (gbq_class == NULL)
+  {
+    do_convert = FALSE;
+  }
+  else if (StringCmp (gbq_class->val, "snRNA") == 0)
+  {
+    rrp->type = 5;
+  }
+  else if (StringCmp (gbq_class->val, "scRNA") == 0)
+  {
+    rrp->type = 6;
+  }
+  else if (StringCmp (gbq_class->val, "snoRNA") == 0)
+  {
+    rrp->type = 7;
+  }
+  else if (IsStringInNcRNAClassList (gbq_class->val))
+  {
+    do_convert = FALSE;
+    rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+    rrp->ext.value.ptrvalue = StringSave (gbq_class->val);
+    RemoveQualByName (sfp, "ncRNA_class");
+  }
+  else
+  {
+    do_convert = FALSE;
+  }
+  if (do_convert)
+  {
+    if (gbq_prod == NULL)
+    {
+      rrp->ext.choice = 0;
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+    }
+    else
+    {
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = gbq_prod->val;
+      gbq_prod->val = NULL;
+    }
+    gbq = sfp->qual;
+    while (gbq != NULL)
+    {
+      gbq_next = gbq->next;
+      if (StringCmp (gbq->qual, "ncRNA_class") == 0
+          || StringCmp (gbq->qual, "product") == 0)
+      {
+        if (gbq_prev == NULL)
+        {
+          sfp->qual = gbq->next;
+        }
+        else
+        {
+          gbq_prev->next = gbq->next;
+        }
+        gbq->next = NULL;
+        gbq = GBQualFree (gbq);
+      }
+      else
+      {
+        gbq_prev = gbq;
+      }
+      gbq = gbq_next;
+    }
+  }
+}
+
+
 static void SetRnaImportExportItems (RnaFormPtr rfp)
 
 {
@@ -6214,91 +6884,126 @@ static void SetRnaImportExportItems (RnaFormPtr rfp)
   }
 }
 
-static void ChangeRnaProc (PopuP p)
+static void SetRnaType (RnaPagePtr rpp, Uint2 subtype)
 
 {
   RnaFormPtr  rfp;
-  RnaPagePtr  rpp;
-  UIEnum      val;
+  RnaRefPtr   rrp = NULL;
 
-  rpp = (RnaPagePtr) GetObjectExtra (p);
-  if (rpp != NULL) {
+  if (rpp != NULL && rpp->rfp != NULL) {
     rfp = rpp->rfp;
-    if (GetEnumPopup (rpp->type, rna_type_alist, &val)) {
-      switch (val) {
-        case 0 :
-          SafeHide (rpp->nameGrp);
-          SafeHide (rpp->rrnaPrompt);
-          SafeHide (rpp->ornaPrompt);
-          SafeHide (rpp->trnaGrp);
-          SafeHide (rfp->product);
-          SafeHide (rfp->usrobjext);
-          break;
-        case 2 :
-          SafeHide (rpp->trnaGrp);
-          SafeHide (rpp->rrnaPrompt);
-          SafeHide (rpp->ornaPrompt);
-          SafeShow (rpp->nameGrp);
-          SafeShow (rfp->product);
-          SafeShow (rfp->usrobjext);
-          break;
-        case 3 :
-          SafeHide (rpp->nameGrp);
-          SafeHide (rpp->rrnaPrompt);
-          SafeHide (rpp->ornaPrompt);
-          SafeShow (rpp->trnaGrp);
-          SafeShow (rfp->product);
-          SafeHide (rfp->usrobjext);
-          break;
-        case 4 :
-          SafeHide (rpp->trnaGrp);
-          SafeHide (rpp->ornaPrompt);
-          SafeShow (rpp->rrnaPrompt);
-          SafeShow (rpp->nameGrp);
-          SafeShow (rfp->product);
-          SafeHide (rfp->usrobjext);
-          break;
-        case 5 :
-          SafeHide (rpp->trnaGrp);
-          SafeHide (rpp->rrnaPrompt);
-          SafeHide (rpp->ornaPrompt);
-          SafeShow (rpp->nameGrp);
-          SafeShow (rfp->product);
-          SafeHide (rfp->usrobjext);
-          break;
-        case 6 :
-          SafeHide (rpp->trnaGrp);
-          SafeHide (rpp->rrnaPrompt);
-          SafeHide (rpp->ornaPrompt);
-          SafeShow (rpp->nameGrp);
-          SafeShow (rfp->product);
-          SafeHide (rfp->usrobjext);
-          break;
-        case 7 :
-          SafeHide (rpp->trnaGrp);
-          SafeHide (rpp->rrnaPrompt);
-          SafeHide (rpp->ornaPrompt);
-          SafeShow (rpp->nameGrp);
-          SafeShow (rfp->product);
-          SafeHide (rfp->usrobjext);
-          break;
-        case 255 :
-          SafeHide (rpp->trnaGrp);
-          SafeHide (rpp->rrnaPrompt);
-          SafeShow (rpp->ornaPrompt);
-          SafeShow (rpp->nameGrp);
-          SafeShow (rfp->product);
-          SafeHide (rfp->usrobjext);
-          break;
-        default :
-          SafeHide (rpp->trnaGrp);
-          SafeHide (rpp->rrnaPrompt);
-          SafeHide (rpp->ornaPrompt);
-          SafeShow (rpp->nameGrp);
-          SafeHide (rfp->product);
-          SafeHide (rfp->usrobjext);
-          break;
-      }
+    switch (subtype) {
+      case 0 :
+        SafeHide (rpp->nameGrp);
+        SafeHide (rpp->rrnaPrompt);
+        SafeHide (rpp->ornaPrompt);
+        SafeHide (rpp->trnaGrp);
+        SafeHide (rfp->product);
+        SafeHide (rfp->usrobjext);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
+        break;
+      case FEATDEF_mRNA:
+        SafeHide (rpp->trnaGrp);
+        SafeHide (rpp->rrnaPrompt);
+        SafeHide (rpp->ornaPrompt);
+        SafeShow (rpp->nameGrp);
+        SafeShow (rfp->product);
+        SafeShow (rfp->usrobjext);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
+        break;
+     case FEATDEF_preRNA :
+        SafeHide (rpp->trnaGrp);
+        SafeHide (rpp->rrnaPrompt);
+        SafeHide (rpp->ornaPrompt);
+        SafeShow (rpp->nameGrp);
+        SafeShow (rfp->product);
+        SafeShow (rfp->usrobjext);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
+        break;
+      case FEATDEF_tRNA :
+        SafeHide (rpp->nameGrp);
+        SafeHide (rpp->rrnaPrompt);
+        SafeHide (rpp->ornaPrompt);
+        SafeShow (rpp->trnaGrp);
+        SafeShow (rfp->product);
+        SafeHide (rfp->usrobjext);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
+        break;
+      case FEATDEF_rRNA :
+        SafeHide (rpp->trnaGrp);
+        SafeHide (rpp->ornaPrompt);
+        SafeShow (rpp->rrnaPrompt);
+        SafeShow (rpp->nameGrp);
+        SafeShow (rfp->product);
+        SafeHide (rfp->usrobjext);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
+        break;
+      case FEATDEF_snRNA :
+      case FEATDEF_scRNA :
+      case FEATDEF_snoRNA :
+        SafeHide (rpp->trnaGrp);
+        SafeHide (rpp->rrnaPrompt);
+        SafeHide (rpp->ornaPrompt);
+        SafeHide (rpp->nameGrp);
+        SafeShow (rfp->product);
+        SafeHide (rfp->usrobjext);
+        SafeShow (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
+        if (subtype == FEATDEF_snRNA) {
+          PointerToDialog (rpp->ncrnaClass, "snRNA");
+          
+        } else if (subtype == FEATDEF_scRNA) {
+          PointerToDialog (rpp->ncrnaClass, "scRNA");
+        } else if (subtype == FEATDEF_snoRNA) {
+          PointerToDialog (rpp->ncrnaClass, "snoRNA");
+        } else if (subtype == FEATDEF_snoRNA) {
+          PointerToDialog (rpp->ncrnaClass, "miscRNA");
+        }
+        break;
+
+      case FEATDEF_ncRNA :
+        SafeHide (rpp->trnaGrp);
+        SafeHide (rpp->rrnaPrompt);
+        SafeHide (rpp->ornaPrompt);
+        SafeHide (rpp->nameGrp);
+        SafeShow (rfp->product);
+        SafeHide (rfp->usrobjext);
+        SafeShow (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
+        break;
+      case FEATDEF_tmRNA :
+        SafeHide (rpp->trnaGrp);
+        SafeHide (rpp->rrnaPrompt);
+        SafeHide (rpp->ornaPrompt);
+        SafeHide (rpp->nameGrp);
+        SafeShow (rfp->product);
+        SafeHide (rfp->usrobjext);
+        SafeHide (rpp->ncrnaGrp);
+        SafeShow (rpp->tmrnaGrp);
+        break;
+      case FEATDEF_otherRNA :
+        SafeHide (rpp->trnaGrp);
+        SafeHide (rpp->rrnaPrompt);
+        SafeShow (rpp->ornaPrompt);
+        SafeShow (rpp->nameGrp);
+        SafeShow (rfp->product);
+        SafeHide (rfp->usrobjext);
+        break;
+      default :
+        SafeHide (rpp->trnaGrp);
+        SafeHide (rpp->rrnaPrompt);
+        SafeHide (rpp->ornaPrompt);
+        SafeShow (rpp->nameGrp);
+        SafeHide (rfp->product);
+        SafeHide (rfp->usrobjext);
+        SafeHide (rpp->ncrnaGrp);
+        SafeHide (rpp->tmrnaGrp);
+        break;
     }
     SetRnaImportExportItems (rpp->rfp);
     Update ();
@@ -6356,6 +7061,173 @@ static CharPtr trnaTabs [] = {
   "Amino Acid", "Codons", "Anticodon", NULL
 };
 
+
+static Uint1 RnaTypeFromFeatdef (Uint2 featdef)
+{
+  switch (featdef) 
+  {
+    case FEATDEF_preRNA:
+      return 1;
+      break;
+    case FEATDEF_mRNA:
+      return 2;
+      break;
+    case FEATDEF_tRNA:
+      return 3;
+      break;
+    case FEATDEF_rRNA:
+      return 4;
+      break;
+    case FEATDEF_snRNA:
+      return 8;
+      break;
+    case FEATDEF_scRNA:
+      return 8;
+      break;
+    case FEATDEF_snoRNA:
+      return 8;
+      break;
+    case FEATDEF_ncRNA:
+      return 8;
+      break;
+    case FEATDEF_tmRNA:
+      return 9; 
+      break;
+    case FEATDEF_otherRNA:
+    default:
+      return 255;
+      break;
+  }
+}
+
+
+static void ChangeRNAType (PopuP p)
+
+{
+  Char             ch;
+  Int2             expev;
+  Int2             geneval;
+  HelpMessageFunc  helpfunc;
+  RnaFormPtr       rfp;
+  RnaFormPtr       newrfp;
+  RnaRefPtr        rrp;
+  RnaPagePtr       rpp;
+  ObjMgrPtr        omp;
+  ObjMgrTypePtr    omtp;
+  CharPtr          ptr;
+  SeqEntryPtr      sep;
+  SeqFeatPtr       sfp;
+  Char             title [128];
+  WindoW           w;
+  UIEnum           val;
+  GBQualPtr        gbq;
+
+  rfp = (RnaFormPtr) GetObjectExtra (p);
+  if (rfp == NULL) return;
+  rpp = (RnaPagePtr) GetObjectExtra (rfp->data);
+  if (rpp == NULL) return;
+  sfp = SeqFeatNew ();
+  if (sfp != NULL) {
+    if (GetEnumPopup (rpp->type, rna_type_alist, &val)) {
+
+      sfp->data.choice = SEQFEAT_RNA;
+      sfp->data.value.ptrvalue = DialogToPointer (rfp->data);
+      sfp->comment = SaveStringFromText (rfp->comment);
+      ptr = sfp->comment;
+      if (ptr != NULL) {
+        ch = *ptr;
+        while (ch != '\0') {
+          if (ch < ' ' || ch > '~') {
+            *ptr = '~';
+          }
+          ptr++;
+          ch = *ptr;
+        }
+      }
+      expev = GetValue (rfp->evidence);
+      if (expev > 0 && expev <= 3) {
+        sfp->exp_ev = expev - 1;
+      } else {
+        sfp->exp_ev = 0;
+      }
+      sfp->partial = GetStatus (rfp->partial);
+      sfp->excpt = GetStatus (rfp->exception);
+      sfp->title = NULL;
+      sfp->product = DialogToPointer (rfp->product);
+      sfp->location = DialogToPointer (rfp->location);
+      sfp->cit = DialogToPointer (rfp->featcits);
+      sfp->dbxref = DialogToPointer (rfp->dbxrefs);
+      sfp->qual = DialogToPointer (rfp->gbquals);
+      CleanupEvidenceGBQuals (&(sfp->qual));
+      VisStringDialogToGbquals (sfp, rfp->experiment, "experiment");
+      InferenceDialogToGBQuals (rfp->inference, sfp, TRUE);
+      AddRnaSpecificQualsForType (sfp, rpp, rpp->prev_rna_type < 0 ? val : rpp->prev_rna_type);
+      if (rpp->prev_rna_type == 8 && val != 8) {
+        RemoveQualByName (sfp, "ncRNA_class");
+      }
+      if (rpp->prev_rna_type == 8 || rpp->prev_rna_type == 9 || rpp->prev_rna_type == 255) {
+        if (val != 8 && val != 9 && val != 255) {
+          ConvertProductQualToRnaRefName (sfp);
+        }
+      } else if (val == 8 || val == 9 || val == 255) {
+        if (rpp->name != NULL && !TextHasNoText (rpp->name)) {
+          gbq = FindOrAddQual (sfp, "product");
+          gbq->val = SaveStringFromText (rpp->name);
+        }
+      }
+
+      SetRNAMiscNameForType (sfp, val);
+      rpp->prev_rna_type = val;
+
+      geneval = GetValue (rfp->gene);
+      sep = GetTopSeqEntryForEntityID (rfp->input_entityID);
+      StringCpy (title, "RNA");
+      if (sfp != NULL && sfp->data.value.ptrvalue != NULL) {
+        rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+        /* set title based on type of RNA feature */
+      }
+      /* need to set subtype to correctly calculate which quals should be suppressed */
+      sfp->idx.subtype = RnaFeatDefFromRnaRef ((RnaRefPtr)sfp->data.value.ptrvalue);
+      w = (WindoW) CreateRnaForm (-50, -33, title, sfp, sep, RnaFeatDefFromRnaRef (rrp),
+                                     StdFeatFormActnProc);
+      newrfp = (RnaFormPtr) GetObjectExtra (w);
+      if (newrfp != NULL) {
+        newrfp->input_entityID = rfp->input_entityID;
+        newrfp->input_itemID = rfp->input_itemID;
+        newrfp->input_itemtype = rfp->input_itemtype;
+        newrfp->this_itemtype = rfp->this_itemtype;
+        newrfp->this_subtype = rfp->this_subtype;
+        if (sfp != NULL) {
+          omp = ObjMgrGet ();
+          if (omp != NULL) {
+            omtp = ObjMgrTypeFind (omp, OBJ_SEQFEAT, NULL, NULL);
+            if (omtp != NULL && omtp->subtypefunc != NULL) {
+              newrfp->this_subtype = (*(omtp->subtypefunc)) (sfp);
+            }
+          }
+        }
+        SendMessageToForm (newrfp->form, VIB_MSG_INIT);
+        SetValue (newrfp->gene, geneval);
+        if (sfp != NULL) {
+          PointerToForm (newrfp->form, (Pointer) sfp);
+        }
+      }
+      Remove (rfp->form);
+      Show (w);
+      Select (w);
+      helpfunc = (HelpMessageFunc) GetAppProperty ("HelpMessageProc");
+      if (helpfunc != NULL) {
+        helpfunc ("Features", title);
+      }
+    }
+    SeqFeatFree (sfp);
+    Update ();
+  }
+}
+
+
+
+
 static DialoG CreateRnaDialog (GrouP h, CharPtr title,
                                Uint2 subtype, SeqEntryPtr sep,
                                SeqFeatPtr sfp, RnaFormPtr rfp)
@@ -6375,6 +7247,8 @@ static DialoG CreateRnaDialog (GrouP h, CharPtr title,
   PrompT      t;
   DialoG      tbs;
   GrouP       x;
+  Uint1       rna_type;
+  Uint2       entityID;
 
   p = HiddenGroup (h, 1, 0, NULL);
   SetGroupSpacing (p, 10, 10);
@@ -6388,6 +7262,8 @@ static DialoG CreateRnaDialog (GrouP h, CharPtr title,
     rpp->fromdialog = RnaPageToRnaRefPtr;
     rpp->testdialog = NULL;
 
+    rpp->prev_rna_type = -1;
+
     if (title != NULL && title [0] != '\0') {
       s = NormalGroup (p, 0, -2, title, systemFont, NULL);
     } else {
@@ -6400,11 +7276,14 @@ static DialoG CreateRnaDialog (GrouP h, CharPtr title,
 
     f = HiddenGroup (m, -2, 0, NULL);
     StaticPrompt (f, "Type", 0, popupMenuHeight, programFont, 'l');
-    rpp->type = PopupList (f, TRUE, ChangeRnaProc);
-    SetObjectExtra (rpp->type, rpp, NULL);
+    rpp->type = PopupList (f, TRUE, ChangeRNAType);
+    SetObjectExtra (rpp->type, rfp, NULL);
     InitEnumPopup (rpp->type, rna_type_alist, NULL);
     SetEnumPopup (rpp->type, rna_type_alist, (UIEnum) 0);
 
+    StaticPrompt (m, "Changing RNA type will recreate the window.",
+                        0, 0, programFont, 'c');
+
     showpseudo = FALSE;
     if (sfp != NULL && sfp->data.choice == SEQFEAT_RNA) {
       rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
@@ -6429,15 +7308,6 @@ static DialoG CreateRnaDialog (GrouP h, CharPtr title,
     x = HiddenGroup (rpp->nameGrp, 0, 0, NULL);
     rpp->rrnaPrompt = StaticPrompt (x, "E.g., 16S ribosomal RNA", 0, 0, programFont, 'c');
     rpp->ornaPrompt = StaticPrompt (x, "E.g., internal transcribed spacer 1", 0, 0, programFont, 'c');
-    if ((sfp != NULL && (sfp->product != NULL || sfp->ext != NULL)) || indexerVersion) {
-      rfp->product = CreateProteinOrMRNAProductDialog (rpp->nameGrp, NULL, "cDNA Product   ", TRUE, sep, NULL, rfp, (BaseFormPtr) rfp);
-      rfp->usrobjext = CreateMrnaUserObjectDialog (rpp->nameGrp, "Protein Product", sep, (BaseFormPtr) rfp);
-    }
-    if ((sfp != NULL && sfp->product != NULL) || indexerVersion) {
-      x = HiddenGroup (rpp->nameGrp, 2, 0, NULL);
-      StaticPrompt (x, "SeqID", 0, dialogTextHeight, programFont, 'l');
-      rfp->prodSeqIdTxt = DialogText (x, "", 6, NULL);
-    }
     AlignObjects (ALIGN_CENTER, (HANDLE) q, (HANDLE) rpp->rrnaPrompt, (HANDLE) rpp->ornaPrompt, NULL);
     Hide (rpp->nameGrp);
 
@@ -6468,81 +7338,38 @@ static DialoG CreateRnaDialog (GrouP h, CharPtr title,
                   (HANDLE) rpp->trnaPages [2], NULL);
     AlignObjects (ALIGN_CENTER, (HANDLE) f, (HANDLE) rpp->nameGrp,
                   (HANDLE) rpp->trnaGrp,  (HANDLE) rpp->pseudo,NULL);
+    Hide (rpp->ncrnaGrp);
+
+    rpp->ncrnaGrp = HiddenGroup (g, 2, 0, NULL);
+    SetGroupSpacing (rpp->ncrnaGrp, 10, 10);
+    StaticPrompt (rpp->ncrnaGrp, "Class", 0, popupMenuHeight, programFont, 'l');
+    rpp->ncrnaClass = CreatencRNAClassDialog (rpp->ncrnaGrp, FALSE, NULL, NULL);
+    StaticPrompt (rpp->ncrnaGrp, "Product", 0, dialogTextHeight, programFont, 'l');
+    rpp->ncrnaProduct = DialogText (rpp->ncrnaGrp, "", 10, NULL);
+    Hide (rpp->ncrnaGrp);
+
+    rpp->tmrnaGrp = HiddenGroup (g, 2, 0, NULL);
+    SetGroupSpacing (rpp->tmrnaGrp, 10, 10);
+    StaticPrompt (rpp->tmrnaGrp, "Tag Peptide", 0, dialogTextHeight, programFont, 'l');
+    rpp->tmrnaTagPeptide = CreateRptUnitRangeDialog (rpp->tmrnaGrp, NULL, NULL, NULL, NULL);
+    StaticPrompt (rpp->tmrnaGrp, "Product", 0, dialogTextHeight, programFont, 'l');
+    rpp->tmrnaProduct = DialogText (rpp->tmrnaGrp, "", 10, NULL);
+    Hide (rpp->tmrnaGrp);
+
+    if (sfp != NULL && sfp->data.choice == SEQFEAT_RNA && sfp->data.value.ptrvalue != NULL) {
+      rna_type = RnaSubtypeFromRnaRef ((RnaRefPtr)sfp->data.value.ptrvalue);
+    } else {
+      rna_type = RnaTypeFromFeatdef (subtype);
+    }
+    SetEnumPopup (rpp->type, rna_type_alist, (UIEnum) rna_type);
+    rpp->prev_rna_type = rna_type;
 
-    switch (subtype) {
-      case 0 :
-        SafeHide (rpp->nameGrp);
-        SafeHide (rpp->rrnaPrompt);
-        SafeHide (rpp->ornaPrompt);
-        SafeHide (rpp->trnaGrp);
-        SafeHide (rfp->product);
-        SafeHide (rfp->usrobjext);
-        break;
-      case FEATDEF_mRNA :
-        SafeHide (rpp->trnaGrp);
-        SafeHide (rpp->rrnaPrompt);
-        SafeHide (rpp->ornaPrompt);
-        SafeShow (rpp->nameGrp);
-        SafeShow (rfp->product);
-        SafeShow (rfp->usrobjext);
-        break;
-      case FEATDEF_tRNA :
-        SafeHide (rpp->nameGrp);
-        SafeHide (rpp->rrnaPrompt);
-        SafeHide (rpp->ornaPrompt);
-        SafeShow (rpp->trnaGrp);
-        SafeShow (rfp->product);
-        SafeHide (rfp->usrobjext);
-        break;
-      case FEATDEF_rRNA :
-        SafeHide (rpp->trnaGrp);
-        SafeHide (rpp->ornaPrompt);
-        SafeShow (rpp->rrnaPrompt);
-        SafeShow (rpp->nameGrp);
-        SafeShow (rfp->product);
-        SafeHide (rfp->usrobjext);
-        break;
-      case FEATDEF_snRNA :
-        SafeHide (rpp->trnaGrp);
-        SafeHide (rpp->ornaPrompt);
-        SafeHide (rpp->rrnaPrompt);
-        SafeShow (rpp->nameGrp);
-        SafeShow (rfp->product);
-        SafeHide (rfp->usrobjext);
-        break;
-      case FEATDEF_scRNA :
-        SafeHide (rpp->trnaGrp);
-        SafeHide (rpp->ornaPrompt);
-        SafeHide (rpp->rrnaPrompt);
-        SafeShow (rpp->nameGrp);
-        SafeShow (rfp->product);
-        SafeHide (rfp->usrobjext);
-        break;
-      case FEATDEF_snoRNA :
-        SafeHide (rpp->trnaGrp);
-        SafeHide (rpp->ornaPrompt);
-        SafeHide (rpp->rrnaPrompt);
-        SafeShow (rpp->nameGrp);
-        SafeShow (rfp->product);
-        SafeHide (rfp->usrobjext);
-        break;
-      case FEATDEF_otherRNA :
-        SafeHide (rpp->trnaGrp);
-        SafeHide (rpp->rrnaPrompt);
-        SafeShow (rpp->ornaPrompt);
-        SafeShow (rpp->nameGrp);
-        SafeShow (rfp->product);
-        SafeHide (rfp->usrobjext);
-        break;
-      default :
-        SafeHide (rpp->trnaGrp);
-        SafeHide (rpp->ornaPrompt);
-        SafeHide (rpp->rrnaPrompt);
-        SafeShow (rpp->nameGrp);
-        SafeHide (rfp->product);
-        SafeHide (rfp->usrobjext);
-        break;
+    if ((sfp != NULL && sfp->product != NULL) || indexerVersion) {
+      entityID = SeqMgrGetEntityIDForSeqEntry(sep);
+      rfp->product = CreateRNATranscriptIDDialog (m, entityID, TRUE, NULL, NULL);
     }
+
+    SetRnaType (rpp, subtype);
   }
 
   return (DialoG) p;
@@ -6741,13 +7568,10 @@ static void RnaFormActivate (WindoW w)
 static void RnaRefPtrToForm (ForM f, Pointer data)
 
 {
-  BioseqPtr     bsp;
-  Char          id [41];
   SeqEntryPtr   oldsep;
   RnaFormPtr    rfp;
   SeqEntryPtr   sep;
   SeqFeatPtr    sfp;
-  SeqIdPtr      sip;
   Int4          val;
 
   rfp = (RnaFormPtr) GetObjectExtra (f);
@@ -6772,16 +7596,6 @@ static void RnaRefPtrToForm (ForM f, Pointer data)
       }
       SeqFeatPtrToCommon ((FeatureFormPtr) rfp, sfp);
       PointerToDialog (rfp->product, sfp->product);
-      if (sfp->product != NULL) {
-        sip = SeqLocId (sfp->product);
-        if (sip != NULL) {
-          bsp = BioseqFind (sip);
-          if (bsp == NULL) {
-            SeqIdWrite (sip, id, PRINTID_FASTA_LONG, sizeof (id));
-            SafeSetTitle (rfp->prodSeqIdTxt, id);
-          }
-        }
-      }
     }
     SeqEntrySetScope (oldsep);
   }
@@ -6875,6 +7689,7 @@ extern ForM CreateRnaForm (Int2 left, Int2 top, CharPtr title,
     s = HiddenGroup (h, -1, 0, NULL);
     SetGroupSpacing (s, 3, 10);
     rfp->data = CreateRnaDialog (s, NULL, subtype, sep, sfp, rfp);
+    SetRnaSpecificQuals (sfp, rfp->data);
     rfp->pages [RNA_PAGE] = s;
     Hide (rfp->pages [RNA_PAGE]);
     rnaFormTabs [0] = NULL;
@@ -6987,7 +7802,7 @@ extern Int2 LIBCALLBACK RnaGenFunc (Pointer data)
   if (sfp != NULL && sfp->data.value.ptrvalue != NULL) {
     rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
     StringNCpy_0 (title,
-                GetEnumName ((UIEnum) rrp->type, rna_type_alist),
+                GetEnumName (RnaSubtypeFromRnaRef(rrp), rna_type_alist),
                 sizeof (title));
     if (StringHasNoText (title)) {
       StringCpy (title, "Unknown RNA");
@@ -7043,27 +7858,16 @@ extern Int2 LIBCALLBACK RnaGenFunc (Pointer data)
       rpp = (RnaPagePtr) GetObjectExtra (rfp->data);
       if (rpp != NULL) {
         SetNewFeatureDefaultInterval ((FeatureFormPtr) rfp);
-        if (subtype >= FEATDEF_preRNA && subtype <= FEATDEF_scRNA) {
-          SetEnumPopup (rpp->type, rna_type_alist,
-                        (UIEnum) check_rna_type (subtype - FEATDEF_preRNA + 1));
-          if (subtype == FEATDEF_tRNA)
-          {
-            /* attempt to provide default location for anticodons */
-            SeqLocPtr tmp_loc = NULL;
-            
-            tmp_loc = DialogToPointer (rpp->rfp->location);
-            PointerToDialog (rpp->anticodon, tmp_loc);
-            SetSequenceAndStrandForIntervalPage (rpp->anticodon);
-            SeqLocFree (tmp_loc);              
-          }
-        } else if (subtype == FEATDEF_snoRNA) {
-          SetEnumPopup (rpp->type, rna_type_alist,
-                        (UIEnum) check_rna_type (7));
-        } else if (subtype == FEATDEF_otherRNA) {
-          SetEnumPopup (rpp->type, rna_type_alist,
-                        (UIEnum) check_rna_type (255));
-        } else {
-          SetEnumPopup (rpp->type, rna_type_alist, (UIEnum) 0);
+        SetEnumPopup (rpp->type, rna_type_alist, RnaTypeFromFeatdef (subtype));
+        if (subtype == FEATDEF_tRNA)
+        {
+          /* attempt to provide default location for anticodons */
+          SeqLocPtr tmp_loc = NULL;
+          
+          tmp_loc = DialogToPointer (rpp->rfp->location);
+          PointerToDialog (rpp->anticodon, tmp_loc);
+          SetSequenceAndStrandForIntervalPage (rpp->anticodon);
+          SeqLocFree (tmp_loc);              
         }
       }
     }
@@ -7077,3 +7881,645 @@ extern Int2 LIBCALLBACK RnaGenFunc (Pointer data)
   return OM_MSG_RET_DONE;
 }
 
+
+typedef struct ncrnaclassdlg {
+  DIALOG_MESSAGE_BLOCK
+  PopuP                ncrnaclass;
+  TexT                 otherclass;
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer              change_userdata;
+  Boolean              is_constraint;
+
+} NcrnaClassDlgData, PNTR NcrnaClassDlgPtr;
+
+static void ChangeNcrnaClass (PopuP p)
+{
+  NcrnaClassDlgPtr dlg;
+
+  dlg = (NcrnaClassDlgPtr) GetObjectExtra (p);
+  if (dlg == NULL) return;
+
+  if (GetValue (dlg->ncrnaclass) == NcrnaOTHER) {
+    Show (dlg->otherclass);
+  } else {
+    Hide (dlg->otherclass);
+  }
+
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void ChangeNcrnaOtherClass (TexT t)
+{
+  NcrnaClassDlgPtr dlg;
+
+  dlg = (NcrnaClassDlgPtr) GetObjectExtra (t);
+  if (dlg == NULL) return;
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void PointerToNcrnaClassDialog (DialoG d, Pointer data)
+{
+  NcrnaClassDlgPtr dlg;
+  CharPtr PNTR     cpp;
+  Int4             pos = NcrnaOTHER;
+
+  dlg = (NcrnaClassDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  if (data == NULL) {
+    if (dlg->is_constraint) {
+      pos = NcrnaOTHER + 1;
+    }
+  } else {
+    if (data != NULL) {
+      for (cpp = ncrnaClassList, pos = 1;
+          *cpp != NULL && pos < NcrnaOTHER;
+          cpp++, pos++) {
+        if (StringCmp (*cpp, (CharPtr) data) == 0) {
+          break;
+        }
+      }
+    }
+  }
+  
+  SetValue (dlg->ncrnaclass, pos);
+  if (pos == NcrnaOTHER) {
+    SetTitle (dlg->otherclass, (CharPtr) data);
+    Show (dlg->otherclass);
+  } else {
+    Hide (dlg->otherclass);
+  }
+}
+
+
+static Pointer NcrnaClassDialogToPointer (DialoG d)
+{
+  NcrnaClassDlgPtr dlg;
+  Int4             pos;
+
+  dlg = (NcrnaClassDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  pos = GetValue (dlg->ncrnaclass);
+  if (pos > 0 && pos < NcrnaOTHER) {
+    return StringSave (ncrnaClassList[pos - 1]);
+  } else if (pos == NcrnaOTHER && !TextHasNoText (dlg->otherclass)) {
+    return SaveStringFromText (dlg->otherclass);
+  } else {
+    return NULL;
+  }  
+}
+
+
+static ValNodePtr TestNcrnaClassDialog (DialoG d)
+{
+  ValNodePtr err_list = NULL;
+
+  NcrnaClassDlgPtr dlg;
+  Int4             pos;
+
+  dlg = (NcrnaClassDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  pos = GetValue (dlg->ncrnaclass);
+
+  if (pos < 1 && !dlg->is_constraint) {
+    ValNodeAddPointer (&err_list, 0, "No ncRNA class");
+  } else if (pos == NcrnaOTHER) {
+    if (TextHasNoText (dlg->otherclass)) {
+      ValNodeAddPointer (&err_list, 0, "No ncRNA class");
+    }
+  } else if (!dlg->is_constraint && pos > NcrnaOTHER) {
+    ValNodeAddPointer (&err_list, 0, "No ncRNA class");
+  }
+  return err_list;
+}
+
+
+extern DialoG CreatencRNAClassDialog (GrouP h, Boolean is_constraint, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  NcrnaClassDlgPtr dlg;
+  GrouP            p;
+  CharPtr PNTR cpp;
+
+  p = HiddenGroup (h, 2, 0, NULL);  
+  dlg = (NcrnaClassDlgPtr) MemNew (sizeof (NcrnaClassDlgData));
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+  
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = PointerToNcrnaClassDialog;
+  dlg->fromdialog = NcrnaClassDialogToPointer;
+  dlg->testdialog = TestNcrnaClassDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+  dlg->is_constraint = is_constraint;
+  
+  dlg->ncrnaclass = PopupList (p, TRUE, ChangeNcrnaClass);
+  SetObjectExtra (dlg->ncrnaclass, dlg, NULL);
+  for (cpp = ncrnaClassList; *cpp != NULL; cpp++) {
+    PopupItem (dlg->ncrnaclass, *cpp);
+  }
+  if (is_constraint) {
+    PopupItem (dlg->ncrnaclass, "Any");
+    SetValue (dlg->ncrnaclass, NcrnaOTHER + 1);
+  } else {
+    SetValue (dlg->ncrnaclass, NcrnaOTHER);
+  }
+  dlg->otherclass = DialogText (p, "", 10, ChangeNcrnaOtherClass);
+  SetObjectExtra (dlg->otherclass, dlg, NULL);
+
+  return (DialoG) p;
+}
+
+
+extern RnaTypePtr RnaTypeFree (RnaTypePtr rtp)
+{
+  if (rtp != NULL)
+  {
+    rtp->ncrna_class = MemFree (rtp->ncrna_class);
+    rtp = MemFree (rtp);
+  }
+  return rtp;
+}
+
+
+extern Boolean MatchesRnaType (SeqFeatPtr sfp, RnaTypePtr rtp)
+{
+  RnaRefPtr rrp;
+  GBQualPtr gbq;
+  Uint1     featdef;
+  Boolean   matches = TRUE;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return FALSE;
+  if (rtp == NULL || rtp->rna_featdef == FEATDEF_ANY) return TRUE;
+
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (rrp == NULL) return FALSE;
+
+  featdef = RnaFeatDefFromRnaRef (rrp);
+  if (featdef != rtp->rna_featdef) return FALSE;
+
+  if (featdef == FEATDEF_ncRNA)
+  {
+    if (rtp->ncrna_class == NULL) {
+      matches = TRUE;
+    } else {
+      gbq = sfp->qual;
+      while (gbq != NULL && StringCmp (gbq->qual, "ncRNA_class") != 0)
+      {
+        gbq = gbq->next;
+      }
+      if (gbq == NULL)
+      {
+        if (rrp->ext.choice == 1 && StringCmp (rrp->ext.value.ptrvalue, rtp->ncrna_class) == 0)
+        {
+          matches = TRUE;
+        }
+        else if (StringDoesHaveText (rtp->ncrna_class)) 
+        {
+          matches = FALSE;
+        }
+      }
+      else if (StringCmp (gbq->val, rtp->ncrna_class) != 0)
+      {
+        matches = FALSE;
+      }
+    }
+  }
+  return matches; 
+}
+
+
+static void ClearRNAProduct (RnaRefPtr rrp)
+{
+  tRNAPtr trna;
+
+  if (rrp == NULL || rrp->ext.choice == 0)
+  {
+    return;
+  }
+  if (rrp->ext.choice == 2)
+  {
+		trna = (tRNAPtr)(rrp->ext.value.ptrvalue);
+    if (trna != NULL) {
+		  trna->anticodon = SeqLocFree(trna->anticodon);
+    }
+  }
+
+  rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+  rrp->ext.choice = 0;
+}
+
+
+static void MoveRnaProductToQual (SeqFeatPtr sfp)
+{
+  RnaRefPtr rrp;
+  CharPtr   product = NULL;
+  GBQualPtr gbq;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL)
+  {
+    return;
+  }
+
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (rrp->ext.choice == 1)
+  { 
+    product = rrp->ext.value.ptrvalue;
+    rrp->ext.value.ptrvalue = NULL;
+  }
+  ClearRNAProduct (rrp);
+  rrp->ext.choice = 1;
+  rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+  if (product != NULL)
+  {
+    gbq = FindOrAddQual (sfp, "product");
+    gbq->val = product;
+  }
+}
+
+
+extern void ApplyRnaTypeToSeqFeat (SeqFeatPtr sfp, RnaTypePtr rtp)
+{
+  RnaRefPtr rrp;
+  GBQualPtr gbq;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA)
+  {
+    return;
+  }
+
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (rrp == NULL)
+  {
+    rrp = RnaRefNew();
+    sfp->data.value.ptrvalue = rrp;
+  }
+
+  if (rtp == NULL || rtp->rna_featdef == FEATDEF_ANY)
+  {
+    return;
+  }
+
+  switch (rtp->rna_featdef)
+  {
+    case FEATDEF_preRNA:
+      rrp->type = 1;
+      break;
+    case FEATDEF_mRNA:
+      rrp->type = 2;
+      break;
+    case FEATDEF_tRNA:
+      rrp->type = 3;
+      break;
+    case FEATDEF_rRNA:
+      rrp->type = 4;
+      break;
+    case FEATDEF_scRNA:
+      rrp->type = 255;
+      MoveRnaProductToQual (sfp);
+      gbq = FindOrAddQual (sfp, "ncRNA_class");
+      gbq->val = MemFree (gbq->val);
+      gbq->val = StringSave ("scRNA");
+      break;
+    case FEATDEF_snRNA:
+      rrp->type = 255;
+      MoveRnaProductToQual (sfp);
+      gbq = FindOrAddQual (sfp, "ncRNA_class");
+      gbq->val = MemFree (gbq->val);
+      gbq->val = StringSave ("snRNA");
+      break;
+    case FEATDEF_snoRNA:
+      rrp->type = 255;
+      MoveRnaProductToQual (sfp);
+      gbq = FindOrAddQual (sfp, "ncRNA_class");
+      gbq->val = MemFree (gbq->val);
+      gbq->val = StringSave ("snoRNA");
+      break;
+    case FEATDEF_ncRNA:
+      rrp->type = 255;
+      MoveRnaProductToQual (sfp);
+      gbq = FindOrAddQual (sfp, "ncRNA_class");
+      gbq->val = MemFree (gbq->val);
+      gbq->val = StringSave (rtp->ncrna_class);
+      break;
+    case FEATDEF_tmRNA:
+      rrp->type = 255;
+      MoveRnaProductToQual (sfp);
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = StringSave ("tmRNA");
+      rrp->ext.choice = 1;
+      break;
+    case FEATDEF_otherRNA:
+      rrp->type = 255;
+      if (rrp->ext.choice == 1 && IsStringInNcRNAClassList (rrp->ext.value.ptrvalue))
+      {
+        gbq = FindOrAddQual (sfp, "ncRNA_class");
+        gbq->val = MemFree (gbq->val);
+        gbq->val = rrp->ext.value.ptrvalue;
+        rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+      }
+      break;
+  }
+
+}
+
+
+extern void AddToComment (SeqFeatPtr sfp, CharPtr comment)
+{
+  CharPtr tmp;
+
+  if (sfp == NULL || StringHasNoText (comment)) return;
+
+  if (StringHasNoText (sfp->comment))
+  {
+    sfp->comment = MemFree (sfp->comment);
+    sfp->comment = StringSave (comment);
+  }
+  else
+  {
+    tmp = (CharPtr) MemNew (sizeof (Char) * (StringLen (sfp->comment) + StringLen (comment) + 3));
+    sprintf (tmp, "%s; %s", sfp->comment, comment);
+    sfp->comment = MemFree (sfp->comment);
+    sfp->comment = tmp;
+  }
+}
+
+
+extern void ApplyProductToRNA (SeqFeatPtr sfp, CharPtr product)
+{
+  RnaRefPtr rrp;
+  GBQualPtr gbq;
+  Uint1     aa;
+  Int4      j;
+  Boolean   justTrnaText = FALSE;
+  Char      codon [16];
+  tRNAPtr   trp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA
+      || sfp->data.value.ptrvalue == NULL)
+  {
+    return;
+  }
+
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (rrp->type == 3)
+  {
+    ClearRNAProduct (rrp);
+
+    aa = ParseTRnaString (product, &justTrnaText, (Uint1Ptr) codon, TRUE);
+    if (aa != 0) 
+    {
+      trp = (tRNAPtr) MemNew (sizeof (tRNA));
+      if (trp != NULL) 
+      {
+        trp->aatype = 2;
+        for (j = 0; j < 6; j++)
+        {
+          trp->codon [j] = 255;
+        }
+        if (justTrnaText)
+        {
+          for (j = 0; j < 6; j++)
+          {
+            trp->codon [j] = codon [j];
+          }
+        }
+        trp->aa = aa;
+        rrp->ext.choice = 2;
+        rrp->ext.value.ptrvalue = (Pointer) trp;
+      }
+    }
+    if (aa == 0 || !justTrnaText)
+    {
+      AddToComment (sfp, product);
+    }
+  }
+  else if (rrp->type == 255 
+           && rrp->ext.choice == 1 
+           && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
+               || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
+               || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))
+  {
+    gbq = FindOrAddQual (sfp, "product");
+    gbq->val = MemFree (gbq->val);
+    gbq->val = StringSave (product);    
+  }
+  else
+  {
+    ClearRNAProduct (rrp);
+    rrp->ext.choice = 1;
+    rrp->ext.value.ptrvalue = StringSave (product);
+  }
+}
+
+
+
+typedef struct rnatypedlg {
+  DIALOG_MESSAGE_BLOCK
+  PopuP                rna_type;
+  DialoG               ncrna_class;
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer              change_userdata;
+  Boolean              is_constraint;
+
+} RnaTypeDlgData, PNTR RnaTypeDlgPtr;
+
+
+static void ChangeRnaTypeDlg (PopuP p)
+{
+  RnaTypeDlgPtr dlg;
+  UIEnum        val;
+
+  dlg = (RnaTypeDlgPtr) GetObjectExtra (p);
+  if (dlg != NULL)
+  {
+    if (GetEnumPopup (dlg->rna_type, rna_type_alist, &val) && val == 8)
+    {
+      Enable (dlg->ncrna_class);
+    }
+    else
+    {
+      Disable (dlg->ncrna_class);
+    }
+    if (dlg->change_notify != NULL)
+    {
+      (dlg->change_notify) (dlg->change_userdata);
+    }
+  }
+}
+
+
+static void PointerToRnaTypeDialog (DialoG d, Pointer data)
+{
+  RnaTypeDlgPtr dlg;
+  RnaTypePtr    rtp = NULL;
+
+  dlg = (RnaTypeDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  rtp = (RnaTypePtr) data;
+  if (rtp == NULL || rtp->rna_featdef == FEATDEF_ANY) 
+  {
+    SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 0);
+    PointerToDialog (dlg->ncrna_class, NULL);
+  }
+  else
+  {
+    switch (rtp->rna_featdef)
+    {
+      case FEATDEF_preRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 1);
+        PointerToDialog (dlg->ncrna_class, NULL);
+        break;
+      case FEATDEF_mRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 2);
+        PointerToDialog (dlg->ncrna_class, NULL);
+        break;
+      case FEATDEF_tRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 3);
+        PointerToDialog (dlg->ncrna_class, NULL);
+        break;
+      case FEATDEF_rRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 4);
+        PointerToDialog (dlg->ncrna_class, NULL);
+        break;
+      case FEATDEF_scRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 8);
+        PointerToDialog (dlg->ncrna_class, "scRNA");
+        break;
+      case FEATDEF_snRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 8);
+        PointerToDialog (dlg->ncrna_class, "snRNA");
+        break;
+      case FEATDEF_snoRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 8);
+        PointerToDialog (dlg->ncrna_class, "snoRNA");
+        break;
+      case FEATDEF_ncRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 8);
+        PointerToDialog (dlg->ncrna_class, rtp->ncrna_class);
+        break;
+      case FEATDEF_tmRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 9);
+        PointerToDialog (dlg->ncrna_class, NULL);
+        break;
+      case FEATDEF_otherRNA:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 255);
+        PointerToDialog (dlg->ncrna_class, NULL);
+        break;
+      default:
+        SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 0);
+        PointerToDialog (dlg->ncrna_class, NULL);
+        break;
+    }
+  }
+  ChangeRnaTypeDlg (dlg->rna_type);
+}
+
+
+static Pointer RnaTypeDialogToPointer (DialoG d)
+{
+  RnaTypeDlgPtr dlg;
+  RnaTypePtr    rtp = NULL;
+  UIEnum        val;
+
+  dlg = (RnaTypeDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  if (GetEnumPopup (dlg->rna_type, rna_type_alist, &val))
+  {
+    rtp = (RnaTypePtr) MemNew (sizeof (RnaTypeData));
+    rtp->rna_featdef = FEATDEF_ANY;
+    rtp->ncrna_class = NULL;
+    switch (val)
+    {
+      case 0:
+        rtp->rna_featdef = FEATDEF_ANY;
+        break;
+      case 1:
+        rtp->rna_featdef = FEATDEF_preRNA;
+        break;
+      case 2:
+        rtp->rna_featdef = FEATDEF_mRNA;
+        break;
+      case 3:
+        rtp->rna_featdef = FEATDEF_tRNA;
+        break;
+      case 4:
+        rtp->rna_featdef = FEATDEF_rRNA;
+        break;
+      case 8:
+        rtp->rna_featdef = FEATDEF_ncRNA;
+        rtp->ncrna_class = DialogToPointer (dlg->ncrna_class);
+        break;
+      case 9:
+        rtp->rna_featdef = FEATDEF_tmRNA;
+        break;
+      case 255:
+        rtp->rna_featdef = FEATDEF_otherRNA;
+        break;
+    }
+  }
+  return rtp;
+}
+ 
+
+static ValNodePtr TestRnaTypeDialog (DialoG d)
+{
+  RnaTypeDlgPtr dlg;
+  ValNodePtr    err_list = NULL;
+  UIEnum        val;
+
+  dlg = (RnaTypeDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  if (GetEnumPopup (dlg->rna_type, rna_type_alist, &val)) {
+    if (val == 8) {
+      err_list = TestDialog (dlg->ncrna_class);
+    }
+  } else {
+    ValNodeAddPointer (&err_list, 0, "RNA type");
+  }
+  return err_list;
+}  
+
+extern DialoG RnaTypeDialog (GrouP h, Boolean is_constraint, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  RnaTypeDlgPtr dlg;
+  GrouP         p;
+  CharPtr       title;
+
+  if (is_constraint) {
+    title = "RNA Type of Feature to be Edited";
+  } else {
+    title = "RNA Type";
+  }
+  
+  p = NormalGroup (h, -1, 0, title, programFont, NULL);  
+  dlg = (RnaTypeDlgPtr) MemNew (sizeof (RnaTypeDlgData));
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+  
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = PointerToRnaTypeDialog;
+  dlg->fromdialog = RnaTypeDialogToPointer;
+  dlg->testdialog = TestRnaTypeDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+  dlg->is_constraint = is_constraint;
+
+  dlg->rna_type = PopupList (p, TRUE, ChangeRnaTypeDlg);
+  SetObjectExtra (dlg->rna_type, dlg, NULL);
+  InitEnumPopup (dlg->rna_type, rna_type_alist, NULL);
+  SetEnumPopup (dlg->rna_type, rna_type_alist, (UIEnum) 0);
+  
+  dlg->ncrna_class = CreatencRNAClassDialog (p, is_constraint, change_notify, change_userdata);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->rna_type, (HANDLE) dlg->ncrna_class, NULL);
+
+  return (DialoG) p;
+}
+
diff --git a/desktop/cdrgn.h b/desktop/cdrgn.h
index 8797ed93..3b19dfef 100644
--- a/desktop/cdrgn.h
+++ b/desktop/cdrgn.h
@@ -29,13 +29,37 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.6 $
+* $Revision: 6.13 $
 *
 * File Description: 
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: cdrgn.h,v $
+* Revision 6.13  2008/01/17 21:18:09  bollin
+* Fixes for RNA dialog for ncRNA product/class handling
+*
+* Revision 6.12  2007/12/21 17:30:27  bollin
+* Changes to dialog for selecting ncRNA class and RNA type - allow ncRNA class
+* Any if selecting RNA type in a constraint context, test dialog to generate
+* error if "other" is the class but no text is specified.
+*
+* Revision 6.11  2007/11/26 21:16:29  bollin
+* Moved CreatencRNAClassDialog proto into cdrgn.h
+*
+* Revision 6.10  2007/09/21 18:05:23  bollin
+* code in place for conversion of old-style misc_RNA, snRNA, scRNA, and snoRNA
+* features to new ncRNA features, commented out until changeover.
+*
+* Revision 6.9  2007/09/10 20:08:51  bollin
+* Correction to MatchesRnaType
+*
+* Revision 6.8  2007/09/10 18:47:11  kans
+* prototype for SetRnaSpecificQuals, cast for codon argument to ParseTRnaString
+*
+* Revision 6.7  2007/09/10 18:33:15  bollin
+* Changes for new ncRNA and tmRNA class editor.
+*
 * Revision 6.6  2007/07/25 13:53:12  bollin
 * Removed local copy of TruncateLocation from sequin3.c, made TruncateLocation
 * function in desktop/cdrgn.c extern and added prototype to cdrgn.h
@@ -94,8 +118,26 @@ extern ForM CreateRnaForm (Int2 left, Int2 top, CharPtr title,
                            Uint2 subtype, FormActnFunc actproc);
 extern Int2 LIBCALLBACK RnaGenFunc (Pointer data);
 
+extern void AddRnaSpecificQuals (SeqFeatPtr sfp, DialoG d);
+extern void ConvertProductQualToRnaRefName (SeqFeatPtr sfp);
+extern void SetRnaSpecificQuals (SeqFeatPtr sfp, DialoG d);
+extern void ConvertToOldRNAFormat (SeqFeatPtr sfp);
+
 extern SeqLocPtr TruncateLocation (SeqLocPtr head, Int4 len);
 
+/* for searching for RNA values of a certain type */
+typedef struct rnatype {
+  Int4    rna_featdef; /* use FEATDEF_ANY for match any RNA */
+  CharPtr ncrna_class; /* value to look for in ncrna_class qual */
+} RnaTypeData, PNTR RnaTypePtr;
+
+extern RnaTypePtr RnaTypeFree (RnaTypePtr rtp);
+extern Boolean MatchesRnaType (SeqFeatPtr sfp, RnaTypePtr rtp);
+extern void ApplyRnaTypeToSeqFeat (SeqFeatPtr sfp, RnaTypePtr rtp);
+extern void ApplyProductToRNA (SeqFeatPtr sfp, CharPtr product);
+extern void AddToComment (SeqFeatPtr sfp, CharPtr comment);
+extern DialoG RnaTypeDialog (GrouP h, Boolean is_constraint, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
+extern DialoG CreatencRNAClassDialog (GrouP h, Boolean is_constraint, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
 
 #ifdef __cplusplus
 }
diff --git a/desktop/dlgutil1.c b/desktop/dlgutil1.c
index cacc2286..ecd9ab58 100644
--- a/desktop/dlgutil1.c
+++ b/desktop/dlgutil1.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.126 $
+* $Revision: 6.136 $
 *
 * File Description: 
 *
@@ -55,6 +55,8 @@
 #include <alignmgr2.h>
 #include <toasn3.h>
 #include <vibforms.h>
+#include <cdrgn.h>
+#include <findrepl.h>
 
 #define NUMBER_OF_SUFFIXES    8
 
@@ -236,6 +238,8 @@ extern Boolean DescFormReplaceWithoutUpdateProc (ForM f)
           sdp->data.ptrvalue = DialogToPointer (dfp->data);
           break;
       }
+      FixSpecialCharactersForObject (OBJ_SEQDESC, sdp, "You may not include special characters in the text.\nIf you do not choose replacement characters, these special characters will be replaced with '#'.", TRUE, NULL);
+
       ompc.output_data = (Pointer) sdp;
       if (ompc.input_entityID == 0) {
         if (! ObjMgrRegister (OBJ_SEQDESC, (Pointer) sdp)) {
@@ -1278,7 +1282,6 @@ extern void SeqFeatPtrToCommon (FeatureFormPtr ffp, SeqFeatPtr sfp)
   }
 }
 
-extern void CleanupEvidenceGBQuals (GBQualPtr PNTR prevgbq);
 extern void CleanupEvidenceGBQuals (GBQualPtr PNTR prevgbq)
 
 {
@@ -1609,7 +1612,6 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
   Char            badInfMssg [32];
   Char            badInfQual [256];
   BioseqPtr       bsp;
-  Char            ch;
   Char            desc [128];
   Int2            expev;
   SeqMgrFeatContext  fcontext;
@@ -1629,7 +1631,6 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
   Boolean         noRight;
   SeqEntryPtr     oldscope;
   OMProcControl   ompc;
-  CharPtr         ptr;
   ReplaceData     rd;
   Boolean         rsult;
   SeqAnnotPtr     sap;
@@ -1677,17 +1678,7 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
           break;
       }
       sfp->comment = SaveStringFromText (ffp->comment);
-      ptr = sfp->comment;
-      if (ptr != NULL) {
-        ch = *ptr;
-        while (ch != '\0') {
-          if (ch < ' ' || ch > '~') {
-            *ptr = '~';
-          }
-          ptr++;
-          ch = *ptr;
-        }
-      }
+      NewlinesToTildes (sfp->comment);
       expev = GetValue (ffp->evidence);
       if (expev > 0 && expev <= 3) {
         sfp->exp_ev = expev - 1;
@@ -1845,11 +1836,18 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
           }
         }
       }
+
       ompc.output_data = (Pointer) sfp;
       if (ompc.input_entityID == 0) {
         sfp->qual = DialogToPointer (ffp->gbquals);
         VisStringDialogToGbquals (sfp, ffp->experiment, "experiment");
         InferenceDialogToGBQuals (ffp->inference, sfp, TRUE);
+        if (sfp->data.choice == SEQFEAT_RNA) {
+          AddRnaSpecificQuals (sfp, ffp->data);
+          /* NOTE - we will remove this line when we convert to the new data format */
+/*          ConvertToOldRNAFormat (sfp); */
+        }
+
         sfp->ext = DialogToPointer (ffp->usrobjext);
         if (ffp->goTermUserObj != NULL) {
           sfp->ext = CombineGOTermUserObjects (sfp->ext, ffp->goTermUserObj);
@@ -1864,6 +1862,7 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
           TextToFeatXref (ffp->fidxref, sfp);
         }
         AddProtRefXref (sfp, ffp->protXrefName, ffp->protXrefDesc);
+        FixSpecialCharactersForObject (OBJ_SEQFEAT, sfp, "You may not include special characters in the text.\nIf you do not choose replacement characters, these special characters will be replaced with '#'.", TRUE, NULL);
         if (! ObjMgrRegister (OBJ_SEQFEAT, (Pointer) sfp)) {
           Message (MSG_ERROR, "ObjMgrRegister failed");
         }
@@ -1874,6 +1873,12 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
         sfp->qual = DialogToPointer (ffp->gbquals);
         VisStringDialogToGbquals (sfp, ffp->experiment, "experiment");
         InferenceDialogToGBQuals (ffp->inference, sfp, TRUE);
+        if (sfp->data.choice == SEQFEAT_RNA) {
+          AddRnaSpecificQuals (sfp, ffp->data);
+          /* NOTE - we will remove this line when we convert to the new data format */
+/*          ConvertToOldRNAFormat (sfp); */
+        }
+
         sfp->ext = DialogToPointer (ffp->usrobjext);
         if (ffp->goTermUserObj != NULL) {
           sfp->ext = CombineGOTermUserObjects (sfp->ext, ffp->goTermUserObj);
@@ -1888,6 +1893,7 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
           TextToFeatXref (ffp->fidxref, sfp);
         }
         AddProtRefXref (sfp, ffp->protXrefName, ffp->protXrefDesc);
+        FixSpecialCharactersForObject (OBJ_SEQFEAT, sfp, "You may not include special characters in the text.\nIf you do not choose replacement characters, these special characters will be replaced with '#'.", TRUE, NULL);
         ompc.output_itemtype = OBJ_SEQFEAT;
         if (ompc.input_itemtype == OBJ_BIOSEQ) {
           bsp = GetBioseqGivenIDs (ompc.input_entityID, ompc.input_itemID, ompc.input_itemtype);
@@ -1925,6 +1931,11 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
         rd.sfp = sfp;
         GatherItem (ompc.input_entityID, ompc.input_itemID, ompc.input_itemtype,
                     (Pointer) &rd, ReplaceFeatureExtras);
+        if (sfp->data.choice == SEQFEAT_RNA) {
+          AddRnaSpecificQuals (sfp, ffp->data);
+          /* NOTE - we will remove this line when we convert to the new data format */
+/*          ConvertToOldRNAFormat (sfp); */
+        }
         if (HasExceptionGBQual (sfp)) {
           sfp->excpt = TRUE;
         }
@@ -1939,6 +1950,7 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
         {
           AddProtRefXref (sfp, ffp->protXrefName, ffp->protXrefDesc);
         }
+        FixSpecialCharactersForObject (OBJ_SEQFEAT, sfp, "You may not include special characters in the text.\nIf you do not choose replacement characters, these special characters will be replaced with '#'.", TRUE, NULL);
         if (! ReplaceDataForProc (&ompc, FALSE)) {
           Message (MSG_ERROR, "ReplaceDataForProc failed");
         }
@@ -1972,6 +1984,7 @@ extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f)
               sfp = CreateNewFeature (sep, NULL, SEQFEAT_GENE, NULL);
               if (sfp != NULL) {
                 sfp->data.value.ptrvalue = (Pointer) grp;
+                FixSpecialCharactersForObject (OBJ_SEQFEAT, sfp, "You may not include special characters in the text.\nIf you do not choose replacement characters, these special characters will be replaced with '#'.", TRUE, NULL);
                 sfp->location = SeqLocFree (sfp->location);
                 sfp->location = DialogToPointer (ffp->location);
                 bsp = GetBioseqGivenSeqLoc (sfp->location, ffp->input_entityID);
@@ -2722,12 +2735,231 @@ static void AuthorDialogMessage (DialoG d, Int2 mssg)
   }
 }
 
+
+static Boolean IsAuthList (CharPtr path)
+{
+  FILE *fp;
+  Char buffer[10];
+  Int4 len;
+  Boolean rval = FALSE;
+
+  fp = FileOpen (path, "r");
+  if (fp == NULL) return FALSE;
+  
+  len = fread (buffer, 1, 9, fp);
+  buffer[9] = 0;
+  if (StringCmp (buffer, "Auth-list") == 0)
+  {
+    rval = TRUE;
+  }
+  FileClose (fp);
+  return rval;
+}
+
+
+static NameStdPtr ReadNameFromString (CharPtr str, CharPtr PNTR next_name, BoolPtr found_special)
+{
+  CharPtr cp_end, cp_space;
+  NameStdPtr n;
+
+  if (StringHasNoText (str)) 
+  {
+    if (next_name != NULL)
+    {
+      *next_name = NULL;
+    }
+    return NULL;
+  }
+
+  /* skip over any leading spaces */
+  str += StringSpn (str, " \t");
+
+  /* skip over "and" if found */
+  if (StringNCmp (str, "and ", 4) == 0)
+  {
+    str += 4;
+  }
+  if (StringHasNoText (str)) return NULL;
+
+  cp_end = StringChr (str, ',');
+  if (cp_end != NULL)
+  {
+    *cp_end = 0;
+    if (next_name != NULL)
+    {
+      if (StringHasNoText (cp_end + 1))
+      {
+        *next_name = NULL;
+      }
+      else
+      {
+        *next_name = cp_end + 1;
+      }
+    }
+  }
+  else if (next_name != NULL)
+  {
+    *next_name = NULL;
+  }
+
+  n = NameStdNew ();  
+  /* look for elements in name */
+  cp_space = StringRChr (str, ' ');
+  if (cp_space == NULL)
+  {
+    n->names[0] = StringSave (str);
+  }
+  else
+  {
+    n->names[0] = StringSave (cp_space + 1);
+    while (isspace (*cp_space))
+    {
+      cp_space--;
+    }
+    *(cp_space + 1) = 0;
+    cp_space = StringChr (str, ' ');
+    if (cp_space == NULL)
+    {
+       n->names[1] = StringSave (str);
+       n->names[4] = (CharPtr) MemNew (sizeof (Char) * 3);
+       sprintf (n->names[4], "%c.", *(n->names[1]));
+    }
+    else
+    {
+      *(cp_space) = 0;
+      n->names[1] = StringSave (str);
+
+      cp_space++;
+      while (isspace (*cp_space))
+      {
+        cp_space++;
+      }
+      
+      n->names[4] = (CharPtr) MemNew (sizeof (Char) * (4 + StringLen (cp_space)));
+      sprintf (n->names[4], "%c.%s.", *(n->names[1]), cp_space);
+    }
+    SpecialCharReplace (&(n->names[1]), NULL, found_special, NULL);
+    SpecialCharReplace (&(n->names[4]), NULL, found_special, NULL);
+  }
+  SpecialCharReplace (&(n->names[0]), NULL, found_special, NULL);
+
+  return n;
+}
+
+
+static Boolean EndsWithComma (CharPtr str)
+{
+  CharPtr cp;
+
+  if (StringHasNoText (str)) return FALSE;
+  cp = str + StringLen (str) - 1;
+  while (isspace (*cp) && cp > str)
+  {
+    cp--;
+  }
+  if (*cp == ',')
+  {
+    return TRUE;
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+
+static CharPtr ExtendToComma (CharPtr line, ReadBufferPtr rbp)
+{
+  CharPtr next_line = NULL, tmp;
+  Boolean end_of_file = FALSE;
+
+  while (!EndsWithComma (line) && !end_of_file)
+  {
+    next_line = AbstractReadFunction (rbp);
+    if (next_line == NULL)
+    {
+      end_of_file = TRUE;
+    }
+    else if (StringHasNoText (next_line))
+    {
+      next_line = MemFree (next_line);
+    }
+    else if (StringHasNoText (line))
+    {
+      line = MemFree (line);
+      line = next_line;
+    }
+    else
+    {
+      tmp = (CharPtr) MemNew (sizeof (Char) * (StringLen (line) + StringLen (next_line) + 2));
+      sprintf (tmp, "%s %s", line, next_line);
+      next_line = MemFree (next_line);
+      line = MemFree (line);
+      line = tmp;
+    }
+  }
+  return line;
+}
+
+
+static AuthListPtr ReadAuthorListFromTextFile (CharPtr path)
+{
+  ReadBufferData rbd;
+  CharPtr        line;
+  AuthListPtr    alp;
+  AuthorPtr      ap;
+  CharPtr        cp, next_cp;
+  NameStdPtr     n;
+  ValNodePtr     names = NULL;
+  Boolean        found_special = FALSE;
+
+  rbd.fp = FileOpen (path, "r");
+  if (rbd.fp == NULL) return FALSE;
+  rbd.current_data = NULL;
+
+  line = ExtendToComma (NULL, &rbd);
+  while (line != NULL) 
+  {
+    cp = line;
+    next_cp = NULL;
+    while (cp != NULL)
+    {
+      n = ReadNameFromString (cp, &next_cp, &found_special);
+      if (n != NULL)
+      {
+        ap = AuthorNew ();
+        ap->name = PersonIdNew ();
+        ap->name->choice = 2;
+        ap->name->data = n;
+        ValNodeAddPointer (&names, 0, ap);
+      }
+      cp = next_cp;
+    }
+    line = MemFree (line);
+    line = ExtendToComma (NULL, &rbd);
+  }
+  if (names != NULL)
+  {
+    alp = AuthListNew ();
+    alp->choice = 1;
+    alp->names = names;
+  }
+  if (found_special)
+  {
+    Message (MSG_OK, "Special characters in names were converted");
+  }
+  
+  FileClose (rbd.fp);
+  return alp;
+}
+
+
 static Boolean ReadAuthorDialog (DialoG d, CharPtr filename)
 
 {
   AuthorDialogPtr  adp;
   AsnIoPtr         aip;
-  AuthListPtr      alp;
+  AuthListPtr      alp = NULL;
   Char             path [PATH_MAX];
 
   path [0] = '\0';
@@ -2735,16 +2967,20 @@ static Boolean ReadAuthorDialog (DialoG d, CharPtr filename)
   adp = (AuthorDialogPtr) GetObjectExtra (d);
   if (adp != NULL) {
     if (path [0] != '\0' || GetInputFileName (path, sizeof (path), "", "TEXT")) {
-      aip = AsnIoOpen (path, "r");
-      if (aip != NULL) {
-        alp = AuthListAsnRead (aip, NULL);
-        AsnIoClose (aip);
-        if (alp != NULL) {
-          PointerToDialog (adp->dialog, (Pointer) alp);
-          alp = AuthListFree (alp);
-          Update ();
-          return TRUE;
+      if (IsAuthList (path)) {
+        aip = AsnIoOpen (path, "r");
+        if (aip != NULL) {
+          alp = AuthListAsnRead (aip, NULL);
+          AsnIoClose (aip);
         }
+      } else {
+        alp = ReadAuthorListFromTextFile (path);
+      }
+      if (alp != NULL) {
+        PointerToDialog (adp->dialog, (Pointer) alp);
+        alp = AuthListFree (alp);
+        Update ();
+        return TRUE;
       }
     }
   }
@@ -7019,6 +7255,7 @@ static void StringToLatLonDlg (DialoG d, Pointer data)
   tmp = (CharPtr) MemNew (sizeof (Char) * len);
   StringNCpy (tmp, str, len - 1);
   tmp [len - 1] = 0;
+  TrimSpacesAroundString (tmp);
   SetTitle (dlg->deg_ns, tmp);
   tmp = MemFree (tmp);
   SetValue (dlg->dir_ns, *ns == 'N' ? 1 : 2);
@@ -7027,6 +7264,7 @@ static void StringToLatLonDlg (DialoG d, Pointer data)
   tmp = (CharPtr) MemNew (sizeof (Char) * len);
   StringNCpy (tmp, ns + 1, len - 1);
   tmp [len - 1] = 0;
+  TrimSpacesAroundString (tmp);
   SetTitle (dlg->deg_ew, tmp);
   tmp = MemFree (tmp);
   SetValue (dlg->dir_ew, *ew == 'E' ? 1 : 2);
@@ -8501,6 +8739,176 @@ extern void CreateStandardEditMenu (WindoW w)
   i = CommandItem (m, "Copy", StdCopyTextProc);
   i = CommandItem (m, "Paste", StdPasteTextProc);
   i = CommandItem (m, "Clear", StdDeleteTextProc);
+}
+
+
+static ValNodePtr sqnTempFiles = NULL;
+
+extern void RememberSqnTempFile (CharPtr file)
+
+{
+  ValNodePtr  vnp;
+
+  if (StringHasNoText (file)) return;
+
+  vnp = ValNodeCopyStr (NULL, 0, file);
+  if (vnp == NULL) return;
+
+  vnp->next = sqnTempFiles;
+  sqnTempFiles = vnp;
+}
+
+extern void FreeSqnTempFiles (void)
+
+{
+  CharPtr     file;
+  ValNodePtr  list;
+  ValNodePtr  vnp;
+
+  if (sqnTempFiles == NULL) return;
+
+  list = sqnTempFiles;
+  sqnTempFiles = NULL;
+
+  for (vnp = list; vnp != NULL; vnp = vnp->next) {
+    file = (CharPtr) vnp->data.ptrvalue;
+    if (StringHasNoText (file)) continue;
+    FileRemove (file);
+  }
+
+  ValNodeFreeData (list);
+}
+
+
+/* This gets a list of the open views */
+NLM_EXTERN ValNodePtr GetBaseFormList ()
+
+{
+  Uint4          j;
+  Uint4          num;
+  ObjMgrPtr      omp;
+  ObjMgrDataPtr  omdp;
+  ObjMgrDataPtr  PNTR omdpp;
+  OMUserDataPtr  omudp;
+  BaseFormPtr    bfp;
+  ValNodePtr     base_form_list = NULL;
+
+  omp = ObjMgrGet ();
+  if (omp == NULL) return NULL;
+  num = omp->currobj;
+  for (j = 0, omdpp = omp->datalist; j < num && omdpp != NULL; j++, omdpp++) {
+    omdp = *omdpp;
+    if (omdp->parentptr == NULL) {
+      for (omudp = omdp->userdata; omudp != NULL; omudp = omudp->next) {
+        if (omudp->proctype == OMPROC_VIEW) {
+          bfp = (BaseFormPtr) omudp->userdata.ptrvalue;
+          ValNodeAddPointer (&base_form_list, 0, bfp);
+        }
+      }
+    }
+  }
+  return base_form_list;
+}
+
+
+/* This gets a list of the top SeqEntry for each open view */
+NLM_EXTERN ValNodePtr GetViewedSeqEntryList (void)
+{
+  ValNodePtr  sep_list = NULL, base_form_list, vnp;
+  BaseFormPtr bfp;
+  SeqEntryPtr sep;
+  
+  base_form_list = GetBaseFormList();
+  for (vnp = base_form_list; vnp != NULL; vnp = vnp->next) {
+    bfp = (BaseFormPtr) vnp->data.ptrvalue;
+    if (bfp != NULL && bfp->input_entityID != 0) {
+      sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+      ValNodeAddPointer (&sep_list, 0, sep);
+    }
+  }
+  base_form_list = ValNodeFree (base_form_list);
+  return sep_list;
+}
+
+
+NLM_EXTERN SeqEntryPtr RestoreFromFile (CharPtr path)
 
+{
+  BioseqPtr     bsp;
+  BioseqSetPtr  bssp;
+  Pointer       dataptr;
+  Uint2         datatype;
+  Uint2         entityID;
+  SeqEntryPtr   rsult;
+  SeqEntryPtr   sep;
+
+  rsult = NULL;
+  if (path != NULL && path [0] != '\0') {
+    dataptr = ObjMgrGenericAsnTextFileRead (path, &datatype, &entityID);
+    if (dataptr != NULL && entityID > 0) {
+      if (datatype == OBJ_SEQSUB || datatype == OBJ_SEQENTRY ||
+          datatype == OBJ_BIOSEQ || datatype == OBJ_BIOSEQSET) {
+        WatchCursor ();
+        sep = GetTopSeqEntryForEntityID (entityID);
+        if (sep == NULL) {
+          sep = SeqEntryNew ();
+          if (sep != NULL) {
+            if (datatype == OBJ_BIOSEQ) {
+              bsp = (BioseqPtr) dataptr;
+              sep->choice = 1;
+              sep->data.ptrvalue = bsp;
+              SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep);
+            } else if (datatype == OBJ_BIOSEQSET) {
+              bssp = (BioseqSetPtr) dataptr;
+              sep->choice = 2;
+              sep->data.ptrvalue = bssp;
+              SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) bssp, sep);
+            } else {
+              sep = SeqEntryFree (sep);
+            }
+          }
+          sep = GetTopSeqEntryForEntityID (entityID);
+        }
+        if (sep != NULL) {
+          rsult = SeqEntryNew ();
+          if (rsult != NULL) {
+            rsult->choice = sep->choice;
+            rsult->data.ptrvalue = sep->data.ptrvalue;
+            sep->data.ptrvalue = NULL;
+            if (datatype == OBJ_SEQSUB) {
+              SeqSubmitFree ((SeqSubmitPtr) dataptr);
+            } else {
+              SeqEntryFree (sep);
+            }
+            /*Message (MSG_OK, "Call new object manager free function");*/
+          }
+        }
+        ArrowCursor ();
+      }
+      /*
+      ObjMgrDelete (entityID);
+      */
+    }
+  }
+  return rsult;
+}
+
+
+NLM_EXTERN Uint2 RestoreEntityIDFromFile (CharPtr path, Uint2 entityID)
+{
+  SeqEntryPtr scope, oldsep, currsep;
+  Uint2 newid = 0;
+
+  scope = SeqEntrySetScope (NULL);
+  oldsep = RestoreFromFile (path);
+  currsep = GetTopSeqEntryForEntityID (entityID);
+  if (oldsep == NULL || currsep == NULL) {
+    SeqEntrySetScope (scope);
+  } else {  
+    ReplaceSeqEntryWithSeqEntry (currsep, oldsep, TRUE);
+    SeqEntrySetScope (NULL);
+    newid = ObjMgrGetEntityIDForChoice (currsep);
+  }
+  return newid;
 }
 
diff --git a/desktop/dlgutil2.c b/desktop/dlgutil2.c
index 22827785..b3d604bd 100644
--- a/desktop/dlgutil2.c
+++ b/desktop/dlgutil2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.164 $
+* $Revision: 6.186 $
 *
 * File Description: 
 *
@@ -54,6 +54,7 @@
 #include <objseq.h>
 #include <toasn3.h>
 #include <explore.h>
+#include <findrepl.h>
 #ifdef WIN_MOTIF
 #include <netscape.h>
 #endif
@@ -100,6 +101,56 @@ extern CharPtr SaveStringFromTextAndStripNewlines (TexT t)
   }
 }
 
+
+extern CharPtr StripNewlines (CharPtr str)
+
+{
+  Char     ch;
+  size_t   len;
+  CharPtr  ptr;
+
+  if (str == NULL) return str;
+  len = StringLen (str);
+  if (len > 0) {
+    ptr = str;
+    ch = *ptr;
+    while (ch != '\0') {
+      if (ch < ' ') {
+        *ptr = ' ';
+      }
+      ptr++;
+      ch = *ptr;
+    }
+    TrimSpacesAroundString (str);
+    if (StringHasNoText (str)) {
+      str = MemFree (str);
+    }
+  } else {
+    str = MemFree (str);
+  }
+  return str;
+}
+
+
+extern void NewlinesToTildes (CharPtr str)
+
+{
+  Uchar    ch;
+  CharPtr  ptr;
+
+  if (StringHasNoText (str)) return;
+  ptr = str;
+  ch = *ptr;
+  while (ch != '\0') {
+    if (ch < ' ') {
+      *ptr = '~';
+    }
+    ptr++;
+    ch = *ptr;
+  }
+}
+
+
 static void DatePtrToDatePage (DialoG d, Pointer data)
 
 {
@@ -1000,6 +1051,37 @@ typedef struct fieldpage {
   ButtoN             PNTR boxes;
 } FieldPage, PNTR FieldPagePtr;
 
+
+static Boolean ShouldSuppressGBQual(Uint1 subtype, CharPtr qual_name)
+{
+  if (StringHasNoText (qual_name)) {
+    return FALSE;
+  }
+
+  /* always suppress experiment and inference quals */
+  if (StringCmp (qual_name, "experiment") == 0 || StringCmp (qual_name, "inference") == 0) {
+    return TRUE;
+  }
+  
+  if (subtype == FEATDEF_ncRNA) {
+    if (StringCmp (qual_name, "product") == 0
+        || StringCmp (qual_name, "ncRNA_class") == 0) {
+      return TRUE;
+    }
+  } else if (subtype == FEATDEF_tmRNA) {
+    if (StringCmp (qual_name, "product") == 0
+        || StringCmp (qual_name, "tag_peptide") == 0) {
+      return TRUE;
+    }
+  } else if (subtype == FEATDEF_otherRNA) {
+    if (StringCmp (qual_name, "product") == 0) {
+      return TRUE;
+    }
+  }
+  return FALSE;
+}
+    
+
 static Boolean ShouldBeAGBQual (Uint1 subtype, Int2 qual, Boolean allowProductGBQual)
 
 {
@@ -1020,6 +1102,8 @@ static Boolean ShouldBeAGBQual (Uint1 subtype, Int2 qual, Boolean allowProductGB
       qual == GBQUAL_rpt_unit ||
       qual == GBQUAL_transposon ||
       qual == GBQUAL_experiment ||
+      qual == GBQUAL_trans_splicing ||
+      qual == GBQUAL_ribosomal_slippage ||
       qual == GBQUAL_inference) {
     return FALSE;
   }
@@ -1030,6 +1114,11 @@ static Boolean ShouldBeAGBQual (Uint1 subtype, Int2 qual, Boolean allowProductGB
       return FALSE;
     }
   }
+
+  if (qual > -1 && ShouldSuppressGBQual (subtype, ParFlat_GBQual_names [qual].name)) {
+    return FALSE;
+  }
+
   return TRUE;
 }
 
@@ -1517,6 +1606,35 @@ static DialoG CreateInferenceDialog (GrouP h, Uint2 rows, Int2 spacing, Int2 wid
 static DialoG NewCreateInferenceDialog (GrouP prnt);
 extern void Nlm_LaunchGeneFeatEd (ButtoN b);
 
+
+static CharPtr GetNameForFeature (SeqFeatPtr sfp)
+{
+  FeatDefPtr curr;
+  Uint1      key;
+  CharPtr    label = NULL;
+  CharPtr    featname = NULL;
+  CharPtr    ptr;
+  Char       ch;
+
+  if (sfp != NULL) {
+    curr = FeatDefFindNext (NULL, &key, &label, sfp->idx.subtype, TRUE);
+    if (curr != NULL) {
+      featname = StringSave (label);
+      ptr = featname;
+      ch = *ptr;
+      while (ch != '\0') {
+        if (IS_UPPER (ch)) {
+          *ptr = TO_LOWER (ch);
+        }
+        ptr++;
+        ch = *ptr;
+      }
+    }
+  }
+  return featname;
+}
+
+
 extern GrouP CreateCommonFeatureGroupEx (GrouP h, FeatureFormPtr ffp,
                                          SeqFeatPtr sfp, Boolean hasGeneControl,
                                          Boolean hasCitationTab, Boolean hasGeneSuppress)
@@ -1544,14 +1662,15 @@ extern GrouP CreateCommonFeatureGroupEx (GrouP h, FeatureFormPtr ffp,
   GrouP      v;
   GrouP      x;
   GrouP      y;
+  CharPtr    featname;
 
   c = NULL;
   if (ffp != NULL) {
     hasQuals = FALSE;
     cdsQuals = FALSE;
     if (ffp->gbquals == NULL && sfp != NULL && sfp->qual != NULL) {
-      for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
-        if (StringCmp (gbq->qual, "experiment") != 0 && StringCmp (gbq->qual, "inference") != 0) {
+      for (gbq = sfp->qual; gbq != NULL && !hasQuals; gbq = gbq->next) {
+        if (!ShouldSuppressGBQual(sfp->idx.subtype, gbq->qual)) {
           hasQuals = TRUE;
         }
       }
@@ -1812,7 +1931,9 @@ extern GrouP CreateCommonFeatureGroupEx (GrouP h, FeatureFormPtr ffp,
     x = NULL;
     if (hasQuals && ffp->gbquals == NULL) {
       x = HiddenGroup (c, -1, 0, NULL);
-      ffp->gbquals = CreateImportFields (x, NULL, sfp, FALSE);
+      featname = GetNameForFeature (sfp);
+      ffp->gbquals = NewCreateImportFields (x, featname, sfp, FALSE);
+      featname = MemFree (featname);
     }
     ffp->commonSubGrp [page] = c;
     Hide (ffp->commonSubGrp [page]);
@@ -4950,14 +5071,16 @@ static ValNodePtr TestSequenceSelectionDialog (DialoG d)
 }
 
 
-extern DialoG SequenceSelectionDialog 
+extern DialoG SequenceSelectionDialogEx 
 (GrouP h,
  Nlm_ChangeNotifyProc     change_notify,
  Pointer                  change_userdata,
  Boolean                  allow_multi,
+ Boolean                  allow_none,
  Boolean                  show_nucs,
  Boolean                  show_prots,
- Uint2                    entityID)
+ Uint2                    entityID,
+ Int4                     list_height)
 
 {
   SequenceSelectionPtr  dlg;
@@ -4994,23 +5117,47 @@ extern DialoG SequenceSelectionDialog
   dlg->dialogmessage = SequenceSelectionDialogMessage;
   dlg->testdialog = TestSequenceSelectionDialog;
 
-  dlg->sequence_choice_list = NULL;
+  if (allow_none) {
+    dlg->sequence_choice_list = ValNodeNew (NULL);
+    dlg->sequence_choice_list->choice = 0;
+    dlg->sequence_choice_list->data.ptrvalue = NULL;
+  } else {
+    dlg->sequence_choice_list = NULL;
+  }
   GetSequenceChoiceList (sep, &dlg->sequence_choice_list, show_nucs, show_prots);
   
   
   for (vnp = dlg->sequence_choice_list; vnp != NULL; vnp = vnp->next) {
     sip = SeqIdFindWorst ((SeqIdPtr) vnp->data.ptrvalue);
-    SeqIdWrite (sip, tmp, PRINTID_REPORT, sizeof (tmp));
+    if (sip == NULL) {
+      sprintf (tmp, " ");
+    } else {
+      SeqIdWrite (sip, tmp, PRINTID_REPORT, sizeof (tmp));
+    }
     ValNodeAddPointer (&choice_name_list, 0, StringSave (tmp));
   }
 
   dlg->sequence_list_dlg = SelectionDialog (p, change_notify, change_userdata,
                                             allow_multi, "sequence",
-                                            choice_name_list, TALL_SELECTION_LIST);
+                                            choice_name_list, list_height);
   ValNodeFreeData (choice_name_list); 
   return (DialoG) p;
 }
 
+
+extern DialoG SequenceSelectionDialog 
+(GrouP h,
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata,
+ Boolean                  allow_multi,
+ Boolean                  show_nucs,
+ Boolean                  show_prots,
+ Uint2                    entityID)
+{
+  return SequenceSelectionDialogEx (h, change_notify, change_userdata, allow_multi, FALSE, show_nucs, show_prots, entityID, TALL_SELECTION_LIST);
+}
+
+
 extern DialoG SubSourceTypeDialog 
 (GrouP                    h,
  Int2                     list_height,
@@ -5304,6 +5451,320 @@ static DialoG CreateInferenceDialog (GrouP h, Uint2 rows, Int2 spacing, Int2 wid
 
 /* inference dialog controls, utility functions */
 
+Uint2 accessionlist_types [] = {
+  TAGLIST_POPUP, TAGLIST_TEXT
+};
+
+Uint2 accessionlist_widths [] = {
+  0, 10
+};
+
+ENUM_ALIST(accn_type_alist)
+  { " ",       0 },
+  { "GenBank", 1 },
+  { "EMBL",    2 },
+  { "DDBJ",    3 },
+  { "INSD",    4 },
+  { "RefSeq",  5 },
+  { "UniProt", 6 },
+  { "Other",   7 },
+END_ENUM_ALIST
+
+static EnumFieldAssocPtr accessionlist_popups [] = {
+  accn_type_alist, NULL
+};
+
+static CharPtr accnTypePrefix [] = {
+  "",
+  "GenBank",
+  "EMBL",
+  "DDBJ",
+  "INSD",
+  "RefSeq",
+  "UniProt",
+  "?",
+  NULL
+};
+
+const Int4 numAccnTypePrefixes = sizeof (accnTypePrefix) / sizeof (CharPtr);
+
+static Int4 GetAccnTypeNum (CharPtr str)
+{
+  Int4 i;
+
+  if (StringHasNoText (str)) return 0;
+
+  for (i = 1; i < numAccnTypePrefixes; i++)
+  {
+    if (StringCmp (accnTypePrefix[i], str) == 0)
+    {
+      return i;
+    }
+  }
+  return 0;
+}
+
+
+static CharPtr ValForOneAccession (CharPtr str)
+{
+  CharPtr cp, val_buf = NULL;
+  CharPtr val_fmt = "%d\t%s";
+  Int4    db;
+
+  if (!StringHasNoText (str))
+  {
+    cp = StringChr (str, '|');
+    if (cp == NULL)
+    {
+      if ((db = GetAccnTypeNum(str)) > 0)
+      {
+        val_buf = MemNew (sizeof (Char) * StringLen (val_fmt));
+        sprintf (val_buf, val_fmt, db, " ");
+      }
+      else
+      {
+        val_buf = MemNew (sizeof (Char) * (StringLen (val_fmt) + StringLen (str)));
+        sprintf (val_buf, val_fmt, 0, str);
+      }
+    }
+    else
+    {
+      *cp = 0;
+      db = GetAccnTypeNum (str);
+      val_buf = MemNew (sizeof (Char) * (StringLen (val_fmt) + StringLen (cp + 1)));
+      sprintf (val_buf, val_fmt, db, cp + 1);
+      *cp = '|';
+    }
+  }
+  return val_buf;
+}
+
+static void AccessionListDataToDialog (DialoG d, Pointer data)
+{
+  TagListPtr    tlp;
+  CharPtr       str, cp, val_buf;
+  ValNodePtr    new_list = NULL, vnp;
+  Int4          j;
+  Int2          scroll_pos;
+
+  tlp = (TagListPtr) GetObjectExtra (d);
+  
+  if (tlp == NULL) return;
+  str = (CharPtr) data;
+  
+  cp = StringChr (str, ',');
+  while (cp != NULL)
+  {
+    *cp = 0;
+    val_buf = ValForOneAccession (str);
+    if (val_buf != NULL)
+    {
+      ValNodeAddPointer (&new_list, 0, val_buf);
+    }
+    *cp = ',';
+    str = cp + 1;
+    cp = StringChr (str, ',');
+  }
+  val_buf = ValForOneAccession (str);
+  if (val_buf != NULL)
+  {
+    ValNodeAddPointer (&new_list, 0, val_buf);
+  }
+
+  scroll_pos = 0;
+  if (tlp->bar != NULL) 
+  {
+    scroll_pos = GetBarValue (tlp->bar);
+  }
+  else if (tlp->left_bar != NULL)
+  {
+    scroll_pos = GetBarValue (tlp->left_bar);
+  }
+
+  SendMessageToDialog (tlp->dialog, VIB_MSG_RESET);
+  tlp->vnp = new_list;
+  for (j = 0, vnp = tlp->vnp; vnp != NULL; j++, vnp = vnp->next) {
+  }
+  tlp->max = MAX ((Int2) 0, (Int2) (j - tlp->rows + 1));
+  CorrectBarMax (tlp->bar, tlp->max);
+  CorrectBarPage (tlp->bar, (Int2) (tlp->rows-1), (Int2) (tlp->rows-1));   
+
+  /* retain scroll position */
+  if (scroll_pos > tlp->max) {
+    scroll_pos = tlp->max;
+  }
+  
+  if (tlp->bar != NULL)
+  {
+    CorrectBarValue (tlp->bar, scroll_pos);      
+  }
+  if (tlp->left_bar != NULL)
+  {
+    CorrectBarValue (tlp->left_bar, scroll_pos);      
+  }
+    
+  SendMessageToDialog (tlp->dialog, VIB_MSG_REDRAW);
+  Update ();
+ 
+}
+
+
+static Pointer AccessionListDialogToData (DialoG d)
+{
+  TagListPtr    tlp;
+  ValNodePtr    vnp;
+  Int4          result_len = 0, db;
+  CharPtr       str, acc_str, result_str = NULL;
+  Boolean       first_item = TRUE;
+  
+  tlp = (TagListPtr) GetObjectExtra (d);
+  
+  if (tlp == NULL) return NULL;
+  
+  for (vnp = tlp->vnp;
+       vnp != NULL;
+       vnp = vnp->next)
+  {
+    acc_str = ExtractTagListColumn ((CharPtr) vnp->data.ptrvalue, 1);
+    str = ExtractTagListColumn ((CharPtr) vnp->data.ptrvalue, 0);
+    if (!StringHasNoText (acc_str) || !StringHasNoText (str))
+    {
+      result_len += StringLen (acc_str);
+      result_len += 1; /* comma */
+      db = atoi (str);
+      if (db >= 0 && db < numAccnTypePrefixes)
+      {
+        result_len += MAX (StringLen (accnTypePrefix[db]), 1);
+      }
+      else
+      {
+        result_len ++; /* will represent with ? */
+      }
+      result_len ++; /* for db/accession separator */
+    }
+    acc_str = MemFree (acc_str);
+    str = MemFree (str);
+  }
+  
+  if (result_len > 0) 
+  {
+    result_str = (CharPtr) MemNew (sizeof (Char) * (result_len + 1));
+    for (vnp = tlp->vnp;
+        vnp != NULL;
+        vnp = vnp->next)
+    {
+      acc_str = ExtractTagListColumn ((CharPtr) vnp->data.ptrvalue, 1);
+      str = ExtractTagListColumn ((CharPtr) vnp->data.ptrvalue, 0);
+      db = (str == NULL ? 0 : atoi (str));
+      str = MemFree (str);
+      if (!StringHasNoText (acc_str) || db > 0)
+      {
+        if (first_item)
+        {
+          first_item = FALSE;
+        }
+        else
+        {
+          StringCat (result_str, ",");
+        }
+
+        if (db > 0 && db < numAccnTypePrefixes)
+        {
+          StringCat (result_str, accnTypePrefix[db]);
+        }
+        else
+        {
+          StringCat (result_str, "?");
+        }
+        StringCat (result_str, "|");
+        if (!StringHasNoText (result_str)) {
+          StringCat (result_str, acc_str);
+        }
+      }
+      acc_str = MemFree (acc_str);
+    }
+    result_str[result_len] = 0;
+  }
+
+  return result_str;
+}
+
+
+static void RemoveEmptyAccessionStrings (CharPtr acc_list)
+{
+  CharPtr cp_prev_end = NULL, cp_src, cp_dst;
+
+  if (acc_list == NULL) return;
+  
+  cp_src = acc_list;
+  cp_dst = acc_list;
+  cp_prev_end = acc_list;
+  while (*cp_src != 0)
+  {
+    if (*cp_src == '|' && (*(cp_src + 1) == ',' || *(cp_src + 1) == 0))
+    {
+      cp_dst = cp_prev_end;
+      cp_prev_end = cp_dst;
+      cp_src++;
+    }
+    else
+    {
+      *cp_dst = *cp_src;      
+      if (*cp_src == ',')
+      {
+        cp_prev_end = cp_dst;
+      }
+      cp_dst++;
+      cp_src++;
+    }
+  }
+  *cp_dst = 0;
+}
+
+
+static CharPtr insdmessage =
+"GenBank, EMBL, and DDBJ records are part of the International Nucleotide " \
+"Sequence Database collaboration.\nThe database prefix for the /inference " \
+"qualifier in these cases is INSD by collaboration policy.";
+
+
+static Boolean ReplaceDatabaseStrings (CharPtr PNTR str)
+{
+  Boolean changed_db = FALSE;
+
+  if (str == NULL || *str == NULL) return FALSE;
+
+  if (StringSearch (*str, "GenBank|") != NULL)
+  {
+    changed_db = TRUE;
+    FindReplaceString (str, "GenBank|", "INSD|", TRUE, FALSE);
+  }
+  if (StringSearch (*str, "EMBL|") != NULL)
+  {
+    changed_db = TRUE;
+    FindReplaceString (str, "EMBL|", "INSD|", TRUE, FALSE);
+  }
+  if (StringSearch (*str, "DDBJ|") != NULL)
+  {
+    changed_db = TRUE;
+    FindReplaceString (str, "DDBJ|", "INSD|", TRUE, FALSE);
+  }
+
+  if (changed_db)
+  {
+    if (GetAppProperty ("InternalNcbiSequin") == NULL) {
+      Message (MSG_OK, "%s", insdmessage);
+    }
+  }
+
+  return changed_db;
+}
+
+
+static void ChangeInferAccessionList (Pointer data); 
+static TaglistCallback AccessionListCallbacks[] = 
+{ ChangeInferAccessionList, ChangeInferAccessionList };
+
 typedef struct inferevid {
   CharPtr  prefix;     /* from inferencePrefix     */
   Boolean  species;    /* optional (same species)  */
@@ -5315,6 +5776,7 @@ typedef struct inferevid {
   CharPtr  version;    /* program version          */
   CharPtr  basis1;     /* profile or motif         */
   CharPtr  basis2;     /*  evidence_basis texts    */
+  CharPtr  accession_list; /* accession list for alignment */
 } InferEvid, PNTR InferEvidPtr;
 
 typedef struct inferdialog {
@@ -5333,6 +5795,12 @@ typedef struct inferdialog {
   TexT          version;
   TexT          basis1;
   TexT          basis2;
+  PrompT        inf_free_program_prompt;
+  PrompT        inf_free_version_prompt;
+  PrompT        accession_list_program_prompt;
+  PrompT        accession_list_version_prompt;
+  PrompT        accession_list_prompt;
+  DialoG        accession_list;
 
   GrouP         inf_accn_group;
   GrouP         other_db_group;
@@ -5372,6 +5840,7 @@ static InferEvidPtr InferEvidFree (
   MemFree (iep->version);
   MemFree (iep->basis1);
   MemFree (iep->basis2);
+  MemFree (iep->accession_list);
 
   return MemFree (iep);
 }
@@ -5430,6 +5899,7 @@ static CharPtr inferencePrefix [] = {
   "nucleotide motif",
   "protein motif",
   "ab initio prediction",
+  "alignment",
   NULL
 };
 
@@ -5446,29 +5916,7 @@ ENUM_ALIST(inference_alist)
   { "nucleotide motif",      9 },
   { "protein motif",        10 },
   { "ab initio prediction", 11 },
-END_ENUM_ALIST
-
-static CharPtr accnTypePrefix [] = {
-  "",
-  "GenBank",
-  "EMBL",
-  "DDBJ",
-  "INSD",
-  "RefSeq",
-  "UniProt",
-  "?",
-  NULL
-};
-
-ENUM_ALIST(accn_type_alist)
-  { " ",       0 },
-  { "GenBank", 1 },
-  { "EMBL",    2 },
-  { "DDBJ",    3 },
-  { "INSD",    4 },
-  { "RefSeq",  5 },
-  { "UniProt", 6 },
-  { "Other",   7 },
+  { "alignment",            12 },
 END_ENUM_ALIST
 
 static CharPtr programPrefix [] = {
@@ -5505,7 +5953,7 @@ static CharPtr PrintInferTable (
 
   len = StringLen (iep->prefix) + StringLen (iep->database) + StringLen (iep->db_other) + StringLen (iep->accession) +
         StringLen (iep->program) + StringLen (iep->pr_other) + StringLen (iep->version) + StringLen (iep->basis1) +
-        StringLen (iep->basis2) + 50;
+        StringLen (iep->basis2) + StringLen (iep->accession_list) + 50;
   buf = MemNew (len);
   if (buf == NULL) return NULL;
 
@@ -5552,6 +6000,11 @@ static CharPtr PrintInferTable (
     if (StringDoesHaveText (iep->basis2)) {
       StringCat (buf, ":");
       StringCat (buf, iep->basis2);
+      if (StringCmp (iep->prefix, "alignment") == 0 && 
+          StringDoesHaveText (iep->accession_list)) {
+        StringCat (buf, ":");
+        StringCat (buf, iep->accession_list);
+      }
     }
   } else {
     StringCat (buf, " ");
@@ -5588,6 +6041,12 @@ static void ShowInferenceGroup (
       SafeHide (idp->species);
       SafeHide (idp->inf_prog_group);
       SafeShow (idp->inf_free_group);
+      SafeHide (idp->accession_list);
+      SafeShow (idp->inf_free_program_prompt);
+      SafeShow (idp->inf_free_version_prompt);
+      SafeHide (idp->accession_list_program_prompt);
+      SafeHide (idp->accession_list_version_prompt);
+      SafeHide (idp->accession_list_prompt);
     } else if (val == 11) {
       SafeHide (idp->inf_accn_group);
       SafeHide (idp->species);
@@ -5600,6 +6059,17 @@ static void ShowInferenceGroup (
         SafeHide (idp->other_pr_group);
       }
       MemFree (str);
+    } else if (val == 12) {
+      SafeHide (idp->inf_accn_group);
+      SafeHide (idp->species);
+      SafeHide (idp->inf_prog_group);
+      SafeShow (idp->inf_free_group);
+      SafeShow (idp->accession_list);
+      SafeHide (idp->inf_free_program_prompt);
+      SafeHide (idp->inf_free_version_prompt);
+      SafeShow (idp->accession_list_program_prompt);
+      SafeShow (idp->accession_list_version_prompt);
+      SafeShow (idp->accession_list_prompt);
     } else {
       SafeHide (idp->inf_accn_group);
       SafeHide (idp->species);
@@ -5665,6 +6135,9 @@ static void ChangeInferTableSelect (
     SafeSetTitle (idp->basis1, iep->basis1);
     SafeSetTitle (idp->basis2, iep->basis2);
 
+    ReplaceDatabaseStrings (&(iep->accession_list));
+    PointerToDialog (idp->accession_list, iep->accession_list);
+
     ShowInferenceGroup (idp);
   }
 
@@ -5741,11 +6214,6 @@ static void ChangeSameSpecies (
   CheckExtendInferTable (idp);
 }
 
-static CharPtr insdmessage =
-"GenBank, EMBL, and DDBJ records are part of the International Nucleotide " \
-"Sequence Database collaboration.\nThe database prefix for the /inference " \
-"qualifier in these cases is INSD by collaboration policy.";
-
 static void ChangeInferDatabase (
   PopuP p
 )
@@ -5960,6 +6428,34 @@ static void ChangeInferBasis2 (
   CheckExtendInferTable (idp);
 }
 
+
+static void ChangeInferAccessionList (Pointer data)
+{
+  InferDialogPtr  idp;
+  InferEvidPtr    iep;
+
+  idp = (InferDialogPtr) data;
+  if (idp == NULL) return;
+  iep = GetInferEvid (idp, idp->currItem);
+  if (iep == NULL) return;
+
+  iep->accession_list = MemFree (iep->accession_list);
+  iep->accession_list = DialogToPointer (idp->accession_list);
+  
+  if (ReplaceDatabaseStrings (&(iep->accession_list)))
+  {
+    PointerToDialog (idp->accession_list, iep->accession_list);
+  }
+
+  ShowInferenceGroup (idp);
+
+  UpdateDocument (idp->inferdoc, idp->currItem, idp->currItem);
+  Update ();
+
+  CheckExtendInferTable (idp);
+}
+
+
 static Boolean StringInList (CharPtr str, CharPtr PNTR list)
 
 {
@@ -5986,7 +6482,7 @@ extern void GBQualsToInferenceDialog (DialoG d, SeqFeatPtr sfp)
   size_t          len;
   CharPtr         rest;
   CharPtr         str;
-  CharPtr         tmp;
+  CharPtr         tmp, tmp2;
 
   idp = (InferDialogPtr) GetObjectExtra (d);
   if (idp == NULL) return;
@@ -6111,8 +6607,19 @@ extern void GBQualsToInferenceDialog (DialoG d, SeqFeatPtr sfp)
       } else {
         iep->basis1 = MemFree (iep->basis1);
         iep->basis1 = StringSaveNoNull (str);
+        tmp2 = NULL;
+        if (StringCmp (iep->prefix, "alignment") == 0)
+        {
+          tmp2 = StringChr (tmp, ':');
+          if (tmp2 != NULL) {
+            *tmp2 = 0;
+            tmp2++;
+          }
+        }
         iep->basis2 = MemFree (iep->basis2);
         iep->basis2 = StringSaveNoNull (tmp);
+        iep->accession_list = MemFree (iep->accession_list);
+        iep->accession_list = StringSaveNoNull (tmp2);
       }
 
     } else {
@@ -6163,7 +6670,7 @@ extern void GBQualsToInferenceDialog (DialoG d, SeqFeatPtr sfp)
 extern void InferenceDialogToGBQuals (DialoG d, SeqFeatPtr sfp, Boolean convertBadToNote)
 
 {
-  CharPtr         first = NULL, second = NULL;
+  CharPtr         first = NULL, second = NULL, accession_list = NULL;
   GBQualPtr       gbq, lastgbq;
   InferDialogPtr  idp;
   InferEvidPtr    iep;
@@ -6194,7 +6701,7 @@ extern void InferenceDialogToGBQuals (DialoG d, SeqFeatPtr sfp, Boolean convertB
     gbq->qual = StringSave ("inference");
 
     if (WhereInEnumPopup (inference_alist, iep->prefix, &val)) {
-      if (val > 0 && val <= 11) {
+      if (val > 0 && val <= 12) {
         prefix = inferencePrefix [(int) val];
       }
     }
@@ -6225,11 +6732,16 @@ extern void InferenceDialogToGBQuals (DialoG d, SeqFeatPtr sfp, Boolean convertB
       if (StringDoesHaveText (iep->basis1)) {
         first = iep->basis1;
         second = iep->basis2;
+        if (StringCmp (iep->prefix, "alignment") == 0) {
+          accession_list = iep->accession_list;
+          RemoveEmptyAccessionStrings (accession_list);
+          ReplaceDatabaseStrings (&accession_list);
+        }
       }
     }
 
-    len = StringLen (prefix) + StringLen (speciesies) + StringLen (first) + StringLen (second);
-    str = MemNew (len + 5);
+    len = StringLen (prefix) + StringLen (speciesies) + StringLen (first) + StringLen (second) + StringLen (accession_list);
+    str = MemNew (len + 6);
     if (str != NULL) {
       StringCpy (str, prefix);
       StringCat (str, speciesies);
@@ -6237,6 +6749,10 @@ extern void InferenceDialogToGBQuals (DialoG d, SeqFeatPtr sfp, Boolean convertB
       StringCat (str, first);
       StringCat (str, ":");
       StringCat (str, second);
+      if (StringCmp (prefix, "alignment") == 0 && accession_list != NULL) {
+        StringCat (str, ":");
+        StringCat (str, accession_list);
+      }
       gbq->val = StringSave (str);
       MemFree (str);
     } else {
@@ -6276,6 +6792,7 @@ extern void InferenceDialogToGBQuals (DialoG d, SeqFeatPtr sfp, Boolean convertB
       lastgbq->next = gbq;
     }
     lastgbq = gbq;
+    accession_list = NULL;
   }
 }
 
@@ -6302,7 +6819,7 @@ static DialoG NewCreateInferenceDialog (
 )
 
 {
-  GrouP           cts, tbl, g0, g1, g2, g3, g4, g5, p;
+  GrouP           cts, tbl, g0, g1, g2, g3, g4, g5, p, prompt_grp;
   FonT            fnt;
   Int2            i, hgt, wid;
   InferDialogPtr  idp;
@@ -6414,14 +6931,26 @@ static DialoG NewCreateInferenceDialog (
   g5 = HiddenGroup (g2, 2, 0, NULL);
   SetGroupSpacing (g5, 5, 5);
 
-  StaticPrompt (g5, "Program or Database", 0, dialogTextHeight, programFont, 'l');
+  prompt_grp = HiddenGroup (g5, 0, 0, NULL);
+  idp->inf_free_program_prompt = StaticPrompt (prompt_grp, "Program or Database", 0, dialogTextHeight, programFont, 'l');
+  idp->accession_list_program_prompt = StaticPrompt (prompt_grp, "Program", 0, dialogTextHeight, programFont, 'l');
   idp->basis1 = DialogText (g5, "", 10, ChangeInferBasis1);
   SetObjectExtra (idp->basis1, idp, NULL);
 
-  StaticPrompt (g5, "Version or Accession", 0, dialogTextHeight, programFont, 'l');
+  prompt_grp = HiddenGroup (g5, 0, 0, NULL);
+  idp->inf_free_version_prompt = StaticPrompt (prompt_grp, "Version or Accession", 0, dialogTextHeight, programFont, 'l');
+  idp->accession_list_version_prompt = StaticPrompt (prompt_grp, "Version", 0, dialogTextHeight, programFont, 'l');
+
   idp->basis2 = DialogText (g5, "", 10, ChangeInferBasis2);
   SetObjectExtra (idp->basis2, idp, NULL);
 
+  idp->accession_list_prompt = StaticPrompt (g5, "Accessions", 0, dialogTextHeight, programFont, 'l');
+  idp->accession_list = CreateTagListDialogEx3 (g5, 3, 2, 2,
+                              accessionlist_types, accessionlist_widths,
+                              accessionlist_popups, TRUE, FALSE, AccessionListDataToDialog, AccessionListDialogToData,
+                              AccessionListCallbacks, idp,
+                              FALSE, FALSE);
+
   idp->inf_free_group = g5;
   Hide (idp->inf_free_group);
 
@@ -6727,6 +7256,17 @@ extern EditApplyPtr EditApplyFree (EditApplyPtr eap)
   return eap;
 }
 
+
+extern EditApplyPtr EditApplyNew (void)
+{
+  EditApplyPtr eap;
+
+  eap = (EditApplyPtr) MemNew (sizeof (EditApplyData));
+  eap->find_location = EditApplyFindLocation_anywhere;
+  return eap;
+}
+
+
 typedef struct EditApplydlg
 {
   DIALOG_MESSAGE_BLOCK
@@ -6905,7 +7445,7 @@ static Pointer DialogToEditApply (DialoG d)
     }
 
     if (dlg->location_choice != NULL) {
-      data->find_location = GetValue (dlg->location_choice);
+      data->find_location = (EditApplyFindLocation) GetValue (dlg->location_choice);
     } else {
       data->find_location = EditApplyFindLocation_anywhere;
     }
@@ -6968,7 +7508,7 @@ static ValNodePtr TestEditApply (DialoG d)
     {
       if (TextHasNoText (dlg->apply_txt))
       {
-        ValNodeAddPointer (&total_err_list, 0, "apply text");
+        ValNodeAddPointer (&total_err_list, 0, StringSave ("apply text"));
       }
     }
     else
@@ -6982,7 +7522,7 @@ static ValNodePtr TestEditApply (DialoG d)
     {
       if (TextHasNoText (dlg->find_txt))
       {
-        ValNodeAddPointer (&total_err_list, 0, "find text");
+        ValNodeAddPointer (&total_err_list, 0, StringSave ("find text"));
       }
     }
     else 
@@ -7010,30 +7550,6 @@ static void EditApplyDialogCopy (ButtoN b)
   str = MemFree (str);
 }
 
-static ValNodePtr ValNodeDupStringList (ValNodePtr vnp)
-{
-  ValNodePtr cpy = NULL, last = NULL, tmp;
-
-  while (vnp != NULL)
-  {
-    tmp = ValNodeNew (NULL);
-    tmp->choice = vnp->choice;
-    tmp->data.ptrvalue = StringSave (vnp->data.ptrvalue);
-    if (last == NULL)
-    {
-      cpy = tmp;
-    }
-    else
-    {
-      last->next = tmp;
-    }
-    last = tmp;
-    vnp = vnp->next;
-  }
-  return cpy;
-}
-      
-
 extern DialoG EditApplyDialog 
 (GrouP                    h,
  Int4                     action_choice, 
@@ -7710,7 +8226,11 @@ typedef struct clickablelist
 {
   DIALOG_MESSAGE_BLOCK
   DoC  doc;
-  DoC  clickable_item_list;  
+  DoC  clickable_item_list;
+  PrompT title1;
+  PrompT title2;
+  PrompT help1;
+  PrompT help2;
   TexT find_txt;
 
   ClickableCallback item_single_click_callback;
@@ -7809,7 +8329,7 @@ static ClickableItemPtr GetSubItem (ValNodePtr item_list, Int2Ptr pitem)
 
 static Int4 CountLevels (ValNodePtr item_list)
 {
-  Int4       num_levels = 1, num, num_sublevels = 0;
+  Int4       num, num_sublevels = 0;
   ValNodePtr vnp;
   ClickableItemPtr cip;
   
@@ -7953,22 +8473,34 @@ static void PopulateClickableList (ClickableListPtr dlg, ValNodePtr list_list)
 
 }
 
-static Int2 PanelOffsetFromCharOffset (ClickableListPtr dlg, Int2 item, Int2 char_offset)
+
+NLM_EXTERN Int2 PanelOffsetFromCharOffsetEx (DoC doc, FonT font, Int2 item, Int2 col, Int2 char_offset)
 {
   Int2 numRows, numCols, lineHeight;
   Int2 left_start, width, inset, char_width;
-  if (dlg == NULL) return 0;
 
-  GetItemParams4 (dlg->doc, item, NULL, &numRows, &numCols, &lineHeight, NULL);
-  GetColParams (dlg->doc, item, numCols, &left_start, &width, &inset, NULL);
+  if (doc == NULL) return 0;
+  GetItemParams4 (doc, item, NULL, &numRows, &numCols, &lineHeight, NULL);
+  GetColParams (doc, item, col, &left_start, &width, &inset, NULL);
 
   /* need to set font so that Nlm_CharWidth works properly */
-  SelectFont (dlg->col_fmt_array_array[0][0].font);
+  SelectFont (font);
   char_width = Nlm_CharWidth ('A');
   return left_start + inset + char_offset * char_width;
 }
 
-static Int2 GetTextSelectCharOffset (PoinT pt, ClickableListPtr dlg, Int2 item, Int2 row, Int2 col)
+
+static Int2 PanelOffsetFromCharOffset (ClickableListPtr dlg, Int2 item, Int2 char_offset)
+{
+  Int2 numCols;
+  if (dlg == NULL) return 0;
+  GetItemParams4 (dlg->doc, item, NULL, NULL, &numCols, NULL, NULL);
+
+  return PanelOffsetFromCharOffsetEx (dlg->doc, dlg->col_fmt_array_array[0][0].font, item, numCols, char_offset);
+}
+
+
+NLM_EXTERN Int2 GetTextSelectCharOffsetEx (PoinT pt, DoC doc, FonT font, Int2 item, Int2 row, Int2 col)
 {
   Int2 pixPos, pixInset;
   Int2 one_char_width;
@@ -7976,18 +8508,18 @@ static Int2 GetTextSelectCharOffset (PoinT pt, ClickableListPtr dlg, Int2 item,
   Int4    len;
   Int2    char_offset;
 
-  if (dlg == NULL) return 0;
+  if (doc == NULL) return 0;
 
-  GetColParams (dlg->doc, item, col, &pixPos,
+  GetColParams (doc, item, col, &pixPos,
                 NULL, &pixInset, NULL);
 
-  SelectFont (dlg->col_fmt_array_array[0][0].font);
+  SelectFont (font);
   one_char_width = Nlm_CharWidth ('A');
   if (one_char_width == 0) return 0;
 
   char_offset = (pt.x - pixPos - pixInset) / one_char_width;
   if (char_offset > 0) {
-    txt = GetDocText (dlg->doc, item, row, col);
+    txt = GetDocText (doc, item, row, col);
     len = StringLen (txt);
     if (char_offset >= len) {
       char_offset = - 1;
@@ -7998,6 +8530,14 @@ static Int2 GetTextSelectCharOffset (PoinT pt, ClickableListPtr dlg, Int2 item,
 }
 
 
+static Int2 GetTextSelectCharOffset (PoinT pt, ClickableListPtr dlg, Int2 item, Int2 row, Int2 col)
+{
+  if (dlg == NULL) return 0;
+
+  return GetTextSelectCharOffsetEx (pt, dlg->doc, dlg->col_fmt_array_array[0][0].font, item, row, col);
+}
+
+
 static void ClickList (DoC d, PoinT pt)
 
 {
@@ -8635,19 +9175,21 @@ CreateClickableListDialogEx
 (GrouP h, 
  CharPtr label1, 
  CharPtr label2,
+ CharPtr help1,
+ CharPtr help2,
  ClickableCallback item_single_click_callback,
  ClickableCallback item_double_click_callback,
  Pointer         item_click_callback_data,
  GetClickableItemText get_item_text,
  Int4            left_width,
  Int4            right_width,
- Boolean         horizontal)
+ Boolean         horizontal,
+ Boolean         show_find)
 {
-  GrouP p, pnl_grp, find_grp;
+  GrouP p, pnl_grp, find_grp = NULL;
   ClickableListPtr dlg;
   RecT             r;
   ButtoN           b;
-  PrompT           p1, p2;
 
   dlg = (ClickableListPtr) MemNew (sizeof (ClickableListData));
   if (dlg == NULL)
@@ -8673,18 +9215,30 @@ CreateClickableListDialogEx
   if (horizontal) {
     pnl_grp = HiddenGroup (p, 2, 0, NULL);
     
-    StaticPrompt (pnl_grp, label1, 0, popupMenuHeight, programFont, 'c');
-    StaticPrompt (pnl_grp, label2, 0, popupMenuHeight, programFont, 'c');
-  
+    if (label1 || label2) {
+      dlg->title1 = StaticPrompt (pnl_grp, label1, left_width, popupMenuHeight, programFont, 'c');
+      dlg->title2 = StaticPrompt (pnl_grp, label2, right_width, popupMenuHeight, programFont, 'c');
+    }
     dlg->doc = DocumentPanel (pnl_grp, left_width, stdLineHeight * 20);
     dlg->clickable_item_list = DocumentPanel (pnl_grp, right_width, stdLineHeight * 20);
+    if (help1 || help2) {
+      dlg->help1 = StaticPrompt (pnl_grp, help1, left_width, popupMenuHeight, programFont, 'c');
+      dlg->help2 = StaticPrompt (pnl_grp, help2, right_width, popupMenuHeight, programFont, 'c');
+    } 
   } else {
     pnl_grp = HiddenGroup (p, -1, 0, NULL);
-    p1 = StaticPrompt (pnl_grp, label1, 0, popupMenuHeight, programFont, 'c');
+    dlg->title1 = StaticPrompt (pnl_grp, label1, left_width, popupMenuHeight, programFont, 'c');
     dlg->doc = DocumentPanel (pnl_grp, left_width, stdLineHeight * 20);
-    p2 = StaticPrompt (pnl_grp, label2, 0, popupMenuHeight, programFont, 'c');
+    if (help1 || help2) {
+      dlg->help1 = StaticPrompt (pnl_grp, help1, left_width, popupMenuHeight, programFont, 'c');
+    }
+    dlg->title2 = StaticPrompt (pnl_grp, label2, right_width, popupMenuHeight, programFont, 'c');
     dlg->clickable_item_list = DocumentPanel (pnl_grp, right_width, stdLineHeight * 20);
-    AlignObjects (ALIGN_CENTER, (HANDLE) p1, (HANDLE) dlg->doc, (HANDLE) p2, (HANDLE) dlg->clickable_item_list, NULL);
+    if (help1 || help2) {
+      dlg->help2 = StaticPrompt (pnl_grp, help2, right_width, popupMenuHeight, programFont, 'c');
+    }
+    AlignObjects (ALIGN_CENTER, (HANDLE) dlg->title1, (HANDLE) dlg->doc, (HANDLE) dlg->title2, (HANDLE) dlg->clickable_item_list, 
+                                (HANDLE) (dlg->help1 == NULL ? dlg->help2 : dlg->help1), (HANDLE) (dlg->help1 == NULL ? NULL : dlg->help2), NULL);
   }
 
   SetObjectExtra (dlg->doc, dlg, NULL);
@@ -8704,19 +9258,37 @@ CreateClickableListDialogEx
   InsetRect (&r, 4, 4);
   clickableColFmt[1].pixWidth = r.right - r.left - clickableColFmt[0].pixWidth;
   
-  find_grp = HiddenGroup (p, 4, 0, NULL);
-  SetGroupSpacing (find_grp, 10, 10);
-  StaticPrompt (find_grp, "Find Text", 0, popupMenuHeight, programFont, 'l');
-  dlg->find_txt = DialogText (find_grp, "", 20, NULL);
-  b = PushButton (find_grp, "<<", FindPreviousClickableText);
-  SetObjectExtra (b, dlg, NULL);
-  b = PushButton (find_grp, ">>", FindClickableText);
-  SetObjectExtra (b, dlg, NULL);
+  if (show_find) {
+    find_grp = HiddenGroup (p, 4, 0, NULL);
+    SetGroupSpacing (find_grp, 10, 10);
+    StaticPrompt (find_grp, "Find Text", 0, popupMenuHeight, programFont, 'l');
+    dlg->find_txt = DialogText (find_grp, "", 20, NULL);
+    b = PushButton (find_grp, "<<", FindPreviousClickableText);
+    SetObjectExtra (b, dlg, NULL);
+    b = PushButton (find_grp, ">>", FindClickableText);
+    SetObjectExtra (b, dlg, NULL);
+  }
   
   AlignObjects (ALIGN_CENTER, (HANDLE) pnl_grp, (HANDLE) find_grp, NULL);
   return (DialoG) p;
 }
 
+extern void SetClickableListDialogTitles (DialoG d, CharPtr title1, CharPtr title2, CharPtr help1, CharPtr help2)
+{
+  ClickableListPtr dlg;
+
+  dlg = (ClickableListPtr) GetObjectExtra (d);
+  if (dlg == NULL)
+  {
+    return;
+  }
+  SafeSetTitle (dlg->title1, title1);
+  SafeSetTitle (dlg->title2, title2);
+  SafeSetTitle (dlg->help1, help1);
+  SafeSetTitle (dlg->help2, help2);
+}
+
+
 extern DialoG 
 CreateClickableListDialog 
 (GrouP h, 
@@ -8727,14 +9299,14 @@ CreateClickableListDialog
  Pointer         item_click_callback_data,
  GetClickableItemText get_item_text)
 {
-  return CreateClickableListDialogEx (h, label1, label2,
+  return CreateClickableListDialogEx (h, label1, label2, NULL, NULL,
                                       item_single_click_callback,
                                       item_double_click_callback,
                                       item_click_callback_data,
                                       get_item_text, 
                                       stdCharWidth * 30,
                                       stdCharWidth * 30 + 5,
-                                      TRUE);
+                                      TRUE, TRUE);
 }
 
 
@@ -8915,6 +9487,202 @@ static CharPtr GetClickableTextFromItemList (ValNodePtr item_list, CharPtr separ
   return txt;
 }
 
+
+static CharPtr
+GetFragmentFromDocRow
+(DoC  doc,
+ Int2 item,
+ Int2 col,
+ Int2 row,
+ Int2 char_start, Int2 char_stop)
+{
+  CharPtr txt = NULL, cp_txt;
+  Int4    len;
+ 
+  txt = GetDocText (doc, item, row, col);
+
+  if (char_start == 0 && char_stop < 0) {
+    /* take all of row */
+    return txt;
+  } else {
+    len = StringLen (txt);
+    if (char_stop >= len) {
+      /* selection was drawn beyond length of text */
+      char_stop = len - 1;
+    } else if (char_stop < 0) {
+      /* take all of row */
+      char_stop = len - 1;
+    }
+    if (char_start >= len) {
+      /* do nothing - selection is not within text */
+      txt = MemFree (txt);
+    } else {
+      cp_txt = (CharPtr) MemNew (sizeof (Char) * (2 + char_stop - char_start));
+      StringNCpy (cp_txt, txt + char_start, 1 + char_stop - char_start);
+      cp_txt[1 + char_stop - char_start] = 0;
+      txt = MemFree (txt);
+      txt = cp_txt;
+    }
+  }  
+  return txt;
+}
+
+
+static CharPtr 
+GetFragmentsFromDocCol
+(DoC  doc,
+ Int2 item,
+ Int2 col,
+ Int2 row_start, Int2 row_stop,
+ Int2 char_start, Int2 char_stop)
+{
+  Int2       row;
+  CharPtr    txt;
+  ValNodePtr fragments = NULL;
+
+  if (row_start == row_stop) {
+    txt = GetFragmentFromDocRow (doc, item, col, row_start, char_start, char_stop);
+    if (StringHasNoText (txt)) {
+      txt = MemFree (txt);
+    } else {
+      ValNodeAddPointer (&fragments, 0, txt);
+    }
+  } else {
+    txt = GetFragmentFromDocRow (doc, item, col, row_start, char_start, -1);
+    if (StringHasNoText (txt)) {
+      txt = MemFree (txt);
+    } else {
+      ValNodeAddPointer (&fragments, 0, txt);
+    }
+    row = row_start + 1;
+    while (row < row_stop) {
+      txt = GetFragmentFromDocRow (doc, item, col, row, 0, -1);
+      if (StringHasNoText (txt)) {
+        txt = MemFree (txt);
+      } else {
+        ValNodeAddPointer (&fragments, 0, txt);
+      }
+      row++;
+    }
+    txt = GetFragmentFromDocRow (doc, item, col, row_stop, 0, char_stop);
+    if (StringHasNoText (txt)) {
+      txt = MemFree (txt);
+    } else {
+      ValNodeAddPointer (&fragments, 0, txt);
+    }
+  }
+  txt = GetClickableTextFromItemList (fragments, " ");
+  fragments = ValNodeFreeData (fragments);
+  return txt;
+}
+
+
+static Boolean CollectFromThisColumn (Int2 col, Int2Ptr only_these_columns, Int2 num_col)
+{
+  Int2 i;
+  Boolean rval = FALSE;
+
+  if (only_these_columns == NULL) {
+    rval = TRUE;
+  } else {
+    for (i = 0; i < num_col; i++) {
+      if (only_these_columns[i] == col) {
+        rval = TRUE;
+      }
+    }
+  }
+  return rval;
+}
+
+ 
+static CharPtr
+GetFragmentsFromDocItem 
+(DoC  doc,
+ Int2 item, 
+ Int2 col_start, Int2 col_stop,
+ Int2 row_start, Int2 row_stop,
+ Int2 char_start, Int2 char_stop,
+ Int2Ptr only_these_columns, Int2 num_col)
+{
+  Int2       col;
+  CharPtr    txt;
+  Int2       num_rows, num_cols;
+  ValNodePtr fragments = NULL;
+
+  GetItemParams4 (doc, item, NULL, &num_rows, &num_cols, NULL, NULL);
+  if (col_stop < 0) {
+    col_stop = num_cols;
+  }
+  if (row_stop < 0) {
+    row_stop = num_rows;
+  }
+
+  if (col_start == col_stop) {
+    if (CollectFromThisColumn (col_start, only_these_columns, num_col)) {
+      txt = GetFragmentsFromDocCol (doc, item, col_start, row_start, row_stop, char_start, char_stop);
+      ValNodeAddPointer (&fragments, 0, txt);
+    }
+  } else {
+    if (CollectFromThisColumn (col_start, only_these_columns, num_col)) {
+      txt = GetFragmentsFromDocCol (doc, item, col_start, row_start, num_rows, char_start, -1);
+      ValNodeAddPointer (&fragments, 0, txt);
+    }
+    col = col_start + 1;
+    while (col < col_stop) {
+      if (CollectFromThisColumn (col, only_these_columns, num_col)) {
+        txt = GetFragmentsFromDocCol (doc, item, col, 1, num_rows, 0, -1);
+        ValNodeAddPointer (&fragments, 0, txt);
+      }
+      col++;
+    }
+    if (CollectFromThisColumn (col_stop, only_these_columns, num_col)) {
+      txt = GetFragmentsFromDocCol (doc, item, col_stop, 1, row_stop, 0, char_stop);
+      ValNodeAddPointer (&fragments, 0, txt);
+    }
+  }
+  txt = GetClickableTextFromItemList (fragments, "\t");
+  fragments = ValNodeFreeData (fragments);
+
+  return txt;
+}
+
+
+NLM_EXTERN CharPtr GetSelectedDocText (DoC doc, Int2 item_start, Int2 row_start, Int2 col_start, Int2 char_start,
+                                       Int2 item_stop, Int2 row_stop, Int2 col_stop, Int2 char_stop,
+                                       Int2Ptr only_these_columns, Int2 num_col)
+{
+  Int2             item;
+  CharPtr          txt;
+  ValNodePtr       fragment_list = NULL;
+  
+  if (doc == NULL || item_start < 1)
+  {
+    return NULL;
+  }
+
+  if (char_start < 0) char_start = 0;
+
+  if (item_start == item_stop) {
+    txt = GetFragmentsFromDocItem (doc, item_start, col_start, col_stop, row_start, row_stop, char_start, char_stop, only_these_columns, num_col); 
+    ValNodeAddPointer (&fragment_list, 0, txt);
+  } else {
+    txt = GetFragmentsFromDocItem (doc, item_start, col_start, -1, row_start, -1, char_start, -1, only_these_columns, num_col);
+    ValNodeAddPointer (&fragment_list, 0, txt);
+    item = item_start + 1;
+    while (item < item_stop) {
+      txt = GetFragmentsFromDocItem (doc, item, 1, -1, 1, -1, 0, -1, only_these_columns, num_col);
+      ValNodeAddPointer (&fragment_list, 0, txt);
+      item++;
+    }
+    txt = GetFragmentsFromDocItem (doc, item, 1, col_stop, 1, row_stop, 0, char_stop, only_these_columns, num_col);
+    ValNodeAddPointer (&fragment_list, 0, txt);
+  }
+
+  txt = GetClickableTextFromItemList (fragment_list, "\r\n");
+  fragment_list = ValNodeFreeData (fragment_list);
+  return txt;
+}
+
 extern CharPtr GetSelectedClickableListText (DialoG d)
 {
   ClickableListPtr dlg;
@@ -9146,12 +9914,6 @@ static Int4 GetYearFromToken (CharPtr token, Int4 token_len)
   return year;
 }
 
-static CharPtr months [12] = 
-{ 
-  "January", "February", "March", "April", "May", "June",
-  "July", "August", "September", "October", "November", "December"
-};
-
 static CharPtr month_abbrevs [12] =
 {
   "Jan", "Feb", "Mar", "Apr", "May", "Jun", 
@@ -9395,7 +10157,6 @@ extern CharPtr ReformatDateStringEx (CharPtr orig_date, Boolean month_first, Boo
   CharPtr month = NULL;
   CharPtr token_list[3];
   Int4    token_lens[3];
-  CharPtr delimiters = " \t,-/";
   CharPtr numbers = "0123456789";
   CharPtr letters = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
   Int4    num_tokens = 0;
@@ -9880,7 +10641,7 @@ typedef struct rptunitrangedlg {
   TexT  range_stop;
 } RptUnitRangeDlgData, PNTR RptUnitRangeDlgPtr;
 
-Boolean ParseRptUnitRangeOkEx (CharPtr txt, Int4Ptr pstart, Int4Ptr pstop)
+static Boolean ParseRptUnitRangeOkEx (CharPtr txt, Int4Ptr pstart, Int4Ptr pstop)
 {
   CharPtr cp;
   Int4    start = -1, stop = -1;
@@ -10003,7 +10764,7 @@ extern DialoG CreateRptUnitRangeDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
   return (DialoG) p;
 }
 
-Boolean ParseRptUnitRangeOk (CharPtr txt)
+static Boolean ParseRptUnitRangeOk (CharPtr txt)
 {
   return ParseRptUnitRangeOkEx (txt, NULL, NULL);
 }
@@ -10147,7 +10908,7 @@ static Pointer MobileElementDialogToString (DialoG d)
 }
 
 
-extern DialoG CreateMobileElementDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
+static DialoG CreateMobileElementDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
                                          TaglistCallback tlp_callback,
                                          Pointer callback_data)
 {
@@ -10230,7 +10991,7 @@ static Pointer TrueFalseDialogToPointer (DialoG d)
   }
 }
 
-extern DialoG TrueFalseDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
+static DialoG TrueFalseDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
                                TaglistCallback tlp_callback,
                                Pointer callback_data)
 {
@@ -10254,7 +11015,7 @@ extern DialoG TrueFalseDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
   return (DialoG) p;
 }
 
-Boolean ParseTrueFalseOk (CharPtr txt)
+static Boolean ParseTrueFalseOk (CharPtr txt)
 {
   if (StringHasNoText (txt) || StringICmp (txt, "TRUE") == 0 || StringICmp (txt, "FALSE") == 0) {
     return TRUE;
@@ -10830,7 +11591,7 @@ static void GBQualEditDialogCopyText (ButtoN b)
   }
 }
 
-extern DialoG CreateSingleGBQualEditDialog (GrouP h, SeqEntryPtr sep, CharPtr name, 
+static DialoG CreateSingleGBQualEditDialog (GrouP h, SeqEntryPtr sep, CharPtr name, 
                                             Boolean force_string,
                                             TaglistCallback tlp_callback, 
                                             Pointer callback_data)
@@ -11143,7 +11904,12 @@ static Pointer NewDialogToImportFields (DialoG d)
   return (Pointer) gbq_list;
 }
 
-static void AddMandatoryAndOptionalQuals (CharPtr name, NewFieldPagePtr fpf, GBQualPtr gbq, Boolean use_rarely_used)
+static void 
+AddMandatoryAndOptionalQuals 
+(CharPtr         name,
+ NewFieldPagePtr fpf,
+ GBQualPtr       gbq, 
+ Boolean         use_rarely_used)
 {
   Int2 index, i, qual;
   SematicFeatPtr  sefp;
@@ -11234,8 +12000,10 @@ extern DialoG NewCreateImportFields (GrouP h, CharPtr name, SeqFeatPtr sfp, Bool
 
     /* add remaining qualifiers last */
     gbq_it = gbq;
-    while (gbq_it != NULL) {
-      AddTemporaryGBQual (&(fpf->new_gbq), gbq_it->qual, gbq, FALSE);
+    while (gbq_it != NULL) {  
+      if (!ShouldSuppressGBQual(fpf->subtype, gbq_it->qual)) {
+        AddTemporaryGBQual (&(fpf->new_gbq), gbq_it->qual, gbq, FALSE);
+      }
       gbq_it = gbq_it->next;
     }
 
@@ -11281,3 +12049,258 @@ extern DialoG NewCreateImportFields (GrouP h, CharPtr name, SeqFeatPtr sfp, Bool
 }
 
 
+typedef struct specialcharacterdialog 
+{
+  TexT PNTR       text_list;
+  ButtoN          accept_btn;
+  Int4            num_chars;
+  ValNodePtr      find_list;
+} SpecialCharacterDialogData, PNTR SpecialCharacterDialogPtr;  
+
+
+static void EnableSpecialCharacterAccept (TexT t)
+{
+  SpecialCharacterDialogPtr sd;
+  Int4                      pos;
+  CharPtr                   str;
+  Boolean                   has_bad = FALSE;
+
+  sd = (SpecialCharacterDialogPtr) GetObjectExtra (t);
+  if (sd == NULL) return;
+
+  for (pos = 0; pos < sd->num_chars && !has_bad; pos++)
+  {
+    str = SaveStringFromText (sd->text_list[pos]);
+    SpecialCharFind (&str, NULL, &has_bad, NULL);
+    str = MemFree (str);
+  }
+  if (has_bad) 
+  {
+    Disable (sd->accept_btn);
+  }
+  else
+  {
+    Enable (sd->accept_btn);
+  }
+}
+
+
+static void SetWindowsSpecialCharacterDefaults (ButtoN b)
+{
+  SpecialCharacterDialogPtr sd;
+  Int4                      pos;
+  CharPtr                   str;
+  ValNodePtr                vnp;
+
+  sd = (SpecialCharacterDialogPtr) GetObjectExtra (b);
+  if (sd == NULL) return;
+
+  for (vnp = sd->find_list, pos = 0; vnp != NULL; vnp = vnp->next, pos++)
+  {
+    str = GetSpecialWinCharacterReplacement ((unsigned char) vnp->choice);
+    SetTitle (sd->text_list[pos], str);
+  }
+}
+
+
+static void SetMacSpecialCharacterDefaults (ButtoN b)
+{
+  SpecialCharacterDialogPtr sd;
+  Int4                      pos;
+  CharPtr                   str;
+  ValNodePtr                vnp;
+
+  sd = (SpecialCharacterDialogPtr) GetObjectExtra (b);
+  if (sd == NULL) return;
+
+  for (vnp = sd->find_list, pos = 0; vnp != NULL; vnp = vnp->next, pos++)
+  {
+    str = GetSpecialMacCharacterReplacement ((unsigned char) vnp->choice);
+    SetTitle (sd->text_list[pos], str);
+  }
+
+}
+
+
+extern Boolean FixSpecialCharactersForStringsInList (ValNodePtr find_list, CharPtr exp_text, Boolean force_fix)
+{
+  ValNodePtr      vnp, context_list, vnp_c;
+  Int4            pos;
+  CharPtr         repl;
+  WindoW          w;
+  GrouP           h, c, g, p1, g2;
+  PrompT          p2;
+  LisT            contexts;
+  ButtoN          b;
+  SpecialCharacterDialogData sd;
+  ModalAcceptCancelData      acd;
+  Char                  label[2];
+  Int4                  num_contexts;
+  Boolean               rval = FALSE;
+
+  if (find_list == NULL) {
+    return TRUE;
+  } 
+
+  ArrowCursor();
+  Update();
+
+  sd.find_list = find_list;
+  sd.num_chars = ValNodeLen (find_list);
+  
+  acd.accepted = FALSE;
+  acd.cancelled = FALSE;
+  
+  w = ModalWindow(-20, -13, -10, -10, NULL);
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+  
+  p1 = MultiLinePrompt (h, exp_text, 27 * stdCharWidth, programFont);
+  p2 = StaticPrompt (h, "Choose replacement characters.", 0, 0, programFont, 'l');
+
+  g = HiddenGroup (h, 3, 0, NULL);
+  StaticPrompt (g, "Character", 0, 0, programFont, 'l');
+  StaticPrompt (g, "Replacement", 0, 0, programFont, 'l');
+  StaticPrompt (g, "Contexts", 0, 0, programFont, 'l');
+
+  sd.text_list = MemNew (sizeof (TexT) * sd.num_chars);
+  label[1] = 0;
+  for (vnp = find_list, pos = 0; vnp != NULL; vnp = vnp->next, pos++)
+  {
+    label[0] = vnp->choice;
+    StaticPrompt (g, label, 0, 0, programFont, 'l');
+    repl = GetSpecialCharacterReplacement (vnp->choice);
+    sd.text_list[pos] = DialogText (g, repl, 5, EnableSpecialCharacterAccept);
+    SetObjectExtra (sd.text_list[pos], &sd, NULL);
+    context_list = vnp->data.ptrvalue;
+    num_contexts = ValNodeLen (context_list);
+    if (num_contexts == 0)
+    {
+      StaticPrompt (g, "", 0, 0, programFont, 'l');
+    }
+    else if (num_contexts == 1)
+    {
+      StaticPrompt (g, *((CharPtr PNTR)context_list->data.ptrvalue), 0, 0, programFont, 'l');
+    }
+    else
+    {
+      contexts = SingleList (g, 16, MIN (num_contexts, 5), NULL);
+      for (vnp_c = context_list; vnp_c != NULL; vnp_c = vnp_c->next)
+      {
+        ListItem (contexts, *((CharPtr PNTR)vnp_c->data.ptrvalue));
+      }
+      SetValue (contexts, 1);
+    }
+  }
+
+  g2 = HiddenGroup (h, 2, 0, NULL);
+  SetGroupSpacing (g2, 10, 10);
+  b = PushButton (g2, "Suggest Windows Replacements", SetWindowsSpecialCharacterDefaults);
+  SetObjectExtra (b, &sd, NULL);
+  b = PushButton (g2, "Suggest Mac Replacements", SetMacSpecialCharacterDefaults);
+  SetObjectExtra (b, &sd, NULL);
+
+  c = HiddenGroup (h, 3, 0, NULL);
+  SetGroupSpacing (c, 10, 10);
+  sd.accept_btn = PushButton (c, "Replace Characters", ModalAcceptButton);
+  SetObjectExtra (sd.accept_btn, &acd, NULL);
+  b = PushButton (c, "Cancel", ModalCancelButton);
+  SetObjectExtra (b, &acd, NULL);
+  AlignObjects (ALIGN_CENTER, (HANDLE) p1, (HANDLE) p2, (HANDLE) g, (HANDLE) g2, (HANDLE) c, NULL);
+  
+  Show(w); 
+  Select (w);
+  while (!acd.accepted && ! acd.cancelled)
+  {
+    ProcessExternalEvent ();
+    Update ();
+  }
+  ProcessAnEvent ();
+  if (acd.accepted)
+  {
+    for (vnp = find_list, pos = 0; vnp != NULL; vnp = vnp->next, pos++)
+    {
+      repl = JustSaveStringFromText (sd.text_list[pos]);
+      label[0] = vnp->choice;
+      for (vnp_c = vnp->data.ptrvalue; vnp_c != NULL; vnp_c = vnp_c->next)
+      {
+        FindReplaceString (vnp_c->data.ptrvalue, label, repl, TRUE, FALSE);
+      }
+      repl = MemFree (repl);
+    }
+
+    rval = TRUE;
+  }
+  else if (force_fix)
+  {
+    for (vnp = find_list; vnp != NULL; vnp = vnp->next)
+    {
+      label[0] = vnp->choice;
+      for (vnp_c = vnp->data.ptrvalue; vnp_c != NULL; vnp_c = vnp_c->next)
+      {
+        FindReplaceString (vnp_c->data.ptrvalue, label, "#", TRUE, FALSE);
+      }
+    }
+    rval = TRUE;
+  }
+
+  Remove (w);
+  return rval;
+
+}
+
+
+NLM_EXTERN Boolean FixSpecialCharacters (Uint2 entityID)
+{
+  ValNodePtr      find_list = NULL;
+  Boolean         rval;
+
+  StringActionInEntity (entityID, FALSE, UPDATE_NEVER, NULL, NULL, NULL, TRUE,
+                        SpecialCharFindWithContext, NULL, &find_list);
+
+  rval = FixSpecialCharactersForStringsInList (find_list,
+              "The ASN.1 contains special characters.\nIf you save it without stripping them,\nyou will be unable to load the file in Sequin.",
+              FALSE);
+
+  find_list = FreeContextList (find_list);
+  if (rval) 
+  {
+    ObjMgrSetDirtyFlag (entityID, TRUE);
+    ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
+  }
+  return rval;
+}
+
+
+NLM_EXTERN Boolean FixSpecialCharactersForObject (Uint2 datatype, Pointer objdata, CharPtr msg, Boolean force_fix, BoolPtr changed)
+{
+  ValNodePtr      find_list = NULL;
+  Boolean         rval;
+
+  StringActionForObject (datatype, objdata, 0, FALSE, UPDATE_NEVER,
+                        SpecialCharFindWithContext, NULL, &find_list);
+
+  rval = FixSpecialCharactersForStringsInList (find_list,
+              msg == NULL ?
+                     "The ASN.1 contains special characters.\nIf you save it without stripping them,\nyou will be unable to load the file in Sequin."
+                     : msg,
+              force_fix);
+
+  if (changed != NULL)
+  {
+    if (find_list == NULL)
+    {
+      *changed = FALSE;
+    }
+    else
+    {
+      *changed = rval;
+    }
+  } 
+
+  find_list = FreeContextList (find_list);
+  return rval;
+}
+
+
+
diff --git a/desktop/dlogutil.h b/desktop/dlogutil.h
index 3e8523ef..f7a5cc96 100644
--- a/desktop/dlogutil.h
+++ b/desktop/dlogutil.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.76 $
+* $Revision: 6.91 $
 *
 * File Description: 
 *
@@ -46,6 +46,7 @@
 #define _DLOGUTIL_
 
 #include <vibrant.h>
+#include <document.h>
 #include <sqnutils.h>
 #include <prtutil.h>
 #include <asn.h>
@@ -327,6 +328,8 @@ typedef void (*HelpMessageFunc) (CharPtr, CharPtr);
 *****************************************************************************/
 
 extern CharPtr SaveStringFromTextAndStripNewlines (TexT t);
+extern CharPtr StripNewlines (CharPtr str);
+extern void NewlinesToTildes (CharPtr str);
 
 /* GetRidOfEmptyFeatsDescStrings takes either an entityID or a SeqEntryPtr */
 
@@ -468,6 +471,17 @@ extern DialoG SequenceSelectionDialog
  Boolean                  show_prots,
  Uint2                    entityID);
 
+extern DialoG SequenceSelectionDialogEx 
+(GrouP h,
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata,
+ Boolean                  allow_multi,
+ Boolean                  allow_none,
+ Boolean                  show_nucs,
+ Boolean                  show_prots,
+ Uint2                    entityID,
+ Int4                     list_height);
+
 extern DialoG SubSourceTypeDialog 
 (GrouP                    h,
  Int2                     list_height,
@@ -504,13 +518,18 @@ CreateClickableListDialogEx
 (GrouP h, 
  CharPtr label1, 
  CharPtr label2,
+ CharPtr help1,
+ CharPtr help2,
  ClickableCallback item_single_click_callback,
  ClickableCallback item_double_click_callback,
  Pointer         item_click_callback_data,
  GetClickableItemText get_item_text,
  Int4            left_width,
  Int4            right_width,
- Boolean         horizontal);
+ Boolean         horizontal,
+ Boolean         show_find);
+
+extern void SetClickableListDialogTitles (DialoG d, CharPtr title1, CharPtr title2, CharPtr help1, CharPtr help2);
 
 extern void ScrollToNextClickableTextDescription (CharPtr txt, DialoG d);
 extern void ScrollToPreviousClickableTextDescription (CharPtr txt, DialoG d);
@@ -575,6 +594,7 @@ typedef struct editapply
 } EditApplyData, PNTR EditApplyPtr;
 
 extern EditApplyPtr EditApplyFree (EditApplyPtr eap);
+extern EditApplyPtr EditApplyNew (void);
 
 typedef enum {
   eEditApplyChoice_Apply = 0,
@@ -683,9 +703,34 @@ extern DialoG CollectionDateDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
                                TaglistCallback tlp_callback,
                                Pointer callback_data);
 
+extern DialoG CreateRptUnitRangeDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
+                                         TaglistCallback tlp_callback,
+                                         Pointer callback_data);
 
 extern void CreateStandardEditMenu (WindoW w);
 
+extern void CleanupEvidenceGBQuals (GBQualPtr PNTR prevgbq);
+extern void VisStringDialogToGbquals (SeqFeatPtr sfp, DialoG d, CharPtr qual);
+
+extern void RememberSqnTempFile (CharPtr file);
+extern void FreeSqnTempFiles (void);
+
+/* For fixing special characters */
+NLM_EXTERN Boolean FixSpecialCharacters (Uint2 entityID);
+extern Boolean FixSpecialCharactersForStringsInList (ValNodePtr find_list, CharPtr exp_text, Boolean force_fix);
+NLM_EXTERN Boolean FixSpecialCharactersForObject (Uint2 datatype, Pointer objdata, CharPtr msg, Boolean force_fix, BoolPtr changed);
+
+/* for functions that act on all open records */
+NLM_EXTERN ValNodePtr GetBaseFormList ();
+NLM_EXTERN ValNodePtr GetViewedSeqEntryList (void);
+NLM_EXTERN SeqEntryPtr RestoreFromFile (CharPtr path);
+NLM_EXTERN Uint2 RestoreEntityIDFromFile (CharPtr path, Uint2 entityID);
+
+NLM_EXTERN Int2 PanelOffsetFromCharOffsetEx (DoC doc, FonT font, Int2 item, Int2 col, Int2 char_offset);
+NLM_EXTERN Int2 GetTextSelectCharOffsetEx (PoinT pt, DoC doc, FonT font, Int2 item, Int2 row, Int2 col);
+NLM_EXTERN CharPtr GetSelectedDocText (DoC doc, Int2 item_start, Int2 row_start, Int2 col_start, Int2 char_start,
+                                       Int2 item_stop, Int2 row_stop, Int2 col_stop, Int2 char_stop,
+                                       Int2Ptr only_these_columns, Int2 num_col);
 
 #ifdef __cplusplus
 }
diff --git a/desktop/gbfview.c b/desktop/gbfview.c
index b83d3740..88968e10 100644
--- a/desktop/gbfview.c
+++ b/desktop/gbfview.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   2/5/97
 *
-* $Revision: 6.94 $
+* $Revision: 6.98 $
 *
 * File Description: 
 *
@@ -48,6 +48,7 @@
 #include <asn2gnbi.h>
 #include <tofasta.h>
 #include <explore.h>
+#include <subutil.h>
 
 static ParData ffParFmt = {FALSE, FALSE, FALSE, FALSE, TRUE, 0, 0};
 static ColData ffColFmt = {0, 0, 80, 0, NULL, 'l', FALSE, FALSE, FALSE, FALSE, TRUE};
@@ -548,24 +549,73 @@ static Uint2 MatchItemInFlatFile (Uint2 entityID, Uint4 itemID, CharPtr str,
   return ms.editItemID;
 }
 
+static CharPtr google_earth_1 =
+  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" \
+  "<kml xmlns=\"http://earth.google.com/kml/2.2\">\n" \
+  "<Document>\n" \
+  "  <name>KmlFile</name>\n" \
+  "  <StyleMap id=\"default_copy0+nicon=http://maps.google.com/mapfiles/kml/pal3/icon60.png+hicon=http://maps.google.com/mapfiles/kml/pal3/icon52.png\">\n" \
+  "    <Pair>\n" \
+  "      <key>normal</key>\n" \
+  "      <styleUrl>#default_copy0+icon=http://maps.google.com/mapfiles/kml/pal3/icon60.png</styleUrl>\n" \
+  "    </Pair>\n" \
+  "    <Pair>\n" \
+  "      <key>highlight</key>\n" \
+  "      <styleUrl>#default_copy0+icon=http://maps.google.com/mapfiles/kml/pal3/icon52.png</styleUrl>\n" \
+  "    </Pair>\n" \
+  "  </StyleMap>\n" \
+  "  <Style id=\"default_copy0+icon=http://maps.google.com/mapfiles/kml/pal3/icon60.png\">\n" \
+  "    <IconStyle>\n" \
+  "      <Icon>\n" \
+  "        <href>http://maps.google.com/mapfiles/kml/pal3/icon60.png</href>\n" \
+  "      </Icon>\n" \
+  "    </IconStyle>\n" \
+  "  </Style>\n" \
+  "  <Placemark>\n";
+
+static CharPtr google_earth_2 =
+  "    <styleUrl>#default_copy0+nicon=http://maps.google.com/mapfiles/kml/pal3/icon60.png+hicon=http://maps.google.com/mapfiles/kml/pal3/icon52.png</styleUrl>\n" \
+  "    <Point>\n";
+
+static CharPtr google_earth_3 =
+  "    </Point>\n" \
+  "  </Placemark>\n" \
+  "</Document>\n" \
+  "</kml>\n";
+
 static void ReleaseIcon (DoC d, PoinT pt)
 
 {
-  BioseqViewPtr  bvp;
-  Char           ch;
-  CharPtr        dst;
-  Uint4          editItemID;
-  Uint2          entityID;
-  Int2           handled;
-  Int2           item;
-  Uint4          itemID;
-  Uint2          itemtype;
-  Int2           row;
-  SeqEntryPtr    sep;
-  Boolean        slashgene;
-  Boolean        slashproduct;
-  CharPtr        src;
-  CharPtr        str;
+  BioSourcePtr       biop;
+  BioseqViewPtr      bvp;
+  Char               ch;
+  SeqMgrDescContext  context;
+  CharPtr            dst;
+  Uint4              editItemID;
+  Uint2              entityID;
+  Boolean            format_ok = FALSE;
+  FILE               *fp;
+  Int2               handled;
+  Int2               item;
+  Uint4              itemID;
+  Uint2              itemtype;
+  FloatHi            lat = 0.0;
+  FloatHi            lon = 0.0;
+  CharPtr            lat_lon = NULL;
+  Boolean            lat_in_range = FALSE;
+  Boolean            lon_in_range = FALSE;
+  Char               path [PATH_MAX];
+  Int2               row;
+  SeqDescPtr         sdp;
+  SeqEntryPtr        sep;
+  Boolean            slashgene;
+  Boolean            slashproduct;
+  CharPtr            src;
+  SubSourcePtr       ssp;
+  CharPtr            str;
+#ifdef OS_UNIX
+  Char               cmmd [256];
+#endif
 
   bvp = (BioseqViewPtr) GetObjectExtra (d);
   if (bvp == NULL) return;
@@ -573,6 +623,56 @@ static void ReleaseIcon (DoC d, PoinT pt)
   if (row != 0 && item != 0 && item == bvp->itemClicked) {
     if (GetIDsFromDoc (d, item, &entityID, &itemID, &itemtype)) {
       if (bvp->wasDoubleClick) {
+
+        if (bvp->wasShiftKey) {
+          if (itemtype == OBJ_SEQDESC) {
+            sdp = SeqMgrGetDesiredDescriptor (entityID, NULL, itemID, 0, NULL, &context);
+            if (sdp != NULL && sdp->choice == Seq_descr_source) {
+              biop = (BioSourcePtr) sdp->data.ptrvalue;
+              if (biop != NULL) {
+                for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
+                  if (ssp->subtype != SUBSRC_lat_lon) continue;
+                  lat_lon = ssp->name;
+                  if (StringHasNoText (lat_lon)) continue;
+                  IsCorrectLatLonFormat (lat_lon, &format_ok, &lat_in_range, &lon_in_range);
+                  if (! format_ok) continue;
+                  if (! lat_in_range) continue;
+                  if (! lon_in_range) continue;
+                  if (! ParseLatLon (lat_lon, &lat, &lon)) continue;
+                  TmpNam (path);
+                  /* write to original temp file, so next temp file name will not collide */
+                  fp = FileOpen (path, "w");
+                  if (fp != NULL) {
+                    fprintf (fp, "\n");
+                    FileClose (fp);
+                    RememberSqnTempFile (path);
+                  }
+                  /* now append .kml extension so proper application is launched */
+                  StringCat (path, ".kml");
+                  fp = FileOpen (path, "w");
+                  if (fp != NULL) {
+                    fprintf (fp, "%s", google_earth_1);
+                    fprintf (fp, "    <name>%s</name>\n", lat_lon);
+                    fprintf (fp, "%s", google_earth_2);
+                    fprintf (fp, "      <coordinates>%lf,%lf</coordinates>\n", (double) lon, (double) lat);
+                    fprintf (fp, "%s", google_earth_3);
+                    FileClose (fp);
+                    RememberSqnTempFile (path);
+#ifdef OS_UNIX
+                    sprintf (cmmd, "open %s", path);
+                    system (cmmd);
+#endif
+#ifdef WIN_MSWIN
+                    Nlm_MSWin_OpenDocument (path);
+#endif
+                  }
+                  return;
+                }
+              }
+            }
+          }
+        }
+
         sep = GetTopSeqEntryForEntityID (entityID);
         if (bvp->launchSubviewers) {
           WatchCursor ();
diff --git a/desktop/import.c b/desktop/import.c
index 2f404826..c87077d7 100644
--- a/desktop/import.c
+++ b/desktop/import.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/18/95
 *
-* $Revision: 6.63 $
+* $Revision: 6.68 $
 *
 * File Description: 
 *
@@ -240,8 +240,6 @@ static void CleanupImportPage (GraphiC g, VoidPtr data)
   MemFree (data);
 }
 
-extern void CleanupEvidenceGBQuals (GBQualPtr PNTR prevgbq);
-extern void VisStringDialogToGbquals (SeqFeatPtr sfp, DialoG d, CharPtr qual);
 
 static void ChangeKey (Handle obj)
 
@@ -2013,21 +2011,23 @@ typedef struct molinfoform {
 } MolInfoForm, PNTR MolInfoFormPtr;
 
 static ENUM_ALIST(molinfo_biomol_alist)
-  {" ",                      0},
-  {"Genomic DNA or RNA",     1},
-  {"Precursor RNA",          2},
-  {"mRNA [cDNA]",            3},
-  {"Ribosomal RNA",          4},
-  {"Transfer RNA",           5},
-  {"Small nuclear RNA",      6},
-  {"Small cytoplasmic RNA",  7},
-  {"Peptide",                8},
-  {"Other-Genetic",          9},
-  {"Genomic-mRNA",          10},
-  {"cRNA",                  11},
-  {"Small nucleolar RNA",   12},
-  {"Transcribed RNA",       13},
-  {"Other",                255},
+  {" ",                       0},
+  {"Genomic DNA or RNA",      1},
+  {"Precursor RNA",           2},
+  {"mRNA [cDNA]",             3},
+  {"Ribosomal RNA",           4},
+  {"Transfer RNA",            5},
+  {"Small nuclear RNA",       6},
+  {"Small cytoplasmic RNA",   7},
+  {"Peptide",                 8},
+  {"Other-Genetic",           9},
+  {"Genomic-mRNA",           10},
+  {"cRNA",                   11},
+  {"Small nucleolar RNA",    12},
+  {"Transcribed RNA",        13},
+  {"Non-coding  RNA",        14},
+  {"Transfer-messenger RNA", 15},
+  {"Other",                 255},
 END_ENUM_ALIST
 
 extern CharPtr GetMoleculeTypeName (Uint1 mol_val)
@@ -2043,38 +2043,42 @@ extern CharPtr GetMoleculeTypeName (Uint1 mol_val)
 
 
 static ENUM_ALIST(molinfo_biomol_nuc_alist)
-  {" ",                      0},
-  {"Genomic DNA or RNA",     1},
-  {"Precursor RNA",          2},
-  {"mRNA [cDNA]",            3},
-  {"Ribosomal RNA",          4},
-  {"Transfer RNA",           5},
-  {"Small nuclear RNA",      6},
-  {"Small cytoplasmic RNA",  7},
-  {"Other-Genetic",          9},
-  {"Genomic-mRNA",          10},
-  {"cRNA",                  11},
-  {"Small nucleolar RNA",   12},
-  {"Transcribed RNA",       13},
-  {"Other",                255},
+  {" ",                       0},
+  {"Genomic DNA or RNA",      1},
+  {"Precursor RNA",           2},
+  {"mRNA [cDNA]",             3},
+  {"Ribosomal RNA",           4},
+  {"Transfer RNA",            5},
+  {"Small nuclear RNA",       6},
+  {"Small cytoplasmic RNA",   7},
+  {"Other-Genetic",           9},
+  {"Genomic-mRNA",           10},
+  {"cRNA",                   11},
+  {"Small nucleolar RNA",    12},
+  {"Transcribed RNA",        13},
+  {"Non-coding  RNA",        14},
+  {"Transfer-messenger RNA", 15},
+  {"Other",                 255},
 END_ENUM_ALIST
 
 static ENUM_ALIST(molinfo_biomol_nucX_alist)
-  {" ",                      0},
-  {"Genomic DNA",          253},
-  {"Genomic RNA",          254},
-  {"Precursor RNA",          2},
-  {"mRNA [cDNA]",            3},
-  {"Ribosomal RNA",          4},
-  {"Transfer RNA",           5},
-  {"Small nuclear RNA",      6},
-  {"Small cytoplasmic RNA",  7},
-  {"Other-Genetic",          9},
-  {"Genomic-mRNA",          10},
-  {"cRNA",                  11},
-  {"Small nucleolar RNA",   12},
-  {"Transcribed RNA",       13},
-  {"Other",                255},
+  {" ",                       0},
+  {"Genomic DNA",           253},
+  {"Genomic RNA",           254},
+  {"Precursor RNA",           2},
+  {"mRNA [cDNA]",             3},
+  {"Ribosomal RNA",           4},
+  {"Transfer RNA",            5},
+  {"Small nuclear RNA",       6},
+  {"Small cytoplasmic RNA",   7},
+  {"Other-Genetic",           9},
+  {"Genomic-mRNA",           10},
+  {"cRNA",                   11},
+  {"Small nucleolar RNA",    12},
+  {"Transcribed RNA",        13},
+  {"Non-coding  RNA",        14},
+  {"Transfer-messenger RNA", 15},
+  {"Other",                 255},
 END_ENUM_ALIST
 
 static ENUM_ALIST(molinfo_biomol_prot_alist)
@@ -2107,6 +2111,7 @@ static ENUM_ALIST(molinfo_tech_alist)
   {"WGS",                20},
   {"Barcode",            21},
   {"Composite-WGS-HTGS", 22},
+  {"TSA",                23},
   {"Other:",            255},
 END_ENUM_ALIST
 
@@ -2128,6 +2133,7 @@ static ENUM_ALIST(molinfo_tech_nuc_alist)
   {"WGS",                20},
   {"Barcode",            21},
   {"Composite-WGS-HTGS", 22},
+  {"TSA",                23},
   {"Other:",            255},
 END_ENUM_ALIST
 
@@ -2181,14 +2187,14 @@ END_ENUM_ALIST
 static Uint1 check_biomol (Uint1 biomol)
 
 {
-  if (biomol > 13 && biomol < 253) return 0;
+  if (biomol > MOLECULE_TYPE_TMRNA && biomol < 253) return 0;
   return biomol;
 }
 
 static Uint1 check_technique (Uint1 tech)
 
 {
-  if (tech > MI_TECH_composite_wgs_htgs && tech != MI_TECH_other) return 0;
+  if (tech > MI_TECH_tsa && tech != MI_TECH_other) return 0;
   return tech;
 }
 
@@ -3496,11 +3502,19 @@ static Pointer VisStrPageToCharPtr (DialoG d)
 {
   CharPtr        title;
   VisStrPagePtr  vpp;
+  ValNodePtr     find_list = NULL;
 
   title = NULL;
   vpp = (VisStrPagePtr) GetObjectExtra (d);
   if (vpp != NULL) {
-    title = SaveStringFromTextAndStripNewlines (vpp->title);
+    title = SaveStringFromText (vpp->title);
+    title = StripNewlines (title);
+    SpecialCharFindWithContext (&title, &find_list, NULL, NULL);
+    FixSpecialCharactersForStringsInList (find_list, "Special characters are not permitted.", TRUE);      
+    if (find_list != NULL) {
+      PointerToDialog (d, title);
+      find_list = FreeContextList (find_list);
+    }
   }
   return (Pointer) title;
 }
diff --git a/desktop/macrodlg.c b/desktop/macrodlg.c
new file mode 100755
index 00000000..96106532
--- /dev/null
+++ b/desktop/macrodlg.c
@@ -0,0 +1,10335 @@
+/*   macrodlg.c
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  macrodlg.c
+*
+* Author:  Colleen Bollin
+*
+* Version Creation Date:   11/23/2007
+*
+* $Revision: 1.61 $
+*
+* File Description: 
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* Date     Name        Description of modification
+* -------  ----------  -----------------------------------------------------
+*
+*
+* ==========================================================================
+*/
+
+#include <objseq.h>
+#include <objfdef.h>
+#include <sqnutils.h>
+#include <vibforms.h>
+#include <document.h>
+#include <dlogutil.h>
+#include <cdrgn.h>
+#include <seqpanel.h>
+#define NLM_GENERATED_CODE_PROTO
+#include <objmacro.h>
+#include <macroapi.h>
+#include <macrodlg.h>
+
+/* macro editor dialog */
+typedef struct macroeditorform {
+  FORM_MESSAGE_BLOCK
+  DoC    macro_summary;
+  ButtoN run_btn;
+  
+  ValNodePtr macro_list;
+  CharPtr    last_filename;
+  Boolean    unsaved;
+  Boolean    indexer_version;
+  FonT       summary_font;
+} MacroEditorFormData, PNTR MacroEditorFormPtr;
+
+static void CleanupMacroEditorForm (GraphiC g, VoidPtr data)
+
+{
+  MacroEditorFormPtr f;
+
+  f = (MacroEditorFormPtr) data;
+  if (f != NULL) {
+    f->macro_list = MacroActionListFree (f->macro_list);
+    f->last_filename = MemFree (f->last_filename);
+  }
+  StdCleanupFormProc (g, data);
+}
+
+
+static void SetupMacroEditorFont (MacroEditorFormPtr f)
+
+{
+  if (f == NULL) return;
+
+#ifdef WIN_MAC
+  f->summary_font = ParseFont ("Times,12");
+#endif
+#ifdef WIN_MSWIN
+  f->summary_font = ParseFont ("Times New Roman,12");
+#endif
+#ifdef WIN_MOTIF
+  f->summary_font = ParseFont ("Times,12");
+#endif
+}
+
+
+static void SetMacroEditorFileItems (MacroEditorFormPtr mefp);
+
+static Boolean SaveMacroFile (ForM f, CharPtr filename)
+
+{
+  MacroEditorFormPtr mefp;
+  Boolean            rval = FALSE;
+  Char               path [PATH_MAX];
+  AsnIoPtr           aip;
+
+  mefp = (MacroEditorFormPtr) GetObjectExtra (f);
+  if (mefp != NULL) {
+    path [0] = '\0';
+    StringNCpy_0 (path, filename, sizeof (path));
+    if (path [0] != '\0' || GetOutputFileName (path, sizeof (path), NULL)) {
+      aip = AsnIoOpen (path, "w");
+      if (aip == NULL) {
+        Message (MSG_ERROR, "Unable to open %s", path);
+      } else {
+        MacroActionListAsnWrite (mefp->macro_list, aip, NULL);
+        AsnIoClose (aip);
+        mefp->last_filename = MemFree (mefp->last_filename);
+        mefp->last_filename = StringSave (path);
+        mefp->unsaved = FALSE;
+        rval = TRUE;
+      }
+    }
+  }
+  return rval;
+}
+
+
+static CharPtr SummarizeMacroAction (ValNodePtr vnp);
+
+static void SummarizeMacro (DoC doc, ValNodePtr macro_list, FonT font)
+{
+  ValNodePtr vnp;
+  CharPtr    str;
+  CharPtr    tmp;
+  RecT       r;
+  ParData    ParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0};
+  ColData    ColFmt[] = 
+  {
+    {12, 0, 1, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE},
+    {12, 0, 1, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE},
+    {12, 0, 1, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE},
+    {12, 0, 1, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE},
+    {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}
+  };
+
+
+  Reset (doc);
+
+  ObjectRect (doc, &r);
+  InsetRect (&r, 4, 4);
+  
+  ColFmt[4].pixWidth = r.right - r.left - 48;
+
+  if (font == NULL) font = programFont;
+
+  if (macro_list == NULL) {
+    AppendText (doc, "(Click here to start a new macro script)", NULL, NULL, font);
+  } else {
+    AppendText (doc, "(Click here to insert an action at the beginning of the script)", NULL, NULL, font);
+    for (vnp = macro_list; vnp != NULL; vnp = vnp->next) {
+      str = SummarizeMacroAction (vnp);
+      tmp = (CharPtr) MemNew (sizeof (Char) * (StringLen (str) + 6));
+      sprintf (tmp, "\t\t\t\t%s\n", str);
+      str = MemFree (str);
+      AppendText (doc, tmp, &ParFmt, ColFmt, font);
+      tmp = MemFree (tmp);
+    }
+    AppendText (doc, "(Click here to insert an action at the end of the script)", NULL, NULL, font);
+  }
+  UpdateDocument (doc, 0, 0);
+}
+
+
+static Boolean OpenMacroFile (ForM f, CharPtr filename)
+
+{
+  MacroEditorFormPtr mefp;
+  Boolean            rval = FALSE;
+  CharPtr            extension;
+  Char               path [PATH_MAX];
+  AsnIoPtr           aip;
+  ValNodePtr         action_list;
+
+  mefp = (MacroEditorFormPtr) GetObjectExtra (f);
+  if (mefp != NULL) {
+    if (mefp->unsaved) {
+      if (Message (MSG_YN, "Do you want to save changes to the current file?") == ANS_YES) {
+        if (!SaveMacroFile(f, mefp->last_filename)) {
+           return FALSE;
+        }
+      }
+    }
+    path [0] = '\0';
+    StringNCpy_0 (path, filename, sizeof (path));
+    extension = NULL;
+    if (path [0] != '\0' || GetInputFileName (path, sizeof (path), extension, "TEXT")) {
+      aip = AsnIoOpen (path, "r");
+      if (aip == NULL) {
+        Message (MSG_ERROR, "Unable to open %s", path);
+      } else {
+        action_list = MacroActionListAsnRead (aip, NULL);
+        if (action_list == NULL) {
+          Message (MSG_ERROR, "Unable to read action list from %s.", path);
+        } else {
+          mefp->macro_list = MacroActionListFree (mefp->macro_list);
+          mefp->macro_list = action_list;
+          mefp->last_filename = MemFree (mefp->last_filename);
+          mefp->last_filename = StringSave (path);
+          mefp->unsaved = FALSE;
+          rval = TRUE;
+          SetMacroEditorFileItems (mefp);
+          SummarizeMacro (mefp->macro_summary, mefp->macro_list, mefp->summary_font);
+          Enable (mefp->run_btn);
+        }
+        AsnIoClose (aip);
+      }
+    }    
+  }
+  return rval;
+}
+
+
+static Boolean ImportMacroFile (ForM f, CharPtr filename)
+
+{
+  MacroEditorFormPtr mefp;
+  Boolean            rval = FALSE;
+  CharPtr            extension;
+  Char               path [PATH_MAX];
+  AsnIoPtr           aip;
+  ValNodePtr         action_list;
+
+  mefp = (MacroEditorFormPtr) GetObjectExtra (f);
+  if (mefp == NULL) return FALSE;
+  path [0] = '\0';
+  StringNCpy_0 (path, filename, sizeof (path));
+  extension = NULL;
+  if (path [0] != '\0' || GetInputFileName (path, sizeof (path), extension, "TEXT")) {
+    aip = AsnIoOpen (path, "r");
+    if (aip == NULL) {
+      Message (MSG_ERROR, "Unable to open %s", path);
+    } else {
+      action_list = MacroActionListAsnRead (aip, NULL);
+      if (action_list == NULL) {
+        Message (MSG_ERROR, "Unable to read action list from %s.", path);
+      } else {
+        ValNodeLink (&(mefp->macro_list), action_list);
+        mefp->unsaved = FALSE;
+        rval = TRUE;
+        SetMacroEditorFileItems (mefp);
+        SummarizeMacro (mefp->macro_summary, mefp->macro_list, mefp->summary_font);
+        Enable (mefp->run_btn);
+      }
+      AsnIoClose (aip);
+    }
+  }
+  return rval;
+}
+
+
+static void SetMacroEditorFileItems (MacroEditorFormPtr mefp)
+
+{
+  IteM  i;
+
+  if (mefp != NULL) {
+    i = FindFormMenuItem ((BaseFormPtr) mefp, VIB_MSG_OPEN);
+    SafeSetTitle (i, "Load Macro File");
+    SafeEnable (i);
+
+    i = FindFormMenuItem ((BaseFormPtr) mefp, VIB_MSG_IMPORT);
+    SafeSetTitle (i, "Add Macros from File to Script");
+    SafeEnable (i);
+
+    i = FindFormMenuItem ((BaseFormPtr) mefp, VIB_MSG_SAVE);
+    SafeSetTitle (i, "Save Macro File");
+    if (mefp->macro_list == NULL) {
+      SafeDisable (i);
+    } else {
+      SafeEnable (i);
+    }
+    i = FindFormMenuItem ((BaseFormPtr) mefp, VIB_MSG_SAVE_AS);
+    SafeSetTitle (i, "Save Macro File As");
+    if (mefp->macro_list == NULL) {
+      SafeDisable (i);
+    } else {
+      SafeEnable (i);
+    }
+  }
+}
+
+
+static void MacroEditorFormMessage (ForM f, Int2 mssg)
+
+{
+  MacroEditorFormPtr  mefp;
+  ValNodePtr          vnp, string_list = NULL;
+  Int4                len = 1;
+  CharPtr             str;
+
+  mefp = (MacroEditorFormPtr) GetObjectExtra (f);
+  if (mefp != NULL) {
+    switch (mssg) {
+      case VIB_MSG_OPEN :
+        OpenMacroFile (f, NULL);
+        break;
+      case VIB_MSG_IMPORT :
+        ImportMacroFile (f, NULL);
+        break;
+      case VIB_MSG_SAVE :
+        SaveMacroFile (f, mefp->last_filename);
+        break;
+      case VIB_MSG_SAVE_AS :
+        SaveMacroFile (f, NULL);
+        break;
+      case VIB_MSG_CUT :
+        StdCutTextProc (NULL);
+        break;
+      case VIB_MSG_COPY :
+        /* get length of entire macro list */
+        for (vnp = mefp->macro_list; vnp != NULL; vnp = vnp->next) {
+          str = SummarizeMacroAction (vnp);
+          len += StringLen (str) + 2;
+          ValNodeAddPointer (&string_list, 0, str);
+        }
+        str = (CharPtr) MemNew (sizeof (Char) * len);
+        str[0] = 0;
+        for (vnp = string_list; vnp != NULL; vnp = vnp->next) {
+          StringCat (str, vnp->data.ptrvalue);
+          StringCat (str, "\r\n");
+        }
+        string_list = ValNodeFreeData (string_list);
+        StringToClipboard (str);
+        str = MemFree (str);
+        break;
+      case VIB_MSG_PASTE :
+        StdPasteTextProc (NULL);
+        break;
+      case VIB_MSG_DELETE :
+        break;
+      case VIB_MSG_CLOSE:
+      case VIB_MSG_QUIT:
+        if (mefp->unsaved) {
+          if (Message (MSG_YN, "Do you want to save changes to the current file?") == ANS_YES) {
+            if (SaveMacroFile(f, mefp->last_filename)) {
+              Remove (mefp->form);
+            }
+          }
+        }
+        Remove (mefp->form);
+        break;
+      default :
+        break;
+    }
+  }
+}
+
+
+static void RunMacro (ButtoN b)
+{
+  MacroEditorFormPtr  f;
+  SeqEntryPtr         sep;
+  ValNodePtr          sep_list, vnp;
+  Uint2               entityID;
+  Int4                num_fields = 0, num_features = 0;
+  Int4                tmp_fields, tmp_features;
+
+  f = (MacroEditorFormPtr) GetObjectExtra (b);
+  if (f == NULL) return;
+
+  if (f->macro_list == NULL) {
+    Message (MSG_ERROR, "No macro loaded!");
+  } else {
+    sep_list = GetViewedSeqEntryList ();
+    if (sep_list == NULL) {
+      Message (MSG_ERROR, "No records open!");
+    } else if (sep_list->next != NULL 
+      && ANS_CANCEL == Message (MSG_OKC, "You have more than one record open - run macro for all open records?")) {
+      /* do nothing */
+    } else {
+      WatchCursor();
+      Update();
+      for (vnp = sep_list; vnp != NULL; vnp = vnp->next) {
+        sep = vnp->data.ptrvalue;
+        entityID = ObjMgrGetEntityIDForChoice(sep);
+        tmp_fields = 0;
+        tmp_features = 0;
+        ApplyMacroToSeqEntry (sep, f->macro_list, &tmp_fields, &tmp_features);
+        num_fields += tmp_fields;
+        num_features += tmp_features;
+        ObjMgrSetDirtyFlag (entityID, TRUE);
+        ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
+      }
+      sep_list = ValNodeFree (sep_list);
+      ArrowCursor ();
+      Update ();   
+      Message (MSG_OK, "Macro script affected %d fields and created %d features", num_fields, num_features);
+    }
+  }
+}
+
+static Boolean EditMacroAction (ValNodePtr action, Boolean indexer_version);
+
+static Boolean EditMacroItem (MacroEditorFormPtr f, Int2 item)
+{
+  Boolean rval = FALSE;
+  ValNodePtr vnp;
+
+  if (f == NULL) return FALSE;
+
+  for (vnp = f->macro_list; vnp != NULL && item > 1; vnp = vnp->next, item--) {}
+  if (vnp != NULL) {
+    rval = EditMacroAction (vnp, f->indexer_version);
+  }
+  return rval;
+}
+
+static AECRActionPtr BuildDefaultAECRAction (Uint1 action_type, Uint1 qual_type)
+{
+  AECRActionPtr action = AECRActionNew();
+  ApplyActionPtr apply;
+  EditActionPtr  edit;
+  ConvertActionPtr convert;
+  CopyActionPtr copy;
+  SwapActionPtr swap;
+  AECRParseActionPtr parse;
+  RemoveActionPtr remove;
+
+  switch (action_type) {
+    case ActionChoice_apply:
+      apply = ApplyActionNew();
+      apply->field = ValNodeNew (NULL);
+      apply->field->choice = qual_type;
+      action->action = ValNodeNew (NULL);
+      action->action->choice = action_type;
+      action->action->data.ptrvalue = apply;
+      break;
+    case ActionChoice_edit:
+      edit = EditActionNew ();
+      edit->field = ValNodeNew (NULL);
+      edit->field->choice = qual_type;
+      action->action = ValNodeNew (NULL);
+      action->action->choice = action_type;
+      action->action->data.ptrvalue = edit;
+      break;
+    case ActionChoice_convert:
+      convert = ConvertActionNew();
+      convert->fields = ValNodeNew (NULL);
+      convert->fields->choice = qual_type;
+      action->action = ValNodeNew (NULL);
+      action->action->choice = action_type;
+      action->action->data.ptrvalue = convert;
+      break;
+    case ActionChoice_copy:
+      copy = CopyActionNew();
+      copy->fields = ValNodeNew (NULL);
+      copy->fields->choice = qual_type;
+      action->action = ValNodeNew (NULL);
+      action->action->choice = action_type;
+      action->action->data.ptrvalue = copy;
+      break;
+    case ActionChoice_swap:
+      swap = SwapActionNew();
+      swap->fields = ValNodeNew (NULL);
+      swap->fields->choice = qual_type;
+      action->action = ValNodeNew (NULL);
+      action->action->choice = action_type;
+      action->action->data.ptrvalue = swap;
+      break;
+    case ActionChoice_remove:
+      remove = RemoveActionNew();
+      remove->field = ValNodeNew (NULL);
+      remove->field->choice = qual_type;
+      action->action = ValNodeNew (NULL);
+      action->action->choice = action_type;
+      action->action->data.ptrvalue = remove;
+      break;
+    case ActionChoice_parse:
+      parse = AECRParseActionNew();
+      parse->fields = ValNodeNew (NULL);
+      parse->fields->choice = qual_type;
+      action->action = ValNodeNew (NULL);
+      action->action->choice = action_type;
+      action->action->data.ptrvalue = parse;
+      break;
+  }
+
+  return action;
+}
+
+
+static ApplyFeatureActionPtr BuildDefaultApplyFeatureAction (Uint2 feat_type)
+{
+  ApplyFeatureActionPtr action;
+  FeatQualLegalValPtr   qual;
+
+  action = ApplyFeatureActionNew ();
+  action->type = feat_type;
+  action->location = ValNodeNew (NULL);
+  action->location->choice = LocationChoice_whole_sequence;
+  action->seq_list = ValNodeNew (NULL);
+  action->seq_list->choice = SequenceListChoice_all;
+  qual = FeatQualLegalValNew ();
+  qual->qual = Feat_qual_legal_codon_start;
+  qual->val = StringSave ("best");
+  action->fields = ValNodeNew (NULL);
+  action->fields->choice = FeatQualLegalValChoice_qual;
+  action->fields->data.ptrvalue = qual;
+  return action;
+}
+
+
+static EditFeatureLocationActionPtr BuildDefaultEditFeatureLocationAction (Uint2 feat_type)
+{
+  EditFeatureLocationActionPtr a;
+  EditLocationStrandPtr strand;
+
+  a = EditFeatureLocationActionNew ();
+  a->type = feat_type;
+  a->action = ValNodeNew (NULL);
+  a->action->choice = LocationEditType_strand;
+  strand = EditLocationStrandNew ();
+  strand->strand_to = Feature_location_strand_to_reverse;
+  a->action->data.ptrvalue = strand;
+  return a;
+}
+
+static ParseActionPtr BuildDefaultParseAction (void)
+{
+  ParseActionPtr parse;
+
+  parse = ParseActionNew();
+  return parse;
+}
+
+
+static RemoveFeatureActionPtr BuildDefaultRemoveFeatureAction (void)
+{
+  RemoveFeatureActionPtr remove;
+
+  remove = RemoveFeatureActionNew ();
+  return remove;
+}
+
+
+static ValNodePtr BuildDefaultNewMacroAction (void)
+{
+  ValNodePtr vnp;
+  ApplyFeatureActionPtr apply_feat;
+
+  apply_feat = BuildDefaultApplyFeatureAction (Feature_type_cds);
+
+  vnp = ValNodeNew (NULL);
+  vnp->choice = MacroActionChoice_add_feature;
+  vnp->data.ptrvalue = apply_feat;
+  return vnp;
+}
+
+
+static void UpdateMacroSummary (MacroEditorFormPtr f, Int4 scroll_pos)
+{
+  Int4 scroll_max;
+  BaR  sb_vert;
+
+  if (f == NULL) return;
+
+  f->unsaved = TRUE;
+  SetMacroEditorFileItems (f);
+  SummarizeMacro (f->macro_summary, f->macro_list, f->summary_font);
+  if (f->macro_list == NULL) {
+    Disable (f->run_btn);
+  } else {
+    Enable (f->run_btn);
+  }
+  if (scroll_pos > 0) {
+    sb_vert = GetSlateVScrollBar ((SlatE) f->macro_summary);
+    scroll_max = GetBarMax (sb_vert);
+    if (scroll_pos > scroll_max) {
+      scroll_pos = scroll_max;
+    }
+    CorrectBarValue (sb_vert, scroll_pos);
+  }
+}
+
+
+static void AddMacroActions (MacroEditorFormPtr f, Int2 item);
+
+static void ClickMacroDoc (DoC d, PoinT pt)
+{
+  Int2               item, row, col;
+  RecT               rct;
+  MacroEditorFormPtr f;
+  ValNodePtr         vnp, vnp_prev = NULL, two_prev = NULL, vnp_next;
+  Boolean            changed_macro = FALSE;
+  BaR                sb_vert = NULL;
+  Int2               scroll_pos = 0;
+  
+  f = (MacroEditorFormPtr) GetObjectExtra (d);
+  if (f == NULL) return;
+  
+  MapDocPoint (d, pt, &item, &row, &col, &rct);
+  if (item == 0 && row == 0 && f->macro_list == NULL) {
+    AddMacroActions (f, 0);
+  } else if (item > 0 && row > 0) {
+    if (item == 1) {
+      /* add to beginning of list */
+      AddMacroActions (f, 0);
+    } else if (item == ValNodeLen (f->macro_list) + 2) {
+      /* add to end of list */
+      AddMacroActions (f, item);
+    } else {
+      /* correct for explanatory line */
+      item--;
+      sb_vert = GetSlateVScrollBar ((SlatE) f->macro_summary);
+      scroll_pos = GetBarValue (sb_vert);
+      switch (col) {
+        case 1:
+          /* delete this item */
+          for (vnp = f->macro_list; vnp != NULL && item > 1; vnp = vnp->next, item--) {
+            vnp_prev = vnp;
+          }
+          if (vnp != NULL) {
+            if (vnp_prev == NULL) {
+              f->macro_list = vnp->next;
+            } else {
+              vnp_prev->next = vnp->next;
+            }
+            vnp->next = NULL;
+            vnp = MacroActionListFree (vnp);
+            changed_macro = TRUE;
+          }
+          break;
+        case 2:
+          /* move this item up */
+          for (vnp = f->macro_list; vnp != NULL && item > 1; vnp = vnp->next, item--) {
+            two_prev = vnp_prev;
+            vnp_prev = vnp;
+          }
+          if (vnp != NULL && vnp_prev != NULL) {
+            vnp_prev->next = vnp->next;
+            vnp->next = vnp_prev;
+            if (two_prev == NULL) {
+              f->macro_list = vnp;
+            } else {
+              two_prev->next = vnp;
+            }
+            /* decrease the scroll position, so cursor will still be over the same item */
+            scroll_pos--;
+            changed_macro = TRUE;
+          }
+          break;
+        case 3:
+          /* move this item down */
+          for (vnp = f->macro_list; vnp != NULL && item > 1; vnp = vnp->next, item--) {
+            vnp_prev = vnp;
+          }
+          if (vnp != NULL && vnp->next != NULL) {
+            vnp_next = vnp->next;
+            vnp->next = vnp_next->next;
+            vnp_next->next = vnp;
+            if (vnp_prev == NULL) {
+              f->macro_list = vnp_next;
+            } else {
+              vnp_prev->next = vnp_next;
+            }
+            /* increase the scroll position, so cursor will still be over the same item */
+            scroll_pos++;
+            changed_macro = TRUE;
+          }
+          break;
+        case 4:
+          /* insert item */
+          if (pt.y >= rct.top && pt.y <= rct.top + 4) {
+            /* insert macro before this one */
+            AddMacroActions (f, item - 1);
+          } else if (pt.y >= rct.bottom - 4 && pt.y <= rct.bottom) {
+            /* insert macro after this one */
+            AddMacroActions (f, item);
+          }
+          break;
+        case 5:
+          /* edit this item */
+          changed_macro = EditMacroItem (f, item);
+          break;
+      }
+    }
+  }
+  if (changed_macro) {
+    UpdateMacroSummary (f, scroll_pos);
+  }
+}
+
+
+static void DrawMacroDocControls (DoC d, RectPtr r, Int2 item, Int2 firstLine)
+
+{
+  MacroEditorFormPtr dlg;
+  RecT               rct;
+  Int4               width;
+  PoinT              pt1, pt2;
+
+  dlg = (MacroEditorFormPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+  /* don't draw controls for explanatory text */
+  if (item == 1 || item >= ValNodeLen (dlg->macro_list) + 2) return;
+
+  if (dlg != NULL && r != NULL && item > 0 && firstLine == 0) {
+    rct = *r;
+
+    width = 10;
+    /* draw X for deletion */
+    pt1.x = rct.left + 1;
+    pt1.y = rct.top + 1;
+    pt2.x = pt1.x + width;
+    pt2.y = pt1.y + width;
+    DrawLine (pt1, pt2);
+    pt1.x = rct.left + 1;
+    pt1.y = rct.top + 1 + width;
+    pt2.x = pt1.x + width;
+    pt2.y = rct.top + 1;
+    DrawLine (pt1, pt2);
+
+    /* draw up arrow for moving step up */
+    if (item > 2) {
+      pt1.x = rct.left + width + 3;
+      pt1.y = rct.top + 3;
+      pt2.x = pt1.x + 5;
+      pt2.y = rct.top + 1;
+      DrawLine (pt1, pt2);
+      pt1.x = pt2.x + 5;
+      DrawLine (pt1, pt2);
+      pt1.x = pt2.x;
+      pt1.y = pt2.y + width;
+      DrawLine (pt1, pt2);
+    }
+    /* draw up arrow for moving step up */
+    if (item < ValNodeLen (dlg->macro_list) + 1) {
+      pt1.x = rct.left + 2 * width + 5;
+      pt1.y = rct.top + width - 2;
+      pt2.x = pt1.x + 5;
+      pt2.y = rct.top + width + 1;
+      DrawLine (pt1, pt2);
+      pt1.x = pt2.x + 5;
+      DrawLine (pt1, pt2);
+      pt1.x = pt2.x;
+      pt1.y = rct.top + 1;
+      DrawLine (pt1, pt2);
+    }
+
+    /* draw insertion controls */
+    pt1.x = rct.left + 3 * width + 7;
+    pt1.y = rct.top + 4;
+    pt2.x = pt1.x + width;
+    pt2.y = rct.top;
+    if (item > 2) {
+      DrawLine (pt1, pt2);
+    }
+    pt1.y = rct.bottom - 4;
+    pt2.y = rct.bottom;
+    if (item < ValNodeLen (dlg->macro_list) + 1) {
+      DrawLine (pt1, pt2);
+    }
+  }
+}
+
+
+NLM_EXTERN void LaunchMacroEditor (IteM i)
+{
+  BaseFormPtr         bfp;
+  WindoW              w;
+  MacroEditorFormPtr  f;
+  GrouP               h, c;
+  MenU                m;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+
+  f = (MacroEditorFormPtr) MemNew (sizeof (MacroEditorFormData));
+  if (f == NULL) return;
+    
+  w = FixedWindow (-50, -33, -10, -10, "Macro Editor", StdCloseWindowProc);
+  SetObjectExtra (w, f, CleanupMacroEditorForm);
+  f->form = (ForM) w;
+  f->input_entityID = bfp->input_entityID;
+
+  f->formmessage = MacroEditorFormMessage;
+
+  f->macro_list = NULL;
+  f->last_filename = NULL;
+  f->unsaved = FALSE;
+  f->indexer_version = TRUE;
+
+  m = PulldownMenu (w, "File");
+  FormCommandItem (m, "Open", (BaseFormPtr)f, VIB_MSG_OPEN);
+  FormCommandItem (m, "Import", (BaseFormPtr)f, VIB_MSG_IMPORT);
+  FormCommandItem (m, "Save", (BaseFormPtr)f, VIB_MSG_SAVE);
+  FormCommandItem (m, "Save As", (BaseFormPtr)f, VIB_MSG_SAVE_AS);
+  SeparatorItem (m);
+  FormCommandItem (m, "Quit", (BaseFormPtr)f, VIB_MSG_QUIT);
+  m = PulldownMenu (w, "Edit");
+  FormCommandItem (m, "Copy All to Clipboard", (BaseFormPtr) f, VIB_MSG_COPY);
+
+  SetupMacroEditorFont (f);
+  SetMacroEditorFileItems (f);
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  f->macro_summary = DocumentPanel (h, stdCharWidth * 50, stdLineHeight * 12);
+  SetObjectExtra (f->macro_summary, f, NULL);
+  SetDocProcs (f->macro_summary, ClickMacroDoc, NULL, NULL, NULL);
+  SetDocShade (f->macro_summary, DrawMacroDocControls, NULL, NULL, NULL);
+
+  c = HiddenGroup (h, 3, 0, NULL);
+  f->run_btn = PushButton (c, "Run", RunMacro);
+  SetObjectExtra (f->run_btn, f, NULL);
+  Disable (f->run_btn);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) f->macro_summary, (HANDLE) c, NULL);
+  SummarizeMacro (f->macro_summary, f->macro_list, f->summary_font);
+  Show (w);
+}
+
+
+static void ClearDialogBtn (ButtoN b)
+{
+  DialoG d;
+  
+  d = (DialoG) GetObjectExtra (b);
+  
+  PointerToDialog (d, NULL);
+}
+
+
+typedef struct textportiondialog
+{
+  DIALOG_MESSAGE_BLOCK
+
+  GrouP  start_choice;
+  TexT   start_text;
+  GrouP  end_choice;
+  TexT   end_text;
+  ButtoN rem_before;
+  ButtoN also_rem_before;
+  ButtoN rem_after;
+  ButtoN also_rem_after;
+  ButtoN insensitive;
+  ButtoN whole_word;
+
+  Boolean inside;
+
+  Nlm_ChangeNotifyProc     change_notify;
+  Pointer                  change_userdata;
+} TextPortionDialogData, PNTR TextPortionDialogPtr;
+
+
+static void OutsideEnableDisable (TextPortionDialogPtr tp)
+{
+  if (tp == NULL || tp->inside)
+  {
+    return;
+  }
+  if (GetStatus (tp->rem_before)) 
+  {
+    Enable (tp->start_text);
+    Enable (tp->also_rem_before);
+  }
+  else
+  {
+    Disable (tp->start_text);
+    Disable (tp->also_rem_before);
+  }
+  if (GetStatus (tp->rem_after)) 
+  {
+    Enable (tp->end_text);
+    Enable (tp->also_rem_after);
+  }
+  else
+  {
+    Disable (tp->end_text);
+    Disable (tp->also_rem_after);
+  }
+}
+
+static void ResetTextPortionDialog (TextPortionDialogPtr tp)
+{
+  if (tp == NULL)
+  {
+    return;
+  }
+  if (tp->inside)
+  {
+    SetValue (tp->start_choice, 1);
+    SetValue (tp->end_choice, 1);
+  }
+  else
+  {
+    SetStatus (tp->rem_before, FALSE);
+    SetStatus (tp->also_rem_before, FALSE);
+    SetStatus (tp->rem_after, FALSE);
+    SetStatus (tp->also_rem_after, FALSE);
+  }
+  SetTitle (tp->start_text, "");
+  SetTitle (tp->end_text, "");
+  SetStatus (tp->insensitive, FALSE);
+  SetStatus (tp->whole_word, FALSE);
+  OutsideEnableDisable (tp);
+}
+
+static void TextPortionToDialog (DialoG d, Pointer data)
+{
+  TextPortionDialogPtr tdlg;
+  TextPortionPtr       tdata;
+  
+  tdlg = (TextPortionDialogPtr) GetObjectExtra (d);
+  if (tdlg == NULL) {
+    return;
+  }
+  tdata = (TextPortionPtr) data;
+  ResetTextPortionDialog (tdlg);  
+  if (tdata != NULL) {
+    if (tdlg->inside) {
+      if (tdata->include_left) {        
+        SetValue (tdlg->start_choice, 2);
+      } else {
+        SetValue (tdlg->start_choice, 1);
+      }
+      if (tdata->include_right) {
+        SetValue (tdlg->end_choice, 2);
+      } else {
+        SetValue (tdlg->end_choice, 1);
+      }
+    } else {
+      SetStatus (tdlg->rem_before, StringHasNoText (tdata->left_text));
+      SetStatus (tdlg->rem_after, StringHasNoText (tdata->right_text));
+      SetStatus (tdlg->also_rem_before, tdata->include_left);
+      SetStatus (tdlg->also_rem_after, tdata->include_right);
+    }
+    if (tdata->left_text != NULL) {
+      SetTitle (tdlg->start_text, tdata->left_text);
+    }
+    if (tdata->right_text != NULL)
+    {
+      SetTitle (tdlg->end_text, tdata->right_text);
+    }
+    SetStatus (tdlg->insensitive, !tdata->case_sensitive);
+    SetStatus (tdlg->whole_word, tdata->whole_word);
+  }
+  OutsideEnableDisable (tdlg);
+}
+
+static Pointer DialogToTextPortion (DialoG d)
+{
+  TextPortionDialogPtr tdlg;
+  TextPortionPtr       tdata;
+
+  tdlg = (TextPortionDialogPtr) GetObjectExtra (d);
+  if (tdlg == NULL) {
+    return NULL;
+  }
+
+  tdata = TextPortionNew();
+  if (tdata != NULL) {
+    if (tdlg->inside) {
+      if (GetValue (tdlg->start_choice) == 1) {
+        tdata->include_left = FALSE;
+      } else {
+        tdata->include_left = TRUE;
+      }
+      tdata->left_text = JustSaveStringFromText (tdlg->start_text);
+
+      if (GetValue (tdlg->end_choice) == 1) {
+        tdata->include_right = FALSE;
+      } else {
+        tdata->include_right = TRUE;
+      }
+      tdata->right_text = JustSaveStringFromText (tdlg->end_text);
+    } else {
+      if (GetStatus (tdlg->rem_before)) {
+        tdata->left_text = JustSaveStringFromText (tdlg->start_text);
+      } else {
+        tdata->left_text = NULL;
+      }
+      if (GetStatus (tdlg->rem_after)) {
+        tdata->right_text = JustSaveStringFromText (tdlg->end_text);
+      } else {
+        tdata->right_text = NULL;
+      }
+
+      tdata->include_left = GetStatus (tdlg->also_rem_before);
+      tdata->include_right = GetStatus (tdlg->also_rem_after);
+    }
+        
+    tdata->case_sensitive = !GetStatus (tdlg->insensitive);
+    tdata->whole_word = GetStatus (tdlg->whole_word);
+    tdata->inside = tdlg->inside;
+  }
+  return tdata;
+}
+
+static void TextPortionMessage (DialoG d, Int2 mssg)
+
+{
+  TextPortionDialogPtr tp;
+
+  tp = (TextPortionDialogPtr) GetObjectExtra (d);
+  if (tp != NULL) {
+    switch (mssg) {
+      case VIB_MSG_INIT :
+        ResetTextPortionDialog (tp);        
+        break;
+      case VIB_MSG_ENTER :
+        Select (tp->start_text);
+        break;
+      default :
+        break;
+    }
+  }
+}
+
+static void ChangeTextPortionGroup (GrouP g)
+{
+  TextPortionDialogPtr tp;
+
+  tp = (TextPortionDialogPtr) GetObjectExtra (g);
+  if (tp == NULL) return;
+
+  if (tp->change_notify != NULL)
+  {
+    (tp->change_notify) (tp->change_userdata);
+  }
+}
+
+static void ChangeTextPortionText (TexT t)
+{
+  TextPortionDialogPtr tp;
+
+  tp = (TextPortionDialogPtr) GetObjectExtra (t);
+  if (tp == NULL) return;
+
+  if (tp->change_notify != NULL)
+  {
+    (tp->change_notify) (tp->change_userdata);
+  }
+}
+
+
+static void ChangeTextPortionBtn (ButtoN b)
+{
+  TextPortionDialogPtr tp;
+
+  tp = (TextPortionDialogPtr) GetObjectExtra (b);
+  if (tp == NULL) return;
+  OutsideEnableDisable (tp);
+
+  if (tp->change_notify != NULL)
+  {
+    (tp->change_notify) (tp->change_userdata);
+  }
+}
+
+
+static ValNodePtr TestTextPortionDialog (DialoG d)
+{
+  TextPortionDialogPtr tp;
+  ValNodePtr err_list = NULL;
+
+  tp = (TextPortionDialogPtr) GetObjectExtra (d);
+  if (tp == NULL) return NULL;
+
+  /* don't actually need to fill anything in.  Could want to copy the entire field. */
+
+  return err_list;
+}
+
+
+static DialoG TextPortionDialog (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  TextPortionDialogPtr tp;
+  GrouP                p, g1, g2;
+  
+  tp = (TextPortionDialogPtr) MemNew (sizeof (TextPortionDialogData));
+  if (tp == NULL)
+  {
+    return NULL;
+  }
+  
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetObjectExtra (p, tp, StdCleanupExtraProc);
+
+  tp->dialog = (DialoG) p;
+  tp->todialog = TextPortionToDialog;
+  tp->fromdialog = DialogToTextPortion;
+  tp->dialogmessage = TextPortionMessage;
+  tp->testdialog = TestTextPortionDialog;
+
+  tp->change_notify = change_notify;
+  tp->change_userdata = change_userdata;
+  tp->inside = inside;
+
+  g1 = HiddenGroup (p, 3, 0, NULL);
+  SetGroupSpacing (g1, 10, 10);
+
+  if (inside) 
+  {
+    StaticPrompt (g1, "Between", 0, popupMenuHeight, programFont, 'r');
+    tp->start_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionGroup);
+    RadioButton (tp->start_choice, "just after");
+    RadioButton (tp->start_choice, "starting at");
+    SetValue (tp->start_choice, 1);
+    SetObjectExtra (tp->start_choice, tp, NULL);
+
+    tp->start_text = DialogText (g1, "", 10, ChangeTextPortionText);
+    SetObjectExtra (tp->start_text, tp, NULL);
+    
+    StaticPrompt (g1, "And", 0, popupMenuHeight, programFont, 'r');
+    tp->end_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionGroup);
+    RadioButton (tp->end_choice, "up to");
+    RadioButton (tp->end_choice, "including");
+    SetValue (tp->end_choice, 1);
+    SetObjectExtra (tp->start_choice, tp, NULL);
+      
+    tp->end_text = DialogText (g1, "", 10, ChangeTextPortionText);
+    SetObjectExtra (tp->start_text, tp, NULL);
+  }
+  else
+  {
+    tp->rem_before = CheckBox (g1, "Before", ChangeTextPortionBtn);
+    SetObjectExtra (tp->rem_before, tp, NULL);
+    tp->start_text = DialogText (g1, "", 10, ChangeTextPortionText);
+    SetObjectExtra (tp->start_text, tp, NULL);
+    tp->also_rem_before = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionBtn);
+
+    tp->rem_after = CheckBox (g1, "After", ChangeTextPortionBtn);
+    SetObjectExtra (tp->rem_after, tp, NULL);
+    tp->end_text = DialogText (g1, "", 10, ChangeTextPortionText);
+    SetObjectExtra (tp->end_text, tp, NULL);
+    tp->also_rem_after = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionBtn);    
+  }
+  
+  g2 = HiddenGroup (p, 2, 0, NULL);
+  tp->insensitive = CheckBox (g2, "Case insensitive", ChangeTextPortionBtn);
+  SetObjectExtra (tp->insensitive, tp, NULL);
+  tp->whole_word = CheckBox (g2, "Whole word", ChangeTextPortionBtn);
+  SetObjectExtra (tp->whole_word, tp, NULL);
+  
+  AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL);
+  
+  ResetTextPortionDialog (tp);
+  return (DialoG) p;
+}
+
+
+typedef struct fieldeditdlg {
+  DIALOG_MESSAGE_BLOCK
+  TexT find_txt;
+  TexT repl_txt;
+  GrouP location;
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer              change_userdata;
+} FieldEditDlgData, PNTR FieldEditDlgPtr;
+
+
+static void ChangeFieldEditText (TexT t)
+{
+  FieldEditDlgPtr dlg;
+
+  dlg = (FieldEditDlgPtr) GetObjectExtra (t);
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    dlg->change_notify (dlg->change_userdata);
+  }
+}
+
+
+static void ChangeFieldEditGroup (GrouP g)
+{
+  FieldEditDlgPtr dlg;
+
+  dlg = (FieldEditDlgPtr) GetObjectExtra (g);
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    dlg->change_notify (dlg->change_userdata);
+  }
+}
+
+
+static void FieldEditToDialog (DialoG d, Pointer data)
+{
+  FieldEditDlgPtr dlg;
+  FieldEditPtr edit;
+
+  dlg = (FieldEditDlgPtr) GetObjectExtra (d);
+
+  if (dlg == NULL) return;
+
+  edit = (FieldEditPtr) data;
+  if (edit == NULL) {
+    SetTitle (dlg->find_txt, "");
+    SetTitle (dlg->repl_txt, "");
+    SetValue (dlg->location, 1);
+  } else {
+    SetTitle (dlg->find_txt, edit->find_txt);
+    SetTitle (dlg->repl_txt, edit->repl_txt);
+    switch (edit->location) {
+      case Field_edit_location_anywhere:
+        SetValue (dlg->location, 1);
+        break;
+      case Field_edit_location_beginning:
+        SetValue (dlg->location, 2);
+        break;
+      case Field_edit_location_end:
+        SetValue (dlg->location, 3);
+        break;
+      default:
+        SetValue (dlg->location, 1);
+        break;
+    }
+  }
+  if (dlg->change_notify != NULL) {
+    dlg->change_notify (dlg->change_userdata);
+  }
+}
+
+
+static Pointer DialogToFieldEdit (DialoG d)
+{
+  FieldEditDlgPtr dlg;
+  FieldEditPtr edit;
+
+  dlg = (FieldEditDlgPtr) GetObjectExtra (d);
+
+  if (dlg == NULL) return NULL;
+
+  if (TextHasNoText (dlg->find_txt)) {
+    return NULL;
+  }
+  edit = FieldEditNew ();
+  edit->find_txt = JustSaveStringFromText (dlg->find_txt);
+  edit->repl_txt = JustSaveStringFromText (dlg->repl_txt);
+  switch (GetValue (dlg->location)) {
+    case 1:
+      edit->location = Field_edit_location_anywhere;
+      break;
+    case 2:
+      edit->location = Field_edit_location_beginning;
+      break;
+    case 3:
+      edit->location = Field_edit_location_end;
+      break;
+    default:
+      edit->location = Field_edit_location_anywhere;
+      break;
+  }
+  return edit;
+}
+
+
+static void FieldEditDlgCopy (ButtoN b)
+{
+  FieldEditDlgPtr dlg;
+  CharPtr         str = NULL;
+
+  dlg = (FieldEditDlgPtr) GetObjectExtra (b);
+  if (dlg == NULL)
+  {
+    return;
+  }
+  str = JustSaveStringFromText (dlg->find_txt);
+  SetTitle (dlg->repl_txt, str);
+  str = MemFree (str);
+}
+
+static ValNodePtr TestFieldEditDialog (DialoG d)
+{
+  FieldEditDlgPtr dlg;
+  ValNodePtr err_list = NULL;
+
+  dlg = (FieldEditDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) {
+    return NULL;
+  }
+
+  if (TextHasNoText (dlg->find_txt)) {
+    ValNodeAddPointer (&err_list, 0, "no find text");
+  }
+  return err_list;
+}
+
+
+static DialoG FieldEditDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  FieldEditDlgPtr dlg;
+  GrouP p, g;
+  ButtoN b;
+
+  p = HiddenGroup (h, -1, 0, NULL);
+  dlg = (FieldEditDlgPtr) MemNew (sizeof (FieldEditDlgData));
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+  dlg->dialog = (DialoG) p;
+  dlg->fromdialog = DialogToFieldEdit;
+  dlg->todialog = FieldEditToDialog;
+  dlg->testdialog = TestFieldEditDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+  
+  g = HiddenGroup (p, 3, 0, NULL);
+  StaticPrompt (g, "Find", 0, dialogTextHeight, systemFont, 'r');
+  dlg->find_txt = DialogText (g, "", 18, ChangeFieldEditText);
+  SetObjectExtra (dlg->find_txt, dlg, NULL);
+  b = PushButton (g, "Copy", FieldEditDlgCopy);
+  SetObjectExtra (b, dlg, NULL);
+  Hide (b);
+  StaticPrompt (g, "Replace", 0, dialogTextHeight, systemFont, 'r');
+  dlg->repl_txt = DialogText (g, "", 18, ChangeFieldEditText);
+  SetObjectExtra (dlg->repl_txt, dlg, NULL);
+  b = PushButton (g, "Copy", FieldEditDlgCopy);
+  SetObjectExtra (b, dlg, NULL);
+
+  dlg->location = HiddenGroup (p, 3, 0, ChangeFieldEditGroup);
+  SetObjectExtra (dlg->location, dlg, NULL);
+  RadioButton (dlg->location, "Anywhere in field");
+  RadioButton (dlg->location, "At the beginning of the field");
+  RadioButton (dlg->location, "At the end of the field");
+  SetValue (dlg->location, 1);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) dlg->location, NULL);
+
+  return (DialoG) p;
+}
+
+
+typedef struct existingtextdlg {
+  DIALOG_MESSAGE_BLOCK
+  GrouP                action_grp;
+  ButtoN               append_btn;
+  ButtoN               prefix_btn;
+  GrouP                delim_grp;
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer              change_userdata;
+} ExistingTextDlgData, PNTR ExistingTextDlgPtr;
+
+static void ChangeExistingTextActionChoice (GrouP g)
+{
+  ExistingTextDlgPtr dlg;
+  Int4               action_choice;
+
+  dlg = (ExistingTextDlgPtr) GetObjectExtra (g);
+  if (dlg == NULL) return;
+  
+  action_choice = GetValue (dlg->action_grp);
+  if (action_choice == 2 || action_choice == 3) {
+    Enable (dlg->delim_grp);
+  } else {
+    Disable (dlg->delim_grp);
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void ExistingTextToDialog (DialoG d, Pointer data)
+{
+  ExistingTextDlgPtr dlg;
+  Uint2 existing_text;
+
+  dlg = (ExistingTextDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+  if (data == NULL) {
+    SetValue (dlg->action_grp, 1);
+    SetValue (dlg->delim_grp, 1);
+  } else {
+    existing_text = (Uint2) data;
+    switch (existing_text) {
+      case ExistingTextOption_append_semi :
+        SetValue (dlg->action_grp, 2);
+        SetValue (dlg->delim_grp, 1);
+        break;
+      case ExistingTextOption_append_space :
+        SetValue (dlg->action_grp, 2);
+        SetValue (dlg->delim_grp, 2);
+        break;
+      case ExistingTextOption_append_colon :
+        SetValue (dlg->action_grp, 2);
+        SetValue (dlg->delim_grp, 3);
+        break;
+      case ExistingTextOption_append_none :
+        SetValue (dlg->action_grp, 2);
+        SetValue (dlg->delim_grp, 4);
+        break;
+      case ExistingTextOption_prefix_semi :
+        SetValue (dlg->action_grp, 3);
+        SetValue (dlg->delim_grp, 1);
+        break;
+      case ExistingTextOption_prefix_space :
+        SetValue (dlg->action_grp, 3);
+        SetValue (dlg->delim_grp, 2);
+        break;
+      case ExistingTextOption_prefix_colon :
+        SetValue (dlg->action_grp, 3);
+        SetValue (dlg->delim_grp, 3);
+        break;
+      case ExistingTextOption_prefix_none :
+        SetValue (dlg->action_grp, 3);
+        SetValue (dlg->delim_grp, 4);
+        break;
+      case ExistingTextOption_leave_old :
+        SetValue (dlg->action_grp, 4);
+        break;
+      case ExistingTextOption_replace_old :
+      default:
+        SetValue (dlg->action_grp, 1);
+        break;
+    }
+  } 
+  ChangeExistingTextActionChoice (dlg->action_grp);
+}
+
+static void ChangeExistingTextDelimChoice (GrouP g)
+{
+  ExistingTextDlgPtr dlg;
+
+  dlg = (ExistingTextDlgPtr) GetObjectExtra (g);
+  if (dlg == NULL) return;
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static Pointer DialogToExistingText (DialoG d)
+{
+  ExistingTextDlgPtr dlg;
+  Int4 action_choice, separator_choice;
+  Uint2 existing_text = ExistingTextOption_replace_old;
+
+  dlg = (ExistingTextDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  action_choice = GetValue (dlg->action_grp);
+  separator_choice = GetValue (dlg->delim_grp);
+  switch (action_choice) {
+    case 1:
+      existing_text = ExistingTextOption_replace_old;
+      break;
+    case 2:
+      switch (separator_choice) {
+        case 1:
+          existing_text = ExistingTextOption_append_semi;
+          break;
+        case 2:
+          existing_text = ExistingTextOption_append_space;
+          break;
+        case 3:
+          existing_text = ExistingTextOption_append_colon;
+          break;
+        case 4:
+          existing_text = ExistingTextOption_append_none;
+          break;
+      }
+      break;
+    case 3:
+      switch (separator_choice) {
+        case 1:
+          existing_text = ExistingTextOption_prefix_semi;
+          break;
+        case 2:
+          existing_text = ExistingTextOption_prefix_space;
+          break;
+        case 3:
+          existing_text = ExistingTextOption_prefix_colon;
+          break;
+        case 4:
+          existing_text = ExistingTextOption_prefix_none;
+          break;
+      }
+      break;
+    case 4:
+      existing_text = ExistingTextOption_leave_old;
+      break;
+  }
+  return (Pointer) existing_text;
+}
+
+
+static ValNodePtr TestExistingTextDialog (DialoG d)
+{
+  ExistingTextDlgPtr dlg;
+  ValNodePtr err_list = NULL;
+  Int2       val;
+
+  dlg = (ExistingTextDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  val = GetValue (dlg->action_grp);
+  if ((val == 2 && !Enabled (dlg->append_btn)) || (val == 3 && !Enabled (dlg->prefix_btn))) {
+    ValNodeAddPointer (&err_list, 0, "invalid existing text option for nontext value");
+  }
+  return err_list;
+}
+
+
+static void EnableNonTextOptions (DialoG d)
+{
+  ExistingTextDlgPtr dlg;
+
+  dlg = (ExistingTextDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  Enable (dlg->append_btn);
+  Enable (dlg->prefix_btn);
+}
+
+
+static void DisableNonTextOptions (DialoG d)
+{
+  ExistingTextDlgPtr dlg;
+
+  dlg = (ExistingTextDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  Disable (dlg->append_btn);
+  Disable (dlg->prefix_btn);
+}
+
+
+static DialoG ExistingTextDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  ExistingTextDlgPtr dlg;
+  GrouP              p;
+  PrompT             ppt;
+
+  dlg = (ExistingTextDlgPtr) MemNew (sizeof (ExistingTextDlgData));
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetGroupSpacing (p, 10, 10);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->fromdialog = DialogToExistingText;
+  dlg->todialog = ExistingTextToDialog;
+  dlg->testdialog = TestExistingTextDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->action_grp = HiddenGroup (p, 4, 0, ChangeExistingTextActionChoice);
+  SetGroupSpacing (dlg->action_grp, 10, 10);
+  SetObjectExtra (dlg->action_grp, dlg, NULL);
+  RadioButton (dlg->action_grp, "Overwrite existing text");
+  dlg->append_btn = RadioButton (dlg->action_grp, "Append");
+  dlg->prefix_btn = RadioButton (dlg->action_grp, "Prefix");
+  RadioButton (dlg->action_grp, "Ignore new text");
+  SetValue (dlg->action_grp, 1);
+
+  ppt = StaticPrompt (p, "Separate new text and old text with", 
+                      0, dialogTextHeight, programFont, 'c');
+  
+  dlg->delim_grp = HiddenGroup (p, 4, 0, ChangeExistingTextDelimChoice);
+  SetObjectExtra (dlg->delim_grp, dlg, NULL);
+  SetGroupSpacing (dlg->delim_grp, 10, 10);
+  RadioButton (dlg->delim_grp, "Semicolon");
+  RadioButton (dlg->delim_grp, "Space");
+  RadioButton (dlg->delim_grp, "Colon");
+  RadioButton (dlg->delim_grp, "Do not separate");
+  SetValue (dlg->delim_grp, 1);
+  Disable (dlg->delim_grp);
+  return (DialoG) p;
+}
+
+
+typedef struct stringconstraintdialog 
+{
+  DIALOG_MESSAGE_BLOCK
+  PopuP  match_choice;
+  TexT   match_text;
+  ButtoN insensitive;
+  ButtoN whole_word;   
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer change_userdata;
+} StringConstraintDialogData, PNTR StringConstraintDialogPtr;
+
+static void ResetStringConstraintDialog (StringConstraintDialogPtr scdp)
+{
+  if (scdp == NULL) return;
+  
+  SetValue (scdp->match_choice, 1);
+  SetTitle (scdp->match_text, "");
+  SetStatus (scdp->insensitive, FALSE);
+  SetStatus (scdp->whole_word, FALSE);
+}
+
+
+static Int4 GetPopupPosForStringConstraint (StringConstraintPtr scp)
+{
+  Int4 rval = 1;
+
+  if (scp == NULL) return 1;
+
+  switch (scp->match_location)
+  {
+    case String_location_contains:
+      if (scp->not_present) 
+      {
+        rval = 2;
+      } else {
+        rval = 1;
+      }
+      break;
+    case String_location_equals:
+      if (scp->not_present) {
+        rval = 4;
+      } else {
+        rval = 3;
+      }
+      break;
+    case String_location_starts:
+      if (scp->not_present) {
+        rval = 9;
+      } else {
+        rval = 5;
+      }
+      break;
+    case String_location_ends:
+      if (scp->not_present) {
+        rval = 10;
+      } else {
+        rval = 6;
+      }
+      break;
+    case String_location_inlist:
+      if (scp->not_present) {
+        rval = 8;
+      } else {
+        rval = 7;
+      }
+      break;
+  }
+  return rval;
+}
+
+
+static void StringConstraintToDialog (DialoG d, Pointer data)
+
+{
+  StringConstraintDialogPtr scdp;
+  StringConstraintPtr       scp;
+
+  scdp = (StringConstraintDialogPtr) GetObjectExtra (d);
+  scp = (StringConstraintPtr) data;
+  if (scdp == NULL)
+  {
+    return;
+  }
+
+  if (scp == NULL)
+  {
+    ResetStringConstraintDialog (scdp);
+  }
+  else
+  {
+    SetValue (scdp->match_choice, GetPopupPosForStringConstraint (scp));
+    
+    if (StringHasNoText (scp->match_text))
+    {
+      SetTitle (scdp->match_text, " ");
+    }
+    else
+    {
+      SetTitle (scdp->match_text, scp->match_text);
+    }
+    
+    SetStatus (scdp->insensitive, !scp->case_sensitive);
+    SetStatus (scdp->whole_word, scp->whole_word);
+  }
+  if (scdp->change_notify != NULL) {
+    (scdp->change_notify) (scdp->change_userdata);
+  }
+}
+
+static Pointer DialogToStringConstraint (DialoG d)
+
+{
+  StringConstraintDialogPtr scdp;
+  StringConstraintPtr       scp;
+  Int4                      match_choice;
+
+  scdp = (StringConstraintDialogPtr) GetObjectExtra (d);
+  if (scdp == NULL)
+  {
+    return NULL;
+  }
+  scp = StringConstraintNew();
+  if (scp != NULL)
+  {
+    scp->match_text = SaveStringFromText (scdp->match_text);
+    scp->case_sensitive = !GetStatus (scdp->insensitive);
+    scp->whole_word = GetStatus (scdp->whole_word);
+    match_choice = GetValue (scdp->match_choice);
+    switch (match_choice)
+    {
+      case 1:
+        scp->match_location = String_location_contains;
+        scp->not_present = FALSE;
+        break;
+      case 2:
+        scp->match_location = String_location_contains;
+        scp->not_present = TRUE;
+        break;
+      case 3:
+        scp->match_location = String_location_equals;
+        scp->not_present = FALSE;
+        break;
+      case 4:
+        scp->match_location = String_location_equals;
+        scp->not_present = TRUE;
+        break;
+      case 5:
+        scp->match_location = String_location_starts;
+        scp->not_present = FALSE;
+        break;
+      case 6:
+        scp->match_location = String_location_ends;
+        scp->not_present = FALSE;
+        break;
+      case 7:
+        scp->match_location = String_location_inlist;
+        scp->not_present = FALSE;
+        break;
+      case 8:
+        scp->match_location = String_location_inlist;
+        scp->not_present = TRUE;
+        break;
+      case 9:
+        scp->match_location = String_location_starts;
+        scp->not_present = TRUE;
+        break;
+      case 10:
+        scp->match_location = String_location_ends;
+        scp->not_present = TRUE;
+        break;
+      default:
+        scp->match_location = String_location_contains;
+        scp->not_present = FALSE;
+        break;
+    }
+  }
+  return scp;
+}
+
+static void StringConstraintMessage (DialoG d, Int2 mssg)
+
+{
+  StringConstraintDialogPtr scdp;
+
+  scdp = (StringConstraintDialogPtr) GetObjectExtra (d);
+  if (scdp != NULL) {
+    switch (mssg) {
+      case VIB_MSG_INIT :
+        ResetStringConstraintDialog (scdp);        
+        break;
+      case VIB_MSG_ENTER :
+        Select (scdp->match_text);
+        break;
+      default :
+        break;
+    }
+  }
+}
+
+
+static void ChangeStringConstraintDialogText (TexT t)
+{
+  StringConstraintDialogPtr dlg;
+
+  dlg = (StringConstraintDialogPtr) GetObjectExtra (t);
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static ValNodePtr TestStringConstraintDialog (DialoG d)
+
+{
+  ValNodePtr err_list = NULL;
+  StringConstraintDialogPtr dlg;
+
+  dlg = (StringConstraintDialogPtr) GetObjectExtra (d);
+  if (dlg != NULL) {
+    if (TextHasNoText (dlg->match_text)) {
+      ValNodeAddPointer (&err_list, 0, "empty string constraint");
+    }
+  }
+  return err_list;
+}
+
+NLM_EXTERN DialoG StringConstraintDialog (GrouP h, CharPtr label, Boolean clear_btn, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+
+{
+  StringConstraintDialogPtr scdp;
+  GrouP                     p, g, k;
+  ButtoN                    b = NULL;
+  
+  scdp = (StringConstraintDialogPtr) MemNew (sizeof (StringConstraintDialogData));
+  if (scdp == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetObjectExtra (p, scdp, StdCleanupExtraProc);
+
+  scdp->dialog = (DialoG) p;
+  scdp->todialog = StringConstraintToDialog;
+  scdp->fromdialog = DialogToStringConstraint;
+  scdp->dialogmessage = StringConstraintMessage;
+  scdp->testdialog = TestStringConstraintDialog;
+  scdp->change_notify = change_notify;
+  scdp->change_userdata = change_userdata;
+
+  g = HiddenGroup (p, 3, 0, NULL);
+  SetGroupSpacing (g, 10, 10);
+  
+  if (!StringHasNoText (label))
+  {
+    StaticPrompt (g, label, 0, dialogTextHeight, systemFont, 'l');
+  }
+  
+  scdp->match_choice = PopupList (g, TRUE, NULL);
+  PopupItem (scdp->match_choice, "Contains");
+  PopupItem (scdp->match_choice, "Does not contain");
+  PopupItem (scdp->match_choice, "Equals");
+  PopupItem (scdp->match_choice, "Does not equal");
+  PopupItem (scdp->match_choice, "Starts with");
+  PopupItem (scdp->match_choice, "Ends with");
+  PopupItem (scdp->match_choice, "Is one of");
+  PopupItem (scdp->match_choice, "Is not one of");
+  PopupItem (scdp->match_choice, "Does not start with");
+  PopupItem (scdp->match_choice, "Does not end with");
+  SetValue (scdp->match_choice, 1);
+  scdp->match_text = DialogText (g, "", 15, ChangeStringConstraintDialogText);
+  SetObjectExtra (scdp->match_text, scdp, NULL);
+  
+  k = HiddenGroup (p, 3, 0, NULL);
+  SetGroupSpacing (k, 10, 10);
+  scdp->insensitive = CheckBox (k, "Case Insensitive", NULL);
+  scdp->whole_word = CheckBox (k, "Whole Word", NULL);
+  
+  if (clear_btn)
+  {
+    b = PushButton (p, "Clear Constraint", ClearDialogBtn);
+    SetObjectExtra (b, p, NULL);
+  }
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) k, (HANDLE) b, NULL);
+    
+  return (DialoG) p;
+}
+
+typedef struct locationconstraintdialog 
+{
+  DIALOG_MESSAGE_BLOCK
+  PopuP  strand;
+  PopuP  sequence_type;  
+
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer change_userdata; 
+} LocationConstraintDialogData, PNTR LocationConstraintDialogPtr;
+
+
+static void ChangeLocationConstraintDialogPopup (PopuP p)
+{
+  LocationConstraintDialogPtr dlg;
+
+  dlg = (LocationConstraintDialogPtr) GetObjectExtra (p);
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void LocationConstraintToDialog (DialoG d, Pointer data)
+{
+  LocationConstraintDialogPtr dlg;
+  LocationConstraintPtr l;
+
+  dlg = (LocationConstraintDialogPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  l = (LocationConstraintPtr) data;
+  if (l == NULL) {
+    SetValue (dlg->strand, 1);
+    SetValue (dlg->sequence_type, 1);
+  } else {
+    switch (l->strand) {
+      case Strand_constraint_any:
+        SetValue (dlg->strand, 1);
+        break;
+      case Strand_constraint_plus:
+        SetValue (dlg->strand, 2);
+        break;
+      case Strand_constraint_minus:
+        SetValue (dlg->strand, 3);
+        break;
+      default:
+        SetValue (dlg->strand, 1);
+        break;
+    }
+    switch (l->seq_type) {
+      case Seqtype_constraint_any:
+        SetValue (dlg->sequence_type, 1);
+        break;
+      case Seqtype_constraint_nuc:
+        SetValue (dlg->sequence_type, 2);
+        break;
+      case Seqtype_constraint_prot:
+        SetValue (dlg->sequence_type, 3);
+        break;
+      default:
+        SetValue (dlg->sequence_type, 1);
+        break;
+     }
+  }
+  ChangeLocationConstraintDialogPopup (dlg->strand);
+}
+
+
+static Pointer DialogToLocationConstraint (DialoG d)
+{
+  LocationConstraintDialogPtr dlg;
+  LocationConstraintPtr l;
+
+  dlg = (LocationConstraintDialogPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  l = LocationConstraintNew();
+  if (l != NULL) {
+    switch (GetValue (dlg->strand)) {
+      case 1:
+        l->strand = Strand_constraint_any;
+        break;
+      case 2:
+        l->strand = Strand_constraint_plus;
+        break;
+      case 3:
+        l->strand = Strand_constraint_minus;
+        break;
+      default:
+        l->strand = Strand_constraint_any;
+        break;
+    }
+    switch (GetValue (dlg->sequence_type)) {
+      case 1:
+        l->seq_type = Seqtype_constraint_any;
+        break;
+      case 2:
+        l->seq_type = Seqtype_constraint_nuc;
+        break;
+      case 3:
+        l->seq_type = Seqtype_constraint_prot;
+        break;
+      default:
+        l->seq_type = Seqtype_constraint_any;
+        break;
+     }
+  }
+  return l;
+}
+
+
+static ValNodePtr TestLocationConstraintDialog (DialoG d)
+{
+  LocationConstraintDialogPtr dlg;
+  ValNodePtr err_list = NULL;
+
+  dlg = (LocationConstraintDialogPtr) GetObjectExtra (d);
+  if (dlg != NULL) {
+    if (GetValue (dlg->sequence_type) == 1 && GetValue (dlg->strand) == 1) {
+      ValNodeAddPointer (&err_list, 0, "empty location constraint");
+    }
+  }
+  return err_list;
+}
+
+
+extern DialoG LocationConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+
+{
+  LocationConstraintDialogPtr dlg;
+  GrouP                     p;
+  ButtoN                    b = NULL;
+  
+  dlg = (LocationConstraintDialogPtr) MemNew (sizeof (LocationConstraintDialogData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, 4, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = LocationConstraintToDialog;
+  dlg->fromdialog = DialogToLocationConstraint;
+  dlg->testdialog = TestLocationConstraintDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  StaticPrompt (p, "on", 0, dialogTextHeight, systemFont, 'l');
+  dlg->strand = PopupList (p, TRUE, ChangeLocationConstraintDialogPopup);
+  SetObjectExtra (dlg->strand, dlg, NULL);
+  PopupItem (dlg->strand, "Any strand");
+  PopupItem (dlg->strand, "Plus strand");
+  PopupItem (dlg->strand, "Minus strand");
+  SetValue (dlg->strand, 1);
+  
+  StaticPrompt (p, "on", 0, dialogTextHeight, systemFont, 'l');
+  dlg->sequence_type = PopupList (p, TRUE, ChangeLocationConstraintDialogPopup);
+  SetObjectExtra (dlg->sequence_type, dlg, NULL);
+  PopupItem (dlg->sequence_type, "nucleotide and protein sequences");
+  PopupItem (dlg->sequence_type, "nucleotide sequences only");
+  PopupItem (dlg->sequence_type, "protein sequences only");
+  SetValue (dlg->sequence_type, 1);
+
+
+  return (DialoG) p;
+}
+
+
+typedef struct sourcequalchoicedialog
+{
+  DIALOG_MESSAGE_BLOCK
+  DialoG dlg;
+  DialoG loc_dlg;
+  DialoG orig_dlg;
+  GrouP  choice_type;
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer change_userdata;
+} SourceQualChoiceDialogData, PNTR SourceQualChoiceDialogPtr;
+
+
+static void ChangeSourceQualChoice (GrouP g)
+{
+  SourceQualChoiceDialogPtr dlg;
+  Int4 val;
+
+  dlg = (SourceQualChoiceDialogPtr) GetObjectExtra (g);
+  if (dlg == NULL || dlg->choice_type == NULL) return;
+
+  val = GetValue (dlg->choice_type);
+  switch (val) {
+    case 1:
+      Show (dlg->dlg);
+      Hide (dlg->loc_dlg);
+      Hide (dlg->orig_dlg);
+      break;
+    case 2:
+      Hide (dlg->dlg);
+      Show (dlg->loc_dlg);
+      Hide (dlg->orig_dlg);
+      break;
+    case 3:
+      Hide (dlg->dlg);
+      Hide (dlg->loc_dlg);
+      Show (dlg->orig_dlg);
+      break;
+    default:
+      Hide (dlg->dlg);
+      Hide (dlg->loc_dlg);
+      Hide (dlg->orig_dlg);
+      break;
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void SourceQualChoiceToDialog (DialoG d, Pointer data)
+{
+  SourceQualChoiceDialogPtr dlg;
+  ValNodePtr                vnp;
+  ValNode                   vn;
+
+  dlg = (SourceQualChoiceDialogPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+  vnp = (ValNodePtr) data;
+
+  if (vnp == NULL) {
+    SafeSetValue (dlg->choice_type, 1);
+    PointerToDialog (dlg->dlg, NULL);
+  } else if (vnp->choice == SourceQualChoice_textqual) {
+    SafeSetValue (dlg->choice_type, 1);
+    vn.choice = 0;
+    vn.next = NULL;
+    vn.data.ptrvalue = GetSourceQualName (vnp->data.intvalue);
+    PointerToDialog (dlg->dlg, &vn);
+  } else if (vnp->choice == SourceQualChoice_location) {
+    SafeSetValue (dlg->choice_type, 2);
+    vn.choice = vnp->data.intvalue;
+    vn.next = NULL;
+    vn.data.ptrvalue = NULL;
+    PointerToDialog (dlg->loc_dlg, &vn);
+  } else if (vnp->choice == SourceQualChoice_origin) {
+    SafeSetValue (dlg->choice_type, 3);
+    vn.choice = vnp->data.intvalue;
+    vn.next = NULL;
+    vn.data.ptrvalue = NULL;
+    PointerToDialog (dlg->orig_dlg, &vn);
+  }
+
+  ChangeSourceQualChoice (dlg->choice_type);
+}
+
+
+static Pointer DialogToSourceQualChoice (DialoG d)
+{
+  SourceQualChoiceDialogPtr dlg;
+  ValNodePtr                vnp, sqc = NULL;
+  Int4                      choice_type = SourceQualChoice_textqual;
+
+  dlg = (SourceQualChoiceDialogPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  if (dlg->choice_type == NULL) {
+    choice_type = SourceQualChoice_textqual;
+  } else {
+    switch (GetValue (dlg->choice_type)) {
+      case 1:
+        choice_type = SourceQualChoice_textqual;
+        break;
+      case 2:
+        choice_type = SourceQualChoice_location;
+        break;
+      case 3:
+        choice_type = SourceQualChoice_origin;
+        break;
+    }
+  }
+  switch (choice_type) {
+    case SourceQualChoice_textqual:
+      vnp = DialogToPointer (dlg->dlg);
+      if (vnp != NULL) { 
+        sqc = ValNodeNew (NULL);
+        sqc->choice = SourceQualChoice_textqual;
+        sqc->data.intvalue = GetSourceQualTypeByName (vnp->data.ptrvalue);
+      }
+      break;
+    case SourceQualChoice_location:
+      vnp = DialogToPointer (dlg->loc_dlg);
+      sqc = ValNodeNew (NULL);
+      sqc->choice = SourceQualChoice_location;
+      if (vnp == NULL) {
+        sqc->data.intvalue = 0;
+      } else {
+        sqc->data.intvalue = vnp->choice;
+      }
+      vnp = ValNodeFree (vnp);
+      break;
+    case SourceQualChoice_origin:
+      vnp = DialogToPointer (dlg->orig_dlg);
+      sqc = ValNodeNew (NULL);
+      sqc->choice = SourceQualChoice_origin;
+      if (vnp == NULL) { 
+        sqc->data.intvalue = 0;
+      } else {
+        sqc->data.intvalue = vnp->choice;
+      }
+      vnp = ValNodeFree (vnp);
+      break;
+  }
+  return sqc;
+}
+
+
+static ValNodePtr TestSourceQualChoiceDialog (DialoG d)
+{
+  SourceQualChoiceDialogPtr dlg;
+  ValNodePtr err_list = NULL;
+  Int4 val;
+
+  dlg = (SourceQualChoiceDialogPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  if (dlg->choice_type == NULL) {
+    err_list = TestDialog (dlg->dlg);
+  } else {
+    val = GetValue (dlg->choice_type);
+    switch (val) {
+      case 1:
+        err_list = TestDialog (dlg->dlg);
+        break;
+      case 2:
+        err_list = TestDialog (dlg->loc_dlg);
+        break;
+      case 3:
+        err_list = TestDialog (dlg->orig_dlg);
+        break;
+      default:
+        ValNodeAddPointer (&err_list, 0, "no source qual choice");
+        break;
+    }
+  }
+  return err_list;
+}
+
+
+static DialoG SourceQualChoiceDialog (GrouP h, Boolean text_only, Boolean for_remove, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  SourceQualChoiceDialogPtr dlg;
+  GrouP                     p, g;
+  ValNodePtr                qual_list, loc_list, orig_list;
+  ButtoN                    b1, b2, b3;
+  ValNode                   vn;
+  
+  dlg = (SourceQualChoiceDialogPtr) MemNew (sizeof (SourceQualChoiceDialogData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, 2, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = SourceQualChoiceToDialog;
+  dlg->fromdialog = DialogToSourceQualChoice;
+  dlg->testdialog = TestSourceQualChoiceDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  if (!text_only) {
+    dlg->choice_type = HiddenGroup (p, 0, 3, ChangeSourceQualChoice);
+    SetObjectExtra (dlg->choice_type, dlg, NULL);
+    b1 = RadioButton (dlg->choice_type, "Text Qualifier");
+    b2 = RadioButton (dlg->choice_type, "Location");
+    b3 = RadioButton (dlg->choice_type, "Origin");
+  }
+  g = HiddenGroup (p, 0, 0, NULL);
+  qual_list = GetSourceQualList ();
+  dlg->dlg = ValNodeSelectionDialog (g, qual_list, SHORT_SELECTION_LIST,
+                                               ValNodeStringName,
+                                               ValNodeSimpleDataFree,
+                                               ValNodeStringCopy,
+                                               ValNodeStringMatch,
+                                               "source qual",
+                                               change_notify, change_userdata, FALSE);
+  if (!text_only) {
+    loc_list = GetLocationList (for_remove);
+    dlg->loc_dlg = ValNodeSelectionDialog (g, loc_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+    if (for_remove) {
+      vn.choice = Source_location_unknown;
+      vn.data.ptrvalue = NULL;
+      vn.next = NULL;
+      PointerToDialog (dlg->loc_dlg, &vn);
+    }
+    orig_list = GetOriginList (for_remove);
+    dlg->orig_dlg = ValNodeSelectionDialog (g, orig_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "origin", 
+                                           change_notify, change_userdata, FALSE);
+    if (for_remove) {
+      vn.choice = Source_origin_unknown;
+      vn.data.ptrvalue = NULL;
+      vn.next = NULL;
+      PointerToDialog (dlg->orig_dlg, &vn);
+    }
+  }
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->dlg, (HANDLE) dlg->loc_dlg, (HANDLE) dlg->orig_dlg, NULL);
+
+  ChangeSourceQualChoice (dlg->choice_type);
+
+  return (DialoG) p;
+}
+
+
+typedef struct sourceconstraintdialog 
+{
+  DIALOG_MESSAGE_BLOCK
+  GrouP  constraint_type;
+
+  DialoG qual_present;
+  GrouP sc_group;
+  DialoG qual_string;
+  DialoG string_constraint;
+  GrouP match_group;
+  DialoG qualmatch1;
+  DialoG qualmatch2;
+
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer change_userdata;
+} SourceConstraintDialogData, PNTR SourceConstraintDialogPtr;
+
+
+static void ChangeSourceConstraintType (GrouP p)
+{
+  SourceConstraintDialogPtr dlg;
+  Int4                      constraint_type;
+
+  dlg = (SourceConstraintDialogPtr) GetObjectExtra (p);
+  if (dlg == NULL)
+  {
+    return;
+  }
+  Hide (dlg->qual_present);
+  Hide (dlg->sc_group);
+  Hide (dlg->match_group);
+  constraint_type = GetValue (dlg->constraint_type);
+  switch (constraint_type) {
+    case 1:
+      Show (dlg->qual_present);
+      break;
+    case 2:
+      Show (dlg->sc_group);
+      break;
+    case 3:
+      Show (dlg->match_group);
+      break;
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify)(dlg->change_userdata);
+  }
+}
+
+
+static void SourceConstraintToDialog (DialoG d, Pointer data)
+{
+  SourceConstraintDialogPtr dlg;
+  SourceConstraintPtr s;
+
+  dlg = (SourceConstraintDialogPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  s = (SourceConstraintPtr) data;
+  SetValue (dlg->constraint_type, 1);
+  PointerToDialog (dlg->qual_present, NULL);
+  PointerToDialog (dlg->qual_string, NULL);
+  PointerToDialog (dlg->string_constraint, NULL);
+  PointerToDialog (dlg->qualmatch1, NULL);
+  PointerToDialog (dlg->qualmatch2, NULL);
+  if (s != NULL) {
+    if (s->field1 != NULL && s->field2 != NULL) {
+      SetValue (dlg->constraint_type, 3);
+      PointerToDialog (dlg->qualmatch1, s->field1);
+      PointerToDialog (dlg->qualmatch2, s->field2);
+    } else if ((s->field1 != NULL || s->field2 != NULL) && s->constraint != NULL) {
+      SetValue (dlg->constraint_type, 2);
+      if (s->field1 != NULL) {
+        PointerToDialog (dlg->qual_string, s->field1);
+      } else if (s->field2 != NULL) {
+        PointerToDialog (dlg->qual_string, s->field2);
+      }
+      PointerToDialog (dlg->string_constraint, s->constraint);
+    } else if (s->field1 != NULL || s->field2 != NULL) {
+      SetValue (dlg->constraint_type, 1);
+      if (s->field1 != NULL) {
+        PointerToDialog (dlg->qual_present, s->field1);
+      } else if (s->field2 != NULL) {
+        PointerToDialog (dlg->qual_present, s->field2);
+      }
+    }
+  }
+  ChangeSourceConstraintType (dlg->constraint_type);
+}
+
+
+static Pointer DialogToSourceConstraint (DialoG d)
+{
+  SourceConstraintDialogPtr dlg;
+  SourceConstraintPtr s = NULL;
+  Int2                constraint_type;
+
+  dlg = (SourceConstraintDialogPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  
+  constraint_type = GetValue (dlg->constraint_type);
+  switch (constraint_type) {
+    case 1:
+      s = SourceConstraintNew();
+      s->field1 = DialogToPointer (dlg->qual_present);
+      break;
+    case 2:
+      s = SourceConstraintNew();
+      s->field1 = DialogToPointer (dlg->qual_string);
+      s->constraint = DialogToPointer (dlg->string_constraint);
+      break;
+    case 3:
+      s = SourceConstraintNew();
+      s->field1 = DialogToPointer (dlg->qualmatch1);
+      s->field2 = DialogToPointer (dlg->qualmatch2);
+      break;
+  }
+  return s;
+}
+
+
+static ValNodePtr TestSourceConstraintDialog (DialoG d)
+{
+  SourceConstraintPtr constraint;
+  ValNodePtr err_list = NULL;
+
+  constraint = DialogToPointer (d);
+  if (IsSourceConstraintEmpty (constraint)) {
+    ValNodeAddPointer (&err_list, 0, "empty source constraint");
+  }
+  constraint = SourceConstraintFree (constraint);
+  return err_list;
+}
+
+
+static DialoG SourceConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+
+{
+  SourceConstraintDialogPtr dlg;
+  GrouP                     p, g;
+  ButtoN                    b = NULL;
+  ButtoN                    b1, b2, b3;
+  
+  dlg = (SourceConstraintDialogPtr) MemNew (sizeof (SourceConstraintDialogData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = SourceConstraintToDialog;
+  dlg->fromdialog = DialogToSourceConstraint;
+  dlg->testdialog = TestSourceConstraintDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->constraint_type = HiddenGroup (p, 3, 0, ChangeSourceConstraintType);
+  SetObjectExtra (dlg->constraint_type, dlg, NULL);
+  b1 = RadioButton (dlg->constraint_type, "When qualifier present");
+  b2 = RadioButton (dlg->constraint_type, "String constraint");
+  b3 = RadioButton (dlg->constraint_type, "When qualifiers match");
+
+  g = HiddenGroup (p, 0, 0, NULL);
+  
+  dlg->qual_present = SourceQualChoiceDialog (g, TRUE, FALSE, change_notify, change_userdata);
+
+  dlg->sc_group = HiddenGroup (g, 2, 0, NULL);
+  dlg->qual_string = SourceQualChoiceDialog (dlg->sc_group, TRUE, FALSE, change_notify, change_userdata);
+  dlg->string_constraint = StringConstraintDialog (dlg->sc_group, NULL, FALSE, change_notify, change_userdata);
+
+  dlg->match_group = HiddenGroup (g, 3, 0, NULL);
+  dlg->qualmatch1 = SourceQualChoiceDialog (dlg->match_group, TRUE, FALSE, change_notify, change_userdata);
+  StaticPrompt (dlg->match_group, "Equals", 0, dialogTextHeight, systemFont, 'l');
+  dlg->qualmatch2 = SourceQualChoiceDialog (dlg->match_group, TRUE, FALSE, change_notify, change_userdata);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->qual_present, (HANDLE) dlg->sc_group, (HANDLE) dlg->match_group, NULL);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->constraint_type, (HANDLE) g, NULL);    
+    
+  SetValue (dlg->constraint_type, 1);
+  ChangeSourceConstraintType (dlg->constraint_type); 
+  return (DialoG) p;
+}
+
+
+static DialoG CDSGeneProtFieldDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
+
+
+typedef struct cdsgeneprotpseudoconstraintdlg {
+  DIALOG_MESSAGE_BLOCK
+  DialoG feat;
+  GrouP  pseudo;
+} CDSGeneProtPseudoConstraintDlgData, PNTR CDSGeneProtPseudoConstraintDlgPtr;
+
+
+static void CDSGeneProtPseudoConstraintToDialog (DialoG d, Pointer data)
+{
+  CDSGeneProtPseudoConstraintDlgPtr dlg;
+  CDSGeneProtPseudoConstraintPtr pseudo;
+  ValNode vn;
+
+  dlg = (CDSGeneProtPseudoConstraintDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) {
+    return;
+  }
+
+  pseudo = (CDSGeneProtPseudoConstraintPtr) data;
+
+  if (pseudo == NULL) {
+    PointerToDialog (dlg->feat, NULL);
+    SetValue (dlg->pseudo, 1);
+  } else {
+    vn.choice = pseudo->feature;
+    vn.data.ptrvalue = NULL;
+    vn.next = NULL;
+    PointerToDialog (dlg->feat, &vn);
+    if (pseudo->is_pseudo) {
+      SetValue (dlg->pseudo, 1);
+    } else {
+      SetValue (dlg->pseudo, 2);
+    }
+  }
+}
+
+
+static Pointer DialogToCDSGeneProtPseudoConstraint (DialoG d)
+{
+  CDSGeneProtPseudoConstraintDlgPtr dlg;
+  CDSGeneProtPseudoConstraintPtr constraint;
+  Uint2 feat_type;
+  ValNodePtr vnp;
+  Int2       val;
+
+  dlg = (CDSGeneProtPseudoConstraintDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) {
+    return NULL;
+  }
+
+  val = GetValue (dlg->pseudo);
+  if (val < 1 || val > 2) {
+    return NULL;
+  }
+  vnp = (ValNodePtr) DialogToPointer (dlg->feat);
+  if (vnp == NULL) return NULL;
+  feat_type = vnp->choice;
+  vnp = ValNodeFree (vnp);
+
+  constraint = CDSGeneProtPseudoConstraintNew ();
+  constraint->feature = feat_type;
+  constraint->is_pseudo = val == 1 ? TRUE : FALSE;
+  
+  return (Pointer) constraint;
+}
+
+
+static ValNodePtr TestCDSGeneProtPseudoConstraintDialog (DialoG d)
+{
+  CDSGeneProtPseudoConstraintDlgPtr dlg;
+  ValNodePtr err_list = NULL;
+  Int4       val;
+
+  dlg = (CDSGeneProtPseudoConstraintDlgPtr) GetObjectExtra (d);
+  if (dlg != NULL) {
+    val = GetValue (dlg->pseudo);
+    if (val < 1 || val > 2) {
+      ValNodeAddPointer (&err_list, 0, "pseudo");
+    }
+    ValNodeLink (&err_list, TestDialog (dlg->feat));
+  }
+  return err_list;
+}
+
+static DialoG CDSGeneProtPseudoConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  CDSGeneProtPseudoConstraintDlgPtr dlg;
+  ValNodePtr feat_list = NULL;
+  GrouP p;
+  
+  p = HiddenGroup (h, -1, 0, NULL);
+  dlg = (CDSGeneProtPseudoConstraintDlgPtr) MemNew (sizeof (CDSGeneProtPseudoConstraintDlgData));
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = CDSGeneProtPseudoConstraintToDialog;
+  dlg->fromdialog = DialogToCDSGeneProtPseudoConstraint;
+  dlg->testdialog = TestCDSGeneProtPseudoConstraintDialog;
+
+  AddAllCDSGeneProtFeaturesToChoiceList (&feat_list);
+  dlg->feat = ValNodeSelectionDialog (p, feat_list, TALL_SELECTION_LIST, ValNodeStringName,
+                                ValNodeSimpleDataFree, ValNodeStringCopy,
+                                ValNodeChoiceMatch, "feature type", 
+                                change_notify, change_userdata, FALSE);
+
+  dlg->pseudo = HiddenGroup (p, 2, 0, NULL);
+  RadioButton (dlg->pseudo, "Is pseudo");
+  RadioButton (dlg->pseudo, "Is not pseudo");
+  SetValue (dlg->pseudo, 1);
+  return (DialoG) p;
+}
+
+
+typedef struct cdsgeneprotqualconstraintdialog 
+{
+  DIALOG_MESSAGE_BLOCK
+  GrouP  constraint_type;
+
+  DialoG qual_present;
+  GrouP sc_group;
+  DialoG qual_string;
+  DialoG string_constraint;
+  GrouP match_group;
+  DialoG qualmatch1;
+  DialoG qualmatch2;
+
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer change_userdata;
+} CDSGeneProtQualConstraintDialogData, PNTR CDSGeneProtQualConstraintDialogPtr;
+
+
+static void ChangeCDSGeneProtQualConstraintType (GrouP p)
+{
+  CDSGeneProtQualConstraintDialogPtr dlg;
+  Int4                      constraint_type;
+
+  dlg = (CDSGeneProtQualConstraintDialogPtr) GetObjectExtra (p);
+  if (dlg == NULL)
+  {
+    return;
+  }
+  Hide (dlg->qual_present);
+  Hide (dlg->sc_group);
+  Hide (dlg->match_group);
+  constraint_type = GetValue (dlg->constraint_type);
+  switch (constraint_type) {
+    case 1:
+      Show (dlg->qual_present);
+      break;
+    case 2:
+      Show (dlg->sc_group);
+      break;
+    case 3:
+      Show (dlg->match_group);
+      break;
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void CDSGeneProtQualConstraintToDialog (DialoG d, Pointer data)
+{
+  CDSGeneProtQualConstraintDialogPtr dlg;
+  CDSGeneProtQualConstraintPtr s;
+
+  dlg = (CDSGeneProtQualConstraintDialogPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  s = (CDSGeneProtQualConstraintPtr) data;
+  SetValue (dlg->constraint_type, 1);
+  PointerToDialog (dlg->qual_present, NULL);
+  PointerToDialog (dlg->qual_string, NULL);
+  PointerToDialog (dlg->string_constraint, NULL);
+  PointerToDialog (dlg->qualmatch1, NULL);
+  PointerToDialog (dlg->qualmatch2, NULL);
+  if (s != NULL) {
+    if (s->field1 != NULL && s->field2 != NULL) {
+      SetValue (dlg->constraint_type, 3);
+      PointerToDialog (dlg->qualmatch1, s->field1);
+      PointerToDialog (dlg->qualmatch2, s->field2);
+    } else if ((s->field1 != NULL || s->field2 != NULL) && s->constraint != NULL) {
+      SetValue (dlg->constraint_type, 2);
+      if (s->field1 != NULL) {
+        PointerToDialog (dlg->qual_string, s->field1);
+      } else if (s->field2 != NULL) {
+        PointerToDialog (dlg->qual_string, s->field2);
+      }
+      PointerToDialog (dlg->string_constraint, s->constraint);
+    } else if (s->field1 != NULL || s->field2 != NULL) {
+      SetValue (dlg->constraint_type, 1);
+      if (s->field1 != NULL) {
+        PointerToDialog (dlg->qual_present, s->field1);
+      } else if (s->field2 != NULL) {
+        PointerToDialog (dlg->qual_present, s->field2);
+      }
+    }
+  }
+  ChangeCDSGeneProtQualConstraintType (dlg->constraint_type);
+}
+
+
+static Pointer DialogToCDSGeneProtQualConstraint (DialoG d)
+{
+  CDSGeneProtQualConstraintDialogPtr dlg;
+  CDSGeneProtQualConstraintPtr s = NULL;
+  Int2                constraint_type;
+
+  dlg = (CDSGeneProtQualConstraintDialogPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  
+  constraint_type = GetValue (dlg->constraint_type);
+  switch (constraint_type) {
+    case 1:
+      s = CDSGeneProtQualConstraintNew();
+      s->field1 = DialogToPointer (dlg->qual_present);
+      break;
+    case 2:
+      s = CDSGeneProtQualConstraintNew();
+      s->field1 = DialogToPointer (dlg->qual_string);
+      s->constraint = DialogToPointer (dlg->string_constraint);
+      break;
+    case 3:
+      s = CDSGeneProtQualConstraintNew();
+      s->field1 = DialogToPointer (dlg->qualmatch1);
+      s->field2 = DialogToPointer (dlg->qualmatch2);
+      break;
+  }
+  return s;
+}
+
+
+static ValNodePtr TestCDSGeneProtQualConstraintDialog (DialoG d)
+{
+  CDSGeneProtQualConstraintPtr constraint;
+  ValNodePtr err_list = NULL;
+
+  constraint = DialogToPointer (d);
+  if (IsCDSGeneProtQualConstraintEmpty (constraint)) {
+    ValNodeAddPointer (&err_list, 0, "empty CDS-gene-prot qual constraint");
+  }
+  constraint = CDSGeneProtQualConstraintFree (constraint);
+  return err_list;
+}
+
+  
+static DialoG CDSGeneProtQualConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+
+{
+  CDSGeneProtQualConstraintDialogPtr dlg;
+  GrouP                     p, g;
+  ButtoN                    b = NULL;
+  ButtoN                    b1, b2, b3;
+  
+  dlg = (CDSGeneProtQualConstraintDialogPtr) MemNew (sizeof (CDSGeneProtQualConstraintDialogData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = CDSGeneProtQualConstraintToDialog;
+  dlg->fromdialog = DialogToCDSGeneProtQualConstraint;
+  dlg->testdialog = TestCDSGeneProtQualConstraintDialog;
+
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->constraint_type = HiddenGroup (p, 3, 0, ChangeCDSGeneProtQualConstraintType);
+  SetObjectExtra (dlg->constraint_type, dlg, NULL);
+  b1 = RadioButton (dlg->constraint_type, "When qualifier present");
+  b2 = RadioButton (dlg->constraint_type, "String constraint");
+  b3 = RadioButton (dlg->constraint_type, "When qualifiers match");
+
+  g = HiddenGroup (p, 0, 0, NULL);
+  
+  dlg->qual_present = CDSGeneProtFieldDialog (g, change_notify, change_userdata);
+
+  dlg->sc_group = HiddenGroup (g, 2, 0, NULL);
+  dlg->qual_string = CDSGeneProtFieldDialog (dlg->sc_group, change_notify, change_userdata);
+  dlg->string_constraint = StringConstraintDialog (dlg->sc_group, NULL, FALSE, change_notify, change_userdata);
+
+  dlg->match_group = HiddenGroup (g, 3, 0, NULL);
+  dlg->qualmatch1 = CDSGeneProtFieldDialog (dlg->match_group, change_notify, change_userdata);
+  StaticPrompt (dlg->match_group, "Equals", 0, dialogTextHeight, systemFont, 'l');
+  dlg->qualmatch2 = CDSGeneProtFieldDialog (dlg->match_group, change_notify, change_userdata);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->qual_present, (HANDLE) dlg->sc_group, (HANDLE) dlg->match_group, NULL);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->constraint_type, (HANDLE) g, NULL);    
+  SetValue (dlg->constraint_type, 1);
+  ChangeCDSGeneProtQualConstraintType (dlg->constraint_type); 
+  return (DialoG) p;
+}
+
+
+typedef struct sequencequaldlg {
+  DIALOG_MESSAGE_BLOCK
+  PopuP field_type;
+  DialoG molecule_dlg;
+  DialoG technique_dlg;
+  DialoG completedness_dlg;
+  DialoG mol_class_dlg;
+  DialoG topology_dlg;
+  DialoG strand_dlg;
+
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer change_userdata;
+} SequenceQualDlgData, PNTR SequenceQualDlgPtr;
+
+
+static void ChangeSequenceQualType (PopuP p)
+{
+  SequenceQualDlgPtr dlg;
+  Int2               val;
+
+  dlg = (SequenceQualDlgPtr) GetObjectExtra (p);
+  if (dlg == NULL) return;
+
+  Hide (dlg->molecule_dlg);
+  Hide (dlg->technique_dlg);
+  Hide (dlg->completedness_dlg);
+  Hide (dlg->mol_class_dlg);
+  Hide (dlg->topology_dlg);
+  Hide (dlg->strand_dlg);
+
+  val = GetValue (dlg->field_type);
+  switch (val) {
+    case 1:
+      Show (dlg->molecule_dlg);
+      break;
+    case 2:
+      Show (dlg->technique_dlg);
+      break;
+    case 3:
+      Show (dlg->completedness_dlg);
+      break;
+    case 4:
+      Show (dlg->mol_class_dlg);
+      break;
+    case 5:
+      Show (dlg->topology_dlg);
+      break;
+    case 6:
+      Show (dlg->strand_dlg);
+      break;
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void SequenceQualToDialog (DialoG d, Pointer data)
+{
+  SequenceQualDlgPtr dlg;
+  ValNodePtr         field;
+  ValNode            vn;
+
+  dlg = (SequenceQualDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  field = (ValNodePtr) data;
+
+  if (field == NULL) {
+    SetValue (dlg->field_type, 1);
+    PointerToDialog (dlg->molecule_dlg, NULL);
+  } else {
+    vn.next = NULL;
+    vn.data.ptrvalue = NULL;
+
+    switch (field->choice) {
+      case MolinfoField_molecule:
+        SetValue (dlg->field_type, 1);
+        vn.choice = field->data.intvalue;
+        PointerToDialog (dlg->molecule_dlg, &vn);
+        break;
+      case MolinfoField_technique:
+        SetValue (dlg->field_type, 2);
+        vn.choice = field->data.intvalue;
+        PointerToDialog (dlg->technique_dlg, &vn);
+        break;
+      case MolinfoField_completedness:
+        SetValue (dlg->field_type, 3);
+        vn.choice = field->data.intvalue;
+        PointerToDialog (dlg->completedness_dlg, &vn);
+        break;
+      case MolinfoField_mol_class:
+        SetValue (dlg->field_type, 4);
+        vn.choice = field->data.intvalue;
+        PointerToDialog (dlg->mol_class_dlg, &vn);
+        break;
+      case MolinfoField_topology:
+        SetValue (dlg->field_type, 5);
+        vn.choice = field->data.intvalue;
+        PointerToDialog (dlg->topology_dlg, &vn);
+        break;
+      case MolinfoField_strand:
+        SetValue (dlg->field_type, 6);
+        vn.choice = field->data.intvalue;
+        PointerToDialog (dlg->strand_dlg, &vn);
+        break;
+      default:
+        SetValue (dlg->field_type, 1);
+        PointerToDialog (dlg->molecule_dlg, NULL);
+        break;
+    }
+  }
+  ChangeSequenceQualType (dlg->field_type);
+}
+
+
+static Pointer DialogToSequenceQual (DialoG d)
+{
+  SequenceQualDlgPtr dlg;
+  ValNodePtr         field = NULL, vnp;
+  Int2               val;
+
+  dlg = (SequenceQualDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  val = GetValue (dlg->field_type);
+  switch (val) {
+    case 1:
+      vnp = DialogToPointer (dlg->molecule_dlg);
+      if (vnp != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoField_molecule;
+        field->data.intvalue = vnp->choice;
+        vnp = ValNodeFree (vnp);
+      }
+      break;
+    case 2:
+      vnp = DialogToPointer (dlg->technique_dlg);
+      if (vnp != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoField_technique;
+        field->data.intvalue = vnp->choice;
+        vnp = ValNodeFree (vnp);
+      }
+      break;
+    case 3:
+      vnp = DialogToPointer (dlg->completedness_dlg);
+      if (vnp != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoField_completedness;
+        field->data.intvalue = vnp->choice;
+        vnp = ValNodeFree (vnp);
+      }
+      break;
+    case 4:
+      vnp = DialogToPointer (dlg->mol_class_dlg);
+      if (vnp != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoField_mol_class;
+        field->data.intvalue = vnp->choice;
+        vnp = ValNodeFree (vnp);
+      }
+      break;
+    case 5:
+      vnp = DialogToPointer (dlg->topology_dlg);
+      if (vnp != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoField_topology;
+        field->data.intvalue = vnp->choice;
+        vnp = ValNodeFree (vnp);
+      }
+      break;
+    case 6:
+      vnp = DialogToPointer (dlg->strand_dlg);
+      if (vnp != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoField_strand;
+        field->data.intvalue = vnp->choice;
+        vnp = ValNodeFree (vnp);
+      }
+      break;
+  }
+
+  return field;    
+  
+}
+
+
+static ValNodePtr TestSequenceQualDialog (DialoG d)
+{
+  SequenceQualDlgPtr dlg;
+  Int2               val;
+  ValNodePtr         err_list = NULL;
+
+  dlg = (SequenceQualDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  val = GetValue (dlg->field_type);
+  if (val < 1 || val > 6) {
+  }
+  switch (val) {
+    case 1:
+      err_list = TestDialog (dlg->molecule_dlg);
+      break;
+    case 2:
+      err_list = TestDialog (dlg->technique_dlg);
+      break;
+    case 3:
+      err_list = TestDialog (dlg->completedness_dlg);
+      break;
+    case 4:
+      err_list = TestDialog (dlg->mol_class_dlg);
+      break;
+    case 5:
+      err_list = TestDialog (dlg->topology_dlg);
+      break;
+    case 6:
+      err_list = TestDialog (dlg->strand_dlg);
+      break;
+    default:
+      ValNodeAddPointer (&err_list, 0, StringSave ("field type"));
+      break;
+  }
+
+  return err_list;
+}
+
+
+static DialoG SequenceQualDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+
+{
+  SequenceQualDlgPtr dlg;
+  GrouP              p, g;
+  ValNodePtr         val_list;
+  
+  dlg = (SequenceQualDlgPtr) MemNew (sizeof (SequenceQualDlgData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = SequenceQualToDialog;
+  dlg->fromdialog = DialogToSequenceQual;
+  dlg->testdialog = TestSequenceQualDialog;
+
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->field_type = PopupList (p, TRUE, ChangeSequenceQualType);
+  SetObjectExtra (dlg->field_type, dlg, NULL);
+  PopupItem (dlg->field_type, "molecule");
+  PopupItem (dlg->field_type, "technique");
+  PopupItem (dlg->field_type, "completedness");
+  PopupItem (dlg->field_type, "class");
+  PopupItem (dlg->field_type, "topology");
+  PopupItem (dlg->field_type, "strand");
+  SetValue (dlg->field_type, 1);
+
+  g = HiddenGroup (p, 0, 0, NULL);
+  
+  val_list = GetMoleculeTypeList ();
+  dlg->molecule_dlg = ValNodeSelectionDialog (g, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetTechniqueTypeList ();
+  dlg->technique_dlg = ValNodeSelectionDialog (g, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetCompletednessTypeList ();
+  dlg->completedness_dlg = ValNodeSelectionDialog (g, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetMoleculeClassTypeList ();
+  dlg->mol_class_dlg = ValNodeSelectionDialog (g, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetTopologyTypeList ();
+  dlg->topology_dlg = ValNodeSelectionDialog (g, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetStrandTypeList ();
+  dlg->strand_dlg = ValNodeSelectionDialog (g, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+
+  AlignObjects (ALIGN_MIDDLE, (HANDLE) dlg->molecule_dlg, 
+                              (HANDLE) dlg->technique_dlg,
+                              (HANDLE) dlg->completedness_dlg,
+                              (HANDLE) dlg->mol_class_dlg,
+                              (HANDLE) dlg->topology_dlg,
+                              (HANDLE) dlg->strand_dlg,
+                              NULL);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->field_type, (HANDLE) g, NULL);    
+  ChangeSequenceQualType (dlg->field_type); 
+  return (DialoG) p;
+}
+
+
+typedef struct sequencequalpairdlg {
+  DIALOG_MESSAGE_BLOCK
+  PopuP field_type;
+  GrouP molecule_grp;
+  DialoG molecule_from_dlg;
+  DialoG molecule_to_dlg;
+  GrouP technique_grp;
+  DialoG technique_from_dlg;
+  DialoG technique_to_dlg;
+  GrouP completedness_grp;
+  DialoG completedness_from_dlg;
+  DialoG completedness_to_dlg;
+  GrouP mol_class_grp;
+  DialoG mol_class_from_dlg;
+  DialoG mol_class_to_dlg;
+  GrouP topology_grp;
+  DialoG topology_from_dlg;
+  DialoG topology_to_dlg;
+  GrouP strand_grp;
+  DialoG strand_from_dlg;
+  DialoG strand_to_dlg;
+
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer change_userdata;
+} SequenceQualPairDlgData, PNTR SequenceQualPairDlgPtr;
+
+
+static void ChangeSequenceQualPairType (PopuP p)
+{
+  SequenceQualPairDlgPtr dlg;
+  Int2                   val;
+
+  dlg = (SequenceQualPairDlgPtr) GetObjectExtra (p);
+  if (dlg == NULL) return;
+
+  Hide (dlg->molecule_grp);
+  Hide (dlg->technique_grp);
+  Hide (dlg->completedness_grp);
+  Hide (dlg->mol_class_grp);
+  Hide (dlg->topology_grp);
+  Hide (dlg->strand_grp);
+
+  val = GetValue (dlg->field_type);
+  switch (val) {
+    case 1:
+      Show (dlg->molecule_grp);
+      break;
+    case 2:
+      Show (dlg->technique_grp);
+      break;
+    case 3:
+      Show (dlg->completedness_grp);
+      break;
+    case 4:
+      Show (dlg->mol_class_grp);
+      break;
+    case 5:
+      Show (dlg->topology_grp);
+      break;
+    case 6:
+      Show (dlg->strand_grp);
+      break;
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void SequenceQualPairToDialog (DialoG d, Pointer data)
+{
+  SequenceQualPairDlgPtr dlg;
+  ValNodePtr m_fields;
+  ValNode    vn;
+
+  dlg = (SequenceQualPairDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  m_fields = (ValNodePtr) data;
+  if (m_fields == NULL) {
+    SetValue (dlg->field_type, 1);
+    PointerToDialog (dlg->molecule_from_dlg, NULL);
+    PointerToDialog (dlg->molecule_to_dlg, NULL);
+  } else {
+    vn.data.ptrvalue = NULL;
+    vn.next = NULL;
+    switch (m_fields->choice) {
+      case MolinfoFieldPair_molecule:
+        SetValue (dlg->field_type, 1);
+        if (m_fields->data.ptrvalue == NULL) {
+          PointerToDialog (dlg->molecule_from_dlg, NULL);
+          PointerToDialog (dlg->molecule_to_dlg, NULL);
+        } else {
+          vn.choice = ((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->from;
+          PointerToDialog (dlg->molecule_from_dlg, &vn);
+          vn.choice = ((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->to;
+          PointerToDialog (dlg->molecule_to_dlg, &vn);
+        }
+        break;
+      case MolinfoFieldPair_technique:
+        SetValue (dlg->field_type, 2);
+        if (m_fields->data.ptrvalue == NULL) {
+          PointerToDialog (dlg->technique_from_dlg, NULL);
+          PointerToDialog (dlg->technique_to_dlg, NULL);
+        } else {
+          vn.choice = ((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->from;
+          PointerToDialog (dlg->technique_from_dlg, &vn);
+          vn.choice = ((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->to;
+          PointerToDialog (dlg->technique_to_dlg, &vn);
+        }
+        break;
+      case MolinfoFieldPair_completedness:
+        SetValue (dlg->field_type, 3);
+        if (m_fields->data.ptrvalue == NULL) {
+          PointerToDialog (dlg->completedness_from_dlg, NULL);
+          PointerToDialog (dlg->completedness_to_dlg, NULL);
+        } else {
+          vn.choice = ((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->from;
+          PointerToDialog (dlg->completedness_from_dlg, &vn);
+          vn.choice = ((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->to;
+          PointerToDialog (dlg->completedness_to_dlg, &vn);
+        }
+        break;
+      case MolinfoFieldPair_mol_class:
+        SetValue (dlg->field_type, 4);
+        if (m_fields->data.ptrvalue == NULL) {
+          PointerToDialog (dlg->mol_class_from_dlg, NULL);
+          PointerToDialog (dlg->mol_class_to_dlg, NULL);
+        } else {
+          vn.choice = ((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->from;
+          PointerToDialog (dlg->mol_class_from_dlg, &vn);
+          vn.choice = ((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->to;
+          PointerToDialog (dlg->mol_class_to_dlg, &vn);
+        }
+        break;
+      case MolinfoFieldPair_topology:
+        SetValue (dlg->field_type, 5);
+        if (m_fields->data.ptrvalue == NULL) {
+          PointerToDialog (dlg->topology_from_dlg, NULL);
+          PointerToDialog (dlg->topology_to_dlg, NULL);
+        } else {
+          vn.choice = ((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->from;
+          PointerToDialog (dlg->topology_from_dlg, &vn);
+          vn.choice = ((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->to;
+          PointerToDialog (dlg->topology_to_dlg, &vn);
+        }
+        break;
+      case MolinfoFieldPair_strand:
+        SetValue (dlg->field_type, 6);
+        if (m_fields->data.ptrvalue == NULL) {
+          PointerToDialog (dlg->strand_from_dlg, NULL);
+          PointerToDialog (dlg->strand_to_dlg, NULL);
+        } else {
+          vn.choice = ((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->from;
+          PointerToDialog (dlg->strand_from_dlg, &vn);
+          vn.choice = ((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->to;
+          PointerToDialog (dlg->strand_to_dlg, &vn);
+        }
+        break;
+      default:
+        SetValue (dlg->field_type, 1);
+        PointerToDialog (dlg->molecule_from_dlg, NULL);
+        PointerToDialog (dlg->molecule_to_dlg, NULL);
+        break;
+    }
+  }
+}
+
+
+static Pointer DialogToSequenceQualPair (DialoG d)
+{
+  SequenceQualPairDlgPtr dlg;
+  Int2                   val;
+  ValNodePtr             field = NULL, vnp_from, vnp_to;
+  MolinfoMoleculePairPtr mol;
+  MolinfoTechniquePairPtr tech;
+  MolinfoCompletednessPairPtr comp;
+  MolinfoMolClassPairPtr mol_class;
+  MolinfoTopologyPairPtr topology;
+  MolinfoStrandPairPtr   strand;
+
+  dlg = (SequenceQualPairDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  val = GetValue (dlg->field_type);
+  switch (val) {
+    case 1:
+      vnp_from = DialogToPointer (dlg->molecule_from_dlg);
+      vnp_to = DialogToPointer (dlg->molecule_to_dlg);
+      if (vnp_from != NULL && vnp_to != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoFieldPair_molecule;
+        mol = MolinfoMoleculePairNew ();
+        mol->from = vnp_from->choice;
+        mol->to = vnp_to->choice;
+        field->data.ptrvalue = mol;
+      }
+      vnp_from = ValNodeFree (vnp_from);
+      vnp_to = ValNodeFree (vnp_to);
+      break;
+    case 2:
+      vnp_from = DialogToPointer (dlg->technique_from_dlg);
+      vnp_to = DialogToPointer (dlg->technique_to_dlg);
+      if (vnp_from != NULL && vnp_to != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoFieldPair_technique;
+        tech = MolinfoTechniquePairNew ();
+        tech->from = vnp_from->choice;
+        tech->to = vnp_to->choice;
+        field->data.ptrvalue = tech;
+      }
+      vnp_from = ValNodeFree (vnp_from);
+      vnp_to = ValNodeFree (vnp_to);
+      break;
+    case 3:
+      vnp_from = DialogToPointer (dlg->completedness_from_dlg);
+      vnp_to = DialogToPointer (dlg->completedness_to_dlg);
+      if (vnp_from != NULL && vnp_to != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoFieldPair_completedness;
+        comp = MolinfoCompletednessPairNew ();
+        comp->from = vnp_from->choice;
+        comp->to = vnp_to->choice;
+        field->data.ptrvalue = comp;
+      }
+      vnp_from = ValNodeFree (vnp_from);
+      vnp_to = ValNodeFree (vnp_to);
+      break;
+    case 4:
+      vnp_from = DialogToPointer (dlg->mol_class_from_dlg);
+      vnp_to = DialogToPointer (dlg->mol_class_to_dlg);
+      if (vnp_from != NULL && vnp_to != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoFieldPair_technique;
+        mol_class = MolinfoMolClassPairNew ();
+        mol_class->from = vnp_from->choice;
+        mol_class->to = vnp_to->choice;
+        field->data.ptrvalue = mol_class;
+      }
+      vnp_from = ValNodeFree (vnp_from);
+      vnp_to = ValNodeFree (vnp_to);
+      break;
+    case 5:
+      vnp_from = DialogToPointer (dlg->topology_from_dlg);
+      vnp_to = DialogToPointer (dlg->topology_to_dlg);
+      if (vnp_from != NULL && vnp_to != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoFieldPair_topology;
+        topology = MolinfoTopologyPairNew ();
+        topology->from = vnp_from->choice;
+        topology->to = vnp_to->choice;
+        field->data.ptrvalue = topology;
+      }
+      vnp_from = ValNodeFree (vnp_from);
+      vnp_to = ValNodeFree (vnp_to);
+      break;
+    case 6:
+      vnp_from = DialogToPointer (dlg->strand_from_dlg);
+      vnp_to = DialogToPointer (dlg->strand_to_dlg);
+      if (vnp_from != NULL && vnp_to != NULL) {
+        field = ValNodeNew (NULL);
+        field->choice = MolinfoFieldPair_strand;
+        strand = MolinfoStrandPairNew ();
+        strand->from = vnp_from->choice;
+        strand->to = vnp_to->choice;
+        field->data.ptrvalue = strand;
+      }
+      vnp_from = ValNodeFree (vnp_from);
+      vnp_to = ValNodeFree (vnp_to);
+      break;
+  }
+  return field;
+}
+
+
+static ValNodePtr TestSequenceQualPairDialog (DialoG d)
+{
+  ValNodePtr err_list = NULL, field;
+
+  field = DialogToPointer (d);
+  if (field == NULL) {
+    ValNodeAddPointer (&err_list, 0, "field");
+  } else {
+    field = MolinfoFieldPairFree (field);
+  }
+
+  return err_list;
+}
+
+
+static DialoG SequenceQualPairDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+
+{
+  SequenceQualPairDlgPtr dlg;
+  GrouP                  p, g;
+  ValNodePtr             val_list;
+  
+  dlg = (SequenceQualPairDlgPtr) MemNew (sizeof (SequenceQualPairDlgData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = SequenceQualPairToDialog;
+  dlg->fromdialog = DialogToSequenceQualPair;
+  dlg->testdialog = TestSequenceQualPairDialog;
+
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->field_type = PopupList (p, TRUE, ChangeSequenceQualPairType);
+  SetObjectExtra (dlg->field_type, dlg, NULL);
+  PopupItem (dlg->field_type, "molecule");
+  PopupItem (dlg->field_type, "technique");
+  PopupItem (dlg->field_type, "completedness");
+  PopupItem (dlg->field_type, "class");
+  PopupItem (dlg->field_type, "topology");
+  PopupItem (dlg->field_type, "strand");
+  SetValue (dlg->field_type, 1);
+
+  g = HiddenGroup (p, 0, 0, NULL);
+
+  dlg->molecule_grp = HiddenGroup (g, 2, 0, NULL);
+  val_list = GetMoleculeTypeList ();
+  dlg->molecule_from_dlg = ValNodeSelectionDialog (dlg->molecule_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetMoleculeTypeList ();
+  dlg->molecule_to_dlg = ValNodeSelectionDialog (dlg->molecule_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+
+  dlg->technique_grp = HiddenGroup (g, 2, 0, NULL);
+  val_list = GetTechniqueTypeList ();
+  dlg->technique_from_dlg = ValNodeSelectionDialog (dlg->technique_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetTechniqueTypeList ();
+  dlg->technique_to_dlg = ValNodeSelectionDialog (dlg->technique_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+
+  dlg->completedness_grp = HiddenGroup (g, 2, 0, NULL);
+  val_list = GetCompletednessTypeList ();
+  dlg->completedness_from_dlg = ValNodeSelectionDialog (dlg->completedness_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetCompletednessTypeList ();
+  dlg->completedness_to_dlg = ValNodeSelectionDialog (dlg->completedness_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+
+  dlg->mol_class_grp = HiddenGroup (g, 2, 0, NULL);
+  val_list = GetMoleculeClassTypeList ();
+  dlg->mol_class_from_dlg = ValNodeSelectionDialog (dlg->mol_class_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetMoleculeClassTypeList ();
+  dlg->mol_class_to_dlg = ValNodeSelectionDialog (dlg->mol_class_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+
+  dlg->topology_grp = HiddenGroup (g, 2, 0, NULL);
+  val_list = GetTopologyTypeList ();
+  dlg->topology_from_dlg = ValNodeSelectionDialog (dlg->topology_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetTopologyTypeList ();
+  dlg->topology_to_dlg = ValNodeSelectionDialog (dlg->topology_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+
+  dlg->strand_grp = HiddenGroup (g, 2, 0, NULL);
+
+  val_list = GetStrandTypeList ();
+  dlg->strand_from_dlg = ValNodeSelectionDialog (dlg->strand_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+  val_list = GetStrandTypeList ();
+  dlg->strand_to_dlg = ValNodeSelectionDialog (dlg->strand_grp, val_list, SHORT_SELECTION_LIST, ValNodeStringName,
+                                           ValNodeSimpleDataFree, ValNodeStringCopy,
+                                           ValNodeChoiceMatch, "location", 
+                                           change_notify, change_userdata, FALSE);
+
+  AlignObjects (ALIGN_MIDDLE, (HANDLE) dlg->molecule_grp, 
+                              (HANDLE) dlg->technique_grp,
+                              (HANDLE) dlg->completedness_grp,
+                              (HANDLE) dlg->mol_class_grp,
+                              (HANDLE) dlg->topology_grp,
+                              (HANDLE) dlg->strand_grp,
+                              NULL);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->field_type, (HANDLE) g, NULL);    
+  ChangeSequenceQualPairType (dlg->field_type); 
+  return (DialoG) p;
+}
+
+
+typedef struct sequenceconstraintdlg {
+  DIALOG_MESSAGE_BLOCK
+  GrouP seqtype;
+  GrouP rna_subtype_grp;
+  DialoG rna_subtype;
+  ButtoN feat_present;
+  DialoG feature_type;
+  DialoG id;
+
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer change_userdata;
+} SequenceConstraintDlgData, PNTR SequenceConstraintDlgPtr;
+
+
+static void ChangeSequenceConstraintButton (ButtoN b)
+{
+  SequenceConstraintDlgPtr dlg;
+
+  dlg = (SequenceConstraintDlgPtr) GetObjectExtra (b);
+  if (dlg == NULL) return;
+
+  if (GetStatus (dlg->feat_present)) {
+    Enable (dlg->feature_type);
+  } else {
+    Disable (dlg->feature_type);
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void ChangeSequenceConstraintGroup (GrouP g)
+{
+  SequenceConstraintDlgPtr dlg;
+
+  dlg = (SequenceConstraintDlgPtr) GetObjectExtra (g);
+  if (dlg == NULL) return;
+
+  if (GetValue (dlg->seqtype) == 4) {
+    Show (dlg->rna_subtype_grp);
+  } else {
+    Hide (dlg->rna_subtype_grp);
+  }
+
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void SequenceConstraintToDialog (DialoG d, Pointer data)
+{
+  SequenceConstraintDlgPtr dlg;
+  SequenceConstraintPtr constraint;
+  ValNode vn;
+
+  dlg = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  constraint = (SequenceConstraintPtr) data;
+  if (constraint == NULL) {
+    SetValue (dlg->seqtype, 1);
+    PointerToDialog (dlg->rna_subtype, NULL);
+    Hide (dlg->rna_subtype_grp);
+    SetStatus (dlg->feat_present, FALSE);
+    PointerToDialog (dlg->feature_type, NULL);
+    PointerToDialog (dlg->id, NULL);
+  } else {
+    if (constraint->seqtype == NULL) {
+      SetValue (dlg->seqtype, 1);
+      PointerToDialog (dlg->rna_subtype, NULL);
+      Hide (dlg->rna_subtype_grp);
+    } else {
+      switch (constraint->seqtype->choice) {
+        case SequenceConstraintMolTypeConstraint_any :
+          SetValue (dlg->seqtype, 1);
+          PointerToDialog (dlg->rna_subtype, NULL);
+          Hide (dlg->rna_subtype_grp);
+          break;
+        case SequenceConstraintMolTypeConstraint_nucleotide :
+          SetValue (dlg->seqtype, 2);
+          PointerToDialog (dlg->rna_subtype, NULL);
+          Hide (dlg->rna_subtype_grp);
+          break;
+        case SequenceConstraintMolTypeConstraint_dna :
+          SetValue (dlg->seqtype, 3);
+          PointerToDialog (dlg->rna_subtype, NULL);
+          Hide (dlg->rna_subtype_grp);
+          break;
+        case SequenceConstraintMolTypeConstraint_rna :
+          SetValue (dlg->seqtype, 4);
+          vn.choice = constraint->seqtype->data.intvalue;
+          vn.data.ptrvalue = NULL;
+          vn.next = NULL;
+          PointerToDialog (dlg->rna_subtype, &vn);
+          Show (dlg->rna_subtype_grp);
+          break;
+        case SequenceConstraintMolTypeConstraint_protein :
+          SetValue (dlg->seqtype, 5);
+          PointerToDialog (dlg->rna_subtype, NULL);
+          Hide (dlg->rna_subtype_grp);
+          break;
+      }
+    }
+  
+    if (constraint->feature == Feature_type_any) {
+      SetStatus (dlg->feat_present, FALSE);
+      PointerToDialog (dlg->feature_type, NULL);
+    } else {
+      SetStatus (dlg->feat_present, TRUE);
+      vn.choice = constraint->feature;
+      vn.data.ptrvalue = NULL;
+      vn.next = NULL;
+      PointerToDialog (dlg->feature_type, &vn);
+    }
+
+    PointerToDialog (dlg->id, constraint->id);
+  }
+  ChangeSequenceConstraintButton (dlg->feat_present);
+}
+
+
+static Pointer SequenceConstraintFromDialog (DialoG d)
+{
+  SequenceConstraintDlgPtr dlg;
+  SequenceConstraintPtr constraint;
+  ValNodePtr vnp;
+  Int4 val;
+
+  dlg = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  constraint = SequenceConstraintNew();
+
+  val = GetValue (dlg->seqtype);
+  switch (val) {
+    case 1:
+      /* don't bother to fill in, it's optional */
+      break;
+    case 2:
+      constraint->seqtype = ValNodeNew (NULL);
+      constraint->seqtype->choice = SequenceConstraintMolTypeConstraint_nucleotide;
+      break;
+    case 3:
+      constraint->seqtype = ValNodeNew (NULL);
+      constraint->seqtype->choice = SequenceConstraintMolTypeConstraint_dna;
+      break;
+    case 4:
+      constraint->seqtype = ValNodeNew (NULL);
+      constraint->seqtype->choice = SequenceConstraintMolTypeConstraint_rna;
+      vnp = DialogToPointer (dlg->rna_subtype);
+      if (vnp == NULL) {
+        constraint->seqtype->data.intvalue = Sequence_constraint_rnamol_any;
+      } else {
+        constraint->seqtype->data.intvalue = vnp->choice;
+      }
+      break;
+    case 5:
+      constraint->seqtype = ValNodeNew (NULL);
+      constraint->seqtype->choice = SequenceConstraintMolTypeConstraint_protein;
+      break;
+  }
+
+  if (GetStatus (dlg->feat_present)) {
+    vnp = DialogToPointer (dlg->feature_type);
+    if (vnp == NULL) {
+      constraint->feature = Feature_type_any;
+    } else {
+      constraint->feature = vnp->choice;
+    }
+    vnp = ValNodeFree (vnp);
+  } else {
+    constraint->feature = Feature_type_any;
+  }
+
+  constraint->id = DialogToPointer (dlg->id);
+  if (IsStringConstraintEmpty (constraint->id)) {
+    constraint->id = StringConstraintFree (constraint->id);
+  }
+  return constraint;
+}
+
+
+NLM_EXTERN DialoG FeatureTypeDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  ValNodePtr feature_list = NULL;
+
+  AddAllFeaturesToChoiceList (&feature_list);
+  return ValNodeSelectionDialog (h, feature_list, TALL_SELECTION_LIST, ValNodeStringName,
+                                ValNodeSimpleDataFree, ValNodeStringCopy,
+                                ValNodeChoiceMatch, "feature type", 
+                                change_notify, change_userdata, FALSE);
+}
+
+
+static ValNodePtr TestSequenceConstraintDialog (DialoG d)
+{
+  SequenceConstraintDlgPtr dlg;
+  ValNodePtr err_list = NULL;
+  SequenceConstraintPtr constraint;
+
+  dlg = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+  if (dlg != NULL) {
+    constraint = DialogToPointer (d);
+    if (IsSequenceConstraintEmpty (constraint)) {
+      ValNodeAddPointer (&err_list, 0, "empty constraint");
+    }
+    constraint = SequenceConstraintFree (constraint);
+  }
+  return err_list;
+}
+   
+
+static DialoG SequenceConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  SequenceConstraintDlgPtr dlg;
+  GrouP p, g;
+  ValNodePtr rna_subtypes = NULL;
+
+  dlg = (SequenceConstraintDlgPtr) MemNew (sizeof (SequenceConstraintDlgData));
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetGroupSpacing (p, 10, 10);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = SequenceConstraintToDialog;
+  dlg->fromdialog = SequenceConstraintFromDialog;
+  dlg->testdialog = TestSequenceConstraintDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->seqtype = HiddenGroup (p, 5, 0, ChangeSequenceConstraintGroup);
+  SetObjectExtra (dlg->seqtype, dlg, NULL);
+  RadioButton (dlg->seqtype, "Any sequence");
+  RadioButton (dlg->seqtype, "Nucleotides");
+  RadioButton (dlg->seqtype, "DNA");
+  RadioButton (dlg->seqtype, "RNA");
+  RadioButton (dlg->seqtype, "Proteins");
+  SetValue (dlg->seqtype, 1);
+  dlg->rna_subtype_grp = HiddenGroup (p, 2, 0, NULL);
+  StaticPrompt (dlg->rna_subtype_grp, "RNA Type", 0, dialogTextHeight, programFont, 'r');
+  AddAllRNASubtypesToChoiceList (&rna_subtypes);
+  dlg->rna_subtype = ValNodeSelectionDialog (dlg->rna_subtype_grp, rna_subtypes, TALL_SELECTION_LIST, ValNodeStringName,
+                                ValNodeSimpleDataFree, ValNodeStringCopy,
+                                ValNodeChoiceMatch, "rna subtype",
+                                change_notify, change_userdata, FALSE);
+
+  Hide (dlg->rna_subtype_grp);
+
+  g = HiddenGroup (p, 2, 0, NULL);
+  dlg->feat_present = CheckBox (g, "Where feature present", ChangeSequenceConstraintButton);
+  SetObjectExtra (dlg->feat_present, dlg, NULL);
+  dlg->feature_type = FeatureTypeDialog (g, change_notify, change_userdata);
+
+  dlg->id = StringConstraintDialog (p, "Where sequence ID", FALSE, change_notify, change_userdata);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->seqtype, (HANDLE) dlg->rna_subtype_grp, (HANDLE) dlg->id, (HANDLE) g, NULL);
+  return (DialoG) p;
+}
+
+
+/* Notes:
+ * There can be more than one constraint, and the user will need to be able to view, edit, add, and delete them.
+ * Should have a DOC that lists the constraints, user can click on buttons to edit or delete, another button to add.
+ * Need to have an Edit window to edit individual constraints.
+ * Let user toggle between types of constraints only when creating a new one?
+ */
+typedef struct editconstraint {
+  PopuP constraint_type;
+
+  DialoG string_dlg;
+  DialoG location_dlg;
+  DialoG src_dlg;
+  DialoG cds_gene_prot_qual_dlg;
+  DialoG cds_gene_prot_pseudo_dlg;
+  DialoG sequence_dlg;
+
+  ButtoN accept_btn;
+} EditConstraintData, PNTR EditConstraintPtr;
+
+
+static void EnableEditConstraintAccept (Pointer data)
+{
+  EditConstraintPtr ecp;
+  Int2 val;
+  ValNodePtr err_list = NULL;
+  Boolean ok_to_accept = TRUE;
+
+  ecp = (EditConstraintPtr) data;
+  if (ecp != NULL && ecp->accept_btn != NULL) {
+    val = GetValue (ecp->constraint_type);
+    switch (val) {
+      case 1:
+        err_list = TestDialog (ecp->string_dlg);
+        break;
+      case 2:
+        err_list = TestDialog (ecp->location_dlg);
+        break;
+      case 3:
+        err_list = TestDialog (ecp->src_dlg);
+        break;
+      case 4:
+        err_list = TestDialog (ecp->cds_gene_prot_qual_dlg);
+        break;
+      case 5:
+        err_list = TestDialog (ecp->cds_gene_prot_pseudo_dlg);
+        break;
+      case 6:
+        err_list = TestDialog (ecp->sequence_dlg);
+        break;
+      default:
+        ok_to_accept = FALSE;
+    }
+    if (err_list != NULL) {
+      ok_to_accept = FALSE;
+      err_list = ValNodeFree (err_list);
+    }
+    if (ok_to_accept) {
+      Enable (ecp->accept_btn);
+    } else {
+      Disable (ecp->accept_btn);
+    }
+  }
+}
+
+
+static void ChangeEditConstraintType (PopuP p)
+{
+  EditConstraintPtr ecp;
+  Int2 val;
+
+  ecp = (EditConstraintPtr) GetObjectExtra (p);
+  if (ecp == NULL) return;
+
+  Hide (ecp->string_dlg);
+  Hide (ecp->location_dlg);
+  Hide (ecp->src_dlg);
+  Hide (ecp->cds_gene_prot_qual_dlg);
+  Hide (ecp->cds_gene_prot_pseudo_dlg);
+  Hide (ecp->sequence_dlg);
+
+  val = GetValue (ecp->constraint_type);
+  switch (val) {
+    case 1:
+      Show (ecp->string_dlg);
+      break;
+    case 2:
+      Show (ecp->location_dlg);
+      break;
+    case 3:
+      Show (ecp->src_dlg);
+      break;
+    case 4:
+      Show (ecp->cds_gene_prot_qual_dlg);
+      break;
+    case 5:
+      Show (ecp->cds_gene_prot_pseudo_dlg);
+      break;
+    case 6:
+      Show (ecp->sequence_dlg);
+      break;
+  }
+  EnableEditConstraintAccept (ecp);
+}
+
+
+static void FreeConstraintData (ValNodePtr constraint)
+{
+  if (constraint == NULL) return;
+
+  switch (constraint->choice) {
+    case ConstraintChoice_string:
+      constraint->data.ptrvalue = StringConstraintFree (constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_location:
+      constraint->data.ptrvalue = LocationConstraintFree (constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_source:
+      constraint->data.ptrvalue = SourceConstraintFree (constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_cdsgeneprot_qual:
+      constraint->data.ptrvalue = CDSGeneProtQualConstraintFree (constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_cdsgeneprot_pseudo:
+      constraint->data.ptrvalue = CDSGeneProtPseudoConstraintFree (constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_sequence:
+      constraint->data.ptrvalue = SequenceConstraintFree (constraint->data.ptrvalue);
+      break;
+  }
+}
+
+
+static Boolean EditConstraint (ValNodePtr constraint)
+{
+  ModalAcceptCancelData acd;
+  EditConstraintData    ecd;
+  Boolean               rval = FALSE;
+  WindoW                w;
+  ButtoN                b;
+  GrouP                 h, g, c;
+  Int2                  val;
+  
+  if (constraint == NULL) return FALSE;
+
+  w = MovableModalWindow(-20, -13, -10, -10, "Constraint", NULL);
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  ecd.constraint_type = PopupList (h, TRUE, ChangeEditConstraintType);
+  SetObjectExtra (ecd.constraint_type, &ecd, NULL);
+  PopupItem (ecd.constraint_type, "String");
+  PopupItem (ecd.constraint_type, "Location");
+  PopupItem (ecd.constraint_type, "Source");
+  PopupItem (ecd.constraint_type, "CDS-Gene-Prot Qualifier");
+  PopupItem (ecd.constraint_type, "CDS-Gene-Prot Pseudo Feature");
+  PopupItem (ecd.constraint_type, "Sequence");
+
+  g = HiddenGroup (h, 0, 0, NULL);
+  ecd.accept_btn = NULL;
+  ecd.string_dlg = StringConstraintDialog (g, "", TRUE, EnableEditConstraintAccept, &ecd);
+  ecd.location_dlg = LocationConstraintDialog (g, EnableEditConstraintAccept, &ecd);
+  ecd.src_dlg = SourceConstraintDialog (g, EnableEditConstraintAccept, &ecd);
+  ecd.cds_gene_prot_qual_dlg = CDSGeneProtQualConstraintDialog (g, EnableEditConstraintAccept, &ecd);
+  ecd.cds_gene_prot_pseudo_dlg = CDSGeneProtPseudoConstraintDialog (g, EnableEditConstraintAccept, &ecd);
+  ecd.sequence_dlg = SequenceConstraintDialog (g, EnableEditConstraintAccept, &ecd);
+  AlignObjects (ALIGN_CENTER, (HANDLE) ecd.string_dlg,
+                              (HANDLE) ecd.location_dlg,
+                              (HANDLE) ecd.src_dlg,
+                              (HANDLE) ecd.cds_gene_prot_qual_dlg,
+                              (HANDLE) ecd.cds_gene_prot_pseudo_dlg,
+                              (HANDLE) ecd.sequence_dlg,
+                              NULL);
+
+  c = HiddenGroup (h, 2, 0, NULL);
+  SetGroupSpacing (c, 10, 10);
+  ecd.accept_btn = PushButton (c, "Accept", ModalAcceptButton);
+  SetObjectExtra (ecd.accept_btn, &acd, NULL);
+  b = PushButton (c, "Cancel", ModalCancelButton);
+  SetObjectExtra (b, &acd, NULL);
+  AlignObjects (ALIGN_CENTER, (HANDLE) ecd.constraint_type,
+                              (HANDLE) g,
+                              (HANDLE) c, 
+                              NULL);
+
+  switch (constraint->choice) {
+    case ConstraintChoice_string:
+      SetValue (ecd.constraint_type, 1);
+      PointerToDialog (ecd.string_dlg, constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_location:
+      SetValue (ecd.constraint_type, 2);
+      PointerToDialog (ecd.location_dlg, constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_source:
+      SetValue (ecd.constraint_type, 3);
+      PointerToDialog (ecd.src_dlg, constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_cdsgeneprot_qual:
+      SetValue (ecd.constraint_type, 4);
+      PointerToDialog (ecd.cds_gene_prot_qual_dlg, constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_cdsgeneprot_pseudo:
+      SetValue (ecd.constraint_type, 5);
+      PointerToDialog (ecd.cds_gene_prot_pseudo_dlg, constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_sequence:
+      SetValue (ecd.constraint_type, 6);
+      PointerToDialog (ecd.sequence_dlg, constraint->data.ptrvalue);
+      break;
+    default:
+      SetValue (ecd.constraint_type, 1);
+      break;
+  }
+
+
+  ChangeEditConstraintType (ecd.constraint_type);
+  Show (w);
+  Select (w);
+  acd.accepted = FALSE;
+  acd.cancelled = FALSE;
+  while (!acd.accepted && ! acd.cancelled)
+  {
+    ProcessExternalEvent ();
+    Update ();
+  }
+  ProcessAnEvent ();
+  if (!acd.cancelled)
+  {
+    val = GetValue (ecd.constraint_type);
+    switch (val) {
+      case 1:
+        FreeConstraintData (constraint);
+        constraint->choice = ConstraintChoice_string;
+        constraint->data.ptrvalue = DialogToPointer (ecd.string_dlg);
+        rval = TRUE;
+        break;
+      case 2:
+        FreeConstraintData (constraint);
+        constraint->choice = ConstraintChoice_location;
+        constraint->data.ptrvalue = DialogToPointer (ecd.location_dlg);
+        rval = TRUE;
+        break;
+      case 3:
+        FreeConstraintData (constraint);
+        constraint->choice = ConstraintChoice_source;
+        constraint->data.ptrvalue = DialogToPointer (ecd.src_dlg);
+        rval = TRUE;
+        break;
+      case 4:
+        FreeConstraintData (constraint);
+        constraint->choice = ConstraintChoice_cdsgeneprot_qual;
+        constraint->data.ptrvalue = DialogToPointer (ecd.cds_gene_prot_qual_dlg);
+        rval = TRUE;
+        break;
+      case 5:
+        FreeConstraintData (constraint);
+        constraint->choice = ConstraintChoice_cdsgeneprot_pseudo;
+        constraint->data.ptrvalue = DialogToPointer (ecd.cds_gene_prot_pseudo_dlg);
+        rval = TRUE;
+        break;
+      case 6:
+        FreeConstraintData (constraint);
+        constraint->choice = ConstraintChoice_sequence;
+        constraint->data.ptrvalue = DialogToPointer (ecd.sequence_dlg);
+        rval = TRUE;
+        break;
+    }
+  }
+  Remove (w);
+  return rval;
+}
+
+
+static CharPtr SummarizeConstraint (ValNodePtr constraint);
+
+typedef struct constraintsetdlg {
+  DIALOG_MESSAGE_BLOCK
+  DoC                  constraint_doc;
+  ValNodePtr           constraint_list;
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer              change_userdata;
+} ConstraintSetDlgData, PNTR ConstraintSetDlgPtr;
+
+static void PopulateConstraintDoc (DoC d, ValNodePtr constraint_list)
+{
+  ValNodePtr vnp;
+  CharPtr    phrase, tmp;
+  RecT       r;
+  ParData    ParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0};
+  ColData    ColFmt[] = 
+  {
+    {12, 0, 1, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE},
+    {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}
+  };
+
+  if (d == NULL) return;
+
+  Reset (d);
+
+  ObjectRect (d, &r);
+  InsetRect (&r, 4, 4);
+  
+  ColFmt[1].pixWidth = r.right - r.left - 12;
+
+  Reset (d);
+
+  for (vnp = constraint_list; vnp != NULL; vnp = vnp->next) {
+    phrase = SummarizeConstraint (vnp);
+    tmp = (CharPtr) MemNew (sizeof (Char) * (StringLen (phrase) + 3));
+    sprintf (tmp, "\t%s\n", phrase);
+    phrase = MemFree (phrase);
+    AppendText (d, tmp, &ParFmt, ColFmt, programFont);
+    tmp = MemFree (tmp);
+  }
+  AppendText (d, "(Click here to add new constraint)", NULL, NULL, programFont);
+  UpdateDocument (d, 0, 0);
+}
+
+static void DrawConstraintDocControls (DoC d, RectPtr r, Int2 item, Int2 firstLine)
+
+{
+  RecT                rct;
+  Int4                width;
+  PoinT               pt1, pt2;
+  ConstraintSetDlgPtr dlg;
+
+  dlg = (ConstraintSetDlgPtr) GetObjectExtra (d);
+  if (dlg != NULL && r != NULL && item > 0 && firstLine == 0 && item <= ValNodeLen (dlg->constraint_list)) {
+    rct = *r;
+  
+    /* draw X for deletion */
+    width = 10;
+    pt1.x = rct.left + 1;
+    pt1.y = rct.top + 1;
+    pt2.x = pt1.x + width;
+    pt2.y = pt1.y + width;
+    DrawLine (pt1, pt2);
+    pt1.x = rct.left + 1;
+    pt1.y = rct.top + 1 + width;
+    pt2.x = pt1.x + width;
+    pt2.y = rct.top + 1;
+    DrawLine (pt1, pt2);
+  }
+}
+
+
+static void ClickConstraintDoc (DoC d, PoinT pt)
+{
+  Int2      item, row, col;
+  RecT      rct;
+  BaR       sb_vert;
+  Int4      scroll_pos = 0, scroll_max;
+  ConstraintSetDlgPtr f;
+  ValNodePtr         vnp, vnp_prev = NULL;
+  Boolean            changed = FALSE;
+  
+  f = (ConstraintSetDlgPtr) GetObjectExtra (d);
+  if (f == NULL) return;
+  
+  MapDocPoint (d, pt, &item, &row, &col, &rct);
+  if (item == 0 && row == 0 && f->constraint_list == NULL) {
+    /* create new constraint */
+    vnp = ValNodeNew (NULL);
+    vnp->choice = ConstraintChoice_string;
+    if (EditConstraint (vnp)) {
+      f->constraint_list = vnp;
+      changed = TRUE;
+    }
+  } else if (item > 0 && row > 0) {
+    if (item == ValNodeLen (f->constraint_list) + 1) {
+      /* create new constraint */
+      vnp = ValNodeNew (NULL);
+      vnp->choice = ConstraintChoice_string;
+      if (EditConstraint (vnp)) {
+        ValNodeLink (&(f->constraint_list), vnp);
+        changed = TRUE;
+      } else {
+        vnp = ConstraintChoiceFree (vnp);
+      }
+    } else {
+      for (vnp = f->constraint_list; vnp != NULL && item > 1; vnp = vnp->next, item--) {
+        vnp_prev = vnp;
+      }
+      if (vnp != NULL) {      
+        sb_vert = GetSlateVScrollBar ((SlatE) f->constraint_doc);
+        scroll_pos = GetBarValue (sb_vert);
+        switch (col) {
+          case 1:
+            /* delete this item */
+            if (vnp_prev == NULL) {
+              f->constraint_list = vnp->next;
+            } else {
+              vnp_prev->next = vnp->next;
+            }
+            vnp->next = NULL;
+            vnp = ConstraintChoiceFree (vnp);
+            changed = TRUE;
+            break;
+          case 2:
+            /* edit */
+            changed = EditConstraint (vnp);
+            break;
+        }
+      }
+    }
+  }
+  if (changed) {
+    PopulateConstraintDoc (f->constraint_doc, f->constraint_list);
+    if (scroll_pos > 0) {
+      sb_vert = GetSlateVScrollBar ((SlatE) f->constraint_doc);
+      scroll_max = GetBarMax (sb_vert);
+      if (scroll_pos > scroll_max) {
+        scroll_pos = scroll_max;
+      }
+      CorrectBarValue (sb_vert, scroll_pos);
+    }
+  }
+}
+
+static void ConstraintSetToDialog (DialoG d, Pointer data)
+{
+  ConstraintSetDlgPtr dlg;
+
+  dlg = (ConstraintSetDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  dlg->constraint_list = ConstraintChoiceSetFree (dlg->constraint_list);
+  if (data != NULL) {
+    dlg->constraint_list = AsnIoMemCopy ((ConstraintChoiceSetPtr) data,
+                                         (AsnReadFunc) ConstraintChoiceSetAsnRead,
+                                         (AsnWriteFunc) ConstraintChoiceSetAsnWrite);
+ }
+ PopulateConstraintDoc (dlg->constraint_doc, dlg->constraint_list);
+ if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static Pointer ConstraintSetFromDialog (DialoG d)
+{
+  ConstraintSetDlgPtr dlg;
+  ValNodePtr constraint_list = NULL;
+
+  dlg = (ConstraintSetDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  if (dlg->constraint_list != NULL) {
+    constraint_list = AsnIoMemCopy ((ConstraintChoiceSetPtr) dlg->constraint_list,
+                                    (AsnReadFunc) ConstraintChoiceSetAsnRead,
+                                    (AsnWriteFunc) ConstraintChoiceSetAsnWrite);
+  }
+  return (Pointer) constraint_list;
+}
+
+static void CleanupConstraintSetDialog (GraphiC g, VoidPtr data)
+
+{
+  ConstraintSetDlgPtr dlg;
+
+  dlg = (ConstraintSetDlgPtr) data;
+  if (dlg != NULL) {
+    dlg->constraint_list = ConstraintChoiceSetFree (dlg->constraint_list);
+  }
+  StdCleanupExtraProc (g, data);
+}
+
+
+static DialoG ConstraintSetDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  ConstraintSetDlgPtr dlg;
+  GrouP               p;
+  PrompT              ppt;
+
+  p = HiddenGroup (h, -1, 0, NULL);
+  dlg = (ConstraintSetDlgPtr) MemNew (sizeof (ConstraintSetDlgData));
+  SetObjectExtra (p, dlg, CleanupConstraintSetDialog);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = ConstraintSetToDialog;
+  dlg->fromdialog = ConstraintSetFromDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+  
+  dlg->constraint_list = NULL;
+  ppt = StaticPrompt (p, "Constraints", 0, dialogTextHeight, programFont, 'c');
+  dlg->constraint_doc = DocumentPanel (p, stdCharWidth * 30, stdLineHeight * 5);
+  SetObjectExtra (dlg->constraint_doc, dlg, NULL);
+  SetDocProcs (dlg->constraint_doc, ClickConstraintDoc, NULL, NULL, NULL);
+  SetDocShade (dlg->constraint_doc, DrawConstraintDocControls, NULL, NULL, NULL);
+  PopulateConstraintDoc (dlg->constraint_doc, dlg->constraint_list);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) ppt, (HANDLE) dlg->constraint_doc, NULL);
+  return (DialoG) p;
+}
+
+
+static DialoG LegalFeatQualChoiceDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  ValNodePtr field_list = NULL;
+
+  AddAllFeatureFieldsToChoiceList (&field_list);
+  return ValNodeSelectionDialog (h, field_list, TALL_SELECTION_LIST, ValNodeStringName,
+                                ValNodeSimpleDataFree, ValNodeStringCopy,
+                                ValNodeChoiceMatch, "field type",
+                                change_notify, change_userdata, FALSE);
+}
+
+
+typedef struct featqualchoicedlg {
+  DIALOG_MESSAGE_BLOCK
+  DialoG legal_qual;
+  DialoG illegal_qual;
+  Boolean is_legal;
+} FeatQualChoiceDlgData, PNTR FeatQualChoiceDlgPtr;
+
+
+static void FeatQualChoiceToDialog (DialoG d, Pointer data)
+{
+  FeatQualChoiceDlgPtr dlg;
+  ValNodePtr vnp;
+  ValNode vn;
+
+  dlg = (FeatQualChoiceDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  vnp = (ValNodePtr) data;
+  if (vnp == NULL) {
+    dlg->is_legal = TRUE;
+    PointerToDialog (dlg->legal_qual, NULL);
+    Show (dlg->legal_qual);
+    Hide (dlg->illegal_qual);
+  } else if (vnp->choice == FeatQualChoice_legal_qual) {
+    dlg->is_legal = TRUE;
+    vn.choice = vnp->data.intvalue;
+    vn.data.ptrvalue = NULL;
+    vn.next = NULL;
+    PointerToDialog (dlg->legal_qual, &vn);
+    Show (dlg->legal_qual);
+    Hide (dlg->illegal_qual);
+  } else if (vnp->choice == FeatQualChoice_illegal_qual) {
+    dlg->is_legal = FALSE;
+    PointerToDialog (dlg->illegal_qual, vnp->data.ptrvalue);
+    Hide (dlg->legal_qual);
+    Show (dlg->illegal_qual);
+  } else {
+    dlg->is_legal = TRUE;
+    PointerToDialog (dlg->legal_qual, NULL);
+    Show (dlg->legal_qual);
+    Hide (dlg->illegal_qual);
+  }
+}
+
+
+static Pointer DialogToFeatQualChoice (DialoG d)
+{
+  FeatQualChoiceDlgPtr dlg;
+  ValNodePtr vnp = NULL, vnp2;
+  StringConstraintPtr scp;
+
+  dlg = (FeatQualChoiceDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  if (dlg->is_legal) {
+    vnp2 = (ValNodePtr) DialogToPointer (dlg->legal_qual);
+    if (vnp2 != NULL) {
+      vnp = ValNodeNew (NULL);
+      vnp->choice = FeatQualChoice_legal_qual;
+      vnp->data.intvalue = vnp2->choice;
+      vnp2 = ValNodeFree (vnp2);
+    }
+  } else {
+    scp = (StringConstraintPtr) DialogToPointer (dlg->illegal_qual);
+    if (scp != NULL) {
+      vnp = ValNodeNew (NULL);
+      vnp->choice = FeatQualChoice_illegal_qual;
+      vnp->data.ptrvalue = scp;
+    }
+  }
+  return vnp;
+}
+
+
+static ValNodePtr TestFeatQualChoiceDialog (DialoG d)
+{
+  FeatQualChoiceDlgPtr dlg;
+  ValNodePtr err_list = NULL;
+  StringConstraintPtr scp;
+
+  dlg = (FeatQualChoiceDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  if (dlg->is_legal) {
+    err_list = TestDialog (dlg->legal_qual);
+  } else {
+    scp = DialogToPointer (dlg->illegal_qual);
+    if (scp == NULL || StringHasNoText (scp->match_text)) {
+      ValNodeAddPointer (&err_list, 0, "match text");
+    }
+  }
+  return err_list;
+}
+
+static DialoG FeatQualChoiceDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  FeatQualChoiceDlgPtr dlg;
+  GrouP                 p;
+  
+  dlg = (FeatQualChoiceDlgPtr) MemNew (sizeof (FeatQualChoiceDlgData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, 0, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = FeatQualChoiceToDialog;
+  dlg->fromdialog = DialogToFeatQualChoice;
+  dlg->testdialog = TestFeatQualChoiceDialog;
+  dlg->is_legal = TRUE;
+
+  dlg->legal_qual = LegalFeatQualChoiceDialog (p, change_notify, change_userdata);
+  dlg->illegal_qual = StringConstraintDialog (p, NULL, FALSE, change_notify, change_userdata);
+  Hide (dlg->illegal_qual);
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->legal_qual, (HANDLE) dlg->illegal_qual, NULL);
+
+  return (DialoG) p;
+}
+
+
+typedef struct cdsgeneprotfielddlg {
+  DIALOG_MESSAGE_BLOCK
+  DialoG dlg;
+} CDSGeneProtFieldDlgData, PNTR CDSGeneProtFieldDlgPtr;
+
+
+static void CDSGeneProtFieldToDialog (DialoG d, Pointer data)
+{
+  CDSGeneProtFieldDlgPtr dlg;
+  ValNodePtr vnp;
+  ValNode vn;
+  
+  dlg = (CDSGeneProtFieldDlgPtr) GetObjectExtra (d);
+  if (dlg != NULL) {
+    vnp = (ValNodePtr) data;
+    if (vnp == NULL) {
+      PointerToDialog (dlg->dlg, NULL);
+    } else {
+      vn.choice = vnp->data.intvalue;
+      vn.data.ptrvalue = NULL;
+      vn.next = NULL;
+      PointerToDialog (dlg->dlg, &vn);
+    }
+  }
+}
+
+static Pointer DialogToCDSGeneProtField (DialoG d)
+{
+  CDSGeneProtFieldDlgPtr dlg;
+  ValNodePtr vnp, field = NULL;
+  
+  dlg = (CDSGeneProtFieldDlgPtr) GetObjectExtra (d);
+  if (dlg != NULL) {
+    vnp = (ValNodePtr) DialogToPointer (dlg->dlg);
+    if (vnp != NULL) {
+      field = ValNodeNew (NULL);
+      field->choice = FieldType_cds_gene_prot;
+      field->data.intvalue = vnp->choice;
+    }
+  }
+  return field;
+}
+
+
+static ValNodePtr TestCDSGeneProtFieldDialog (DialoG d)
+{
+  CDSGeneProtFieldDlgPtr dlg;
+  ValNodePtr err_list = NULL;
+
+  dlg = (CDSGeneProtFieldDlgPtr) GetObjectExtra (d);
+  if (dlg != NULL) {
+    err_list = TestDialog (dlg->dlg);
+  }
+  return err_list;
+}
+
+
+static DialoG CDSGeneProtFieldDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  CDSGeneProtFieldDlgPtr dlg;
+  GrouP                  p;
+  ValNodePtr             field_list = NULL;
+  
+  dlg = (CDSGeneProtFieldDlgPtr) MemNew (sizeof (CDSGeneProtFieldDlgData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, 0, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = CDSGeneProtFieldToDialog;
+  dlg->fromdialog = DialogToCDSGeneProtField;
+  dlg->testdialog = TestCDSGeneProtFieldDialog;
+
+  AddAllCDSGeneProtFieldsToChoiceList (&field_list);
+  dlg->dlg = ValNodeSelectionDialog (p, field_list, TALL_SELECTION_LIST, ValNodeStringName,
+                                ValNodeSimpleDataFree, ValNodeStringCopy,
+                                ValNodeChoiceMatch, "field type",
+                                change_notify, change_userdata, FALSE);
+
+  return (DialoG) p;
+}
+
+
+typedef struct fieldtypedlg {
+  DIALOG_MESSAGE_BLOCK
+  Uint1 field_type;
+  DialoG src_qual;
+  GrouP feature_field_grp;
+  DialoG feature_type;
+  DialoG feature_field;
+  DialoG cdsgeneprot;
+  DialoG sequence_qual;
+} FieldTypeDlgData, PNTR FieldTypeDlgPtr;
+
+
+static void FieldTypeToDialog (DialoG d, Pointer data)
+{
+  FieldTypeDlgPtr dlg;
+  FeatureFieldPtr ffp;
+  ValNodePtr vnp;
+  ValNode vn;
+
+  dlg = (FieldTypeDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  SafeHide (dlg->src_qual);
+  SafeHide (dlg->feature_field_grp);
+  SafeHide (dlg->cdsgeneprot);
+  SafeHide (dlg->sequence_qual);
+  vnp = (ValNodePtr) data;
+  if (vnp != NULL) {
+    switch (vnp->choice) {
+      case FieldType_source_qual:
+        SafeShow (dlg->src_qual);
+        PointerToDialog (dlg->src_qual, vnp->data.ptrvalue);
+        dlg->field_type = FieldType_source_qual;
+        break;
+      case FieldType_feature_field:
+        SafeShow (dlg->feature_field_grp);
+        ffp = (FeatureFieldPtr) vnp->data.ptrvalue;
+        if (ffp == NULL) {
+          PointerToDialog (dlg->feature_type, NULL);
+          PointerToDialog (dlg->feature_field, NULL);
+        } else {
+          vn.choice = ffp->type;
+          vn.data.ptrvalue = NULL;
+          vn.next = NULL;
+          PointerToDialog (dlg->feature_type, &vn);
+          PointerToDialog (dlg->feature_field, ffp->field);
+        }
+        dlg->field_type = FieldType_feature_field;
+        break;
+      case FieldType_cds_gene_prot:
+        SafeShow (dlg->cdsgeneprot);
+        PointerToDialog (dlg->cdsgeneprot, vnp);
+        dlg->field_type = FieldType_cds_gene_prot;
+        break;
+      case FieldType_molinfo_field:
+        SafeShow (dlg->sequence_qual);
+        PointerToDialog (dlg->sequence_qual, vnp->data.ptrvalue);
+        dlg->field_type = FieldType_molinfo_field;
+        break;
+    }
+  }
+}
+
+
+static Pointer DialogToFieldType (DialoG d)
+{
+  FieldTypeDlgPtr dlg;
+  FeatureFieldPtr ffp;
+  ValNodePtr vnp = NULL, vnp2;
+
+  dlg = (FieldTypeDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  switch (dlg->field_type) {
+    case FieldType_source_qual:
+      vnp = ValNodeNew(NULL);
+      vnp->choice = FieldType_source_qual;
+      vnp->data.ptrvalue = DialogToPointer (dlg->src_qual);
+      break;
+    case FieldType_feature_field:
+      vnp2 = DialogToPointer (dlg->feature_type);
+      if (vnp2 != NULL) {
+        ffp = FeatureFieldNew();
+        ffp->type = vnp2->choice;
+        ffp->field = DialogToPointer (dlg->feature_field);
+        vnp = ValNodeNew (NULL);
+        vnp->choice = FieldType_feature_field;
+        vnp->data.ptrvalue = ffp;
+      }
+      break;
+    case FieldType_cds_gene_prot:
+      vnp = DialogToPointer (dlg->cdsgeneprot);
+      break;
+    case FieldType_molinfo_field:
+      vnp = ValNodeNew (NULL);
+      vnp->choice = FieldType_molinfo_field;
+      vnp->data.ptrvalue = DialogToPointer (dlg->sequence_qual);
+      break;
+  }
+  return vnp;
+}
+
+
+static ValNodePtr TestFieldTypeDialog (DialoG d)
+{
+  FieldTypeDlgPtr dlg;
+  ValNodePtr      err_list = NULL;
+
+  dlg = (FieldTypeDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  switch (dlg->field_type) {
+    case FieldType_source_qual:
+      ValNodeLink (&err_list, TestDialog (dlg->src_qual));
+      break;
+    case FieldType_feature_field:
+      ValNodeLink (&err_list, TestDialog (dlg->feature_type));
+      ValNodeLink (&err_list, TestDialog (dlg->feature_field));
+      break;
+    case FieldType_cds_gene_prot:
+      ValNodeLink (&err_list, TestDialog (dlg->cdsgeneprot));
+      break;
+    case FieldType_molinfo_field:
+      ValNodeLink (&err_list, TestDialog (dlg->sequence_qual));
+      break;
+    default :
+      ValNodeAddPointer (&err_list, 0, "No field type chosen");
+      break;
+  }
+  return err_list;  
+}
+
+
+static DialoG FieldTypeDialog (GrouP h, Boolean text_only, Boolean for_remove, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  FieldTypeDlgPtr dlg;
+  GrouP                 p;
+  
+  dlg = (FieldTypeDlgPtr) MemNew (sizeof (FieldTypeDlgData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, 0, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = FieldTypeToDialog;
+  dlg->fromdialog = DialogToFieldType;
+  dlg->testdialog = TestFieldTypeDialog;
+
+  dlg->src_qual = SourceQualChoiceDialog (p, text_only, for_remove, change_notify, change_userdata);
+  dlg->feature_field_grp = HiddenGroup (p, 2, 0, NULL);
+  dlg->feature_type = FeatureTypeDialog (dlg->feature_field_grp, change_notify, change_userdata);
+  dlg->feature_field = FeatQualChoiceDialog (dlg->feature_field_grp, change_notify, change_userdata);
+  dlg->cdsgeneprot = CDSGeneProtFieldDialog (p, change_notify, change_userdata);
+  dlg->sequence_qual = SequenceQualDialog (p, change_notify, change_userdata);
+
+  SafeHide (dlg->src_qual);
+  SafeHide (dlg->feature_field_grp);
+  SafeHide (dlg->cdsgeneprot);
+  SafeHide (dlg->sequence_qual);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->src_qual,
+                              (HANDLE) dlg->feature_field_grp,
+                              (HANDLE) dlg->cdsgeneprot,
+                              (HANDLE) dlg->sequence_qual,
+                              NULL);
+
+  return (DialoG) p;
+}
+
+
+typedef struct fieldpairtypedlg {
+  DIALOG_MESSAGE_BLOCK
+  Uint1 field_type;
+  GrouP src_qual_grp;
+  DialoG src_qual_from;
+  DialoG src_qual_to;
+  GrouP feature_field_grp;
+  DialoG feature_type;
+  DialoG feature_field_from;
+  DialoG feature_field_to;
+  GrouP cdsgeneprot_grp;
+  DialoG cdsgeneprot_from;
+  DialoG cdsgeneprot_to;
+  DialoG molinfo_dlg;
+} FieldPairTypeDlgData, PNTR FieldPairTypeDlgPtr;
+
+
+static void FieldPairTypeToDialog (DialoG d, Pointer data)
+{
+  FieldPairTypeDlgPtr dlg;
+  ValNodePtr vnp;
+  ValNode      vn;
+  FieldTypePtr from_field, to_field;  
+  FeatureFieldPairPtr ffp;
+  CDSGeneProtFieldPairPtr cgp;
+
+  dlg = (FieldPairTypeDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  SafeHide (dlg->src_qual_grp);
+  SafeHide (dlg->feature_field_grp);
+  SafeHide (dlg->cdsgeneprot_grp);
+  SafeHide (dlg->molinfo_dlg);
+  vnp = (ValNodePtr) data;
+  if (vnp == NULL) {
+    dlg->field_type = 0;
+  } else {
+    switch (vnp->choice) {
+      case FieldPairType_source_qual:
+        SafeShow (dlg->src_qual_grp);
+        from_field = GetFromFieldFromFieldPair (vnp);
+        if (from_field == NULL) {
+          PointerToDialog (dlg->src_qual_from, NULL);
+        } else {
+          PointerToDialog (dlg->src_qual_from, from_field->data.ptrvalue);
+        }
+        from_field = FieldTypeFree (from_field);
+        to_field = GetToFieldFromFieldPair (vnp);
+        if (to_field == NULL) {
+          PointerToDialog (dlg->src_qual_to, NULL);
+        } else {
+          PointerToDialog (dlg->src_qual_to, to_field->data.ptrvalue);
+        }
+        to_field = FieldTypeFree (to_field);
+        dlg->field_type = FieldType_source_qual;
+        break;
+      case FieldPairType_feature_field:
+        SafeShow (dlg->feature_field_grp);
+        ffp = (FeatureFieldPairPtr) vnp->data.ptrvalue;
+        if (ffp == NULL) {
+          PointerToDialog (dlg->feature_type, NULL);
+          PointerToDialog (dlg->feature_field_from, NULL);
+          PointerToDialog (dlg->feature_field_to, NULL);
+        } else {
+          vn.choice = ffp->type;
+          vn.data.ptrvalue = NULL;
+          vn.next = NULL;
+          PointerToDialog (dlg->feature_type, &vn);
+          PointerToDialog (dlg->feature_field_from, ffp->field_from);
+          PointerToDialog (dlg->feature_field_to, ffp->field_to);
+        }
+        dlg->field_type = FieldType_feature_field;
+        break;
+      case FieldPairType_cds_gene_prot:
+        SafeShow (dlg->cdsgeneprot_grp);
+        cgp = (CDSGeneProtFieldPairPtr) vnp->data.ptrvalue;
+        if (cgp == NULL) {
+          PointerToDialog (dlg->cdsgeneprot_from, NULL);
+          PointerToDialog (dlg->cdsgeneprot_to, NULL);
+        } else {
+          from_field = GetFromFieldFromFieldPair (vnp);
+          PointerToDialog (dlg->cdsgeneprot_from, from_field);
+          from_field = FieldTypeFree (from_field);
+          to_field = GetToFieldFromFieldPair (vnp);
+          PointerToDialog (dlg->cdsgeneprot_to, to_field);
+          to_field = FieldTypeFree (to_field);
+        }
+        dlg->field_type = FieldType_cds_gene_prot;
+        break;
+      case FieldPairType_molinfo_field:
+        SafeShow (dlg->molinfo_dlg);
+        PointerToDialog (dlg->molinfo_dlg, vnp->data.ptrvalue);
+        dlg->field_type = FieldPairType_molinfo_field;
+        break;
+    }
+  }
+}
+
+
+static Pointer DialogToFieldPairType (DialoG d)
+{
+  FieldPairTypeDlgPtr dlg;
+  ValNodePtr vnp = NULL, vnp1, vnp2;
+  SourceQualPairPtr sqp;
+  FeatureFieldPairPtr ffp;
+  CDSGeneProtFieldPairPtr cgp;
+
+  dlg = (FieldPairTypeDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  switch (dlg->field_type) {
+    case FieldPairType_source_qual:
+      vnp1 = DialogToPointer (dlg->src_qual_from);
+      vnp2 = DialogToPointer (dlg->src_qual_to);
+      if (vnp1 != NULL && vnp2 != NULL && vnp1->choice == SourceQualChoice_textqual && vnp2->choice == SourceQualChoice_textqual) {
+        sqp = SourceQualPairNew ();
+        sqp->field_from = vnp1->data.intvalue;
+        sqp->field_to = vnp2->data.intvalue;
+        vnp = ValNodeNew (NULL);
+        vnp->choice = FieldPairType_source_qual;
+        vnp->data.ptrvalue = sqp;
+      }
+      vnp1 = SourceQualChoiceFree (vnp1);
+      vnp2 = SourceQualChoiceFree (vnp2); 
+      break;
+    case FieldPairType_feature_field:
+      vnp2 = (ValNodePtr) DialogToPointer (dlg->feature_type);
+      if (vnp2 != NULL) {
+        ffp = FeatureFieldPairNew ();
+        ffp->type = vnp2->choice;
+        vnp2 = ValNodeFree (vnp2);
+        ffp->field_from = DialogToPointer (dlg->feature_field_from);
+        ffp->field_to = DialogToPointer (dlg->feature_field_to);
+        vnp = ValNodeNew (NULL);
+        vnp->choice = FieldPairType_feature_field;
+        vnp->data.ptrvalue = ffp;
+      }
+      break;
+    case FieldPairType_cds_gene_prot:
+      vnp1 = DialogToPointer (dlg->cdsgeneprot_from);
+      vnp2 = DialogToPointer (dlg->cdsgeneprot_to);
+      if (vnp1 != NULL && vnp2 != NULL) {
+        cgp = CDSGeneProtFieldPairNew ();
+        cgp->field_from = vnp1->data.intvalue;
+        cgp->field_to = vnp2->data.intvalue;
+        vnp = ValNodeNew (NULL);
+        vnp->choice = FieldPairType_cds_gene_prot;
+        vnp->data.ptrvalue = cgp;
+      }
+      vnp1 = ValNodeFree (vnp1);
+      vnp2 = ValNodeFree (vnp2);
+      break;
+    case FieldPairType_molinfo_field:
+      vnp1 = DialogToPointer (dlg->molinfo_dlg);
+      if (vnp1 != NULL) {
+        vnp = ValNodeNew (NULL);
+        vnp->choice = FieldPairType_molinfo_field;
+        vnp->data.ptrvalue = vnp1;
+      }
+      break;
+  }
+
+  return vnp;
+}
+
+
+static ValNodePtr TestFieldPairTypeDialog (DialoG d)
+{
+  FieldPairTypeDlgPtr dlg;
+  ValNodePtr err_list = NULL;
+
+  dlg = (FieldPairTypeDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) {
+    return NULL;
+  }
+
+  switch (dlg->field_type) {
+    case FieldPairType_source_qual:
+      err_list = TestDialog (dlg->src_qual_from);
+      ValNodeLink (&err_list, TestDialog (dlg->src_qual_to));
+      break;
+    case FieldPairType_feature_field:
+      err_list = TestDialog (dlg->feature_type);
+      ValNodeLink (&err_list, TestDialog (dlg->feature_field_from));
+      ValNodeLink (&err_list, TestDialog (dlg->feature_field_to));
+      break;
+    case FieldPairType_cds_gene_prot:
+      ValNodeLink (&err_list, TestDialog (dlg->cdsgeneprot_from));
+      ValNodeLink (&err_list, TestDialog (dlg->cdsgeneprot_to));
+      break;
+    case FieldPairType_molinfo_field:
+      ValNodeLink (&err_list, TestDialog (dlg->molinfo_dlg));
+      break;
+    default:
+      ValNodeAddPointer (&err_list, 0, "No field type");
+      break;
+  }
+  return err_list;
+}
+    
+
+static DialoG FieldPairTypeDialog (GrouP h, Boolean for_convert, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  FieldPairTypeDlgPtr dlg;
+  GrouP                 p;
+  
+  dlg = (FieldPairTypeDlgPtr) MemNew (sizeof (FieldPairTypeDlgData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, 0, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = FieldPairTypeToDialog;
+  dlg->fromdialog = DialogToFieldPairType;
+  dlg->testdialog = TestFieldPairTypeDialog;
+
+  dlg->src_qual_grp = HiddenGroup (p, 2, 0, NULL);
+  dlg->src_qual_from = SourceQualChoiceDialog (dlg->src_qual_grp, TRUE, FALSE, change_notify, change_userdata);
+  dlg->src_qual_to = SourceQualChoiceDialog (dlg->src_qual_grp, TRUE, FALSE, change_notify, change_userdata);
+
+  dlg->feature_field_grp = HiddenGroup (p, 3, 0, NULL);
+  dlg->feature_type = FeatureTypeDialog (dlg->feature_field_grp, change_notify, change_userdata);
+  dlg->feature_field_from = FeatQualChoiceDialog (dlg->feature_field_grp, change_notify, change_userdata);
+  dlg->feature_field_to = FeatQualChoiceDialog (dlg->feature_field_grp, change_notify, change_userdata);
+  
+  dlg->cdsgeneprot_grp = HiddenGroup (p, 2, 0, NULL);
+  dlg->cdsgeneprot_from = CDSGeneProtFieldDialog (dlg->cdsgeneprot_grp, change_notify, change_userdata);
+  dlg->cdsgeneprot_to = CDSGeneProtFieldDialog (dlg->cdsgeneprot_grp, change_notify, change_userdata);
+
+  if (for_convert) {
+    dlg->molinfo_dlg = SequenceQualPairDialog (p, change_notify, change_userdata);
+  }
+
+  SafeHide (dlg->src_qual_grp);
+  SafeHide (dlg->feature_field_grp);
+  SafeHide (dlg->cdsgeneprot_grp);
+  SafeHide (dlg->molinfo_dlg);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->src_qual_grp,
+                              (HANDLE) dlg->feature_field_grp,
+                              (HANDLE) dlg->cdsgeneprot_grp, 
+                              (HANDLE) dlg->molinfo_dlg,
+                              NULL);
+
+  return (DialoG) p;
+}
+
+
+typedef struct editaecractiondlg {
+  DIALOG_MESSAGE_BLOCK
+  PopuP qual_type;
+  DialoG field_dlg;
+  TexT   value_txt;
+  DialoG edit;
+  DialoG text_portion;
+  ButtoN remove_from_parsed;
+  DialoG existing_text;
+  DialoG constraint_dlg;
+  ButtoN accept_btn;
+
+  Uint1      action_type;
+
+  Nlm_ChangeNotifyProc     change_notify;
+  Pointer                  change_userdata;
+  Nlm_ChangeNotifyProc     redraw_notify;
+  Pointer                  redraw_userdata;
+} EditAECRActionDlgData, PNTR EditAECRActionDlgPtr;
+
+
+static void ChangeAECRQualPopup (PopuP p)
+{
+  EditAECRActionDlgPtr d;
+
+  d = (EditAECRActionDlgPtr) GetObjectExtra (p);
+  if (d != NULL && d->redraw_notify != NULL) {
+    d->redraw_notify(d->redraw_userdata);
+  }
+}
+
+
+static Uint1 ActionTypeChoiceFromPopupValue (Int4 i)
+{
+  Uint1 action_type_choice = ActionChoice_apply;
+
+  switch (i) {
+    case 2:
+      action_type_choice = ActionChoice_apply;
+      break;
+    case 3:
+      action_type_choice = ActionChoice_edit;
+      break;
+    case 4:
+      action_type_choice = ActionChoice_convert;
+      break;
+    case 5:
+      action_type_choice = ActionChoice_copy;
+      break;
+    case 6:
+      action_type_choice = ActionChoice_swap;
+      break;
+    case 8:
+      action_type_choice = ActionChoice_remove;
+      break;
+    case 7:
+      action_type_choice = ActionChoice_parse;
+      break;
+  }
+  return action_type_choice;
+}
+
+
+static Uint1 FieldTypeChoiceFromPopupValue (Int4 i)
+{
+  Uint1 field_type_choice = FieldType_source_qual;
+  switch (i) {
+    case 1: 
+      field_type_choice = FieldType_source_qual;
+      break;
+    case 2: 
+      field_type_choice = FieldType_feature_field;
+      break;
+    case 3:
+      field_type_choice = FieldType_cds_gene_prot;
+      break;
+    case 4:
+      field_type_choice = FieldType_molinfo_field;
+      break;
+  }
+  return field_type_choice;
+}
+
+
+static Uint1 FieldTypeChoiceFromEditAECRActionDialog (DialoG d)
+{
+  EditAECRActionDlgPtr dlg;
+  
+  dlg = (EditAECRActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) {
+    return FieldType_source_qual;
+  } else {
+    return FieldTypeChoiceFromPopupValue (GetValue (dlg->qual_type));
+  }
+}
+
+
+static Boolean IsFieldTypeNonText (ValNodePtr field_type)
+{
+  ValNodePtr      vnp;
+  FeatureFieldPtr ffp;
+  Boolean         rval = FALSE;
+
+  if (field_type == NULL) {
+    return FALSE;
+  } 
+  switch (field_type->choice) {
+    case FieldType_source_qual :
+      vnp = (ValNodePtr) field_type->data.ptrvalue;
+      if (vnp != NULL) {
+        if (vnp->choice == SourceQualChoice_location || vnp->choice == SourceQualChoice_origin) {
+          rval = TRUE;
+        } else if (vnp->choice == SourceQualChoice_textqual) {
+          if (IsNonTextSourceQual (vnp->data.intvalue)) {
+            rval = TRUE;
+          }
+        }
+      }
+      break;
+    case FieldType_feature_field :
+      ffp = (FeatureFieldPtr) field_type->data.ptrvalue;
+      if (ffp != NULL && ffp->field != NULL && ffp->field->choice == FeatQualChoice_legal_qual
+          && ffp->field->data.intvalue == Feat_qual_legal_pseudo) {
+        rval = TRUE;
+      }
+      break;
+    case FieldType_molinfo_field :
+      rval = TRUE;
+      break;
+  } 
+  return rval;
+}
+
+
+static void ChangeDialogForApplyFieldChoice (EditAECRActionDlgPtr dlg)
+{
+  ValNodePtr field;
+
+  if (dlg == NULL) return;
+  field = DialogToPointer (dlg->field_dlg);
+  if (IsFieldTypeNonText (field)) {
+    DisableNonTextOptions (dlg->existing_text);
+    Hide (dlg->value_txt);
+  } else {
+    EnableNonTextOptions (dlg->existing_text);
+    Show (dlg->value_txt);
+  }
+  field = FieldTypeFree (field);
+}
+
+
+static void ChangeApplyFieldType (Pointer data)
+{
+  EditAECRActionDlgPtr dlg;
+
+  dlg = (EditAECRActionDlgPtr) data;
+  if (dlg == NULL) return;
+  ChangeDialogForApplyFieldChoice (dlg);
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static ValNodePtr TestAECRActionDialog (DialoG d)
+{
+  EditAECRActionDlgPtr dlg;
+  Int2 field_type;
+  ValNodePtr err_list = NULL;
+  ValNodePtr field;
+  Boolean    field_is_nontext = FALSE;
+
+  dlg = (EditAECRActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  field_type = GetValue (dlg->qual_type);
+  if (field_type < 1 || field_type > 4) {
+    ValNodeAddPointer (&err_list, 0, "field type");
+  }
+
+  ValNodeLink (&err_list, TestDialog (dlg->field_dlg));
+  ValNodeLink (&err_list, TestDialog (dlg->existing_text));
+
+  field = DialogToPointer (dlg->field_dlg);
+  field_is_nontext = IsFieldTypeNonText (field);
+  field = FieldTypeFree (field);
+
+  switch (dlg->action_type) {
+    case ActionChoice_apply:
+      if (TextHasNoText (dlg->value_txt) && !field_is_nontext) {
+        ValNodeAddPointer (&err_list, 0, "no apply text");
+      }
+      break;
+    case ActionChoice_edit:
+      if (field_is_nontext) {
+        ValNodeAddPointer (&err_list, 0, "invalid action for field type");
+      }
+      ValNodeLink (&err_list, TestDialog (dlg->edit));
+      break;
+    case ActionChoice_convert:
+      if (field_is_nontext && field_type != 4) {
+        ValNodeAddPointer (&err_list, 0, "invalid action for field type");
+      }
+      ValNodeLink (&err_list, TestDialog (dlg->edit));
+      break;
+    case ActionChoice_copy:
+      if (field_is_nontext) {
+        ValNodeAddPointer (&err_list, 0, "invalid action for field type");
+      }
+      ValNodeLink (&err_list, TestDialog (dlg->edit));
+      break;
+    case ActionChoice_swap:
+      if (field_is_nontext) {
+        ValNodeAddPointer (&err_list, 0, "invalid action for field type");
+      }
+      ValNodeLink (&err_list, TestDialog (dlg->edit));
+      break;
+    case ActionChoice_remove:
+      break;
+    case ActionChoice_parse:
+      if (field_is_nontext) {
+        ValNodeAddPointer (&err_list, 0, "invalid action for field type");
+      }
+      ValNodeLink (&err_list, TestDialog (dlg->edit));
+      ValNodeLink (&err_list, TestDialog (dlg->text_portion));
+      break;
+  }
+  
+  return err_list;
+}
+
+
+static void ChangeEditAECRActionDialogText (TexT t)
+{
+  EditAECRActionDlgPtr dlg;
+
+  dlg = (EditAECRActionDlgPtr) GetObjectExtra (t);
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    (dlg->change_notify)(dlg->change_userdata);
+  }
+}
+
+
+static Pointer AECRActionFromEditDialog (DialoG d)
+{
+  EditAECRActionDlgPtr dlg;
+  AECRActionPtr      action = NULL;
+  Uint1              qual_type;
+  ApplyActionPtr     apply;
+  EditActionPtr      edit;
+  ConvertActionPtr   convert;
+  CopyActionPtr      copy;
+  SwapActionPtr      swap;
+  AECRParseActionPtr parse;
+  RemoveActionPtr    remove;
+
+  dlg = (EditAECRActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  action = AECRActionNew ();
+
+  qual_type = FieldTypeChoiceFromPopupValue (GetValue (dlg->qual_type));
+
+  switch (dlg->action_type) {
+    case ActionChoice_apply:
+      apply = ApplyActionNew();
+      apply->field = DialogToPointer (dlg->field_dlg); 
+      if (IsFieldTypeNonText (apply->field)) {
+        apply->value = StringSave ("TRUE");
+      } else {
+        apply->value = SaveStringFromText (dlg->value_txt);
+      }        
+      apply->existing_text = (Uint2) DialogToPointer (dlg->existing_text);
+      action->action = ValNodeNew (NULL);
+      action->action->choice = dlg->action_type;
+      action->action->data.ptrvalue = apply;
+      break;
+    case ActionChoice_edit:
+      edit = EditActionNew ();
+      edit->field = DialogToPointer (dlg->field_dlg);
+      edit->edit = DialogToPointer (dlg->edit);
+      action->action = ValNodeNew (NULL);
+      action->action->choice = dlg->action_type;
+      action->action->data.ptrvalue = edit;
+      break;
+    case ActionChoice_convert:
+      convert = ConvertActionNew();
+      convert->fields = DialogToPointer (dlg->field_dlg);
+      convert->existing_text = (Uint2) DialogToPointer (dlg->existing_text);
+      action->action = ValNodeNew (NULL);
+      action->action->choice = dlg->action_type;
+      action->action->data.ptrvalue = convert;
+      break;
+    case ActionChoice_copy:
+      copy = CopyActionNew();
+      copy->fields = DialogToPointer (dlg->field_dlg);
+      copy->existing_text = (Uint2) DialogToPointer (dlg->existing_text);
+      action->action = ValNodeNew (NULL);
+      action->action->choice = dlg->action_type;
+      action->action->data.ptrvalue = copy;
+      break;
+    case ActionChoice_swap:
+      swap = SwapActionNew();
+      swap->fields = DialogToPointer (dlg->field_dlg);
+      action->action = ValNodeNew (NULL);
+      action->action->choice = dlg->action_type;
+      action->action->data.ptrvalue = swap;
+      break;
+    case ActionChoice_remove:
+      remove = RemoveActionNew();
+      remove->field = DialogToPointer (dlg->field_dlg);
+      action->action = ValNodeNew (NULL);
+      action->action->choice = dlg->action_type;
+      action->action->data.ptrvalue = remove;
+      break;
+    case ActionChoice_parse:
+      parse = AECRParseActionNew();
+      parse->fields = DialogToPointer (dlg->field_dlg);
+      parse->portion = DialogToPointer (dlg->text_portion);
+      parse->remove_from_parsed = GetStatus (dlg->remove_from_parsed);
+      parse->existing_text = (Uint2) DialogToPointer (dlg->existing_text);
+      action->action = ValNodeNew (NULL);
+      action->action->choice = dlg->action_type;
+      action->action->data.ptrvalue = parse;
+      break;
+  }
+
+  action->constraint = DialogToPointer (dlg->constraint_dlg);
+
+  return (Pointer) action;
+}
+
+
+static Boolean MolInfoAllowed (Int4 action_type)
+{
+  if (action_type != ActionChoice_edit
+      && action_type != ActionChoice_copy
+      && action_type != ActionChoice_swap
+      && action_type != ActionChoice_parse) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+
+static void FieldToAECRDialog (ValNodePtr field, DialoG dlg, Int4 action_type, Int4 field_type)
+{
+  ValNode               vn;
+
+  if (field == NULL) {
+    PointerToDialog (dlg, NULL);
+  } else if (field_type == FieldType_molinfo_field && !MolInfoAllowed (action_type)) {
+    vn.choice = FieldType_source_qual;
+    vn.data.ptrvalue = NULL;
+    vn.next = NULL;
+    PointerToDialog (dlg, &vn);
+  } else {
+    PointerToDialog (dlg, field);
+  }  
+}
+
+
+  
+static DialoG 
+EditAECRActionDialog 
+(GrouP h,
+ AECRActionPtr action,
+ Boolean indexer_version,
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata,
+ Nlm_ChangeNotifyProc     redraw_notify,
+ Pointer                  redraw_userdata)
+{
+  EditAECRActionDlgPtr dlg;
+  GrouP                 p;
+  Uint1                 field_type;
+  GrouP                 control_group;
+  ApplyActionPtr        apply;
+  EditActionPtr         edit;
+  AECRParseActionPtr    parse;
+  RemoveActionPtr       remove;
+  ConvertActionPtr      convert;
+  CopyActionPtr         copy;
+  SwapActionPtr         swap;
+
+  dlg = (EditAECRActionDlgPtr) MemNew (sizeof (EditAECRActionDlgData));
+
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = NULL;
+  dlg->fromdialog = AECRActionFromEditDialog;
+  dlg->testdialog = TestAECRActionDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+  dlg->redraw_notify = redraw_notify;
+  dlg->redraw_userdata = redraw_userdata;
+
+  if (action == NULL || action->action == NULL) {
+    dlg->action_type = ActionChoice_apply;
+  } else {
+    dlg->action_type = action->action->choice;
+  }
+
+  dlg->qual_type = PopupList (p, TRUE, ChangeAECRQualPopup);
+  SetObjectExtra (dlg->qual_type, dlg, NULL);
+  PopupItem (dlg->qual_type, "Source Qual");
+  PopupItem (dlg->qual_type, "Feature Qual");
+  PopupItem (dlg->qual_type, "CDS-Gene-Prot Qual");
+  if (MolInfoAllowed (dlg->action_type)) {
+    PopupItem (dlg->qual_type, "MolInfo Qual");
+  }
+  field_type = FieldTypeFromAECRAction (action);
+  switch (field_type) {
+    case FieldType_source_qual:
+      SetValue (dlg->qual_type, 1);
+      break;
+    case FieldType_feature_field:
+      SetValue (dlg->qual_type, 2);
+      break;
+    case FieldType_cds_gene_prot:
+      SetValue (dlg->qual_type, 3);
+      break;
+    case FieldType_molinfo_field:
+      if (MolInfoAllowed(dlg->action_type)) {
+        SetValue (dlg->qual_type, 4);
+      } else {
+        SetValue (dlg->qual_type, 1);
+      }
+      break;
+    default:
+      SetValue (dlg->qual_type, 1);
+      break;
+  }
+
+  dlg->field_dlg = NULL;
+  dlg->value_txt = NULL;
+  dlg->existing_text = NULL;
+
+  control_group = HiddenGroup (p, -1, 0, NULL);
+  switch (dlg->action_type) {
+    case ActionChoice_apply:
+      dlg->field_dlg = FieldTypeDialog (control_group, FALSE, FALSE, ChangeApplyFieldType, dlg);
+      dlg->value_txt = DialogText (control_group, "", 20, ChangeEditAECRActionDialogText);
+      SetObjectExtra (dlg->value_txt, dlg, NULL);
+      AlignObjects (ALIGN_CENTER, (HANDLE) dlg->field_dlg, (HANDLE) dlg->value_txt, NULL);
+      dlg->existing_text = ExistingTextDialog (p, change_notify, change_userdata);
+      if (action != NULL && action->action != NULL && action->action->data.ptrvalue != NULL) {
+        apply = (ApplyActionPtr) action->action->data.ptrvalue;
+        PointerToDialog (dlg->field_dlg, apply->field);
+        SetTitle (dlg->value_txt, apply->value);
+        PointerToDialog (dlg->existing_text, (Pointer) apply->existing_text);
+      }
+      ChangeDialogForApplyFieldChoice (dlg);
+      break;
+    case ActionChoice_edit:
+      dlg->field_dlg = FieldTypeDialog (control_group, TRUE, FALSE, change_notify, change_userdata);
+      dlg->edit = FieldEditDialog (control_group, change_notify, change_userdata);
+      AlignObjects (ALIGN_CENTER, (HANDLE) dlg->field_dlg, (HANDLE) dlg->edit, NULL);
+      if (action != NULL && action->action != NULL 
+          && action->action->data.ptrvalue != NULL) {
+        edit = (EditActionPtr) action->action->data.ptrvalue;
+        PointerToDialog (dlg->edit, edit->edit);
+        FieldToAECRDialog (edit->field, dlg->field_dlg, dlg->action_type, field_type);
+      }
+        
+      break;
+    case ActionChoice_remove:
+      dlg->field_dlg = FieldTypeDialog (control_group, FALSE, TRUE, change_notify, change_userdata);
+      if (action != NULL && action->action != NULL && action->action->data.ptrvalue != NULL) {
+        remove = (RemoveActionPtr) action->action->data.ptrvalue;
+        PointerToDialog (dlg->field_dlg, remove->field);
+      }
+      break;
+    case ActionChoice_convert:
+      dlg->field_dlg = FieldPairTypeDialog (control_group, TRUE, change_notify, change_userdata);
+      dlg->existing_text = ExistingTextDialog (p, change_notify, change_userdata);
+      if (action != NULL && action->action != NULL && action->action->data.ptrvalue != NULL) {
+        convert = (ConvertActionPtr) action->action->data.ptrvalue;
+        PointerToDialog (dlg->field_dlg, convert->fields);
+        PointerToDialog (dlg->existing_text, (Pointer) convert->existing_text);
+      }
+      break;
+    case ActionChoice_copy:
+      dlg->field_dlg = FieldPairTypeDialog (control_group, FALSE, change_notify, change_userdata);
+      dlg->existing_text = ExistingTextDialog (p, change_notify, change_userdata);
+      if (action != NULL && action->action != NULL 
+          && action->action->data.ptrvalue != NULL) {
+        copy = (CopyActionPtr) action->action->data.ptrvalue;
+        FieldToAECRDialog (copy->fields, dlg->field_dlg, dlg->action_type, field_type);
+        PointerToDialog (dlg->existing_text, (Pointer) copy->existing_text);
+      }
+      break;
+    case ActionChoice_swap:
+      dlg->field_dlg = FieldPairTypeDialog (control_group, FALSE, change_notify, change_userdata);
+      if (action != NULL && action->action != NULL
+          && action->action->data.ptrvalue != NULL) {
+        swap = (SwapActionPtr) action->action->data.ptrvalue;
+        FieldToAECRDialog (swap->fields, dlg->field_dlg, dlg->action_type, field_type);
+      }
+      break;
+    case ActionChoice_parse:
+      dlg->field_dlg = FieldPairTypeDialog (control_group, FALSE, change_notify, change_userdata);
+      dlg->text_portion = TextPortionDialog (control_group, TRUE, change_notify, change_userdata);
+      dlg->remove_from_parsed = CheckBox (control_group, "Remove from parsed field", NULL);
+      AlignObjects (ALIGN_CENTER, (HANDLE) dlg->field_dlg, (HANDLE) dlg->text_portion, (HANDLE) dlg->remove_from_parsed, NULL);
+      dlg->existing_text = ExistingTextDialog (p, change_notify, change_userdata);
+      if (action != NULL && action->action != NULL
+          && action->action->data.ptrvalue != NULL) {
+        parse = (AECRParseActionPtr) action->action->data.ptrvalue;
+        FieldToAECRDialog (parse->fields, dlg->field_dlg, dlg->action_type, field_type);
+        PointerToDialog (dlg->text_portion, parse->portion);
+        SetStatus (dlg->remove_from_parsed, parse->remove_from_parsed);
+        PointerToDialog (dlg->existing_text, (Pointer) parse->existing_text);
+      }
+      break;
+  }
+
+  dlg->constraint_dlg = ConstraintSetDialog (p, change_notify, change_userdata);
+  if (action != NULL) {
+    PointerToDialog (dlg->constraint_dlg, action->constraint);
+  }
+  
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->qual_type,
+                              (HANDLE) dlg->constraint_dlg,
+                              (HANDLE) control_group,
+                              (HANDLE) dlg->existing_text,
+                              NULL);
+  return (DialoG) p;
+}
+
+
+typedef struct applyfeatureactiondlg {
+  DIALOG_MESSAGE_BLOCK
+  DialoG                   feature_type_dlg;
+  ButtoN                   apply_to_parts;
+  TexT                     only_this_part;
+  ButtoN                   partial5;
+  ButtoN                   partial3;
+  GrouP                    strand_group;
+  GrouP                    use_whole_interval;
+  TexT                     left_end;
+  TexT                     right_end;
+  GrouP                    all_or_some_group;
+  TexT                     accession_list_txt;
+  ButtoN                   add_redundant;
+  /* for CDS */
+  ButtoN                   add_mrna;
+  PopuP                    reading_frame;
+  TexT                     protein_name;
+  TexT                     protein_description;
+
+  /* for RNA */
+  DialoG                   ncrna_class;
+  TexT                     rna_name;
+
+  /* for import features */
+  DialoG                   quals;
+  
+  /* for all */
+  TexT                     gene_locus;
+  TexT                     gene_description;
+  TexT                     comment;
+
+  Nlm_ChangeNotifyProc     change_notify;
+  Pointer                  change_userdata;
+
+
+} ApplyFeatureActionDlgData, PNTR ApplyFeatureActionDlgPtr;
+
+
+static ValNodePtr TestApplyFeatureActionDialog (DialoG d)
+{
+  ApplyFeatureActionDlgPtr dlg;
+  ValNodePtr err_list = NULL;
+
+  dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) {
+    return NULL;
+  }
+
+  err_list = TestDialog (dlg->feature_type_dlg);
+
+  return err_list;
+}
+
+
+static void ChangeApplyFeatureActionDlg (ApplyFeatureActionDlgPtr dlg)
+{
+  if (dlg == NULL) return;
+
+  if (GetStatus (dlg->apply_to_parts)) {
+    SafeEnable (dlg->only_this_part);
+  } else {
+    SafeDisable (dlg->only_this_part);
+  }
+
+  if (dlg->use_whole_interval != NULL) {
+    if (GetValue (dlg->use_whole_interval) == 2) {
+      Enable (dlg->left_end);
+      Enable (dlg->right_end);
+    } else {
+      Disable (dlg->left_end);
+      Disable (dlg->right_end);
+    }
+  }
+
+  if (dlg->all_or_some_group != NULL) {
+    if (GetValue (dlg->all_or_some_group) == 2) {
+      Enable (dlg->accession_list_txt);
+    } else {
+      Disable (dlg->accession_list_txt);
+    }
+  }
+
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static CharPtr SequenceListWrite (ValNodePtr seq_list)
+{
+  Int4 len = 0;
+  ValNodePtr vnp;
+  CharPtr    txt = NULL;
+
+  if (seq_list == NULL) return NULL;
+  for (vnp = seq_list; vnp != NULL; vnp = vnp->next) {
+    len += StringLen (vnp->data.ptrvalue) + 2;
+  }
+
+  txt = (CharPtr) MemNew (sizeof (Char) * len);
+  for (vnp = seq_list; vnp != NULL; vnp = vnp->next) {
+    StringCat (txt, vnp->data.ptrvalue);
+    if (vnp->next != NULL) {
+      StringCat (txt, ";");
+    }
+  }
+  return txt;
+}
+
+
+static ValNodePtr SequenceListCollect (CharPtr txt)
+{
+  ValNodePtr seq_list = NULL;
+  CharPtr    cp;
+
+  if (StringHasNoText (txt)) {
+    return NULL;
+  }
+  cp = StringChr (txt, ';');
+  while (cp != NULL && *txt != 0) {
+    *cp = 0;
+    if (!StringHasNoText (txt)) {
+      ValNodeAddPointer (&seq_list, 0, StringSave (txt));
+    }
+    *cp = ';';
+    txt = cp + 1;
+    cp = StringChr (txt, ':');
+  }
+  if (!StringHasNoText (txt)) {
+    ValNodeAddPointer (&seq_list, 0, StringSave (txt));
+  }
+  return seq_list;
+}
+
+
+static CharPtr FindFeatQualValue (ValNodePtr vnp, Int4 featqual)
+{
+  FeatQualLegalValPtr q;
+  CharPtr str = NULL;
+  while (vnp != NULL && str == NULL) {
+    q = (FeatQualLegalValPtr) vnp->data.ptrvalue;
+    if (q != NULL && q->qual == featqual) {
+      str = q->val;
+    }
+    vnp = vnp->next;
+  }
+  if (str == NULL) {
+    str = "";
+  }
+  return str;
+}
+
+
+static void SetFeatQualValue (ValNodePtr PNTR fields, Int4 featqual, CharPtr val)
+{
+  FeatQualLegalValPtr q;
+
+  q = FeatQualLegalValNew ();
+  q->qual = featqual;
+  q->val = StringSave (val);
+  ValNodeAddPointer (fields, 1, q);
+}
+
+
+static SeqFeatPtr CreateFeatureWithImportFeatureQuals (ApplyFeatureActionPtr action)
+{
+  SeqFeatPtr sfp;
+  ValNodePtr vnp;
+  FeatQualLegalValPtr q;
+  GBQualPtr gbq;
+  CharPtr   qualname, cp;
+
+  sfp = SeqFeatNew();
+  sfp->idx.subtype = GetFeatdefFromFeatureType (action->type);
+  sfp->data.choice = FindFeatFromFeatDefType (sfp->idx.subtype);
+
+  for (vnp = action->fields; vnp != NULL; vnp = vnp->next) {
+    q = (FeatQualLegalValPtr) vnp->data.ptrvalue;
+    if (q != NULL && q->qual != Feat_qual_legal_gene && q->qual != Feat_qual_legal_gene_description && q->qual != Feat_qual_legal_note) {
+      gbq = GBQualNew ();
+      qualname = StringSave (GetFeatQualName(q->qual));
+      cp = StringChr (qualname, '-');
+      while (cp != NULL) {
+        *cp = '_';
+        cp = StringChr (cp + 1, '-');
+      }
+      gbq->qual = qualname;
+      gbq->val = StringSave (q->val);
+      gbq->next = sfp->qual;
+      sfp->qual = gbq;
+    }
+  }
+  return sfp;  
+}
+
+
+static void AddGBQualsToActionFields (GBQualPtr gbq, ApplyFeatureActionPtr action)
+{
+  Int4 qualtype;
+
+  if (action == NULL) return;
+
+  while (gbq != NULL) {
+    qualtype = GetFeatQualByName (gbq->qual);
+    if (qualtype > -1) {
+      SetFeatQualValue (&(action->fields), qualtype, gbq->val);
+    }
+    gbq = gbq->next;
+  }
+}
+
+
+static void ApplyFeatureActionToDialog (DialoG d, Pointer data)
+{
+  ApplyFeatureActionDlgPtr dlg;
+  ApplyFeatureActionPtr    action;
+  Char                     num[20];
+  LocationIntervalPtr      lint;
+  CharPtr                  txt;
+  ValNode                  vn;
+
+  dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) {
+    return;
+  }
+
+  action = (ApplyFeatureActionPtr) data;
+
+  if (action == NULL) {
+    PointerToDialog (dlg->feature_type_dlg, NULL);
+    SetStatus (dlg->apply_to_parts, FALSE);
+    SetTitle (dlg->only_this_part, "");
+    SetStatus (dlg->partial5, FALSE);
+    SetStatus (dlg->partial3, FALSE);
+    SetValue (dlg->strand_group, 1);
+    SetValue (dlg->use_whole_interval, 1);
+    SetTitle (dlg->left_end, "");
+    SetTitle (dlg->right_end, "");
+    SetValue (dlg->all_or_some_group, 1);
+    SetTitle (dlg->accession_list_txt, "");
+    SetStatus (dlg->add_redundant, FALSE);
+
+    /* for CDS */
+    SafeSetStatus (dlg->add_mrna, FALSE);
+    SafeSetValue (dlg->reading_frame, 4);
+    SafeSetTitle (dlg->protein_name, "");
+    SafeSetTitle (dlg->protein_description, "");
+
+    /* for RNA */
+    PointerToDialog (dlg->ncrna_class, NULL);
+    SafeSetTitle (dlg->rna_name, "");
+
+    /* for import features */
+    PointerToDialog (dlg->quals, NULL);
+  
+    /* for all */
+    SafeSetTitle (dlg->gene_locus, "");
+    SafeSetTitle (dlg->gene_description, "");
+    SafeSetTitle (dlg->comment, "");
+  } else {
+    vn.choice = (Uint1) action->type;
+    vn.next = NULL;
+    vn.data.ptrvalue = NULL;
+    PointerToDialog (dlg->feature_type_dlg, &vn);
+
+    SetStatus (dlg->apply_to_parts, action->apply_to_parts);
+    if (action->only_seg_num > -1) {
+      sprintf (num, "%d", action->only_seg_num);  
+      SetTitle (dlg->only_this_part, num);
+    } else {
+      SetTitle (dlg->only_this_part, "");
+    }
+    SetStatus (dlg->partial5, action->partial5);
+    SetStatus (dlg->partial3, action->partial3);
+    if (action->plus_strand) {
+      SetValue (dlg->strand_group, 1);
+    } else {
+      SetValue (dlg->strand_group, 2);
+    }
+    if (action->location == NULL || action->location->choice == LocationChoice_whole_sequence) {    
+      SetValue (dlg->use_whole_interval, 1);
+      SetTitle (dlg->left_end, "");
+      SetTitle (dlg->right_end, "");
+    } else {
+      SetValue (dlg->use_whole_interval, 2);
+      lint = (LocationIntervalPtr) action->location->data.ptrvalue;
+      if (lint == NULL) {
+        SetTitle (dlg->left_end, "");
+        SetTitle (dlg->right_end, "");
+      } else {
+        sprintf (num, "%d", lint->from);  
+        SetTitle (dlg->left_end, num);
+        sprintf (num, "%d", lint->to);  
+        SetTitle (dlg->right_end, num);
+      }
+    }
+
+    if (action->seq_list == NULL || action->seq_list->choice == SequenceListChoice_all) {
+      SetValue (dlg->all_or_some_group, 1);
+      SetTitle (dlg->accession_list_txt, "");
+    } else {
+      txt = SequenceListWrite (action->seq_list->data.ptrvalue);
+      SetValue (dlg->all_or_some_group, 2);
+      SetTitle (dlg->accession_list_txt, txt);
+      txt = MemFree (txt);
+    }
+
+    SetStatus (dlg->add_redundant, action->add_redundant);
+
+    /* for CDS */
+    SafeSetStatus (dlg->add_mrna, action->add_mrna);
+    txt = FindFeatQualValue (action->fields, Feat_qual_legal_codon_start);
+    if (StringICmp (txt, "best") == 0) {
+      SafeSetValue (dlg->reading_frame, 4);
+    } else {
+      SafeSetValue (dlg->reading_frame, atoi (txt));
+    }
+
+    SafeSetTitle (dlg->protein_name, FindFeatQualValue (action->fields, Feat_qual_legal_product));
+    SafeSetTitle (dlg->protein_description, FindFeatQualValue (action->fields, Feat_qual_legal_description));
+
+    /* for RNA */
+    PointerToDialog (dlg->ncrna_class, FindFeatQualValue (action->fields, Feat_qual_legal_ncRNA_class));
+    SafeSetTitle (dlg->rna_name, FindFeatQualValue (action->fields, Feat_qual_legal_product));
+  
+    /* for all */
+    SafeSetTitle (dlg->gene_locus, FindFeatQualValue (action->fields, Feat_qual_legal_gene));
+    SafeSetTitle (dlg->gene_description, FindFeatQualValue (action->fields, Feat_qual_legal_gene_description));
+    SafeSetTitle (dlg->comment, FindFeatQualValue (action->fields, Feat_qual_legal_note));
+  }
+
+  ChangeApplyFeatureActionDlg (dlg);
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static Pointer DialogToApplyFeatureAction (DialoG d)
+{
+  ApplyFeatureActionDlgPtr dlg;
+  ApplyFeatureActionPtr    action;
+  CharPtr                  num_txt, txt;
+  Char                     num[15];
+  LocationIntervalPtr      lint;
+  Int4                     frame;
+  GBQualPtr                gbq;
+  ValNodePtr               vnp;
+
+  dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) {
+    return NULL;
+  }
+
+  vnp = DialogToPointer (dlg->feature_type_dlg);
+  if (vnp == NULL) {
+    return NULL;
+  }
+
+  action = ApplyFeatureActionNew();
+
+  action->type = vnp->choice;
+  vnp = ValNodeFree (vnp);
+
+  action->apply_to_parts = GetStatus (dlg->apply_to_parts);
+  if (action->apply_to_parts && !TextHasNoText (dlg->only_this_part)) {
+    num_txt = SaveStringFromText (dlg->only_this_part);
+    action->only_seg_num = atoi (num_txt);
+    num_txt = MemFree (num_txt);
+  }
+
+  action->partial5 = GetStatus (dlg->partial5);
+  action->partial3 = GetStatus (dlg->partial3);
+  if (GetValue (dlg->strand_group) == 1) {
+    action->plus_strand = TRUE;
+  } else {
+    action->plus_strand = FALSE;
+  }
+
+  if (GetValue (dlg->use_whole_interval) == 1) {
+    action->location = ValNodeNew(NULL);
+    action->location->choice = LocationChoice_whole_sequence;
+  } else {
+    lint = LocationIntervalNew ();
+    num_txt = SaveStringFromText (dlg->left_end);
+    lint->from = atoi (num_txt);
+    num_txt = MemFree (num_txt);
+    num_txt = SaveStringFromText (dlg->right_end);
+    lint->to = atoi (num_txt);
+    num_txt = MemFree (num_txt);
+    action->location = ValNodeNew(NULL);
+    action->location->choice = LocationChoice_interval;
+    action->location->data.ptrvalue = lint;
+  }
+
+  if (GetValue (dlg->all_or_some_group) == 1) {
+    action->seq_list = ValNodeNew(NULL);
+    action->seq_list->choice = SequenceListChoice_all;
+  } else {
+    num_txt = SaveStringFromText (dlg->accession_list_txt);
+    action->seq_list = ValNodeNew(NULL);
+    action->seq_list->choice = SequenceListChoice_list;
+    action->seq_list->data.ptrvalue = SequenceListCollect (num_txt);
+    num_txt = MemFree (num_txt);
+  }
+
+  action->add_redundant = GetStatus (dlg->add_redundant);
+
+  /* for CDS */
+  if (dlg->add_mrna != NULL && GetStatus (dlg->add_mrna)) {
+    action->add_mrna = TRUE;
+  } else {
+    action->add_mrna = FALSE;
+  }
+
+  if (dlg->reading_frame != NULL) {
+    frame = GetValue (dlg->reading_frame);
+    if (frame > 0 && frame < 4) {
+      sprintf (num, "%d", frame);
+      SetFeatQualValue (&(action->fields), Feat_qual_legal_codon_start, num);
+    } else {
+      SetFeatQualValue (&(action->fields), Feat_qual_legal_codon_start, "best");
+    }
+  }
+
+  if (dlg->protein_name != NULL && !TextHasNoText (dlg->protein_name)) {
+    txt = SaveStringFromText (dlg->protein_name);
+    SetFeatQualValue (&(action->fields), Feat_qual_legal_product, txt);
+    txt = MemFree (txt);
+  }
+  if (dlg->protein_name != NULL && !TextHasNoText (dlg->protein_description)) {
+    txt = SaveStringFromText (dlg->protein_description);
+    SetFeatQualValue (&(action->fields), Feat_qual_legal_description, txt);
+    txt = MemFree (txt);
+  }
+
+  /* for RNA */
+  if (dlg->ncrna_class != NULL) {
+    txt = DialogToPointer (dlg->ncrna_class);
+    if (!StringHasNoText (txt)) {
+      SetFeatQualValue (&(action->fields), Feat_qual_legal_ncRNA_class, txt);
+    }
+    txt = MemFree (txt);
+  }
+  if (dlg->rna_name != NULL && !TextHasNoText (dlg->rna_name)) {
+    txt = SaveStringFromText (dlg->rna_name);
+    SetFeatQualValue (&(action->fields), Feat_qual_legal_product, txt);
+    txt = MemFree (txt);
+  }
+
+  /* for import features */
+  if (dlg->quals != NULL) {
+    gbq = DialogToPointer (dlg->quals);
+    AddGBQualsToActionFields (gbq, action);
+    gbq = GBQualFree (gbq);
+  }
+  
+  /* for all */
+  if (dlg->gene_locus != NULL && !TextHasNoText (dlg->gene_locus)) {
+    txt = SaveStringFromText (dlg->gene_locus);
+    SetFeatQualValue (&(action->fields), Feat_qual_legal_gene, txt);
+    txt = MemFree (txt);
+  }
+  if (dlg->gene_description != NULL && !TextHasNoText (dlg->gene_description)) {
+    txt = SaveStringFromText (dlg->gene_description);
+    SetFeatQualValue (&(action->fields), Feat_qual_legal_gene_description, txt);
+    txt = MemFree (txt);
+  }
+  if (dlg->comment != NULL && !TextHasNoText (dlg->comment)) {
+    txt = SaveStringFromText (dlg->comment);
+    SetFeatQualValue (&(action->fields), Feat_qual_legal_note, txt);
+    txt = MemFree (txt);
+  }
+
+  return action;
+}
+
+
+static void AddTextToComment (ButtoN b, CharPtr text)
+{
+  ApplyFeatureActionDlgPtr dlg;
+  CharPtr                  orig_comment;
+  CharPtr                  new_comment;
+  
+  dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (b);
+  if (dlg == NULL || StringHasNoText (text))
+  {
+    return;
+  }
+  
+  orig_comment = SaveStringFromText (dlg->comment);
+  if (StringHasNoText (orig_comment))
+  {
+    SetTitle (dlg->comment, text);
+  }
+  else
+  {
+    new_comment = (CharPtr) MemNew ((StringLen (orig_comment) + StringLen (text) + 3) * sizeof (Char));
+    if (new_comment != NULL)
+    {
+      StringCpy (new_comment, orig_comment);
+      StringCat (new_comment, "; ");
+      StringCat (new_comment, text);
+      SetTitle (dlg->comment, new_comment);
+      new_comment = MemFree (new_comment);
+    }
+  } 
+  orig_comment = MemFree (orig_comment);
+}
+
+
+static void Add18SITS28SToComment (ButtoN b) 
+{
+  AddTextToComment (b, "contains 18S ribosomal RNA, internal transcribed spacer 1, 5.8S ribosomal RNA, internal transcribed spacer 2, and 28S ribosomal RNA");
+}
+
+
+static void Add16SIGS23SToComment (ButtoN b)
+{
+  AddTextToComment (b, "contains 16S ribosomal RNA, 16S-23S ribosomal RNA intergenic spacer, and 23S ribosomal RNA");
+}
+
+
+static void ChangeApplyFeatureActionDlgBtn (ButtoN b)
+{
+  ApplyFeatureActionDlgPtr dlg;
+
+  dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (b);
+  if (dlg == NULL) return;
+  ChangeApplyFeatureActionDlg (dlg);
+}
+
+
+static void ChangeApplyFeatureActionDlgGrp (GrouP g)
+{
+  ApplyFeatureActionDlgPtr dlg;
+
+  dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (g);
+  if (dlg == NULL) return;
+  ChangeApplyFeatureActionDlg (dlg);
+}
+
+
+static DialoG 
+ApplyFeatureActionDialog 
+(GrouP h,
+ ApplyFeatureActionPtr action,
+ Boolean indexer_version, 
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata,
+ Nlm_ChangeNotifyProc     redraw_notify,
+ Pointer                  redraw_userdata)
+{
+  ApplyFeatureActionDlgPtr dlg;
+  GrouP                 p, g, parts_group, x, indexer_only_group;
+  GrouP                 r, r2, r3, r4, frame_grp = NULL, comment_btns_grp = NULL;
+  ButtoN                comment_btn;
+  ValNodePtr            feature_type_list = NULL;
+  SeqFeatPtr            sfp;
+
+  dlg = (ApplyFeatureActionDlgPtr) MemNew (sizeof (ApplyFeatureActionDlgData));
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetGroupSpacing (p, 10, 10);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = ApplyFeatureActionToDialog;
+  dlg->fromdialog = DialogToApplyFeatureAction;
+  dlg->dialogmessage = NULL;
+  dlg->testdialog = TestApplyFeatureActionDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  ValNodeAddPointer (&feature_type_list, Feature_type_cds, StringSave ("CDS"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_gene, StringSave ("gene"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_preRNA, StringSave ("precursor RNA"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_mRNA, StringSave ("mRNA"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_tRNA, StringSave ("tRNA"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_rRNA, StringSave ("rRNA"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_snRNA, StringSave ("snRNA"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_scRNA, StringSave ("scRNA"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_otherRNA, StringSave ("misc RNA"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_ncRNA, StringSave ("ncRNA"));
+  ValNodeAddPointer (&feature_type_list, Feature_type_tmRNA, StringSave ("tmRNA"));
+  AddImportFeaturesToChoiceList (&feature_type_list);
+
+  /* note - the ValNodeSelectionDialog will free feature_type_list when done */                                            
+  dlg->feature_type_dlg = ValNodeSelectionDialog (p, feature_type_list, TALL_SELECTION_LIST, ValNodeStringName,
+                                ValNodeSimpleDataFree, ValNodeStringCopy,
+                                ValNodeChoiceMatch, "feature type", 
+                                redraw_notify, redraw_userdata, FALSE);
+
+  parts_group = HiddenGroup (p, 1, 0, NULL);
+  dlg->apply_to_parts = CheckBox (parts_group, "Apply to segmented parts, not segmented sequence", ChangeApplyFeatureActionDlgBtn);
+  SetObjectExtra (dlg->apply_to_parts, dlg, NULL);
+  x = HiddenGroup (parts_group, 2, 0, NULL);
+  StaticPrompt (x, "Apply only to particular numbered segment", 0, dialogTextHeight, programFont, 'l');
+  dlg->only_this_part = DialogText (x, "", 4, NULL);
+  Disable (dlg->only_this_part);
+
+  
+  g = HiddenGroup (p, 2, 0, NULL);
+  dlg->partial5 = CheckBox (g, "Incomplete at 5' end", NULL);
+  dlg->partial3 = CheckBox (g, "Incomplete at 3' end", NULL);
+
+  /* group for strand */
+  dlg->strand_group = HiddenGroup (p, 2, 0, NULL);
+  SetObjectExtra (dlg->strand_group, dlg, NULL);
+  RadioButton (dlg->strand_group, "Plus Strand");
+  RadioButton (dlg->strand_group, "Minus Strand");
+  SetValue (dlg->strand_group, 1);
+
+  /* coordinates */
+  if (indexer_version)
+  {
+    indexer_only_group = HiddenGroup (p, -1, 0, NULL);
+    r2 = HiddenGroup (indexer_only_group, 5, 0, NULL);
+    dlg->use_whole_interval = HiddenGroup (r2, 0, 2, ChangeApplyFeatureActionDlgGrp);
+    SetObjectExtra (dlg->use_whole_interval, dlg, NULL);
+    RadioButton (dlg->use_whole_interval, "Use Whole Sequence Interval");
+    RadioButton (dlg->use_whole_interval, "Use these coordinates:");
+    r3 = HiddenGroup (r2, 0, 2, NULL);
+    StaticPrompt (r3, "", 0, dialogTextHeight, programFont, 'l');
+    r4 = HiddenGroup (r3, 4, 0, NULL);
+    StaticPrompt (r4, "From", 0, dialogTextHeight, programFont, 'l');
+    dlg->left_end = DialogText (r4, "1", 5, NULL);
+    StaticPrompt (r4, "To", 0, dialogTextHeight, programFont, 'l');
+    dlg->right_end = DialogText (r4, "1", 5, NULL);
+    SetValue (dlg->use_whole_interval, 1);
+    
+    /* apply to some sequences or all sequences */
+    dlg->all_or_some_group = HiddenGroup (indexer_only_group, 1, 0, ChangeApplyFeatureActionDlgGrp);
+    SetObjectExtra (dlg->all_or_some_group, dlg, NULL);
+    RadioButton (dlg->all_or_some_group, "Apply to all sequences");
+    RadioButton (dlg->all_or_some_group, "Apply to sequences in this list");
+    dlg->accession_list_txt = DialogText (dlg->all_or_some_group, "", 25, NULL);
+    SetValue (dlg->all_or_some_group, 1);
+    
+    dlg->add_redundant = CheckBox (indexer_only_group, "Add even if feature of same type already present", ChangeApplyFeatureActionDlgBtn);
+    SetObjectExtra (dlg->add_redundant, dlg, NULL);
+    if (action != NULL && action->type == Feature_type_cds) {
+      dlg->add_mrna = CheckBox (indexer_only_group, "Also add mRNA", ChangeApplyFeatureActionDlgBtn);
+      SetObjectExtra (dlg->add_mrna, dlg, NULL);
+    }
+
+    AlignObjects (ALIGN_CENTER, (HANDLE) r2, (HANDLE) dlg->all_or_some_group, (HANDLE) dlg->add_redundant, (HANDLE) dlg->add_mrna, NULL);
+  }  
+
+  if (action != NULL && action->type == Feature_type_cds) {
+    frame_grp = HiddenGroup (p, 2, 0, NULL);
+    StaticPrompt (frame_grp, "Reading Frame", 0, dialogTextHeight, programFont, 'l');
+    dlg->reading_frame = PopupList (frame_grp, TRUE, NULL);
+    PopupItem (dlg->reading_frame, "1");
+    PopupItem (dlg->reading_frame, "2");
+    PopupItem (dlg->reading_frame, "3");
+    PopupItem (dlg->reading_frame, "Best");
+    SetValue (dlg->reading_frame, 4);
+  }    
+  r = HiddenGroup (p, 2, 0, NULL);
+  if (action != NULL && action->type == Feature_type_cds) {
+
+    StaticPrompt (r, "Protein Name", 0, dialogTextHeight, programFont, 'l');
+    dlg->protein_name = DialogText (r, "", 20, NULL);
+    StaticPrompt (r, "Protein Description", 0, dialogTextHeight, programFont, 'l');
+    dlg->protein_description = DialogText (r, "", 20, NULL);
+  } else if (action != NULL && (action->type == Feature_type_preRNA
+                                || action->type == Feature_type_mRNA
+                                || action->type == Feature_type_tRNA
+                                || action->type == Feature_type_rRNA
+                                || action->type == Feature_type_snRNA
+                                || action->type == Feature_type_scRNA 
+                                || action->type == Feature_type_otherRNA
+                                || action->type == Feature_type_tmRNA
+                                || action->type == Feature_type_ncRNA)) {
+    /* RNA name */
+    StaticPrompt (r, "RNA Name", 0, dialogTextHeight, programFont, 'l');
+    dlg->rna_name = DialogText (r, "", 20, NULL);
+    /* ncRNA class */
+    if (action->type == Feature_type_ncRNA) {
+      StaticPrompt (r, "ncRNA Class", 0, dialogTextHeight, programFont, 'l');
+      dlg->ncrna_class = CreatencRNAClassDialog (r, FALSE, NULL, NULL);
+    }
+  } else if (action != NULL && action->type != Feature_type_gene) {
+    StaticPrompt (r, "Qualifiers", 0, dialogTextHeight, programFont, 'l');
+    sfp = CreateFeatureWithImportFeatureQuals (action);
+    dlg->quals = NewCreateImportFields (r, GetFeatureNameFromFeatureType (action->type), sfp, FALSE);
+    sfp = SeqFeatFree (sfp);
+  }
+
+  /* gene qualifiers ( for all ) */
+  StaticPrompt (r, "Gene Locus", 0, dialogTextHeight, programFont, 'l');
+  dlg->gene_locus = DialogText (r, "", 20, NULL);
+  StaticPrompt (r, "Gene Description", 0, dialogTextHeight, programFont, 'l');
+  dlg->gene_description = DialogText (r, "", 20, NULL);
+  StaticPrompt (r, "Comment", 0, dialogTextHeight, programFont, 'l');
+  dlg->comment = DialogText (r, "", 20, NULL);  
+  if (action != NULL && action->type == Feature_type_otherRNA && indexer_version) {
+    comment_btns_grp = HiddenGroup (p, 2, 0, NULL);
+    comment_btn = PushButton (comment_btns_grp, "Add '18S-ITS-5.8S-ITS-28S' to comment", Add18SITS28SToComment);
+    SetObjectExtra (comment_btn, dlg, NULL);
+    comment_btn = PushButton (comment_btns_grp, "Add '16S-IGS-23S' to comment", Add16SIGS23SToComment);
+    SetObjectExtra (comment_btn, dlg, NULL);
+  }
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg,
+                              (HANDLE) parts_group,
+                              (HANDLE) g,
+                              (HANDLE) dlg->strand_group,
+                              (HANDLE) indexer_only_group,
+                              (HANDLE) r,
+                              (HANDLE) (frame_grp != NULL ? frame_grp : comment_btns_grp),
+                              NULL);
+
+  return (DialoG) p;  
+}
+
+
+typedef struct removefeatureactiondlg {
+  DIALOG_MESSAGE_BLOCK
+  DialoG                   feature_type_dlg;
+  DialoG                   constraint_dlg;
+  Nlm_ChangeNotifyProc     change_notify;
+  Pointer                  change_userdata;
+} RemoveFeatureActionDlgData, PNTR RemoveFeatureActionDlgPtr;
+
+
+static void RemoveFeatureActionToDialog (DialoG d, Pointer data)
+{
+  RemoveFeatureActionDlgPtr dlg;
+  RemoveFeatureActionPtr    action;
+  ValNode                   vn;
+
+  dlg = (RemoveFeatureActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  action = (RemoveFeatureActionPtr) data;
+  if (action == NULL) {
+    PointerToDialog (dlg->feature_type_dlg, NULL);
+    PointerToDialog (dlg->constraint_dlg, NULL);
+  } else {
+    vn.choice = action->type;
+    vn.data.ptrvalue = NULL;
+    vn.next = NULL;
+    PointerToDialog (dlg->feature_type_dlg, &vn);
+    PointerToDialog (dlg->constraint_dlg, action->constraint);
+  }
+
+}
+
+
+static Pointer DialogToRemoveFeatureAction (DialoG d)
+{
+  RemoveFeatureActionDlgPtr dlg;
+  RemoveFeatureActionPtr    action;
+  ValNodePtr                vnp;
+
+  dlg = (RemoveFeatureActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  vnp = DialogToPointer (dlg->feature_type_dlg);
+  if (vnp == NULL) return NULL;
+
+  action = RemoveFeatureActionNew ();
+  action->type = vnp->choice;
+  vnp = ValNodeFree (vnp);
+  action->constraint = DialogToPointer (dlg->constraint_dlg);
+  return action;
+}
+
+
+static ValNodePtr TestRemoveFeatureActionDialog (DialoG d)
+{
+  RemoveFeatureActionDlgPtr dlg;
+  dlg = (RemoveFeatureActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  return TestDialog (dlg->feature_type_dlg);
+}
+
+
+static DialoG 
+RemoveFeatureActionDialog 
+(GrouP h,
+ Boolean indexer_version, 
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata)
+{
+  RemoveFeatureActionDlgPtr dlg;
+  GrouP                     p;
+
+  dlg = (RemoveFeatureActionDlgPtr) MemNew (sizeof (RemoveFeatureActionDlgData));
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetGroupSpacing (p, 10, 10);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = RemoveFeatureActionToDialog;
+  dlg->fromdialog = DialogToRemoveFeatureAction;
+  dlg->dialogmessage = NULL;
+  dlg->testdialog = TestRemoveFeatureActionDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->feature_type_dlg = FeatureTypeDialog (p, change_notify, change_userdata);
+  dlg->constraint_dlg = ConstraintSetDialog (p, change_notify, change_userdata);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg, (HANDLE) dlg->constraint_dlg, NULL);
+
+  return (DialoG) p;
+}
+
+
+typedef struct editfeaturelocationactiondlg {
+  DIALOG_MESSAGE_BLOCK
+  DialoG                   feature_type_dlg;
+  PopuP                    feature_edit_type;
+  GrouP                    strand_edit_grp;
+  PopuP                    strand_from;
+  PopuP                    strand_to;                   
+  GrouP                    set_5_partial_grp;
+  PopuP                    set_5_type;
+  ButtoN                   extend5;
+  PopuP                    clear_5_type;
+  GrouP                    set_3_partial_grp;
+  PopuP                    set_3_type;
+  ButtoN                   extend3;
+  PopuP                    clear_3_type;
+  PopuP                    convert_loc;
+  DialoG                   constraint_dlg;
+  Nlm_ChangeNotifyProc     change_notify;
+  Pointer                  change_userdata;
+} EditFeatureLocationActionDlgData, PNTR EditFeatureLocationActionDlgPtr;
+
+
+static void ChangeFeatureLocationEditType (PopuP p)
+{
+  EditFeatureLocationActionDlgPtr dlg;
+  Int2 val;
+
+  dlg = (EditFeatureLocationActionDlgPtr) GetObjectExtra (p);
+  if (dlg == NULL) return;
+  
+  Hide (dlg->strand_edit_grp);
+  Hide (dlg->set_5_partial_grp);
+  Hide (dlg->clear_5_type);
+  Hide (dlg->set_3_partial_grp);
+  Hide (dlg->clear_3_type);
+  Hide (dlg->convert_loc);
+
+  val = GetValue (dlg->feature_edit_type);
+  switch (val) {
+    case 1:
+      Show (dlg->strand_edit_grp);
+      break;
+    case 2:
+      Show (dlg->set_5_partial_grp);
+      break;
+    case 3:
+      Show (dlg->clear_5_type);
+      break;
+    case 4:
+      Show (dlg->set_3_partial_grp);
+      break;
+    case 5:
+      Show (dlg->clear_3_type);
+      break;
+    case 6:
+      Show (dlg->convert_loc);
+      break;
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void ResetFeatureLocationActionEditType (EditFeatureLocationActionDlgPtr dlg)
+{
+  if (dlg != NULL) {
+    SetValue (dlg->feature_edit_type, 1);
+    SetValue (dlg->strand_from, 1);
+    SetValue (dlg->strand_to, 1);
+  }
+}
+
+
+static void EditFeatureLocationActionToDialog (DialoG d, Pointer data)
+{
+  EditFeatureLocationActionDlgPtr dlg;
+  EditFeatureLocationActionPtr    action;
+  ValNode                   vn;
+  EditLocationStrandPtr    strand;
+  Partial5SetActionPtr     set5;
+  Partial3SetActionPtr     set3;
+
+  dlg = (EditFeatureLocationActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  action = (EditFeatureLocationActionPtr) data;
+  if (action == NULL) {
+    PointerToDialog (dlg->feature_type_dlg, NULL);
+    ResetFeatureLocationActionEditType (dlg);
+    PointerToDialog (dlg->constraint_dlg, NULL);
+  } else {
+    vn.choice = action->type;
+    vn.data.ptrvalue = NULL;
+    vn.next = NULL;
+    PointerToDialog (dlg->feature_type_dlg, &vn);
+    PointerToDialog (dlg->constraint_dlg, action->constraint);
+    if (action->action == NULL) {
+      ResetFeatureLocationActionEditType (dlg);
+    } else {
+      switch (action->action->choice) {
+        case LocationEditType_strand:
+          SetValue (dlg->feature_edit_type, 1);
+          strand = (EditLocationStrandPtr) action->action->data.ptrvalue;
+          if (strand == NULL) {
+            SetValue (dlg->strand_from, 1);
+            SetValue (dlg->strand_to, 1);
+          } else {
+            switch (strand->strand_from) {
+              case Feature_location_strand_from_any:
+                SetValue (dlg->strand_from, 1);
+                break;
+              case Feature_location_strand_from_plus:
+                SetValue (dlg->strand_from, 2);
+                break;
+              case Feature_location_strand_from_minus:
+                SetValue (dlg->strand_from, 3);
+                break;
+              case Feature_location_strand_from_unknown:
+                SetValue (dlg->strand_from, 4);
+                break;
+              case Feature_location_strand_from_both:
+                SetValue (dlg->strand_from, 5);
+                break;
+              default:
+                SetValue (dlg->strand_from, 1);
+                break;
+            }
+            switch (strand->strand_to) {
+              case Feature_location_strand_to_plus:
+                SetValue (dlg->strand_to, 1);
+                break;
+              case Feature_location_strand_to_minus:
+                SetValue (dlg->strand_to, 2);
+                break;
+              case Feature_location_strand_to_unknown:
+                SetValue (dlg->strand_to, 3);
+                break;
+              case Feature_location_strand_to_both:
+                SetValue (dlg->strand_to, 4);
+                break;
+              case Feature_location_strand_to_reverse:
+                SetValue (dlg->strand_to, 5);
+                break;
+              default:
+                SetValue (dlg->strand_to, 1);
+                break;
+            }
+          }
+          break;
+        case LocationEditType_set_5_partial:
+          SetValue (dlg->feature_edit_type, 2);
+          set5 = (Partial5SetActionPtr) action->action->data.ptrvalue;
+          if (set5 == NULL) {
+            SetValue (dlg->set_5_type, 1);
+            SetStatus (dlg->extend5, FALSE);
+          } else {
+            switch (set5->constraint) {
+              case Partial_5_set_constraint_all:
+                SetValue (dlg->set_5_type, 1);
+                break;
+              case Partial_5_set_constraint_at_end:
+                SetValue (dlg->set_5_type, 2);
+                break;
+              case Partial_5_set_constraint_bad_start:
+                SetValue (dlg->set_5_type, 3);
+                break;
+              case Partial_5_set_constraint_frame_not_one:
+                SetValue (dlg->set_5_type, 4);
+                break;
+              default:
+                SetValue (dlg->set_5_type, 1);
+                break;
+            }
+            SetStatus (dlg->extend5, set5->extend);
+          }
+          break;   
+        case LocationEditType_clear_5_partial:
+          SetValue (dlg->feature_edit_type, 3);
+          switch (action->action->data.intvalue) {
+            case Partial_5_clear_constraint_all:
+              SetValue (dlg->clear_5_type, 1);
+              break;
+            case Partial_5_clear_constraint_not_at_end:
+              SetValue (dlg->clear_5_type, 2);
+              break;
+            case Partial_5_clear_constraint_good_start:
+              SetValue (dlg->clear_5_type, 3);
+              break;
+            default:
+              SetValue (dlg->clear_5_type, 1);
+              break;
+          }
+          break;
+        case LocationEditType_set_3_partial:
+          SetValue (dlg->feature_edit_type, 4);
+          set3 = (Partial3SetActionPtr) action->action->data.ptrvalue;
+          if (set3 == NULL) {
+            SetValue (dlg->set_3_type, 1);
+            SetStatus (dlg->extend3, FALSE);
+          } else {
+            switch (set3->constraint) {
+              case Partial_3_set_constraint_all:
+                SetValue (dlg->set_3_type, 1);
+                break;
+              case Partial_3_set_constraint_at_end:
+                SetValue (dlg->set_3_type, 2);
+                break;
+              case Partial_3_set_constraint_bad_end:
+                SetValue (dlg->set_3_type, 3);
+                break;
+              default:
+                SetValue (dlg->set_3_type, 1);
+                break;
+            }
+            SetStatus (dlg->extend3, set3->extend);
+          }
+          break;   
+        case LocationEditType_clear_3_partial:
+          SetValue (dlg->feature_edit_type, 5);
+          switch (action->action->data.intvalue) {
+            case Partial_3_clear_constraint_all:
+              SetValue (dlg->clear_3_type, 1);
+              break;
+            case Partial_3_clear_constraint_not_at_end:
+              SetValue (dlg->clear_3_type, 2);
+              break;
+            case Partial_3_clear_constraint_good_end:
+              SetValue (dlg->clear_3_type, 3);
+              break;
+            default:
+              SetValue (dlg->clear_3_type, 1);
+              break;
+          }
+          break;
+        case LocationEditType_convert:
+          SetValue (dlg->feature_edit_type, 6);
+          switch (action->action->data.intvalue) {
+            case Convert_location_type_join:
+              SetValue (dlg->convert_loc, 1);
+              break;
+            case Convert_location_type_order:
+              SetValue (dlg->convert_loc, 2);
+              break;
+            case Convert_location_type_merge:
+              SetValue (dlg->convert_loc, 3);
+              break;
+            default:
+              SetValue (dlg->convert_loc, 1);
+              break;
+          }
+          break;
+        default:
+          ResetFeatureLocationActionEditType (dlg);
+          break;
+      }
+    }
+  }
+  ChangeFeatureLocationEditType (dlg->feature_edit_type);
+}
+
+
+static Pointer DialogToEditFeatureLocationAction (DialoG d)
+{
+  EditFeatureLocationActionDlgPtr dlg;
+  EditFeatureLocationActionPtr    action;
+  ValNodePtr                vnp;
+  Int2                      val, val2;
+  EditLocationStrandPtr    strand;
+  Partial5SetActionPtr     set5;
+  Partial3SetActionPtr     set3;
+
+  dlg = (EditFeatureLocationActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  vnp = DialogToPointer (dlg->feature_type_dlg);
+  if (vnp == NULL) return NULL;
+
+  action = EditFeatureLocationActionNew ();
+  action->type = vnp->choice;
+  vnp = ValNodeFree (vnp);
+  action->constraint = DialogToPointer (dlg->constraint_dlg);
+
+  val = GetValue (dlg->feature_edit_type);
+  switch (val) {
+    case 1:
+      strand = EditLocationStrandNew ();
+      action->action = ValNodeNew (NULL);
+      action->action->choice = LocationEditType_strand;
+      action->action->data.ptrvalue = strand;
+      val2 = GetValue (dlg->strand_from);
+      switch (val2) {
+        case 1:
+          strand->strand_from = Feature_location_strand_from_any;
+          break;
+        case 2:
+          strand->strand_from = Feature_location_strand_from_plus;
+          break;
+        case 3:
+          strand->strand_from = Feature_location_strand_from_minus;
+          break;
+        case 4:
+          strand->strand_from = Feature_location_strand_from_unknown;
+          break;
+        case 5:
+          strand->strand_from = Feature_location_strand_from_both;
+          break;
+        default:
+          action = EditFeatureLocationActionFree (action);
+          return NULL;
+      }
+      val2 = GetValue (dlg->strand_to);
+      switch (val2) {
+        case 1:
+          strand->strand_to = Feature_location_strand_to_plus;
+          break;
+        case 2:
+          strand->strand_to = Feature_location_strand_to_minus;
+          break;
+        case 3:
+          strand->strand_to = Feature_location_strand_to_unknown;
+          break;
+        case 4:
+          strand->strand_to = Feature_location_strand_to_both;
+          break;
+        case 5:
+          strand->strand_to = Feature_location_strand_to_reverse;
+          break;
+        default:
+          action = EditFeatureLocationActionFree (action);
+          break;
+      }
+      break;
+    case 2:
+      set5 = Partial5SetActionNew ();
+      action->action = ValNodeNew (NULL);
+      action->action->choice = LocationEditType_set_5_partial;
+      action->action->data.ptrvalue = set5;
+      set5->extend = GetStatus (dlg->extend5);
+      val2 = GetValue (dlg->set_5_type);
+      switch (val2) {
+        case 1:
+          set5->constraint = Partial_5_set_constraint_all;
+          break;
+        case 2:
+          set5->constraint = Partial_5_set_constraint_at_end;
+          break;
+        case 3:
+          set5->constraint = Partial_5_set_constraint_bad_start;
+          break;
+        case 4:
+          set5->constraint = Partial_5_set_constraint_frame_not_one;
+          break;
+        default:
+          action = EditFeatureLocationActionFree (action);
+          return NULL;
+          break;
+      }
+      break;
+    case 3:
+      action->action = ValNodeNew (NULL);
+      action->action->choice = LocationEditType_clear_5_partial;
+      val2 = GetValue (dlg->clear_5_type);
+      switch (val2) {
+        case 1:
+          action->action->data.intvalue = Partial_5_clear_constraint_all;
+          break;
+        case 2:
+          action->action->data.intvalue = Partial_5_clear_constraint_not_at_end;
+          break;
+        case 3:
+          action->action->data.intvalue = Partial_5_clear_constraint_good_start;
+          break;
+        default:
+          action = EditFeatureLocationActionFree (action);
+          return NULL;
+          break;
+      }
+      break;
+    case 4:
+      set3 = Partial3SetActionNew ();
+      action->action = ValNodeNew (NULL);
+      action->action->choice = LocationEditType_set_3_partial;
+      action->action->data.ptrvalue = set3;
+      set3->extend = GetStatus (dlg->extend3);
+      val2 = GetValue (dlg->set_3_type);
+      switch (val2) {
+        case 1:
+          set3->constraint = Partial_3_set_constraint_all;
+          break;
+        case 2:
+          set3->constraint = Partial_3_set_constraint_at_end;
+          break;
+        case 3:
+          set3->constraint = Partial_3_set_constraint_bad_end;
+          break;
+        default:
+          action = EditFeatureLocationActionFree (action);
+          return NULL;
+          break;
+      }
+      break;
+    case 5:
+      action->action = ValNodeNew (NULL);
+      action->action->choice = LocationEditType_clear_3_partial;
+      val2 = GetValue (dlg->clear_3_type);
+      switch (val2) {
+        case 1:
+          action->action->data.intvalue = Partial_3_clear_constraint_all;
+          break;
+        case 2:
+          action->action->data.intvalue = Partial_3_clear_constraint_not_at_end;
+          break;
+        case 3:
+          action->action->data.intvalue = Partial_3_clear_constraint_good_end;
+          break;
+        default:
+          action = EditFeatureLocationActionFree (action);
+          return NULL;
+          break;
+      }
+      break;
+    case 6:
+      action->action = ValNodeNew (NULL);
+      action->action->choice = LocationEditType_convert;
+      val2 = GetValue (dlg->convert_loc);
+      switch (val2) {
+        case 1:
+          action->action->data.intvalue = Convert_location_type_join;
+          break;
+        case 2:
+          action->action->data.intvalue = Convert_location_type_order;
+          break;
+        case 3:
+          action->action->data.intvalue = Convert_location_type_merge;
+          break;
+        default:
+          action = EditFeatureLocationActionFree (action);
+          return NULL;
+          break;
+      }
+      break;
+    default:
+      action = EditFeatureLocationActionFree (action);
+      break;
+  }
+
+  return action;
+}
+
+
+static ValNodePtr TestEditFeatureLocationActionDialog (DialoG d)
+{
+  EditFeatureLocationActionDlgPtr dlg;
+  EditFeatureLocationActionPtr a;
+  ValNodePtr err_list = NULL;
+
+  dlg = (EditFeatureLocationActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  a = (EditFeatureLocationActionPtr) DialogToPointer (d);
+  if (a == NULL) {
+    ValNodeAddPointer (&err_list, 0, "bad action");
+  } else {
+    a = EditFeatureLocationActionFree (a);
+    err_list = TestDialog (dlg->feature_type_dlg);
+  }
+  return err_list;
+}
+
+
+static void ChangeEditFeatureLocationPopup (PopuP p)
+{
+  EditFeatureLocationActionDlgPtr dlg;
+
+  dlg = (EditFeatureLocationActionDlgPtr) GetObjectExtra (p);
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void ChangeEditFeatureLocationButton (ButtoN b)
+{
+  EditFeatureLocationActionDlgPtr dlg;
+
+  dlg = (EditFeatureLocationActionDlgPtr) GetObjectExtra (b);
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static DialoG 
+EditFeatureLocationActionDialog 
+(GrouP h,
+ Boolean indexer_version, 
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata)
+{
+  EditFeatureLocationActionDlgPtr dlg;
+  GrouP                     p;
+  GrouP                     g;
+
+  dlg = (EditFeatureLocationActionDlgPtr) MemNew (sizeof (EditFeatureLocationActionDlgData));
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetGroupSpacing (p, 10, 10);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = EditFeatureLocationActionToDialog;
+  dlg->fromdialog = DialogToEditFeatureLocationAction;
+  dlg->dialogmessage = NULL;
+  dlg->testdialog = TestEditFeatureLocationActionDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->feature_type_dlg = FeatureTypeDialog (p, change_notify, change_userdata);
+
+  dlg->feature_edit_type = PopupList (p, TRUE, ChangeFeatureLocationEditType);
+  SetObjectExtra (dlg->feature_edit_type, dlg, NULL);
+  PopupItem (dlg->feature_edit_type, "Edit Strand");
+  PopupItem (dlg->feature_edit_type, "Set 5' Partial");
+  PopupItem (dlg->feature_edit_type, "Clear 5' Partial");
+  PopupItem (dlg->feature_edit_type, "Set 3' Partial");
+  PopupItem (dlg->feature_edit_type, "Clear 3' Partial");
+  PopupItem (dlg->feature_edit_type, "Convert location");
+  SetValue (dlg->feature_edit_type, 1);
+
+  g = HiddenGroup (p, 0, 0, NULL);
+  dlg->strand_edit_grp = HiddenGroup (g, 4, 0, NULL);
+
+  /* strand */
+  StaticPrompt (dlg->strand_edit_grp, "Convert location strand from", 0, dialogTextHeight, systemFont, 'l');
+  dlg->strand_from = PopupList (dlg->strand_edit_grp, TRUE, ChangeEditFeatureLocationPopup);
+  SetObjectExtra (dlg->strand_from, dlg, NULL);
+  PopupItem (dlg->strand_from, "Any");
+  PopupItem (dlg->strand_from, "Plus");
+  PopupItem (dlg->strand_from, "Minus");
+  PopupItem (dlg->strand_from, "Unknown");
+  PopupItem (dlg->strand_from, "Both");
+  SetValue (dlg->strand_from, 1);
+  dlg->strand_to = PopupList (dlg->strand_edit_grp, TRUE, ChangeEditFeatureLocationPopup);
+  SetObjectExtra (dlg->strand_to, dlg, NULL);
+  PopupItem (dlg->strand_to, "Plus");
+  PopupItem (dlg->strand_to, "Minus");
+  PopupItem (dlg->strand_to, "Unknown");
+  PopupItem (dlg->strand_to, "Both");
+  PopupItem (dlg->strand_to, "Reverse");
+  SetValue (dlg->strand_to, 5);
+
+  /* partials */
+  dlg->set_5_partial_grp = HiddenGroup (g, 2, 0, NULL);
+  dlg->set_5_type = PopupList (dlg->set_5_partial_grp, TRUE, ChangeEditFeatureLocationPopup);
+  SetObjectExtra (dlg->set_5_type, dlg, NULL);
+  PopupItem (dlg->set_5_type, "All");
+  PopupItem (dlg->set_5_type, "If 5' end at end of sequence");
+  PopupItem (dlg->set_5_type, "If bad start codon");
+  PopupItem (dlg->set_5_type, "If CDS frame > 1");
+  SetValue (dlg->set_5_type, 1);
+  dlg->extend5 = CheckBox (dlg->set_5_partial_grp, "Extend to 5' end if partial is set", ChangeEditFeatureLocationButton);
+  SetObjectExtra (dlg->extend5, dlg, NULL);
+
+  dlg->clear_5_type = PopupList (g, TRUE, ChangeEditFeatureLocationPopup);
+  SetObjectExtra (dlg->clear_5_type, dlg, NULL);
+  PopupItem (dlg->clear_5_type, "All");
+  PopupItem (dlg->clear_5_type, "If 5' end not at end of sequence");
+  PopupItem (dlg->clear_5_type, "If good start codon");
+  SetValue (dlg->clear_5_type, 1);
+
+  dlg->set_3_partial_grp = HiddenGroup (g, 2, 0, NULL);
+  dlg->set_3_type = PopupList (dlg->set_3_partial_grp, TRUE, ChangeEditFeatureLocationPopup);
+  SetObjectExtra (dlg->set_3_type, dlg, NULL);
+  PopupItem (dlg->set_3_type, "All");
+  PopupItem (dlg->set_3_type, "If 3' end at end of sequence");
+  PopupItem (dlg->set_3_type, "If bad stop codon");
+  SetValue (dlg->set_3_type, 1);
+  dlg->extend3 = CheckBox (dlg->set_3_partial_grp, "Extend to 3' end if partial is set", ChangeEditFeatureLocationButton);
+  SetObjectExtra (dlg->extend3, dlg, NULL);
+
+  dlg->clear_3_type = PopupList (g, TRUE, ChangeEditFeatureLocationPopup);
+  SetObjectExtra (dlg->clear_3_type, dlg, NULL);
+  PopupItem (dlg->clear_3_type, "All");
+  PopupItem (dlg->clear_3_type, "If 3' end not at end of sequence");
+  PopupItem (dlg->clear_3_type, "If good stop codon");
+  SetValue (dlg->clear_3_type, 1);
+
+  /* convert location */
+  dlg->convert_loc = PopupList (g, TRUE, ChangeEditFeatureLocationPopup);
+  SetObjectExtra (dlg->convert_loc, dlg, NULL);
+  PopupItem (dlg->convert_loc, "Join");
+  PopupItem (dlg->convert_loc, "Order");
+  PopupItem (dlg->convert_loc, "Single Interval");
+  SetValue (dlg->convert_loc, 1);
+
+  AlignObjects (ALIGN_MIDDLE, (HANDLE) dlg->strand_edit_grp,
+                              (HANDLE) dlg->set_5_partial_grp,
+                              (HANDLE) dlg->clear_5_type,
+                              (HANDLE) dlg->set_3_partial_grp,
+                              (HANDLE) dlg->clear_3_type,
+                              (HANDLE) dlg->convert_loc,
+                              (HANDLE) NULL);
+
+  dlg->constraint_dlg = ConstraintSetDialog (p, change_notify, change_userdata);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg,
+                              (HANDLE) dlg->feature_edit_type,
+                              (HANDLE) g,
+                              (HANDLE) dlg->constraint_dlg,
+                              NULL);
+
+  ChangeFeatureLocationEditType (dlg->feature_edit_type);
+
+  return (DialoG) p;
+}
+
+
+typedef struct parsesrcdlg {
+ DIALOG_MESSAGE_BLOCK
+ PopuP main_choice;
+ GrouP src_grp;
+ DialoG src_qual_choice;
+ GrouP feat_or_desc;
+ TexT  structured_comment_field;
+ Nlm_ChangeNotifyProc change_notify;
+ Pointer              change_userdata;
+} ParseSrcDlgData, PNTR ParseSrcDlgPtr;
+
+
+const CharPtr kTaxnameAfterBinomialString = "Taxname after binomial";
+
+static void ChangeParseSrcDialogPopup (PopuP p)
+{
+  ParseSrcDlgPtr dlg;
+  Int2           val;
+
+  dlg = (ParseSrcDlgPtr) GetObjectExtra (p);
+  if (dlg == NULL) return;
+
+  val = GetValue (dlg->main_choice);
+  switch (val) {
+    case 4:
+      Show (dlg->src_grp);
+      Hide (dlg->structured_comment_field);
+      break;
+    case 7:
+      Show (dlg->structured_comment_field);
+      Hide (dlg->src_grp);
+      break;
+    default:
+      Hide (dlg->structured_comment_field);
+      Hide (dlg->src_grp);
+      break;
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void ChangeParseSrcDialogText (TexT t)
+{
+  ParseSrcDlgPtr dlg;
+
+  dlg = (ParseSrcDlgPtr) GetObjectExtra (t);
+  if (dlg == NULL) return;
+
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void ParseSrcToDialog (DialoG d, Pointer data)
+{
+  ParseSrcDlgPtr dlg;
+  ValNodePtr src;
+  ParseSrcOrgPtr org;
+  ValNode        vn;
+
+  dlg = (ParseSrcDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  src = (ValNodePtr) data;
+  if (src == NULL) {
+    SetValue (dlg->main_choice, 4);
+    vn.choice = 0;
+    vn.data.ptrvalue = kTaxnameAfterBinomialString;
+    vn.next = NULL;
+    PointerToDialog (dlg->src_qual_choice, &vn);
+    SetValue (dlg->feat_or_desc, 1);
+  } else {
+    switch (src->choice) {
+      case ParseSrc_defline:
+        SetValue (dlg->main_choice, 1);
+        break;
+      case ParseSrc_flatfile:
+        SetValue (dlg->main_choice, 2);
+        break;
+      case ParseSrc_local_id:
+        SetValue (dlg->main_choice, 3);
+        break;
+      case ParseSrc_org:
+        SetValue (dlg->main_choice, 4);
+        org = (ParseSrcOrgPtr) src->data.ptrvalue;
+        if (org == NULL) {
+          SetValue (dlg->feat_or_desc, 1);
+          PointerToDialog (dlg->src_qual_choice, NULL);
+        } else {
+          switch (org->type) {
+            case Object_type_constraint_any:
+              SetValue (dlg->feat_or_desc, 1);
+              break;
+            case Object_type_constraint_feature:
+              SetValue (dlg->feat_or_desc, 2);
+              break;
+            case Object_type_constraint_descriptor:
+              SetValue (dlg->feat_or_desc, 3);
+              break;
+            default:
+              SetValue (dlg->feat_or_desc, 1);
+              break;
+          }
+          if (org->field == NULL) {
+             PointerToDialog (dlg->src_qual_choice, NULL);
+          } else if (org->field->choice == ParseSrcOrgChoice_taxname_after_binomial) {
+            vn.choice = 0;
+            vn.data.ptrvalue = kTaxnameAfterBinomialString;
+            vn.next = NULL;
+            PointerToDialog (dlg->src_qual_choice, &vn);
+          } else if (org->field->choice == ParseSrcOrgChoice_source_qual) {
+            vn.choice = 0;
+            vn.data.ptrvalue = GetSourceQualName (org->field->data.intvalue);
+            vn.next = NULL;
+            PointerToDialog (dlg->src_qual_choice, &vn);
+          } else {
+            PointerToDialog (dlg->src_qual_choice, NULL);
+          }
+        }
+        break;
+      case ParseSrc_comment:
+        SetValue (dlg->main_choice, 5);
+        break;
+      case ParseSrc_bankit_comment:
+        SetValue (dlg->main_choice, 6);
+        break;
+      case ParseSrc_structured_comment:
+        SetValue (dlg->main_choice, 7);
+        SetTitle (dlg->structured_comment_field, src->data.ptrvalue);
+        break;
+      case ParseSrc_file_id:
+        SetValue (dlg->main_choice, 8);
+        break;
+      default:
+        SetValue (dlg->main_choice, 0);
+        break;
+    }
+  }
+
+  ChangeParseSrcDialogPopup (dlg->main_choice);
+}
+
+
+static Pointer DialogToParseSrc (DialoG d)
+{
+  ParseSrcDlgPtr dlg;
+  ParseSrcOrgPtr org;
+  ValNodePtr     src = NULL, vnp;
+  Int2           val;
+
+  dlg = (ParseSrcDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  val = GetValue (dlg->main_choice);
+  switch (val) {
+    case 1:
+      src = ValNodeNew (NULL);
+      src->choice = ParseSrc_defline;
+      break;
+    case 2:
+      src = ValNodeNew (NULL);
+      src->choice = ParseSrc_flatfile;
+      break;
+    case 3:
+      src = ValNodeNew (NULL);
+      src->choice = ParseSrc_local_id;
+      break;
+    case 4:
+      org = ParseSrcOrgNew ();
+      switch (GetValue (dlg->feat_or_desc)) {
+        case 1:
+          org->type = Object_type_constraint_any;
+          break;
+        case 2:
+          org->type = Object_type_constraint_feature;
+          break;
+        case 3:
+          org->type = Object_type_constraint_descriptor;
+          break;
+        default:
+          org->type = Object_type_constraint_any;
+          break;
+      }
+      vnp = (ValNodePtr) DialogToPointer (dlg->src_qual_choice);
+      if (vnp != NULL) {
+        org->field = ValNodeNew (NULL);
+        if (StringCmp (vnp->data.ptrvalue, kTaxnameAfterBinomialString) == 0) {
+          org->field->choice = ParseSrcOrgChoice_taxname_after_binomial;
+        } else {
+          org->field->choice = ParseSrcOrgChoice_source_qual;
+          org->field->data.intvalue = GetSourceQualTypeByName (vnp->data.ptrvalue);
+        }
+        vnp = ValNodeFree (vnp);
+      }
+      src = ValNodeNew (NULL);
+      src->choice = ParseSrc_org;
+      src->data.ptrvalue = org;
+      break;
+    case 5:
+      src = ValNodeNew (NULL);
+      src->choice = ParseSrc_comment;
+      break;
+    case 6:
+      src = ValNodeNew (NULL);
+      src->choice = ParseSrc_bankit_comment;
+      break;
+    case 7:
+      src = ValNodeNew (NULL);
+      src->choice = ParseSrc_structured_comment;
+      src->data.ptrvalue = SaveStringFromText (dlg->structured_comment_field);
+      break;
+    case 8:
+      src = ValNodeNew (NULL);
+      src->choice = ParseSrc_file_id;
+      break;
+  } 
+  return src;
+}
+
+
+static ValNodePtr TestParseSrcDialog (DialoG d)
+{
+  ParseSrcDlgPtr dlg;
+  Int2 val;
+  ValNodePtr err_list = NULL;
+
+  dlg = (ParseSrcDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  val = GetValue (dlg->main_choice);
+  if (val < 1 || val > 8) {
+    ValNodeAddPointer (&err_list, 0, "main choice");
+  } else if (val == 4) {
+    ValNodeLink (&err_list, TestDialog (dlg->src_qual_choice));
+  } else if (val == 7 && TextHasNoText (dlg->structured_comment_field)) {
+    ValNodeAddPointer (&err_list, 0, "structured comment field");
+  }
+  return err_list;
+}
+
+
+static DialoG ParseSrcDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  ParseSrcDlgPtr dlg;
+  GrouP          p, g;
+  ValNodePtr     qual_list;
+  ValNode        vn;
+
+  p = HiddenGroup (h, 2, 0, NULL);
+  SetGroupSpacing (p, 10, 10);
+
+  dlg = (ParseSrcDlgPtr) MemNew (sizeof (ParseSrcDlgData));
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->fromdialog = DialogToParseSrc;
+  dlg->todialog = ParseSrcToDialog;
+  dlg->testdialog = TestParseSrcDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->main_choice = PopupList (p, TRUE, ChangeParseSrcDialogPopup);
+  SetObjectExtra (dlg->main_choice, dlg, NULL);
+  PopupItem (dlg->main_choice, "Defline");
+  PopupItem (dlg->main_choice, "FlatFile");
+  PopupItem (dlg->main_choice, "Local ID");
+  PopupItem (dlg->main_choice, "Source Qualifier");
+  PopupItem (dlg->main_choice, "Comment");
+  PopupItem (dlg->main_choice, "BankIT Comment");
+  PopupItem (dlg->main_choice, "Structured Comment");
+  PopupItem (dlg->main_choice, "File ID");
+  SetValue (dlg->main_choice, 4);
+
+  g = HiddenGroup (p, 0, 0, NULL);
+  dlg->src_grp = HiddenGroup (g, -1, 0, NULL);
+  qual_list = ValNodeNew (NULL);
+  qual_list->choice = 0;
+  qual_list->data.ptrvalue = StringSave (kTaxnameAfterBinomialString);
+  qual_list->next = GetSourceQualList ();  
+  dlg->src_qual_choice = ValNodeSelectionDialog (dlg->src_grp, qual_list, SHORT_SELECTION_LIST,
+                                               ValNodeStringName,
+                                               ValNodeSimpleDataFree,
+                                               ValNodeStringCopy,
+                                               ValNodeStringMatch,
+                                               "source qual",
+                                               change_notify, change_userdata, FALSE);
+  vn.choice = 0;
+  vn.data.ptrvalue = "Taxname after binomial";
+  vn.next = NULL;
+  PointerToDialog (dlg->src_qual_choice, &vn);
+  dlg->feat_or_desc = HiddenGroup (dlg->src_grp, 3, 0, NULL);
+  RadioButton (dlg->feat_or_desc, "Descriptors and Features");
+  RadioButton (dlg->feat_or_desc, "Descriptors Only");
+  RadioButton (dlg->feat_or_desc, "Features Only");
+  SetValue (dlg->feat_or_desc, 1);
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->src_qual_choice, (HANDLE) dlg->feat_or_desc, NULL);
+
+  dlg->structured_comment_field = DialogText (g, "", 20, ChangeParseSrcDialogText);
+  SetObjectExtra (dlg->structured_comment_field, dlg, NULL);
+  Hide (dlg->structured_comment_field);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->src_grp, (HANDLE) dlg->structured_comment_field, NULL);
+
+  return (DialoG) p;
+}
+
+
+typedef struct parsedstdlg {
+ DIALOG_MESSAGE_BLOCK
+ PopuP main_choice;
+ GrouP src_grp;
+ DialoG src_qual_choice;
+ GrouP feat_or_desc;
+ GrouP  feature_field_grp;
+ DialoG feature_type_choice;
+ DialoG feature_field_choice;
+ TexT  dbxref_db;
+ Nlm_ChangeNotifyProc change_notify;
+ Pointer              change_userdata;
+} ParseDstDlgData, PNTR ParseDstDlgPtr;
+
+
+static void ChangeParseDstDialogPopup (PopuP p) 
+{
+  ParseDstDlgPtr dlg;
+  Int2 val;
+
+  dlg = (ParseDstDlgPtr) GetObjectExtra (p);
+  if (dlg == NULL) return;
+
+  val = GetValue (dlg->main_choice);
+  switch (val) {
+    case 2:
+      Show (dlg->src_grp);
+      Hide (dlg->feature_field_grp);
+      Hide (dlg->dbxref_db);
+      break;
+    case 3:
+      Hide (dlg->src_grp);
+      Show (dlg->feature_field_grp);
+      Hide (dlg->dbxref_db);
+      break;
+    case 4:
+      Hide (dlg->src_grp);
+      Hide (dlg->feature_field_grp);
+      Show (dlg->dbxref_db);
+      break;
+    default:
+      Hide (dlg->src_grp);
+      Hide (dlg->feature_field_grp);
+      Hide (dlg->dbxref_db);
+      break;
+  }
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify)(dlg->change_userdata);
+  }
+}
+
+
+static void ChangeParseDstDialogText (TexT t) 
+{
+  ParseDstDlgPtr dlg;
+
+  dlg = (ParseDstDlgPtr) GetObjectExtra (t);
+  if (dlg == NULL) return;
+
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify)(dlg->change_userdata);
+  }
+}
+
+
+static void ParseDstToDialog (DialoG d, Pointer data)
+{
+  ParseDstDlgPtr dlg;
+  ValNodePtr     dst;
+  ParseDstOrgPtr org;
+  FeatureFieldLegalPtr ffp;
+  ValNode        vn;
+
+  dlg = (ParseDstDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  dst = (ValNodePtr) data;
+  if (dst == NULL) {
+    SetValue (dlg->main_choice, 1);
+  } else {
+    switch (dst->choice) {
+      case ParseDest_defline:
+        SetValue (dlg->main_choice, 1);
+        break;
+      case ParseDest_org:
+        SetValue (dlg->main_choice, 2);
+        org = (ParseDstOrgPtr) dst->data.ptrvalue;
+        if (org == NULL) {
+          PointerToDialog (dlg->src_qual_choice, NULL);
+          SetValue (dlg->feat_or_desc, 1);
+        } else {
+          switch (org->type) {
+            case Object_type_constraint_any:
+              SetValue (dlg->feat_or_desc, 1);
+              break;
+            case Object_type_constraint_feature:
+              SetValue (dlg->feat_or_desc, 2);
+              break;
+            case Object_type_constraint_descriptor:
+              SetValue (dlg->feat_or_desc, 3);
+              break;
+            default:
+              SetValue (dlg->feat_or_desc, 1);
+              break;
+          }
+          if (org->field == NULL) {
+            PointerToDialog (dlg->src_qual_choice, NULL);
+          } else {
+            vn.choice = 0;
+            vn.data.ptrvalue = GetSourceQualName (org->field->data.intvalue);
+            vn.next = NULL;
+            PointerToDialog (dlg->src_qual_choice, &vn);
+          }
+        }
+        break;
+      case ParseDest_featqual:
+        SetValue (dlg->main_choice, 3);
+        ffp = (FeatureFieldLegalPtr) dst->data.ptrvalue;
+        if (ffp == NULL) {
+          PointerToDialog (dlg->feature_type_choice, NULL);
+          PointerToDialog (dlg->feature_field_choice, NULL);
+        } else {
+          vn.choice = ffp->type;
+          vn.data.ptrvalue = NULL;
+          vn.next = NULL;
+          PointerToDialog (dlg->feature_type_choice, &vn);
+          vn.choice = ffp->field;
+          PointerToDialog (dlg->feature_field_choice, &vn);
+        }
+        break;
+      case ParseDest_dbxref:
+        SetValue (dlg->main_choice, 4);
+        SetTitle (dlg->dbxref_db, dst->data.ptrvalue);
+        break;
+    }
+  }
+
+  ChangeParseDstDialogPopup (dlg->main_choice);
+}
+
+
+static Pointer DialogToParseDst (DialoG d)
+{
+  ParseDstDlgPtr dlg;
+  ParseDstOrgPtr org;
+  FeatureFieldLegalPtr ffp;
+  ValNodePtr     dst = NULL, vnp;
+  Int2           val;
+
+  dlg = (ParseDstDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  val = GetValue (dlg->main_choice);
+  switch (val) {
+    case 1:
+      dst = ValNodeNew (NULL);
+      dst->choice = ParseDest_defline;
+      break;
+    case 2:
+      org = ParseDstOrgNew ();
+      switch (GetValue (dlg->feat_or_desc)) {
+        case 1:
+          org->type = Object_type_constraint_any;
+          break;
+        case 2:
+          org->type = Object_type_constraint_feature;
+          break;
+        case 3:
+          org->type = Object_type_constraint_descriptor;
+          break;
+        default:
+          org->type = Object_type_constraint_any;
+          break;
+      }
+      vnp = (ValNodePtr) DialogToPointer (dlg->src_qual_choice);
+      if (vnp != NULL) {
+        org->field = ValNodeNew (NULL);
+        org->field->choice = SourceQualChoice_textqual;
+        org->field->data.intvalue = GetSourceQualTypeByName (vnp->data.ptrvalue);
+        vnp = ValNodeFree (vnp);
+      }      
+      dst = ValNodeNew (NULL);
+      dst->choice = ParseDest_org;
+      dst->data.ptrvalue = org;
+      break;
+    case 3:
+      ffp = FeatureFieldLegalNew ();
+      vnp = (ValNodePtr) DialogToPointer (dlg->feature_type_choice);
+      if (vnp != NULL) {
+        ffp->type = vnp->choice;
+        vnp = ValNodeFree (vnp);
+      }
+      vnp = (ValNodePtr) DialogToPointer (dlg->feature_field_choice);
+      if (vnp != NULL) {
+        ffp->field = vnp->choice;
+        vnp = ValNodeFree (vnp);
+      }
+      dst = ValNodeNew (NULL);
+      dst->choice = ParseDest_featqual;
+      dst->data.ptrvalue = ffp;
+      break;
+    case 4:
+      dst = ValNodeNew (NULL);
+      dst->choice = ParseDest_dbxref;
+      dst->data.ptrvalue = SaveStringFromText (dlg->dbxref_db);
+      break;
+  }
+  return dst;
+}
+
+
+static ValNodePtr TestParseDstDialog (DialoG d)
+{
+  ParseDstDlgPtr dlg;
+  ValNodePtr     err_list = NULL;
+  Int2           val;
+
+  dlg = (ParseDstDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  val = GetValue (dlg->main_choice);
+  if (val < 1 || val > 4) {
+    ValNodeAddPointer (&err_list, 0, "main choice");
+  } else if (val == 2) {
+    ValNodeLink (&err_list, TestDialog (dlg->src_qual_choice));
+  } else if (val == 3) {
+    ValNodeLink (&err_list, TestDialog (dlg->feature_type_choice));
+    ValNodeLink (&err_list, TestDialog (dlg->feature_field_choice));
+  } else if (val == 4 && TextHasNoText (dlg->dbxref_db)) {
+    ValNodeAddPointer (&err_list, 0, "dbxref db");
+  }
+  return err_list;
+}
+  
+
+static DialoG ParseDstDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  ParseDstDlgPtr dlg;
+  GrouP          p, g;
+  ValNodePtr     qual_list;
+
+  p = HiddenGroup (h, 2, 0, NULL);
+  SetGroupSpacing (p, 10, 10);
+
+  dlg = (ParseDstDlgPtr) MemNew (sizeof (ParseDstDlgData));
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = ParseDstToDialog;
+  dlg->fromdialog = DialogToParseDst;
+  dlg->testdialog = TestParseDstDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->main_choice = PopupList (p, TRUE, ChangeParseDstDialogPopup);
+  SetObjectExtra (dlg->main_choice, dlg, NULL);
+  PopupItem (dlg->main_choice, "Defline");
+  PopupItem (dlg->main_choice, "Source Qualifier");
+  PopupItem (dlg->main_choice, "Feature Qualifier");
+  PopupItem (dlg->main_choice, "Dbxref");
+  SetValue (dlg->main_choice, 1);
+
+  g = HiddenGroup (p, 0, 0, NULL);
+  dlg->src_grp = HiddenGroup (g, -1, 0, NULL);
+  qual_list = GetSourceQualList ();  
+  dlg->src_qual_choice = ValNodeSelectionDialog (dlg->src_grp, qual_list, SHORT_SELECTION_LIST,
+                                               ValNodeStringName,
+                                               ValNodeSimpleDataFree,
+                                               ValNodeStringCopy,
+                                               ValNodeStringMatch,
+                                               "source qual",
+                                               change_notify, change_userdata, FALSE);
+  dlg->feat_or_desc = HiddenGroup (dlg->src_grp, 3, 0, NULL);
+  RadioButton (dlg->feat_or_desc, "Descriptors and Features");
+  RadioButton (dlg->feat_or_desc, "Descriptors Only");
+  RadioButton (dlg->feat_or_desc, "Features Only");
+  SetValue (dlg->feat_or_desc, 1);
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->src_qual_choice, (HANDLE) dlg->feat_or_desc, NULL);
+  Hide (dlg->src_grp);
+
+  dlg->feature_field_grp = HiddenGroup (g, 2, 0, NULL);
+  dlg->feature_type_choice = FeatureTypeDialog (dlg->feature_field_grp, change_notify, change_userdata);
+  dlg->feature_field_choice = LegalFeatQualChoiceDialog (dlg->feature_field_grp, change_notify, change_userdata);
+  Hide (dlg->feature_field_grp);
+
+  dlg->dbxref_db = DialogText (g, "", 20, ChangeParseDstDialogText);
+  SetObjectExtra (dlg->dbxref_db, dlg, NULL);
+  Hide (dlg->dbxref_db);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->src_grp, (HANDLE) dlg->feature_field_grp, (HANDLE) dlg->dbxref_db, NULL);
+
+  return (DialoG) p;
+}
+
+
+typedef struct parseactiondlg {
+ DIALOG_MESSAGE_BLOCK
+ DialoG text_portion;
+ DialoG src;
+ DialoG dst;
+ GrouP  cap_change;
+ ButtoN remove_from_parsed;
+ DialoG existing_text;
+ Nlm_ChangeNotifyProc change_notify;
+ Pointer              change_userdata;
+ Nlm_ChangeNotifyProc redraw_notify;
+ Pointer              redraw_userdata;
+} ParseActionDlgData, PNTR ParseActionDlgPtr;
+
+
+static void ParseActionToDialog (DialoG d, Pointer data)
+{
+  ParseActionDlgPtr dlg;
+  ParseActionPtr action;
+
+  dlg = (ParseActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  action = (ParseActionPtr) data;
+  if (action == NULL) {
+    PointerToDialog (dlg->text_portion, NULL);
+    PointerToDialog (dlg->src, NULL);
+    PointerToDialog (dlg->dst, NULL);
+    SetValue (dlg->cap_change, 1);
+    SetStatus (dlg->remove_from_parsed, FALSE);
+    PointerToDialog (dlg->existing_text, NULL);
+  } else {
+    PointerToDialog (dlg->text_portion, action->portion);
+    PointerToDialog (dlg->src, action->src);
+    PointerToDialog (dlg->dst, action->dest);
+    switch (action->capitalization) {
+      case Cap_change_none:
+        SetValue (dlg->cap_change, 1);
+        break;
+      case Cap_change_tolower:
+        SetValue (dlg->cap_change, 2);
+        break;
+      case Cap_change_toupper:
+        SetValue (dlg->cap_change, 3);
+        break;
+      case Cap_change_firstcap:
+        SetValue (dlg->cap_change, 4);
+        break;
+      default:
+        SetValue (dlg->cap_change, 1);
+        break;
+    }
+    SetStatus (dlg->remove_from_parsed, action->remove_from_parsed);
+    PointerToDialog (dlg->existing_text, (Pointer) action->existing_text);
+  }    
+}
+
+
+static Pointer DialogToParseAction (DialoG d)
+{
+  ParseActionDlgPtr dlg;
+  ParseActionPtr    action;
+
+  dlg = (ParseActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  action = ParseActionNew();
+  action->portion = DialogToPointer (dlg->text_portion);
+  action->src = DialogToPointer (dlg->src);
+  action->dest = DialogToPointer (dlg->dst);
+  action->remove_from_parsed = GetStatus (dlg->remove_from_parsed);
+  switch (GetValue (dlg->cap_change)) {
+    case 1:
+      action->capitalization = Cap_change_none;
+      break;
+    case 2:
+      action->capitalization = Cap_change_tolower;
+      break;
+    case 3:
+      action->capitalization = Cap_change_toupper;
+      break;
+    case 4:
+      action->capitalization = Cap_change_firstcap;
+      break;
+    default:
+      action->capitalization = Cap_change_none;
+      break;
+  }
+  action->existing_text = (Uint2) DialogToPointer (dlg->existing_text);
+  return action;
+}
+
+
+static ValNodePtr TestParseActionDialog (DialoG d)
+{
+  ParseActionDlgPtr dlg;
+  ValNodePtr err_list = NULL;
+  Int2 val;
+
+  dlg = (ParseActionDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  ValNodeLink (&err_list, TestDialog (dlg->text_portion));
+  ValNodeLink (&err_list, TestDialog (dlg->src));
+  ValNodeLink (&err_list, TestDialog (dlg->dst));
+  ValNodeLink (&err_list, TestDialog (dlg->existing_text));
+  val = GetValue (dlg->cap_change);
+  if (val < 1 || val > 4) {
+    ValNodeAddPointer (&err_list, 0, "cap change");
+  }
+  return err_list;
+}
+
+
+static DialoG 
+ParseActionDialog 
+(GrouP h,
+ Boolean indexer_version, 
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata,
+ Nlm_ChangeNotifyProc     redraw_notify,
+ Pointer                  redraw_userdata)
+{
+  ParseActionDlgPtr dlg;
+  GrouP                 p, g;
+
+  dlg = (ParseActionDlgPtr) MemNew (sizeof (ParseActionDlgData));
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetGroupSpacing (p, 10, 10);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = ParseActionToDialog;
+  dlg->fromdialog = DialogToParseAction;
+  dlg->dialogmessage = NULL;
+  dlg->testdialog = TestParseActionDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->text_portion = TextPortionDialog (p, TRUE, change_notify, change_userdata);
+
+  g = HiddenGroup (p, 2, 0, NULL);
+  StaticPrompt (g, "From", 0, popupMenuHeight, programFont, 'r');
+  dlg->src = ParseSrcDialog (g, change_notify, change_userdata);
+  StaticPrompt (g, "And place in", 0, popupMenuHeight, programFont, 'r');
+  dlg->dst = ParseDstDialog (g, change_notify, change_userdata);
+  dlg->cap_change = NormalGroup (p, 3, 0, "Capitalization", programFont, NULL);
+  SetGroupSpacing (dlg->cap_change, 10, 10);
+
+  RadioButton (dlg->cap_change, "No change");
+  RadioButton (dlg->cap_change, "To lower");
+  RadioButton (dlg->cap_change, "To upper");
+  RadioButton (dlg->cap_change, "First cap, rest lower");
+  SetValue (dlg->cap_change, 1);
+
+  dlg->remove_from_parsed = CheckBox (p, "Remove from parsed field", NULL);
+
+  dlg->existing_text = ExistingTextDialog (p, change_notify, change_userdata);
+
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->cap_change,
+                              (HANDLE) dlg->remove_from_parsed,
+                              (HANDLE) dlg->existing_text,
+                              (HANDLE) dlg->text_portion,
+                              (HANDLE) g,
+                              NULL);
+
+  return (DialoG) p;  
+}
+
+  
+typedef struct editmacroaction {
+  PopuP action_type;
+
+  DialoG action_dlg;
+
+  ButtoN accept_btn;
+  ButtoN test_btn;
+  ButtoN undo_btn;
+  ButtoN leave_dlg_up;
+  Boolean rebuild_window;
+  Char    undo_file [PATH_MAX];
+} EditMacroActionData, PNTR EditMacroActionPtr;
+
+
+/* rebuild dialog with new feature type */
+static void ChangeMacroAction (Pointer data)
+{
+  EditMacroActionPtr e;
+
+  e = (EditMacroActionPtr) data;
+  if (e != NULL) {
+    e->rebuild_window = TRUE;
+  }
+}
+
+
+static void ChangeMacroActionPopup (PopuP p)
+{
+  ChangeMacroAction (GetObjectExtra (p));
+}
+
+
+static void EnableEditMacroActionAccept (Pointer data)
+{
+  EditMacroActionPtr e;
+  ValNodePtr err_list = NULL;
+
+  e = (EditMacroActionPtr) data;
+  if (e != NULL) {
+    err_list = TestDialog (e->action_dlg);
+    if (err_list == NULL) {
+      Enable (e->accept_btn);
+      Enable (e->test_btn);
+    } else {
+      Disable (e->accept_btn);
+      Disable (e->test_btn);
+    }
+    err_list = ValNodeFree (err_list);
+  }
+}  
+
+
+static void RunMacroInEditor (ButtoN b)
+{
+  EditMacroActionPtr e;
+  ValNodePtr  action;
+  ValNodePtr  sep_list, vnp;
+  SeqEntryPtr sep;
+  Uint2       entityID;
+  Int4        num_fields = 0, num_features = 0;
+  Int4        tmp_fields, tmp_features;
+
+  e = (EditMacroActionPtr) GetObjectExtra (b);
+  if (e == NULL) return;
+
+  action = ValNodeNew (NULL);
+  switch (GetValue (e->action_type)) {
+    case 1:
+      action->choice = MacroActionChoice_add_feature;
+      action->data.ptrvalue = DialogToPointer (e->action_dlg);
+      break;
+    case 2:
+    case 3:
+    case 4:
+    case 5:
+    case 6:
+    case 7:
+    case 8:
+      action->choice = MacroActionChoice_aecr;
+      action->data.ptrvalue = DialogToPointer (e->action_dlg);
+      break;
+    case 9:
+      action->choice = MacroActionChoice_parse;
+      action->data.ptrvalue = DialogToPointer (e->action_dlg);
+      break;
+    case 10:
+      action->choice = MacroActionChoice_remove_feature;
+      action->data.ptrvalue = DialogToPointer (e->action_dlg);
+      break;
+    case 11:
+      action->choice = MacroActionChoice_edit_location;
+      action->data.ptrvalue = DialogToPointer (e->action_dlg);
+      break;
+  }
+
+  sep_list = GetViewedSeqEntryList ();
+  if (sep_list == NULL) {
+    Message (MSG_ERROR, "No records open!");
+  } else if (sep_list->next != NULL 
+    && ANS_CANCEL == Message (MSG_OKC, "You have more than one record open - run macro for all open records?")) {
+    /* do nothing */
+  } else {
+    WatchCursor();
+    Update();
+    for (vnp = sep_list; vnp != NULL; vnp = vnp->next) {
+      sep = vnp->data.ptrvalue;
+      entityID = ObjMgrGetEntityIDForChoice(sep);
+      tmp_fields = 0;
+      tmp_features = 0;
+      ApplyMacroToSeqEntry (sep, action, &tmp_fields, &tmp_features);
+      num_fields += tmp_fields;
+      num_features += tmp_features;
+      ObjMgrSetDirtyFlag (entityID, TRUE);
+      ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
+    }
+    sep_list = ValNodeFree (sep_list);
+    ArrowCursor ();
+    Update ();  
+    Message (MSG_OK, "Macro action affected %d fields and created %d features", num_fields, num_features); 
+  }  
+
+  action = MacroActionChoiceFree (action);
+  Enable (e->undo_btn);
+}
+
+
+static Boolean SaveBackupSeqEntryList (CharPtr path)
+{
+  ValNodePtr sep_list, vnp;
+  AsnIoPtr   aip;
+
+  aip = AsnIoOpen (path, "w");
+  if (aip == NULL) {
+    Message (MSG_ERROR, "Unable to open file for backup");
+    return FALSE;
+  }
+
+  sep_list = GetViewedSeqEntryList ();
+  if (sep_list == NULL) {
+    AsnIoClose (aip);
+    return FALSE;
+  }
+
+  for (vnp = sep_list; vnp != NULL; vnp = vnp->next) {
+    SeqEntryAsnWrite (vnp->data.ptrvalue, aip, NULL);
+  }
+
+  AsnIoClose (aip);
+  sep_list = ValNodeFree (sep_list);
+  return TRUE;  
+}
+
+
+static ValNodePtr ReadBackupSeqEntryList (CharPtr path)
+{
+  AsnIoPtr   aip;
+  ValNodePtr sep_list = NULL;
+  SeqEntryPtr sep;
+
+  aip = AsnIoOpen (path, "r");
+  if (aip == NULL) {
+    Message (MSG_ERROR, "Unable to open %s", path);
+  } else {
+    while ((sep = SeqEntryAsnRead (aip, NULL)) != NULL) {
+      ValNodeAddPointer (&sep_list, 0, sep);
+    }
+    AsnIoClose (aip);
+  }
+  return sep_list;  
+}
+
+
+static void RestoreList (ValNodePtr curr_sep_list, ValNodePtr backup_sep_list)
+{
+  ValNodePtr vnp_c, vnp_b;
+  SeqEntryPtr sep_c, sep_b;
+  Uint2       entityID;
+
+  if (curr_sep_list == NULL) return;
+  if (ValNodeLen (curr_sep_list) != ValNodeLen (backup_sep_list)) {
+    Message (MSG_ERROR, "Backup list does not match current list.  Unable to undo.");
+    return;
+  }
+
+  for (vnp_c = curr_sep_list, vnp_b = backup_sep_list; vnp_c != NULL && vnp_b != NULL; vnp_c = vnp_c->next, vnp_b = vnp_b->next) {
+    sep_c = vnp_c->data.ptrvalue;
+    sep_b = vnp_b->data.ptrvalue;
+    SeqEntrySetScope (NULL);
+    ReplaceSeqEntryWithSeqEntry (sep_c, sep_b, TRUE);
+    entityID = ObjMgrGetEntityIDForChoice (sep_c);
+    ObjMgrSetDirtyFlag (entityID, TRUE);
+    ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
+  }
+  Update();
+}
+
+
+static void UndoMacroActionTest (ButtoN b)
+{
+  EditMacroActionPtr e;
+  ValNodePtr         curr_list;
+  ValNodePtr         backup_list;
+  
+  e = (EditMacroActionPtr) GetObjectExtra (b);
+  if (e == NULL) return;
+
+  curr_list = GetViewedSeqEntryList ();
+  if (curr_list == NULL) {
+    Message (MSG_ERROR, "No records to undo");
+    Disable (e->undo_btn);
+    return;
+  } else {
+    backup_list = ReadBackupSeqEntryList (e->undo_file);
+    RestoreList (curr_list, backup_list);
+    Disable (e->undo_btn);
+    curr_list = ValNodeFree (curr_list);
+    backup_list = ValNodeFree (backup_list);
+  }
+  
+}
+
+
+static WindoW 
+BuildEditMacroActionWindow 
+(ValNodePtr action,
+ Boolean indexer_version,
+ EditMacroActionPtr d,
+ ModalAcceptCancelPtr acp,
+ Boolean adding_new)
+{
+  ValNodePtr            feature_type_list = NULL;
+  AECRActionPtr         aecr = NULL;
+  ApplyFeatureActionPtr apply_feat = NULL;
+  RemoveFeatureActionPtr remove_feat = NULL;
+  EditFeatureLocationActionPtr edit_loc = NULL;
+  ParseActionPtr        parse = NULL;
+  WindoW                w;
+  GrouP                 h, c;
+  ButtoN                b;
+  Int2                  action_type;
+
+  w = MovableModalWindow(-20, -13, -10, -10, "Edit Action", NULL);
+#ifndef WIN_MAC
+  CreateStandardEditMenu (w);
+#endif
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  d->action_type = PopupList (h, TRUE, ChangeMacroActionPopup);
+  SetObjectExtra (d->action_type, d, NULL);
+  PopupItem (d->action_type, "Apply Feature");
+  PopupItem (d->action_type, "Apply Qualifier");
+  PopupItem (d->action_type, "Edit Qualifier");
+  PopupItem (d->action_type, "Convert Qualifier");
+  PopupItem (d->action_type, "Copy Qualifier");
+  PopupItem (d->action_type, "Swap Qualifier");
+  PopupItem (d->action_type, "Parse Qualifier");
+  PopupItem (d->action_type, "Remove Qualifier");
+  PopupItem (d->action_type, "Parse Text");
+  PopupItem (d->action_type, "Remove Feature");
+  PopupItem (d->action_type, "Edit Feature Location");
+
+  if (action == NULL) {
+    SetValue (d->action_type, 1);
+  } else {
+    switch (action->choice) {
+      case MacroActionChoice_add_feature:
+        SetValue (d->action_type, 1);
+        apply_feat = (ApplyFeatureActionPtr) action->data.ptrvalue;
+        break;
+      case MacroActionChoice_aecr:
+        aecr = (AECRActionPtr) action->data.ptrvalue;
+        if (aecr == NULL || aecr->action == NULL) {
+          SetValue (d->action_type, 2);
+        } else {
+          switch (aecr->action->choice) {
+            case ActionChoice_apply:
+              SetValue (d->action_type, 2);
+              break;
+            case ActionChoice_edit:
+              SetValue (d->action_type, 3);
+              break;
+            case ActionChoice_convert:
+              SetValue (d->action_type, 4);
+              break;
+            case ActionChoice_copy:
+              SetValue (d->action_type, 5);
+              break;
+            case ActionChoice_swap:
+              SetValue (d->action_type, 6);
+              break;
+            case ActionChoice_parse:
+              SetValue (d->action_type, 7);
+              break;
+            case ActionChoice_remove:
+              SetValue (d->action_type, 8);
+              break;
+            default:
+              SetValue (d->action_type, 2);
+              break;
+          }
+        }
+        break;
+      case MacroActionChoice_parse:
+        SetValue (d->action_type, 9);
+        parse = (ParseActionPtr) action->data.ptrvalue;
+        break;
+      case MacroActionChoice_remove_feature:
+        SetValue (d->action_type, 10);
+        remove_feat = (RemoveFeatureActionPtr) action->data.ptrvalue;
+        break;
+      case MacroActionChoice_edit_location:
+        SetValue (d->action_type, 11);
+        edit_loc = (EditFeatureLocationActionPtr) action->data.ptrvalue;
+        break;
+      default:
+        SetValue (d->action_type, 1);
+        break;
+    }
+  } 
+  d->action_dlg = NULL;
+
+  action_type = GetValue (d->action_type);
+  /* set up remaining controls */
+  switch (action_type) {
+    case 1:  
+      d->action_dlg = ApplyFeatureActionDialog (h, apply_feat, indexer_version, EnableEditMacroActionAccept, d, ChangeMacroAction, d);
+      PointerToDialog (d->action_dlg, apply_feat);
+      break;
+    case 2:
+    case 3:
+    case 4:
+    case 5:
+    case 6:
+    case 7:
+    case 8:
+      d->action_dlg = EditAECRActionDialog (h, aecr, indexer_version, EnableEditMacroActionAccept, d, ChangeMacroAction, d);
+      PointerToDialog (d->action_dlg, aecr);
+      break;
+    case 9:
+      d->action_dlg = ParseActionDialog (h, indexer_version, EnableEditMacroActionAccept, d, ChangeMacroAction, d);
+      PointerToDialog (d->action_dlg, parse);
+      break;
+    case 10:
+      d->action_dlg = RemoveFeatureActionDialog (h, indexer_version, EnableEditMacroActionAccept, d);
+      PointerToDialog (d->action_dlg, remove_feat);
+      break;
+    case 11:
+      d->action_dlg = EditFeatureLocationActionDialog (h, indexer_version, EnableEditMacroActionAccept, d);
+      PointerToDialog (d->action_dlg, edit_loc);
+      break;
+  }
+  c = HiddenGroup (h, 4, 0, NULL);
+  SetGroupSpacing (c, 10, 10);
+  d->accept_btn = PushButton (c, "Accept", ModalAcceptButton);
+  SetObjectExtra (d->accept_btn, acp, NULL);
+  if (d->undo_file[0] != 0) {
+    d->test_btn = PushButton (c, "Test", RunMacroInEditor);
+    SetObjectExtra (d->test_btn, d, NULL);
+    d->undo_btn = PushButton (c, "Undo", UndoMacroActionTest);
+    SetObjectExtra (d->undo_btn, d, NULL);
+    Disable (d->undo_btn);
+  }
+  b = PushButton (c, "Cancel", ModalCancelButton);
+  SetObjectExtra (b, acp, NULL);
+
+  if (adding_new) {
+    d->leave_dlg_up = CheckBox (h, "Leave dialog up (and add more macro actions)", NULL);
+  }
+  AlignObjects (ALIGN_CENTER, (HANDLE) c, 
+                              (HANDLE) d->action_type,
+                              (HANDLE) d->action_dlg,
+                              (HANDLE) d->leave_dlg_up,
+                              NULL);
+  EnableEditMacroActionAccept (d);
+  return w;
+}
+
+
+static Boolean EditMacroAction (ValNodePtr action, Boolean indexer_version)
+{
+  EditMacroActionData   d;
+  ModalAcceptCancelData acd;
+  Boolean               rval = FALSE;
+  WindoW                w, repl_w;
+  ValNodePtr            action_copy = NULL;
+  Int2                  action_type;
+  
+  if (action == NULL) return FALSE;
+
+  d.accept_btn = NULL;
+  d.test_btn = NULL;
+  d.leave_dlg_up = NULL;
+
+  TmpNam (d.undo_file);
+  if (!SaveBackupSeqEntryList (d.undo_file)) {
+    d.undo_file[0] = 0;
+  }
+
+  action_copy = AsnIoMemCopy (action, (AsnReadFunc) MacroActionChoiceAsnRead, (AsnWriteFunc) MacroActionChoiceAsnWrite);
+  w = BuildEditMacroActionWindow (action_copy, indexer_version, &d, &acd, FALSE);
+  d.rebuild_window = FALSE;
+      
+  Show (w);
+  Select (w);
+  acd.accepted = FALSE;
+  acd.cancelled = FALSE;
+  while (!acd.accepted && ! acd.cancelled)
+  {
+    ProcessExternalEvent ();
+    if (d.rebuild_window) {
+      /* copy data from dialog if compatible */
+      action_type = GetValue (d.action_type);
+      if (action_type == 1 && action_copy != NULL && action_copy->choice == MacroActionChoice_add_feature) {
+        action_copy = MacroActionChoiceFree (action_copy);
+        action_copy = ValNodeNew (NULL);
+        action_copy->choice = MacroActionChoice_add_feature;
+        action_copy->data.ptrvalue = DialogToPointer (d.action_dlg);
+      } else if (action_type > 1 && action_type < 9 && action_copy != NULL && action_copy->choice == MacroActionChoice_aecr) {
+        action_copy = MacroActionChoiceFree (action_copy);
+        action_copy = ValNodeNew (NULL);
+        action_copy->choice = MacroActionChoice_aecr;
+        action_copy->data.ptrvalue = BuildDefaultAECRAction (ActionTypeChoiceFromPopupValue (action_type), FieldTypeChoiceFromEditAECRActionDialog (d.action_dlg));      
+      } else {
+        action_copy = MacroActionChoiceFree (action_copy);
+        if (action_type == 1) {
+          action_copy = ValNodeNew (NULL);
+          action_copy->choice = MacroActionChoice_add_feature;
+          action_copy->data.ptrvalue = BuildDefaultApplyFeatureAction (Feature_type_cds);
+        } else if (action_type >1 && action_type < 9) {
+          action_copy = ValNodeNew (NULL);
+          action_copy->choice = MacroActionChoice_aecr;
+          action_copy->data.ptrvalue = BuildDefaultAECRAction (ActionTypeChoiceFromPopupValue (action_type), FieldTypeChoiceFromEditAECRActionDialog (d.action_dlg));      
+        } else if (action_type == 9) {
+          action_copy = ValNodeNew (NULL);
+          action_copy->choice = MacroActionChoice_parse;
+          action_copy->data.ptrvalue = BuildDefaultParseAction ();
+        } else if (action_type == 10) {
+          action_copy = ValNodeNew (NULL);
+          action_copy->choice = MacroActionChoice_remove_feature;
+          action_copy->data.ptrvalue = BuildDefaultRemoveFeatureAction ();
+        } else if (action_type == 11) {
+          action_copy = ValNodeNew (NULL);
+          action_copy->choice = MacroActionChoice_edit_location;
+          action_copy->data.ptrvalue = BuildDefaultEditFeatureLocationAction (Feature_type_gene);
+        }
+      }
+
+      /* replace window */
+      Remove (w);
+      repl_w = BuildEditMacroActionWindow (action_copy, indexer_version, &d, &acd, FALSE);
+      w = repl_w;
+      Show (w);
+      Select (w);
+      d.rebuild_window = FALSE;
+    }        
+    Update ();
+  }
+  ProcessAnEvent ();
+  if (!acd.cancelled)
+  {
+    rval = TRUE;
+    switch (action->choice) {
+      case MacroActionChoice_aecr:
+        action->data.ptrvalue = AECRActionFree (action->data.ptrvalue);
+        break;
+      case MacroActionChoice_parse:
+        action->data.ptrvalue = ParseActionFree (action->data.ptrvalue);
+        break;
+      case MacroActionChoice_add_feature:
+        action->data.ptrvalue = ApplyFeatureActionFree (action->data.ptrvalue);
+        break;
+      case MacroActionChoice_remove_feature:
+        action->data.ptrvalue = RemoveFeatureActionFree (action->data.ptrvalue);
+        break;
+      case MacroActionChoice_edit_location:
+        action->data.ptrvalue = EditFeatureLocationActionFree (action->data.ptrvalue);
+        break;
+    }
+    switch (GetValue (d.action_type)) {
+      case 1:
+        action->choice = MacroActionChoice_add_feature;
+        action->data.ptrvalue = DialogToPointer (d.action_dlg);
+        break;
+      case 2:
+      case 3:
+      case 4:
+      case 5:
+      case 6:
+      case 7:
+      case 8:
+        action->choice = MacroActionChoice_aecr;
+        action->data.ptrvalue = DialogToPointer (d.action_dlg);
+        break;
+      case 9:
+        action->choice = MacroActionChoice_parse;
+        action->data.ptrvalue = DialogToPointer (d.action_dlg);
+        break;
+      case 10:
+        action->choice = MacroActionChoice_remove_feature;
+        action->data.ptrvalue = DialogToPointer (d.action_dlg);
+        break;
+      case 11:
+        action->choice = MacroActionChoice_edit_location;
+        action->data.ptrvalue = DialogToPointer (d.action_dlg);
+        break;
+    }
+  }
+  Remove (w);
+  FileRemove (d.undo_file);
+
+  action_copy = MacroActionChoiceFree (action_copy);
+  return rval;
+}
+
+
+static void AddMacroActions (MacroEditorFormPtr f, Int2 item)
+{
+  EditMacroActionData   d;
+  ModalAcceptCancelData acd;
+  Boolean               rval = FALSE;
+  WindoW                w, repl_w;
+  ValNodePtr            action_copy = NULL, new_action, prev_action = NULL;
+  Int2                  pos;
+  Int2                  action_type;
+  Boolean               done = FALSE, leave_up;
+  Int4                  scroll_pos;
+  BaR                   sb_vert;
+
+  if (f == NULL) return;
+
+  if (item > 0 && f->macro_list != NULL) {
+    pos = 1;
+    prev_action = f->macro_list;
+    while (pos < item && prev_action->next != NULL) {
+      pos++;
+      prev_action = prev_action->next;
+    }
+  }  
+  
+  action_copy = BuildDefaultNewMacroAction ();
+  d.accept_btn = NULL;
+  d.test_btn = NULL;
+  d.leave_dlg_up = NULL;
+  TmpNam (d.undo_file);
+  if (!SaveBackupSeqEntryList (d.undo_file)) {
+    d.undo_file[0] = 0;
+  }
+  w = BuildEditMacroActionWindow (action_copy, f->indexer_version, &d, &acd, TRUE);
+  d.rebuild_window = FALSE;
+    
+  Show (w);
+  Select (w);
+  while (!done) {
+    acd.accepted = FALSE;
+    acd.cancelled = FALSE;
+    while (!acd.accepted && ! acd.cancelled)
+    {
+      ProcessExternalEvent ();
+      if (d.rebuild_window) {
+        /* copy data from dialog if compatible */
+        action_type = GetValue (d.action_type);
+        if (action_type == 1 && action_copy != NULL && action_copy->choice == MacroActionChoice_add_feature) {
+          action_copy = MacroActionChoiceFree (action_copy);
+          action_copy = ValNodeNew (NULL);
+          action_copy->choice = MacroActionChoice_add_feature;
+          action_copy->data.ptrvalue = DialogToPointer (d.action_dlg);
+        } else if (action_type > 1 && action_type < 9 && action_copy != NULL && action_copy->choice == MacroActionChoice_aecr) {
+          action_copy = MacroActionChoiceFree (action_copy);
+          action_copy = ValNodeNew (NULL);
+          action_copy->choice = MacroActionChoice_aecr;
+          action_copy->data.ptrvalue = BuildDefaultAECRAction (ActionTypeChoiceFromPopupValue (action_type), FieldTypeChoiceFromEditAECRActionDialog (d.action_dlg));      
+        } else {
+          action_copy = MacroActionChoiceFree (action_copy);
+          if (action_type == 1) {
+            action_copy = ValNodeNew (NULL);
+            action_copy->choice = MacroActionChoice_add_feature;
+            action_copy->data.ptrvalue = BuildDefaultApplyFeatureAction (Feature_type_cds);
+          } else if (action_type > 1 && action_type < 9) {
+            action_copy = ValNodeNew (NULL);
+            action_copy->choice = MacroActionChoice_aecr;
+            action_copy->data.ptrvalue = BuildDefaultAECRAction (ActionTypeChoiceFromPopupValue (action_type), FieldTypeChoiceFromEditAECRActionDialog (d.action_dlg));      
+          } else if (action_type == 9) {
+            action_copy = ValNodeNew (NULL);
+            action_copy->choice = MacroActionChoice_parse;
+            action_copy->data.ptrvalue = BuildDefaultParseAction ();
+          } else if (action_type == 10) {
+            action_copy = ValNodeNew (NULL);
+            action_copy->choice = MacroActionChoice_remove_feature;
+            action_copy->data.ptrvalue = BuildDefaultRemoveFeatureAction ();
+          } else if (action_type == 11) {
+            action_copy = ValNodeNew (NULL);
+            action_copy->choice = MacroActionChoice_edit_location;
+            action_copy->data.ptrvalue = BuildDefaultEditFeatureLocationAction (Feature_type_gene);
+          }
+        }
+
+        /* replace window */
+        leave_up = GetStatus (d.leave_dlg_up);
+        Remove (w);
+        repl_w = BuildEditMacroActionWindow (action_copy, f->indexer_version, &d, &acd, TRUE);
+        SetStatus (d.leave_dlg_up, leave_up);
+        w = repl_w;
+        Show (w);
+        Select (w);
+        d.rebuild_window = FALSE;
+      }        
+      Update ();
+    }
+    ProcessAnEvent ();
+    if (acd.cancelled) {
+      done = TRUE;
+    } else {
+      /* get current scroll position */
+      sb_vert = GetSlateVScrollBar ((SlatE) f->macro_summary);
+      scroll_pos = GetBarValue (sb_vert);
+      /* we will want to increase the scroll position after each addition
+       * note that we need to get the scroll bar and check the initial position
+       * each time - if there was no scroll bar after the last update, scroll_pos
+       * needs to be zero to start.
+       */
+      scroll_pos++;
+
+      rval = TRUE;
+      /* create new action based on contents of dialog */
+      new_action = ValNodeNew (NULL);
+      switch (GetValue (d.action_type)) {
+        case 1:
+          new_action->choice = MacroActionChoice_add_feature;
+          new_action->data.ptrvalue = DialogToPointer (d.action_dlg);
+          break;
+        case 2:
+        case 3:
+        case 4:
+        case 5:
+        case 6:
+        case 7:
+        case 8:
+          new_action->choice = MacroActionChoice_aecr;
+          new_action->data.ptrvalue = DialogToPointer (d.action_dlg);
+          break;
+        case 9:
+          new_action->choice = MacroActionChoice_parse;
+          new_action->data.ptrvalue = DialogToPointer (d.action_dlg);
+          break;
+        case 10:
+          new_action->choice = MacroActionChoice_remove_feature;
+          new_action->data.ptrvalue = DialogToPointer (d.action_dlg);
+          break;
+        case 11:
+          new_action->choice = MacroActionChoice_edit_location;
+          new_action->data.ptrvalue = DialogToPointer (d.action_dlg);
+          break;
+      }
+      /* add action to macro list */
+      if (prev_action == NULL) {
+        /* put at start of list */
+        new_action->next = f->macro_list;
+        f->macro_list = new_action;
+      } else {
+        /* insert in list */
+        new_action->next = prev_action->next;
+        prev_action->next = new_action;
+      }
+      /* next action will be inserted after this one */
+      prev_action = new_action; 
+      /* update summary */
+      UpdateMacroSummary (f, scroll_pos);
+
+      /* done if leave_dlg_up not checked */
+      if (!GetStatus (d.leave_dlg_up)) {
+        done = TRUE;
+      }
+    }
+  }
+  Remove (w);
+  action_copy = MacroActionChoiceFree (action_copy);
+}
+
+
+/* Functions for summarizing macro actions for display */
+
+static CharPtr SummarizeExistingText (Uint2 existing_text)
+{
+  CharPtr str = NULL;
+
+  switch (existing_text) {
+    case ExistingTextOption_append_semi :
+      str = "append separated by semicolon";
+      break;
+    case ExistingTextOption_append_space :
+      str = "append separated by space";
+      break;
+    case ExistingTextOption_append_colon :
+      str = "append separated by colon";
+      break;
+    case ExistingTextOption_append_none :
+      str = "append (no separator)";
+      break;
+    case ExistingTextOption_prefix_semi :
+      str = "prefix separated by semicolon";
+      break;
+    case ExistingTextOption_prefix_space :
+      str = "prefix separated by space";
+      break;
+    case ExistingTextOption_prefix_colon :
+      str = "prefix separated by colon";
+      break;
+    case ExistingTextOption_prefix_none :
+      str = "prefix (no separator)";
+      break;
+    case ExistingTextOption_leave_old :
+      str = "ignore new text when existing text is present";
+      break;
+    case ExistingTextOption_replace_old :
+      str = "overwrite existing text";
+      break;
+    default:
+      str = "invalid existing_text option";
+      break;
+  }
+  return str;    
+}
+
+
+static CharPtr GetStringLocationPhrase (Uint2 match_location, Boolean not_present)
+{
+  CharPtr location_word = NULL;
+
+  switch (match_location) {
+    case String_location_contains :
+      if (not_present) {
+        location_word = "does not contain";
+      } else {
+        location_word = "contains";
+      }
+      break;
+    case String_location_equals :
+      if (not_present) {
+        location_word = "does not equal";
+      } else {
+        location_word = "equals";
+      }
+      break;
+    case String_location_starts :
+      if (not_present) {
+        location_word = "does not start with";
+      } else {
+        location_word = "starts with";
+      }
+      break;
+    case String_location_ends :
+      if (not_present) {
+        location_word = "does not end with";
+      } else {
+        location_word = "ends with";
+      }
+      break;
+    case String_location_inlist :
+      if (not_present) {
+        location_word = "is not one of";
+      } else {
+        location_word = "is one of";
+      }
+      break;
+  }
+  return location_word;
+}
+
+
+/* summarizing constraints */
+static CharPtr SummarizeStringConstraint (StringConstraintPtr constraint)
+{
+  CharPtr location_word = NULL;
+  CharPtr case_sensitive = "case-sensitive";
+  CharPtr whole_word = "whole word";
+  CharPtr str = NULL;
+  Int4 len;
+  CharPtr fmt = "%s '%s'";
+
+  if (constraint == NULL || constraint->match_text == NULL) return NULL;
+
+  location_word = GetStringLocationPhrase (constraint->match_location, constraint->not_present);
+  if (location_word == NULL) return NULL;
+  len = StringLen (location_word) + StringLen (constraint->match_text) + StringLen (fmt);
+  if (constraint->case_sensitive) {
+    len += StringLen (case_sensitive) + 3;
+  }
+  if (constraint->whole_word) {
+    len += StringLen (whole_word) + 3;
+  }
+  str = (CharPtr) MemNew (sizeof (Char) * len);
+  sprintf (str, fmt, location_word, constraint->match_text);
+  if (constraint->case_sensitive || constraint->whole_word) {
+    StringCat (str, " (");
+  }
+  if (constraint->case_sensitive) {
+    StringCat (str, case_sensitive);
+    if (constraint->whole_word) {
+      StringCat (str, ", ");
+    }
+  }
+  if (constraint->whole_word) {
+    StringCat (str, whole_word);
+  }
+  if (constraint->case_sensitive || constraint->whole_word) {
+    StringCat (str, ")");
+  }
+
+  return str;
+}
+
+
+static CharPtr SummarizeLocationConstraint (LocationConstraintPtr constraint)
+{
+  CharPtr str = NULL;
+  CharPtr strand_word = NULL, seq_word = NULL;
+  CharPtr fmt = "only objects";
+  Int4    len = 0;
+
+  if (constraint == NULL 
+      || (constraint->strand == Strand_constraint_any
+          && constraint->seq_type == Seqtype_constraint_any)) {
+    return NULL;
+  }
+  if (constraint->seq_type == Seqtype_constraint_nuc) {
+    seq_word = "nucleotide sequences";
+  } else if (constraint->seq_type == Seqtype_constraint_prot) {
+    seq_word = "protein sequences";
+  }
+
+  if (constraint->strand == Strand_constraint_plus) {
+    strand_word = " on plus strands";
+  } else if (constraint->strand == Strand_constraint_minus) {
+    strand_word = " on minus strands";
+  }
+
+  if (seq_word == NULL && strand_word == NULL) {
+    return NULL;
+  }
+  len = StringLen (fmt) + 1;
+  if (strand_word != NULL) {
+    len += StringLen (strand_word);
+  }
+  if (seq_word != NULL) {
+    len += StringLen (seq_word) + 4;
+  }
+  str = (CharPtr) MemNew (sizeof (Char) * len);
+  sprintf (str, fmt);
+  if (strand_word == NULL) {
+    StringCat (str, " on ");
+    StringCat (str, seq_word);
+  } else {
+    StringCat (str, strand_word);
+    if (seq_word != NULL) {
+      StringCat (str, " of ");
+      StringCat (str, seq_word);
+    }
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeSourceConstraint (SourceConstraintPtr constraint)
+{
+  CharPtr string, intro = NULL, field1, field2;
+  CharPtr match_fmt = "%s %s matches %s";
+  CharPtr present_fmt = "%s %s is present";
+  CharPtr text_fmt = "%s text %s";
+  CharPtr two_match_fmt = "%s %s matches %s and %s %s";
+  CharPtr one_match_fmt = "%s %s %s";
+  CharPtr summ = NULL;
+
+  if (constraint == NULL) return NULL;
+
+  string = SummarizeStringConstraint (constraint->constraint);
+  field1 = SummarizeSourceQual (constraint->field1);
+  field2 = SummarizeSourceQual (constraint->field2);
+
+  if (constraint->field1 == NULL && constraint->field2 == NULL && string == NULL) {
+    if (constraint->type_constraint == Object_type_constraint_feature) {
+      summ = "where source is a feature";
+    } else if (constraint->type_constraint == Object_type_constraint_descriptor) {
+      summ = "where source is a descriptor";
+    }
+  } else { 
+    if (constraint->type_constraint == Object_type_constraint_any) {
+      intro = "where source";
+    } else if (constraint->type_constraint == Object_type_constraint_feature) {
+      intro = "where source feature";
+    } else if (constraint->type_constraint == Object_type_constraint_descriptor) {
+      intro = "where source descriptor";
+    } else {
+      string = MemFree (string);
+      field1 = MemFree (field1);
+      field2 = MemFree (field2);
+      return NULL;
+    }
+
+    if (string == NULL) {
+      if (field1 == NULL && field2 == NULL) {
+        if (constraint->type_constraint == Object_type_constraint_feature) {
+          summ = StringSave ("where source is a feature");
+        } else if (constraint->type_constraint == Object_type_constraint_descriptor) {
+          summ = StringSave ("where source is a descriptor");
+        }
+      } else if (field1 != NULL && field2 != NULL) {
+        summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (match_fmt) + StringLen (intro) + StringLen (field1) + StringLen (field2)));
+        sprintf (summ, match_fmt, intro, field1, field2);
+      } else if (field1 != NULL) {
+        summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (present_fmt) + StringLen (intro) + StringLen (field1)));
+        sprintf (summ, present_fmt, intro, field1);
+      } else if (field2 != NULL) {
+        summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (present_fmt) + StringLen (intro) + StringLen (field2)));
+        sprintf (summ, present_fmt, intro, field2);
+      }
+    } else {
+      if (field1 == NULL && field2 == NULL) {
+        summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (text_fmt) + StringLen (intro) + StringLen (string)));
+        sprintf (summ, text_fmt, intro, string);
+      } else if (field1 != NULL && field2 != NULL) {
+        summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (two_match_fmt) + StringLen (intro) 
+                                                   + 2 * StringLen (field1) + StringLen (field2) + StringLen (string)));
+        sprintf (summ, two_match_fmt, intro, field1, field2, field1, string);
+      } else if (field1 != NULL) {
+        summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (one_match_fmt) + StringLen (intro) + StringLen (field1) + StringLen (string)));
+        sprintf (summ, one_match_fmt, intro, field1, string);
+      } else if (field2 != NULL) {
+        summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (one_match_fmt) + StringLen (intro) + StringLen (field2) + StringLen (string)));
+        sprintf (summ, one_match_fmt, intro, field2, string);
+      }
+    }
+  }
+  string = MemFree (string);
+  field1 = MemFree (field1);
+  field2 = MemFree (field2);
+  return summ;
+}
+
+
+
+static CharPtr SummarizeCDSGeneProtPseudoConstraint (CDSGeneProtPseudoConstraintPtr constraint)
+{
+  CharPtr summ = NULL, pseudo_feat;
+  CharPtr is_pseudo_fmt = "where %s is pseudo";
+  CharPtr not_pseudo_fmt = "where %s is not pseudo";
+
+  if (constraint != NULL) {
+    pseudo_feat = CDSGeneProtFeatureNameFromFeatureType (constraint->feature);
+    if (pseudo_feat != NULL) {
+      if (constraint->is_pseudo) {
+        summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (is_pseudo_fmt) + StringLen (pseudo_feat)));
+        sprintf (summ, is_pseudo_fmt, pseudo_feat);
+      } else {
+        summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (not_pseudo_fmt) + StringLen (pseudo_feat)));
+        sprintf (summ, not_pseudo_fmt, pseudo_feat);
+      }
+    }
+  }
+     
+  return summ;
+}
+
+
+static CharPtr SummarizeCDSGeneProtQualConstraint (CDSGeneProtQualConstraintPtr constraint)
+{
+  CharPtr string, field1 = NULL, field2 = NULL;
+  CharPtr match_fmt = "where %s matches %s";
+  CharPtr present_fmt = "where %s is present";
+  CharPtr text_fmt = "where CDS-gene-prot text %s";
+  CharPtr two_match_fmt = "where %s matches %s and %s %s";
+  CharPtr one_match_fmt = "where %s %s";
+  CharPtr summ = NULL;
+
+  if (constraint == NULL) return NULL;
+
+  string = SummarizeStringConstraint (constraint->constraint);
+  if (constraint->field1 != NULL) {
+    field1 = CDSGeneProtNameFromField (constraint->field1->data.intvalue);
+  }
+  if (constraint->field2 != NULL) {
+    field2 = CDSGeneProtNameFromField (constraint->field2->data.intvalue);
+  }
+
+  if (string == NULL) {
+    if (field1 != NULL && field2 != NULL) {
+      summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (match_fmt) + StringLen (field1) + StringLen (field2)));
+      sprintf (summ, match_fmt, field1, field2);
+    } else if (field1 != NULL) {
+      summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (present_fmt) + StringLen (field1)));
+      sprintf (summ, present_fmt, field1);
+    } else if (field2 != NULL) {
+      summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (present_fmt) + StringLen (field2)));
+      sprintf (summ, present_fmt, field2);
+    }
+  } else {
+    if (field1 == NULL && field2 == NULL) {
+      summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (text_fmt) + StringLen (string)));
+      sprintf (summ, text_fmt, string);
+    } else if (field1 != NULL && field2 != NULL) {
+      summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (two_match_fmt)  
+                                                  + 2 * StringLen (field1) + StringLen (field2) + StringLen (string)));
+      sprintf (summ, two_match_fmt, field1, field2, field1, string);
+    } else if (field1 != NULL) {
+      summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (one_match_fmt) + StringLen (field1) + StringLen (string)));
+      sprintf (summ, one_match_fmt, field1, string);
+    } else if (field2 != NULL) {
+      summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (one_match_fmt) + StringLen (field2) + StringLen (string)));
+      sprintf (summ, one_match_fmt, field2, string);
+    }
+  }
+  
+  string = MemFree (string);
+  /* note - field1 and field2 aren't allocated, so we don't need to free them */
+
+  return summ;
+}
+
+
+static CharPtr SummarizeSequenceConstraint (SequenceConstraintPtr constraint)
+{
+  CharPtr summ = NULL;
+  CharPtr seq_word = NULL, featpresent = NULL, id = NULL;
+  Int4    len = 0;
+  CharPtr seq_word_intro = "where sequence type is ";
+  CharPtr feat_after = " is present";
+  CharPtr id_intro = "sequence ID ";
+  
+  if (IsSequenceConstraintEmpty (constraint)) {
+    summ = StringSave ("Missing sequence constraint");
+  } else {
+    if (constraint->seqtype != NULL && constraint->seqtype->choice != SequenceConstraintMolTypeConstraint_any) {
+      switch (constraint->seqtype->choice) {
+        case SequenceConstraintMolTypeConstraint_nucleotide:
+          seq_word = "nucleotide";
+          break;
+        case SequenceConstraintMolTypeConstraint_dna:
+          seq_word = "DNA";
+          break;
+        case SequenceConstraintMolTypeConstraint_rna:
+          if (constraint->seqtype->data.intvalue == Sequence_constraint_rnamol_any) {
+            seq_word = "RNA";
+          } else {
+            seq_word = GetBiomolNameForRnaType (constraint->seqtype->data.intvalue);
+          }
+          break;
+        case SequenceConstraintMolTypeConstraint_protein:
+          seq_word = "protein";
+          break;
+      }
+    }
+
+    if (constraint->feature != Feature_type_any) {
+      featpresent = GetFeatureNameFromFeatureType (constraint->feature);
+    }
+
+    if (!IsStringConstraintEmpty (constraint->id)) {
+      id = SummarizeStringConstraint (constraint->id);
+    }
+ 
+    if (seq_word != NULL) {
+      len += StringLen (seq_word) + StringLen (seq_word_intro);
+    }
+
+    if (featpresent != NULL) {
+      if (len == 0) {
+        len += 6;
+      } else {
+        len += 5;
+      }
+      len += StringLen (featpresent);
+      len += StringLen (feat_after);
+    }
+
+    if (id != NULL) {
+      if (len == 0) {
+        len += 6;
+      } else {
+        len += 5;
+      }
+      len += StringLen (id_intro);
+      len += StringLen (id);
+    }
+
+    if (len == 0) {
+      summ = StringSave ("missing sequence constraint");
+    } else {
+      len++;
+      summ = (CharPtr) MemNew (sizeof (Char) * len);
+      summ[0] = 0;
+      if (seq_word != NULL) {
+        StringCat (summ, seq_word_intro);
+        StringCat (summ, seq_word);
+      }
+      if (featpresent != NULL) {
+        if (seq_word == NULL) {
+          StringCat (summ, "where ");
+        } else {
+          StringCat (summ, " and ");
+        }
+        StringCat (summ, featpresent);
+        StringCat (summ, feat_after);
+      }
+      if (id != NULL) {
+        if (seq_word == NULL && featpresent == NULL) {
+          StringCat (summ, "where ");
+        } else {
+          StringCat (summ, " and ");
+        }
+        StringCat (summ, id_intro);
+        StringCat (summ, id);
+      }
+    }
+    id = MemFree (id);
+  }
+  return summ;
+}
+
+static CharPtr SummarizeConstraint (ValNodePtr constraint)
+{
+  CharPtr phrase = NULL, tmp;
+  CharPtr fmt = "where object text %s";
+
+  if (constraint == NULL) return NULL;
+  switch (constraint->choice) {
+    case ConstraintChoice_string:
+      tmp = SummarizeStringConstraint (constraint->data.ptrvalue);
+      if (tmp != NULL) {
+        phrase = (CharPtr) MemNew (sizeof (Char) * (StringLen (tmp) + StringLen (fmt)));
+        sprintf (phrase, fmt, tmp);
+        tmp = MemFree (tmp);
+      }
+      break;
+    case ConstraintChoice_location:
+      phrase = SummarizeLocationConstraint (constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_source:
+      phrase = SummarizeSourceConstraint (constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_cdsgeneprot_qual:
+      phrase = SummarizeCDSGeneProtQualConstraint (constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_cdsgeneprot_pseudo:
+      phrase = SummarizeCDSGeneProtPseudoConstraint (constraint->data.ptrvalue);
+      break;
+    case ConstraintChoice_sequence:
+      phrase = SummarizeSequenceConstraint (constraint->data.ptrvalue);
+      break;
+  }
+  return phrase;
+}
+
+
+static CharPtr SummarizeConstraintSet (ValNodePtr constraint_set)
+{
+  ValNodePtr phrases = NULL, vnp;
+  Int4 len = 0;
+  CharPtr phrase, str = NULL;
+
+  while (constraint_set != NULL) {
+    phrase = SummarizeConstraint (constraint_set);
+    if (phrase != NULL) {
+      ValNodeAddPointer (&phrases, 0, phrase);
+      if (len > 0) {
+        len += 5; /* for " and " */
+      } else {
+        len += 1; /* for terminal NULL */
+      }
+      len += StringLen (phrase);
+    }
+    constraint_set = constraint_set->next;
+  }
+  if (len > 0) {
+    str = (CharPtr) MemNew (sizeof (Char) * len);
+    for (vnp = phrases; vnp != NULL; vnp = vnp->next) {
+      StringCat (str, vnp->data.ptrvalue);
+      if (vnp->next != NULL) {
+        StringCat (str, " and ");
+      }
+    }
+  }
+  return str;
+}
+
+/* summarizing AECR actions */
+static CharPtr SummarizeFieldPairType (ValNodePtr vnp, CharPtr connect_word)
+{
+  FeatureFieldPairPtr ffp;
+  CDSGeneProtFieldPairPtr cgp;
+  SourceQualPairPtr     quals;
+  MolinfoFieldPairPtr   m_fields;
+  CharPtr str = NULL;
+  CharPtr from_label = NULL, to_label = NULL;
+  CharPtr label_fmt = "%s %s %s";
+  CharPtr type_label_fmt = "%s %s %s %s";
+  CharPtr    label = NULL;
+
+  if (connect_word == NULL) {
+    connect_word = "to";
+  }
+  if (vnp == NULL) {
+    str = StringSave ("missing field");
+  } else {
+    switch (vnp->choice) {
+      case FieldPairType_source_qual:
+        if (vnp->data.ptrvalue != NULL) {
+          quals = (SourceQualPairPtr) vnp->data.ptrvalue;
+          from_label = GetSourceQualName (quals->field_from);
+          to_label = GetSourceQualName (quals->field_to);
+        }
+        if (from_label != NULL && to_label != NULL) {
+          str = (CharPtr) MemNew (sizeof (Char) *
+                                  StringLen (from_label) + StringLen (connect_word) + StringLen (to_label)
+                                  + 3);
+          sprintf (str, "%s %s %s", from_label, connect_word, to_label);
+        } else {
+          str = StringSave ("missing field");
+        }
+        break;
+      case FieldPairType_feature_field:
+        ffp = (FeatureFieldPairPtr) vnp->data.ptrvalue;
+        if (ffp == NULL || ffp->field_from == NULL || ffp->field_to == NULL) {
+          str = StringSave ("missing field");
+        } else {
+          label = GetFeatureNameFromFeatureType (ffp->type);
+          from_label = FeatureFieldLabel (label, ffp->field_from);
+          to_label = FeatureFieldLabel (label, ffp->field_to);
+          str = (CharPtr) MemNew (sizeof (Char) * 
+                                  (StringLen (label_fmt) 
+                                   + StringLen (from_label) + StringLen (to_label)
+                                   + StringLen (connect_word)));
+          sprintf (str, label_fmt, from_label, connect_word, to_label);
+          from_label = MemFree (from_label);
+          to_label = MemFree (to_label);
+        }
+        break;
+      case FieldPairType_cds_gene_prot:
+        cgp = (CDSGeneProtFieldPairPtr) vnp->data.ptrvalue;
+        from_label = CDSGeneProtNameFromField (cgp->field_from);
+        to_label = CDSGeneProtNameFromField (cgp->field_to);
+        str = (CharPtr) MemNew (sizeof (Char) *
+                                StringLen (from_label) + StringLen (connect_word) + StringLen (to_label)
+                                + 3);
+        sprintf (str, "%s %s %s", from_label, connect_word, to_label);
+        break;
+      case FieldPairType_molinfo_field:
+        m_fields = (MolinfoFieldPairPtr) vnp->data.ptrvalue;
+        from_label = NULL;
+        to_label = NULL;
+        label = NULL;
+        switch (m_fields->choice) {
+          case MolinfoFieldPair_molecule:
+            from_label = BiomolNameFromBiomol (BiomolFromMoleculeType (((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->from));
+            to_label = BiomolNameFromBiomol (BiomolFromMoleculeType (((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->to));
+            label = "molecule";
+            break;
+          case MolinfoFieldPair_technique:
+            from_label = TechNameFromTech (TechFromTechniqueType (((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->from));
+            to_label = TechNameFromTech (TechFromTechniqueType (((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->to));
+            label = "technique";
+            break;
+          case MolinfoFieldPair_completedness:
+            from_label = CompletenessNameFromCompleteness (CompletenessFromCompletednessType (((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->from));
+            to_label = CompletenessNameFromCompleteness (CompletenessFromCompletednessType (((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->to));
+            label = "completeness";
+            break;
+          case MolinfoFieldPair_mol_class:
+            from_label = MolNameFromMol (MolFromMoleculeClassType (((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->from));
+            to_label = MolNameFromMol (MolFromMoleculeClassType (((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->to));
+            label = "class";
+            break;
+          case MolinfoFieldPair_topology:
+            from_label = TopologyNameFromTopology (TopologyFromTopologyType (((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->from));
+            to_label = TopologyNameFromTopology (TopologyFromTopologyType (((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->to));
+            label = "topology";
+            break;
+          case MolinfoFieldPair_strand:
+            from_label = StrandNameFromStrand (StrandFromStrandType (((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->from));
+            to_label = StrandNameFromStrand (StrandFromStrandType (((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->to));
+            label = "strand";
+            break;
+        }
+        if (from_label == NULL) {
+          from_label = "Unknown value";
+        }
+        if (to_label == NULL) {
+          to_label = "Unknown value";
+        }
+        if (label == NULL) {
+          label = "Unknown molinfo field";
+        }
+        str = (CharPtr) MemNew (sizeof (Char) * (StringLen (type_label_fmt)
+                                                 + StringLen (label)
+                                                 + StringLen (from_label)
+                                                 + StringLen (to_label)
+                                                 + StringLen (connect_word)));
+        sprintf (str, type_label_fmt, label, from_label, connect_word, to_label);
+        break;
+      default:
+        str = StringSave ("Invalid field type");
+        break;
+    }
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeTextPortion (TextPortionPtr text_portion)
+{
+  CharPtr summ = NULL;
+  CharPtr left_fmt = NULL, right_fmt = NULL;
+  Int4 len = 6;
+
+  if (text_portion == NULL 
+      || ((text_portion->left_text == NULL || text_portion->left_text[0] == 0)
+          && (text_portion->right_text == NULL || text_portion->right_text[0] == 0))) {
+    summ = StringSave ("entire text");
+  } else if (text_portion->inside) {
+    if (text_portion->left_text != NULL && text_portion->left_text[0] != 0) {
+      if (text_portion->include_left) {
+        left_fmt = "starting with ";
+      } else {
+        left_fmt = "just after ";
+      }
+      len += StringLen (left_fmt) + StringLen (text_portion->left_text) + 3;
+    }
+    if (text_portion->right_text != NULL && text_portion->right_text[0] != 0) {
+      if (text_portion->include_right) {
+        right_fmt = "up to and including ";
+      } else {
+        right_fmt = "up to ";
+      }
+      len += StringLen (right_fmt) + StringLen (text_portion->right_text) + 3;
+      if (left_fmt != NULL) {
+        len += 2;
+      }
+    }
+    if (left_fmt == NULL && right_fmt == NULL) {
+      summ = StringSave ("entire text");
+    } else {
+      summ = (CharPtr) MemNew (sizeof (Char) * len);
+      StringCat (summ, "text ");
+      if (left_fmt != NULL) {
+        StringCat (summ, left_fmt);
+        StringCat (summ, "'");
+        StringCat (summ, text_portion->left_text);
+        StringCat (summ, "'");
+        if (right_fmt != NULL) {
+          StringCat (summ, ", ");
+        }
+      }
+      if (right_fmt != NULL) {
+        StringCat (summ, right_fmt);
+        StringCat (summ, "'");
+        StringCat (summ, text_portion->right_text);
+        StringCat (summ, "'");
+      }
+    }      
+  } else {
+    if (text_portion->right_text != NULL && text_portion->right_text[0] != 0) {
+      if (text_portion->include_right) {
+        right_fmt = "starting with ";
+      } else {
+        right_fmt = "after ";
+      }
+      len += StringLen (right_fmt) + StringLen (text_portion->right_text) + 3;
+    }
+    if (text_portion->left_text != NULL && text_portion->left_text[0] != 0) {
+      if (text_portion->include_left) {
+        left_fmt = "up to and including ";
+      } else {
+        left_fmt = "before ";
+      }
+      len += StringLen (left_fmt) + StringLen (text_portion->left_text) + 3;
+      if (right_fmt != NULL) {
+        len += 5;
+      }
+    }
+
+    if (left_fmt == NULL && right_fmt == NULL) {
+      summ = StringSave ("entire text");
+    } else {
+      summ = (CharPtr) MemNew (sizeof (Char) * len);
+      StringCat (summ, "text ");
+      if (right_fmt != NULL) {
+        StringCat (summ, right_fmt);
+        StringCat (summ, "'");
+        StringCat (summ, text_portion->right_text);
+        StringCat (summ, "'");
+        if (left_fmt != NULL) {
+          StringCat (summ, " and ");
+        }
+      }
+      if (left_fmt != NULL) {
+        StringCat (summ, left_fmt);
+        StringCat (summ, "'");
+        StringCat (summ, text_portion->left_text);
+        StringCat (summ, "'");
+      }
+    }          
+  }
+  return summ;
+}
+
+
+static CharPtr SummarizeApplyAction (ApplyActionPtr a)
+{
+  CharPtr str = NULL;
+  CharPtr fmt = "Apply %s to %s (%s)";
+  CharPtr nontextqual_fmt = "Apply %s (%s)";
+  CharPtr field, existing_text;
+
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else if (a->value == NULL || a->field == NULL) {
+    str = StringSave ("Invalid action");
+  } else {
+    field = SummarizeFieldType (a->field);
+    existing_text = SummarizeExistingText (a->existing_text);
+    if (IsFieldTypeNonText (a->field)) {
+      str = (CharPtr) MemNew (sizeof (Char) * StringLen (nontextqual_fmt) + StringLen (field) + StringLen (existing_text));
+      sprintf (str, nontextqual_fmt, field, existing_text);
+    } else {
+      str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (a->value) + StringLen (field) + StringLen (existing_text)));
+      sprintf (str, fmt, a->value, field, existing_text);
+    }
+    field = MemFree (field);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeEditAction (EditActionPtr a)
+{
+  CharPtr str = NULL;
+  CharPtr fmt = "Edit %s replace '%s' with '%s'";
+  CharPtr field;
+
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else if (a->field == NULL || a->field == NULL || a->edit == NULL || a->edit->find_txt == NULL) {
+    str = StringSave ("Invalid action");
+  } else {
+    field = SummarizeFieldType (a->field);
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (field) + StringLen (a->edit->find_txt) + StringLen (a->edit->repl_txt)));
+    sprintf (str, fmt, field, a->edit->find_txt, a->edit->repl_txt == NULL ? "" : a->edit->repl_txt);
+    field = MemFree (field);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeConvertAction (ConvertActionPtr a)
+{
+  CharPtr str = NULL;
+  CharPtr fmt = "Convert %s (%s)";
+  CharPtr fields, existing_text;
+
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else if (a->fields == NULL || a->fields == NULL) {
+    str = StringSave ("Invalid action");
+  } else {
+    fields = SummarizeFieldPairType (a->fields, "to");
+    existing_text = SummarizeExistingText (a->existing_text);
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (fields) + StringLen (existing_text)));
+    sprintf (str, fmt, fields, existing_text);
+    fields = MemFree (fields);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeCopyAction (CopyActionPtr a)
+{
+  CharPtr str = NULL;
+  CharPtr fmt = "Copy %s (%s)";
+  CharPtr fields, existing_text;
+
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else if (a->fields == NULL) {
+    str = StringSave ("Invalid action");
+  } else {
+    fields = SummarizeFieldPairType (a->fields, "to");
+    existing_text = SummarizeExistingText (a->existing_text);
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (fields) + StringLen (existing_text)));
+    sprintf (str, fmt, fields, existing_text);
+    fields = MemFree (fields);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeSwapAction (SwapActionPtr a)
+{
+  CharPtr str = NULL;
+  CharPtr fmt = "Swap %s";
+  CharPtr fields;
+
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else if (a->fields == NULL) {
+    str = StringSave ("Invalid action");
+  } else {
+    fields = SummarizeFieldPairType (a->fields, "with");
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (fields)));
+    sprintf (str, fmt, fields);
+    fields = MemFree (fields);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeAECRParseAction (AECRParseActionPtr a)
+{
+  CharPtr str = NULL;
+  CharPtr fmt = "Parse %s from %s (%s)";
+  CharPtr fields, existing_text, text_portion;
+
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else if (a->fields == NULL) {
+    str = StringSave ("Invalid action");
+  } else {
+    fields = SummarizeFieldPairType (a->fields, "to");
+    existing_text = SummarizeExistingText (a->existing_text);
+    text_portion = SummarizeTextPortion (a->portion);
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (text_portion) + StringLen (fields) + StringLen (existing_text)));
+    sprintf (str, fmt, text_portion, fields, existing_text);
+    fields = MemFree (fields);
+    text_portion = MemFree (text_portion);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeRemoveAction (RemoveActionPtr a)
+{
+  CharPtr str = NULL;
+  CharPtr fmt = "Remove %s";
+  CharPtr field;
+
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else if (a->field == NULL || a->field == NULL) {
+    str = StringSave ("Invalid action");
+  } else {
+    field = SummarizeFieldType (a->field);
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (field)));
+    sprintf (str, fmt, field);
+    field = MemFree (field);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeAECRAction (AECRActionPtr a)
+{
+  CharPtr str = NULL, act = NULL, constraint = NULL;
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else if (a->action == NULL) {
+    str = StringSave ("Invalid command");
+  } else {
+    switch (a->action->choice) {
+      case ActionChoice_apply:
+        act = SummarizeApplyAction (a->action->data.ptrvalue);
+        break;
+      case ActionChoice_edit:
+        act = SummarizeEditAction (a->action->data.ptrvalue);
+        break;
+      case ActionChoice_convert:
+        act = SummarizeConvertAction (a->action->data.ptrvalue);
+        break;
+      case ActionChoice_copy:
+        act = SummarizeCopyAction (a->action->data.ptrvalue);
+        break;
+      case ActionChoice_swap:
+        act = SummarizeSwapAction (a->action->data.ptrvalue);
+        break;
+      case ActionChoice_remove:
+        act = SummarizeRemoveAction (a->action->data.ptrvalue);
+        break;
+      case ActionChoice_parse:
+        act = SummarizeAECRParseAction (a->action->data.ptrvalue);
+        break;
+    }
+    if (act == NULL) {
+      str = StringSave ("Invalid action");
+    } else {
+      constraint = SummarizeConstraintSet (a->constraint);
+      if (constraint == NULL) {
+        str = act;
+      } else {
+        str = (CharPtr) MemNew (sizeof (Char) * (StringLen(act) + 2 + StringLen (constraint)));
+        sprintf (str, "%s %s", act, constraint);
+        act = MemFree (act);
+        constraint = MemFree (constraint);
+      }
+    }
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeParseSrc (ValNodePtr src)
+{
+  CharPtr summ = NULL;
+  CharPtr fmt = "structured comment field %s";
+  ParseSrcOrgPtr src_org;
+  Boolean need_to_save = TRUE;
+  
+  if (src != NULL) {
+    switch (src->choice) {
+      case ParseSrc_defline:
+        summ = "defline";
+        break;
+      case ParseSrc_flatfile:
+        summ = "flat file";
+        break;
+      case ParseSrc_local_id:
+        summ = "local ID";
+        break;
+      case ParseSrc_org:
+        src_org = (ParseSrcOrgPtr) src->data.ptrvalue;
+        if (src_org != NULL) {
+          if (src_org->field != NULL) {
+            if (src_org->field->choice == ParseSrcOrgChoice_taxname_after_binomial) {
+              summ = kTaxnameAfterBinomialString;
+            } else if (src_org->field->choice == ParseSrcOrgChoice_source_qual) {
+              summ = GetSourceQualName (src_org->field->data.intvalue);
+            }
+          }
+        }
+        break;
+      case ParseSrc_comment:
+        summ = "comment";
+        break;
+      case ParseSrc_bankit_comment:
+        summ = "BankIT comment";
+        break;
+      case ParseSrc_structured_comment:
+        if (!StringHasNoText (src->data.ptrvalue)) {
+          summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (src->data.ptrvalue) + StringLen (fmt)));
+          sprintf (summ, fmt, src->data.ptrvalue);
+          need_to_save = FALSE;
+        }
+        break;
+      case ParseSrc_file_id:
+        summ = "file ID";
+        break;
+    }
+  }
+  if (summ == NULL) {
+    summ = StringSave ("missing field");
+  } else if (need_to_save) {
+    summ = StringSave (summ);
+  } 
+  return summ;
+}
+
+
+static CharPtr SummarizeParseDst (ValNodePtr dst)
+{
+  CharPtr summ = NULL;
+  CharPtr fmt = "%s %s";
+  CharPtr feature, field;
+  ParseDstOrgPtr dst_org;
+  Boolean need_to_save = TRUE;
+  FeatureFieldLegalPtr ffp;
+  
+  if (dst != NULL) {
+    switch (dst->choice) {
+      case ParseDest_defline:
+        summ = "defline";
+        break;
+      case ParseDest_org:
+        dst_org = (ParseDstOrgPtr) dst->data.ptrvalue;
+        if (dst_org != NULL) {
+          if (dst_org->field != NULL) {
+            switch (dst_org->field->choice) {
+              case SourceQualChoice_textqual:
+                summ = GetSourceQualName (dst_org->field->data.intvalue);
+                break;
+              case SourceQualChoice_location:
+                summ = "location";
+                break;
+              case SourceQualChoice_origin:
+                summ = "origin";
+                break;
+            }
+          }
+        }
+        break;
+      case ParseDest_featqual:
+        ffp = (FeatureFieldLegalPtr) dst->data.ptrvalue;
+        if (ffp != NULL) {
+          feature = GetFeatureNameFromFeatureType (ffp->type);
+          field = GetFeatQualName (ffp->field);
+          summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (feature) + StringLen (field)));
+          sprintf (summ, fmt, feature, field);
+          need_to_save = FALSE;
+        }
+        break;
+      case ParseDest_dbxref:
+        summ = "dbxref";
+        break;
+    }
+  }
+  if (summ == NULL) {
+    summ = StringSave ("missing field");
+  } else if (need_to_save) {
+    summ = StringSave (summ);
+  } 
+  return summ;
+}
+
+
+static CharPtr SummarizeParseAction (ParseActionPtr p)
+{
+  CharPtr field_from = NULL, field_to = NULL;
+  CharPtr existing_text = NULL, text_portion = NULL;
+  CharPtr summ = NULL;
+  CharPtr fmt = "Parse %s from %s to %s (%s)";
+
+  if (p == NULL) {
+    summ = StringSave ("No action");
+  } else {
+    field_from = SummarizeParseSrc (p->src);
+    field_to = SummarizeParseDst (p->dest);
+    existing_text = SummarizeExistingText (p->existing_text);
+    text_portion = SummarizeTextPortion (p->portion);
+    summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (text_portion) + StringLen (field_from) + StringLen (field_to) + StringLen (existing_text)));
+    sprintf (summ, fmt, text_portion, field_from, field_to, existing_text);
+    text_portion = MemFree (text_portion);
+    field_from = MemFree (field_from);
+    field_to = MemFree (field_to);
+  }
+  return summ;
+}
+
+
+static CharPtr SummarizeApplyFeatureAction (ApplyFeatureActionPtr a)
+{
+  CharPtr    label = NULL;
+  CharPtr    str;
+  CharPtr    fmt = "Apply %s";
+
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else {
+    label = GetFeatureNameFromFeatureType (a->type);
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (label)));
+    sprintf (str, fmt, label);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeRemoveFeatureAction (RemoveFeatureActionPtr a)
+{
+  CharPtr    label = NULL;
+  CharPtr    constraint, str;
+  CharPtr    fmt = "Remove %s";
+  CharPtr    constraint_fmt = "Remove %s %s";
+
+  if (a == NULL) {
+    str = StringSave ("No action");
+  } else {
+    label = GetFeatureNameFromFeatureType (a->type);
+    constraint = SummarizeConstraintSet (a->constraint);
+    if (constraint == NULL) {
+      str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (label)));
+      sprintf (str, fmt, label);
+    } else {
+      str = (CharPtr) MemNew (sizeof (Char) * (StringLen (constraint_fmt) + StringLen (label) + StringLen (constraint)));
+      sprintf (str, constraint_fmt, label, constraint);
+      constraint = MemFree (constraint);
+    }
+  }
+
+  return str;
+}
+
+
+static CharPtr SummarizeEditLocationStrand (EditLocationStrandPtr strand)
+{
+  CharPtr from_label = NULL, to_label = NULL;
+  CharPtr fmt = "Convert %s strand to %s";
+  CharPtr str = NULL;
+
+  if (strand == NULL) return NULL;
+
+  switch (strand->strand_from) {
+    case Feature_location_strand_from_any:
+      from_label = "any";
+      break;
+    case Feature_location_strand_from_plus:
+      from_label = "plus";
+      break;
+    case Feature_location_strand_from_minus:
+      from_label = "minus";
+      break;
+    case Feature_location_strand_from_unknown:
+      from_label = "unknown";
+      break;
+    case Feature_location_strand_from_both:
+      from_label = "both";
+      break;
+  }
+
+  switch (strand->strand_to) {
+    case Feature_location_strand_to_plus:
+      to_label = "plus";
+      break;
+    case Feature_location_strand_to_minus:
+      to_label = "minus";
+      break;
+    case Feature_location_strand_to_unknown:
+      to_label = "unknown";
+      break;
+    case Feature_location_strand_to_both:
+      to_label = "both";
+      break;
+    case Feature_location_strand_to_reverse:
+      to_label = "reverse";
+      break;
+  }
+
+  if (from_label != NULL && to_label != NULL) {
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (from_label) + StringLen (to_label)));
+    sprintf (str, fmt, from_label, to_label);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizePartial5SetAction (Partial5SetActionPtr a)
+{
+  CharPtr str = NULL;
+  CharPtr constraint = NULL, extend = NULL;
+  CharPtr fmt = "Set 5' partial%s%s";
+
+  if (a == NULL) return NULL;
+
+  switch (a->constraint) {
+    case Partial_5_set_constraint_all:
+      constraint = "";
+      break;
+    case Partial_5_set_constraint_at_end:
+      constraint = " when 5' end of location is at end of sequence";
+      break;
+    case Partial_5_set_constraint_bad_start:
+      constraint = " when coding region has no start codon";
+      break;
+    case Partial_5_set_constraint_frame_not_one:
+      constraint = " when coding region frame > 1";
+      break;
+  }
+  if (a->extend) {
+    extend = ", extend 5' end of feature to end of sequence";
+  } else {
+    extend = "";
+  }
+  if (constraint != NULL) {
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt)
+                                             + StringLen (constraint) 
+                                             + StringLen (extend)));
+    sprintf (str, fmt, constraint, extend);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizePartial5ClearAction (Int4 a)
+{
+  CharPtr str = NULL;
+
+  switch (a) {
+    case Partial_5_clear_constraint_all:
+      str = StringSave ("Clear 5' partial");
+      break;
+    case Partial_5_clear_constraint_not_at_end:
+      str = StringSave ("Clear 5' partial when 5' end of feature is not at end of sequence");
+      break;
+    case Partial_5_clear_constraint_good_start:
+      str = StringSave ("Clear 5' partial when coding region has start codon");
+      break;
+  }
+  return str;
+}
+
+
+static CharPtr SummarizePartial3SetAction (Partial3SetActionPtr a)
+{
+  CharPtr str = NULL;
+  CharPtr constraint = NULL, extend = NULL;
+  CharPtr fmt = "Set 3' partial%s%s";
+
+  if (a == NULL) return NULL;
+
+  switch (a->constraint) {
+    case Partial_3_set_constraint_all:
+      constraint = "";
+      break;
+    case Partial_3_set_constraint_at_end:
+      constraint = " when 3' end of location is at end of sequence";
+      break;
+    case Partial_3_set_constraint_bad_end:
+      constraint = " when coding region has no stop codon";
+      break;
+  }
+  if (a->extend) {
+    extend = ", extend 3' end of feature to end of sequence";
+  } else {
+    extend = "";
+  }
+  if (constraint != NULL) {
+    str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt)
+                                             + StringLen (constraint) 
+                                             + StringLen (extend)));
+    sprintf (str, fmt, constraint, extend);
+  }
+  return str;
+}
+
+
+static CharPtr SummarizePartial3ClearAction (Int4 a)
+{
+  CharPtr str = NULL;
+
+  switch (a) {
+    case Partial_3_clear_constraint_all:
+      str = StringSave ("Clear 3' partial");
+      break;
+    case Partial_3_clear_constraint_not_at_end:
+      str = StringSave ("Clear 3' partial when 3' end of feature is not at end of sequence");
+      break;
+    case Partial_3_clear_constraint_good_end:
+      str = StringSave ("Clear 3' partial when coding region has stop codon");
+      break;
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeConvertLoc (Int4 a)
+{
+  CharPtr str = NULL;
+
+  switch (a) {
+    case Convert_location_type_join:
+      str = StringSave ("Convert location to join");
+      break;
+    case Convert_location_type_order:
+      str = StringSave ("Convert location to order");
+      break;
+    case Convert_location_type_merge:
+      str = StringSave ("Convert location to single interval");
+      break;
+  }
+  return str;
+}
+
+
+static CharPtr SummarizeEditFeatureLocationAction (EditFeatureLocationActionPtr a)
+{
+  CharPtr str = NULL, action_label = NULL, constraint, feature;
+  CharPtr fmt = "%s for %s features";
+  CharPtr constraint_fmt = "%s for %s features %s";
+
+  if (a == NULL || a->action == NULL) {
+    str = StringSave ("No action");
+  } else {
+    
+    switch (a->action->choice) {
+      case LocationEditType_strand:
+        action_label = SummarizeEditLocationStrand (a->action->data.ptrvalue);
+        break;
+      case LocationEditType_set_5_partial:
+        action_label = SummarizePartial5SetAction (a->action->data.ptrvalue);
+        break;
+      case LocationEditType_clear_5_partial:
+        action_label = SummarizePartial5ClearAction (a->action->data.intvalue);
+        break;
+      case LocationEditType_set_3_partial:
+        action_label = SummarizePartial3SetAction (a->action->data.ptrvalue);
+        break;
+      case LocationEditType_clear_3_partial:
+        action_label = SummarizePartial3ClearAction (a->action->data.intvalue);
+        break;
+      case LocationEditType_convert:
+        action_label = SummarizeConvertLoc (a->action->data.intvalue);
+        break;
+    }
+    if (action_label == NULL) {
+      str = StringSave ("Invalid action");
+    } else {
+      feature = GetFeatureNameFromFeatureType (a->type);
+      constraint = SummarizeConstraintSet (a->constraint);
+      if (constraint == NULL) {
+        str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (action_label) + StringLen (feature)));
+        sprintf (str, fmt, action_label, feature);
+      } else {
+        str = (CharPtr) MemNew (sizeof (Char) * (StringLen (constraint_fmt) + StringLen (action_label) + StringLen (feature) + StringLen (constraint)));
+        sprintf (str, constraint_fmt, action_label, feature, constraint);
+        constraint = MemFree (constraint);
+      }
+    }
+  } 
+  return str;
+}
+
+
+
+static CharPtr SummarizeMacroAction (ValNodePtr vnp)
+{
+  CharPtr str = NULL;
+
+  if (vnp == NULL) {
+    return StringSave ("No action");
+  }
+  switch (vnp->choice) {
+    case MacroActionChoice_aecr:
+      str = SummarizeAECRAction (vnp->data.ptrvalue);
+      break;
+    case MacroActionChoice_parse:
+      str = SummarizeParseAction (vnp->data.ptrvalue);
+      break;
+    case MacroActionChoice_add_feature:
+      str = SummarizeApplyFeatureAction (vnp->data.ptrvalue);
+      break;
+    case MacroActionChoice_remove_feature:
+      str = SummarizeRemoveFeatureAction (vnp->data.ptrvalue);
+      break;
+    case MacroActionChoice_edit_location:
+      str = SummarizeEditFeatureLocationAction (vnp->data.ptrvalue);
+      break;
+    default:
+      str = StringSave ("Invalid action");
+      break;
+  }
+  return str;
+}
+
+
+/* For using macro functions to apply tables */
+typedef struct tabcolumnconfigdlg {
+  DIALOG_MESSAGE_BLOCK
+  PopuP                    column_action;
+  GrouP                    qual_grp;
+  DialoG                   src_qual;
+  GrouP                    feature_field_grp;
+  DialoG                   feature_type;
+  DialoG                   feature_field;
+  DialoG                   cdsgeneprot;
+
+  ButtoN                   change_mrna;
+  GrouP                    apply_options;
+  ButtoN                   erase_when_blank;
+  DialoG                   existing_text;
+
+  Nlm_ChangeNotifyProc     change_notify;
+  Pointer                  change_userdata;
+} TabColumnConfigDlgData, PNTR TabColumnConfigDlgPtr;
+
+static void TabColumnConfigPopupChange (PopuP p)
+{
+  TabColumnConfigDlgPtr dlg;
+
+  dlg = (TabColumnConfigDlgPtr) GetObjectExtra (p);
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void TabColumnConfigFieldChange (Pointer data)
+{
+  TabColumnConfigDlgPtr dlg;
+  TabColumnConfigPtr    config;
+
+  dlg = (TabColumnConfigDlgPtr) data;
+  if (dlg != NULL) {
+    config = (TabColumnConfigPtr) DialogToPointer (dlg->dialog);
+    if (config == NULL || !IsFieldTypeCDSProduct(config->field)) {
+      Disable (dlg->change_mrna);
+    } else {
+      Enable (dlg->change_mrna);
+    }
+    config = TabColumnConfigFree (config);
+    if (dlg->change_notify != NULL) {
+      (dlg->change_notify) (dlg->change_userdata);
+    }
+  }
+}
+
+
+static Pointer TabColumnConfigDialogToChoice (DialoG d)
+{
+  TabColumnConfigDlgPtr dlg;
+  TabColumnConfigPtr    f;
+  Int2                  val;
+  FeatureFieldPtr       ff;
+  ValNodePtr            vnp;
+
+  dlg = (TabColumnConfigDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  f = TabColumnConfigNew ();
+  f->match_mrna = FALSE;
+  
+  val = GetValue (dlg->column_action);
+  if (val < 2) {
+    f = TabColumnConfigFree (f);
+  } else if (val < 8) {
+    f->match_type = val - 1;
+    f->existing_text = ExistingTextOption_replace_old;
+    f->skip_blank = TRUE;
+  } else {
+    if (val == 8) {
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FieldType_source_qual;
+      f->field->data.ptrvalue = DialogToPointer (dlg->src_qual);
+    } else if (val == 9) {
+      f->field = ValNodeNew (NULL);
+      f->field->choice = FieldType_feature_field;
+      ff = FeatureFieldNew ();
+      vnp = DialogToPointer (dlg->feature_type);
+      if (vnp != NULL) {
+        ff->type = vnp->choice;
+        vnp = ValNodeFree (vnp);
+      }
+      vnp = DialogToPointer (dlg->feature_field);
+      if (vnp != NULL) {
+        ValNodeAddInt (&(ff->field), FeatQualChoice_legal_qual, vnp->choice);
+        ValNodeFree (vnp);
+      }
+      f->field->data.ptrvalue = ff;
+    } else if (val == 10) {
+      f->field = DialogToPointer (dlg->cdsgeneprot);
+    }
+
+    if (dlg->erase_when_blank == NULL) {
+      f->skip_blank = TRUE;
+    } else {
+      f->skip_blank = !GetStatus (dlg->erase_when_blank);
+    }
+    if (IsFieldTypeCDSProduct (f->field)) {
+      f->match_mrna = GetStatus (dlg->change_mrna);
+    }
+
+    f->existing_text = (Uint2) DialogToPointer (dlg->existing_text);
+  }
+
+  return f;
+}
+
+
+static void TabColumnActionChange (PopuP p)
+{
+  TabColumnConfigDlgPtr dlg;
+  TabColumnConfigPtr    config;
+  Int2 val;
+
+  dlg = (TabColumnConfigDlgPtr) GetObjectExtra (p);
+  if (dlg == NULL) return;
+
+  val = GetValue (p);
+
+  switch (val) {
+    case 1:
+    case 2:
+    case 3:
+    case 4:
+    case 5:
+    case 6:
+    case 7:
+      /* matching, hide apply controls */
+      Hide (dlg->qual_grp);
+      Disable (dlg->apply_options);
+      break;
+    case 8:
+      /* show source qual, hide others */
+      Show (dlg->qual_grp);
+      Show (dlg->src_qual);
+      Hide (dlg->feature_field_grp);
+      Hide (dlg->cdsgeneprot);
+      Disable (dlg->change_mrna);
+      Enable (dlg->apply_options);
+      break;
+    case 9:
+      /* show feature qual, hide others */
+      Show (dlg->qual_grp);
+      Hide (dlg->src_qual);
+      Show (dlg->feature_field_grp);
+      Hide (dlg->cdsgeneprot);
+      config = DialogToPointer (dlg->dialog);
+      if (config == NULL || !IsFieldTypeCDSProduct (config->field)) {
+        SafeDisable (dlg->change_mrna);
+      } else {
+        SafeEnable (dlg->change_mrna);
+      }
+      config = TabColumnConfigFree (config);
+      Enable (dlg->apply_options);
+      break;
+    case 10:
+      /* show cds-gene-prot qual, hide others */
+      Show (dlg->qual_grp);
+      Hide (dlg->src_qual);
+      Hide (dlg->feature_field_grp);
+      Show (dlg->cdsgeneprot);
+      config = DialogToPointer (dlg->dialog);
+      if (config == NULL || !IsFieldTypeCDSProduct (config->field)) {
+        SafeDisable (dlg->change_mrna);
+      } else {
+        SafeEnable (dlg->change_mrna);
+      }
+      config = TabColumnConfigFree (config);
+      Enable (dlg->apply_options);
+      break;
+  }
+
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void TabColumnConfigToDialog (DialoG d, Pointer data)
+{
+  TabColumnConfigDlgPtr dlg;
+  TabColumnConfigPtr    f;
+  FeatureFieldPtr       ff;
+  ValNode               vn;
+
+  dlg = (TabColumnConfigDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+  f = (TabColumnConfigPtr) data;
+  if (f == NULL) {
+    SetValue (dlg->column_action, 1);
+  } else {
+    if (f->match_type > 0) {
+      SetValue (dlg->column_action, f->match_type + 1);
+    } else if (f->field == NULL) {
+      SetValue (dlg->column_action, 1);
+    } else {
+      if (f->field->choice == FieldType_source_qual) {
+        SetValue (dlg->column_action, 8);
+        PointerToDialog (dlg->src_qual, f->field->data.ptrvalue);
+      } else if (f->field->choice == FieldType_feature_field) {
+        SetValue (dlg->column_action, 9);
+        ff = (FeatureFieldPtr) f->field->data.ptrvalue;
+        if (ff == NULL) {
+          PointerToDialog (dlg->feature_type, NULL);
+          PointerToDialog (dlg->feature_field, NULL);
+        } else {
+          vn.choice = ff->type;
+          vn.data.ptrvalue = NULL;
+          vn.next = NULL;
+          PointerToDialog (dlg->feature_type, &vn);
+          if (ff->field == NULL || ff->field->choice != FeatQualChoice_legal_qual) {
+            PointerToDialog (dlg->feature_field, NULL);
+          } else {
+            vn.choice = ff->field->data.intvalue;
+            vn.data.ptrvalue = NULL;
+            vn.next = NULL;
+            PointerToDialog (dlg->feature_field, &vn);
+          }
+        }          
+      } else if (f->field->choice == FieldType_cds_gene_prot) {
+        SetValue (dlg->column_action, 10);
+        PointerToDialog (dlg->cdsgeneprot, &vn);
+      }
+        
+      SafeSetStatus (dlg->change_mrna, f->match_mrna);
+      SafeSetStatus (dlg->erase_when_blank, !f->skip_blank);
+      PointerToDialog (dlg->existing_text, (Pointer) f->existing_text);
+    }
+  }
+  TabColumnActionChange (dlg->column_action);
+}
+
+
+static void TabColumnConfigButtonChange (ButtoN b)
+{
+  TabColumnConfigDlgPtr dlg;
+
+  dlg = (TabColumnConfigDlgPtr) GetObjectExtra (b);
+  if (dlg != NULL && dlg->change_notify != NULL) {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static void SetTabColumnConfigDialogTitle (DialoG d, CharPtr title, Int4 num_blank)
+{
+  CharPtr real_title;
+  CharPtr title_fmt = "(%d are blank)%s";
+  TabColumnConfigDlgPtr dlg;
+
+  if (title == NULL) {
+    real_title = "";
+  } else if (num_blank > 0) {
+    real_title = (CharPtr) MemNew (sizeof (Char) * (StringLen (title_fmt) + StringLen (title) + 15));
+    sprintf (real_title, title_fmt, num_blank, title);
+  } else {
+    real_title = title;
+  }
+
+  SetTitle (d, real_title);
+
+  if (real_title != title) {
+    real_title = MemFree (real_title);
+  }  
+
+  dlg = (TabColumnConfigDlgPtr) GetObjectExtra (d);
+  if (dlg != NULL) {  
+    if (num_blank == 0) {
+      SafeDisable (dlg->erase_when_blank);
+    } else {
+      SafeEnable (dlg->erase_when_blank);
+    }
+  }
+}
+
+
+NLM_EXTERN DialoG TabColumnConfigDialog 
+(GrouP                    h,
+ CharPtr                  title,
+ Int4                     num_blank,
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata)
+{
+  TabColumnConfigDlgPtr dlg;
+  GrouP p;
+  CharPtr real_title;
+  CharPtr title_fmt = "(%d are blank)%s";
+  Boolean free_title = FALSE;
+
+  dlg = (TabColumnConfigDlgPtr) MemNew (sizeof (TabColumnConfigDlgData));
+
+  if (title == NULL) {
+    real_title = "";
+  } else if (num_blank > 0) {
+    real_title = (CharPtr) MemNew (sizeof (Char) * (StringLen (title_fmt) + StringLen (title) + 15));
+    sprintf (real_title, title_fmt, num_blank, title);
+    free_title = TRUE;
+  } else {
+    real_title = title;
+  }
+
+  p = NormalGroup (h, -1, 0, real_title, programFont, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  if (free_title) {
+    real_title = MemFree (real_title);
+  }
+  dlg->dialog = (DialoG) p;
+  dlg->fromdialog = TabColumnConfigDialogToChoice;
+  dlg->todialog = TabColumnConfigToDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->column_action = PopupList (p, TRUE, TabColumnActionChange);
+  SetObjectExtra (dlg->column_action, dlg, NULL);
+  PopupItem (dlg->column_action, "Ignore column");
+  PopupItem (dlg->column_action, "Match to Feature ID");
+  PopupItem (dlg->column_action, "Match to Gene locus tag");
+  PopupItem (dlg->column_action, "Match to Protein ID");
+  PopupItem (dlg->column_action, "Match to Dbxref");
+  PopupItem (dlg->column_action, "Match to Nucleotide ID");
+  PopupItem (dlg->column_action, "Match to Taxname");
+  PopupItem (dlg->column_action, "Apply to Source Qual");
+  PopupItem (dlg->column_action, "Apply to Feature Field");
+  PopupItem (dlg->column_action, "Apply to CDS-Gene-Prot Field");
+  SetValue (dlg->column_action, 1);
+  
+  dlg->qual_grp = HiddenGroup (p, 0, 0, NULL);
+  dlg->src_qual = SourceQualChoiceDialog (dlg->qual_grp, TRUE, FALSE, change_notify, change_userdata);
+  dlg->feature_field_grp = HiddenGroup (dlg->qual_grp, 2, 0, NULL);
+  dlg->feature_type = FeatureTypeDialog (dlg->feature_field_grp, TabColumnConfigFieldChange, dlg);
+  dlg->feature_field = LegalFeatQualChoiceDialog (dlg->feature_field_grp, TabColumnConfigFieldChange, dlg);
+  dlg->cdsgeneprot = CDSGeneProtFieldDialog (dlg->qual_grp, TabColumnConfigFieldChange, dlg);
+
+  dlg->change_mrna = CheckBox (p, "Also change mRNA product name", TabColumnConfigButtonChange);
+  SetObjectExtra (dlg->change_mrna, dlg, NULL);
+  Disable (dlg->change_mrna);
+
+  dlg->apply_options = HiddenGroup (p, -1, 0, NULL);
+  if (num_blank > 0 || title == NULL) {
+    dlg->erase_when_blank = CheckBox (dlg->apply_options, "Erase field when table cell is blank", NULL);
+    if (num_blank == 0) {
+      Disable (dlg->erase_when_blank);
+    }
+  } else {
+    dlg->erase_when_blank = NULL;
+  }
+  dlg->existing_text = ExistingTextDialog (dlg->apply_options, change_notify, change_userdata);
+
+  Disable (dlg->apply_options);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->existing_text,
+                              (HANDLE) dlg->erase_when_blank, 
+                              NULL);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->qual_grp, (HANDLE) dlg->apply_options, (HANDLE) dlg->change_mrna, NULL);
+
+  return (DialoG) p;
+}
+
+
+static CharPtr SummarizeTabColumnConfig (TabColumnConfigPtr t)
+{
+  CharPtr summ = NULL;
+  CharPtr apply_fmt = "Apply to %s (%s)";
+  CharPtr field;
+  CharPtr erase_when_blank = ", remove field when cell is blank";
+  CharPtr also_mrna = ", make mRNA product match new CDS product";
+  CharPtr existing_text;
+  Int4    summ_len = 0;
+
+  if (t == NULL) return StringSave ("Ignore column");
+
+  switch (t->match_type) {
+    case 0:
+      field = SummarizeFieldType (t->field);
+      if (field == NULL) {
+        field = StringSave ("unspecified field");
+      }
+      existing_text = SummarizeExistingText (t->existing_text);
+      summ_len = StringLen (apply_fmt) + StringLen (field) + StringLen (existing_text);
+      if (!t->skip_blank) {
+        summ_len += StringLen (erase_when_blank);
+      }
+      if (t->match_mrna) {
+        summ_len += StringLen (also_mrna);
+      }
+      summ = (CharPtr) MemNew (sizeof (Char) * summ_len);
+      sprintf (summ, apply_fmt, field, existing_text);
+      if (!t->skip_blank) {
+        StringCat (summ, erase_when_blank);
+      }
+      if (t->match_mrna) {
+        StringCat (summ, also_mrna);
+      }
+      field = MemFree (field);
+      break;
+    case eTableMatchFeatureID:
+      summ = StringSave ("Match to feature ID");
+      break;
+    case eTableMatchGeneLocusTag:
+      summ = StringSave ("Match to gene locus tag");
+      break;
+    case eTableMatchProteinID:
+      summ = StringSave ("Match to protein ID");
+      break;
+    case eTableMatchDbxref:
+      summ = StringSave ("Match to feature dbxref");
+      break;
+    case eTableMatchNucID:
+      summ = StringSave ("Match to nucleotide ID");
+      break;
+    case eTableMatchBioSource:
+      summ = StringSave ("Match to taxname");
+      break;
+  }
+  return summ;
+}
+
+
+typedef struct tabcolumnconfiglistdialog {
+  DIALOG_MESSAGE_BLOCK
+  DoC                  column_list_doc;
+  DialoG               edit_col_dlg;
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer              change_userdata;
+  TabColumnConfigPtr PNTR column_list;
+  CharPtr PNTR            first_values;
+  Int4Ptr                 blank_list;
+  Int4                    num_columns;
+  Int4                    current_column;
+} TabColumnConfigListDlgData, PNTR TabColumnConfigListDlgPtr;
+
+
+static void CleanupTabColumnConfigListDialog (GraphiC g, VoidPtr data)
+
+{
+  TabColumnConfigListDlgPtr dlg;
+  Int4 i;
+
+  dlg = (TabColumnConfigListDlgPtr) data;
+  if (dlg != NULL) {
+    for (i = 0; i < dlg->num_columns; i++) {
+      dlg->column_list[i] = TabColumnConfigFree (dlg->column_list[i]);
+      dlg->first_values[i] = MemFree (dlg->first_values[i]);
+    }
+    dlg->column_list = MemFree (dlg->column_list);
+    dlg->first_values = MemFree (dlg->first_values);
+    dlg->blank_list = MemFree (dlg->blank_list);
+  }
+  StdCleanupExtraProc (g, data);
+}
+
+
+
+
+static Pointer DialogToTabColumnConfigList (DialoG d)
+{
+  TabColumnConfigListDlgPtr dlg;
+  Int4 i;
+  ValNodePtr column_list = NULL;
+
+  dlg = (TabColumnConfigListDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+  for (i = 0; i < dlg->num_columns; i++) {
+    ValNodeAddPointer (&column_list, 0, TabColumnConfigCopy (dlg->column_list[i]));
+  }
+  return (Pointer) column_list;
+}
+
+
+static ValNodePtr TestTabColumnConfigListDialog (DialoG d)
+{
+  TabColumnConfigListDlgPtr dlg;
+  Int4 i;
+  ValNodePtr err_list = NULL;
+  Int4 num_match = 0;
+  Boolean have_apply = FALSE;
+
+  dlg = (TabColumnConfigListDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  for (i = 0; i < dlg->num_columns; i++) {
+    if (dlg->column_list[i] != NULL) {
+      if (dlg->column_list[i]->match_type > 0) {
+        num_match++;
+      } else if (!IsFieldTypeEmpty(dlg->column_list[i]->field)) {
+        have_apply = TRUE;
+      }
+    }
+  }
+  if (num_match == 0) {
+    ValNodeAddPointer (&err_list, 0, "No match column");
+  } else if (num_match > 1) {
+    ValNodeAddPointer (&err_list, 0, "Too many match columns");
+  }
+  if (!have_apply) {
+    ValNodeAddPointer (&err_list, 0, "No apply column");
+  }
+  return err_list;
+}
+
+
+static void PopulateTabConfigListColumnListDoc (DialoG d)
+{
+  TabColumnConfigListDlgPtr dlg;
+  Int4 i, len;
+  CharPtr str, tmp;
+  CharPtr    row_fmt = "%d\t%s\t%s\n";
+  RecT       r;
+  FonT       font = programFont;
+  ParData    ParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0};
+  ColData    ColFmt[] = 
+  {
+    {0, 0, 4, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE}, /* column number */
+    {0, 0, 1, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE}, /* action */
+    {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}   /* first value */
+  };
+
+  dlg = (TabColumnConfigListDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  Reset (dlg->column_list_doc);
+
+  ObjectRect (dlg->column_list_doc, &r);
+  InsetRect (&r, 4, 4);
+  
+  if (dlg->num_columns < 10) {    
+    ColFmt[0].pixWidth = stdCharWidth * 2;
+  } else {
+    ColFmt[0].pixWidth = stdCharWidth * 3;
+  }
+  ColFmt[1].pixWidth = (r.right - r.left - ColFmt[0].pixWidth) / 2;
+  ColFmt[2].pixWidth = ColFmt[1].pixWidth;
+  for (i = 0; i < dlg->num_columns; i++) {
+    str = SummarizeTabColumnConfig (dlg->column_list[i]);
+    len = StringLen (str) + StringLen (dlg->first_values[i]) + 15 + StringLen (row_fmt);
+    tmp = (CharPtr) MemNew (sizeof (Char) * len);
+    sprintf (tmp, row_fmt, i + 1, str, dlg->first_values[i]);
+    str = MemFree (str);
+    AppendText (dlg->column_list_doc, tmp, &ParFmt, ColFmt, font);
+    tmp = MemFree (tmp);
+  }
+  UpdateDocument (dlg->column_list_doc, 0, 0);
+}
+
+
+static void ClickColumnListDoc (DoC d, PoinT pt)
+{
+  Int2               item, row, col;
+  RecT               rct;
+  TabColumnConfigListDlgPtr dlg;
+  
+  dlg = (TabColumnConfigListDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+  
+  MapDocPoint (d, pt, &item, &row, &col, &rct);
+  if (item > 0) {
+    dlg->current_column = item - 1;
+    PointerToDialog (dlg->edit_col_dlg, dlg->column_list[item - 1]);
+    SetTabColumnConfigDialogTitle (dlg->edit_col_dlg, dlg->first_values[item - 1], dlg->blank_list[item - 1]);
+  }
+}
+
+
+static void ChangeTabColumnConfig (Pointer userdata)
+{
+  TabColumnConfigListDlgPtr dlg;
+
+  dlg = (TabColumnConfigListDlgPtr) userdata;
+  if (dlg == NULL) return;
+
+  dlg->column_list[dlg->current_column] = TabColumnConfigFree (dlg->column_list[dlg->current_column]);
+  dlg->column_list[dlg->current_column] = DialogToPointer (dlg->edit_col_dlg);
+  PopulateTabConfigListColumnListDoc (dlg->dialog);
+  if (dlg->change_notify != NULL) {
+    (dlg->change_notify)(dlg->change_userdata);
+  }
+}
+
+
+NLM_EXTERN DialoG TabColumnConfigListDialog (GrouP h, ValNodePtr first_values, ValNodePtr blank_list, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  TabColumnConfigListDlgPtr dlg;
+  GrouP                p;
+  ValNodePtr           vnp_v, vnp_b;
+  Int4                 i;
+  
+  dlg = (TabColumnConfigListDlgPtr) MemNew (sizeof (TabColumnConfigListDlgData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+  
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetObjectExtra (p, dlg, CleanupTabColumnConfigListDialog);
+
+  dlg->dialog = (DialoG) p;
+  dlg->fromdialog = DialogToTabColumnConfigList;
+  dlg->testdialog = TestTabColumnConfigListDialog;
+
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+
+  dlg->column_list_doc = DocumentPanel (p, stdCharWidth * 50, stdLineHeight * 12);
+  SetObjectExtra (dlg->column_list_doc, dlg, NULL);
+  SetDocProcs (dlg->column_list_doc, ClickColumnListDoc, NULL, NULL, NULL);
+  dlg->edit_col_dlg = TabColumnConfigDialog (p, NULL, 0, ChangeTabColumnConfig, dlg);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->column_list_doc, (HANDLE) dlg->edit_col_dlg, NULL);
+
+  /* populate column list */
+  dlg->num_columns = ValNodeLen (blank_list);
+  dlg->column_list = (TabColumnConfigPtr PNTR) MemNew (sizeof (TabColumnConfigPtr) * dlg->num_columns);
+  dlg->first_values = MemNew (sizeof (CharPtr) * dlg->num_columns);
+  dlg->blank_list = (Int4Ptr) MemNew (sizeof (Int4) * dlg->num_columns);
+
+  vnp_v = first_values;
+  vnp_b = blank_list;
+  i = 0;
+  while (vnp_b != NULL) {
+    dlg->blank_list[i] = vnp_b->data.intvalue;
+    if (vnp_v == NULL || StringHasNoText (vnp_v->data.ptrvalue)) {
+      dlg->first_values[i] = StringSave ("First row value is blank");
+    } else {
+      dlg->first_values[i] = StringSave (vnp_v->data.ptrvalue);
+    }
+    dlg->column_list[i] = NULL;
+    vnp_b = vnp_b->next;
+    if (vnp_v != NULL) {
+      vnp_v = vnp_v->next;
+    }
+    i++;
+  }
+    
+  PopulateTabConfigListColumnListDoc ((DialoG) p);
+
+  dlg->current_column = 0;
+  PointerToDialog (dlg->edit_col_dlg, dlg->column_list[0]);
+  SetTabColumnConfigDialogTitle (dlg->edit_col_dlg, dlg->first_values[0], dlg->blank_list[0]);
+    
+  return (DialoG) p;
+}
diff --git a/desktop/macrodlg.h b/desktop/macrodlg.h
new file mode 100755
index 00000000..a7c26cfa
--- /dev/null
+++ b/desktop/macrodlg.h
@@ -0,0 +1,63 @@
+/*   macrodlg.h
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*            National Center for Biotechnology Information (NCBI)
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government do not place any restriction on its use or reproduction.
+*  We would, however, appreciate having the NCBI and the author cited in
+*  any work or product based on this material
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+* ===========================================================================
+*
+* File Name:  macrodlg.h
+*
+* Author:  Colleen Bollin
+*
+* Version Creation Date:   11/23/2007
+*
+* $Revision: 1.7 $
+*
+* File Description: 
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* Date     Name        Description of modification
+* -------  ----------  -----------------------------------------------------
+*
+*
+* ==========================================================================
+*/
+
+#ifndef MACRODLG_H
+#define MACRODLG_H
+
+#include <objmacro.h>
+
+NLM_EXTERN void LaunchMacroEditor (IteM i);
+NLM_EXTERN DialoG TabColumnConfigDialog 
+(GrouP                    h,
+ CharPtr                  title,
+ Int4                     num_blank,
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata);
+NLM_EXTERN DialoG TabColumnConfigListDialog (GrouP h, ValNodePtr first_values, ValNodePtr blank_list, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
+
+NLM_EXTERN DialoG FeatureTypeDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
+NLM_EXTERN DialoG StringConstraintDialog (GrouP h, CharPtr label, Boolean clear_btn, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
+
+
+#endif
diff --git a/desktop/pubdesc.c b/desktop/pubdesc.c
index a9a28b5a..6397f881 100644
--- a/desktop/pubdesc.c
+++ b/desktop/pubdesc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/28/95
 *
-* $Revision: 6.62 $
+* $Revision: 6.66 $
 *
 * File Description:
 *
@@ -46,6 +46,8 @@
 #include <utilpub.h>
 #include <explore.h>
 #include <toasn3.h>
+#include <mla2api.h>
+#include <dlogutil.h>
 
 #define FIRST_PAGE      0
 
@@ -714,6 +716,9 @@ static Pointer PubdescPageToPubdescPtr (DialoG d)
   Int2                  val;
   CitRetractPtr         crp;
   UIEnum                uieval;
+  /* for fixing special characters */
+  SeqDescrPtr           sdp_tmp;
+  Boolean               fixed_chars = FALSE;
 
   pdp = NULL;
   ppp = (PubdescPagePtr) GetObjectExtra (d);
@@ -959,6 +964,19 @@ static Pointer PubdescPageToPubdescPtr (DialoG d)
       }
     }
   }
+
+  /* fix special characters before returning */
+  sdp_tmp = SeqDescrNew(NULL);
+  sdp_tmp->choice = Seq_descr_pub;
+  sdp_tmp->data.ptrvalue = pdp;
+  FixSpecialCharactersForObject (OBJ_SEQDESC, sdp_tmp, "You may not include special characters in publication text.\nIf you do not choose replacement characters, these special characters will be replaced with '#'.", TRUE, &fixed_chars);
+  sdp_tmp->data.ptrvalue = NULL;
+  sdp_tmp = SeqDescrFree (sdp_tmp);
+  if (fixed_chars)
+  {
+    PointerToDialog (d, pdp);
+  }
+
   return (Pointer) pdp;
 }
 
@@ -1712,6 +1730,41 @@ static CitGenPtr ConvertCitArtToCitGen (CitArtPtr cap)
   return cgp;
 }
 
+static void FixEPubOnlyJournal (PubdescPagePtr ppp, Boolean only_if_ahead_of_print)
+
+{
+  Char    str [256];
+  Int2    starting_year;
+  UIEnum  val;
+  Int2    year = 0;
+
+  if (ppp == NULL) return;
+
+  GetTitle (ppp->year, str, sizeof (str));
+  if (StringDoesHaveText (str)) {
+    StrToInt (str, &year);
+    if (year < 1900) {
+      year = 0;
+    }
+  }
+
+  GetTitle (ppp->journal, str, sizeof (str) - 1);
+  if (StringHasNoText (str)) return;
+
+  if (! Mla2IsEPubOnlyJournal (str, &starting_year)) return;
+
+  if (starting_year > 0) {
+    if (year < starting_year) return;
+  }
+
+  if (only_if_ahead_of_print) {
+    if (GetEnumPopup (ppp->pubstatus, pubstatus_alist, &val) && val > 0) {
+      if ((Uint1) val != PUBSTATUS_aheadofprint) return;
+    }
+  }
+
+  SetEnumPopup (ppp->pubstatus, pubstatus_alist, (UIEnum) PUBSTATUS_epublish);
+}
 
 static ValNodePtr LookupAnArticle (PubEquivLookupProc lookup, ValNodePtr oldpep, Boolean byMuid)
 
@@ -1871,6 +1924,7 @@ static void LookupCommonProc (ButtoN b, Boolean byMuid, Boolean byPmid)
         PointerToDialog (ppp->dialog, (Pointer) pdp);
       }
       PubdescFree (pdp);
+      FixEPubOnlyJournal (ppp, FALSE);
       Select (ParentWindow (b));
       Update ();
     }
@@ -2000,12 +2054,14 @@ static void LookupISOJournalProc (ButtoN b)
         if (len > 1) {
           if (ChooseFromMultipleJournals (str, sizeof (str) - 1, allTitles)) {
             SetTitle (ppp->journal, str);
+            FixEPubOnlyJournal (ppp, FALSE);
           } else {
             Message (MSG_OK, "Unable to match journal");
           }
         } else if (len == 1 && StringDoesHaveText (allTitles->data.ptrvalue) &&
                    allTitles->choice == Cit_title_iso_jta) {
           SetTitle (ppp->journal, allTitles->data.ptrvalue);
+          FixEPubOnlyJournal (ppp, FALSE);
         } else {
           Message (MSG_OK, "Unable to match journal");
         }
@@ -2716,6 +2772,7 @@ static void PubdescAcceptFormButtonProc (ButtoN b)
     return;
   }
   pdp = (PubdescPtr) DialogToPointer (pfp->data);
+
   copy = AsnIoMemCopy ((Pointer) pdp,
                        (AsnReadFunc) PubdescAsnRead,
                        (AsnWriteFunc) PubdescAsnWrite); 
@@ -3352,6 +3409,7 @@ static Boolean ReplaceAllCallback (GatherObjectPtr gop)
       if (PubEquivMatch (pdp->pub, radp->deleteThis->pub) == 0) {
         serial_number = GetSerialNumber (pdp->pub);
         pdp->pub = PubEquivFree (pdp->pub);
+
         pdp->pub = AsnIoMemCopy (radp->replaceWith->pub, (AsnReadFunc) PubEquivAsnRead,
                                  (AsnWriteFunc) PubEquivAsnWrite);
         SetSerialNumber (pdp->pub, serial_number);
@@ -4355,14 +4413,12 @@ extern Int2 LIBCALLBACK PubdescGenFunc (Pointer data)
 
 typedef struct citart_inpress_struct {
 
-  FILE *logfile;	
   Boolean error;	
       
-  CharPtr   f_last_name, f_first_name, l_last_name, l_first_name; 
+  CharPtr   f_last_name, l_last_name; 
   CharPtr  jour_title, jour_volume,  jour_page, art_title;
 
   Int2 year;
-  Int1 rank;
 
   ByteStorePtr uids_bs;  /*pmids*/
 
@@ -4395,6 +4451,8 @@ typedef struct citationupdateform {
   ButtoN          Extra_Term;
   TexT            extra_term_text;
 
+  ButtoN          expand_year;
+
   PopuP           new_query;
   DoC             rdoc;          
   ButtoN          action;           
@@ -4679,13 +4737,33 @@ static  void AddPage(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st)
   EntrezAddToBooleanRequest (e2rp, NULL, 0, "PAGE",term, NULL, 0, 0, NULL, NULL, FALSE, FALSE);
 }
 
-static  void AddYear(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st)
+static  void AddYear(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st, Boolean expand)
 {
+  Int4 year;
+  Char year_buf[10];
   if (StringHasNoText (term)) return;
   if (!is_1st) {
     EntrezAddToBooleanRequest (e2rp, NULL, ENTREZ_OP_AND, NULL, NULL, NULL, 0, 0, NULL, NULL, FALSE, FALSE);  
   }
-  EntrezAddToBooleanRequest (e2rp, NULL, 0, "EDAT", term, NULL, 0, 0, NULL, NULL, FALSE, FALSE);
+  if (expand) {
+    year = atoi (term);
+    if (year > 0) {
+      EntrezAddToBooleanRequest (e2rp, NULL, ENTREZ_OP_LEFT_PAREN, NULL, NULL, NULL, 0, 0, NULL, NULL, FALSE, FALSE); 
+      sprintf (year_buf, "%d", year - 1);
+      EntrezAddToBooleanRequest (e2rp, NULL, 0, "EDAT", year_buf, NULL, 0, 0, NULL, NULL, FALSE, FALSE);
+      EntrezAddToBooleanRequest (e2rp, NULL, ENTREZ_OP_OR, NULL, NULL, NULL, 0, 0, NULL, NULL, FALSE, FALSE); 
+      sprintf (year_buf, "%d", year);
+      EntrezAddToBooleanRequest (e2rp, NULL, 0, "EDAT", year_buf, NULL, 0, 0, NULL, NULL, FALSE, FALSE);
+      EntrezAddToBooleanRequest (e2rp, NULL, ENTREZ_OP_OR, NULL, NULL, NULL, 0, 0, NULL, NULL, FALSE, FALSE); 
+      sprintf (year_buf, "%d", year + 1);
+      EntrezAddToBooleanRequest (e2rp, NULL, 0, "EDAT", year_buf, NULL, 0, 0, NULL, NULL, FALSE, FALSE);
+      EntrezAddToBooleanRequest (e2rp, NULL, ENTREZ_OP_RIGHT_PAREN, NULL, NULL, NULL, 0, 0, NULL, NULL, FALSE, FALSE);
+    } else {
+      EntrezAddToBooleanRequest (e2rp, NULL, 0, "EDAT", term, NULL, 0, 0, NULL, NULL, FALSE, FALSE);
+    }
+  } else {
+    EntrezAddToBooleanRequest (e2rp, NULL, 0, "EDAT", term, NULL, 0, 0, NULL, NULL, FALSE, FALSE);
+  }
 }
 
 static  void AddAll(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st)
@@ -4698,72 +4776,62 @@ static  void AddAll(Entrez2RequestPtr e2rp, CharPtr term, Boolean is_1st)
 }
 
 
+static Entrez2RequestPtr QueryFromForm (CitationUpdateFormPtr cufp, Boolean use_all)
+{
+  Entrez2RequestPtr e2rp = NULL;
+  Boolean is_first_term = TRUE;
+  Char    val_str[256];
 
+  if (cufp == NULL) return NULL;
 
-/*****************************************************************************
-*
-*  Function:   FormDefaultQuery
-*              constructs entrez2 query from information passed in, execute
-*              the query, and get back the uids from entrezReplyPtr. 
-********************************pass uids back as bs of caipp. returns void.
-*  Argument:   CitArtInPressPtr
-*
-*  Returns:    void
-*
-*****************************************************************************/
-static void FormDefaultQuery (Entrez2RequestPtr e2rp, CitArtInPressPtr caipp) {
-
-  Char  year [16];
- 
-  if (caipp->year != -1) {
-    sprintf(year, "%d", (int) caipp->year); 
+  /* for new term in query, add to [all], then automatically go through Term mapping*/
+  /* add exta term (user supplied) as ALL, no specific field */
+  /* debug:  assuming this is a well-formed query string, let the add func. parse it*/
+  if ( !TextHasNoText (cufp->extra_term_text) && (use_all || GetStatus (cufp->Extra_Term))) {
+    GetTitle (cufp->extra_term_text, val_str, sizeof (val_str));
+    e2rp = EntrezCreateBooleanRequest (TRUE, FALSE, "PubMed", val_str, 0, 0, NULL, 20, 0); 
+    is_first_term = FALSE;
+  } else {
+    e2rp = EntrezCreateBooleanRequest (TRUE, FALSE, "PubMed", NULL, 0, 0, NULL, 20, 0);
   }
 
-  /* add all available fields as indicated by rank*/
-  if (caipp->rank == 10) {      /* add title, page, vol */
-
-    AddJournal(e2rp,  caipp->jour_title, TRUE);  /* add first term*/
-    AddVolume(e2rp,  caipp->jour_volume, FALSE);  
-    AddPage(e2rp,  caipp->jour_page, FALSE); 
+  if ( ! TextHasNoText (cufp->f_auth_text) && (use_all || GetStatus (cufp->First_Author))) {
+    GetTitle (cufp->f_auth_text, val_str, sizeof (val_str));
+    AddAuthor(e2rp, val_str, is_first_term);
+    is_first_term = FALSE;
   }
-  
-  else {    
-    
-    if (caipp->rank > 4) {    /* add author in all cases*/
 
-      /***** term  can be capital letter or lower case,  (ENTREZ_OP_NONE is 0)  */
-      AddAuthor(e2rp,  caipp->f_last_name, TRUE);  /* add first term */
+  if ( !TextHasNoText (cufp->l_auth_text) && (use_all || GetStatus (cufp->Last_Author))) {
+    GetTitle (cufp->l_auth_text, val_str, sizeof (val_str));
+    AddAuthor(e2rp, val_str, is_first_term);    
+    is_first_term = FALSE;
+  }
 
-      if(StringCmp(caipp->l_last_name, "null") && StringCmp(caipp->l_last_name, caipp->f_last_name)) {
-      AddAuthor(e2rp,  caipp->l_last_name, FALSE); 
-      }
-    }
-    
-    if (caipp->rank == 6) {  /* add year, takes StringSave(year-1900)?? */   
-      AddYear(e2rp,  year, FALSE);        
-    }     
+  if ( !TextHasNoText (cufp->journal_text) && (use_all || GetStatus (cufp->Journal))) {
+    GetTitle (cufp->journal_text, val_str, sizeof (val_str));
+    AddJournal(e2rp, val_str, is_first_term);
+    is_first_term = FALSE;
+  }
 
-    if (caipp->rank > 6) {  /* add jour_title */
-      AddJournal(e2rp,  caipp->jour_title, FALSE);  /* NOT first term*/
-    }
-    
-    if (caipp->rank == 9) {       /* add vol and year */
-      AddVolume(e2rp,  caipp->jour_volume, FALSE);  
-      AddYear(e2rp,  year, FALSE); 
-    }
+  if ( !TextHasNoText (cufp->volume_text) && (use_all || GetStatus (cufp->Volume))) {
+    GetTitle (cufp->volume_text, val_str, sizeof (val_str));
+    AddVolume(e2rp, val_str, is_first_term);
+    is_first_term = FALSE;
+  }
 
-    if (caipp->rank == 8) {  /* add year or volume */
-      
-      if (caipp->year != -1) {
-	AddYear(e2rp,  year, FALSE); 	
-      }
-      else {
-	AddVolume(e2rp,  caipp->jour_volume, FALSE);
-      }		       
-    }   /* end rank 8*/ 		     
-  }  
-}	
+  if ( !TextHasNoText (cufp->page_text) && (use_all || GetStatus (cufp->Page))) {
+    GetTitle (cufp->page_text, val_str, sizeof (val_str));
+    AddPage(e2rp, val_str, is_first_term);
+    is_first_term = FALSE;
+  }
 
+  if ( !TextHasNoText (cufp->year_text) && (use_all || GetStatus (cufp->Year))) {
+    GetTitle (cufp->year_text, val_str, sizeof (val_str));
+    AddYear(e2rp, val_str, is_first_term, GetStatus (cufp->expand_year));
+    is_first_term = FALSE;
+  }
+  return e2rp;  
+}
 
 
 /*****************************************************************************
@@ -4788,17 +4856,6 @@ static void SendQuery (ButtoN b)
   Entrez2RequestPtr  e2rp = NULL;
 
 
-  Char               f_auth [64];
-  Char               l_auth [64];
-  Char               journal [64];
-  Char               volume [64];
-  Char               page [64];
-  Char               year [64];
-  Char               new_term [256];
-
-  Boolean            is_first_term = TRUE;
-
-
   cufp = (CitationUpdateFormPtr) GetObjectExtra (b);
   if (cufp == NULL) return;
 
@@ -4813,74 +4870,7 @@ static void SendQuery (ButtoN b)
   /*** trick:  must make sure to add Op : AND, after the first term, can't
    add one before!! */
 
-  if (choice == 1) {               /* precess default query*/
-
-    e2rp = EntrezCreateBooleanRequest (TRUE, FALSE, "PubMed", NULL, 0, 0, NULL, 20, 0);
-
-    FormDefaultQuery (e2rp,  caipp);
-    
-
-    /* add exta term (user supplied) as ALL, no specific field */
-    if ( GetStatus (cufp->Extra_Term) ) {
-      GetTitle (cufp->extra_term_text, new_term, sizeof (f_auth));
-      AddAll(e2rp, new_term, FALSE);
-      is_first_term = FALSE;
-    }
-  }
-     
-  if (choice == 2) {        /*user specify query*/
-
-    /* for new term in query, add to [all], then automatically go through Term mapping*/
-    /* add exta term (user supplied) as ALL, no specific field */
-    /* debug:  assuming this is a well-formed query string, let the add func. parse it*/
-    if ( GetStatus (cufp->Extra_Term) ) {
-      GetTitle (cufp->extra_term_text, new_term, sizeof (f_auth));
-      e2rp = EntrezCreateBooleanRequest (TRUE, FALSE, "PubMed", new_term, 0, 0, NULL, 20, 0); 
-      is_first_term = FALSE;
-    }
-    else{
-      e2rp = EntrezCreateBooleanRequest (TRUE, FALSE, "PubMed", NULL, 0, 0, NULL, 20, 0);
-    }
-
-    if ( GetStatus (cufp->First_Author) ) {
-      GetTitle (cufp->f_auth_text, f_auth, sizeof (f_auth));
-      AddAuthor(e2rp, f_auth, is_first_term);
-      is_first_term = FALSE;
-    }
-
-    if ( GetStatus (cufp->Last_Author) ) {
-      GetTitle (cufp->l_auth_text, l_auth, sizeof (l_auth));
-      AddAuthor(e2rp, l_auth, is_first_term);    
-      is_first_term = FALSE;
-    }
-
-    if ( GetStatus (cufp->Journal) ) {
-      GetTitle (cufp->journal_text, journal, sizeof (journal));
-      AddJournal(e2rp, journal, is_first_term);
-      is_first_term = FALSE;
-    }
-
-    if ( GetStatus (cufp->Volume) ) {
-      GetTitle (cufp->volume_text, volume, sizeof (volume));
-      AddVolume(e2rp, volume, is_first_term);
-      is_first_term = FALSE;
-    }
-
-    if ( GetStatus (cufp->Page) ) {
-      GetTitle (cufp->page_text, volume, sizeof (page));
-      AddPage(e2rp, page, is_first_term);
-      is_first_term = FALSE;
-    }
-
-    if ( GetStatus (cufp->Year) ) {
-      GetTitle (cufp->year_text, year, sizeof (year));
-      AddYear(e2rp, year, is_first_term);
-      is_first_term = FALSE;
-    }      
-  }
-
-  SetValue (cufp->new_query, 2); /* reset the popup list to display customize item*/
-
+  e2rp = QueryFromForm (cufp, choice == 1);
 
   /* process query, get Uids, populate the caipp field*/
   GetUidListFromE2Request (caipp, e2rp, cufp->rdoc);
@@ -5029,6 +5019,26 @@ static void Quit (ButtoN b)
 }
 
 
+static void SetRequestType (ButtoN b)
+{
+  CitationUpdateFormPtr  cufp;
+
+  cufp = (CitationUpdateFormPtr) GetObjectExtra (b);
+  if (cufp == NULL) return;
+
+  if (GetStatus (cufp->First_Author)
+      || GetStatus (cufp->Last_Author)
+      || GetStatus (cufp->Journal)
+      || GetStatus (cufp->Volume)
+      || GetStatus (cufp->Page)
+      || GetStatus (cufp->Year)
+      || GetStatus (cufp->Extra_Term)) {
+    SetValue (cufp->new_query, 2);
+  } else {
+    SetValue (cufp->new_query, 1);
+  }  
+}
+
 
 /*****************************************************************************
 *  Function:     CreateCitationUpdateWindow_detail
@@ -5089,26 +5099,34 @@ static WindoW CreateCitationUpdateWindow_detail (Pointer userdata)
   authors = HiddenGroup (cit_fields, 4, 0, NULL);
   SetGroupSpacing (authors, 5, 3);
 
-  cufp->First_Author  = CheckBox (authors, "First Author", NULL);
+  cufp->First_Author  = CheckBox (authors, "First Author", SetRequestType);
+  SetObjectExtra (cufp->First_Author, cufp, NULL);
   cufp->f_auth_text = DialogText (authors,  "", 12, NULL);
 
-  cufp->Last_Author = CheckBox (authors, "Last Author", NULL);
+  cufp->Last_Author = CheckBox (authors, "Last Author", SetRequestType);
+  SetObjectExtra (cufp->Last_Author, cufp, NULL);
   cufp->l_auth_text = DialogText (authors,  "", 12, NULL);
 
   journal = HiddenGroup (cit_fields, 2, 0, NULL);
   SetGroupSpacing (journal, 5, 3);
 
-  cufp->Journal = CheckBox (journal, "Journal", NULL);
+  cufp->Journal = CheckBox (journal, "Journal", SetRequestType);
+  SetObjectExtra (cufp->Journal, cufp, NULL);
   cufp->journal_text = DialogText (journal,  "", 30, NULL);
 
-  imprint = HiddenGroup (cit_fields, 6, 0, NULL);
+  imprint = HiddenGroup (cit_fields, 7, 0, NULL);
   SetGroupSpacing (imprint, 5, 3);
 
-  cufp->Year = CheckBox (imprint, "Year", NULL);
+  cufp->Year = CheckBox (imprint, "Year", SetRequestType);
+  SetObjectExtra (cufp->Year, cufp, NULL);
   cufp->year_text = DialogText (imprint, "", 6, NULL);
-  cufp->Volume = CheckBox (imprint, "Volume", NULL);
+  cufp->expand_year = CheckBox (imprint, "+/- 1 Year", NULL);
+  SetStatus (cufp->expand_year, TRUE);
+  cufp->Volume = CheckBox (imprint, "Volume", SetRequestType);
+  SetObjectExtra (cufp->Volume, cufp, NULL);
   cufp->volume_text  = DialogText (imprint, "", 6, NULL);
-  cufp->Page = CheckBox (imprint, "Page", NULL);
+  cufp->Page = CheckBox (imprint, "Page", SetRequestType);
+  SetObjectExtra (cufp->Page, cufp, NULL);
   cufp->page_text = DialogText (imprint, "", 6, NULL);
 
 
@@ -5116,7 +5134,7 @@ static WindoW CreateCitationUpdateWindow_detail (Pointer userdata)
   SetGroupSpacing (title, 5, 3);
 
   StaticPrompt (title, "Article Title:", 0, dialogTextHeight, systemFont, 'l');
-  cufp->art_title_text = ScrollText (title, 30, 1, systemFont, TRUE, NULL);
+  cufp->art_title_text = ScrollText (title, 30, 2, systemFont, TRUE, NULL);
   SafeSetTitle (cufp->art_title_text, "");
 
   i = HiddenGroup (h, 2, 0, NULL);     /*3rd vertical item in h*/
@@ -5126,7 +5144,8 @@ static WindoW CreateCitationUpdateWindow_detail (Pointer userdata)
   StaticPrompt (i, " ", 0, popupMenuHeight, programFont, 'l');
   StaticPrompt (i, " ", 0, popupMenuHeight, programFont, 'l');
 
-  cufp->Extra_Term = CheckBox (i, "Add these terms to new query", NULL);
+  cufp->Extra_Term = CheckBox (i, "Add these terms to new query", SetRequestType);
+  SetObjectExtra (cufp->Extra_Term, cufp, NULL);
   cufp->extra_term_text = DialogText (i, "", 25, NULL);
 
 
@@ -5200,6 +5219,22 @@ static WindoW CreateCitationUpdateWindow_detail (Pointer userdata)
   return w;
 }
 
+
+static CharPtr GetLastNameFromPersonId (PersonIdPtr pid)
+{
+  NameStdPtr nsp;
+  CharPtr lname = NULL;
+
+  if (pid != NULL && pid->choice == 2) {		     
+		nsp = (NameStdPtr) pid->data;  
+		if (nsp->names != NULL) {    		
+      lname = nsp->names[0];
+    }
+  }
+  return lname;
+}
+
+
 /*****************************************************************************
 *  Function:     PopulateWindow
 *  Description:	 use pdp to populate a caipp structure. No default query!!
@@ -5224,30 +5259,22 @@ static void PopulateWindow( WindoW w, PubdescPtr pdp)
   CitJourPtr cjp;
   ImprintPtr ImpPtr;
   AuthListPtr alp;  
-  AuthorPtr f_author_p, l_author_p, ap;  /* first and last authors*/
-  PersonIdPtr pid_p, pid;
-  NameStdPtr nsp;
+  AuthorPtr f_author_p = NULL, l_author_p = NULL, ap;  /* first and last authors*/
+  PersonIdPtr pid;
 
   ValNodePtr title_vnp, auth_vnp, art_title_vnp;
 
-  /*could get rid of full names*/
-  CharPtr f_first_name = NULL, f_last_name = NULL, l_first_name = NULL, l_last_name = NULL;
-  CharPtr jour_title = NULL, jour_volume, jour_page, art_title = NULL;
+  CharPtr f_last_name = NULL, l_last_name = NULL;
+  CharPtr jour_title = NULL, jour_volume = NULL, jour_page = NULL, art_title = NULL;
   
-  Int2 year;
-  Int1 rank;
+  Int2 year = -1;
 
-  Boolean has_author, has_title, has_volume, has_page, has_year, is_article;
-  has_author =  has_title = has_volume = has_page = has_year = is_article = FALSE;
+  Boolean is_article = FALSE;;
 
   cufp = (CitationUpdateFormPtr) GetObjectExtra (w);
   if (cufp == NULL) return;
 
 
-  if ( (caipp = MemNew(sizeof(CitArtInPress))) == NULL) {
-    return;
-  }
-
   pubdesc = pdp;      /* don't really need this could use pubdesc*/   
   if(pubdesc == NULL) return;
 
@@ -5256,237 +5283,99 @@ static void PopulateWindow( WindoW w, PubdescPtr pdp)
 
   for (pub=pubdesc->pub, cap=NULL; pub; pub=pub->next) {
     if (pub->choice == PUB_Article) {
-
       is_article = TRUE;
       cap = (CitArtPtr) pub->data.ptrvalue;
       if (cap == NULL) return; 
       
       /* look for cit-art from journals only*/
-      if (cap->from ==1) {
-	
-	cjp = (CitJourPtr) cap->fromptr;
-	if (cjp == NULL) return; 
-	
-	ImpPtr =(ImprintPtr) cjp->imp;	      
-	if(ImpPtr == NULL) return; 
+      if (cap->from ==1) {	
+	      cjp = (CitJourPtr) cap->fromptr;
+	      if (cjp == NULL) return; 
+      	
+	      ImpPtr =(ImprintPtr) cjp->imp;	      
+	      if(ImpPtr == NULL) return; 
 	      
-
-	  /* get article title */
-	  if( !cap->title ) { art_title = StringSave("No title was available"); }
-	  for (art_title_vnp=cap->title; art_title_vnp; art_title_vnp=art_title_vnp->next) {
-	    /*could combine the four*/
-	    if((art_title_vnp->choice == Cit_title_name) || (art_title_vnp->choice == Cit_title_tsub)|| (art_title_vnp->choice == Cit_title_trans)) {
-	      art_title = art_title_vnp->data.ptrvalue;		    
-	    }
-	  }	 
-
-	  /* get journal title */
-	  if( !cjp->title ) { jour_title = StringSave("null"); }
-	  for (title_vnp=cjp->title; title_vnp; title_vnp=title_vnp->next) {
-	    /*could combine the four*/
-	    if (title_vnp->choice == Cit_title_iso_jta) {
-	      jour_title = title_vnp->data.ptrvalue;		    
-	    }
-	    else if (title_vnp->choice == Cit_title_ml_jta) {
-	      jour_title = title_vnp->data.ptrvalue;
-	    }
-	    else if (title_vnp->choice == Cit_title_jta) {
-	      jour_title = title_vnp->data.ptrvalue;
-	    }
-	    else if (title_vnp->choice == Cit_title_name) {
-	      jour_title = title_vnp->data.ptrvalue;
-	      /* break;            don't need break ??? */
-	    }
-	    else { 
-	      jour_title = StringSave("this journal got a WEIRD title");
-	    }
-	    has_title = TRUE;  
-	  }
+	      /* get article title */
+	      for (art_title_vnp=cap->title; art_title_vnp; art_title_vnp=art_title_vnp->next) {
+	        /*could combine the four*/
+	        if((art_title_vnp->choice == Cit_title_name) || (art_title_vnp->choice == Cit_title_tsub)|| (art_title_vnp->choice == Cit_title_trans)) {
+	          art_title = art_title_vnp->data.ptrvalue;		    
+	        }
+	      }
+
+	      /* get journal title */
+	      for (title_vnp=cjp->title; title_vnp; title_vnp=title_vnp->next) {
+	        /*could combine the four*/
+	        if (title_vnp->choice == Cit_title_iso_jta) {
+	          jour_title = title_vnp->data.ptrvalue;		    
+	        }
+	        else if (title_vnp->choice == Cit_title_ml_jta) {
+	          jour_title = title_vnp->data.ptrvalue;
+	        }
+	        else if (title_vnp->choice == Cit_title_jta) {
+	          jour_title = title_vnp->data.ptrvalue;
+	        }
+	        else if (title_vnp->choice == Cit_title_name) {
+	          jour_title = title_vnp->data.ptrvalue;
+	          /* break;            don't need break ??? */
+	        }
+	        else { 
+	          jour_title = "this journal got a WEIRD title";
+	        }
+	      }
 	  
 	  
-	  if (ImpPtr->volume) {
-	    jour_volume =  ImpPtr->volume;
-	    has_volume = TRUE;  
-	  }
-	  else {  jour_volume = StringSave("null"); }	 
-	  
-	  if (ImpPtr->pages) { 
-	    jour_page =  ImpPtr->pages;
-	    has_page = TRUE;  
-	  }
-	  else {  jour_page = StringSave("null"); }
+	      if (ImpPtr->volume) {
+	        jour_volume =  ImpPtr->volume;
+	      }
+    	  
+	      if (ImpPtr->pages) { 
+	        jour_page =  ImpPtr->pages;
+	      }
 	
 	  
-	  /* not ideal behavior, although date is required in imp*/
-	  if ((DatePtr)ImpPtr->date == NULL) { return; }
-	  
-		year = -1;
-		DateRead (ImpPtr->date, &year, NULL, NULL, NULL);
-		if (year != -1) { has_year = TRUE; }				
-		
-		alp = (AuthListPtr) cap->authors; 
-		if (alp == NULL) {
-		  
-		  if (caipp->logfile) {                   
- 
-		    fprintf(caipp->logfile,"|this in-press cit-art has no author| %s | %s| %s | %d\n", jour_title, jour_volume, jour_page, year);
-		  }
-		   return;
-		}		
-		 		 			
-		/*get ptr to both 1st and last author*/	 
-		auth_vnp = (ValNodePtr) alp->names; /*get the first node */ 
-		
-		f_author_p = (AuthorPtr)auth_vnp->data.ptrvalue;
-		l_author_p =(AuthorPtr)auth_vnp->data.ptrvalue;
-		
-		/* get the node for the last author, but ignore consortium */
-		while (auth_vnp->next) {
-		  auth_vnp = auth_vnp->next;
-		  ap = (AuthorPtr) auth_vnp->data.ptrvalue;
-		  if (ap != NULL) {
-		    pid = (PersonIdPtr) ap->name;
-		    if (pid != NULL) {
-		      if (pid->choice == 2) {
-		        l_author_p =(AuthorPtr)auth_vnp->data.ptrvalue;
-		      }
+	      /* not ideal behavior, although date is required in imp*/
+	      if ((DatePtr)ImpPtr->date != NULL) {	  
+		      DateRead (ImpPtr->date, &year, NULL, NULL, NULL);
 		    }
-		  }
-		}
-		
-		/* should be analyzing the value of alp->choice,  not alp->names->choice*/
-		if (alp->choice == 1) {   
-		  /*could make this (getting name from author_p) a function */		   
-		   pid_p = (PersonIdPtr) f_author_p->name;
-		   
-		   if (pid_p->choice ==2) { 			 
-		     
-		     nsp = (NameStdPtr) pid_p -> data;  
-		     
-		     /* why didnot this work?? * 			 
-			if (!( nsp->names[0])) */		    
-		     
-		     if (nsp->names[0] != NULL ) {
-		       
-		       f_last_name =  nsp->names[0];	
-		       has_author = TRUE;		       
-		       
-		       if (nsp->names[1]!= NULL) {
-			 f_first_name =  nsp->names[1];	
-		       }
-		       else { f_first_name = StringSave("null"); }		       	
-		       
-		     }
-		     /* set to null!! */
-		     else {  f_last_name = StringSave("null"); 
-		     f_first_name = StringSave("null");			     
-		     }
-		   }
-		   
-		   
-		   /*now do the last author */
-		   
-		   if (l_author_p->name == f_author_p->name) {  /*single author*/
-		     l_first_name = f_first_name;
-		     l_last_name =f_last_name;
-		   }
-		   else {
-		     
-		     pid_p = (PersonIdPtr) l_author_p->name;
-		     if (pid_p->choice ==2) { 			 
-		       nsp = (NameStdPtr) pid_p -> data;  
-		       
-		       if (nsp->names[0] != NULL ) {
-			 
-			 l_last_name =  nsp->names[0];	
-			 if (nsp->names[1]!= NULL) {
-			   l_first_name =  nsp->names[1];	
-			 }
-			 else { l_first_name = StringSave("null"); }
-		       }		      
-		       else {  l_last_name = StringSave("null"); 
-		       l_first_name = StringSave("null");	
-		       }
-		     }
-		   } /*end of last author */
-		 }  /* end alp-> choice is std */
-		 
-		 
-		 /* here, if author list is not std names */ 			      
-		 else if (alp->choice == 2) {  
-		   
-		   /* full name as last name*/	       
-		   f_last_name = (CharPtr)f_author_p;
-		   f_first_name = StringSave ("null");
-		   has_author = TRUE;	
-
-		   l_last_name = (CharPtr)l_author_p;
-		   l_first_name = StringSave ("null");
-		 }
-		 else {  
-		   /* full name as last name*/	       
-		   f_last_name = (CharPtr)f_author_p;
-		   f_first_name = StringSave ("null");
-		   has_author = TRUE;	
-
-		   l_last_name = (CharPtr)l_author_p;
-		   l_first_name = StringSave ("null");
-		 }	      		     		   
-		
-
-
-		rank = 0;
-		 /*caculate rank*/
-	
-		if (has_page && has_volume && has_title) {
-		   rank = 10;
-		}
-		else if (has_author) {
-		  if (has_title) {
-		    if(has_year && has_volume) { rank = 9; }
-		    else if (has_year || has_volume) { rank = 8; }
-		     else { rank = 7; }                /* auth + journal_title only*/
-		  }
-		  else if (has_year) { rank = 6; }   /* auth + year only*/
-		  else { rank = 5; } /* author  but no journal_title case */
-		}		 
-		else { rank = 0; }  /*ignore all other combo*/	     
-
-
-		rank = 0;
-		 /*caculate rank*/
-		/*   better set flags as key individual fields are collected!! 
-		 *    avoid many calls to StringCmp */
-		/* must have first author, or (journal_title, volume and page)*/
-		
-		if (has_page && has_volume && has_title) {
-		   rank = 10;
-		}
-		else if (has_author) {
-		  if (has_title) {
-		    if(has_year && has_volume) { rank = 9; }
-		    else if (has_year || has_volume) { rank = 8; }
-		     else { rank = 7; }                /* auth + journal_title only*/
-		  }
-		  else if (has_year) { rank = 6; }   /* auth + year only*/
-		  else { rank = 5; } /* author  but no journal_title case */
-		}		 
-		else { rank = 0; }  /*ignore all other combo*/	     
-
-
-		  /*  safe practice to save a new copy if the struct my go away. */     
-		  caipp->jour_title =  StringSave(jour_title);
-		  caipp->f_last_name = StringSave(f_last_name);
-		  caipp->f_first_name =StringSave(f_first_name);
-		  caipp->l_last_name = StringSave(l_last_name);
-		  caipp->l_first_name = StringSave(l_first_name);
-		  caipp->jour_volume = StringSave(jour_volume);
-		  caipp->jour_page = StringSave(jour_page);
-		  caipp->year = year;
-		  caipp->art_title = StringSave(art_title);
-		  caipp->rank = rank;
-			
-	/*}       end if prepub*/  	
+
+		    alp = (AuthListPtr) cap->authors; 
+		    if (alp != NULL) {		  		 		 			
+		      /*get ptr to both 1st and last author*/	 
+		      auth_vnp = (ValNodePtr) alp->names; /*get the first node */ 
+      		
+		      f_author_p = (AuthorPtr)auth_vnp->data.ptrvalue;
+		      l_author_p =(AuthorPtr)auth_vnp->data.ptrvalue;
+      		
+		      /* get the node for the last author, but ignore consortium */
+		      while (auth_vnp->next) {
+		        auth_vnp = auth_vnp->next;
+		        ap = (AuthorPtr) auth_vnp->data.ptrvalue;
+		        if (ap != NULL) {
+		          pid = (PersonIdPtr) ap->name;
+		          if (pid != NULL) {
+		            if (pid->choice == 2) {
+		              l_author_p =(AuthorPtr)auth_vnp->data.ptrvalue;
+		            }
+		          }
+		        }
+		      }
+    		
+		      /* should be analyzing the value of alp->choice,  not alp->names->choice*/
+		      if (alp->choice == 1) {
+            /* std */   
+            f_last_name = GetLastNameFromPersonId (f_author_p->name);
+		        l_last_name = GetLastNameFromPersonId (l_author_p->name);
+		      } else if (alp->choice == 2) {  		   
+            /* full name as last name*/	       
+		        f_last_name = (CharPtr)f_author_p;
+		        l_last_name = (CharPtr)l_author_p;
+		      } else {  
+		        /* full name as last name*/	       
+		        f_last_name = (CharPtr)f_author_p;
+		        l_last_name = (CharPtr)l_author_p;
+		      }	      		     		   
+		    }			
       }        /*end if cit-art*/      
     }          /*end if Pub_article*/    
   }  /* end for, looped through all valnodes of pub*/
@@ -5498,9 +5387,20 @@ static void PopulateWindow( WindoW w, PubdescPtr pdp)
     ArrowCursor ();
     Update ();
 
-    MemFree(caipp);
     return;
   }
+
+  if ( (caipp = MemNew(sizeof(CitArtInPress))) == NULL) {
+    return;
+  }
+
+	caipp->jour_title =  StringSave(jour_title);
+	caipp->f_last_name = StringSave(f_last_name);
+	caipp->l_last_name = StringSave(l_last_name);
+	caipp->jour_volume = StringSave(jour_volume);
+	caipp->jour_page = StringSave(jour_page);
+	caipp->year = year;
+	caipp->art_title = StringSave(art_title);
   
   cufp->caipp = caipp;
 
@@ -5532,17 +5432,45 @@ static void UpdateWindow( CitationUpdateFormPtr cufp, CitArtInPressPtr caipp)
 
   if (caipp == NULL) return;
 
-  year = MemNew(5);
-  sprintf(year, "%d", caipp->year); 
+  if (caipp->year > -1) {
+    year = MemNew(5);
+    sprintf(year, "%d", caipp->year); 
+    SafeSetTitle (cufp->year_text, year);
+  } else {
+    SetTitle (cufp->year_text, "");
+  }
 
-  SafeSetTitle (cufp->f_auth_text,caipp->f_last_name);
-  SafeSetTitle (cufp->l_auth_text,caipp->l_last_name);
-  SafeSetTitle (cufp->journal_text,caipp->jour_title);
-  SafeSetTitle (cufp->year_text, year);
-  SafeSetTitle (cufp->volume_text,caipp->jour_volume);
-  SafeSetTitle (cufp->page_text,caipp->jour_page);
+  if (caipp->f_last_name == NULL) {
+    SetTitle (cufp->f_auth_text, "");
+  } else {
+    SafeSetTitle (cufp->f_auth_text, caipp->f_last_name);
+  }
+  if (caipp->l_last_name == NULL) {
+    SetTitle (cufp->l_auth_text, "");
+  } else {
+    SafeSetTitle (cufp->l_auth_text,caipp->l_last_name);
+  }
+  if (caipp->jour_title == NULL) {
+    SetTitle (cufp->journal_text, "");
+  } else {
+    SafeSetTitle (cufp->journal_text,caipp->jour_title);
+  }
+  if (caipp->jour_volume == NULL) {
+    SetTitle (cufp->volume_text, "");
+  } else {
+    SafeSetTitle (cufp->volume_text,caipp->jour_volume);
+  }
+  if (caipp->jour_page== NULL) {
+    SetTitle (cufp->page_text, "");
+  } else {
+    SafeSetTitle (cufp->page_text,caipp->jour_page);
+  }
 
-  SafeSetTitle (cufp->art_title_text, caipp->art_title);
+  if (caipp->art_title == NULL) {
+    SetTitle (cufp->art_title_text, "");
+  } else {
+    SafeSetTitle (cufp->art_title_text, caipp->art_title);
+  }
   SafeSetTitle (cufp->extra_term_text, "");
 
   SetValue (cufp->new_query, 1); /* reset the popup to default query after an update*/
diff --git a/desktop/salpanel.c b/desktop/salpanel.c
index bfa4a3a2..472fc76c 100644
--- a/desktop/salpanel.c
+++ b/desktop/salpanel.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/27/96
 *
-* $Revision: 6.88 $
+* $Revision: 6.92 $
 *
 * File Description: 
 *
@@ -54,6 +54,7 @@
 #include <dlogutil.h>
 #include <import.h>
 #include <seqpanel.h>
+#include <cdrgn.h>
 
 #define OBJ_VIRT 254
 
@@ -4616,7 +4617,7 @@ typedef struct batchapplyfeaturedetailsdlg
   TexT           rnaName;
   TexT           featcomment;
   DialoG         featdef_choice_dlg;
-  PopuP          rnaSubType;
+  DialoG         rnaType;
   PopuP          reading_frame;
   Int4           feattype;
   Nlm_ChangeNotifyProc     change_notify;
@@ -4631,9 +4632,10 @@ BatchApplyFeatureDetailsFree
   {
     bafdp->defline = MemFree (bafdp->defline);
     bafdp->geneName = MemFree (bafdp->geneName);
-	bafdp->geneDesc = MemFree (bafdp->geneDesc);
+	  bafdp->geneDesc = MemFree (bafdp->geneDesc);
     bafdp->protName = MemFree (bafdp->protName);
     bafdp->protDesc = MemFree (bafdp->protDesc);
+    bafdp->rnaType = RnaTypeFree (bafdp->rnaType);
     bafdp->rnaName = MemFree (bafdp->rnaName);
     bafdp->featcomment = MemFree (bafdp->featcomment);
     bafdp->featdef_name = MemFree (bafdp->featdef_name);
@@ -4659,24 +4661,11 @@ extern BatchApplyFeatureDetailsPtr BatchApplyFeatureDetailsNew (void)
     bafdp->featdef_name = NULL;
     bafdp->featdef_choice = FEATDEF_GENE;
     bafdp->reading_frame = 4;
-    bafdp->rnaSubType = 4;
+    bafdp->rnaType = NULL;
   }
   return bafdp;
 }
 
-static ENUM_ALIST(rnax_subtype_alist)
-  {" ",           99},
-  {"unknown",      0},
-  {"preRna",       1},
-  {"mRNA",         2},
-  {"tRNA",         3},
-  {"rRNA",         4},
-  {"snRNA",        5},
-  {"scRNA",        6},
-  {"snoRNA",       7},
-  {"misc_RNA",   255},
-END_ENUM_ALIST
-
 static void BatchApplyFeatureDetailsToDialog (DialoG d, Pointer data)
 {
   BatchApplyFeatureDetailsDlgPtr dlg;
@@ -4709,7 +4698,7 @@ static void BatchApplyFeatureDetailsToDialog (DialoG d, Pointer data)
       vn.data.ptrvalue = NULL;
       PointerToDialog (dlg->featdef_choice_dlg, &vn);
     }
-    SafeSetValue (dlg->rnaSubType, 4);
+    PointerToDialog (dlg->rnaType, NULL);
   }
   else
   {
@@ -4774,7 +4763,7 @@ static void BatchApplyFeatureDetailsToDialog (DialoG d, Pointer data)
       vn.data.ptrvalue = NULL;
       PointerToDialog (dlg->featdef_choice_dlg, &vn);
     }
-    SafeSetValue (dlg->rnaSubType, bafdp->rnaSubType);
+    PointerToDialog (dlg->rnaType, bafdp->rnaType);
   } 
   if (dlg->change_notify != NULL)
   {
@@ -4787,7 +4776,6 @@ static Pointer BatchApplyFeatureDetailsDialogToData (DialoG d)
   BatchApplyFeatureDetailsDlgPtr dlg;
   BatchApplyFeatureDetailsPtr    bafdp;
   ValNodePtr                     vnp;
-  UIEnum                         val;
   
   dlg = (BatchApplyFeatureDetailsDlgPtr) GetObjectExtra (d);
   if (dlg == NULL)
@@ -4893,21 +4881,7 @@ static Pointer BatchApplyFeatureDetailsDialogToData (DialoG d)
     }
   }
 
-  if (dlg->rnaSubType == NULL)
-  {
-    bafdp->rnaSubType = 4;
-  }
-  else
-  {
-    if (GetEnumPopup (dlg->rnaSubType, rnax_subtype_alist, &val))
-    {
-      bafdp->rnaSubType = val;
-    }
-    else
-    {
-      bafdp->rnaSubType = 4;
-    }
-  }
+  bafdp->rnaType = DialogToPointer (dlg->rnaType);
   
   return bafdp;  
 }
@@ -5079,6 +5053,7 @@ static void AddTextToComment (ButtoN b, CharPtr text)
   BatchApplyFeatureDetailsDlgPtr dlg;
   CharPtr                        orig_comment;
   CharPtr                        new_comment;
+  RnaTypeData                    rtd;
   
   dlg = (BatchApplyFeatureDetailsDlgPtr) GetObjectExtra (b);
   if (dlg == NULL || StringHasNoText (text))
@@ -5105,7 +5080,9 @@ static void AddTextToComment (ButtoN b, CharPtr text)
   } 
   orig_comment = MemFree (orig_comment);
 
-  SetEnumPopup (dlg->rnaSubType, rnax_subtype_alist, (UIEnum) 255);
+  rtd.ncrna_class = NULL;
+  rtd.rna_featdef = FEATDEF_otherRNA;
+  PointerToDialog (dlg->rnaType, &rtd);
 }
 
 static void Add18SITS28SToComment (ButtoN b)
@@ -5149,6 +5126,7 @@ BatchApplyFeatureDetailsDialog (GrouP parent, Int4 feattype, Nlm_ChangeNotifyPro
   Nlm_EnumFieldAssocPtr          ap;
   Int4                           j;
   Boolean                        is_indexer = FALSE;
+  RnaTypeData                    rtd;
   
   dlg = (BatchApplyFeatureDetailsDlgPtr) MemNew (sizeof (BatchApplyFeatureDetailsDlgData));
   if (dlg == NULL)
@@ -5190,11 +5168,10 @@ BatchApplyFeatureDetailsDialog (GrouP parent, Int4 feattype, Nlm_ChangeNotifyPro
   }
   else if (dlg->feattype == ADD_RRNA) 
   {
-    r = HiddenGroup (p, 2, 0, NULL);
-    StaticPrompt (r, "RNA subtype", 0, dialogTextHeight, programFont, 'l');
-    dlg->rnaSubType = PopupList (r, TRUE, NULL);
-    InitEnumPopup (dlg->rnaSubType, rnax_subtype_alist, NULL);
-    SetEnumPopup (dlg->rnaSubType, rnax_subtype_alist, (UIEnum) 4);
+    dlg->rnaType = RnaTypeDialog (p, FALSE, change_notify, change_userdata);
+    rtd.ncrna_class = NULL;
+    rtd.rna_featdef = FEATDEF_rRNA;
+    PointerToDialog (dlg->rnaType, &rtd);
   }
 
   text_group = HiddenGroup (p, 0, 2, NULL);
@@ -5757,6 +5734,41 @@ ApplyOneCodingRegion
   return sfp;
 }
 
+
+typedef struct hasrna {
+  Boolean hasrna;
+  RnaTypePtr rtp;
+} HasRnaData, PNTR HasRnaPtr;
+
+static void AlreadyHasRNACallback (SeqFeatPtr sfp, Pointer userdata)
+{
+  HasRnaPtr hp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || userdata == NULL)
+  {
+    return;
+  }
+
+  hp = (HasRnaPtr) userdata;
+
+  if (!hp->hasrna && MatchesRnaType (sfp, hp->rtp))
+  {
+    hp->hasrna = TRUE;
+  }
+}
+
+
+extern Boolean AlreadyHasRNA (SeqEntryPtr sep, RnaTypePtr rtp)
+{
+  HasRnaData hrd;
+
+  hrd.rtp = NULL;
+  hrd.hasrna = FALSE;
+  VisitFeaturesInSep (sep, &hrd, AlreadyHasRNACallback);
+  return hrd.hasrna;
+}
+
+
 static SeqFeatPtr ApplyOneRNA 
 (BatchApplyFeatureDetailsPtr feature_details_data,
  SeqEntryPtr                 sep, 
@@ -5772,27 +5784,21 @@ static SeqFeatPtr ApplyOneRNA
     return NULL;
   }
   
-  if (suppressDups && entityID > 0 &&
-	     AlreadyHasFeatOrDesc (sep, SEQFEAT_RNA, 0, feature_details_data->rnaSubType))
+  if (suppressDups && entityID > 0 && AlreadyHasRNA (sep, feature_details_data->rnaType))
   {
     return NULL;
   }
   
   rrp = RnaRefNew ();
-  if (rrp == NULL)
-  {
-    return NULL;
-  }
-
-  rrp->type = feature_details_data->rnaSubType;
-  if (! StringHasNoText (feature_details_data->rnaName)) {
-    rrp->ext.choice = 1;
-    rrp->ext.value.ptrvalue = StringSave (feature_details_data->rnaName);
-  }
   sfp = CreateNewFeature (nsep, NULL, SEQFEAT_RNA, NULL);
   if (sfp != NULL) {
     sfp->data.value.ptrvalue = (Pointer) rrp;
   }
+  ApplyRnaTypeToSeqFeat (sfp, feature_details_data->rnaType);
+  if (! StringHasNoText (feature_details_data->rnaName)) {
+    ApplyProductToRNA (sfp, feature_details_data->rnaName);
+  }
+
   return sfp;
 }
 
@@ -6131,7 +6137,10 @@ static void DoApplyFeatureToAlignment (ButtoN b)
                                  &errcount, &ambigList);
         AddProductForCDS (sfp, feature_details_data, sep, nsep, aafdp->entityID);
       }
-      
+      else if (aafdp->feattype == ADD_RRNA)
+      {
+/*        ConvertToOldRNAFormat (sfp); */
+      }
     }
     
     if (sfp != NULL
@@ -6192,10 +6201,7 @@ static void DoApplyFeatureToAlignment (ButtoN b)
     else
     {
       /* add comment */
-      if (!StringHasNoText (feature_details_data->featcomment))
-      {
-        sfp->comment = StringSave (feature_details_data->featcomment);
-      }
+      AddToComment (sfp, feature_details_data->featcomment);
     }
     
     slp_this = slp_next;
diff --git a/desktop/salpanel.h b/desktop/salpanel.h
index 5a8ae5a4..c702126f 100644
--- a/desktop/salpanel.h
+++ b/desktop/salpanel.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/27/96
 *
-* $Revision: 6.16 $
+* $Revision: 6.17 $
 *
 * File Description: 
 *
@@ -51,6 +51,7 @@
 #include <txalign.h>
 #include <explore.h>
 #include <dlogutil.h>
+#include <cdrgn.h>
 
 extern WindoW getwindow_frompanel (PaneL pnl);
 extern PaneL GetPanelFromWindow (WindoW w);
@@ -127,11 +128,11 @@ typedef struct batchapplyfeaturedetails
   CharPtr protName;
   CharPtr protDesc;
   CharPtr rnaName;
+  RnaTypePtr rnaType;
   CharPtr featcomment;
   Int4    featdef_choice;
   CharPtr featdef_name;
   Int4    reading_frame;
-  Int4    rnaSubType;
   
 } BatchApplyFeatureDetailsData, PNTR BatchApplyFeatureDetailsPtr;
 
@@ -148,6 +149,7 @@ extern void SortEnumFieldAssocPtrArray (EnumFieldAssocPtr alist, CompareFunc com
 extern DialoG 
 BatchApplyFeatureDetailsDialog (GrouP parent, Int4 feattype, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
 extern Boolean OkToAcceptBatchApplyFeatureDetails (DialoG d);
+extern Boolean AlreadyHasRNA (SeqEntryPtr sep, RnaTypePtr rtp);
 
 extern void 
 ApplyFeatureToAlignment 
diff --git a/desktop/salsa.c b/desktop/salsa.c
index acb4ad53..5bcb6e2e 100644
--- a/desktop/salsa.c
+++ b/desktop/salsa.c
@@ -28,7 +28,7 @@
 *
 * Version Creation Date:   1/27/96
 *
-* $Revision: 6.180 $
+* $Revision: 6.183 $
 *
 * File Description: 
 *
@@ -2722,21 +2722,7 @@ static void SalsaNewFeaturesMenu (MenU m, Boolean is_na)
               while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT,
                       omtp->datatype, 0, ompp)) != NULL) {
                 subtype = ompp->subinputtype;
-                if (subtype == fdp->featdef_key &&
-                    subtype != FEATDEF_PUB &&
-                    subtype != FEATDEF_IMP &&
-                    subtype != FEATDEF_Imp_CDS &&
-                    subtype != FEATDEF_misc_RNA &&
-                    subtype != FEATDEF_precursor_RNA &&
-                    subtype != FEATDEF_mat_peptide &&
-                    subtype != FEATDEF_sig_peptide &&
-                    subtype != FEATDEF_transit_peptide &&
-                    subtype != FEATDEF_source &&
-                    subtype != FEATDEF_virion &&
-                    subtype != FEATDEF_mutation &&
-                    subtype != FEATDEF_allele &&
-                    subtype != FEATDEF_site_ref &&
-                    subtype != FEATDEF_gap) {
+                if (subtype == fdp->featdef_key && OkToListFeatDefInRemainingFeatures (subtype)) {
                   i = CommandItem (sub, ompp->proclabel, SalsaNewFeatureMenuProc);
                   nfp = (NewFeaturePtr) MemNew (sizeof (NewFeatureData));
                   if (nfp != NULL) {
@@ -6592,6 +6578,24 @@ static Boolean DisplayFarPointerData (FarPointerPtr fpp, Int4 num)
   return acd.accepted;
 }
 
+
+static CharPtr FindFarPointerID (CharPtr str)
+{
+  CharPtr tmp = NULL;
+  if (StringHasNoText (str)) return NULL;
+
+  if (StringNICmp (str, "acc", 3) == 0) {
+    tmp = str + 3;
+  } else {
+    tmp = StringSearch (str, "|acc");
+    if (tmp != NULL) {
+      tmp += 4;
+    }
+  }
+  return tmp;
+}
+
+
 /* This function will replace a sequence in an alignment record with one
  * downloaded from GenBank.  It will also adjust the alignment starts
  * for that sequence if the GenBank sequence is not identical to the
@@ -6640,9 +6644,8 @@ static ValNodePtr CCNormalizeSeqAlignId (SeqAlignPtr salp, ValNodePtr vnp)
 
     /* is this a farpointer ID? */
     SeqIdWrite (far_pointer_list[i].sip_local, str, PRINTID_FASTA_LONG, sizeof (str) - 1);
-    tmp = StringISearch (str, "acc");
+    tmp = FindFarPointerID (str);
     if (tmp!=NULL) {
-      tmp += 3;
       if (*tmp == '|')
          tmp++;   
       id_start = tmp;
@@ -7372,9 +7375,8 @@ static Boolean check_dbid_seqalign (SeqAlignPtr salp)
            sip->next = NULL;
            SeqIdWrite (sip, str, PRINTID_FASTA_LONG, 50);
            sip->next = next;
-           tmp = StringStr (str, "acc");
+           tmp = FindFarPointerID (str);
            if (tmp!=NULL) {
-              tmp++; tmp++; tmp++;
               if (*tmp == '|')
                  tmp++;
               TmpBuff = tmp;
diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c
index b901c260..fd55fa25 100644
--- a/desktop/seqpanel.c
+++ b/desktop/seqpanel.c
@@ -1,4 +1,4 @@
-/* $Id: seqpanel.c,v 6.212 2007/07/18 16:00:17 bollin Exp $
+/* $Id: seqpanel.c,v 6.219 2008/02/28 20:24:30 bollin Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -47,6 +47,7 @@
 #include <algo/blast/api/blast_seqalign.h>
 #include <alignval.h>
 #include <salptool.h>
+#include <vsm.h>
 
 enum ESeqNum   { eNumNone=1, eNumSide=2, eNumTop=3 };
 enum EDrawGrid { eDrawGridOn=1, eDrawGridOff=2 };
@@ -1251,6 +1252,7 @@ static void DrawAlignment
   /* finally draw everything */
   best_id = SeqIdFindBestAccession (bsp->id);
   alnlabel_len = (bvp->SeqStartPosX / bvp->CharWidth) - 10;
+  if (alnlabel_len < 10) alnlabel_len = 10;
   alnlabel = (CharPtr) MemNew (sizeof (Char) * (alnlabel_len + 1)); 
 
   SeqIdWrite (best_id, alnlabel, PRINTID_TEXTID_ACCESSION, alnlabel_len);        /* Get label           */
@@ -2466,11 +2468,12 @@ static void DrawSeqPanel (BioseqViewPtr bvp)
   Int4             aln_idx;
   Int4             start;
   PaneL            p;
+  Int4             vis_seq_start_line, vis_seq_start, vis_seq_stop;
   
   if (bvp == NULL || bvp->bsp == NULL || bvp->SeqPanLines == NULL) return;
   bsp = bvp->bsp;
   p = bvp->seqView;
-  spp = SeqPortNew (bsp, 0, bsp->length-1, Seq_strand_plus, Seq_code_iupacna);
+
   buf = MemNew (SEQ_GROUP_SIZE+1);
   if (bvp->seqAlignMode) { /* allocate it here, to speed up drawing of alignments */
     seqbuf = MemNew (bvp->BlocksAtLine * SEQ_GROUP_SIZE + 3);
@@ -2494,6 +2497,20 @@ static void DrawSeqPanel (BioseqViewPtr bvp)
       aln_idx++;
     }
   }
+
+  splp = bvp->SeqPanLines[line];
+  vis_seq_start_line = splp->bioSeqLine;
+  vis_seq_start = vis_seq_start_line * bvp->CharsAtLine;
+  if (vis_seq_start > bsp->length - 1)
+  {
+    spp = NULL;
+  }
+  else
+  {
+    vis_seq_stop = vis_seq_start + ((r.bottom - 3 * SEQ_Y_OFFSET - r.top) / (bvp->LineHeight == 0 ? 1 : bvp->LineHeight)) * bvp->CharsAtLine;
+    vis_seq_stop = MIN (vis_seq_stop, bsp->length - 1);
+    spp = SeqPortNew (bsp, vis_seq_start, vis_seq_stop, Seq_strand_plus, Seq_code_iupacna); 
+  }
   
   for (line = start; line < bvp->TotalLines  &&  y <= r.bottom-2*SEQ_Y_OFFSET; line++) {
     if (IsInRange(y, updateRect.top,updateRect.bottom) || 
@@ -2512,11 +2529,11 @@ static void DrawSeqPanel (BioseqViewPtr bvp)
           break;
         case eTypeSequence:
           if (GetValue(bvp->newNumControl) != eNumNone) DrawSeqSideLineNumbers(x, y, splp->bioSeqLine, bvp); /* Draw line numbers    */
-          DrawSequence(x, y, splp->bioSeqLine, spp, buf, bvp);                /* Draw the sequence    */
+          DrawSequence(x, y, splp->bioSeqLine - vis_seq_start_line, spp, buf, bvp);                /* Draw the sequence    */
           if (bvp->DrawGrid) DrawLtGrid(x, y+bvp->LineSpace/2, r.right, y+bvp->LineSpace/2);
           break;
         case eTypeSequenceComplement:
-          DrawSequenceComplement(x, y, splp->bioSeqLine, spp, buf, bvp);                       /* Draw the sequence    */
+          DrawSequenceComplement(x, y, splp->bioSeqLine - vis_seq_start_line, spp, buf, bvp);  /* Draw the sequence    */
           if (bvp->DrawGrid) DrawLtGrid(x, y+bvp->LineSpace/2, r.right, y+bvp->LineSpace/2);
           break;
         case eTypeAlignSequence:
@@ -3133,8 +3150,8 @@ GetSeqChapterFeatureInfo
          || (fcontext.left <= chapter_start && fcontext.right > chapter_stop)))
     {
       Boolean coding   = fcontext.seqfeattype == SEQFEAT_CDREGION;
-      Int4    paraFrom = floor(fcontext.left / lineLength);      /* feature starting paragraph */
-      Int4    paraTo   = ceil (fcontext.right / lineLength) + 1;  /* feature ending paragraph   */
+      Int4    paraFrom = (Int4)floor(fcontext.left / lineLength);      /* feature starting paragraph */
+      Int4    paraTo   = (Int4)ceil (fcontext.right / lineLength) + 1;  /* feature ending paragraph   */
       /*BioseqPtr bsp_prot = BioseqFind (SeqLocId(sfp->product));*/
       start = SeqLocStart (sfp->location);
       stop = SeqLocStop (sfp->location);
@@ -3228,7 +3245,7 @@ static void UnindexSeqPanChapter (BioseqViewPtr bvp, ValNodePtr chapter_vnp, Int
   if (chapter_vnp == NULL || bvp == NULL) return;
   
   old_lines = CountChapterLines (chapter_vnp, bvp);
-  num_paragraphs = floor(bvp->bsp->length / bvp->CharsAtLine) + 1; /* sequence length */ 
+  num_paragraphs = (Int4) floor(bvp->bsp->length / bvp->CharsAtLine) + 1; /* sequence length */ 
 
   InitSeqPanChapter ((SeqPanParaPtr) chapter_vnp->data.ptrvalue, 
                      chapter_number * SEQ_PAN_CHAPTER_SIZE, num_paragraphs);
@@ -4743,7 +4760,7 @@ static void SeqEdTranslateAndJournalOneCDS (SeqFeatPtr sfp, SeqEdFormPtr sefp)
   sejp->next = end;
   end->prev = sejp;
   sefp->last_journal_entry = sejp;
-  SeqEdTranslateOneCDS (sfp, sefp->bfp->bvd.bsp, sefp->input_entityID);	
+  SeqEdTranslateOneCDS (sfp, sefp->bfp->bvd.bsp, sefp->input_entityID, Sequin_GlobalAlign2Seq);	
 
   SetUndoRedoStatus (sefp);
 }
@@ -7839,21 +7856,7 @@ static void SeqEdNewFeaturesMenu (MenU m, Boolean is_na)
               while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT,
                       omtp->datatype, 0, ompp)) != NULL) {
                 subtype = ompp->subinputtype;
-                if (subtype == fdp->featdef_key &&
-                    subtype != FEATDEF_PUB &&
-                    subtype != FEATDEF_IMP &&
-                    subtype != FEATDEF_Imp_CDS &&
-                    subtype != FEATDEF_misc_RNA &&
-                    subtype != FEATDEF_precursor_RNA &&
-                    subtype != FEATDEF_mat_peptide &&
-                    subtype != FEATDEF_sig_peptide &&
-                    subtype != FEATDEF_transit_peptide &&
-                    subtype != FEATDEF_source &&
-                    subtype != FEATDEF_virion &&
-                    subtype != FEATDEF_mutation &&
-                    subtype != FEATDEF_allele &&
-                    subtype != FEATDEF_site_ref &&
-                    subtype != FEATDEF_gap) {
+                if (subtype == fdp->featdef_key && OkToListFeatDefInRemainingFeatures (subtype)) {
                   i = CommandItem (sub, ompp->proclabel, SeqEditNewFeatureMenuProc);
                   nfp = (NewFeaturePtr) MemNew (sizeof (NewFeatureData));
                   if (nfp != NULL) {
@@ -9615,349 +9618,6 @@ BioseqPageData seqAlnPnlPageData = {
   NULL, NULL, ResizeSeqView, NULL
 };
 
-/* The following section of code is used for retranslating a CDS and updating
- * the protein features based on an alignment between the old and new protein
- * sequences.
- */
-static Int4 SeqEdRemapCoord (SeqAlignPtr salp, Int4 coord, Boolean move_up, Int4 len)
-
-{
-  Int4 aln_pos;
-  
-  if (salp == NULL) return -1;
-  aln_pos = AlnMgr2MapBioseqToSeqAlign (salp, coord, 1);
-  while (aln_pos == -1)
-  {
-  	if (move_up)
-  	{
-  	  if (coord >= len - 1)
-  	  {
-  	  	return len - 1;
-  	  }
-  	  else
-  	  {
-  	  	coord ++;
-  	  }
-  	}
-  	else
-  	{
-  	  if (coord <= 0)
-  	  {
-  	  	return 0;
-  	  }
-  	  else
-  	  {
-  	  	coord --;
-  	  }
-  	}
-  	aln_pos = AlnMgr2MapBioseqToSeqAlign (salp, coord, 1);
-  }
-  return AlnMgr2MapSeqAlignToBioseq (salp, aln_pos, 2);
-}
-
-
-static void SeqEdRemapSeqIntLoc (SeqAlignPtr salp, SeqIntPtr sintp, Int4 seq_len)
-
-{  
-  if (salp == NULL || sintp == NULL) return;
-  sintp->from = SeqEdRemapCoord (salp, sintp->from, TRUE, seq_len);
-  sintp->to = SeqEdRemapCoord (salp, sintp->to, FALSE, seq_len); 
-}
-
-static void SeqEdRemapSeqPntLoc (SeqAlignPtr salp, SeqPntPtr spp, Int4 seq_len)
-
-{  
-  if (salp == NULL || spp == NULL) return;
-  
-  spp->point = SeqEdRemapCoord (salp, spp->point, FALSE, seq_len);
-}
-
-
-static void SeqEdRemapPackSeqPnt (SeqAlignPtr salp, PackSeqPntPtr pspp, Int4 seq_len)
-
-{
-  Uint1          used;
-
-  if (salp == NULL || pspp == NULL) return;
-  for (used = 0; used < pspp->used; used++) 
-  {
-    pspp->pnts [used] = SeqEdRemapCoord (salp, pspp->pnts [used], FALSE, seq_len);
-  }
-}
-
-
-NLM_EXTERN void SeqEdRemapLocation (SeqAlignPtr salp, SeqLocPtr slp, Int4 seq_len)
-
-{
-
-  if (slp == NULL) return;
-  switch (slp->choice) {
-    case SEQLOC_INT :
-      SeqEdRemapSeqIntLoc (salp, slp->data.ptrvalue, seq_len);
-      break;
-    case SEQLOC_PNT :
-      SeqEdRemapSeqPntLoc (salp, slp->data.ptrvalue, seq_len);
-      break;
-    case SEQLOC_PACKED_PNT :
-      SeqEdRemapPackSeqPnt (salp, slp->data.ptrvalue, seq_len);
-      break;
-    default :
-      break;
-  }
-}
-
-static void MakeLocationMatchEntireSequence (SeqLocPtr slp, BioseqPtr bsp)
-{
-  SeqIntPtr sip;
-  
-  if (slp == NULL || bsp == NULL) return;
-  
-  if (slp->choice == SEQLOC_WHOLE)
-  {
-  	SeqIdFree (slp->data.ptrvalue);
-  	slp->data.ptrvalue = SeqIdDup (bsp->id);
-  }
-  else if (slp->choice == SEQLOC_INT)
-  {
-    sip = (SeqIntPtr) slp->data.ptrvalue;
-    if (sip == NULL)
-    {
-      sip = SeqIntNew ();
-      slp->data.ptrvalue = sip;
-    }
-    if (sip != NULL)
-    {
-      sip->from = 0;
-      sip->to = bsp->length - 1;
-    }
-  }
-}
-
-NLM_EXTERN Boolean SeqEdFixProteinFeatures (BioseqPtr oldbsp, BioseqPtr newbsp, Boolean force_fix)
-{
-  SeqAlignPtr       salp = NULL;
-  Boolean           revcomp = FALSE;
-  SeqFeatPtr        sfp;
-  SeqMgrFeatContext fcontext;
-  Boolean           tried_to_get_alignment = FALSE;
-  Boolean           unmappable_feats = FALSE;
-  SeqLocPtr         slp_tmp = NULL;
-  
-  if (oldbsp == NULL || newbsp == NULL) return FALSE;
-
-  /* get alignment between old and new proteins */
-
-  if (ISA_na (oldbsp->mol) != ISA_na (newbsp->mol)) return FALSE;
-
-  /* iterate through the features on the old protein.  Full length features
-   * should be set to the new length.  Other features should be mapped through
-   * the alignment (if possible), otherwise warn the user that they could not
-   * be remapped. */      
-
-  if (!force_fix)
-  {
-    for (sfp = SeqMgrGetNextFeature (oldbsp, NULL, 0, 0, &fcontext);
-         sfp != NULL && !unmappable_feats;
-         sfp = SeqMgrGetNextFeature (oldbsp, sfp, 0, 0, &fcontext))
-    {
-      if (sfp->idx.subtype != FEATDEF_PROT)
-      {
-        if (salp == NULL)
-        {
-          salp = Sequin_GlobalAlign2Seq (oldbsp, newbsp, &revcomp);
-        }
-        if (salp == NULL)
-        {
-          unmappable_feats = TRUE;
-        } 
-        else
-        {
-          slp_tmp = (SeqLocPtr) AsnIoMemCopy (sfp->location,
-                                              (AsnReadFunc) SeqLocAsnRead,
-                                              (AsnWriteFunc) SeqLocAsnWrite);
-          SeqEdRemapLocation (salp, slp_tmp, newbsp->length);	  	  	
-          if (slp_tmp == NULL)
-          {
-            unmappable_feats = TRUE;
-          }
-          else
-          {
-            slp_tmp = SeqLocFree (slp_tmp);
-          }
-        }
-      }
-    }
-    if (unmappable_feats)
-    {
-      return FALSE;
-    }
-  }
-  
-  for (sfp = SeqMgrGetNextFeature (oldbsp, NULL, 0, 0, &fcontext);
-       sfp != NULL;
-       sfp = SeqMgrGetNextFeature (oldbsp, sfp, 0, 0, &fcontext))
-  {
-    if (sfp->idx.subtype == FEATDEF_PROT)
-    {
-      /* make new location match new sequence length */
-      MakeLocationMatchEntireSequence (sfp->location, newbsp);
-    }
-    else
-    {
-      if (salp == NULL && !tried_to_get_alignment)
-      {
-        salp = Sequin_GlobalAlign2Seq (oldbsp, newbsp, &revcomp);
-        tried_to_get_alignment = TRUE;
-      }
-      if (salp != NULL)
-      {
-        SeqEdRemapLocation (salp, sfp->location, newbsp->length);	  	  	
-      }
-      else
-      {
-        unmappable_feats = TRUE;
-      }
-    }
-  } 
-        
-  if (salp != NULL)
-  {
-    SeqAlignFree (salp);
-  }
-  if (unmappable_feats)
-  {
-    return FALSE;
-  }
-  else
-  {
-    return TRUE;
-  }
-}
-
-
-NLM_EXTERN void SeqEdTranslateOneCDS (SeqFeatPtr sfp, BioseqPtr featbsp, Uint2 entityID)
-{
-  ByteStorePtr  bs;
-  Char          ch;
-  CharPtr       prot;
-  CharPtr       ptr;
-  Int4          star_at_end = 0;
-  BioseqPtr     old_prot;
-  SeqIdPtr      new_prot_id;
-  SeqEntryPtr   parent, new_prot_sep;
-  SeqLocPtr     slp;
-  Uint1         seq_data_type;
-  Int4          old_length;
-  BioseqPtr     newbsp;
-  ProtRefPtr    prp;
-  SeqFeatPtr    prot_sfp;
-  SeqDataPtr    sdp;
-  
-  if (featbsp == NULL || sfp == NULL || sfp->location == NULL 
-      || sfp->data.choice != SEQFEAT_CDREGION) 
-  {
-  	return;
-  }
-  
-  old_prot = BioseqFindFromSeqLoc (sfp->product);
-  new_prot_id = SeqIdDup (SeqLocId (sfp->product));
-  if (new_prot_id == NULL)
-  {
-  	new_prot_id = MakeNewProteinSeqId (sfp->location, featbsp->id);
-  }
-  	
-  bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
-  if (bs != NULL) {
-    prot = BSMerge (bs, NULL);
-    bs = BSFree (bs);
-    if (prot != NULL) {
-      ptr = prot;
-      ch = *ptr;
-      while (ch != '\0') {
-        *ptr = TO_UPPER (ch);
-        if (ch == '*') {
-          star_at_end = 1;
-        } else {
-          star_at_end = 0;
-        }
-        ptr++;
-        ch = *ptr;
-      }
-      if (star_at_end)
-      {
-      	*(ptr - 1) = 0;
-      }
-      bs = BSNew (1000);
-      if (bs != NULL) {
-        ptr = prot;
-        BSWrite (bs, (VoidPtr) ptr, (Int4) StringLen (ptr));
-      }
-      MemFree (prot);
-    }
-    newbsp = BioseqNew ();
-    if (newbsp != NULL) {
-      newbsp->id = SeqIdParse ("lcl|CdRgnTransl");
-      newbsp->repr = Seq_repr_raw;
-      newbsp->mol = Seq_mol_aa;
-      newbsp->seq_data_type = Seq_code_ncbieaa;
-      newbsp->seq_data = (SeqDataPtr) bs;
-      newbsp->length = BSLen (bs);
-      
-      if (old_prot == NULL)
-      {
-  	    /* need to create a new protein sequence */
-  	    SeqIdFree (newbsp->id);
-  	    newbsp->id = new_prot_id;
-  	    new_prot_sep = SeqEntryNew ();
-  	    new_prot_sep->choice = 1;
-  	    new_prot_sep->data.ptrvalue = newbsp;
-  	    parent = GetBestTopParentForData (entityID, featbsp);
-  	    if (parent != NULL)
-  	    {
-  	      AddSeqEntryToSeqEntry (parent, new_prot_sep, TRUE);
-  	    }
-  	    slp = ValNodeNew (NULL);
-  	    if (slp != NULL)
-  	    {
-  	      slp->choice = SEQLOC_WHOLE;
-  	      slp->data.ptrvalue = SeqIdDup (new_prot_id);
-  	    }
-  	    sfp->product = slp;
-  	    
-  	    /* create full length protein feature */
-        prp = ProtRefNew ();
-        prot_sfp = CreateNewFeature (new_prot_sep, NULL, SEQFEAT_PROT, NULL);
-        if (prot_sfp != NULL) {
-          prot_sfp->data.value.ptrvalue = (Pointer) prp;
-        }
-      }
-      else
-      {
-        /* propagate features to new protein */
-        if (!SeqEdFixProteinFeatures (old_prot, newbsp, TRUE))
-        {
-          Message (MSG_ERROR, "Unable to construct alignment between old and new "
-                  "proteins - you will need to adjust the protein features "
-                  "manually.");
-        }
-             	
-      	/* then replace old protein with new */
-      	seq_data_type = old_prot->seq_data_type;
-      	sdp = old_prot->seq_data;
-      	old_length = old_prot->length;
-      	old_prot->seq_data_type = newbsp->seq_data_type;
-      	old_prot->seq_data = newbsp->seq_data;
-      	old_prot->length = newbsp->length;
-      	newbsp->seq_data_type = seq_data_type;
-      	newbsp->seq_data = sdp;
-      	newbsp->length = old_length;
-      	BioseqFree (newbsp);
-      }
-    }
-  }
-}
-
-
 #define SEQ_ED_TRANSLATE_BUFFER_SIZE 32000
 NLM_EXTERN SeqEdJournalPtr SeqEdJournalNewTranslate
 (SeqFeatPtr sfp,
@@ -10108,7 +9768,7 @@ static Boolean PlayOneTranslationJournalEntry (SeqEdJournalPtr sejp)
     AsnIoMemClose(aimp);					  /* close it */    
   }
   	
-  SeqEdTranslateOneCDS (sejp->sfp, sejp->bsp, sejp->entityID);	
+  SeqEdTranslateOneCDS (sejp->sfp, sejp->bsp, sejp->entityID, Sequin_GlobalAlign2Seq);	
   return TRUE;
 }
 
diff --git a/desktop/seqpanel.h b/desktop/seqpanel.h
index 2cd617d6..82201279 100644
--- a/desktop/seqpanel.h
+++ b/desktop/seqpanel.h
@@ -1,4 +1,4 @@
-/* $Id: seqpanel.h,v 6.17 2006/12/05 13:49:46 bollin Exp $
+/* $Id: seqpanel.h,v 6.18 2007/11/30 14:32:28 bollin Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -54,9 +54,6 @@ WriteAlignmentInterleaveToFileEx
 
 extern ForM CreateSeqEditorWindow (Int2 left, Int2 top, CharPtr windowname, BioseqPtr bsp);
 
-NLM_EXTERN void SeqEdTranslateOneCDS (SeqFeatPtr sfp, BioseqPtr featbsp, Uint2 entityID);
-NLM_EXTERN void SeqEdRemapLocation (SeqAlignPtr salp, SeqLocPtr slp, Int4 seq_len);
-NLM_EXTERN Boolean SeqEdFixProteinFeatures (BioseqPtr oldbsp, BioseqPtr newbsp, Boolean force_fix);
 NLM_EXTERN SeqAlignPtr Sequin_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp);
 extern ForM CreateAlnEditorWindow (Int2 left, Int2 top, CharPtr windowname, SeqAlignPtr salp, Uint2 entityID);
 NLM_EXTERN CharPtr FeatureLocationAlignment (SeqFeatPtr sfp, SeqAlignPtr salp, Int4 begin, Int4 fin);
diff --git a/desktop/seqsub.c b/desktop/seqsub.c
index d3e19864..9d6d0df5 100644
--- a/desktop/seqsub.c
+++ b/desktop/seqsub.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.34 $
+* $Revision: 6.36 $
 *
 * File Description: 
 *
@@ -3763,6 +3763,122 @@ static Boolean GetBioSourceFromSeqSubmit (SeqSubmitPtr ssp, BioSourcePtr PNTR pb
   return rval;
 }
 
+
+static CitSubPtr GetCitSubFromPub (PubdescPtr pdp)
+{
+  ValNodePtr   vnp;
+  CitSubPtr    cit = NULL;
+
+  if (pdp == NULL) return NULL;
+  for (vnp = pdp->pub; vnp != NULL && cit == NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == PUB_Sub)
+    {
+      cit = vnp->data.ptrvalue;
+    }
+  }
+  return cit;
+}
+
+
+static ContactInfoPtr ContactInfoFromAuthList (AuthListPtr auth_list)
+{
+  ContactInfoPtr contact_info = NULL;
+  AffilPtr       affil = NULL;
+  ValNodePtr     vnp;
+  AuthorPtr      author = NULL;
+
+  if (auth_list == NULL) return NULL;
+
+  for (vnp = auth_list->names; vnp != NULL && author == NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == 1)
+    {
+      author = vnp->data.ptrvalue;
+    }
+  }
+
+  if (author != NULL)
+  {
+    contact_info = ContactInfoNew();
+    contact_info->contact = (AuthorPtr) AsnIoMemCopy (author, (AsnReadFunc) AuthorAsnRead, (AsnWriteFunc) AuthorAsnWrite);
+    if (contact_info->contact->affil == NULL && auth_list->affil != NULL)
+    {
+      contact_info->contact->affil = (AffilPtr) AsnIoMemCopy (auth_list->affil, (AsnReadFunc) AffilAsnRead, (AsnWriteFunc) AffilAsnWrite);
+    }
+  }
+
+  return contact_info;
+}
+
+
+static SubmitBlockPtr SubmitBlockFromSeqEntry (SeqEntryPtr sep)
+{
+  BioseqPtr    bsp;
+  BioseqSetPtr bssp;
+  SeqDescrPtr  sdp = NULL;
+  CitSubPtr    cit = NULL;
+  SubmitBlockPtr sbp = NULL;
+
+  if (sep == NULL || sep->data.ptrvalue == NULL) return NULL;
+  if (IS_Bioseq (sep))
+  {
+    bsp = (BioseqPtr) sep->data.ptrvalue;
+    sdp = bsp->descr;
+  }
+  else if (IS_Bioseq_set (sep))
+  {
+    bssp = (BioseqSetPtr) sep->data.ptrvalue;
+    sdp = bssp->descr;
+  }
+  while (sdp != NULL && cit == NULL)
+  {
+    if (sdp->choice == Seq_descr_pub && sdp->data.ptrvalue != NULL)
+    {
+      cit = GetCitSubFromPub (sdp->data.ptrvalue);
+    }
+    sdp = sdp->next;
+  }
+      
+  if (cit != NULL)
+  { 
+    sbp = SubmitBlockNew ();
+    sbp->cit = (CitSubPtr) AsnIoMemCopy (cit, (AsnReadFunc) CitSubAsnRead, (AsnWriteFunc) CitSubAsnWrite);
+    sbp->contact = ContactInfoFromAuthList (sbp->cit->authors);
+  }
+  
+  return sbp;
+}
+
+
+static void ListDescriptorsCallback (SeqDescrPtr sdp, Pointer data, Uint1 desc_choice)
+{
+  SeqDescrPtr tmp;
+
+  if (sdp != NULL && sdp->choice == desc_choice && data != NULL)
+  {
+    if (sdp->choice != Seq_descr_pub 
+        || GetCitSubFromPub (sdp->data.ptrvalue) == NULL)
+    {
+      tmp = sdp->next;
+      sdp->next = NULL;
+      ValNodeLink ((ValNodePtr PNTR) data, AsnIoMemCopy (sdp, (AsnReadFunc) SeqDescrAsnRead, (AsnWriteFunc) SeqDescrAsnWrite));
+      sdp->next = tmp;
+    }
+  }
+}
+
+
+static void ListCommentsCallback (SeqDescrPtr sdp, Pointer data)
+{
+  ListDescriptorsCallback (sdp, data, Seq_descr_comment);
+}
+
+static void ListPubsCallback (SeqDescrPtr sdp, Pointer data)
+{
+  ListDescriptorsCallback (sdp, data, Seq_descr_pub);
+}
+
 static Boolean ImportSeqSubmitForm (ForM f, CharPtr filename)
 {
   SubmitTemplateEditorPtr dlg;
@@ -3773,11 +3889,12 @@ static Boolean ImportSeqSubmitForm (ForM f, CharPtr filename)
   Uint2                   datatype;
   Uint2                   entityID;
   FILE                    *fp;
-  SubmitBlockPtr          sbp = NULL;
+  SubmitBlockPtr          sbp = NULL, t_sbp;
   SeqDescrPtr             sdp_comment, sdp_pub = NULL;
   CharPtr                 comment = NULL;
   BioSourcePtr            biop = NULL;
   MolInfoPtr              mip = NULL;
+  SeqEntryPtr             sep = NULL;
   
   dlg = (SubmitTemplateEditorPtr) GetObjectExtra (f);
   if (dlg == NULL)
@@ -3851,6 +3968,44 @@ static Boolean ImportSeqSubmitForm (ForM f, CharPtr filename)
         sbp = (SubmitBlockPtr) dataptr;
       }
     }
+    else if (datatype == OBJ_SEQENTRY)
+    {
+      sep = (SeqEntryPtr) dataptr;
+      t_sbp = SubmitBlockFromSeqEntry (sep);
+      if (t_sbp != NULL)
+      {
+        if (sbp != NULL)
+        {
+          Message (MSG_ERROR, "Found more than one SubmitBlock!  Bad file!");
+          bad_data_found = TRUE;
+        }
+        else if (ssp != NULL)
+        {
+          Message (MSG_ERROR, "Found Separate SeqSubmit and SubmitBlock!  Bad file!");
+          bad_data_found = TRUE;
+        }
+        else
+        {
+          sbp = t_sbp;
+          VisitDescriptorsInSep (sep, &sdp_pub, ListPubsCallback);
+          sdp_comment = NULL;
+          VisitDescriptorsInSep (sep, &sdp_comment, ListCommentsCallback);
+          if (sdp_comment != NULL)
+          {
+            if (comment != NULL)
+            {
+              Message (MSG_ERROR, "Found more than one comment!  Cannot edit this file!");
+              bad_data_found = TRUE;
+            }
+            else
+            {
+              comment = StringSave (sdp_comment->data.ptrvalue);
+            }
+            sdp_comment = SeqDescrFree (sdp_comment);
+          }
+        }
+      }
+    }
     else if (datatype == OBJ_SEQDESC)
     {
       sdp_comment = (SeqDescrPtr) dataptr;
diff --git a/desktop/vsm.c b/desktop/vsm.c
index d5ba0196..4d49c64e 100644
--- a/desktop/vsm.c
+++ b/desktop/vsm.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   11-29-94
 *
-* $Revision: 6.31 $
+* $Revision: 6.37 $
 *
 * File Description: 
 *
@@ -561,6 +561,35 @@ Boolean LIBCALL VSMAddToMenu (MenU m, Int2 menutype)
 	return TRUE;
 }
 
+NLM_EXTERN Boolean OkToListFeatDefInRemainingFeatures (Uint2 subtype)
+{
+  if (subtype != FEATDEF_PUB &&
+      subtype != FEATDEF_IMP &&
+      subtype != FEATDEF_Imp_CDS &&
+      subtype != FEATDEF_misc_RNA &&
+      subtype != FEATDEF_precursor_RNA &&
+      subtype != FEATDEF_mat_peptide &&
+      subtype != FEATDEF_sig_peptide &&
+      subtype != FEATDEF_transit_peptide &&
+      subtype != FEATDEF_source &&
+      subtype != FEATDEF_virion &&
+      subtype != FEATDEF_mutation &&
+      subtype != FEATDEF_allele &&
+      subtype != FEATDEF_site_ref &&
+      subtype != FEATDEF_old_sequence &&
+      subtype != FEATDEF_5clip &&
+      subtype != FEATDEF_3clip &&
+      subtype != FEATDEF_repeat_unit &&
+      subtype != FEATDEF_snRNA &&
+      subtype != FEATDEF_scRNA &&
+      subtype != FEATDEF_snoRNA &&
+      subtype != FEATDEF_gap) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
 /*****************************************************************************
 *
 *   VSMAddMenu(WindoW w, Int2 menutype)
@@ -694,36 +723,22 @@ Boolean LIBCALL VSMAddMenu (WindoW w, Int2 menutype)
 						}
 					}
 				}
-                sub2 = SubMenu (sub, "Remaining Features");
-                fdp = NULL;
-                while ((fdp = FeatDefFindNext (fdp, &key, &label, 0, FALSE)) != NULL) {
-                  if (key != FEATDEF_BAD) {
-                    ompp = NULL;
-                    while ((ompp = ObjMgrProcFindNext (omp, proctype,
-				            omtp->datatype, 0, ompp)) != NULL) {
+        sub2 = SubMenu (sub, "Remaining Features");
+        fdp = NULL;
+        while ((fdp = FeatDefFindNext (fdp, &key, &label, 0, FALSE)) != NULL) {
+          if (key != FEATDEF_BAD) {
+            ompp = NULL;
+            while ((ompp = ObjMgrProcFindNext (omp, proctype,
+				                                        omtp->datatype, 0, ompp)) != NULL) {
 				      subtype = ompp->subinputtype;
-                      if (subtype == fdp->featdef_key &&
-                          subtype != FEATDEF_PUB &&
-                          subtype != FEATDEF_IMP &&
-                          subtype != FEATDEF_Imp_CDS &&
-                          subtype != FEATDEF_misc_RNA &&
-                          subtype != FEATDEF_precursor_RNA &&
-                          subtype != FEATDEF_mat_peptide &&
-                          subtype != FEATDEF_sig_peptide &&
-                          subtype != FEATDEF_transit_peptide &&
-                          subtype != FEATDEF_source &&
-                          subtype != FEATDEF_virion &&
-                          subtype != FEATDEF_mutation &&
-                          subtype != FEATDEF_allele &&
-                          subtype != FEATDEF_site_ref &&
-                          subtype != FEATDEF_gap) {
-                        i = CommandItem (sub2, ompp->proclabel, VSeqMgrStdMenuProc);
-                        SetObjectExtra(i, (VoidPtr)ompp, NULL);
-                        ctr++;
-                      }
-                    }
-                  }
-                }
+              if (subtype == fdp->featdef_key && OkToListFeatDefInRemainingFeatures (subtype)) {
+                i = CommandItem (sub2, ompp->proclabel, VSeqMgrStdMenuProc);
+                SetObjectExtra(i, (VoidPtr)ompp, NULL);
+                ctr++;
+              }
+            }
+          }
+        }
 			} else {
 				sub = SubMenu (m, omtp->label);
 				do
@@ -966,7 +981,7 @@ static Boolean IsSeqEntryInAlignment (SeqAlignPtr salp, SeqEntryPtr sep)
 
 static void FindAlignmentCallback (SeqAnnotPtr sap, Pointer userdata)
 {
-    WarnIfAlignmentPtr wiap;
+  WarnIfAlignmentPtr wiap;
 	SeqAlignPtr        salp;
 
 	if (sap == NULL || sap->type != 2 || userdata == NULL) {
@@ -974,11 +989,33 @@ static void FindAlignmentCallback (SeqAnnotPtr sap, Pointer userdata)
 	}
 	wiap = (WarnIfAlignmentPtr) userdata;
 	if (wiap->found) return;
-    salp = (SeqAlignPtr) sap->data;
+  salp = (SeqAlignPtr) sap->data;
 	if (salp == NULL) return;
 	wiap->found = IsSeqEntryInAlignment (salp, wiap->lookingfor);
 }
 
+
+static void RemoveSeqEntryFromAlignments (SeqEntryPtr topsep, SeqEntryPtr sep)
+{
+	BioseqPtr bsp;
+	BioseqSetPtr bssp;
+	Boolean found = FALSE;
+	SeqEntryPtr this_sep;
+
+	if (IS_Bioseq (sep)) {
+		bsp = (BioseqPtr) sep->data.ptrvalue;
+    RemoveSequenceFromAlignments (topsep, bsp->id);
+	} else if (IS_Bioseq_set (sep)) {
+		bssp = (BioseqSetPtr) sep->data.ptrvalue;
+		for (this_sep = bssp->seq_set;
+			this_sep != NULL && !found;
+			this_sep = this_sep->next) {
+      RemoveSeqEntryFromAlignments (topsep, this_sep);
+	  }
+	}
+}
+
+
 static void WarnIfAlignment (Uint2 type, Pointer ptr, Uint2 input_entityID)
 {
 	SeqEntryPtr sep;
@@ -996,7 +1033,9 @@ static void WarnIfAlignment (Uint2 type, Pointer ptr, Uint2 input_entityID)
 
 	VisitAnnotsInSep (topsep, &wiad, FindAlignmentCallback);
 	if (wiad.found) {
-	    Message (MSG_OK, "Warning - this sequence is part of an alignment.");
+	  if (ANS_YES == Message (MSG_YN, "This sequence is part of an alignment.  Would you like to remove it from the alignment?")) {
+      RemoveSeqEntryFromAlignments (topsep, sep);
+    }
 	}
 }
 
diff --git a/desktop/vsm.h b/desktop/vsm.h
index 0407605f..4f313d84 100644
--- a/desktop/vsm.h
+++ b/desktop/vsm.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   11-29-94
 *
-* $Revision: 6.1 $
+* $Revision: 6.2 $
 *
 * File Description: 
 *
@@ -125,6 +125,8 @@ Boolean LIBCALL VSMAddMenu PROTO((WindoW w, Int2 menutype));
 #define VSM_VIEW_MENU 3     /* viewers */
 #define VSM_EDIT_MENU 4     /* editors */
 
+NLM_EXTERN Boolean OkToListFeatDefInRemainingFeatures (Uint2 subtype);
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/desktop/vsmfile.c b/desktop/vsmfile.c
index 4fc0f1b4..957c4e07 100644
--- a/desktop/vsmfile.c
+++ b/desktop/vsmfile.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   11-29-94
 *
-* $Revision: 6.20 $
+* $Revision: 6.22 $
 *
 * File Description: 
 *
@@ -73,6 +73,9 @@ Boolean LIBCALL VSMFileInit(void)
                            VSMGenericTextAsnOpen, PROC_PRIORITY_DEFAULT);
    
                          /*** SAVE ***/   
+  ObjMgrProcLoad(OMPROC_SAVE, "Save Descriptor File", "Descriptor file", 0,0,0,0,NULL,
+                           VSMDescriptorAsnSave, PROC_PRIORITY_DEFAULT);
+                           
 	ObjMgrProcLoad(OMPROC_SAVE, "Export Protein Feature Table","Protein Feature Table", 0,0,0,0,NULL,
                            VSMExportProteinFeatureTable, PROC_PRIORITY_DEFAULT);
 
@@ -138,7 +141,7 @@ Boolean LIBCALL VSMFileInit(void)
                            
 	ObjMgrProcLoad(OMPROC_SAVE, "Save As Text ASN1 File","ASN.1 text file", 0,0,0,0,NULL,
                            VSMGenericTextAsnSave, PROC_PRIORITY_DEFAULT);
-                           
+
 	return TRUE;
 }
 
@@ -1171,3 +1174,135 @@ Int2 LIBCALLBACK VSMGenericBinAsnSave ( Pointer data )
 }
 
 
+static Boolean AddToSaveList (GatherContextPtr gcp)
+
+{
+  ValNodePtr PNTR list;
+
+  list = (ValNodePtr PNTR) gcp->userdata;
+  if (list == NULL) return TRUE;
+  ValNodeAddPointer (list, gcp->thistype, gcp->thisitem);
+  return TRUE;
+}
+
+
+typedef struct savesetsdp {
+  AsnIoPtr aip;
+  Boolean  already_have_molinfo;  
+} SaveSetSdpData, PNTR SaveSetSdpPtr;
+
+
+static void SaveSetDescriptors (SeqDescrPtr sdp, Pointer userdata)
+{
+  SaveSetSdpPtr sp;
+  MolInfoPtr    mip;
+
+  if (sdp == NULL || userdata == NULL) return;
+  if (sdp->choice != Seq_descr_source
+      && sdp->choice != Seq_descr_pub
+      && sdp->choice != Seq_descr_molinfo
+      && sdp->choice != Seq_descr_comment) return;
+
+  sp = (SaveSetSdpPtr) userdata;
+  if (sdp->choice == Seq_descr_molinfo
+      && (mip = (MolInfoPtr) sdp->data.ptrvalue) != NULL)
+  {
+    if (mip->biomol == MOLECULE_TYPE_PEPTIDE || sp->already_have_molinfo) 
+    {
+      return;
+    }
+    else
+    {
+      sp->already_have_molinfo = TRUE;
+    }
+  }
+  SeqDescAsnWrite (sdp, sp->aip, NULL);
+  AsnPrintNewLine (sp->aip);
+  AsnIoFlush (sp->aip);
+}
+
+Int2 LIBCALLBACK VSMDescriptorAsnSave (Pointer data)
+{
+  OMProcControlPtr ompcp;
+  Char filename[255];
+  SelStructPtr  ssp, sel;
+  SeqDescrPtr   sdp;
+  BioseqPtr     bsp;
+  SeqEntryPtr   sep;
+  SeqMgrDescContext dcontext;
+#ifdef WIN_MAC
+  FILE * fp;
+#endif
+  ValNodePtr entity_list = NULL, vnp;
+  SaveSetSdpData sd;
+  ValNodePtr obj_list = NULL;
+
+  ompcp = (OMProcControlPtr)data;
+  if (ompcp == NULL) return OM_MSG_RET_ERROR;
+
+  sd.already_have_molinfo = FALSE;
+  ssp = ObjMgrGetSelected();
+  if (ssp == NULL)
+	{
+    Message (MSG_ERROR, "You must select a sequence or set from which descriptors should be saved");
+    return OM_MSG_RET_DONE;
+  } else {
+	  for (sel = ssp; sel != NULL; sel = sel->next)
+	  {
+      GatherItem (sel->entityID, sel->itemID, sel->itemtype,
+                (Pointer) &obj_list, AddToSaveList);
+    }
+  }
+
+  /* get file name to use */	
+	filename[0] = '\0';
+	if (GetOutputFileName(filename, (size_t)254, NULL))
+	{
+		WatchCursor();
+#ifdef WIN_MAC
+		fp = FileOpen (filename, "r");
+		if (fp != NULL) {
+			FileClose (fp);
+		} else {
+			FileCreate (filename, "TEXT", "ttxt");
+		}
+#endif
+
+		sd.aip = AsnIoOpen(filename, "w");
+	  for (vnp = obj_list; vnp != NULL; vnp = vnp->next)
+	  {
+      switch (vnp->choice) {
+        case OBJ_SEQDESC:
+          sdp = (SeqDescrPtr) vnp->data.ptrvalue;
+          SeqDescAsnWrite (sdp, sd.aip, NULL);
+          AsnPrintNewLine (sd.aip);
+          AsnIoFlush (sd.aip);
+          break;
+        case OBJ_BIOSEQ:
+          bsp = (BioseqPtr) vnp->data.ptrvalue;
+          for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
+               sdp != NULL;
+               sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext)) {
+            if (sdp->choice != Seq_descr_source
+                && sdp->choice != Seq_descr_pub
+                && sdp->choice != Seq_descr_molinfo
+                && sdp->choice != Seq_descr_comment) continue;
+            SeqDescAsnWrite (sdp, sd.aip, NULL);
+            AsnPrintNewLine (sd.aip);
+            AsnIoFlush (sd.aip);
+          }
+          break;
+        case OBJ_BIOSEQSET:
+          sep = SeqMgrGetSeqEntryForData (vnp->data.ptrvalue);
+          VisitDescriptorsInSep (sep, &sd, SaveSetDescriptors);
+          break;
+      }              
+    }   
+		AsnIoClose(sd.aip);
+		ArrowCursor();
+	}
+	
+	return OM_MSG_RET_DONE;  
+}
+
+
diff --git a/desktop/vsmfile.h b/desktop/vsmfile.h
index 32cfa81c..426c43e7 100644
--- a/desktop/vsmfile.h
+++ b/desktop/vsmfile.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   11-29-94
 *
-* $Revision: 6.6 $
+* $Revision: 6.7 $
 *
 * File Description: 
 *
@@ -84,6 +84,7 @@ Int2 LIBCALLBACK VSMExportNucFeatureTableSelectedFeatures (Pointer data);
 Int2 LIBCALLBACK VSMExportNucFeatureTableSelectedFeaturesSuppressProteinIDs (Pointer data);
 Int2 LIBCALLBACK VSMExportProteinFeatureTable (Pointer data);
 Int2 LIBCALLBACK VSMFastaSortedProtSave (Pointer data);
+Int2 LIBCALLBACK VSMDescriptorAsnSave (Pointer data);
 NLM_EXTERN void ViewSortedProteins (SeqEntryPtr sep);
 
 extern void ExportSeqAnnotFeatureTable (FILE *fp, SeqAnnotPtr sap);
diff --git a/desktop/vsmutil.c b/desktop/vsmutil.c
index fb09c052..71189ef5 100644
--- a/desktop/vsmutil.c
+++ b/desktop/vsmutil.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   3/3/95
 *
-* $Revision: 6.47 $
+* $Revision: 6.55 $
 *
 * File Description: 
 *
@@ -114,6 +114,19 @@ typedef struct validextra {
   FormActnFunc   revalProc;
   ButtoN         revalBtn;
   Boolean        okaytosetviewtarget;
+  Boolean        indexerVersion;
+  Int2           selected_text_start_item;
+  Int2           selected_text_start_col;
+  Int2           selected_text_start_row;
+  Int4           selected_text_start_offset;
+  Int2           selected_text_end_item;
+  Int2           selected_text_end_col;
+  Int2           selected_text_end_row;
+  Int4           selected_text_end_offset;
+  Int2           selected_text_anchor_item;
+  Int2           selected_text_anchor_col;
+  Int2           selected_text_anchor_row;
+  Int4           selected_text_anchor_offset;
 } ValidExtra, PNTR ValidExtraPtr;
 
 static WindoW  validWindow = NULL;
@@ -156,6 +169,71 @@ static void InvalBorder (DoC d, Int2 item)
   }
 }
 
+
+static Int2 val_columns_for_copy[] = {1, 2, 3, 5};
+
+static void DrawTextSelection (DoC doc, ValidExtraPtr vep, Int2 item, RectPtr r)
+{
+  Int2 lineHeight, numRows, numCols;
+  Int2 last_right;
+  Int2 left_start;
+  Int4 top, line_y;
+  CharPtr txt;
+
+  if (vep == NULL || r == NULL
+      || item < vep->selected_text_start_item
+      || item > vep->selected_text_end_item) {
+    return;
+  }
+
+  if (vep->selected_text_start_item == vep->selected_text_end_item
+      && vep->selected_text_start_row == vep->selected_text_end_row
+      && vep->selected_text_start_offset == vep->selected_text_end_offset) {
+    /* if we've only selected one char, and it's blank, don't draw it. */
+    txt = GetSelectedDocText (doc, vep->selected_text_start_item, vep->selected_text_start_row,
+                              vep->selected_text_start_col, vep->selected_text_start_offset,
+                              vep->selected_text_end_item, vep->selected_text_end_row,
+                              vep->selected_text_end_col, vep->selected_text_end_offset,
+                              val_columns_for_copy, sizeof (val_columns_for_copy));
+    if (StringHasNoText (txt)) {
+      MemFree (txt);
+      return;
+    }
+    MemFree (txt);
+  }
+
+  GetItemParams4 (doc, item, &top, &numRows, &numCols, &lineHeight, NULL);
+
+  /* calculate missing rows from end first */
+  if (vep->selected_text_end_item == item) {
+    numRows = vep->selected_text_end_row;
+    last_right = PanelOffsetFromCharOffsetEx (doc, vep->font, item, vep->selected_text_end_col, vep->selected_text_end_offset);
+  } else {
+    last_right = r->right;
+  }
+
+  if (vep->selected_text_start_item == item) {
+    left_start = PanelOffsetFromCharOffsetEx (doc, vep->font, item, vep->selected_text_start_col, vep->selected_text_start_offset);
+    line_y = r->top + (vep->selected_text_start_row) * lineHeight - 1;
+    numRows -= vep->selected_text_start_row - 1;
+  } else {
+    left_start = PanelOffsetFromCharOffsetEx (doc, vep->font, item, 1, 0);
+    line_y = r->top + lineHeight - 1;
+  }
+
+  while (numRows > 1) {
+    MoveTo (left_start, line_y);
+    left_start = PanelOffsetFromCharOffsetEx (doc, vep->font, item, numCols, 0);
+    LineTo (r->right, line_y);
+    line_y += lineHeight;
+    numRows--;
+  }
+  MoveTo (left_start, line_y);
+  LineTo (last_right, line_y);
+
+}
+
+
 static void DrawValid (DoC d, RectPtr r, Int2 item, Int2 firstLine)
 
 {
@@ -169,19 +247,62 @@ static void DrawValid (DoC d, RectPtr r, Int2 item, Int2 firstLine)
       rct.right = rct.left + 4;
       PaintRect (&rct);
     }
+    if (vep->indexerVersion && vep->selected_text_start_item > -1) {
+      DrawTextSelection (d, vep, item, r);
+    }
   }
 }
 
+
+static void UpdateValidTextSelection (ValidExtraPtr vep, DoC d, PoinT pt)
+{
+  Int2           item, row, col, offset;
+
+  if (vep == NULL) return;
+
+  MapDocPoint (d, pt, &item, &row, &col, NULL);
+
+  if (item < 1 || row < 1 || col < 1) return;
+  offset = GetTextSelectCharOffsetEx (pt, d, vep->font, item, row, col);
+  if (item > vep->selected_text_anchor_item
+      || (item == vep->selected_text_anchor_item 
+          && (col > vep->selected_text_anchor_col
+              || (col == vep->selected_text_anchor_col
+                  && (row > vep->selected_text_anchor_row
+                      || (row == vep->selected_text_anchor_row
+                          && offset >= vep->selected_text_anchor_offset)))))) {
+    vep->selected_text_start_item = vep->selected_text_anchor_item;
+    vep->selected_text_start_row = vep->selected_text_anchor_row;
+    vep->selected_text_start_col = vep->selected_text_anchor_col;
+    vep->selected_text_start_offset = vep->selected_text_anchor_offset;
+    vep->selected_text_end_item = item;
+    vep->selected_text_end_row = row;
+    vep->selected_text_end_col = col;
+    vep->selected_text_end_offset = offset;
+  } else {
+    vep->selected_text_start_item = item;
+    vep->selected_text_start_row = row;
+    vep->selected_text_start_col = col;
+    vep->selected_text_start_offset = offset;
+    vep->selected_text_end_item = vep->selected_text_anchor_item;
+    vep->selected_text_end_row = vep->selected_text_anchor_row;
+    vep->selected_text_end_col = vep->selected_text_anchor_col;
+    vep->selected_text_end_offset = vep->selected_text_anchor_offset;
+  }
+  InvalDocRows (d, 0, 0, 0);
+} 
+
+
 static void ClickValid (DoC d, PoinT pt)
 
 {
   Int2           item;
-  Int2           row;
+  Int2           row, col;
   ValidExtraPtr  vep;
 
   vep = GetObjectExtra (d);
   if (vep != NULL) {
-    MapDocPoint (d, pt, &item, &row, NULL, NULL);
+    MapDocPointEx (d, pt, &item, &row, &col, NULL, TRUE);
     if (item > 0 && row > 0 && vep->clicked == item) {
       vep->dblClick = dblClick;
     } else {
@@ -191,10 +312,29 @@ static void ClickValid (DoC d, PoinT pt)
     vep->shftKey = shftKey;
     if (item > 0 && row > 0) {
       vep->clicked = item;
+      if (vep->indexerVersion) {
+        vep->selected_text_anchor_item = item;
+        vep->selected_text_anchor_col = col;
+        vep->selected_text_anchor_row = row;
+        vep->selected_text_anchor_offset = GetTextSelectCharOffsetEx (pt, d, vep->font, item, row, col);
+        UpdateValidTextSelection (vep, d, pt);
+      }
     }
   }
 }
 
+
+static void DragValid (DoC d, PoinT pt)
+{
+  ValidExtraPtr   vep;
+
+  vep = GetObjectExtra (d);
+  if (vep != NULL && vep->indexerVersion) {
+    UpdateValidTextSelection (vep, d, pt);
+  }
+}
+
+
 static Boolean FindSfpItem (GatherContextPtr gcp)
 
 {
@@ -650,10 +790,10 @@ static void RepopVal (PopuP p)
 
 static CharPtr FormatConsensusSpliceReport (CharPtr doc_line)
 {
-  CharPtr cp, cp2;
+  CharPtr cp, cp2, feat_start, feat_end = NULL;
   CharPtr report_str = NULL;
   CharPtr msg_abbrev = NULL;
-  Char    ch;
+  Char    ch, ch_2;
   Int4    pos;
 
   cp = StringChr (doc_line, '\n');
@@ -669,14 +809,34 @@ static CharPtr FormatConsensusSpliceReport (CharPtr doc_line)
   cp = StringSearch (cp, "position ");
   cp2 = StringSearch (cp, "FEATURE:");
   if (cp2 != NULL) {
+    feat_start = cp2 + 8;
+    if (feat_start != NULL) {
+      feat_end = StringChr (feat_start, ':');
+      if (feat_end != NULL) {
+        ch_2 = *feat_end;
+        *feat_end = 0;
+      }
+    }
     ch = *cp2;
     *cp2 = 0;
-    report_str = (CharPtr) MemNew (sizeof (Char) * StringLen (cp));
+    if (feat_start == NULL) {
+      report_str = (CharPtr) MemNew (sizeof (Char) * StringLen (cp));
+    } else {
+      report_str = (CharPtr) MemNew (sizeof (Char) * (StringLen (cp) + StringLen (feat_start) + 2));
+    }
     if (sscanf (cp, "position %ld of %s", &pos, report_str) == 2) {
-      sprintf (report_str + StringLen (report_str), "\t%s at %ld", msg_abbrev, pos);
+      if (feat_start == NULL) {
+        sprintf (report_str + StringLen (report_str), "\t%s at %ld", msg_abbrev, pos);
+      } else {
+        sprintf (report_str + StringLen (report_str), "\t%s\t%s at %ld", feat_start, msg_abbrev, pos);
+      }
     } else {
       report_str = MemFree (report_str);
     }
+    if (feat_end != NULL) {
+      *feat_end = ch_2;
+    }
+    *cp2 = ch;
   }
 
   return report_str;
@@ -748,7 +908,7 @@ static CharPtr GetEcNumberReport (SeqFeatPtr sfp)
         ec_number = StringSave (str);
       } else {
         tmp = (CharPtr) MemNew (sizeof (Char) * (StringLen (ec_number) + StringLen (str) + 2));
-        sprintf (tmp, "%s;%s", ec_number, gbq->val);
+        sprintf (tmp, "%s;%s", ec_number, str);
         ec_number = MemFree (ec_number);
         ec_number = tmp;
       }
@@ -927,6 +1087,214 @@ extern Boolean WriteBadSpecificHostTable (ValNodePtr bad_biop_list, FILE *fp)
   return any_in_list;
 }
 
+
+typedef struct validatoreporttype {
+  ButtoN PNTR btn_array;
+  ValNodePtr  errorfilter;
+} ValidatorReportTypeData, PNTR ValidatorReportTypePtr;
+
+
+static void EnableValidatorReportTypeButtons (ButtoN b)
+{
+  ValidatorReportTypePtr data;
+  ValNodePtr             vnp, vnp2;
+  Int4                   pos, pos2;
+  ErrFltrPtr             efp;
+
+  data = (ValidatorReportTypePtr) GetObjectExtra (b);
+  if (data == NULL) return;
+
+  for (vnp = data->errorfilter, pos = 0;
+       vnp != NULL;
+       vnp = vnp->next, pos++)
+  {
+    if (data->btn_array[pos] == b)
+    {
+      efp = (ErrFltrPtr) vnp->data.ptrvalue;
+      if (efp != NULL && efp->subcode == INT_MIN)
+      {
+        if (GetStatus (b)) 
+        {
+          /* main category checked, disable subcategories */
+          for (vnp2 = vnp->next, pos2 = pos + 1;
+               vnp2 != NULL && (vnp2->data.ptrvalue == NULL 
+                                || ((ErrFltrPtr)vnp2->data.ptrvalue)->errcode == efp->errcode);
+               vnp2 = vnp2->next, pos2++)
+          {
+            Disable (data->btn_array[pos2]);
+          }
+        } 
+        else
+        {
+          /* main category unchecked, enable subcategories */
+          for (vnp2 = vnp->next, pos2 = pos + 1;
+               vnp2 != NULL && (vnp2->data.ptrvalue == NULL || ((ErrFltrPtr)vnp2->data.ptrvalue)->errcode == efp->errcode);
+               vnp2 = vnp2->next, pos2++)
+          {
+            Enable (data->btn_array[pos2]);
+          }
+        } 
+      }
+      break;
+    }
+  }
+}
+
+
+static ValNodePtr CollectValidatorReportTypes (ValidExtraPtr vep)
+{
+  ErrFltrPtr  efp;
+  ValNodePtr  chosen = NULL, vnp;
+  WindoW      w, h, btn_grp, g1 = NULL, c;
+  Int4        num_buttons, i;
+  ValidatorReportTypeData data;
+  ButtoN PNTR btn_array;
+  ButtoN      b;
+  int         last_errcode = 0;
+  ModalAcceptCancelData acd;
+  
+  if (vep == NULL || vep->errorfilter == NULL) return NULL;
+
+  /* if only one, just select the one */
+  if (vep->errorfilter->next == NULL) 
+  {
+    ValNodeAddPointer (&chosen, 0, vep->errorfilter->data.ptrvalue);
+    return chosen;
+  }
+
+  num_buttons = ValNodeLen (vep->errorfilter);
+  btn_array = (ButtoN PNTR) MemNew (sizeof (ButtoN) * num_buttons);
+
+  data.btn_array = btn_array;
+  data.errorfilter = vep->errorfilter;
+
+  w = MovableModalWindow (-50, -33, -10, -10, "Choose Report Items", NULL);
+  SetGroupSpacing (w, 10, 10);
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  btn_grp = HiddenGroup (h, 3, 0, NULL);
+  for (vnp = vep->errorfilter, i = 0; vnp != NULL; vnp = vnp->next, i++) {
+    efp = (ErrFltrPtr) vnp->data.ptrvalue;
+    if (efp == NULL) continue;
+    if (efp->subcode == INT_MIN) {
+      g1 = NormalGroup (btn_grp, 0, 10, efp->text2, programFont, NULL);
+      btn_array[i] = CheckBox (g1, "All", EnableValidatorReportTypeButtons);
+      SetObjectExtra (btn_array[i], &data, NULL);
+      last_errcode = efp->errcode;
+    } else {
+      if (last_errcode != efp->errcode) {
+        g1 = NULL;
+      }
+      btn_array[i] = CheckBox (g1 == NULL ? btn_grp : g1, efp->text3 == NULL ? "" : efp->text3, NULL);
+    }
+  }
+
+  c = HiddenGroup (w, 4, 0, NULL);
+  SetGroupSpacing (c, 10, 2);
+  b = DefaultButton (c, "Accept", ModalAcceptButton);
+  SetObjectExtra (b, &acd, NULL);
+  b = PushButton (c, "Cancel", ModalCancelButton);
+  SetObjectExtra (b, &acd, NULL);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) btn_grp, (HANDLE) c, NULL);
+  RealizeWindow (w);
+
+  Show (w);
+  Select (w);
+  Update ();
+
+  acd.accepted = FALSE;
+  acd.cancelled = FALSE;
+  
+  while (!acd.accepted && ! acd.cancelled)
+  {
+    while (!acd.accepted && ! acd.cancelled)
+    {
+      ProcessExternalEvent ();
+      Update ();
+    }
+    ProcessAnEvent ();
+
+    if (acd.accepted)
+    {
+      for (vnp = vep->errorfilter, i = 0; vnp != NULL; vnp = vnp->next, i++)
+      {
+        if (vnp->data.ptrvalue != NULL && GetStatus (btn_array[i])) 
+        {
+          ValNodeAddPointer (&chosen, 0, vnp->data.ptrvalue);
+        }
+      }
+    }
+  }
+  btn_array = MemFree (btn_array);
+  Remove (w);
+  return chosen;
+}
+
+
+static Int4 FindReportPositionForError (ErrItemPtr eip, ValNodePtr chosen)
+{
+  Int4       pos;
+  ValNodePtr vnp;
+  ErrFltrPtr efp;
+
+  if (eip == NULL || chosen == NULL) return -1;
+
+  for (vnp = chosen, pos = 0; vnp != NULL; vnp = vnp->next, pos++)
+  {
+    efp = (ErrFltrPtr) vnp->data.ptrvalue;
+    if (efp != NULL && efp->errcode == eip->errcode 
+        && (efp->subcode == INT_MIN || efp->subcode == eip->subcode))
+    {
+      return pos;
+    }
+  }
+  return -1;
+}
+
+
+static Boolean MakeStandardReports (ValNodePtr chosen, ValNodePtr PNTR reports_list, FILE *fp)
+{
+  ValNodePtr chosen_vnp, item_vnp;
+  ErrFltrPtr efp;
+  Int4       i;
+  CharPtr    cp;
+  Boolean    found_any = FALSE;
+  CharPtr    label;
+
+  if (chosen == NULL || reports_list == NULL || fp == NULL) return FALSE;
+  
+  for (chosen_vnp = chosen, i = 0; chosen_vnp != NULL; chosen_vnp = chosen_vnp->next, i++)
+  {
+    efp = (ErrFltrPtr) chosen_vnp->data.ptrvalue;
+    if (efp != NULL && reports_list[i] != NULL) 
+    {
+      fprintf (fp, "%s%s%s\n", efp->text2 == NULL ? "" : efp->text2,
+                               efp->subcode == INT_MIN || efp->text3 != NULL ? ":" : "",
+                               efp->subcode == INT_MIN ? "ALL" : efp->text3 == NULL ? "" : efp->text3);
+      for (item_vnp = reports_list[i]; item_vnp != NULL; item_vnp = item_vnp->next)
+      {
+        cp = GetDiscrepancyItemText (item_vnp);
+        if (cp != NULL)
+        {
+          label = GetParentLabelForDiscrepancyItem (item_vnp);
+          if (label != NULL) {
+            fprintf (fp, "%s:", label);
+            label = MemFree (label);
+          }
+          fprintf (fp, "%s", cp);
+          found_any = TRUE;
+          cp = MemFree (cp);
+        }
+      }
+      fprintf (fp, "\n");
+    }
+  }
+  return found_any;
+}
+
+
 static void MakeValidatorReport (ButtoN b)
 {
   ValidExtraPtr  vep;
@@ -938,21 +1306,29 @@ static void MakeValidatorReport (ButtoN b)
   Boolean        found_any = FALSE;
   FILE           *fp;
   ValNodePtr     consensus_splice_list = NULL;
-  ValNodePtr     stop_codon_list = NULL;
   ValNodePtr     ecnumber_list = NULL;
   ValNodePtr     specific_host_list = NULL;
-  ValNodePtr     its_does_not_abut_list = NULL;
   SeqFeatPtr     sfp;
   SeqDescrPtr    sdp;
+  BioseqPtr      bsp;
   CharPtr        str;
   Char           ch;
   CharPtr        tmp;
   SeqMgrFeatContext fcontext;
   SeqMgrDescContext dcontext;
+  ValNodePtr        chosen = NULL;
+  ValNodePtr PNTR   report_lists = NULL;
+  Int4              num_reports, pos;
 
   vep = (ValidExtraPtr) GetObjectExtra (b);
   if (vep == NULL) return;
 
+  chosen = CollectValidatorReportTypes (vep);
+  if (chosen == NULL) return;
+  num_reports = ValNodeLen (chosen);
+  report_lists = (ValNodePtr PNTR) MemNew (sizeof (ValNodePtr) * num_reports);
+  MemSet (report_lists, 0, sizeof (ValNodePtr) * num_reports);
+
   TmpNam (path); 
 #ifdef WIN_MAC
   fp = FileOpen (path, "r");
@@ -970,6 +1346,9 @@ static void MakeValidatorReport (ButtoN b)
       item++;
       eip = (ErrItemPtr) vnp->data.ptrvalue;
       if (eip != NULL) {
+        pos = FindReportPositionForError (eip, chosen);
+        if (pos == -1) continue;
+
         if (eip->errcode == 5 && (eip->subcode == 16 || eip->subcode == 137 || eip->subcode == 138 || eip->subcode == 139)) {
           /* ERR_SEQ_FEAT_NotSpliceConsensus */
           str = GetDocText (vep->doc, item, 0, 5);
@@ -990,18 +1369,13 @@ static void MakeValidatorReport (ButtoN b)
           if (cp != NULL) {
             ValNodeAddPointer (&consensus_splice_list, 0, cp);
           }
-        } else if (eip->errcode == 5 && eip->subcode == 9) {
-          sfp = SeqMgrGetDesiredFeature (eip->entityID, NULL, eip->itemID, 0, NULL, &fcontext);
-          if (sfp != NULL) {
-            ValNodeAddPointer (&stop_codon_list, OBJ_SEQFEAT, sfp);
-          }
         } else if (eip->errcode == 5 && (eip->subcode == 124 || eip->subcode == 125 || eip->subcode == 126)) {
           /* ERR_SEQ_FEAT_BadEcNumberValue */
           sfp = SeqMgrGetDesiredFeature (eip->entityID, NULL, eip->itemID, 0, NULL, &fcontext);
           if (sfp != NULL) {
             ValNodeAddPointer (&ecnumber_list, OBJ_SEQFEAT, sfp);
           }
-        } else if (eip->errcode == 2 && eip->subcode == 29 && StringCmp (eip->message, "Invalid value for specific host") == 0) {
+        } else if (eip->errcode == 2 && eip->subcode == 50) {
           if (eip->itemtype == OBJ_SEQDESC) {
             sdp = SeqMgrGetDesiredDescriptor (eip->entityID, NULL, eip->itemID, 0, NULL, &dcontext);
             if (sdp != NULL) {
@@ -1013,10 +1387,20 @@ static void MakeValidatorReport (ButtoN b)
               ValNodeAddPointer (&specific_host_list, OBJ_SEQFEAT, sfp);
             }
           }
-        } else if (eip->errcode == 5 && eip->subcode == 116 && eip->itemtype == OBJ_SEQFEAT) {
+        } else if (eip->itemtype == OBJ_SEQFEAT) {
           sfp = SeqMgrGetDesiredFeature (eip->entityID, NULL, eip->itemID, 0, NULL, &fcontext);
           if (sfp != NULL) {
-            ValNodeAddPointer (&its_does_not_abut_list, OBJ_SEQFEAT, sfp);
+            ValNodeAddPointer (&(report_lists[pos]), OBJ_SEQFEAT, sfp);
+          }
+        } else if (eip->itemtype == OBJ_SEQDESC) {
+          sdp = SeqMgrGetDesiredDescriptor (eip->entityID, NULL, eip->itemID, 0, NULL, &dcontext);
+          if (sdp != NULL) {
+            ValNodeAddPointer (&(report_lists[pos]), OBJ_SEQDESC, sdp);
+          }
+        } else if (eip->itemtype == OBJ_BIOSEQ) {
+          bsp = GetBioseqGivenIDs (eip->entityID, eip->itemID, OBJ_BIOSEQ);
+          if (bsp != NULL) {
+            ValNodeAddPointer (&(report_lists[pos]), OBJ_BIOSEQ, bsp);
           }
         }
       }
@@ -1028,23 +1412,11 @@ static void MakeValidatorReport (ButtoN b)
     for (vnp = consensus_splice_list; vnp != NULL; vnp = vnp->next) {
       fprintf (fp, "%s\n", vnp->data.ptrvalue);
     }
+    fprintf (fp, "\n");
     found_any = TRUE;
     consensus_splice_list = ValNodeFreeData (consensus_splice_list);
   }
 
-  if (stop_codon_list != NULL) {
-    fprintf (fp, "Internal Stop Codons\n");
-    for (vnp = stop_codon_list; vnp != NULL; vnp = vnp->next) {
-      cp = GetDiscrepancyItemText (vnp);
-      if (cp != NULL) {
-        fprintf (fp, "%s", cp);
-        found_any = TRUE;
-        cp = MemFree (cp);
-      }
-    }
-    stop_codon_list = ValNodeFree (stop_codon_list);
-  }
-
   if (ecnumber_list != NULL) {
     fprintf (fp, "EC Number Errors\n");
     for (vnp = ecnumber_list; vnp != NULL; vnp = vnp->next) {
@@ -1055,6 +1427,7 @@ static void MakeValidatorReport (ButtoN b)
         cp = MemFree (cp);
       }
     }
+    fprintf (fp, "\n");
     ecnumber_list = ValNodeFree (ecnumber_list);
   }
  
@@ -1064,18 +1437,13 @@ static void MakeValidatorReport (ButtoN b)
     found_any = TRUE;
   }
 
-  if (its_does_not_abut_list != NULL) {
-    fprintf (fp, "ITS Features that do not Abut rRNA\n");
-    for (vnp = its_does_not_abut_list; vnp != NULL; vnp = vnp->next) {
-      cp = GetDiscrepancyItemText (vnp);
-      if (cp != NULL) {
-        fprintf (fp, "%s", cp);
-        found_any = TRUE;
-        cp = MemFree (cp);
-      }
-    }
-    its_does_not_abut_list = ValNodeFree (its_does_not_abut_list);
-  }    
+  found_any |= MakeStandardReports (chosen, report_lists, fp);
+
+  for (pos = 0; pos < num_reports; pos++) {
+    report_lists[pos] = ValNodeFree (report_lists[pos]);
+  }
+  report_lists = MemFree (report_lists);
+  chosen = ValNodeFree (chosen);      
 
   FileClose (fp);
   if (found_any) {
@@ -1349,16 +1717,27 @@ static void CopyValToClipboard (ValidExtraPtr vep)
 {
   FILE         *fp;
   Char         path [PATH_MAX];
+  CharPtr      selected_text;
 
   if (vep == NULL) return;
-  TmpNam (path);
-  fp = FileOpen (path, "w");
-  if (fp != NULL) {
-    SaveDocument (vep->doc, fp);
-    FileClose (fp);
-    FileToClipboard (path);
+  selected_text = GetSelectedDocText (vep->doc, vep->selected_text_start_item, vep->selected_text_start_row,
+                                      vep->selected_text_start_col, vep->selected_text_start_offset,
+                                      vep->selected_text_end_item, vep->selected_text_end_row,
+                                      vep->selected_text_end_col, vep->selected_text_end_offset,
+                                      val_columns_for_copy, sizeof (val_columns_for_copy));
+  if (StringHasNoText (selected_text)) {      
+    TmpNam (path);
+    fp = FileOpen (path, "w");
+    if (fp != NULL) {
+      SaveDocument (vep->doc, fp);
+      FileClose (fp);
+      FileToClipboard (path);
+    }
+    FileRemove (path);
+  } else {
+    StringToClipboard (selected_text);
   }
-  FileRemove (path);
+  selected_text = MemFree (selected_text);
 }
 
 static void PrintValProc (ValidExtraPtr vep)
@@ -1476,6 +1855,7 @@ extern void CreateValidateWindowEx (ErrNotifyProc notify, CharPtr title,
   if (validWindow == NULL) {
     vep = (ValidExtraPtr) MemNew (sizeof (ValidExtra));
     if (vep != NULL) {
+      vep->indexerVersion = indexerVersion;
       if (title == NULL || title [0] == '\0') {
         title = "Validation Errors";
       }
@@ -1583,7 +1963,7 @@ extern void CreateValidateWindowEx (ErrNotifyProc notify, CharPtr title,
         vep->doc = DocumentPanel (g, stdCharWidth * 30, stdLineHeight * 20);
         SetObjectExtra (vep->doc, vep, NULL);
         SetDocAutoAdjust (vep->doc, FALSE);
-        SetDocProcs (vep->doc, ClickValid, NULL, ReleaseValid, NULL);
+        SetDocProcs (vep->doc, ClickValid, DragValid, ReleaseValid, NULL);
         SetDocShade (vep->doc, DrawValid, NULL, NULL, NULL);
         vep->font = font;
 
diff --git a/doc/blast/blast.html b/doc/blast/blast.html
index 39c9f632..e17ea04c 100644
--- a/doc/blast/blast.html
+++ b/doc/blast/blast.html
@@ -13,7 +13,7 @@
 <pre>
 README for stand-alone BLAST
 
-$Date: 2005/05/05 13:53:10 $
+$Date: 2007/10/29 13:30:52 $
 
 Table of contents
 -----------------
@@ -33,14 +33,15 @@ Introduction
 
 NCBI provides binaries for the following platforms:
 
-Apple MacOS X (ppc32)
+Apple MacOS X (ppc32/ia32)
 FreeBSD 4.5 (ia32)
 IBM AIX 5.1 (ppc64)
-Linux (kernel 2.4, glibc 2.3.2) (ia32, ia64, amd64)
+Linux (kernel 2.6, glibc 2.3) (ia32, ia64, x64)
 Microsoft Windows 2000 (ia32)
 SGI IRIX 6.5 (mips64)
 Sun Solaris 9 (ia32)
-Sun Solaris 8 (sparc64)
+Sun Solaris 10 (sparc64)
+Sun Solaris 10 (x64)
 
 We will attempt to produce binaries for other platforms upon request.
 
diff --git a/doc/fwd_check.sh b/doc/fwd_check.sh
index cc530dc5..7b48e97a 100755
--- a/doc/fwd_check.sh
+++ b/doc/fwd_check.sh
@@ -1,5 +1,5 @@
 #! /bin/sh
-# $Id: fwd_check.sh,v 1.27 2006/05/25 19:40:23 lavr Exp $
+# $Id: fwd_check.sh,v 1.42 2008/02/27 17:19:43 lavr Exp $
 # Author:   Denis Vakatov (vakatov@ncbi,nlm.nih.gov)
 # Modified: Anton Lavrentiev (lavr@ncbi.nlm.nih.gov)
 #
@@ -16,35 +16,43 @@ EOF
 
 {
 cat <<EOF
-;130.14.22.1	5853	RETIRED
-;130.14.22.2	5859	RETIRED
-;130.14.22.8	5840	RETIRED
-;130.14.22.30	5810	RETIRED
-;130.14.22.31	5812	RETIRED
-;130.14.22.32	5811	RETIRED
-;130.14.22.12	5845	RETIRED
-130.14.25.13	5555	INTERNAL
-130.14.29.112	5860	OK
+;130.14.25.13	5555	RETIRED
+10.10.150.7	5555	INTERNAL
+130.14.29.112	5860	RESERVED
 130.14.29.112	5861	RESERVED
 130.14.29.112	5862	RESERVED
 130.14.29.112	5863	RESERVED
-130.14.29.112	5864	RESERVED
-130.14.29.112	5865	RESERVED
+130.14.29.112	5864	OK
+130.14.29.112	5865	OK
 130.14.29.112	5866	RESERVED
 130.14.29.112	5867	OK
 130.14.29.112	5868	OK
 130.14.29.112	5869	OK
-130.14.29.112	5870	OK
+130.14.29.112	5870	RESERVED
+130.14.29.112	4444	RETIRED
+130.14.29.112	4445	RESERVED
+130.14.29.112	4446	RESERVED
+130.14.29.112	4447	RESERVED
+130.14.29.112	4448	OK
+130.14.29.112	4449	OK
+130.14.29.112	4450	RESERVED
+130.14.29.112	4451	OK
+130.14.29.112	4452	OK
+130.14.29.112	4453	OK
+130.14.29.112	4454	RESERVED
 EOF
 } |
 while read x_host x_port x_status ; do
     test "`echo $x_host | grep -c '^[;]'`" != "0"  &&  continue
+    if [ "$x_port" -lt "5860" -o "$x_port" -gt "5870" ]; then
+        test -z "$HTTP_CAF" -o -n "$HTTP_CAF_EXTERNAL"  &&  continue
+    fi
     if [ "$x_status" = "RETIRED"  -o \
-         "$x_status" = "RESERVED" -o \
-         "$x_status" = "READYING" ]; then
+         "$x_status" = "RESERVED" ]; then
         echo "${x_host}:${x_port}	$x_status"
         continue
     fi
+    test "$x_status" = "READYING"  &&  unset x_status
     ( echo ; sleep $delay_sec ) | telnet $x_host $x_port >/tmp/$$ 2>&1 &
     pid=$!
     trap 'rm -f /tmp/$$; kill $pid >/dev/null 2>&1' 1 2 15
@@ -52,11 +60,15 @@ while read x_host x_port x_status ; do
     guard=$!
     wait $pid >/dev/null 2>&1
     kill $guard >/dev/null 2>&1
-    grep -s 'NCBI Firewall Daemon:  Invalid ticket\.  *Connection closed\.' /tmp/$$ >/dev/null 2>&1
-    if test $? -eq 0 ; then
-        echo "${x_host}:${x_port}	${x_status}"
+    test -n "$HTTP_CAF_EXTERNAL"  || \
+        cp="`tail +4 /tmp/$$ 2>/dev/null | grep -s '^[0-9]\{1,3\}[.][0-9]\{1,3\}[.][0-9]\{1,3\}[.][0-9]\{1,3\}:[0-9]\{1,5\}'`"
+    grep -qs 'NCBI Firewall Daemon:  Invalid ticket\.  *Connection closed\.' /tmp/$$ >/dev/null 2>&1
+    if   [ $? -eq 0 ]; then
+        echo "${x_host}:${x_port}	${x_status:-OKAY}${cp:+	}${cp}"
+    elif [ -z "$x_status" ]; then
+        echo "${x_host}:${x_port}	READYING"
     else
-        echo "${x_host}:${x_port}	FAILED  ( telnet $x_host $x_port )"
+        echo "${x_host}:${x_port}	FAILED	( telnet $x_host $x_port )"
     fi
     rm -f /tmp/$$
 done 2>&1 | grep -v 'Terminated'
diff --git a/doc/man/Nentrez.1 b/doc/man/Nentrez.1
deleted file mode 100644
index 55d19028..00000000
--- a/doc/man/Nentrez.1
+++ /dev/null
@@ -1,19 +0,0 @@
-.TH NENTREZ 1 2001-11-21 NCBI "NCBI Tools User's Manual"
-.SH NAME
-Nentrez \- a graphical client for the NCBI Entrez retrieval system
-.SH SYNOPSIS
-.B Nentrez
-.SH DESCRIPTION
-\fBNentrez\fP (Network Entrez) is a TCP/IP-based client-server version
-of WWW Entrez. This means it makes a direct connection with the NCBI
-databases over the Internet to retrieve its data. The data comes in a
-binary form taking up less network bandwidth during transfer.
-.SH OPTIONS
-None.
-.SH AUTHOR
-The National Center for Biotechnology Information.
-.SH SEE ALSO
-.ad l
-.BR entrez2 (1),
-.BR netentcf (1),
-<http://www.ncbi.nlm.nih.gov/Entrez/Network/nentrez.overview.html>
diff --git a/doc/man/asn2all.1 b/doc/man/asn2all.1
index 3166882c..19f76172 100644
--- a/doc/man/asn2all.1
+++ b/doc/man/asn2all.1
@@ -1,4 +1,4 @@
-.TH ASN2ALL 1 2005-05-16 NCBI "NCBI Tools User's Manual"
+.TH ASN2ALL 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 asn2all \- generate reports from ASN.1 biological data
 .SH SYNOPSIS
@@ -14,6 +14,7 @@ asn2all \- generate reports from ASN.1 biological data
 [\|\fB\-f\fP\ \fIformat\fP\|]
 [\|\fB\-h\fP\|]
 [\|\fB\-i\fP\ \fIfilename\fP\|]
+[\|\fB\-k\fP\|]
 [\|\fB\-l\fP\|]
 [\|\fB\-n\fP\ \fIpolicy\fP\|]
 [\|\fB\-o\fP\ \fIfilename\fP\|]
@@ -130,6 +131,9 @@ Display extra Help message
 \fB\-i\fP\ \fIfilename\fP
 Input file name (standard input by default)
 .TP
+\fB\-k\fP
+Enable local fetching
+.TP
 \fB\-l\fP
 Lock components in advance
 .TP
diff --git a/doc/man/asn2gb.1 b/doc/man/asn2gb.1
index 5e2b2c58..a7357724 100644
--- a/doc/man/asn2gb.1
+++ b/doc/man/asn2gb.1
@@ -1,4 +1,4 @@
-.TH ASN2GB 1 2006-05-29 NCBI "NCBI Tools User's Manual"
+.TH ASN2GB 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 asn2gb \- convert ASN.1 biological data to a GenBank-style flat format
 .SH SYNOPSIS
@@ -206,10 +206,14 @@ oldasn2gb/newasn2gb
 Custom flags (all default to off):
 .RS
 .PD 0
-.IP 2
-Hide most imported features
 .IP 4
-Hide SNP features
+Hide features
+.IP 1792
+Hide references
+.IP 8192
+Hide sources
+.IP 262144
+Hide translations
 .PD
 .RE
 .\" .TP
@@ -227,4 +231,5 @@ The National Center for Biotechnology Information.
 .BR asn2fsa (1),
 .BR asn2xml (1),
 .BR asndhuff (1),
-.BR insdseqget (1).
+.BR insdseqget (1),
+asn2gb.txt.
diff --git a/doc/man/asn2idx.1 b/doc/man/asn2idx.1
index 5bf2d04e..87a57839 100644
--- a/doc/man/asn2idx.1
+++ b/doc/man/asn2idx.1
@@ -1,12 +1,14 @@
-.TH ASN2IDX 1 2005-05-16 NCBI "NCBI Tools User's Manual"
+.TH ASN2IDX 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 asn2idx \- index ASN.1 Bioseq-sets for fast access to individual sequences
 .SH SYNOPSIS
 .B asn2idx
 [\|\fB\-\fP\|]
 [\|\fB\-b\fP\|]
-[\|\fB\-d\fP\ \fIstr\fP\|]
-\fB\-p\fP\ \fIstr\fP
+[\|\fB\-d\fP\ \fIdir\fP\|]
+[\|\fB\-f\fP\ \fIfilter\fP\|]
+\fB\-p\fP\ \fIpath\fP
+[\|\fB\-r\fP\ \fIpath\fP\|]
 [\|\fB\-t\fP\|]
 [\|\fB\-x\fP\ \fIstr\fP\|]
 .SH DESCRIPTION
@@ -23,17 +25,23 @@ Print usage message
 \fB\-b\fP
 Bioseq-sets are Binary
 .TP
-\fB\-d\fP\ \fIstr\fP
+\fB\-d\fP\ \fIdir\fP
 Required Subdirectory
 .TP
-\fB\-p\fP\ \fIstr\fP
+\fB\-f\fP\ \fIfilter\fP
+Filter (default = \fBgbcon,gbest,gbgss,gbsts\fP)
+.TP
+\fB\-p\fP\ \fIpath\fP
 Path to Files
 .TP
+\fB\-p\fP\ \fIpath\fP
+Path for Results
+.TP
 \fB\-t\fP
 Recurse
 .TP
 \fB\-x\fP\ \fIstr\fP
-File Selection Substring (default = .aso)
+File Selection Substring (default = \fB.aso\fP)
 .SH AUTHOR
 The National Center for Biotechnology Information.
 .SH SEE ALSO
diff --git a/doc/man/asnval.1 b/doc/man/asnval.1
index c53ded12..29673f03 100644
--- a/doc/man/asnval.1
+++ b/doc/man/asnval.1
@@ -1,4 +1,4 @@
-.TH ASNVAL 1 2006-05-29 NCBI "NCBI Tools User's Manual"
+.TH ASNVAL 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 asnval \- validate ASN.1 biological sequence records
 .SH SYNOPSIS
@@ -11,16 +11,19 @@ asnval \- validate ASN.1 biological sequence records
 [\|\fB\-J\fP\|]
 [\|\fB\-L\fP\ \fIfilename\fP\|]
 [\|\fB\-M\fP\|]
+[\|\fB\-N\fP\ \fIflags\fP\|]
 [\|\fB\-P\fP\ \fIN\fP\|]
 [\|\fB\-Q\fP\ \fIN\fP\|]
 [\|\fB\-R\fP\ \fIN\fP\|]
 [\|\fB\-S\fP\ \fIN\fP\|]
 [\|\fB\-T\fP\|]
+[\|\fB\-X\fP\|]
 [\|\fB\-Y\fP\|]
 [\|\fB\-Z\fP\|]
 [\|\fB\-a\fP\ \fItype\fP\|]
 [\|\fB\-b\fP\|]
 [\|\fB\-c\fP\|]
+[\|\fB\-d\fP\ \fIpath\fP\|]
 [\|\fB\-e\fP\|]
 [\|\fB\-i\fP\ \fIfilename\fP\|]
 [\|\fB\-k\fP\|]
@@ -61,6 +64,21 @@ Log File
 \fB\-M\fP
 Match locus_tag against General ID
 .TP
+\fB\-N\fP\ \fIflags\fP
+Latitude-longitude / country flags
+.RS
+.PD 0
+.IP 0
+none
+.IP 1
+test state/province
+.IP 2
+ignore water exception
+.IP 3
+both of the above
+.PD
+.RE
+.TP
 \fB\-P\fP\ \fIN\fP
 Highest severity for error to show:
 .RS
@@ -90,6 +108,9 @@ Skip count
 \fB\-T\fP
 Use Threads
 .TP
+\fB\-X\fP
+Exon splice check
+.TP
 \fB\-Y\fP
 Check against old IDs
 .TP
@@ -123,6 +144,9 @@ Batch file is Binary
 \fB\-c\fP
 Batch file is Compressed
 .TP
+\fB\-d\fP\ \fIpath\fP
+Path to Indexed Binary ASN.1 Data
+.TP
 \fB\-e\fP
 Ignore transcription/translation Exceptions
 .TP
@@ -139,7 +163,7 @@ Lock components in advance
 Single output file
 .TP
 \fB\-p\fP\ \fIpath\fP
-Path to ASN.1 Files [String]
+Path to ASN.1 Files
 .TP
 \fB\-r\fP
 Remote Fetching from ID
@@ -155,4 +179,5 @@ File selection substring (\fB.ent\fP by default)
 .SH AUTHOR
 The National Center for Biotechnology Information.
 .SH SEE ALSO
+.BR cleanasn (1),
 .BR sequin (1).
diff --git a/doc/man/blast.1 b/doc/man/blast.1
index 9f787531..e6205e04 100644
--- a/doc/man/blast.1
+++ b/doc/man/blast.1
@@ -1,4 +1,4 @@
-.TH BLAST 1 2006-05-29 NCBI "NCBI Tools User's Manual"
+.TH BLAST 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 bl2seq, blast, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop \- Basic Local Alignment Search Tool
 .SH SYNOPSIS
@@ -61,8 +61,8 @@ bl2seq, blast, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rp
 [\|\fB\-c\fP\|]
 [\|\fB\-d\fP\ \fIstr\fP\|]
 [\|\fB\-e\fP\ \fIX\fP\|]
-[\|\fB\-f\fP\ \fIN\fP\|]
-[\|\fB\-g\fP\ \fIN\fP\|]
+[\|\fB\-f\fP\ \fIX\fP\|]
+[\|\fB\-g\fP\|]
 [\|\fB\-h\fP\ \fIN\fP\|]
 [\|\fB\-i\fP\ \fIfilename\fP\|]
 [\|\fB\-j\fP\ \fIfilename\fP\|]
@@ -111,7 +111,7 @@ bl2seq, blast, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rp
 [\|\fB\-b\fP\ \fIN\fP\|]
 [\|\fB\-d\fP\ \fIstr\fP\|]
 [\|\fB\-e\fP\ \fIX\fP\|]
-[\|\fB\-f\fP\ \fIN\fP\|]
+[\|\fB\-f\fP\ \fIX\fP\|]
 [\|\fB\-g\ F\fP\|]
 [\|\fB\-i\fP\ \fIfilename\fP\|]
 [\|\fB\-l\fP\ \fIstr\fP\|]
@@ -157,7 +157,7 @@ bl2seq, blast, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rp
 [\|\fB\-b\fP\ \fIN\fP\|]
 [\|\fB\-d\fP\ \fIstr\fP\|]
 [\|\fB\-e\fP\ \fIX\fP\|]
-[\|\fB\-f\fP\ \fIN\fP\|]
+[\|\fB\-f\fP\ \fIX\fP\|]
 [\|\fB\-g\ F\fP\|]
 [\|\fB\-i\fP\ \fIfilename\fP\|]
 [\|\fB\-l\fP\ \fIstr\fP\|]
@@ -201,7 +201,7 @@ bl2seq, blast, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rp
 [\|\fB\-b\fP\ \fIN\fP\|]
 [\|\fB\-d\fP\ \fIstr\fP\|]
 [\|\fB\-e\fP\ \fIX\fP\|]
-[\|\fB\-f\fP\ \fIN\fP\|]
+[\|\fB\-f\fP\ \fIX\fP\|]
 [\|\fB\-g\ F\fP\|]
 [\|\fB\-i\fP\ \fIfilename\fP\|]
 [\|\fB\-m\fP\ \fIN\fP\|]
@@ -314,6 +314,7 @@ bl2seq, blast, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rp
 [\|\fB\-V\fP\|]
 [\|\fB\-W\fP\ \fIN\fP\|]
 [\|\fB\-X\fP\ \fIN\fP\|]
+[\|\fB\-Y\fP\ \fIX\fP\|]
 [\|\fB\-Z\fP\ \fIN\fP\|]
 [\|\fB\-a\fP\ \fIN\fP\|]
 [\|\fB\-b\fP\ \fIN\fP\|]
@@ -346,7 +347,6 @@ bl2seq, blast, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rp
 [\|\fB\-P\fP\ \fIN\fP\|]
 [\|\fB\-T\fP\|]
 [\|\fB\-U\fP\|]
-[\|\fB\-V\fP\|]
 [\|\fB\-X\fP\ \fIN\fP\|]
 [\|\fB\-Y\fP\ \fIX\fP\|]
 [\|\fB\-Z\fP\ \fIN\fP\|]
@@ -378,6 +378,7 @@ bl2seq, blast, blastall, blastall_old, blastcl3, blastpgp, impala, megablast, rp
 [\|\fB\-X\fP\ \fIN\fP\|]
 [\|\fB\-d\fP\ \fIstr\fP\|]
 [\|\fB\-e\fP\ \fIX\fP\|]
+[\|\fB\-f\fP\|]
 [\|\fB\-i\fP\ \fIfilename\fP\|]
 [\|\fB\-k\fP\ \fIfilename\fP\|]
 [\|\fB\-o\fP\ \fIfilename\fP\|]
@@ -481,20 +482,23 @@ Print usage message
 Input sequences in the form of accession.version
 .TP
 \fB\-A\fP\ \fIN\fP (blastall, blastall_old, blastcl3, blastpgp, megablast)
-Multiple Hits window size (default is 40 for blastpgp and 0 for other
-commands, but blastall, blastall_old, and blastcl3 interpret 0 as 40
-for all programs but blastn and megablast)
+Multiple Hits window size; generally defaults to 0 (for single-hit
+extensions), but defaults to 40 when using discontiguous templates.
 .TP
 \fB\-B\fP\ \fIN\fP (blast)
-Produce on-the-fly tabular output:
+Produce on-the-fly output:
 .RS
 .PD 0
 .IP 0
 none (default)
 .IP 1
-just offsets and quality values
+table of offsets and quality values
 .IP 2
 add sequence data
+.IP 3
+text ASN.1
+.IP 4
+binary ASN.1
 .PD
 .RE
 .TP
@@ -505,11 +509,11 @@ Number of concatenated queries, in blastn or tblastn mode
 Input Alignment File for PSI-BLAST Restart
 .TP
 \fB\-C\fP\ \fIX\fP (blast, blastall, blastall_old, blastcl3)
-Use composition-based statistics for tblastn:
+Use composition-based statistics for blastp or tblastn:
 .RS
 .PD 0
 .IP "D or d"
-Default (equivalent to F)
+Default (equivalent to \fBT\fP)
 .IP "0, F, or f"
 No composition-based statistics
 .IP "1, T, or t"
@@ -522,6 +526,12 @@ Composition-based score adjustment as in \fIBioinformatics\fP 21:902-911,
 2005, unconditionally
 .PD
 .RE
+.RS
+When enabling statistics in blastall, blastall_old, or blastcl3 (\fIi.e.\fP,
+not blast), appending \fBu\fP (case-insensitive) to the mode enables
+use of unified p-values combining alignment and compositional p-values
+in round 1 only.
+.RE
 .TP
 \fB\-C\fP\ \fIfilename\fP (blastpgp)
 Output File for PSI-BLAST Checkpointing
@@ -556,6 +566,10 @@ all ungapped segments endpoints
 traditional BLAST output (default)
 .IP 3
 tab-delimited one line format
+.IP 4
+incremental text ASN.1
+.IP 5
+incremental binary ASN.1
 .PD
 .RE
 .TP
@@ -742,7 +756,7 @@ two simultaneous
 rpsblast)
 Use lower case filtering for the query sequence
 .TP
-\fB\-V\fP (bl2seq, blastall, megablast, rpsblast)
+\fB\-V\fP (bl2seq, blastall, megablast)
 Force use of legacy engine
 .TP
 \fB\-V\fP (blast)
@@ -765,7 +779,7 @@ commands vary with "program": 30 for blastn, 20 for megablast, 0 for
 tblastx, and 15 for everything else.)
 .TP
 \fB\-Y\fP\ \fIX\fP (bl2seq, blast, blastall, blastall_old, blastcl3,
-blastpgp, rpsblast)
+blastpgp, megablast, rpsblast)
 Effective length of the search space (use zero for the real size)
 .TP
 \fB\-Z\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3, blastpgp,
@@ -775,7 +789,7 @@ bits (default is 50 for blastn and megablast, 0 for tblastx, 25 for
 others)
 .TP
 \fB\-a\fP\ \fIfilename\fP (bl2seq)
-Write SeqAnnot output to \fIfilename\fP
+Write text ASN.1 output to \fIfilename\fP
 .TP
 \fB\-a\fP\ \fIN\fP (blast, blastall, blastall_old, blastcl3, blastpgp,
 impala, megablast, rpsblast)
@@ -805,7 +819,7 @@ RPS BLAST Database
 \fB\-e\fP\ \fIX\fP
 Expectation value (E) (default = 10.0)
 .TP
-\fB\-f\fP\ \fIN\fP (blastall, blastall_old, blastcl3)
+\fB\-f\fP\ \fIX\fP (blast, blastall, blastall_old, blastcl3)
 Threshold for extending hits, default if zero: 0 for blastn and
 megablast, 11 for blastp, 12 for blastx, and 13 for tblasn and
 tblastx.
@@ -816,27 +830,18 @@ Threshold for extending hits (default 11)
 \fB\-f\fP (megablast)
 Show full IDs in the output (default - only GIs or accessions)
 .TP
+\fB\-f\fP (seedtop)
+Force searching for patterns even if they are too likely
+.TP
 \fB\-g\ F\fP (bl2seq, blastall, blastall_old, blastcl3)
 Do not perform gapped alignment (N/A for tblastx)
 .TP
-\fB\-g\fP\ \fIN\fP (blast)
-Use greedy algorithm for gapped extensions:
-.RS
-.PD 0
-.IP 0
-no (default)
-.IP 1
-one-step
-.IP 2
-two-step
-.IP 3
-two-step with ungapped
-.PD
-.RE
+\fB\-g\fP (blast)
+Use greedy algorithm for gapped extensions
 .TP
 \fB\-g\ F\fP (megablast)
-Generate words for every fourth base of the database (only relevant
-for discontiguous words)
+Make discontiguous megablast generate words for every base of the
+database (mandatory with the current BLAST engine)
 .TP
 \fB\-h\fP\ \fIN\fP (blast)
 Frame shift penalty for out-of-frame gapping (blastx, tblastn only;
@@ -963,8 +968,7 @@ Reward for a nucleotide match (blastn only) (default = 10 for seedtop,
 -10 for everything else)
 .TP
 \fB\-s\fP (blast)
-Generate words for every base of the database (default is every 4th;
-may only be used with discontiguous words)
+No-op (formerly requested generating words for every base of the database)
 .TP
 \fB\-s\fP (blastall, blastall_old, blastcl3, blastpgp)
 Compute locally optimal Smith-Waterman alignments.
diff --git a/doc/man/cleanasn.1 b/doc/man/cleanasn.1
index a6a6e2f6..b0ccaae9 100644
--- a/doc/man/cleanasn.1
+++ b/doc/man/cleanasn.1
@@ -1,54 +1,59 @@
-.TH CLEANASN 1 2006-05-29 NCBI "NCBI Tools User's Manual"
+.TH CLEANASN 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
-cleanasn \- clean up irregularities in NCBI ASN.1 Seq-entry objects
+cleanasn \- clean up irregularities in NCBI ASN.1 objects
 .SH SYNOPSIS
 .B cleanasn
 [\|\fB\-\fP\|]
+[\|\fB\-F\fP\ \fIstr\fP\|]
+[\|\fB\-K\fP\ \fIstr\fP\|]
+[\|\fB\-N\fP\ \fIstr\fP\|]
 [\|\fB\-R\fP\|]
-[\|\fB\-c\fP\ \fIstr\fP\|]
+[\|\fB\-T\fP\|]
+[\|\fB\-a\fP\ \fIstr\fP\|]
+[\|\fB\-b\fP\|]
+[\|\fB\-c\fP\|]
 [\|\fB\-f\fP\ \fIstr\fP\|]
-[\|\fB\-l\fP\ \fIstr\fP\|]
-\fB\-p\fP\ \fIpath\fP
+[\|\fB\-i\fP\ \fIfilename\fP\|]
+[\|\fB\-l\fP\ \fIfilename\fP\|]
+[\|\fB\-o\fP\ \fIfilename\fP\|]
+[\|\fB\-p\fP\ \fIpath\fP\|]
 [\|\fB\-r\fP\ \fIpath\fP\|]
-[\|\fB\-t\fP\|]
+[\|\fB\-x\fP\ \fIext\fP\|]
 .SH DESCRIPTION
 \fBcleanasn\fP is a utility program to clean up irregularities in NCBI
-ASN.1 Seq-entry or Seq-submit objects.
+ASN.1 objects.
 .SH OPTIONS
 A summary of options is included below.
 .TP
 \fB\-\fP
 Print usage message
 .TP
-\fB\-R\fP
-Enable remote fetching from NCBI's ID database
-.TP
-\fB\-c\fP\ \fIstr\fP
-Perform general clean-ups, per the flags in \fIstr\fP:
+\fB\-F\fP\ \fIstr\fP
+Clean up features, per the flags in str:
 .RS
 .PD 0
-.IP b
-BasicSeqEntryCleanup
-.IP s
-SeriousSeqEntryCleanup
+.IP u
+Remove User-objects
+.IP d
+Remove db_xrefs
+.IP r
+Remove redundant gene xrefs
 .PD
 .RE
 .TP
-\fB\-f\fP\ \fIstr\fP
-Remove extraneous features, per the flags in \fIstr\fP:
+\fB\-K\fP\ \fIstr\fP
+Perform a general cleanup, per the flags in str:
 .RS
 .PD 0
-.IP u
-Remove User objects
-.IP d
-Remove Database cross-references
-.IP r
-Remove Redundant gene cross-references
+.IP b
+BasicSeqEntryCleanup
+.IP s
+SeriousSeqEntryCleanup
 .PD
 .RE
 .TP
-\fB\-l\fP\ \fIstr\fP
-Link related features, per the flags in \fIstr\fP:
+\fB\-N\fP\ \fIstr\fP
+Clean up links, per the flags in str:
 .RS
 .PD 0
 .IP o
@@ -57,16 +62,64 @@ LinkCDSmRNAbyOverlap
 LinkCDSmRNAbyProduct
 .IP r
 ReassignFeatureIDs
+.IP c
+ClearFeatureIDs
 .PD
 .RE
 .TP
+\fB\-R\fP
+Remote fetching from ID (NCBI sequence databases)
+.TP
+\fB\-T\fP
+Taxonomy Lookup
+.TP
+\fB\-a\fP\ \fIstr\fP
+ASN.1 type
+.RS
+.PD 0
+.IP a
+Any (default)
+.IP e
+Seq-entry
+.IP b
+Bioseq
+.IP s
+Bioseq-set
+.IP m
+Seq-submit
+.IP t
+Batch Processing [String]
+.PD
+.RE
+.TP
+\fB\-b\fP
+Input ASN.1 is Binary
+.TP
+\fB\-c\fP
+Input ASN.1 is Compressed
+.TP
+\fB\-f\fP\ \fIstr\fP
+Substring filter
+.TP
+\fB\-i\fP\ \fIfilename\fP
+Single input file (defaults to stdin)
+.TP
+\fB\-l\fP\ \fIfilename\fP
+Log file
+.TP
+\fB\-o\fP\ \fIfilename\fP
+Single output file (defaults to stdout)
+.TP
 \fB\-p\fP\ \fIpath\fP
-Path to input files
+Process all matching files in \fIpath\fP
 .TP
 \fB\-r\fP\ \fIpath\fP
-Path for Results (changes are otherwise made in place)
+Path for results
 .TP
-\fB\-t\fP
-Enable Taxonomy lookup
+\fB\-x\fP\ \fIext\fP
+File selection suffix for use with \fB\-p\fP (defaults to \fB.ent\fP)
 .SH AUTHOR
 The National Center for Biotechnology Information.
+.SH SEE ALSO
+asnval (1),
+sequin (1).
diff --git a/doc/man/entrcmd.1 b/doc/man/entrcmd.1
deleted file mode 100644
index 7bead9ca..00000000
--- a/doc/man/entrcmd.1
+++ /dev/null
@@ -1,102 +0,0 @@
-.TH ENTRCMD 1 2001-10-03 NCBI "NCBI Tools User's Manual"
-.SH NAME
-entrcmd \- non-interactive command line interface for Entrez
-.SH SYNOPSIS
-.B entrcmd
-[\|\fB\-\fP\|]
-[\|\fB\-c\fP\|]
-[\|\fB\-d\fP\ \fIstr\fP\|]
-[\|\fB\-e\fP\ \fIstr\fP\|]
-[\|\fB\-f\fP\|]
-[\|\fB\-g\ F\fP\|]
-[\|\fB\-h\fP\|]
-[\|\fB\-i\fP\ \fIstr\fP\|]
-[\|\fB\-l\fP\ \fIstr\fP\|]
-[\|\fB\-n\fP\ \fIfilename\fP\|]
-[\|\fB\-o\fP\ \fIfilename\fP\|]
-\fB\-p\fP\ \fIstr\fP
-[\|\fB\-r\fP\|]
-[\|\fB\-s\fP\|]
-[\|\fB\-t\fP\ \fIstr\fP\|]
-[\|\fB\-u\fP\ \fIstr\fP\|]
-[\|\fB\-w\fP\ \fIstr\fP\|]
-[\|\fB\-x\fP\ \fIstr\fP\|]
-[\|\fB\-y\fP\ \fIN\fP\|]
-.SH DESCRIPTION
-\fBentrcmd\fP is a non-interactive command-line interface which allows
-a user to perform a series of neighboring and output operations, based
-upon an initial set of UIDs or a boolean expression which describes a
-set of UIDs.  Alternatively, it can be used to display an
-alphabetically sorted list of terms near an initial term.
-.SH OPTIONS
-A summary of options is included below.
-.TP
-\fB\-\fP
-Print usage message
-.TP
-\fB\-c\fP
-\&'Check' WWW output Forms
-.TP
-\fB\-d\fP\ \fIstr\fP
-Initial database (default = m)
-.TP
-\fB\-e\fP\ \fIstr\fP
-Boolean expression
-.TP
-\fB\-f\fP
-For WWW output, use Forms
-.TP
-\fB\-g\ F\fP
-Do not use WWW-style encoding for special input characters
-.TP
-\fB\-h\fP
-Print detailed help.  Requires, but ignores, \fB\-p\fP\ \fIstr\fP
-.TP
-\fB\-i\fP\ \fIstr\fP
-Comma-delimited list of files to import for named UID list
-.TP
-\fB\-l\fP\ \fIstr\fP
-Taxonomy lookup string
-.TP
-\fB\-n\fP\ \fIfilename\fP
-On-the-fly neighboring from \fIfilename\fP
-.TP
-\fB\-o\fP\ \fIfilename\fP
-Output file (default = stdout)
-.TP
-\fB\-p\fP\ \fIstr\fP
-Program of commands
-.TP
-\fB\-r\fP
-Get sequences from ID Repository
-.TP
-\fB\-s\fP
-Display status report
-.TP
-\fB\-t\fP\ \fIstr\fP
-Produce a list of terms
-.TP
-\fB\-u\fP\ \fIstr\fP
-Comma-delimited list of UIDs
-.TP
-\fB\-w\fP\ \fIstr\fP
-Produce WWW/HTML formatted output, using \fIstr\fP (/htbin is
-recommended) as the directory prefix for linked hypertext items.
-.TP
-\fB\-x\fP\ \fIstr\fP
-Name of export file for named UID list
-.TP
-\fB\-y\fP\ \fIN\fP
-Complexity:
-.RS
-.PD 0
-.IP 1
-bioseq only
-.IP 2
-bioseq set
-.IP 3
-nuc-prot set (default)
-.PD
-.RE
-.SH AUTHOR
-The National Center for Biotechnology Information.
diff --git a/doc/man/entrez2.1 b/doc/man/entrez2.1
index 4a6e2c09..91194df4 100644
--- a/doc/man/entrez2.1
+++ b/doc/man/entrez2.1
@@ -1,4 +1,4 @@
-.TH ENTREZ2 1 2001-11-21 NCBI "NCBI Tools User's Manual"
+.TH ENTREZ2 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 entrez2 \- a graphical client for the NCBI Entrez retrieval system
 .SH SYNOPSIS
@@ -14,6 +14,4 @@ None.
 The National Center for Biotechnology Information.
 .SH SEE ALSO
 .ad l
-.BR Nentrez (1),
-.BR netentcf (1),
 <http://www.ncbi.nlm.nih.gov/Entrez/Network/nentrez.overview.html>
diff --git a/doc/man/formatdb.1 b/doc/man/formatdb.1
index 4c5c04bd..23e4e233 100644
--- a/doc/man/formatdb.1
+++ b/doc/man/formatdb.1
@@ -1,4 +1,4 @@
-.TH FORMATDB 1 2005-11-04 NCBI "NCBI Tools User's Manual"
+.TH FORMATDB 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 formatdb \- format protein or nucleotide databases for BLAST
 .SH SYNOPSIS
@@ -99,9 +99,9 @@ Title for database file [String]
 .TP
 \fB\-v\fP\ \fIN\fP
 Break up large FASTA files into 'volumes' of size \fIN\fP million
-letters.  As part of the creation of a volume, \fBformatdb\fP writes a
-new type of BLAST database file, called an alias file, with the
-extension 'nal' or 'pal'.
+letters (4000 by default).  As part of the creation of a volume,
+\fBformatdb\fP writes a new type of BLAST database file, called an
+alias file, with the extension 'nal' or 'pal'.
 .SH AUTHOR
 The National Center for Biotechnology Information.
 .SH SEE ALSO
diff --git a/doc/man/getfeat.1 b/doc/man/getfeat.1
deleted file mode 100644
index 8f32b4b3..00000000
--- a/doc/man/getfeat.1
+++ /dev/null
@@ -1,64 +0,0 @@
-.TH GETFEAT 1 2002-08-23 NCBI "NCBI Tools User's Manual"
-.SH NAME
-getfeat \- extract information about sequences' coding regions
-.SH SYNOPSIS
-.B getfeat
-[\|\fB\-\fP\|]
-[\|\fB\-a\fP\|]
-[\|\fB\-b\fP\|]
-[\|\fB\-g\fP\ \fIN\fP\|]
-[\|\fB\-i\fP\ \fIstr\fP\|]
-[\|\fB\-l\ F\fP\|]
-[\|\fB\-o\fP\ \fIfilename\fP\|]
-[\|\fB\-p\fP\|]
-[\|\fB\-r\fP\ \fIN\fP\|]
-[\|\fB\-s\ F\fP\|]
-.SH DESCRIPTION
-\fBgetfeat\fP retrieves biological sequences over the network and
-extracts information about their coding regions.
-.SH OPTIONS
-A summary of options is included below.
-.TP
-\fB\-\fP
-Print usage message
-.TP
-\fB\-a\fP
-ID is GenBank accession
-.TP
-\fB\-b\fP
-ID is PIR accession
-.TP
-\fB\-g\fP\ \fIN\fP
-GenInfo Import ID
-.TP
-\fB\-i\fP\ \fIstr\fP
-Input string id (default = \fBANANIFDR1\fP)
-.TP
-\fB\-l\ F\fP
-ID is NOT GenBank locus
-.TP
-\fB\-o\fP\ \fIfilename\fP
-Output File Name (default = \fBgetfeat.out\fP)
-.TP
-\fB\-p\fP
-ID is PIR locus
-.TP
-\fB\-r\fP\ \fIN\fP
-Return type:
-.RS
-.PD 0
-.IP 1
-Bioseq
-.IP 2
-Seg-set
-.IP 3
-Nuc-prot (default)
-.IP 4
-Pub-set
-.PD
-.RE
-.TP
-\fB\-s\ F\fP
-Do not output a Seq-entry.
-.SH AUTHOR
-The National Center for Biotechnology Information.
diff --git a/doc/man/idfetch.1 b/doc/man/idfetch.1
index 188deff1..4d378114 100644
--- a/doc/man/idfetch.1
+++ b/doc/man/idfetch.1
@@ -1,4 +1,4 @@
-.TH IDFETCH 1 2005-06-24 NCBI "NCBI Tools User's Manual"
+.TH IDFETCH 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 idfetch \- retrieve biological data from the NCBI ID1 server
 .SH SYNOPSIS
@@ -30,7 +30,7 @@ Print usage message
 .TP
 \fB\-F\fP\ \fIstr\fP
 Add the specified feature types (comma-delimited); allowed values are
-CDD, SNP, SNP_graph, MGC, HPRD, and STS.
+CDD, SNP, SNP_graph, MGC, HPRD, STS, tRNA, and microRNA.
 .TP
 \fB\-G\fP\ \fIfilename\fP
 File with list of GIs, (versioned) accessions, FASTA SeqID's to dump
diff --git a/doc/man/netentcf.1 b/doc/man/netentcf.1
deleted file mode 100644
index bc7e23d3..00000000
--- a/doc/man/netentcf.1
+++ /dev/null
@@ -1,16 +0,0 @@
-.TH NETENTCF 1 2001-10-05 NCBI "NCBI Tools User's Manual"
-.SH NAME
-netentcf \- change Entrez network configuration
-.SH SYNOPSIS
-.B netentcf
-.SH DESCRIPTION
-\fBnetentcf\fP lets you configure Network Entrez's firewall and proxy
-settings.
-.SH OPTIONS
-None.
-.SH AUTHOR
-The National Center for Biotechnology Information.
-.SH SEE ALSO
-.ad l
-.BR Nentrez (1),
-<http://www.ncbi.nlm.nih.gov/Entrez/Network/nentrez.overview.html>
diff --git a/doc/man/nps2gps.1 b/doc/man/nps2gps.1
index 5540b3d3..eaf43926 100644
--- a/doc/man/nps2gps.1
+++ b/doc/man/nps2gps.1
@@ -1,16 +1,17 @@
-.TH NPS2GPS 1 2005-11-04 NCBI "NCBI Tools User's Manual"
+.TH NPS2GPS 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 nps2gps \- convert nucleotide-protein sets to ASN.1 genomic product sets
 .SH SYNOPSIS
 .B nps2gps
 [\|\fB\-\fP\|]
+[\|\fB\-F\fP\|]
 [\|\fB\-L\fP\|]
 [\|\fB\-R\fP\|]
 [\|\fB\-f\fP\ \fIstr\fP\|]
 [\|\fB\-i\fP\ \fIfilename\fP\|]
 [\|\fB\-o\fP\ \fIfilename\fP\|]
-[\|\fB\-p\fP\ \fIstr\fP\|]
-[\|\fB\-r\fP\ \fIstr\fP\|]
+[\|\fB\-p\fP\ \fIpath\fP\|]
+[\|\fB\-r\fP\ \fIpath\fP\|]
 [\|\fB\-x\fP\ \fIstr\fP\|]
 .SH DESCRIPTION
 \fBnps2gps\fP converts NCBI Bioseq-sets from simple nucleotide-protein
@@ -22,6 +23,9 @@ A summary of options is included below.
 \fB\-\fP
 Print usage message
 .TP
+\fB\-F\fP
+Map by Feature ID
+.TP
 \fB\-L\fP
 Lock components in advance
 .TP
@@ -37,10 +41,10 @@ Single input file (default = stdin)
 \fB\-o\fP\ \fIfilename\fP
 Single output file (default = stdout)
 .TP
-\fB\-p\fP\ \fIstr\fP
+\fB\-p\fP\ \fIpath\fP
 Path to files for batch conversion
 .TP
-\fB\-r\fP\ \fIstr\fP
+\fB\-r\fP\ \fIpath\fP
 Path for results of batch conversion
 .TP
 \fB\-x\fP\ \fIstr\fP
diff --git a/doc/man/tbl2asn.1 b/doc/man/tbl2asn.1
index 0ca7ba6f..e1b984c6 100644
--- a/doc/man/tbl2asn.1
+++ b/doc/man/tbl2asn.1
@@ -1,4 +1,4 @@
-.TH TBL2ASN 1 2006-05-29 NCBI "NCBI Tools User's Manual"
+.TH TBL2ASN 1 2007-10-19 NCBI "NCBI Tools User's Manual"
 .SH NAME
 tbl2asn \- prepare a GenBank submission using an ASCII feature table
 .SH SYNOPSIS
@@ -6,18 +6,22 @@ tbl2asn \- prepare a GenBank submission using an ASCII feature table
 [\|\fB\-\fP\|]
 [\|\fB\-B\fP\ \fIstr\fP\|]
 [\|\fB\-C\fP\ \fIstr\fP\|]
+[\|\fB\-D\fP\ \fIfilename\fP\|]
 [\|\fB\-E\fP\ \fIstr\fP\|]
-[\|\fB\-F\fP\|]
+[\|\fB\-F\fP\ \fIstr\fP|]
 [\|\fB\-G\fP\ \fIstr\fP\|]
 [\|\fB\-H\fP\|]
+[\|\fB\-K\fP\|]
 [\|\fB\-L\fP\|]
 [\|\fB\-M\fP\ \fIstr\fP\|]
+[\|\fB\-O\fP\|]
 [\|\fB\-P\fP\|]
 [\|\fB\-Q\fP\|]
 [\|\fB\-R\fP\|]
 [\|\fB\-S\fP\|]
 [\|\fB\-T\fP\|]
 [\|\fB\-U\fP\|]
+[\|\fB\-W\fP\|]
 [\|\fB\-X\fP\ \fIstr\fP\|]
 [\|\fB\-Y\fP\ \fIfilename\fP\|]
 [\|\fB\-a\fP\ \fIstr\fP\|]
@@ -25,6 +29,7 @@ tbl2asn \- prepare a GenBank submission using an ASCII feature table
 [\|\fB\-c\fP\|]
 [\|\fB\-d\fP\|]
 [\|\fB\-e\fP\|]
+[\|\fB\-f\fP\ \fIfilename\fP\|]
 [\|\fB\-g\fP\|]
 [\|\fB\-h\fP\|]
 [\|\fB\-i\fP\ \fIfilename\fP\|]
@@ -64,11 +69,14 @@ Alignment Beginning gap characters
 \fB\-C\fP\ \fIstr\fP
 Genome Center tag
 .TP
+\fB\-D\fP\ \fIfilename\fP
+Descriptors file
+.TP
 \fB\-E\fP\ \fIstr\fP
 Alignment End gap characters
 .TP
 \fB\-F\fP
-Feature ID links
+Feature ID links (\fBo\fP by Overlap, \fBp\fP by Product)
 .TP
 \fB\-G\fP\ \fIstr\fP
 Alignment middle Gap characters
@@ -76,12 +84,18 @@ Alignment middle Gap characters
 \fB\-H\fP
 Implicit gaps
 .TP
+\fB\-K\fP
+Safe Bioseq-set
+.TP
 \fB\-L\fP
 Force Local protein_id/transcript_id
 .TP
 \fB\-M\fP\ \fIstr\fP
 Alignment Match characters
 .TP
+\fB\-O\fP
+Allow run-on ORFs
+.TP
 \fB\-P\fP
 Alignment is Proteins
 .TP
@@ -100,6 +114,9 @@ Remote Taxonomy lookup
 \fB\-U\fP
 Remove Unnecessary gene xref
 .TP
+\fB\-W\fP
+Log progress
+.TP
 \fB\-X\fP\ \fIstr\fP
 Alignment missing characters
 .TP
@@ -121,6 +138,9 @@ Read FASTAs as Delta
 \fB\-e\fP
 Read PHRAP/ACE format
 .TP
+\fB\-f\fP\ \fIfilename\fP
+Single table file
+.TP
 \fB\-g\fP
 Input is a genomic product set
 .TP
diff --git a/doc/sdk.doc b/doc/sdk.doc
index 602a2efe..a5bfba61 100644
--- a/doc/sdk.doc
+++ b/doc/sdk.doc
diff --git a/doc/tbl2asn.txt b/doc/tbl2asn.txt
index 6b7bb4c0..7f4fa2d4 100755
--- a/doc/tbl2asn.txt
+++ b/doc/tbl2asn.txt
@@ -62,16 +62,16 @@ that has a .tbl suffix, and then generate a .sqn file.
 The -t command-line argument specifies the template file.
 
 Normally a single FASTA sequence per .fsa file is expected.  If there are
-multiple sequences, only the first is processed, unless one of two other
-flags is given.  These are discussed below.
+multiple sequences, only the first is processed, unless one of two -a flag
+variants are given.  These are discussed below.
 
-The -s flag tells tbl2asn to package the multiple FASTA components as a set
+The -a s flag tells tbl2asn to package the multiple FASTA components as a set
 of unrelated sequences.  This accommodates users who create a single file
-instead of one file per sequence. A single FASTA component can now have gap
+instead of one file per sequence.  A single FASTA component can now have gap
 indications (e.g., >?unk100) on a separate line as long as it is followed
 immediately by more sequence lines, with no > and a mock identifier.
 
-The -d flag tells the program to make a delta sequence out of the multiple
+The -a d flag tells the program to make a delta sequence out of the multiple
 components.  This can be used for HTGS submissions where the sequence of
 the BAC/PAC clone has not been completely determined.  By convention, gaps
 of 100 base pairs should be inserted in between the actual sequence
@@ -89,20 +89,21 @@ transcripts, and all proteins will be entered into the database and given
 accessions.  Note, however, that -g cannot be used for records submitted to
 GenBank.  It is only suitable for records going into RefSeq.
 
-If a feature table is not given, the -c flag tells tbl2asn to annotate the
-longest Open Reading Frame (ORF) on each record.  The -m flag allows
+If a feature table is not given, the -k c flag tells tbl2asn to annotate the
+longest Open Reading Frame (ORF) on each record.  The -k m flag allows
 alternative start codons to be used when finding the ORF.  The protein will
 be named 'unknown' unless the name is present in the .fsa file definition
-line, e.g., [protein=helicase].
+line, e.g., [protein=helicase].  The two flags can be combined as -k cm.
 
-Data records will be validated when the -v flag is indicated.  Output is
+Data records will be validated when the -V v flag is indicated.  Output is
 saved to files with a .val suffix.  The validator checks for many things,
 including internal stops in CDS features and mismatches between the CDS
 translation and the supplied protein sequence.  Errors need to be corrected
 before submitting files to GenBank.
 
-GenBank format output is generated when the -b flag is used.  Resulting
-files have a .gbf suffix.
+GenBank format output is generated when the -V b flag is used.  Resulting
+files have a .gbf suffix.  The validation and flatfile generation flags can
+be combined as -V vb.
 
 
 NUCLEOTIDE SEQUENCE FORMAT
diff --git a/errmsg/valid.msg b/errmsg/valid.msg
index ea171b43..c17a4f2b 100644
--- a/errmsg/valid.msg
+++ b/errmsg/valid.msg
@@ -404,6 +404,14 @@ The lat_lon coordinate does not map to the indicated country.
 $^   LatLonState, 49
 The lat_lon coordinate does not map to the indicated state or province.
 
+$^   BadSpecificHost, 50
+A BioSource descriptor or feature has a specific host value that may
+require a taxonomy consult.
+
+$^   RefGeneTrackingIllegalStatus, 51
+The RefGeneTracking user object has an illegal Status value.
+
+
 $$ GENERIC, 3
 
 $^   NonAsciiAsn, 1
@@ -490,7 +498,7 @@ Bioseq packaged in the set, perhaps within a nuc-prot set.  RefSeq records may
 however be referenced remotely.
 
 $^   InconsistentMolInfoBiomols, 12
-Mol-info.biomol is inconsistent within a segset or parts set.
+Mol-info.biomol is inconsistent within a segset, parts set, or pop/phy/mut/eco set.
 
 $^   ArchaicFeatureLocation, 13
 A feature location should refer to the accession or gi number, not a local or general ID.
@@ -1080,6 +1088,18 @@ and wobble expansion of the anticodon sequence.
 $^   BadAnticodonStrand, 147
 The tRNA feature location and anticodon location are not on the same strand.
 
+$^   UndesiredGeneSynonym, 148
+The gene synonym is uninformative.
+
+$^   UndesiredProteinName, 149
+The protein name is uninformative.
+
+$^ FeatureBeginsOrEndsInGap, 150
+The feature starts or stops within a sequence gap.
+
+$^ GeneOntologyTermMissingGOID, 151
+A Gene Ontology (GO) term is missing the GO Identifier.
+
 $$ SEQ_ALIGN, 6
 
 $^   SeqIdProblem, 1
diff --git a/link/mswin/asnmacro.rc b/link/mswin/asnmacro.rc
new file mode 100644
index 00000000..56ba660a
--- /dev/null
+++ b/link/mswin/asnmacro.rc
@@ -0,0 +1,11 @@
+#include <windows.h>
+#include "ncbirc.h"
+
+STRINGTABLE
+   BEGIN
+   STR_PROGRAM, "Asn Barcode Validator"
+   END
+
+ICO_PROGRAM  ICON ncbilogo.ico
+ICO_NCBILOGO ICON ncbilogo.ico
+
diff --git a/link/mswin/cleanasn.rc b/link/mswin/cleanasn.rc
new file mode 100644
index 00000000..1008aa99
--- /dev/null
+++ b/link/mswin/cleanasn.rc
@@ -0,0 +1,10 @@
+#include <windows.h>
+#include "ncbirc.h"
+
+STRINGTABLE
+   BEGIN
+   STR_PROGRAM, "Cleanasn"
+   END
+
+ICO_PROGRAM  ICON ncbilogo.ico
+ICO_NCBILOGO ICON ncbilogo.ico
diff --git a/link/mswin/cspeedtest.rc b/link/mswin/cspeedtest.rc
new file mode 100644
index 00000000..f2f22922
--- /dev/null
+++ b/link/mswin/cspeedtest.rc
@@ -0,0 +1,10 @@
+#include <windows.h>
+#include "ncbirc.h"
+
+STRINGTABLE
+   BEGIN
+   STR_PROGRAM, "cspeedtest"
+   END
+
+ICO_PROGRAM  ICON ncbilogo.ico
+ICO_NCBILOGO ICON ncbilogo.ico
diff --git a/link/mswin/raw2delt.rc b/link/mswin/raw2delt.rc
new file mode 100644
index 00000000..33730107
--- /dev/null
+++ b/link/mswin/raw2delt.rc
@@ -0,0 +1,11 @@
+#include <windows.h>
+#include "ncbirc.h"
+
+STRINGTABLE
+   BEGIN
+   STR_PROGRAM, "raw2delt"
+   END
+
+ICO_PROGRAM  ICON ncbilogo.ico
+ICO_NCBILOGO ICON ncbilogo.ico
+
diff --git a/make/makeall.unx b/make/makeall.unx
index fdc924c4..cdf8971b 100644
--- a/make/makeall.unx
+++ b/make/makeall.unx
@@ -1,6 +1,6 @@
 #	makefile for asntool and ncbi core routines,
 #
-#	$Id: makeall.unx,v 6.286 2007/08/03 12:42:48 lavr Exp $
+#	$Id: makeall.unx,v 6.291 2008/01/25 19:56:25 ucko Exp $
 #
 #	cdromlib data access functions, vibrant, and entrez
 #	SunOS with unbundled ANSI compiler [ make LCL=acc RAN=ranlib CC=acc ]
@@ -188,18 +188,18 @@ SRC1 =	ncbimain.c $(SRC1e)
 SRC2 =	objacces.c objalign.c objall.c objbibli.c \
 	objfeat.c objgen.c objloc.c objmedli.c objpub.c \
 	objres.c objscoremat.c objseq.c objblock.c objcode.c objsset.c \
-	objsub.c objprt.c objfdef.c objalignloc.c \
-	objpubme.c objmdrs.c objproj.c objgbseq.c objtseq.c objinsdseq.c \
+	objsub.c objprt.c objfdef.c objalignloc.c objtable.c \
+	objpubme.c objmdrs.c objproj.c objgbseq.c objtseq.c objinsdseq.c objmacro.c \
 	objent2.c ent2api.c pmfapi.c objtax3.c tax3api.c objegkludge.c objentgene.c \
 	objmla2.c mla2api.c qblastapi.c vecscnapi.c objmim.c mimapi.c cddapi.c seqport.c \
 	sequtil.c prtutil.c simple.c tofasta.c tofile.c tomedlin.c \
 	valid.c alignmgr.c aliparse.c aliread.c alignval.c sqnutil1.c sqnutil2.c sqnutil3.c \
-	subutil.c edutil.c asn2ff1.c asn2ff2.c asn2ff3.c asn2ff4.c \
+	sqnutil4.c subutil.c edutil.c asn2ff1.c asn2ff2.c asn2ff3.c asn2ff4.c \
 	asn2ff5.c asn2ff6.c asn2gnb1.c asn2gnb2.c asn2gnb3.c asn2gnb4.c \
 	asn2gnb5.c asn2gnb6.c ftusrstr.c gbfeat.c gbftglob.c \
 	gbparint.c utilpars.c utilpub.c ffprint.c wprint.c satutil.c \
 	seqmgr.c objmgr.c gather.c accmmdbs.c acccn3ds.c lsqfetch.c findrepl.c \
-	codon.c jzcoll.c jzmisc.c maputil.c mconsist.c \
+	codon.c jzcoll.c jzmisc.c maputil.c mconsist.c macroapi.c \
 	salpedit.c salpstat.c salpacc.c salprop.c salsap.c salstruc.c salutil.c \
 	udvseq.c blocks.c pgppop.c samutil.c ddvcolor.c viewmgr.c ddvcreate.c \
 	jsavlt.c needleman.c txalign.c fdlobj.c alignmgr2.c alnread.c
@@ -232,7 +232,7 @@ SRC20 = drawseq.c dotmatrx.c fea2seg.c fstyle.c smdlg1.c smdlg2.c smdlg3.c \
 	vsm.c vsmfile.c vsmutil.c udvgraph.c udvopen.c udvpanel.c dotvibrant.c \
 	dlgutil1.c dlgutil2.c e2trmlst.c e2docsum.c asn2graphic.c \
 	medview.c bspview.c gbfview.c gphview.c gphdraw.c gxydraw.c gtrdraw.c \
-	seqpanel.c ingengraph.c ingenext.c ingenwin.c \
+	seqpanel.c ingengraph.c ingenext.c ingenwin.c macrodlg.c \
 	biosrc.c cdrgn.c import.c pubdesc.c seqsub.c mapgene.c prtgene.c salogif.c
 
 SRC45 = ddvclick.c ddvgraph.c ddvopen.c ddvpanel.c
@@ -304,6 +304,9 @@ SRC61 = blast_api.c blast_format.c blast_input.c blast_mtlock.c \
         seqsrc_multiseq.c seqsrc_readdb.c twoseq_api.c dust_filter.c \
         blast_message_api.c
 
+SRCALL = $(THR_SRC) $(SRC1) $(SRC2) $(SRC3) $(SRC4) $(SRC5) $(SRC20) $(SRC22) \
+    $(SRC23) $(SRC28) $(SRC30) $(SRC50) $(SRC60) $(SRC61) $(SRCCOMPADJ)
+
 # objects needed for versions of asntool and entrez
 
 THR_OBJ = ncbithr.o
@@ -329,18 +332,18 @@ OBJ1 =	ncbimain.o $(OBJ1e)
 OBJ2 =	objacces.o objalign.o objall.o objbibli.o \
 	objfeat.o objgen.o objloc.o objmedli.o objpub.o \
 	objres.o objscoremat.o objseq.o objblock.o objcode.o objsset.o \
-	objsub.o objprt.o objfdef.o objalignloc.o \
-	objpubme.o objmdrs.o objproj.o objgbseq.o objtseq.o objinsdseq.o \
+	objsub.o objprt.o objfdef.o objalignloc.o objtable.o \
+	objpubme.o objmdrs.o objproj.o objgbseq.o objtseq.o objinsdseq.o objmacro.o \
 	objent2.o ent2api.o pmfapi.o objtax3.o tax3api.o objegkludge.o objentgene.o \
 	objmla2.o mla2api.o qblastapi.o vecscnapi.o objmim.o mimapi.o cddapi.o seqport.o \
 	sequtil.o prtutil.o simple.o tofasta.o tofile.o tomedlin.o \
 	valid.o alignmgr.o aliparse.o aliread.o alignval.o sqnutil1.o sqnutil2.o sqnutil3.o \
-	subutil.o edutil.o asn2ff1.o asn2ff2.o asn2ff3.o asn2ff4.o \
+	sqnutil4.o subutil.o edutil.o asn2ff1.o asn2ff2.o asn2ff3.o asn2ff4.o \
 	asn2ff5.o asn2ff6.o asn2gnb1.o asn2gnb2.o asn2gnb3.o asn2gnb4.o \
 	asn2gnb5.o asn2gnb6.o ftusrstr.o gbfeat.o gbftglob.o \
 	gbparint.o utilpars.o utilpub.o ffprint.o wprint.o satutil.o \
 	seqmgr.o objmgr.o gather.o accmmdbs.o acccn3ds.o lsqfetch.o findrepl.o \
-	codon.o jzcoll.o jzmisc.o maputil.o mconsist.o \
+	codon.o jzcoll.o jzmisc.o maputil.o mconsist.o macroapi.o \
 	salpedit.o salpstat.o salpacc.o salprop.o salsap.o salstruc.o salutil.o \
 	udvseq.o blocks.o pgppop.o samutil.o ddvcolor.o viewmgr.o ddvcreate.o \
 	jsavlt.o needleman.o txalign.o fdlobj.o alignmgr2.o alnread.o
@@ -383,7 +386,7 @@ OBJ20 = drawseq.o dotmatrx.o fea2seg.o fstyle.o smdlg1.o smdlg2.o smdlg3.o \
 	vsm.o vsmfile.o vsmutil.o udvgraph.o udvopen.o udvpanel.o dotvibrant.o \
 	dlgutil1.o dlgutil2.o e2trmlst.o e2docsum.o asn2graphic.o \
 	medview.o bspview.o gbfview.o gphview.o gphdraw.o gxydraw.o gtrdraw.o \
-	seqpanel.o ingengraph.o ingenext.o ingenwin.o \
+	seqpanel.o ingengraph.o ingenext.o ingenwin.o macrodlg.o \
 	biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o salogif.o
 
 OBJ45 = ddvclick.o ddvgraph.o ddvopen.o ddvpanel.o
@@ -483,8 +486,7 @@ nocopy : sources $(THR_OBJ) $(LIB1) $(LIB2) $(LIB3) $(DLIB4) $(DLIB400) \
 	$(DLIB28) $(DLIB30) $(DLIB3000) \
 	$(DLIB34) $(DLIB37) $(DLIB38) $(LIB50) $(LIB60) $(LIB61) $(NCBI_SHLIBS)
 
-sources : $(THR_SRC) $(SRC1) $(SRC2) $(SRC3) $(SRC4) $(SRC5) $(SRC20) $(SRC22) \
-    $(SRC23) $(SRC28) $(SRC30) $(SRC50) $(SRC60) $(SRC61) $(SRCCOMPADJ)
+sources : $(SRCALL)
 
 ## To clean out the directory without removing make
 ##
@@ -669,6 +671,8 @@ shlib.alf :
 ## get all the source files
 ##
 
+$(SRCALL) : copy
+
 copy :
 	-chmod -R ug+rw,o+r . ../include
 	$(SRCCOPY) ../corelib/tsprintf.h ../include
@@ -714,6 +718,7 @@ copy :
 	-mkdir -p ../include/util/creaders
 	cp -fp ../util/creaders/*.h ../include/util/creaders
 	$(SRCCOPY) ../ctools/*.c .
+	$(SRCCOPY) ../ctools/*.h .
 	-mkdir ../include/ctools
 	-chmod ug+rw,o+r ../include/ctools
 	cp -fp ../ctools/*.h ../include/ctools
diff --git a/make/makeallchives b/make/makeallchives
index 2e8a1826..6c841e7a 100755
--- a/make/makeallchives
+++ b/make/makeallchives
@@ -1,6 +1,6 @@
 #!/bin/sh
 #
-# $Id: makeallchives,v 1.83 2006/08/30 12:10:29 ivanov Exp $
+# $Id: makeallchives 117677 2008-01-18 17:07:17Z vakatov $
 #
 #
 # Creates all archives from a directory above 'ncbi'
diff --git a/make/makedemo.unx b/make/makedemo.unx
index 6a89a7df..f1d6c534 100644
--- a/make/makedemo.unx
+++ b/make/makedemo.unx
@@ -1,6 +1,6 @@
 #	makefile for demo programs
 #
-#	$Id: makedemo.unx,v 6.87 2006/11/16 15:36:19 coulouri Exp $
+#	$Id: makedemo.unx,v 6.88 2008/01/25 19:56:25 ucko Exp $
 #
 #	Sun with unbundled ANSI compiler [ make CC=acc ]
 #	Sun with Gnu C [ make CC=gcc ]
@@ -150,6 +150,8 @@ clean :
 ## get all the source files
 ##
 
+$(SRC1) : copy
+
 copy :
 	$(SRCCOPY) ../demo/*.* .
 	$(SRCCOPY) ../regexp/test/*.* .
diff --git a/make/makedis.csh b/make/makedis.csh
index 3f977b8b..98f1e39e 100755
--- a/make/makedis.csh
+++ b/make/makedis.csh
@@ -1,6 +1,6 @@
 #!/bin/csh -f
 #
-# $Id: makedis.csh,v 1.116 2007/05/09 16:06:55 ucko Exp $
+# $Id: makedis.csh 117677 2008-01-18 17:07:17Z vakatov $
 #
 ##                            PUBLIC DOMAIN NOTICE                          
 #               National Center for Biotechnology Information
diff --git a/make/makeindx.unx b/make/makeindx.unx
index 365c5967..d7be0dae 100644
--- a/make/makeindx.unx
+++ b/make/makeindx.unx
@@ -1,6 +1,6 @@
 #	makefile for flat2asn
 #
-#	$Id: makeindx.unx,v 6.5 2002/06/17 14:27:20 ivanov Exp $
+#	$Id: makeindx.unx,v 6.6 2008/01/25 19:56:25 ucko Exp $
 #
 #	Sun with unbundled ANSI compiler [ make LCL=acc RAN=ranlib CC=acc ]
 #	Sun with Gnu C [ make LCL=gcc RAN=ranlib CC=gcc ]
@@ -61,6 +61,8 @@ SRC_P = add.c asci_blk.c citation.c flat2asn.c flatargs.c \
 		nucprot.c ref.c sp_global.c sp_ref.c sp_ascii.c\
 		taxcash.c utilfeat.c utilref.c 
 
+SRC_ALL = $(SRC_I) $(SRC_P)
+
 # objects needed for indexing and parsing
 
 OBJ_I = indx_blk.o block.o entry.o gb_index.o em_index.o \
@@ -77,7 +79,7 @@ all : copy .WAIT nocopy flat2asn
 
 nocopy : sources $(LIBPARSE)
 
-sources : $(SRC_I) $(SRC_P)
+sources : $(SRC_ALL)
 
 ## To clean out the directory without removing make
 ##
@@ -96,6 +98,8 @@ clean :
 ## get all the source files
 ##
 
+$(SRC_ALL) : copy
+
 copy :
 	- chmod -R ug+rw,o+r .
 	$(SRCCOPY) ../internal/parser/*.h ../include
diff --git a/make/makenet.unx b/make/makenet.unx
index 7df93375..46839d7e 100644
--- a/make/makenet.unx
+++ b/make/makenet.unx
@@ -1,6 +1,6 @@
 #   makefile for network demo programs and network entrez
 #
-#	$Id: makenet.unx,v 6.219 2007/04/18 15:52:34 kans Exp $
+#	$Id: makenet.unx,v 6.224 2008/01/25 19:56:25 ucko Exp $
 #   test, ignore
 #
 #   Sun with unbundled ANSI compiler [ make CC=acc RAN=ranlib ]
@@ -85,6 +85,7 @@ BLIB12 = libncbitax.a
 BLIB13 = libncbiid0.a
 #BLIB14 = libncbibls0.a
 BLIB19 = libncbispel.a
+BLIB22 = libncbimmdb.a
 BLIB23 = libncbitool.a
 BLIBCOMPADJ = libblastcompadj.a
 BLIB24 = libncbisugg.a
@@ -252,7 +253,7 @@ SRC27 = indexlist.c isamlist.c memmap.c miscutils.c
 
 SRC31 = netcnfg.c trmlst.c docsum.c
 
-SRC33 = smartnet.c
+SRC33 = smartnet.c namedpipe.c
 
 SRC35 = ssputil.c
 
@@ -300,7 +301,7 @@ OBJ27 = indexlist.o isamlist.o memmap.o miscutils.o
 
 OBJ31 = netcnfg.o trmlst.o docsum.o
 
-OBJ33 = smartnet.o
+OBJ33 = smartnet.o namedpipe.o
 
 OBJ35 = ssputil.o
 
@@ -366,6 +367,8 @@ SERV_SRC = $(SRCENTSRV)
 
 SERVERS = $(EXESUGGSRV) $(EXEQUERY) $(EXESEQUIN) $(EXEPSEQUIN) $(EXESBTEDIT) $(EXENQUERY)
 
+ALL_SRC = $(NET_LIBS_SRC) $(CLI_SRC) $(SERV_SRC)
+
 ## All things to make
 ##
 all : ln-if-absent copy .WAIT nocopy
@@ -378,7 +381,7 @@ nocopy : sources $(BLIB6) $(BLIB7) $(BLIB8) $(BLIB9) \
    $(DLIB31) $(DLIB33) $(NCBI_SHLIBS) $(CLIENTS) $(VIB) \
    $(DLIB42) $(DLIB43) $(DLIB44)
 
-sources : $(NET_LIBS_SRC) $(CLI_SRC)
+sources : $(ALL_SRC)
 
 servers : $(SERV_SRC) $(SERVERS)
 
@@ -386,7 +389,7 @@ utilities : $(EXEUTIL)
 
 vibutilities : $(EXEUTILVIB)
 
-.NO_PARALLEL:	copy nocopy Tentrez sequin Psequin sbtedit Ssequin elecpcr asn2fast asn2asn cleanasn Nbatch Nbatch3 Nentrcmd seqget idfetch test_ncbi_socket test_ncbi_dsock debug_server rtestval rasn2ff asn2gb asn2gb_psf asn2fsa asn2fsa_psf tbl2asn tbl2asn_psf asn2all gene2xml asnval asnval_psf asndisc asndisc_psf asnstrip flint gbseqget insdseqget trna2sap trna2tbl testent2 entrez2 spidey dotmatrix ingenue condense bl2seq
+.NO_PARALLEL:	copy nocopy Tentrez sequin Psequin sbtedit Ssequin elecpcr asn2fast asn2asn cleanasn cspeedtest Nbatch Nbatch3 Nentrcmd seqget idfetch test_ncbi_socket test_ncbi_dsock debug_server rtestval rasn2ff asn2gb asn2gb_psf asn2fsa asn2fsa_psf tbl2asn tbl2asn_psf raw2delt asn2all gene2xml asnval asnval_psf asndisc asndisc_psf asnmacro asnstrip flint gbseqget insdseqget trna2sap trna2tbl testent2 entrez2 spidey dotmatrix ingenue condense bl2seq
 
 .WAIT:
 	echo Waiting...go
@@ -451,6 +454,8 @@ shlib.alf :
 	rm -f ../shlib/*.a
 
 
+$(ALL_SRC) : copy
+
 copy :
 	$(SRCCOPY) ../connect/test/*.c .
 	$(SRCCOPY) ../network/entrez/client/*.h ../include
@@ -515,6 +520,7 @@ copy :
 	$(SRCCOPY) ../demo/asn2fast.c .
 	$(SRCCOPY) ../demo/asn2asn.c .
 	$(SRCCOPY) ../demo/cleanasn.c .
+	$(SRCCOPY) ../demo/cspeedtest.c .
 	$(SRCCOPY) ../demo/fetchent.c .
 	$(SRCCOPY) ../demo/udvmain.c .
 	$(SRCCOPY) ../demo/rtestval.c .
@@ -525,8 +531,10 @@ copy :
 	$(SRCCOPY) ../demo/gene2xml.c .
 	$(SRCCOPY) ../demo/asnval.c .
 	$(SRCCOPY) ../demo/asndisc.c .
+	$(SRCCOPY) ../demo/asnmacro.c .
 	$(SRCCOPY) ../demo/asnstrip.c .
 	$(SRCCOPY) ../demo/tbl2asn.c .
+	$(SRCCOPY) ../demo/raw2delt.c .
 	$(SRCCOPY) ../demo/flint.c .
 	$(SRCCOPY) ../demo/gbseqget.c .
 	$(SRCCOPY) ../demo/insdseqget.c .
@@ -694,6 +702,8 @@ docsum.o : docsum.c
 	$(CC) $(CFLAGS) docsum.c
 smartnet.o : smartnet.c
 	$(CC) $(CFLAGS) smartnet.c
+namedpipe.o : namedpipe.c
+	$(CC) $(CFLAGS) namedpipe.c
 ssputil.o : ssputil.c
 	$(CC) $(CFLAGS) ssputil.c
 objblst3.o : objblst3.c
@@ -986,7 +996,7 @@ asn2all :	asn2all.c
 # tbl2asn
 tbl2asn : tbl2asn.c 
 	$(CC) -o tbl2asn $(LDFLAGS) tbl2asn.c $(LIB23) $(LIBCOMPADJ) \
-		$(LIB2) $(NETCLILIB) $(LIB1) $(OTHERLIBS) 
+		$(LIB2) $(NETCLILIB) $(LIB1) $(OTHERLIBS)
 
 # tbl2asn_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
 # should be used only internally within NCBI.
@@ -995,6 +1005,11 @@ tbl2asn_psf : tbl2asn.c
 	$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(NCBI_SYBLIBS_CT_r) \
 	$(OTHERLIBS) $(THREAD_OTHERLIBS)
 
+# raw2delt
+raw2delt : raw2delt.c 
+	$(CC) -o raw2delt $(LDFLAGS) raw2delt.c $(LIB22) $(LIBCOMPADJ) \
+		$(LIB2) $(NETCLILIB) $(LIB1) $(OTHERLIBS)
+
 # gene2xml program (gene2xml)
 gene2xml :	gene2xml.c
 	$(CC) -g -o gene2xml $(LDFLAGS) gene2xml.c $(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS)
@@ -1032,10 +1047,15 @@ asndisc_psf :	asndisc.c
 	$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(NCBI_SYBLIBS_CT_r) \
 	$(OTHERLIBS) $(THREAD_OTHERLIBS)
 
+# asnmacro
+asnmacro : asnmacro.c 
+	$(CC) -o asnmacro $(LDFLAGS) asnmacro.c $(LIB61) $(LIB60) $(LIB23) $(LIBCOMPADJ) \
+		$(LIB2) $(LIB1) $(OTHERLIBS)
+
 # asnstrip program (asnstrip)
 asnstrip : asnstrip.c 
 	$(CC) -o asnstrip $(LDFLAGS) asnstrip.c $(LIB23) $(LIBCOMPADJ) \
-		$(LIB2) $(NETCLILIB) $(LIB1) $(OTHERLIBS) 
+		$(LIB2) $(NETCLILIB) $(LIB1) $(OTHERLIBS)
 
 # flint program (flint)
 flint :	flint.c
@@ -1118,6 +1138,11 @@ asn2asn : asn2asn.c
 cleanasn : cleanasn.c
 	$(CC) -o cleanasn $(LDFLAGS) cleanasn.c $(LIB41) $(LIB23) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS)
 
+# demo program (cspeedtest)
+
+cspeedtest : cspeedtest.c
+	$(CC) -o cspeedtest $(LDFLAGS) cspeedtest.c $(LIB41) $(LIB23) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS)
+
 # demo program (fetchent)
 
 fetchent : fetchent.c
diff --git a/make/msvc800_prj/algo/blast/api/blastapi.vcproj b/make/msvc800_prj/algo/blast/api/blastapi.vcproj
index 5883b749..0dd9f4c3 100644
--- a/make/msvc800_prj/algo/blast/api/blastapi.vcproj
+++ b/make/msvc800_prj/algo/blast/api/blastapi.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="blastapi"
-	ProjectGUID="{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}"
+	ProjectGUID="{6058EDC4-453A-48B1-8E27-83820FFB7203}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/algo/blast/composition_adjustment/blastcompadj.vcproj b/make/msvc800_prj/algo/blast/composition_adjustment/blastcompadj.vcproj
index 2183be1b..60792fad 100644
--- a/make/msvc800_prj/algo/blast/composition_adjustment/blastcompadj.vcproj
+++ b/make/msvc800_prj/algo/blast/composition_adjustment/blastcompadj.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="blastcompadj"
-	ProjectGUID="{F7164C61-0D7C-4EC8-9209-88A760907B6B}"
+	ProjectGUID="{A2E2AE46-C7B9-4544-B138-6F7662DF2216}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/algo/blast/core/blast.vcproj b/make/msvc800_prj/algo/blast/core/blast.vcproj
index 1bb205dc..97107994 100644
--- a/make/msvc800_prj/algo/blast/core/blast.vcproj
+++ b/make/msvc800_prj/algo/blast/core/blast.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="blast"
-	ProjectGUID="{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}"
+	ProjectGUID="{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/all.vcproj b/make/msvc800_prj/all.vcproj
index 4a9058d2..ba359739 100644
--- a/make/msvc800_prj/all.vcproj
+++ b/make/msvc800_prj/all.vcproj
@@ -3,8 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="all"
-	ProjectGUID="{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}"
-	RootNamespace="all"
+	ProjectGUID="{347672C9-B4CA-4B21-8281-51955A9C50AC}"
 	Keyword="MakeFileProj"
 	>
 	<Platforms>
diff --git a/make/msvc800_prj/all_demo.vcproj b/make/msvc800_prj/all_demo.vcproj
index 1ce4f9f5..7839af29 100644
--- a/make/msvc800_prj/all_demo.vcproj
+++ b/make/msvc800_prj/all_demo.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="all_demo"
-	ProjectGUID="{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}"
+	ProjectGUID="{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}"
 	Keyword="MakeFileProj"
 	>
 	<Platforms>
diff --git a/make/msvc800_prj/all_exe.vcproj b/make/msvc800_prj/all_exe.vcproj
index e8ece846..51da1032 100644
--- a/make/msvc800_prj/all_exe.vcproj
+++ b/make/msvc800_prj/all_exe.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="all_exe"
-	ProjectGUID="{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}"
+	ProjectGUID="{4DFAAB85-944C-4B34-A3C0-70370B655451}"
 	Keyword="MakeFileProj"
 	>
 	<Platforms>
diff --git a/make/msvc800_prj/all_lib.vcproj b/make/msvc800_prj/all_lib.vcproj
index e5f64496..63933af6 100644
--- a/make/msvc800_prj/all_lib.vcproj
+++ b/make/msvc800_prj/all_lib.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="all_lib"
-	ProjectGUID="{0204EA88-C175-4970-922F-6F2C4FDA52EE}"
+	ProjectGUID="{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}"
 	Keyword="MakeFileProj"
 	>
 	<Platforms>
diff --git a/make/msvc800_prj/all_ncbi.vcproj b/make/msvc800_prj/all_ncbi.vcproj
index e28e3ded..69b59a83 100644
--- a/make/msvc800_prj/all_ncbi.vcproj
+++ b/make/msvc800_prj/all_ncbi.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="all_ncbi"
-	ProjectGUID="{04452BB8-39AC-4DC3-8C42-58384D285FED}"
+	ProjectGUID="{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}"
 	Keyword="MakeFileProj"
 	>
 	<Platforms>
diff --git a/make/msvc800_prj/asnlib/asntool/exe_asntool.vcproj b/make/msvc800_prj/asnlib/asntool/exe_asntool.vcproj
index bca835b5..5af45993 100644
--- a/make/msvc800_prj/asnlib/asntool/exe_asntool.vcproj
+++ b/make/msvc800_prj/asnlib/asntool/exe_asntool.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="exe_asntool"
-	ProjectGUID="{9AA6C9C9-1442-48CD-BD94-F134953418A9}"
+	ProjectGUID="{95BF266E-0195-4BEB-B306-B99489EE3991}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/biostruc/ncbimmdb.vcproj b/make/msvc800_prj/biostruc/ncbimmdb.vcproj
index dfad6d5f..e2a67143 100644
--- a/make/msvc800_prj/biostruc/ncbimmdb.vcproj
+++ b/make/msvc800_prj/biostruc/ncbimmdb.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbimmdb"
-	ProjectGUID="{98C1A680-89B6-4911-8C36-42D14F43B868}"
+	ProjectGUID="{2DD94017-2F95-470D-94F5-9F10AD650BDC}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/cdromlib/ncbiacc/ncbiacc.vcproj b/make/msvc800_prj/cdromlib/ncbiacc/ncbiacc.vcproj
index 23933a32..99b8be41 100644
--- a/make/msvc800_prj/cdromlib/ncbiacc/ncbiacc.vcproj
+++ b/make/msvc800_prj/cdromlib/ncbiacc/ncbiacc.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbiacc"
-	ProjectGUID="{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}"
+	ProjectGUID="{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/cdromlib/ncbicdr/ncbicdr.vcproj b/make/msvc800_prj/cdromlib/ncbicdr/ncbicdr.vcproj
index 90a39aec..bf841265 100644
--- a/make/msvc800_prj/cdromlib/ncbicdr/ncbicdr.vcproj
+++ b/make/msvc800_prj/cdromlib/ncbicdr/ncbicdr.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbicdr"
-	ProjectGUID="{3C4476FB-5518-425A-9D4E-44DD91068776}"
+	ProjectGUID="{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/cdromlib/ncbinacc/ncbinacc.vcproj b/make/msvc800_prj/cdromlib/ncbinacc/ncbinacc.vcproj
index 106cef91..fc08b41f 100644
--- a/make/msvc800_prj/cdromlib/ncbinacc/ncbinacc.vcproj
+++ b/make/msvc800_prj/cdromlib/ncbinacc/ncbinacc.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbinacc"
-	ProjectGUID="{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}"
+	ProjectGUID="{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/cn3d/ncbicn3d/ncbicn3d.vcproj b/make/msvc800_prj/cn3d/ncbicn3d/ncbicn3d.vcproj
index cae62497..4e6567d4 100644
--- a/make/msvc800_prj/cn3d/ncbicn3d/ncbicn3d.vcproj
+++ b/make/msvc800_prj/cn3d/ncbicn3d/ncbicn3d.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbicn3d"
-	ProjectGUID="{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}"
+	ProjectGUID="{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/cn3d/ncbicn3d_ogl/ncbicn3d_ogl.vcproj b/make/msvc800_prj/cn3d/ncbicn3d_ogl/ncbicn3d_ogl.vcproj
index 424e6ea1..113625b2 100644
--- a/make/msvc800_prj/cn3d/ncbicn3d_ogl/ncbicn3d_ogl.vcproj
+++ b/make/msvc800_prj/cn3d/ncbicn3d_ogl/ncbicn3d_ogl.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbicn3d_ogl"
-	ProjectGUID="{B5934B23-8476-4D68-9769-2A65BF5C33A4}"
+	ProjectGUID="{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/http_connector_hit/http_connector_hit.vcproj b/make/msvc800_prj/connect/test/http_connector_hit/http_connector_hit.vcproj
index 18775d5e..35ae2ecf 100644
--- a/make/msvc800_prj/connect/test/http_connector_hit/http_connector_hit.vcproj
+++ b/make/msvc800_prj/connect/test/http_connector_hit/http_connector_hit.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="http_connector_hit"
-	ProjectGUID="{A73BBA44-40FF-4306-AF50-94737CD49839}"
+	ProjectGUID="{6266F193-8E41-4543-BB84-4DEA87146A44}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/socket_io_bouncer/socket_io_bouncer.vcproj b/make/msvc800_prj/connect/test/socket_io_bouncer/socket_io_bouncer.vcproj
index 9d559d67..962ae180 100644
--- a/make/msvc800_prj/connect/test/socket_io_bouncer/socket_io_bouncer.vcproj
+++ b/make/msvc800_prj/connect/test/socket_io_bouncer/socket_io_bouncer.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="socket_io_bouncer"
-	ProjectGUID="{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}"
+	ProjectGUID="{BC50422E-D841-4EDF-B987-5135EC4D8F11}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_buffer/test_ncbi_buffer.vcproj b/make/msvc800_prj/connect/test/test_ncbi_buffer/test_ncbi_buffer.vcproj
index d0788f36..7fe90d3d 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_buffer/test_ncbi_buffer.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_buffer/test_ncbi_buffer.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_buffer"
-	ProjectGUID="{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}"
+	ProjectGUID="{2EDD4E60-025D-4167-B827-9A700DFA6D72}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_connutil_hit/test_ncbi_connutil_hit.vcproj b/make/msvc800_prj/connect/test/test_ncbi_connutil_hit/test_ncbi_connutil_hit.vcproj
index 5f07c0d6..d143e972 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_connutil_hit/test_ncbi_connutil_hit.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_connutil_hit/test_ncbi_connutil_hit.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_connutil_hit"
-	ProjectGUID="{AD565A88-01DA-4401-8E8F-53CCF8C759B5}"
+	ProjectGUID="{760EA748-5473-48CE-8BE0-76538A0CE1B2}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_connutil_misc/test_ncbi_connutil_misc.vcproj b/make/msvc800_prj/connect/test/test_ncbi_connutil_misc/test_ncbi_connutil_misc.vcproj
index 5b0c5f40..c7853310 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_connutil_misc/test_ncbi_connutil_misc.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_connutil_misc/test_ncbi_connutil_misc.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_connutil_misc"
-	ProjectGUID="{E85F8917-C596-477B-8D92-851E3726DE96}"
+	ProjectGUID="{9218C976-8194-4AD4-BC5C-7CBC456C2475}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_core/test_ncbi_core.vcproj b/make/msvc800_prj/connect/test/test_ncbi_core/test_ncbi_core.vcproj
index 13d1424c..85685766 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_core/test_ncbi_core.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_core/test_ncbi_core.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_core"
-	ProjectGUID="{A6AC837C-8852-48B3-9232-57A2493AEDA4}"
+	ProjectGUID="{167BDE33-267C-49EE-9AC5-6177D283D799}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_disp/test_ncbi_disp.vcproj b/make/msvc800_prj/connect/test/test_ncbi_disp/test_ncbi_disp.vcproj
index 98414ac1..d2373d3a 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_disp/test_ncbi_disp.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_disp/test_ncbi_disp.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_disp"
-	ProjectGUID="{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}"
+	ProjectGUID="{087A2516-3C90-4D46-AEA9-670592894CB4}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_dsock/test_ncbi_dsock.vcproj b/make/msvc800_prj/connect/test/test_ncbi_dsock/test_ncbi_dsock.vcproj
index bedfe9a0..77e43d4e 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_dsock/test_ncbi_dsock.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_dsock/test_ncbi_dsock.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_dsock"
-	ProjectGUID="{032E43BB-816C-4BEE-9ABD-1E0B599C007A}"
+	ProjectGUID="{3B976840-4F3F-46A9-832D-4AB79417F712}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_file_connector/test_ncbi_file_connector.vcproj b/make/msvc800_prj/connect/test/test_ncbi_file_connector/test_ncbi_file_connector.vcproj
index 44c26c42..affa74e0 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_file_connector/test_ncbi_file_connector.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_file_connector/test_ncbi_file_connector.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_file_connector"
-	ProjectGUID="{57BABFE8-331D-41A9-8776-314F2D8791E2}"
+	ProjectGUID="{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_http_connector/test_ncbi_http_connector.vcproj b/make/msvc800_prj/connect/test/test_ncbi_http_connector/test_ncbi_http_connector.vcproj
index 36805175..ed177417 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_http_connector/test_ncbi_http_connector.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_http_connector/test_ncbi_http_connector.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_http_connector"
-	ProjectGUID="{8B6B0E08-62BA-4E92-8672-06CCA7432096}"
+	ProjectGUID="{862D2BCD-67ED-4398-A811-7E247C2029E5}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_http_get/test_ncbi_http_get.vcproj b/make/msvc800_prj/connect/test/test_ncbi_http_get/test_ncbi_http_get.vcproj
index 1be6af23..471d873a 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_http_get/test_ncbi_http_get.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_http_get/test_ncbi_http_get.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_http_get"
-	ProjectGUID="{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}"
+	ProjectGUID="{DD51F357-26FE-46F2-9AC9-5B682DBC198C}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_memory_connector/test_ncbi_memory_connector.vcproj b/make/msvc800_prj/connect/test/test_ncbi_memory_connector/test_ncbi_memory_connector.vcproj
index ccd5db0d..ee528472 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_memory_connector/test_ncbi_memory_connector.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_memory_connector/test_ncbi_memory_connector.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_memory_connector"
-	ProjectGUID="{42140DF3-03C5-4A99-9D7B-F4385733D694}"
+	ProjectGUID="{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_sendmail/test_ncbi_sendmail.vcproj b/make/msvc800_prj/connect/test/test_ncbi_sendmail/test_ncbi_sendmail.vcproj
index 076a3a86..1a29a535 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_sendmail/test_ncbi_sendmail.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_sendmail/test_ncbi_sendmail.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_sendmail"
-	ProjectGUID="{AA4B7095-5FBB-41E5-AE2A-39247638EC14}"
+	ProjectGUID="{E459338E-39A8-49C9-9DFC-612E47863CE3}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_service_connector/test_ncbi_service_connector.vcproj b/make/msvc800_prj/connect/test/test_ncbi_service_connector/test_ncbi_service_connector.vcproj
index c242b4b7..ea5e7655 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_service_connector/test_ncbi_service_connector.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_service_connector/test_ncbi_service_connector.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_service_connector"
-	ProjectGUID="{A40959E8-B640-49F7-B2E0-806A03544AB5}"
+	ProjectGUID="{7719A61E-FAE1-4564-AD24-416318E48967}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_socket/test_ncbi_socket.vcproj b/make/msvc800_prj/connect/test/test_ncbi_socket/test_ncbi_socket.vcproj
index e3e9b960..2bd0bb4d 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_socket/test_ncbi_socket.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_socket/test_ncbi_socket.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_socket"
-	ProjectGUID="{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}"
+	ProjectGUID="{E6CE793E-7882-4E77-9D26-22C950DE0AFE}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/test_ncbi_socket_connector/test_ncbi_socket_connector.vcproj b/make/msvc800_prj/connect/test/test_ncbi_socket_connector/test_ncbi_socket_connector.vcproj
index e8309ed5..d34ce1e4 100644
--- a/make/msvc800_prj/connect/test/test_ncbi_socket_connector/test_ncbi_socket_connector.vcproj
+++ b/make/msvc800_prj/connect/test/test_ncbi_socket_connector/test_ncbi_socket_connector.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_ncbi_socket_connector"
-	ProjectGUID="{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}"
+	ProjectGUID="{9AAE2D3F-4D37-43B6-96EB-593DE7679811}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/connect/test/xconntest.vcproj b/make/msvc800_prj/connect/test/xconntest.vcproj
index a3f1d3bb..e48a44ac 100644
--- a/make/msvc800_prj/connect/test/xconntest.vcproj
+++ b/make/msvc800_prj/connect/test/xconntest.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="xconntest"
-	ProjectGUID="{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}"
+	ProjectGUID="{A9561C14-6DAF-4A28-9F59-297D39432D0B}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/corelib/ncbi/ncbi.vcproj b/make/msvc800_prj/corelib/ncbi/ncbi.vcproj
index abcc3d23..3b76d224 100644
--- a/make/msvc800_prj/corelib/ncbi/ncbi.vcproj
+++ b/make/msvc800_prj/corelib/ncbi/ncbi.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbi"
-	ProjectGUID="{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}"
+	ProjectGUID="{F6DB30E7-94C5-4760-92FA-449884953A9D}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/corelib/ncbiconfig.vcproj b/make/msvc800_prj/corelib/ncbiconfig.vcproj
index 6a44c2fa..41138539 100644
--- a/make/msvc800_prj/corelib/ncbiconfig.vcproj
+++ b/make/msvc800_prj/corelib/ncbiconfig.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbiconfig"
-	ProjectGUID="{CF596340-202E-4E79-B041-F4310A422C20}"
+	ProjectGUID="{74B970B2-6C7F-4AEE-9031-27CC087D7214}"
 	Keyword="MakeFileProj"
 	>
 	<Platforms>
diff --git a/make/msvc800_prj/corelib/ncbimain/ncbimain.vcproj b/make/msvc800_prj/corelib/ncbimain/ncbimain.vcproj
index 921e705f..c6a20e57 100644
--- a/make/msvc800_prj/corelib/ncbimain/ncbimain.vcproj
+++ b/make/msvc800_prj/corelib/ncbimain/ncbimain.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbimain"
-	ProjectGUID="{35C18E88-9F42-49EA-9881-C3128245490F}"
+	ProjectGUID="{610E62DA-4DD6-479E-8D85-1FB87126D750}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/ddv/ddv/exe_ddv.vcproj b/make/msvc800_prj/ddv/ddv/exe_ddv.vcproj
index 565074fe..60ae1b37 100644
--- a/make/msvc800_prj/ddv/ddv/exe_ddv.vcproj
+++ b/make/msvc800_prj/ddv/ddv/exe_ddv.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="exe_ddv"
-	ProjectGUID="{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}"
+	ProjectGUID="{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/ddv/ddvlib/ddvlib.vcproj b/make/msvc800_prj/ddv/ddvlib/ddvlib.vcproj
index e3c49019..4c3375b8 100644
--- a/make/msvc800_prj/ddv/ddvlib/ddvlib.vcproj
+++ b/make/msvc800_prj/ddv/ddvlib/ddvlib.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ddvlib"
-	ProjectGUID="{3D2820CB-F5E6-4807-864C-2C751ADC556D}"
+	ProjectGUID="{D2059A10-7A4D-471A-BAEA-76479FD2773D}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/asn2all/demo_asn2all.vcproj b/make/msvc800_prj/demo/asn2all/demo_asn2all.vcproj
index 78ea5ec3..ab5e6e9b 100644
--- a/make/msvc800_prj/demo/asn2all/demo_asn2all.vcproj
+++ b/make/msvc800_prj/demo/asn2all/demo_asn2all.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_asn2all"
-	ProjectGUID="{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}"
+	ProjectGUID="{D3E7608D-BA37-41A8-8012-9DC2E44E2703}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/asn2ff/demo_asn2ff.vcproj b/make/msvc800_prj/demo/asn2ff/demo_asn2ff.vcproj
index b17387a1..054bd5a6 100644
--- a/make/msvc800_prj/demo/asn2ff/demo_asn2ff.vcproj
+++ b/make/msvc800_prj/demo/asn2ff/demo_asn2ff.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_asn2ff"
-	ProjectGUID="{D3D92BB5-1C47-4797-8486-4441926F2A54}"
+	ProjectGUID="{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/asn2fsa/demo_asn2fsa.vcproj b/make/msvc800_prj/demo/asn2fsa/demo_asn2fsa.vcproj
index c8267bc6..b0e73cbd 100644
--- a/make/msvc800_prj/demo/asn2fsa/demo_asn2fsa.vcproj
+++ b/make/msvc800_prj/demo/asn2fsa/demo_asn2fsa.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_asn2fsa"
-	ProjectGUID="{2675C4D0-0894-426B-B291-2807B4B79D3F}"
+	ProjectGUID="{A901D889-28AD-4B69-9F81-5817D0B7120F}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/asn2gb/demo_asn2gb.vcproj b/make/msvc800_prj/demo/asn2gb/demo_asn2gb.vcproj
index b95bcad1..b3c0e819 100644
--- a/make/msvc800_prj/demo/asn2gb/demo_asn2gb.vcproj
+++ b/make/msvc800_prj/demo/asn2gb/demo_asn2gb.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_asn2gb"
-	ProjectGUID="{9CC7403B-4370-4C93-9155-697EA11A8810}"
+	ProjectGUID="{1DDF5590-54DA-48B9-9168-E970F443F224}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/asn2idx/demo_asn2idx.vcproj b/make/msvc800_prj/demo/asn2idx/demo_asn2idx.vcproj
index 926c5323..33815320 100644
--- a/make/msvc800_prj/demo/asn2idx/demo_asn2idx.vcproj
+++ b/make/msvc800_prj/demo/asn2idx/demo_asn2idx.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_asn2idx"
-	ProjectGUID="{06636583-FBC6-4274-9BD8-B5956A23B5C8}"
+	ProjectGUID="{A546FCD9-97BD-475F-975E-04AB9AC4E077}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/asn2xml/demo_asn2xml.vcproj b/make/msvc800_prj/demo/asn2xml/demo_asn2xml.vcproj
index b0f5a9e0..3c8aed76 100644
--- a/make/msvc800_prj/demo/asn2xml/demo_asn2xml.vcproj
+++ b/make/msvc800_prj/demo/asn2xml/demo_asn2xml.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_asn2xml"
-	ProjectGUID="{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}"
+	ProjectGUID="{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/asnbarval/demo_asnbarval.vcproj b/make/msvc800_prj/demo/asnbarval/demo_asnbarval.vcproj
new file mode 100644
index 00000000..b062850a
--- /dev/null
+++ b/make/msvc800_prj/demo/asnbarval/demo_asnbarval.vcproj
@@ -0,0 +1,953 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="8.00"
+	Name="demo_asnbarval"
+	ProjectGUID="{1136C677-E611-42A1-8BBF-C68BBFE19470}"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"
+		/>
+		<Platform
+			Name="x64"
+		/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="DebugDLL|Win32"
+			OutputDirectory=".\DebugDLL"
+			IntermediateDirectory=".\DebugDLL"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_asnbarval.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnbarval.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnbarval.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/asnbarval.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnbarval.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\Release"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_asnbarval.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="0"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnbarval.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnbarval.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/asnbarval.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnbarval.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="ReleaseDLL|Win32"
+			OutputDirectory=".\ReleaseDLL"
+			IntermediateDirectory=".\ReleaseDLL"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_asnbarval.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnbarval.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnbarval.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/asnbarval.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnbarval.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\Debug"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_asnbarval.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="1"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnbarval.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnbarval.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/asnbarval.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnbarval.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="DebugDLL|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_asnbarval.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnbarval.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnbarval.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/asnbarval.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnbarval.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_asnbarval.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="0"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnbarval.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnbarval.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/asnbarval.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnbarval.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="ReleaseDLL|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_asnbarval.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnbarval.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnbarval.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/asnbarval.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnbarval.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Debug|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_asnbarval.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="1"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnbarval.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnbarval.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/asnbarval.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnbarval.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+			>
+			<File
+				RelativePath="..\..\..\..\demo\asnbarval.c"
+				>
+				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="..\..\..\..\link\mswin\asnbarval.rc"
+				>
+				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl"
+			>
+		</Filter>
+		<File
+			RelativePath="..\..\..\..\link\mswin\ncbilogo.ico"
+			>
+		</File>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>
+
diff --git a/make/msvc800_prj/demo/asndhuff/demo_asndhuff.vcproj b/make/msvc800_prj/demo/asndhuff/demo_asndhuff.vcproj
index e9e74dbd..4016b498 100644
--- a/make/msvc800_prj/demo/asndhuff/demo_asndhuff.vcproj
+++ b/make/msvc800_prj/demo/asndhuff/demo_asndhuff.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_asndhuff"
-	ProjectGUID="{6E9207DA-5998-4B79-8850-D019EEA4251D}"
+	ProjectGUID="{95AE7147-09C4-4C87-A6AB-9B5714D51714}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/asndisc/demo_asndisc.vcproj b/make/msvc800_prj/demo/asndisc/demo_asndisc.vcproj
index 485a1d46..2ed9b377 100644
--- a/make/msvc800_prj/demo/asndisc/demo_asndisc.vcproj
+++ b/make/msvc800_prj/demo/asndisc/demo_asndisc.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_asndisc"
-	ProjectGUID="{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}"
+	ProjectGUID="{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/asnstrip/demo_asnstrip.vcproj b/make/msvc800_prj/demo/asnstrip/demo_asnstrip.vcproj
new file mode 100644
index 00000000..21cfb0e3
--- /dev/null
+++ b/make/msvc800_prj/demo/asnstrip/demo_asnstrip.vcproj
@@ -0,0 +1,949 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="8.00"
+	Name="demo_asnstrip"
+	ProjectGUID="{24B6F0A3-B354-4089-B489-560DEF53C75C}"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"
+		/>
+		<Platform
+			Name="x64"
+		/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="DebugDLL|Win32"
+			OutputDirectory=".\DebugDLL"
+			IntermediateDirectory=".\DebugDLL"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_asnstrip.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnstrip.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnstrip.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/asnstrip.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnstrip.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\Debug"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_asnstrip.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="1"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnstrip.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnstrip.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/asnstrip.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnstrip.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\Release"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_asnstrip.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="0"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnstrip.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnstrip.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/asnstrip.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnstrip.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="ReleaseDLL|Win32"
+			OutputDirectory=".\ReleaseDLL"
+			IntermediateDirectory=".\ReleaseDLL"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_asnstrip.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnstrip.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnstrip.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/asnstrip.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnstrip.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="DebugDLL|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_asnstrip.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnstrip.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnstrip.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/asnstrip.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnstrip.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Debug|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_asnstrip.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="1"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnstrip.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnstrip.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/asnstrip.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnstrip.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_asnstrip.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="0"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnstrip.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnstrip.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/asnstrip.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnstrip.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="ReleaseDLL|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_asnstrip.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\connect,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object,..\..\..\..\cdromlib,..\..\..\..\biostruc,..\..\..\..\tools"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_asnstrip.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/asnstrip.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/asnstrip.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_asnstrip.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+			>
+			<File
+				RelativePath="..\..\..\..\demo\asnstrip.c"
+				>
+				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="..\..\..\..\link\mswin\asnstrip.rc"
+				>
+				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl"
+			>
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>
+
diff --git a/make/msvc800_prj/demo/asnval/demo_asnval.vcproj b/make/msvc800_prj/demo/asnval/demo_asnval.vcproj
index a71cf566..1ac619a0 100644
--- a/make/msvc800_prj/demo/asnval/demo_asnval.vcproj
+++ b/make/msvc800_prj/demo/asnval/demo_asnval.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_asnval"
-	ProjectGUID="{D13243FE-FD39-476C-BAB7-14C583B3BC9E}"
+	ProjectGUID="{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/bl2seq/demo_bl2seq.vcproj b/make/msvc800_prj/demo/bl2seq/demo_bl2seq.vcproj
index 7e88f6ee..b83969c8 100644
--- a/make/msvc800_prj/demo/bl2seq/demo_bl2seq.vcproj
+++ b/make/msvc800_prj/demo/bl2seq/demo_bl2seq.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_bl2seq"
-	ProjectGUID="{E778C1FD-C2F7-47A9-A453-259F6F520B4A}"
+	ProjectGUID="{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/blast/demo_blast.vcproj b/make/msvc800_prj/demo/blast/demo_blast.vcproj
index 4dddf849..88bc6e35 100644
--- a/make/msvc800_prj/demo/blast/demo_blast.vcproj
+++ b/make/msvc800_prj/demo/blast/demo_blast.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_blast"
-	ProjectGUID="{F832691F-2EF5-4937-BBB4-626EE814A383}"
+	ProjectGUID="{4E04088C-D796-4227-8227-2539E30F04BD}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/blastall/demo_blastall.vcproj b/make/msvc800_prj/demo/blastall/demo_blastall.vcproj
index 46c1e4a6..e74203c6 100644
--- a/make/msvc800_prj/demo/blastall/demo_blastall.vcproj
+++ b/make/msvc800_prj/demo/blastall/demo_blastall.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_blastall"
-	ProjectGUID="{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}"
+	ProjectGUID="{36A2447A-460B-4A29-9327-18BE2B7007CB}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/blastclust/demo_blastclust.vcproj b/make/msvc800_prj/demo/blastclust/demo_blastclust.vcproj
index 47718034..287920a4 100644
--- a/make/msvc800_prj/demo/blastclust/demo_blastclust.vcproj
+++ b/make/msvc800_prj/demo/blastclust/demo_blastclust.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_blastclust"
-	ProjectGUID="{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}"
+	ProjectGUID="{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/blastpgp/demo_blastpgp.vcproj b/make/msvc800_prj/demo/blastpgp/demo_blastpgp.vcproj
index f6da827e..7db75c7c 100644
--- a/make/msvc800_prj/demo/blastpgp/demo_blastpgp.vcproj
+++ b/make/msvc800_prj/demo/blastpgp/demo_blastpgp.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_blastpgp"
-	ProjectGUID="{AA8B7736-A934-41FD-A1F2-92FA47FE518E}"
+	ProjectGUID="{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/ccp/demo_ccp.vcproj b/make/msvc800_prj/demo/ccp/demo_ccp.vcproj
index da0f0ff6..387c5cb1 100644
--- a/make/msvc800_prj/demo/ccp/demo_ccp.vcproj
+++ b/make/msvc800_prj/demo/ccp/demo_ccp.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_ccp"
-	ProjectGUID="{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}"
+	ProjectGUID="{F8DA831A-6128-4FB6-A41F-D4051D736D81}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/ccpv/demo_ccpv.vcproj b/make/msvc800_prj/demo/ccpv/demo_ccpv.vcproj
index 9b4c54d4..79fab6ad 100644
--- a/make/msvc800_prj/demo/ccpv/demo_ccpv.vcproj
+++ b/make/msvc800_prj/demo/ccpv/demo_ccpv.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_ccpv"
-	ProjectGUID="{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}"
+	ProjectGUID="{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/cdscan/demo_cdscan.vcproj b/make/msvc800_prj/demo/cdscan/demo_cdscan.vcproj
index 54e29923..6816abde 100644
--- a/make/msvc800_prj/demo/cdscan/demo_cdscan.vcproj
+++ b/make/msvc800_prj/demo/cdscan/demo_cdscan.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_cdscan"
-	ProjectGUID="{D221EDFA-64EB-479A-B15B-792A90ADE47D}"
+	ProjectGUID="{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/checksub/demo_checksub.vcproj b/make/msvc800_prj/demo/checksub/demo_checksub.vcproj
index 13da8d9b..9ce5f193 100644
--- a/make/msvc800_prj/demo/checksub/demo_checksub.vcproj
+++ b/make/msvc800_prj/demo/checksub/demo_checksub.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_checksub"
-	ProjectGUID="{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}"
+	ProjectGUID="{D6205067-CD94-494E-A553-C3706C7CFB3B}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/cnsgn/demo_cnsgn.vcproj b/make/msvc800_prj/demo/cnsgn/demo_cnsgn.vcproj
index 9da37a4f..a9ed9ca1 100644
--- a/make/msvc800_prj/demo/cnsgn/demo_cnsgn.vcproj
+++ b/make/msvc800_prj/demo/cnsgn/demo_cnsgn.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_cnsgn"
-	ProjectGUID="{2874FAEF-31B3-4A57-9CD4-998089E73480}"
+	ProjectGUID="{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/cnsgnv/demo_cnsgnv.vcproj b/make/msvc800_prj/demo/cnsgnv/demo_cnsgnv.vcproj
index 396d1f38..259e8a84 100644
--- a/make/msvc800_prj/demo/cnsgnv/demo_cnsgnv.vcproj
+++ b/make/msvc800_prj/demo/cnsgnv/demo_cnsgnv.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_cnsgnv"
-	ProjectGUID="{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}"
+	ProjectGUID="{27575CBA-8AD7-4999-995C-694483047B3C}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/cnsrt/demo_cnsrt.vcproj b/make/msvc800_prj/demo/cnsrt/demo_cnsrt.vcproj
index ff21eb0a..2d1abbe7 100644
--- a/make/msvc800_prj/demo/cnsrt/demo_cnsrt.vcproj
+++ b/make/msvc800_prj/demo/cnsrt/demo_cnsrt.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_cnsrt"
-	ProjectGUID="{487B891B-190D-4534-9B6F-120C53FB4BB9}"
+	ProjectGUID="{8D7875E5-8DC6-44CA-8B25-6501CC30C301}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/cnsrtv/demo_cnsrtv.vcproj b/make/msvc800_prj/demo/cnsrtv/demo_cnsrtv.vcproj
index c7056c01..48d9b5c9 100644
--- a/make/msvc800_prj/demo/cnsrtv/demo_cnsrtv.vcproj
+++ b/make/msvc800_prj/demo/cnsrtv/demo_cnsrtv.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_cnsrtv"
-	ProjectGUID="{750C92D0-CF2F-413E-8D46-CE2D01901322}"
+	ProjectGUID="{6A9781AB-D45C-4D85-971D-04ED02400001}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/copymat/demo_copymat.vcproj b/make/msvc800_prj/demo/copymat/demo_copymat.vcproj
index ed87fd95..b1c0035b 100644
--- a/make/msvc800_prj/demo/copymat/demo_copymat.vcproj
+++ b/make/msvc800_prj/demo/copymat/demo_copymat.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_copymat"
-	ProjectGUID="{1DC69786-C012-46C5-8B82-92C093434D05}"
+	ProjectGUID="{090B589F-7704-4D2F-9778-F884AFFB2359}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/dosimple/demo_dosimple.vcproj b/make/msvc800_prj/demo/dosimple/demo_dosimple.vcproj
index fe830be8..bc6223e9 100644
--- a/make/msvc800_prj/demo/dosimple/demo_dosimple.vcproj
+++ b/make/msvc800_prj/demo/dosimple/demo_dosimple.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_dosimple"
-	ProjectGUID="{4F4585B4-7710-4BCA-86CE-4766F0F905E8}"
+	ProjectGUID="{C6348B36-F5C4-43A9-8577-4F6646B3D78D}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/dust/demo_dust.vcproj b/make/msvc800_prj/demo/dust/demo_dust.vcproj
index ef57015b..f7074734 100644
--- a/make/msvc800_prj/demo/dust/demo_dust.vcproj
+++ b/make/msvc800_prj/demo/dust/demo_dust.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_dust"
-	ProjectGUID="{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}"
+	ProjectGUID="{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/dustv/demo_dustv.vcproj b/make/msvc800_prj/demo/dustv/demo_dustv.vcproj
index 9ae0ce28..ecfc128b 100644
--- a/make/msvc800_prj/demo/dustv/demo_dustv.vcproj
+++ b/make/msvc800_prj/demo/dustv/demo_dustv.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_dustv"
-	ProjectGUID="{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}"
+	ProjectGUID="{C19E4244-4CAD-40A7-900A-7942991DFB75}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/entrez2/demo_entrez2.vcproj b/make/msvc800_prj/demo/entrez2/demo_entrez2.vcproj
index 2e77fd3a..41428bbd 100644
--- a/make/msvc800_prj/demo/entrez2/demo_entrez2.vcproj
+++ b/make/msvc800_prj/demo/entrez2/demo_entrez2.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_entrez2"
-	ProjectGUID="{053F419B-7D93-4051-A624-C6753A0B1A43}"
+	ProjectGUID="{7BFFD010-510A-4C0C-BD77-5845016DABBA}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/epi/demo_epi.vcproj b/make/msvc800_prj/demo/epi/demo_epi.vcproj
index 53c4ef63..fd6be956 100644
--- a/make/msvc800_prj/demo/epi/demo_epi.vcproj
+++ b/make/msvc800_prj/demo/epi/demo_epi.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_epi"
-	ProjectGUID="{DAF15754-B721-430A-A1B9-55D6D67C036D}"
+	ProjectGUID="{B487568D-8168-46AC-80AA-86F955301F21}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/epiv/demo_epiv.vcproj b/make/msvc800_prj/demo/epiv/demo_epiv.vcproj
index 895d64f4..2b6f4b84 100644
--- a/make/msvc800_prj/demo/epiv/demo_epiv.vcproj
+++ b/make/msvc800_prj/demo/epiv/demo_epiv.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_epiv"
-	ProjectGUID="{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}"
+	ProjectGUID="{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/fa2htgs/demo_fa2htgs.vcproj b/make/msvc800_prj/demo/fa2htgs/demo_fa2htgs.vcproj
index 4b84a508..374a9bc8 100644
--- a/make/msvc800_prj/demo/fa2htgs/demo_fa2htgs.vcproj
+++ b/make/msvc800_prj/demo/fa2htgs/demo_fa2htgs.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_fa2htgs"
-	ProjectGUID="{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}"
+	ProjectGUID="{051B2ABA-EDD6-455D-8600-53B8EB79DF21}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/fastacmd/demo_fastacmd.vcproj b/make/msvc800_prj/demo/fastacmd/demo_fastacmd.vcproj
index b86d0d05..4f856fe7 100644
--- a/make/msvc800_prj/demo/fastacmd/demo_fastacmd.vcproj
+++ b/make/msvc800_prj/demo/fastacmd/demo_fastacmd.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_fastacmd"
-	ProjectGUID="{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}"
+	ProjectGUID="{531E4D12-C794-4509-8160-A6B6FCB1FE0C}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/flint/demo_flint.vcproj b/make/msvc800_prj/demo/flint/demo_flint.vcproj
index 88bf69fd..31098e47 100644
--- a/make/msvc800_prj/demo/flint/demo_flint.vcproj
+++ b/make/msvc800_prj/demo/flint/demo_flint.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_flint"
-	ProjectGUID="{3EFBB872-C18C-4F90-BA06-286C205E8A8A}"
+	ProjectGUID="{00DEC39E-11F7-40B4-8840-0556F331A964}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/formatdb/demo_formatdb.vcproj b/make/msvc800_prj/demo/formatdb/demo_formatdb.vcproj
index 1947a862..efc4626b 100644
--- a/make/msvc800_prj/demo/formatdb/demo_formatdb.vcproj
+++ b/make/msvc800_prj/demo/formatdb/demo_formatdb.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_formatdb"
-	ProjectGUID="{3218262E-1A52-4542-8F22-A49D06C334AC}"
+	ProjectGUID="{FE555145-82E8-4721-B2CB-A60B94658A65}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/formatrpsdb/demo_formatrpsdb.vcproj b/make/msvc800_prj/demo/formatrpsdb/demo_formatrpsdb.vcproj
index 485d96dc..ebe890e6 100644
--- a/make/msvc800_prj/demo/formatrpsdb/demo_formatrpsdb.vcproj
+++ b/make/msvc800_prj/demo/formatrpsdb/demo_formatrpsdb.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_formatrpsdb"
-	ProjectGUID="{1DF27097-97DB-4932-BD3B-6F14A92816A3}"
+	ProjectGUID="{C2B3A6D5-5498-4D73-826A-4A839EBA9571}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/gbseqget/demo_gbseqget.vcproj b/make/msvc800_prj/demo/gbseqget/demo_gbseqget.vcproj
index dea18050..a75184c6 100644
--- a/make/msvc800_prj/demo/gbseqget/demo_gbseqget.vcproj
+++ b/make/msvc800_prj/demo/gbseqget/demo_gbseqget.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_gbseqget"
-	ProjectGUID="{F2092248-A59C-4CC3-8571-F6F6809919A5}"
+	ProjectGUID="{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/gene2xml/demo_gene2xml.vcproj b/make/msvc800_prj/demo/gene2xml/demo_gene2xml.vcproj
index f633c686..a028df30 100644
--- a/make/msvc800_prj/demo/gene2xml/demo_gene2xml.vcproj
+++ b/make/msvc800_prj/demo/gene2xml/demo_gene2xml.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_gene2xml"
-	ProjectGUID="{A276E338-0D0C-4A5C-88C7-531574422EBA}"
+	ProjectGUID="{CCEA00C6-F850-4BDA-B420-6214E40A3469}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/getmesh/demo_getmesh.vcproj b/make/msvc800_prj/demo/getmesh/demo_getmesh.vcproj
index 55d2e9a7..8429048f 100644
--- a/make/msvc800_prj/demo/getmesh/demo_getmesh.vcproj
+++ b/make/msvc800_prj/demo/getmesh/demo_getmesh.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_getmesh"
-	ProjectGUID="{A250CCFC-47DA-4895-BC62-66CADA053A52}"
+	ProjectGUID="{EB8FB82E-5466-4430-9BD2-17CF562E8349}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/getpub/demo_getpub.vcproj b/make/msvc800_prj/demo/getpub/demo_getpub.vcproj
index 8c4f8d2f..f2ac9ba5 100644
--- a/make/msvc800_prj/demo/getpub/demo_getpub.vcproj
+++ b/make/msvc800_prj/demo/getpub/demo_getpub.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_getpub"
-	ProjectGUID="{876560CC-AE03-49C7-9FA8-D1656CB7F040}"
+	ProjectGUID="{1557FB61-9785-4955-ACB3-259F8695AA61}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/gil2bin/demo_gil2bin.vcproj b/make/msvc800_prj/demo/gil2bin/demo_gil2bin.vcproj
index 7e71d9d5..0d8e20e5 100644
--- a/make/msvc800_prj/demo/gil2bin/demo_gil2bin.vcproj
+++ b/make/msvc800_prj/demo/gil2bin/demo_gil2bin.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_gil2bin"
-	ProjectGUID="{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}"
+	ProjectGUID="{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/impala/demo_impala.vcproj b/make/msvc800_prj/demo/impala/demo_impala.vcproj
index f7bca06e..53bab9e5 100644
--- a/make/msvc800_prj/demo/impala/demo_impala.vcproj
+++ b/make/msvc800_prj/demo/impala/demo_impala.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_impala"
-	ProjectGUID="{D962509C-BBA8-43AC-BDB9-4D420B16D099}"
+	ProjectGUID="{B641C7E0-F29C-422C-B3C0-BC3C103BC973}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/indexpub/demo_indexpub.vcproj b/make/msvc800_prj/demo/indexpub/demo_indexpub.vcproj
index 20dc8442..5c7a2931 100644
--- a/make/msvc800_prj/demo/indexpub/demo_indexpub.vcproj
+++ b/make/msvc800_prj/demo/indexpub/demo_indexpub.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_indexpub"
-	ProjectGUID="{86E2DEFE-91A2-400B-A093-82B0DE4968C0}"
+	ProjectGUID="{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/insdseqget/demo_insdseqget.vcproj b/make/msvc800_prj/demo/insdseqget/demo_insdseqget.vcproj
index e445fb71..dbab06d2 100644
--- a/make/msvc800_prj/demo/insdseqget/demo_insdseqget.vcproj
+++ b/make/msvc800_prj/demo/insdseqget/demo_insdseqget.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_insdseqget"
-	ProjectGUID="{D3399079-037C-4873-AB41-8535E0F5124E}"
+	ProjectGUID="{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/makemat/demo_makemat.vcproj b/make/msvc800_prj/demo/makemat/demo_makemat.vcproj
index bafd8c4c..143aa8e7 100644
--- a/make/msvc800_prj/demo/makemat/demo_makemat.vcproj
+++ b/make/msvc800_prj/demo/makemat/demo_makemat.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_makemat"
-	ProjectGUID="{9B82B22D-3287-4512-9C61-054CF931C402}"
+	ProjectGUID="{939AD270-6758-4304-9B42-F776B03B2B30}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/megablast/demo_megablast.vcproj b/make/msvc800_prj/demo/megablast/demo_megablast.vcproj
index 9eeaf831..c60c2869 100644
--- a/make/msvc800_prj/demo/megablast/demo_megablast.vcproj
+++ b/make/msvc800_prj/demo/megablast/demo_megablast.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_megablast"
-	ProjectGUID="{6B0FCA0A-B988-4994-9343-8860CABDD9D2}"
+	ProjectGUID="{7B92691D-13E1-400B-BFDA-1C085DB12DC7}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/nentrez/demo_nentrez.vcproj b/make/msvc800_prj/demo/nentrez/demo_nentrez.vcproj
index c7586233..94754cd8 100644
--- a/make/msvc800_prj/demo/nentrez/demo_nentrez.vcproj
+++ b/make/msvc800_prj/demo/nentrez/demo_nentrez.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_nentrez"
-	ProjectGUID="{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}"
+	ProjectGUID="{02F5DB27-2C2D-4995-AE03-AE866FD0D726}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/nentrez_ogl/demo_nentrez_ogl.vcproj b/make/msvc800_prj/demo/nentrez_ogl/demo_nentrez_ogl.vcproj
index 650b9ed1..f02cf558 100644
--- a/make/msvc800_prj/demo/nentrez_ogl/demo_nentrez_ogl.vcproj
+++ b/make/msvc800_prj/demo/nentrez_ogl/demo_nentrez_ogl.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_nentrez_ogl"
-	ProjectGUID="{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}"
+	ProjectGUID="{13E51223-EDBF-46E1-A98A-895FB3685000}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/netentcf/demo_netentcf.vcproj b/make/msvc800_prj/demo/netentcf/demo_netentcf.vcproj
index 46e63955..8f6f0020 100644
--- a/make/msvc800_prj/demo/netentcf/demo_netentcf.vcproj
+++ b/make/msvc800_prj/demo/netentcf/demo_netentcf.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_netentcf"
-	ProjectGUID="{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}"
+	ProjectGUID="{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/raw2delt/demo_raw2delt.vcproj b/make/msvc800_prj/demo/raw2delt/demo_raw2delt.vcproj
new file mode 100644
index 00000000..a45aef6d
--- /dev/null
+++ b/make/msvc800_prj/demo/raw2delt/demo_raw2delt.vcproj
@@ -0,0 +1,949 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="8.00"
+	Name="demo_raw2delt"
+	ProjectGUID="{E6270A0D-B665-450E-BA6A-B9D648D5B145}"
+	>
+	<Platforms>
+		<Platform
+			Name="Win32"
+		/>
+		<Platform
+			Name="x64"
+		/>
+	</Platforms>
+	<ToolFiles>
+	</ToolFiles>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\Debug"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_raw2delt.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="1"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_raw2delt.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/raw2delt.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/raw2delt.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_raw2delt.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="DebugDLL|Win32"
+			OutputDirectory=".\DebugDLL"
+			IntermediateDirectory=".\DebugDLL"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_raw2delt.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_raw2delt.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/raw2delt.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/raw2delt.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_raw2delt.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\Release"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_raw2delt.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="0"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_raw2delt.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/raw2delt.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/raw2delt.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_raw2delt.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="ReleaseDLL|Win32"
+			OutputDirectory=".\ReleaseDLL"
+			IntermediateDirectory=".\ReleaseDLL"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="1"
+				TypeLibraryName="$(OutDir)/demo_raw2delt.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_raw2delt.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/raw2delt.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/raw2delt.pdb"
+				SubSystem="1"
+				TargetMachine="1"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_raw2delt.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Debug|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_raw2delt.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="1"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_raw2delt.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/raw2delt.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/raw2delt.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_raw2delt.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="DebugDLL|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_raw2delt.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object"
+				PreprocessorDefinitions="_CONSOLE;WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_raw2delt.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/raw2delt.exe"
+				LinkIncremental="2"
+				SuppressStartupBanner="true"
+				GenerateDebugInformation="true"
+				ProgramDatabaseFile="$(OutDir)/raw2delt.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_raw2delt.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="Release|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_raw2delt.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="0"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_raw2delt.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/raw2delt.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/raw2delt.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_raw2delt.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+		<Configuration
+			Name="ReleaseDLL|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			ConfigurationType="1"
+			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="false"
+			>
+			<Tool
+				Name="VCPreBuildEventTool"
+			/>
+			<Tool
+				Name="VCCustomBuildTool"
+			/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"
+			/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"
+			/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="true"
+				SuppressStartupBanner="true"
+				TargetEnvironment="3"
+				TypeLibraryName="$(OutDir)/demo_raw2delt.tlb"
+				HeaderFileName=""
+			/>
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="..\..\..\..,..\..\..\..\corelib,..\..\..\..\api,..\..\..\..\asnstat,..\..\..\..\asnlib,..\..\..\..\access,..\..\..\..\object"
+				PreprocessorDefinitions="_CONSOLE;WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="true"
+				RuntimeTypeInfo="true"
+				PrecompiledHeaderFile="$(IntDir)/demo_raw2delt.pch"
+				AssemblerListingLocation="$(IntDir)/"
+				ObjectFile="$(IntDir)/"
+				ProgramDataBaseFileName="$(IntDir)/"
+				WarningLevel="3"
+				SuppressStartupBanner="true"
+			/>
+			<Tool
+				Name="VCManagedResourceCompilerTool"
+			/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"
+			/>
+			<Tool
+				Name="VCPreLinkEventTool"
+			/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="oldnames.lib wsock32.lib"
+				OutputFile="$(OutDir)/raw2delt.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="true"
+				ProgramDatabaseFile="$(OutDir)/raw2delt.pdb"
+				SubSystem="1"
+				TargetMachine="17"
+			/>
+			<Tool
+				Name="VCALinkTool"
+			/>
+			<Tool
+				Name="VCManifestTool"
+			/>
+			<Tool
+				Name="VCXDCMakeTool"
+			/>
+			<Tool
+				Name="VCBscMakeTool"
+				SuppressStartupBanner="true"
+				OutputFile="$(OutDir)/demo_raw2delt.bsc"
+			/>
+			<Tool
+				Name="VCFxCopTool"
+			/>
+			<Tool
+				Name="VCAppVerifierTool"
+			/>
+			<Tool
+				Name="VCWebDeploymentTool"
+			/>
+			<Tool
+				Name="VCPostBuildEventTool"
+			/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+			>
+			<File
+				RelativePath="..\..\..\..\demo\raw2delt.c"
+				>
+				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="..\..\..\..\link\mswin\raw2delt.rc"
+				>
+				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCResourceCompilerTool"
+						PreprocessorDefinitions=""
+						AdditionalIncludeDirectories="\ivanov\ncbi\link\mswin"
+					/>
+				</FileConfiguration>
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl"
+			>
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>
+
diff --git a/make/msvc800_prj/demo/rpsblast/demo_rpsblast.vcproj b/make/msvc800_prj/demo/rpsblast/demo_rpsblast.vcproj
index fda59283..e55acf1a 100644
--- a/make/msvc800_prj/demo/rpsblast/demo_rpsblast.vcproj
+++ b/make/msvc800_prj/demo/rpsblast/demo_rpsblast.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_rpsblast"
-	ProjectGUID="{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}"
+	ProjectGUID="{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/searchv/demo_searchv.vcproj b/make/msvc800_prj/demo/searchv/demo_searchv.vcproj
index 5d315a8c..b047ba87 100644
--- a/make/msvc800_prj/demo/searchv/demo_searchv.vcproj
+++ b/make/msvc800_prj/demo/searchv/demo_searchv.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_searchv"
-	ProjectGUID="{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}"
+	ProjectGUID="{478B9CE3-2141-4C1C-A54C-984865DF5930}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/seedtop/demo_seedtop.vcproj b/make/msvc800_prj/demo/seedtop/demo_seedtop.vcproj
index 1f820a8c..ef243d51 100644
--- a/make/msvc800_prj/demo/seedtop/demo_seedtop.vcproj
+++ b/make/msvc800_prj/demo/seedtop/demo_seedtop.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_seedtop"
-	ProjectGUID="{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}"
+	ProjectGUID="{136554B9-6A33-46F2-9595-5B3E90A00553}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/seqtest/demo_seqtest.vcproj b/make/msvc800_prj/demo/seqtest/demo_seqtest.vcproj
index c8c7aee5..11ef80f1 100644
--- a/make/msvc800_prj/demo/seqtest/demo_seqtest.vcproj
+++ b/make/msvc800_prj/demo/seqtest/demo_seqtest.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_seqtest"
-	ProjectGUID="{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}"
+	ProjectGUID="{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/sigme/demo_sigme.vcproj b/make/msvc800_prj/demo/sigme/demo_sigme.vcproj
index f6701560..14160b4a 100644
--- a/make/msvc800_prj/demo/sigme/demo_sigme.vcproj
+++ b/make/msvc800_prj/demo/sigme/demo_sigme.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_sigme"
-	ProjectGUID="{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}"
+	ProjectGUID="{2861713F-5EA6-486E-AE98-55CC4200305E}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/sigmev/demo_sigmev.vcproj b/make/msvc800_prj/demo/sigmev/demo_sigmev.vcproj
index 68355018..a5cd921b 100644
--- a/make/msvc800_prj/demo/sigmev/demo_sigmev.vcproj
+++ b/make/msvc800_prj/demo/sigmev/demo_sigmev.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_sigmev"
-	ProjectGUID="{AED09298-117B-4D01-8C01-45F820D3BDE8}"
+	ProjectGUID="{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/spidey/demo_spidey.vcproj b/make/msvc800_prj/demo/spidey/demo_spidey.vcproj
index 22cf153d..300307cc 100644
--- a/make/msvc800_prj/demo/spidey/demo_spidey.vcproj
+++ b/make/msvc800_prj/demo/spidey/demo_spidey.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_spidey"
-	ProjectGUID="{E85FC734-1E47-413F-82E3-A83908FC3A77}"
+	ProjectGUID="{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/srchaa/demo_srchaa.vcproj b/make/msvc800_prj/demo/srchaa/demo_srchaa.vcproj
index f1deb033..d53ef88d 100644
--- a/make/msvc800_prj/demo/srchaa/demo_srchaa.vcproj
+++ b/make/msvc800_prj/demo/srchaa/demo_srchaa.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_srchaa"
-	ProjectGUID="{D2928CA0-E664-4C71-9254-AD1B1CB9A201}"
+	ProjectGUID="{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/srchnt/demo_srchnt.vcproj b/make/msvc800_prj/demo/srchnt/demo_srchnt.vcproj
index 1ba2744d..4d810aff 100644
--- a/make/msvc800_prj/demo/srchnt/demo_srchnt.vcproj
+++ b/make/msvc800_prj/demo/srchnt/demo_srchnt.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_srchnt"
-	ProjectGUID="{924EF5EC-35C3-41A2-AB29-827D491DA574}"
+	ProjectGUID="{29EAEDFD-B486-433D-8809-7C4B298BFF17}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/tbl2asn/demo_tbl2asn.vcproj b/make/msvc800_prj/demo/tbl2asn/demo_tbl2asn.vcproj
index 4df1de21..c335c47b 100644
--- a/make/msvc800_prj/demo/tbl2asn/demo_tbl2asn.vcproj
+++ b/make/msvc800_prj/demo/tbl2asn/demo_tbl2asn.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_tbl2asn"
-	ProjectGUID="{42E5A984-7EA8-4DF0-9918-970247935C64}"
+	ProjectGUID="{F7125366-276A-455F-A1AA-80846F7BE09F}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/testcore/demo_testcore.vcproj b/make/msvc800_prj/demo/testcore/demo_testcore.vcproj
index a6c2afa4..c0b2a6c8 100644
--- a/make/msvc800_prj/demo/testcore/demo_testcore.vcproj
+++ b/make/msvc800_prj/demo/testcore/demo_testcore.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_testcore"
-	ProjectGUID="{3684FA7A-0E39-4377-876F-17FA3C6869F2}"
+	ProjectGUID="{986196FD-0900-451E-818F-7373FBAFF793}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/testobj/demo_testobj.vcproj b/make/msvc800_prj/demo/testobj/demo_testobj.vcproj
index 3f1157a9..c2e47817 100644
--- a/make/msvc800_prj/demo/testobj/demo_testobj.vcproj
+++ b/make/msvc800_prj/demo/testobj/demo_testobj.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_testobj"
-	ProjectGUID="{69D59444-9FA8-41D4-82AC-1CA12A8F160F}"
+	ProjectGUID="{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/twop/demo_twop.vcproj b/make/msvc800_prj/demo/twop/demo_twop.vcproj
index 4d8c544d..2113d9ae 100644
--- a/make/msvc800_prj/demo/twop/demo_twop.vcproj
+++ b/make/msvc800_prj/demo/twop/demo_twop.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_twop"
-	ProjectGUID="{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}"
+	ProjectGUID="{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/twopv/demo_twopv.vcproj b/make/msvc800_prj/demo/twopv/demo_twopv.vcproj
index afedf012..a6e09e12 100644
--- a/make/msvc800_prj/demo/twopv/demo_twopv.vcproj
+++ b/make/msvc800_prj/demo/twopv/demo_twopv.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_twopv"
-	ProjectGUID="{8C72F165-0AC2-4462-BAB9-8AE276273AC0}"
+	ProjectGUID="{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/udv/demo_udv.vcproj b/make/msvc800_prj/demo/udv/demo_udv.vcproj
index 15b72cb2..df9a1cce 100644
--- a/make/msvc800_prj/demo/udv/demo_udv.vcproj
+++ b/make/msvc800_prj/demo/udv/demo_udv.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_udv"
-	ProjectGUID="{914A88CB-0667-40BC-8F0F-4594BA7B9D85}"
+	ProjectGUID="{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/demo/vecscreen/demo_vecscreen.vcproj b/make/msvc800_prj/demo/vecscreen/demo_vecscreen.vcproj
index 971994cd..6e730bd8 100644
--- a/make/msvc800_prj/demo/vecscreen/demo_vecscreen.vcproj
+++ b/make/msvc800_prj/demo/vecscreen/demo_vecscreen.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_vecscreen"
-	ProjectGUID="{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}"
+	ProjectGUID="{B9B3203E-0C07-46DB-BABE-3024B22F923C}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/desktop/ncbidesk.vcproj b/make/msvc800_prj/desktop/ncbidesk.vcproj
index 2d1b0434..769d0fe6 100644
--- a/make/msvc800_prj/desktop/ncbidesk.vcproj
+++ b/make/msvc800_prj/desktop/ncbidesk.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbidesk"
-	ProjectGUID="{FD5A8225-8809-4FFB-9190-B6403A2AD467}"
+	ProjectGUID="{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}"
 	>
 	<Platforms>
 		<Platform
@@ -2601,6 +2601,82 @@
 				</FileConfiguration>
 			</File>
 			<File
+				RelativePath="..\..\..\desktop\macrodlg.c"
+				>
+				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+			</File>
+			<File
 				RelativePath="..\..\..\desktop\mapgene.c"
 				>
 				<FileConfiguration
@@ -5126,6 +5202,10 @@
 				>
 			</File>
 			<File
+				RelativePath="..\..\..\desktop\macrodlg.h"
+				>
+			</File>
+			<File
 				RelativePath="..\..\..\desktop\mapgene.h"
 				>
 			</File>
diff --git a/make/msvc800_prj/gif/vibgif.vcproj b/make/msvc800_prj/gif/vibgif.vcproj
index 4ab41f7c..6cb4b078 100644
--- a/make/msvc800_prj/gif/vibgif.vcproj
+++ b/make/msvc800_prj/gif/vibgif.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="vibgif"
-	ProjectGUID="{08C550B7-3DA6-46A6-96EB-A48806F1900C}"
+	ProjectGUID="{A0F67E98-8A07-4319-A3E8-B983D522D8CA}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/internal/all_internal.vcproj b/make/msvc800_prj/internal/all_internal.vcproj
index 43b489bf..88ed831e 100644
--- a/make/msvc800_prj/internal/all_internal.vcproj
+++ b/make/msvc800_prj/internal/all_internal.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="all_internal"
-	ProjectGUID="{FEA214E0-E333-43A5-BD15-E5902264A91A}"
+	ProjectGUID="{53EC88ED-74CA-4F01-8FDB-94989A896E22}"
 	Keyword="MakeFileProj"
 	>
 	<Platforms>
diff --git a/make/msvc800_prj/internal/smart/smartnet/smartnet.vcproj b/make/msvc800_prj/internal/smart/smartnet/smartnet.vcproj
index 04470847..1b0cfddc 100644
--- a/make/msvc800_prj/internal/smart/smartnet/smartnet.vcproj
+++ b/make/msvc800_prj/internal/smart/smartnet/smartnet.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="smartnet"
-	ProjectGUID="{2B743DB7-9F8B-4652-B45D-04E23AE2B547}"
+	ProjectGUID="{43337FCD-B171-4441-B44E-D1C90C2700EE}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/ncbi.sln b/make/msvc800_prj/ncbi.sln
index 0a5bc3dd..5d1b3554 100644
--- a/make/msvc800_prj/ncbi.sln
+++ b/make/msvc800_prj/ncbi.sln
@@ -1,1248 +1,1296 @@
 
 Microsoft Visual Studio Solution File, Format Version 9.00
 # Visual Studio 2005
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all", "all.vcproj", "{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}"
-	ProjectSection(ProjectDependencies) = postProject
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE} = {0204EA88-C175-4970-922F-6F2C4FDA52EE}
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6} = {4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C} = {D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_demo", "all_demo.vcproj", "{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}"
-	ProjectSection(ProjectDependencies) = postProject
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD} = {8FBFAE5E-50CA-42EF-B614-BEA3252064BD}
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5} = {BD7E75D1-DEDC-450E-A3E5-4823C06100D5}
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9} = {67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}
-		{A40959E8-B640-49F7-B2E0-806A03544AB5} = {A40959E8-B640-49F7-B2E0-806A03544AB5}
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14} = {AA4B7095-5FBB-41E5-AE2A-39247638EC14}
-		{42140DF3-03C5-4A99-9D7B-F4385733D694} = {42140DF3-03C5-4A99-9D7B-F4385733D694}
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9} = {C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096} = {8B6B0E08-62BA-4E92-8672-06CCA7432096}
-		{57BABFE8-331D-41A9-8776-314F2D8791E2} = {57BABFE8-331D-41A9-8776-314F2D8791E2}
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A} = {032E43BB-816C-4BEE-9ABD-1E0B599C007A}
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB} = {AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4} = {A6AC837C-8852-48B3-9232-57A2493AEDA4}
-		{E85F8917-C596-477B-8D92-851E3726DE96} = {E85F8917-C596-477B-8D92-851E3726DE96}
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5} = {AD565A88-01DA-4401-8E8F-53CCF8C759B5}
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63} = {9149ED1B-E896-4A64-A3D2-C42FC10A7F63}
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F} = {1F10C6E1-3C88-4C78-9C18-05AC31B2421F}
-		{A73BBA44-40FF-4306-AF50-94737CD49839} = {A73BBA44-40FF-4306-AF50-94737CD49839}
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1} = {805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85} = {914A88CB-0667-40BC-8F0F-4594BA7B9D85}
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0} = {8C72F165-0AC2-4462-BAB9-8AE276273AC0}
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0} = {C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F} = {69D59444-9FA8-41D4-82AC-1CA12A8F160F}
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2} = {3684FA7A-0E39-4377-876F-17FA3C6869F2}
-		{42E5A984-7EA8-4DF0-9918-970247935C64} = {42E5A984-7EA8-4DF0-9918-970247935C64}
-		{924EF5EC-35C3-41A2-AB29-827D491DA574} = {924EF5EC-35C3-41A2-AB29-827D491DA574}
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201} = {D2928CA0-E664-4C71-9254-AD1B1CB9A201}
-		{E85FC734-1E47-413F-82E3-A83908FC3A77} = {E85FC734-1E47-413F-82E3-A83908FC3A77}
-		{AED09298-117B-4D01-8C01-45F820D3BDE8} = {AED09298-117B-4D01-8C01-45F820D3BDE8}
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84} = {6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221} = {4B5696EE-C2E8-49D1-A0ED-4E54AF811221}
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098} = {33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96} = {8BA07548-3F40-4D95-8BF5-ED3F257ACB96}
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3} = {8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C} = {CCA73A4F-96E8-48BE-A1B6-77EC3697584C}
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA} = {D0B197BF-1409-4108-81C0-A2754CD97ADA}
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E} = {AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF} = {0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9} = {3657A377-E327-4B16-9EE9-16E0E1ECFCE9}
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2} = {6B0FCA0A-B988-4994-9343-8860CABDD9D2}
-		{9B82B22D-3287-4512-9C61-054CF931C402} = {9B82B22D-3287-4512-9C61-054CF931C402}
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0} = {86E2DEFE-91A2-400B-A093-82B0DE4968C0}
-		{D3399079-037C-4873-AB41-8535E0F5124E} = {D3399079-037C-4873-AB41-8535E0F5124E}
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099} = {D962509C-BBA8-43AC-BDB9-4D420B16D099}
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4} = {FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040} = {876560CC-AE03-49C7-9FA8-D1656CB7F040}
-		{A250CCFC-47DA-4895-BC62-66CADA053A52} = {A250CCFC-47DA-4895-BC62-66CADA053A52}
-		{A276E338-0D0C-4A5C-88C7-531574422EBA} = {A276E338-0D0C-4A5C-88C7-531574422EBA}
-		{F2092248-A59C-4CC3-8571-F6F6809919A5} = {F2092248-A59C-4CC3-8571-F6F6809919A5}
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3} = {1DF27097-97DB-4932-BD3B-6F14A92816A3}
-		{3218262E-1A52-4542-8F22-A49D06C334AC} = {3218262E-1A52-4542-8F22-A49D06C334AC}
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A} = {3EFBB872-C18C-4F90-BA06-286C205E8A8A}
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0} = {C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614} = {0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13} = {7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}
-		{DAF15754-B721-430A-A1B9-55D6D67C036D} = {DAF15754-B721-430A-A1B9-55D6D67C036D}
-		{053F419B-7D93-4051-A624-C6753A0B1A43} = {053F419B-7D93-4051-A624-C6753A0B1A43}
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43} = {D3DCCB97-8DA8-4F61-BE14-F7078635FE43}
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50} = {EC823D54-D2D0-4E00-A831-2BA12DF2AD50}
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8} = {4F4585B4-7710-4BCA-86CE-4766F0F905E8}
-		{1DC69786-C012-46C5-8B82-92C093434D05} = {1DC69786-C012-46C5-8B82-92C093434D05}
-		{750C92D0-CF2F-413E-8D46-CE2D01901322} = {750C92D0-CF2F-413E-8D46-CE2D01901322}
-		{487B891B-190D-4534-9B6F-120C53FB4BB9} = {487B891B-190D-4534-9B6F-120C53FB4BB9}
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A} = {F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}
-		{2874FAEF-31B3-4A57-9CD4-998089E73480} = {2874FAEF-31B3-4A57-9CD4-998089E73480}
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C} = {83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D} = {D221EDFA-64EB-479A-B15B-792A90ADE47D}
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B} = {4C2CCC7D-3D19-4E13-9317-3927894F0F3B}
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC} = {1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E} = {AA8B7736-A934-41FD-A1F2-92FA47FE518E}
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F} = {1C14632F-22E1-40D3-B0C8-1E53C72ED92F}
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B} = {3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}
-		{F832691F-2EF5-4937-BBB4-626EE814A383} = {F832691F-2EF5-4937-BBB4-626EE814A383}
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A} = {E778C1FD-C2F7-47A9-A453-259F6F520B4A}
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038} = {D1B78D4D-E0B1-4430-AA1A-20E870FBC038}
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E} = {D13243FE-FD39-476C-BAB7-14C583B3BC9E}
-		{049092E8-80F0-40F6-81F1-0AF99640134D} = {049092E8-80F0-40F6-81F1-0AF99640134D}
-		{6E9207DA-5998-4B79-8850-D019EEA4251D} = {6E9207DA-5998-4B79-8850-D019EEA4251D}
-		{9CC7403B-4370-4C93-9155-697EA11A8810} = {9CC7403B-4370-4C93-9155-697EA11A8810}
-		{2675C4D0-0894-426B-B291-2807B4B79D3F} = {2675C4D0-0894-426B-B291-2807B4B79D3F}
-		{D3D92BB5-1C47-4797-8486-4441926F2A54} = {D3D92BB5-1C47-4797-8486-4441926F2A54}
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E} = {C817F26E-4541-45D0-A6DA-59E58DB9DB7E}
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8} = {06636583-FBC6-4274-9BD8-B5956A23B5C8}
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D} = {CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_exe", "all_exe.vcproj", "{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}"
-	ProjectSection(ProjectDependencies) = postProject
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6} = {6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98} = {BB120D1D-3A68-4107-A8A1-427E448DEA98}
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46} = {002CC81D-C6AF-4AED-8624-301D0E13ED46}
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9} = {3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9} = {74C9A79B-EAE3-46B3-848E-73C3B5F679B9}
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9} = {9AA6C9C9-1442-48CD-BD94-F134953418A9}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_internal", "internal\all_internal.vcproj", "{FEA214E0-E333-43A5-BD15-E5902264A91A}"
-	ProjectSection(ProjectDependencies) = postProject
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C} = {ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547} = {2B743DB7-9F8B-4652-B45D-04E23AE2B547}
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE} = {808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_lib", "all_lib.vcproj", "{0204EA88-C175-4970-922F-6F2C4FDA52EE}"
-	ProjectSection(ProjectDependencies) = postProject
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{21191422-314F-421D-93A8-EABF933C3065} = {21191422-314F-421D-93A8-EABF933C3065}
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C} = {08C550B7-3DA6-46A6-96EB-A48806F1900C}
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B} = {94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340} = {47BB9C01-3751-4E25-87AE-6B4BAAA00340}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC} = {45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94} = {A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{98C1A680-89B6-4911-8C36-42D14F43B868} = {98C1A680-89B6-4911-8C36-42D14F43B868}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4} = {B5934B23-8476-4D68-9769-2A65BF5C33A4}
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2} = {0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09} = {AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB} = {4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D} = {3D2820CB-F5E6-4807-864C-2C751ADC556D}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_ncbi", "all_ncbi.vcproj", "{04452BB8-39AC-4DC3-8C42-58384D285FED}"
-	ProjectSection(ProjectDependencies) = postProject
-		{FEA214E0-E333-43A5-BD15-E5902264A91A} = {FEA214E0-E333-43A5-BD15-E5902264A91A}
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE} = {0204EA88-C175-4970-922F-6F2C4FDA52EE}
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6} = {4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C} = {D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all", "all.vcproj", "{347672C9-B4CA-4B21-8281-51955A9C50AC}"
+	ProjectSection(ProjectDependencies) = postProject
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C} = {4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}
+		{4DFAAB85-944C-4B34-A3C0-70370B655451} = {4DFAAB85-944C-4B34-A3C0-70370B655451}
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E} = {B2AEBA00-E619-4FD2-80DA-9F713DD0306E}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_demo", "all_demo.vcproj", "{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}"
+	ProjectSection(ProjectDependencies) = postProject
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25} = {08AA84EC-97CC-4997-BFFF-7CDC535A5C25}
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145} = {E6270A0D-B665-450E-BA6A-B9D648D5B145}
+		{1136C677-E611-42A1-8BBF-C68BBFE19470} = {1136C677-E611-42A1-8BBF-C68BBFE19470}
+		{B6875C47-6809-4972-A89D-0085058670C9} = {B6875C47-6809-4972-A89D-0085058670C9}
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811} = {9AAE2D3F-4D37-43B6-96EB-593DE7679811}
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE} = {E6CE793E-7882-4E77-9D26-22C950DE0AFE}
+		{7719A61E-FAE1-4564-AD24-416318E48967} = {7719A61E-FAE1-4564-AD24-416318E48967}
+		{E459338E-39A8-49C9-9DFC-612E47863CE3} = {E459338E-39A8-49C9-9DFC-612E47863CE3}
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F} = {6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C} = {DD51F357-26FE-46F2-9AC9-5B682DBC198C}
+		{862D2BCD-67ED-4398-A811-7E247C2029E5} = {862D2BCD-67ED-4398-A811-7E247C2029E5}
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B} = {F171E3D9-FC0B-4404-B96F-AD98C055CD8B}
+		{3B976840-4F3F-46A9-832D-4AB79417F712} = {3B976840-4F3F-46A9-832D-4AB79417F712}
+		{087A2516-3C90-4D46-AEA9-670592894CB4} = {087A2516-3C90-4D46-AEA9-670592894CB4}
+		{167BDE33-267C-49EE-9AC5-6177D283D799} = {167BDE33-267C-49EE-9AC5-6177D283D799}
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475} = {9218C976-8194-4AD4-BC5C-7CBC456C2475}
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2} = {760EA748-5473-48CE-8BE0-76538A0CE1B2}
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72} = {2EDD4E60-025D-4167-B827-9A700DFA6D72}
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11} = {BC50422E-D841-4EDF-B987-5135EC4D8F11}
+		{6266F193-8E41-4543-BB84-4DEA87146A44} = {6266F193-8E41-4543-BB84-4DEA87146A44}
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C} = {B9B3203E-0C07-46DB-BABE-3024B22F923C}
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8} = {5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F} = {FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0} = {B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020} = {09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}
+		{986196FD-0900-451E-818F-7373FBAFF793} = {986196FD-0900-451E-818F-7373FBAFF793}
+		{F7125366-276A-455F-A1AA-80846F7BE09F} = {F7125366-276A-455F-A1AA-80846F7BE09F}
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17} = {29EAEDFD-B486-433D-8809-7C4B298BFF17}
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A} = {A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1} = {931A5E4E-E25D-4895-B202-E1D1B3F37ED1}
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A} = {00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}
+		{2861713F-5EA6-486E-AE98-55CC4200305E} = {2861713F-5EA6-486E-AE98-55CC4200305E}
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6} = {05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}
+		{136554B9-6A33-46F2-9595-5B3E90A00553} = {136554B9-6A33-46F2-9595-5B3E90A00553}
+		{478B9CE3-2141-4C1C-A54C-984865DF5930} = {478B9CE3-2141-4C1C-A54C-984865DF5930}
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875} = {84BE55F0-B6BE-4DFA-B387-4D09C24B4875}
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098} = {8EFB0853-50E8-4167-88A5-2C71DAB74098}
+		{82933EEE-EB79-486D-A8E2-B440D33D924A} = {82933EEE-EB79-486D-A8E2-B440D33D924A}
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D} = {4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}
+		{13E51223-EDBF-46E1-A98A-895FB3685000} = {13E51223-EDBF-46E1-A98A-895FB3685000}
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726} = {02F5DB27-2C2D-4995-AE03-AE866FD0D726}
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7} = {7B92691D-13E1-400B-BFDA-1C085DB12DC7}
+		{939AD270-6758-4304-9B42-F776B03B2B30} = {939AD270-6758-4304-9B42-F776B03B2B30}
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5} = {7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A} = {DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973} = {B641C7E0-F29C-422C-B3C0-BC3C103BC973}
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E} = {61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}
+		{1557FB61-9785-4955-ACB3-259F8695AA61} = {1557FB61-9785-4955-ACB3-259F8695AA61}
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349} = {EB8FB82E-5466-4430-9BD2-17CF562E8349}
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469} = {CCEA00C6-F850-4BDA-B420-6214E40A3469}
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD} = {D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571} = {C2B3A6D5-5498-4D73-826A-4A839EBA9571}
+		{FE555145-82E8-4721-B2CB-A60B94658A65} = {FE555145-82E8-4721-B2CB-A60B94658A65}
+		{00DEC39E-11F7-40B4-8840-0556F331A964} = {00DEC39E-11F7-40B4-8840-0556F331A964}
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C} = {531E4D12-C794-4509-8160-A6B6FCB1FE0C}
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21} = {051B2ABA-EDD6-455D-8600-53B8EB79DF21}
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC} = {CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}
+		{B487568D-8168-46AC-80AA-86F955301F21} = {B487568D-8168-46AC-80AA-86F955301F21}
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA} = {7BFFD010-510A-4C0C-BD77-5845016DABBA}
+		{C19E4244-4CAD-40A7-900A-7942991DFB75} = {C19E4244-4CAD-40A7-900A-7942991DFB75}
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB} = {7D38F129-EF19-4A07-8EDC-AED9E364E2CB}
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D} = {C6348B36-F5C4-43A9-8577-4F6646B3D78D}
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0} = {28B5A386-FA1C-4106-AB6E-5DA967D979E0}
+		{090B589F-7704-4D2F-9778-F884AFFB2359} = {090B589F-7704-4D2F-9778-F884AFFB2359}
+		{6A9781AB-D45C-4D85-971D-04ED02400001} = {6A9781AB-D45C-4D85-971D-04ED02400001}
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301} = {8D7875E5-8DC6-44CA-8B25-6501CC30C301}
+		{27575CBA-8AD7-4999-995C-694483047B3C} = {27575CBA-8AD7-4999-995C-694483047B3C}
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292} = {9BCA1F30-F3E2-4F16-8974-C0C2D3902292}
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8} = {5F755177-01B3-44E5-BC77-6FCF825CE0C8}
+		{D6205067-CD94-494E-A553-C3706C7CFB3B} = {D6205067-CD94-494E-A553-C3706C7CFB3B}
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57} = {A8DC9C13-504F-4ED7-B299-ED251D8D7D57}
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3} = {3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81} = {F8DA831A-6128-4FB6-A41F-D4051D736D81}
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E} = {9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9} = {61F9752D-4AE9-4B68-8D20-FF5CF31631A9}
+		{36A2447A-460B-4A29-9327-18BE2B7007CB} = {36A2447A-460B-4A29-9327-18BE2B7007CB}
+		{4E04088C-D796-4227-8227-2539E30F04BD} = {4E04088C-D796-4227-8227-2539E30F04BD}
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F} = {CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5} = {6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE} = {43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}
+		{24B6F0A3-B354-4089-B489-560DEF53C75C} = {24B6F0A3-B354-4089-B489-560DEF53C75C}
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714} = {95AE7147-09C4-4C87-A6AB-9B5714D51714}
+		{1DDF5590-54DA-48B9-9168-E970F443F224} = {1DDF5590-54DA-48B9-9168-E970F443F224}
+		{A901D889-28AD-4B69-9F81-5817D0B7120F} = {A901D889-28AD-4B69-9F81-5817D0B7120F}
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152} = {DD4C129E-9390-41EC-90E8-CEDF4C6F7152}
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703} = {D3E7608D-BA37-41A8-8012-9DC2E44E2703}
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077} = {A546FCD9-97BD-475F-975E-04AB9AC4E077}
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F} = {C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_exe", "all_exe.vcproj", "{4DFAAB85-944C-4B34-A3C0-70370B655451}"
+	ProjectSection(ProjectDependencies) = postProject
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F} = {028EEC3D-499E-453C-A1F4-5A4478BBB39F}
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983} = {67436D24-0D70-48D5-B1AE-6E8DFA978983}
+		{86F47145-3ABB-45BA-8D51-89C24997882F} = {86F47145-3ABB-45BA-8D51-89C24997882F}
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E} = {49F50B13-96C8-44F1-9B8C-68197E0DBE7E}
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D} = {0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}
+		{95BF266E-0195-4BEB-B306-B99489EE3991} = {95BF266E-0195-4BEB-B306-B99489EE3991}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_internal", "internal\all_internal.vcproj", "{53EC88ED-74CA-4F01-8FDB-94989A896E22}"
+	ProjectSection(ProjectDependencies) = postProject
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D} = {8B58713F-B6F4-4A76-9888-309FDDFB985D}
+		{43337FCD-B171-4441-B44E-D1C90C2700EE} = {43337FCD-B171-4441-B44E-D1C90C2700EE}
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D} = {7469FFC1-059F-45B2-A9B8-B17CD881CA8D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_lib", "all_lib.vcproj", "{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}"
+	ProjectSection(ProjectDependencies) = postProject
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B} = {A9561C14-6DAF-4A28-9F59-297D39432D0B}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{C0B91754-0757-42BD-8F53-C05964FFFB66} = {C0B91754-0757-42BD-8F53-C05964FFFB66}
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA} = {A0F67E98-8A07-4319-A3E8-B983D522D8CA}
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69} = {E2180D54-5F75-47B7-8D77-00D04A6BEF69}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86} = {DE96F5AB-AC39-44FF-9BAB-36805FE07A86}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{759991FD-441C-4267-A364-1BB2236C67B8} = {759991FD-441C-4267-A364-1BB2236C67B8}
+		{C2857848-3327-46C6-929C-192629A21F60} = {C2857848-3327-46C6-929C-192629A21F60}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D} = {DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59} = {2F198E60-4B02-46C3-8FEF-CE86D69E2C59}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58} = {8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{2746DC43-68A9-42FE-80F0-1806679538FA} = {2746DC43-68A9-42FE-80F0-1806679538FA}
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D} = {D2059A10-7A4D-471A-BAEA-76479FD2773D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "all_ncbi", "all_ncbi.vcproj", "{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}"
+	ProjectSection(ProjectDependencies) = postProject
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22} = {53EC88ED-74CA-4F01-8FDB-94989A896E22}
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C} = {4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}
+		{4DFAAB85-944C-4B34-A3C0-70370B655451} = {4DFAAB85-944C-4B34-A3C0-70370B655451}
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E} = {B2AEBA00-E619-4FD2-80DA-9F713DD0306E}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "blast", "algo\blast\core\blast.vcproj", "{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "blast", "algo\blast\core\blast.vcproj", "{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "blastapi", "algo\blast\api\blastapi.vcproj", "{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "blastapi", "algo\blast\api\blastapi.vcproj", "{6058EDC4-453A-48B1-8E27-83820FFB7203}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "blastcompadj", "algo\blast\composition_adjustment\blastcompadj.vcproj", "{F7164C61-0D7C-4EC8-9209-88A760907B6B}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "blastcompadj", "algo\blast\composition_adjustment\blastcompadj.vcproj", "{A2E2AE46-C7B9-4544-B138-6F7662DF2216}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ddvlib", "ddv\ddvlib\ddvlib.vcproj", "{3D2820CB-F5E6-4807-864C-2C751ADC556D}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ddvlib", "ddv\ddvlib\ddvlib.vcproj", "{D2059A10-7A4D-471A-BAEA-76479FD2773D}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2all", "demo\asn2all\demo_asn2all.vcproj", "{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2all", "demo\asn2all\demo_asn2all.vcproj", "{D3E7608D-BA37-41A8-8012-9DC2E44E2703}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2ff", "demo\asn2ff\demo_asn2ff.vcproj", "{D3D92BB5-1C47-4797-8486-4441926F2A54}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2ff", "demo\asn2ff\demo_asn2ff.vcproj", "{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2fsa", "demo\asn2fsa\demo_asn2fsa.vcproj", "{2675C4D0-0894-426B-B291-2807B4B79D3F}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2fsa", "demo\asn2fsa\demo_asn2fsa.vcproj", "{A901D889-28AD-4B69-9F81-5817D0B7120F}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2gb", "demo\asn2gb\demo_asn2gb.vcproj", "{9CC7403B-4370-4C93-9155-697EA11A8810}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2gb", "demo\asn2gb\demo_asn2gb.vcproj", "{1DDF5590-54DA-48B9-9168-E970F443F224}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2idx", "demo\asn2idx\demo_asn2idx.vcproj", "{06636583-FBC6-4274-9BD8-B5956A23B5C8}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2idx", "demo\asn2idx\demo_asn2idx.vcproj", "{A546FCD9-97BD-475F-975E-04AB9AC4E077}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2xml", "demo\asn2xml\demo_asn2xml.vcproj", "{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asn2xml", "demo\asn2xml\demo_asn2xml.vcproj", "{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asnbarval", "demo\asnbarval\demo_asnbarval.vcproj", "{E95696E6-C316-4957-853A-547A1088D338}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asnbarval", "demo\asnbarval\demo_asnbarval.vcproj", "{1136C677-E611-42A1-8BBF-C68BBFE19470}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09} = {AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{98C1A680-89B6-4911-8C36-42D14F43B868} = {98C1A680-89B6-4911-8C36-42D14F43B868}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58} = {8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asndhuff", "demo\asndhuff\demo_asndhuff.vcproj", "{6E9207DA-5998-4B79-8850-D019EEA4251D}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asndhuff", "demo\asndhuff\demo_asndhuff.vcproj", "{95AE7147-09C4-4C87-A6AB-9B5714D51714}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09} = {AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58} = {8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asndisc", "demo\asndisc\demo_asndisc.vcproj", "{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asndisc", "demo\asndisc\demo_asndisc.vcproj", "{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asnstrip", "demo\asnstrip\demo_asnstrip.vcproj", "{049092E8-80F0-40F6-81F1-0AF99640134D}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asnmacro", "demo\asnmacro\demo_asnmacro.vcproj", "{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{759991FD-441C-4267-A364-1BB2236C67B8} = {759991FD-441C-4267-A364-1BB2236C67B8}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asnval", "demo\asnval\demo_asnval.vcproj", "{D13243FE-FD39-476C-BAB7-14C583B3BC9E}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asnstrip", "demo\asnstrip\demo_asnstrip.vcproj", "{24B6F0A3-B354-4089-B489-560DEF53C75C}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_bl2seq", "demo\bl2seq\demo_bl2seq.vcproj", "{E778C1FD-C2F7-47A9-A453-259F6F520B4A}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_asnval", "demo\asnval\demo_asnval.vcproj", "{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_blast", "demo\blast\demo_blast.vcproj", "{F832691F-2EF5-4937-BBB4-626EE814A383}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_bl2seq", "demo\bl2seq\demo_bl2seq.vcproj", "{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{98C1A680-89B6-4911-8C36-42D14F43B868} = {98C1A680-89B6-4911-8C36-42D14F43B868}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_blastall", "demo\blastall\demo_blastall.vcproj", "{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_blast", "demo\blast\demo_blast.vcproj", "{4E04088C-D796-4227-8227-2539E30F04BD}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_blastclust", "demo\blastclust\demo_blastclust.vcproj", "{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_blastall", "demo\blastall\demo_blastall.vcproj", "{36A2447A-460B-4A29-9327-18BE2B7007CB}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_blastpgp", "demo\blastpgp\demo_blastpgp.vcproj", "{AA8B7736-A934-41FD-A1F2-92FA47FE518E}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_blastclust", "demo\blastclust\demo_blastclust.vcproj", "{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_ccp", "demo\ccp\demo_ccp.vcproj", "{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}"
-	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_blastpgp", "demo\blastpgp\demo_blastpgp.vcproj", "{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}"
+	ProjectSection(ProjectDependencies) = postProject
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_ccpv", "demo\ccpv\demo_ccpv.vcproj", "{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}"
-	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_ccp", "demo\ccp\demo_ccp.vcproj", "{F8DA831A-6128-4FB6-A41F-D4051D736D81}"
+	ProjectSection(ProjectDependencies) = postProject
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_ccpv", "demo\ccpv\demo_ccpv.vcproj", "{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cdscan", "demo\cdscan\demo_cdscan.vcproj", "{D221EDFA-64EB-479A-B15B-792A90ADE47D}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cdscan", "demo\cdscan\demo_cdscan.vcproj", "{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09} = {AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58} = {8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_checksub", "demo\checksub\demo_checksub.vcproj", "{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_checksub", "demo\checksub\demo_checksub.vcproj", "{D6205067-CD94-494E-A553-C3706C7CFB3B}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cnsgn", "demo\cnsgn\demo_cnsgn.vcproj", "{2874FAEF-31B3-4A57-9CD4-998089E73480}"
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cleanasn", "demo\cleanasn\demo_cleanasn.vcproj", "{5F755177-01B3-44E5-BC77-6FCF825CE0C8}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC} = {45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cnsgnv", "demo\cnsgnv\demo_cnsgnv.vcproj", "{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}"
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cnsgn", "demo\cnsgn\demo_cnsgn.vcproj", "{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{759991FD-441C-4267-A364-1BB2236C67B8} = {759991FD-441C-4267-A364-1BB2236C67B8}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cnsrt", "demo\cnsrt\demo_cnsrt.vcproj", "{487B891B-190D-4534-9B6F-120C53FB4BB9}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cnsgnv", "demo\cnsgnv\demo_cnsgnv.vcproj", "{27575CBA-8AD7-4999-995C-694483047B3C}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cnsrtv", "demo\cnsrtv\demo_cnsrtv.vcproj", "{750C92D0-CF2F-413E-8D46-CE2D01901322}"
-	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_copymat", "demo\copymat\demo_copymat.vcproj", "{1DC69786-C012-46C5-8B82-92C093434D05}"
-	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_dosimple", "demo\dosimple\demo_dosimple.vcproj", "{4F4585B4-7710-4BCA-86CE-4766F0F905E8}"
-	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_dust", "demo\dust\demo_dust.vcproj", "{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cnsrt", "demo\cnsrt\demo_cnsrt.vcproj", "{8D7875E5-8DC6-44CA-8B25-6501CC30C301}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_dustv", "demo\dustv\demo_dustv.vcproj", "{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cnsrtv", "demo\cnsrtv\demo_cnsrtv.vcproj", "{6A9781AB-D45C-4D85-971D-04ED02400001}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-	EndProjectSection
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_copymat", "demo\copymat\demo_copymat.vcproj", "{090B589F-7704-4D2F-9778-F884AFFB2359}"
+	ProjectSection(ProjectDependencies) = postProject
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_entrez2", "demo\entrez2\demo_entrez2.vcproj", "{053F419B-7D93-4051-A624-C6753A0B1A43}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_cspeedtest", "demo\cspeedtest\demo_cspeedtest.vcproj", "{28B5A386-FA1C-4106-AB6E-5DA967D979E0}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{98C1A680-89B6-4911-8C36-42D14F43B868} = {98C1A680-89B6-4911-8C36-42D14F43B868}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_epi", "demo\epi\demo_epi.vcproj", "{DAF15754-B721-430A-A1B9-55D6D67C036D}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_dosimple", "demo\dosimple\demo_dosimple.vcproj", "{C6348B36-F5C4-43A9-8577-4F6646B3D78D}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_epiv", "demo\epiv\demo_epiv.vcproj", "{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_dust", "demo\dust\demo_dust.vcproj", "{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_fa2htgs", "demo\fa2htgs\demo_fa2htgs.vcproj", "{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_dustv", "demo\dustv\demo_dustv.vcproj", "{C19E4244-4CAD-40A7-900A-7942991DFB75}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_fastacmd", "demo\fastacmd\demo_fastacmd.vcproj", "{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_entrez2", "demo\entrez2\demo_entrez2.vcproj", "{7BFFD010-510A-4C0C-BD77-5845016DABBA}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_flint", "demo\flint\demo_flint.vcproj", "{3EFBB872-C18C-4F90-BA06-286C205E8A8A}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_epi", "demo\epi\demo_epi.vcproj", "{B487568D-8168-46AC-80AA-86F955301F21}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_formatdb", "demo\formatdb\demo_formatdb.vcproj", "{3218262E-1A52-4542-8F22-A49D06C334AC}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_epiv", "demo\epiv\demo_epiv.vcproj", "{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_formatrpsdb", "demo\formatrpsdb\demo_formatrpsdb.vcproj", "{1DF27097-97DB-4932-BD3B-6F14A92816A3}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_fa2htgs", "demo\fa2htgs\demo_fa2htgs.vcproj", "{051B2ABA-EDD6-455D-8600-53B8EB79DF21}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_gbseqget", "demo\gbseqget\demo_gbseqget.vcproj", "{F2092248-A59C-4CC3-8571-F6F6809919A5}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_fastacmd", "demo\fastacmd\demo_fastacmd.vcproj", "{531E4D12-C794-4509-8160-A6B6FCB1FE0C}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_gene2xml", "demo\gene2xml\demo_gene2xml.vcproj", "{A276E338-0D0C-4A5C-88C7-531574422EBA}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_flint", "demo\flint\demo_flint.vcproj", "{00DEC39E-11F7-40B4-8840-0556F331A964}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_getmesh", "demo\getmesh\demo_getmesh.vcproj", "{A250CCFC-47DA-4895-BC62-66CADA053A52}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_formatdb", "demo\formatdb\demo_formatdb.vcproj", "{FE555145-82E8-4721-B2CB-A60B94658A65}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_getpub", "demo\getpub\demo_getpub.vcproj", "{876560CC-AE03-49C7-9FA8-D1656CB7F040}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_formatrpsdb", "demo\formatrpsdb\demo_formatrpsdb.vcproj", "{C2B3A6D5-5498-4D73-826A-4A839EBA9571}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_gil2bin", "demo\gil2bin\demo_gil2bin.vcproj", "{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_gbseqget", "demo\gbseqget\demo_gbseqget.vcproj", "{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_impala", "demo\impala\demo_impala.vcproj", "{D962509C-BBA8-43AC-BDB9-4D420B16D099}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_gene2xml", "demo\gene2xml\demo_gene2xml.vcproj", "{CCEA00C6-F850-4BDA-B420-6214E40A3469}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_indexpub", "demo\indexpub\demo_indexpub.vcproj", "{86E2DEFE-91A2-400B-A093-82B0DE4968C0}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_getmesh", "demo\getmesh\demo_getmesh.vcproj", "{EB8FB82E-5466-4430-9BD2-17CF562E8349}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_insdseqget", "demo\insdseqget\demo_insdseqget.vcproj", "{D3399079-037C-4873-AB41-8535E0F5124E}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_getpub", "demo\getpub\demo_getpub.vcproj", "{1557FB61-9785-4955-ACB3-259F8695AA61}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_makemat", "demo\makemat\demo_makemat.vcproj", "{9B82B22D-3287-4512-9C61-054CF931C402}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_gil2bin", "demo\gil2bin\demo_gil2bin.vcproj", "{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_megablast", "demo\megablast\demo_megablast.vcproj", "{6B0FCA0A-B988-4994-9343-8860CABDD9D2}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_impala", "demo\impala\demo_impala.vcproj", "{B641C7E0-F29C-422C-B3C0-BC3C103BC973}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_nentrez", "demo\nentrez\demo_nentrez.vcproj", "{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_indexpub", "demo\indexpub\demo_indexpub.vcproj", "{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{98C1A680-89B6-4911-8C36-42D14F43B868} = {98C1A680-89B6-4911-8C36-42D14F43B868}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC} = {45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D} = {3D2820CB-F5E6-4807-864C-2C751ADC556D}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2} = {0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340} = {47BB9C01-3751-4E25-87AE-6B4BAAA00340}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_nentrez_ogl", "demo\nentrez_ogl\demo_nentrez_ogl.vcproj", "{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_insdseqget", "demo\insdseqget\demo_insdseqget.vcproj", "{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09} = {AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{98C1A680-89B6-4911-8C36-42D14F43B868} = {98C1A680-89B6-4911-8C36-42D14F43B868}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC} = {45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D} = {3D2820CB-F5E6-4807-864C-2C751ADC556D}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4} = {B5934B23-8476-4D68-9769-2A65BF5C33A4}
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340} = {47BB9C01-3751-4E25-87AE-6B4BAAA00340}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_netentcf", "demo\netentcf\demo_netentcf.vcproj", "{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_makemat", "demo\makemat\demo_makemat.vcproj", "{939AD270-6758-4304-9B42-F776B03B2B30}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340} = {47BB9C01-3751-4E25-87AE-6B4BAAA00340}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_regexp", "regexp\demo\demo_regexp.vcproj", "{D0B197BF-1409-4108-81C0-A2754CD97ADA}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_megablast", "demo\megablast\demo_megablast.vcproj", "{7B92691D-13E1-400B-BFDA-1C085DB12DC7}"
 	ProjectSection(ProjectDependencies) = postProject
-		{21191422-314F-421D-93A8-EABF933C3065} = {21191422-314F-421D-93A8-EABF933C3065}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_regexp_grep", "regexp\demo\demo_regexp_grep.vcproj", "{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_nentrez", "demo\nentrez\demo_nentrez.vcproj", "{02F5DB27-2C2D-4995-AE03-AE866FD0D726}"
 	ProjectSection(ProjectDependencies) = postProject
-		{21191422-314F-421D-93A8-EABF933C3065} = {21191422-314F-421D-93A8-EABF933C3065}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{759991FD-441C-4267-A364-1BB2236C67B8} = {759991FD-441C-4267-A364-1BB2236C67B8}
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D} = {D2059A10-7A4D-471A-BAEA-76479FD2773D}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59} = {2F198E60-4B02-46C3-8FEF-CE86D69E2C59}
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86} = {DE96F5AB-AC39-44FF-9BAB-36805FE07A86}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_rpsblast", "demo\rpsblast\demo_rpsblast.vcproj", "{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}"
-	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_nentrez_ogl", "demo\nentrez_ogl\demo_nentrez_ogl.vcproj", "{13E51223-EDBF-46E1-A98A-895FB3685000}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58} = {8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{759991FD-441C-4267-A364-1BB2236C67B8} = {759991FD-441C-4267-A364-1BB2236C67B8}
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D} = {D2059A10-7A4D-471A-BAEA-76479FD2773D}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D} = {DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86} = {DE96F5AB-AC39-44FF-9BAB-36805FE07A86}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_searchv", "demo\searchv\demo_searchv.vcproj", "{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}"
-	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_netentcf", "demo\netentcf\demo_netentcf.vcproj", "{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86} = {DE96F5AB-AC39-44FF-9BAB-36805FE07A86}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_raw2delt", "demo\raw2delt\demo_raw2delt.vcproj", "{E6270A0D-B665-450E-BA6A-B9D648D5B145}"
+	ProjectSection(ProjectDependencies) = postProject
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_regexp", "regexp\demo\demo_regexp.vcproj", "{82933EEE-EB79-486D-A8E2-B440D33D924A}"
+	ProjectSection(ProjectDependencies) = postProject
+		{C0B91754-0757-42BD-8F53-C05964FFFB66} = {C0B91754-0757-42BD-8F53-C05964FFFB66}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_regexp_grep", "regexp\demo\demo_regexp_grep.vcproj", "{8EFB0853-50E8-4167-88A5-2C71DAB74098}"
+	ProjectSection(ProjectDependencies) = postProject
+		{C0B91754-0757-42BD-8F53-C05964FFFB66} = {C0B91754-0757-42BD-8F53-C05964FFFB66}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_rpsblast", "demo\rpsblast\demo_rpsblast.vcproj", "{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}"
+	ProjectSection(ProjectDependencies) = postProject
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_searchv", "demo\searchv\demo_searchv.vcproj", "{478B9CE3-2141-4C1C-A54C-984865DF5930}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_seedtop", "demo\seedtop\demo_seedtop.vcproj", "{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_seedtop", "demo\seedtop\demo_seedtop.vcproj", "{136554B9-6A33-46F2-9595-5B3E90A00553}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_seqtest", "demo\seqtest\demo_seqtest.vcproj", "{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_seqtest", "demo\seqtest\demo_seqtest.vcproj", "{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_sigme", "demo\sigme\demo_sigme.vcproj", "{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_sigme", "demo\sigme\demo_sigme.vcproj", "{2861713F-5EA6-486E-AE98-55CC4200305E}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_sigmev", "demo\sigmev\demo_sigmev.vcproj", "{AED09298-117B-4D01-8C01-45F820D3BDE8}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_sigmev", "demo\sigmev\demo_sigmev.vcproj", "{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_spidey", "demo\spidey\demo_spidey.vcproj", "{E85FC734-1E47-413F-82E3-A83908FC3A77}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_spidey", "demo\spidey\demo_spidey.vcproj", "{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_srchaa", "demo\srchaa\demo_srchaa.vcproj", "{D2928CA0-E664-4C71-9254-AD1B1CB9A201}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_srchaa", "demo\srchaa\demo_srchaa.vcproj", "{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94} = {A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{C2857848-3327-46C6-929C-192629A21F60} = {C2857848-3327-46C6-929C-192629A21F60}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_srchnt", "demo\srchnt\demo_srchnt.vcproj", "{924EF5EC-35C3-41A2-AB29-827D491DA574}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_srchnt", "demo\srchnt\demo_srchnt.vcproj", "{29EAEDFD-B486-433D-8809-7C4B298BFF17}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_tbl2asn", "demo\tbl2asn\demo_tbl2asn.vcproj", "{42E5A984-7EA8-4DF0-9918-970247935C64}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_tbl2asn", "demo\tbl2asn\demo_tbl2asn.vcproj", "{F7125366-276A-455F-A1AA-80846F7BE09F}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_testcore", "demo\testcore\demo_testcore.vcproj", "{3684FA7A-0E39-4377-876F-17FA3C6869F2}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_testcore", "demo\testcore\demo_testcore.vcproj", "{986196FD-0900-451E-818F-7373FBAFF793}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_testobj", "demo\testobj\demo_testobj.vcproj", "{69D59444-9FA8-41D4-82AC-1CA12A8F160F}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_testobj", "demo\testobj\demo_testobj.vcproj", "{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_twop", "demo\twop\demo_twop.vcproj", "{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_twop", "demo\twop\demo_twop.vcproj", "{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_twopv", "demo\twopv\demo_twopv.vcproj", "{8C72F165-0AC2-4462-BAB9-8AE276273AC0}"
-	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_udv", "demo\udv\demo_udv.vcproj", "{914A88CB-0667-40BC-8F0F-4594BA7B9D85}"
-	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D} = {3D2820CB-F5E6-4807-864C-2C751ADC556D}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340} = {47BB9C01-3751-4E25-87AE-6B4BAAA00340}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_vecscreen", "demo\vecscreen\demo_vecscreen.vcproj", "{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}"
-	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_asntool", "asnlib\asntool\exe_asntool.vcproj", "{9AA6C9C9-1442-48CD-BD94-F134953418A9}"
-	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_blastcl3", "network\blast3\blastcl3\exe_blastcl3.vcproj", "{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}"
-	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC} = {45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_ddv", "ddv\ddv\exe_ddv.vcproj", "{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}"
-	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D} = {3D2820CB-F5E6-4807-864C-2C751ADC556D}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340} = {47BB9C01-3751-4E25-87AE-6B4BAAA00340}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
-	EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_idfetch", "network\idfetch\exe_idfetch.vcproj", "{BB120D1D-3A68-4107-A8A1-427E448DEA98}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_twopv", "demo\twopv\demo_twopv.vcproj", "{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_udv", "demo\udv\demo_udv.vcproj", "{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D} = {D2059A10-7A4D-471A-BAEA-76479FD2773D}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86} = {DE96F5AB-AC39-44FF-9BAB-36805FE07A86}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "demo_vecscreen", "demo\vecscreen\demo_vecscreen.vcproj", "{B9B3203E-0C07-46DB-BABE-3024B22F923C}"
+	ProjectSection(ProjectDependencies) = postProject
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_asntool", "asnlib\asntool\exe_asntool.vcproj", "{95BF266E-0195-4BEB-B306-B99489EE3991}"
+	ProjectSection(ProjectDependencies) = postProject
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_blastcl3", "network\blast3\blastcl3\exe_blastcl3.vcproj", "{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}"
+	ProjectSection(ProjectDependencies) = postProject
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{759991FD-441C-4267-A364-1BB2236C67B8} = {759991FD-441C-4267-A364-1BB2236C67B8}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_ddv", "ddv\ddv\exe_ddv.vcproj", "{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}"
+	ProjectSection(ProjectDependencies) = postProject
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D} = {D2059A10-7A4D-471A-BAEA-76479FD2773D}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86} = {DE96F5AB-AC39-44FF-9BAB-36805FE07A86}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
+	EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_idfetch", "network\idfetch\exe_idfetch.vcproj", "{67436D24-0D70-48D5-B1AE-6E8DFA978983}"
 	ProjectSection(ProjectDependencies) = postProject
-		{35C18E88-9F42-49EA-9881-C3128245490F} = {35C18E88-9F42-49EA-9881-C3128245490F}
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{707F859C-FE05-486E-BB82-A447A6CD5036} = {707F859C-FE05-486E-BB82-A447A6CD5036}
+		{610E62DA-4DD6-479E-8D85-1FB87126D750} = {610E62DA-4DD6-479E-8D85-1FB87126D750}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF} = {85E82D79-6144-4151-A3E7-8140E9ED01CF}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_sbtedit", "sequin\sbtedit\exe_sbtedit.vcproj", "{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_sbtedit", "sequin\sbtedit\exe_sbtedit.vcproj", "{028EEC3D-499E-453C-A1F4-5A4478BBB39F}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB} = {4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94} = {A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-		{98C1A680-89B6-4911-8C36-42D14F43B868} = {98C1A680-89B6-4911-8C36-42D14F43B868}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC} = {45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340} = {47BB9C01-3751-4E25-87AE-6B4BAAA00340}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{2746DC43-68A9-42FE-80F0-1806679538FA} = {2746DC43-68A9-42FE-80F0-1806679538FA}
+		{C2857848-3327-46C6-929C-192629A21F60} = {C2857848-3327-46C6-929C-192629A21F60}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{759991FD-441C-4267-A364-1BB2236C67B8} = {759991FD-441C-4267-A364-1BB2236C67B8}
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86} = {DE96F5AB-AC39-44FF-9BAB-36805FE07A86}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_sequin", "sequin\sequin\exe_sequin.vcproj", "{002CC81D-C6AF-4AED-8624-301D0E13ED46}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_sequin", "sequin\sequin\exe_sequin.vcproj", "{86F47145-3ABB-45BA-8D51-89C24997882F}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB} = {4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94} = {A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-		{98C1A680-89B6-4911-8C36-42D14F43B868} = {98C1A680-89B6-4911-8C36-42D14F43B868}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC} = {45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340} = {47BB9C01-3751-4E25-87AE-6B4BAAA00340}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{2746DC43-68A9-42FE-80F0-1806679538FA} = {2746DC43-68A9-42FE-80F0-1806679538FA}
+		{C2857848-3327-46C6-929C-192629A21F60} = {C2857848-3327-46C6-929C-192629A21F60}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{759991FD-441C-4267-A364-1BB2236C67B8} = {759991FD-441C-4267-A364-1BB2236C67B8}
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86} = {DE96F5AB-AC39-44FF-9BAB-36805FE07A86}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_ssequin", "sequin\ssequin\exe_ssequin.vcproj", "{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "exe_ssequin", "sequin\ssequin\exe_ssequin.vcproj", "{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B} = {F7164C61-0D7C-4EC8-9209-88A760907B6B}
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F} = {96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED} = {CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C} = {ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF} = {F8CD481D-462C-40ED-98FA-C6EEF477B5CF}
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16} = {F2107221-7687-4F18-AEAC-FAA7C4EFCC16}
-		{3C4476FB-5518-425A-9D4E-44DD91068776} = {3C4476FB-5518-425A-9D4E-44DD91068776}
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223} = {E2B932C9-4C8A-4922-9DFF-9FB646184223}
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2} = {3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}
-		{327A10DD-2251-4191-8425-17E535235D30} = {327A10DD-2251-4191-8425-17E535235D30}
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB} = {4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94} = {A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467} = {FD5A8225-8809-4FFB-9190-B6403A2AD467}
-		{98C1A680-89B6-4911-8C36-42D14F43B868} = {98C1A680-89B6-4911-8C36-42D14F43B868}
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0} = {32AB53DD-66B1-4E17-B411-FEB804E62CF0}
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC} = {45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340} = {47BB9C01-3751-4E25-87AE-6B4BAAA00340}
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547} = {2B743DB7-9F8B-4652-B45D-04E23AE2B547}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216} = {A2E2AE46-C7B9-4544-B138-6F7662DF2216}
+		{6058EDC4-453A-48B1-8E27-83820FFB7203} = {6058EDC4-453A-48B1-8E27-83820FFB7203}
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A} = {B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D} = {8B58713F-B6F4-4A76-9888-309FDDFB985D}
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0} = {7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}
+		{25806259-F586-4AAC-BDD1-50C1B227147D} = {25806259-F586-4AAC-BDD1-50C1B227147D}
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF} = {F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}
+		{AB9DEE32-64FD-4700-84DF-485166A3E367} = {AB9DEE32-64FD-4700-84DF-485166A3E367}
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786} = {7C0D1F06-0B97-49A1-A25D-93D5E7A96786}
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7} = {14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}
+		{2746DC43-68A9-42FE-80F0-1806679538FA} = {2746DC43-68A9-42FE-80F0-1806679538FA}
+		{C2857848-3327-46C6-929C-192629A21F60} = {C2857848-3327-46C6-929C-192629A21F60}
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD} = {BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC} = {2DD94017-2F95-470D-94F5-9F10AD650BDC}
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937} = {19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}
+		{759991FD-441C-4267-A364-1BB2236C67B8} = {759991FD-441C-4267-A364-1BB2236C67B8}
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86} = {DE96F5AB-AC39-44FF-9BAB-36805FE07A86}
+		{43337FCD-B171-4441-B44E-D1C90C2700EE} = {43337FCD-B171-4441-B44E-D1C90C2700EE}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "http_connector_hit", "connect\test\http_connector_hit\http_connector_hit.vcproj", "{A73BBA44-40FF-4306-AF50-94737CD49839}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "http_connector_hit", "connect\test\http_connector_hit\http_connector_hit.vcproj", "{6266F193-8E41-4543-BB84-4DEA87146A44}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "medarch", "network\medarch\client\medarch.vcproj", "{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "medarch", "network\medarch\client\medarch.vcproj", "{2746DC43-68A9-42FE-80F0-1806679538FA}"
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbi", "corelib\ncbi\ncbi.vcproj", "{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbi", "corelib\ncbi\ncbi.vcproj", "{F6DB30E7-94C5-4760-92FA-449884953A9D}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbiacc", "cdromlib\ncbiacc\ncbiacc.vcproj", "{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbiacc", "cdromlib\ncbiacc\ncbiacc.vcproj", "{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbicdr", "cdromlib\ncbicdr\ncbicdr.vcproj", "{3C4476FB-5518-425A-9D4E-44DD91068776}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbicdr", "cdromlib\ncbicdr\ncbicdr.vcproj", "{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbicn3d", "cn3d\ncbicn3d\ncbicn3d.vcproj", "{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbicn3d", "cn3d\ncbicn3d\ncbicn3d.vcproj", "{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbicn3d_ogl", "cn3d\ncbicn3d_ogl\ncbicn3d_ogl.vcproj", "{B5934B23-8476-4D68-9769-2A65BF5C33A4}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbicn3d_ogl", "cn3d\ncbicn3d_ogl\ncbicn3d_ogl.vcproj", "{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbiconfig", "corelib\ncbiconfig.vcproj", "{CF596340-202E-4E79-B041-F4310A422C20}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbiconfig", "corelib\ncbiconfig.vcproj", "{74B970B2-6C7F-4AEE-9031-27CC087D7214}"
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbidesk", "desktop\ncbidesk.vcproj", "{FD5A8225-8809-4FFB-9190-B6403A2AD467}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbidesk", "desktop\ncbidesk.vcproj", "{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbiid1", "network\id1arch\ncbiid1.vcproj", "{707F859C-FE05-486E-BB82-A447A6CD5036}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbiid1", "network\id1arch\ncbiid1.vcproj", "{85E82D79-6144-4151-A3E7-8140E9ED01CF}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbimain", "corelib\ncbimain\ncbimain.vcproj", "{35C18E88-9F42-49EA-9881-C3128245490F}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbimain", "corelib\ncbimain\ncbimain.vcproj", "{610E62DA-4DD6-479E-8D85-1FB87126D750}"
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbimmdb", "biostruc\ncbimmdb.vcproj", "{98C1A680-89B6-4911-8C36-42D14F43B868}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbimmdb", "biostruc\ncbimmdb.vcproj", "{2DD94017-2F95-470D-94F5-9F10AD650BDC}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbinacc", "cdromlib\ncbinacc\ncbinacc.vcproj", "{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbinacc", "cdromlib\ncbinacc\ncbinacc.vcproj", "{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbiobj", "object\ncbiobj.vcproj", "{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbiobj", "object\ncbiobj.vcproj", "{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbispel", "network\spell\client\ncbispel.vcproj", "{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbispel", "network\spell\client\ncbispel.vcproj", "{8B58713F-B6F4-4A76-9888-309FDDFB985D}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbitool", "tools\ncbitool.vcproj", "{32AB53DD-66B1-4E17-B411-FEB804E62CF0}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbitool", "tools\ncbitool.vcproj", "{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbitxc2", "network\taxon1\taxon2\ncbitxc2.vcproj", "{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ncbitxc2", "network\taxon1\taxon2\ncbitxc2.vcproj", "{C2857848-3327-46C6-929C-192629A21F60}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "netblast", "network\blast3\netblast\netblast.vcproj", "{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "netblast", "network\blast3\netblast\netblast.vcproj", "{759991FD-441C-4267-A364-1BB2236C67B8}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "netcli", "network\nsclilib\netcli.vcproj", "{327A10DD-2251-4191-8425-17E535235D30}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "netcli", "network\nsclilib\netcli.vcproj", "{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "netentr", "network\entrez\client\netentr.vcproj", "{E2B932C9-4C8A-4922-9DFF-9FB646184223}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "netentr", "network\entrez\client\netentr.vcproj", "{AB9DEE32-64FD-4700-84DF-485166A3E367}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "regexp", "regexp\regexp.vcproj", "{21191422-314F-421D-93A8-EABF933C3065}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "regexp", "regexp\regexp.vcproj", "{C0B91754-0757-42BD-8F53-C05964FFFB66}"
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "smartnet", "internal\smart\smartnet\smartnet.vcproj", "{2B743DB7-9F8B-4652-B45D-04E23AE2B547}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "smartnet", "internal\smart\smartnet\smartnet.vcproj", "{43337FCD-B171-4441-B44E-D1C90C2700EE}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "socket_io_bouncer", "connect\test\socket_io_bouncer\socket_io_bouncer.vcproj", "{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "socket_io_bouncer", "connect\test\socket_io_bouncer\socket_io_bouncer.vcproj", "{BC50422E-D841-4EDF-B987-5135EC4D8F11}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_buffer", "connect\test\test_ncbi_buffer\test_ncbi_buffer.vcproj", "{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_buffer", "connect\test\test_ncbi_buffer\test_ncbi_buffer.vcproj", "{2EDD4E60-025D-4167-B827-9A700DFA6D72}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_connutil_hit", "connect\test\test_ncbi_connutil_hit\test_ncbi_connutil_hit.vcproj", "{AD565A88-01DA-4401-8E8F-53CCF8C759B5}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_connutil_hit", "connect\test\test_ncbi_connutil_hit\test_ncbi_connutil_hit.vcproj", "{760EA748-5473-48CE-8BE0-76538A0CE1B2}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_connutil_misc", "connect\test\test_ncbi_connutil_misc\test_ncbi_connutil_misc.vcproj", "{E85F8917-C596-477B-8D92-851E3726DE96}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_connutil_misc", "connect\test\test_ncbi_connutil_misc\test_ncbi_connutil_misc.vcproj", "{9218C976-8194-4AD4-BC5C-7CBC456C2475}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_core", "connect\test\test_ncbi_core\test_ncbi_core.vcproj", "{A6AC837C-8852-48B3-9232-57A2493AEDA4}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_core", "connect\test\test_ncbi_core\test_ncbi_core.vcproj", "{167BDE33-267C-49EE-9AC5-6177D283D799}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_disp", "connect\test\test_ncbi_disp\test_ncbi_disp.vcproj", "{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_disp", "connect\test\test_ncbi_disp\test_ncbi_disp.vcproj", "{087A2516-3C90-4D46-AEA9-670592894CB4}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_dsock", "connect\test\test_ncbi_dsock\test_ncbi_dsock.vcproj", "{032E43BB-816C-4BEE-9ABD-1E0B599C007A}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_dsock", "connect\test\test_ncbi_dsock\test_ncbi_dsock.vcproj", "{3B976840-4F3F-46A9-832D-4AB79417F712}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_file_connector", "connect\test\test_ncbi_file_connector\test_ncbi_file_connector.vcproj", "{57BABFE8-331D-41A9-8776-314F2D8791E2}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_file_connector", "connect\test\test_ncbi_file_connector\test_ncbi_file_connector.vcproj", "{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_http_connector", "connect\test\test_ncbi_http_connector\test_ncbi_http_connector.vcproj", "{8B6B0E08-62BA-4E92-8672-06CCA7432096}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_http_connector", "connect\test\test_ncbi_http_connector\test_ncbi_http_connector.vcproj", "{862D2BCD-67ED-4398-A811-7E247C2029E5}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70} = {8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B} = {A9561C14-6DAF-4A28-9F59-297D39432D0B}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_http_get", "connect\test\test_ncbi_http_get\test_ncbi_http_get.vcproj", "{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_http_get", "connect\test\test_ncbi_http_get\test_ncbi_http_get.vcproj", "{DD51F357-26FE-46F2-9AC9-5B682DBC198C}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_memory_connector", "connect\test\test_ncbi_memory_connector\test_ncbi_memory_connector.vcproj", "{42140DF3-03C5-4A99-9D7B-F4385733D694}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_memory_connector", "connect\test\test_ncbi_memory_connector\test_ncbi_memory_connector.vcproj", "{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70} = {8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B} = {A9561C14-6DAF-4A28-9F59-297D39432D0B}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_sendmail", "connect\test\test_ncbi_sendmail\test_ncbi_sendmail.vcproj", "{AA4B7095-5FBB-41E5-AE2A-39247638EC14}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_sendmail", "connect\test\test_ncbi_sendmail\test_ncbi_sendmail.vcproj", "{E459338E-39A8-49C9-9DFC-612E47863CE3}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_service_connector", "connect\test\test_ncbi_service_connector\test_ncbi_service_connector.vcproj", "{A40959E8-B640-49F7-B2E0-806A03544AB5}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_service_connector", "connect\test\test_ncbi_service_connector\test_ncbi_service_connector.vcproj", "{7719A61E-FAE1-4564-AD24-416318E48967}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70} = {8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B} = {A9561C14-6DAF-4A28-9F59-297D39432D0B}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_socket", "connect\test\test_ncbi_socket\test_ncbi_socket.vcproj", "{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_socket", "connect\test\test_ncbi_socket\test_ncbi_socket.vcproj", "{E6CE793E-7882-4E77-9D26-22C950DE0AFE}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_socket_connector", "connect\test\test_ncbi_socket_connector\test_ncbi_socket_connector.vcproj", "{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_ncbi_socket_connector", "connect\test\test_ncbi_socket_connector\test_ncbi_socket_connector.vcproj", "{9AAE2D3F-4D37-43B6-96EB-593DE7679811}"
 	ProjectSection(ProjectDependencies) = postProject
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D} = {E29B255C-2B3A-4E74-85E1-6CD033DFA55D}
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70} = {8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}
+		{F6DB30E7-94C5-4760-92FA-449884953A9D} = {F6DB30E7-94C5-4760-92FA-449884953A9D}
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B} = {A9561C14-6DAF-4A28-9F59-297D39432D0B}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_regexp", "regexp\test\test_regexp.vcproj", "{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_regexp", "regexp\test\test_regexp.vcproj", "{B6875C47-6809-4972-A89D-0085058670C9}"
 	ProjectSection(ProjectDependencies) = postProject
-		{21191422-314F-421D-93A8-EABF933C3065} = {21191422-314F-421D-93A8-EABF933C3065}
+		{C0B91754-0757-42BD-8F53-C05964FFFB66} = {C0B91754-0757-42BD-8F53-C05964FFFB66}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "vibgif", "gif\vibgif.vcproj", "{08C550B7-3DA6-46A6-96EB-A48806F1900C}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "vibgif", "gif\vibgif.vcproj", "{A0F67E98-8A07-4319-A3E8-B983D522D8CA}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "vibnet", "network\vibnet\vibnet.vcproj", "{47BB9C01-3751-4E25-87AE-6B4BAAA00340}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "vibnet", "network\vibnet\vibnet.vcproj", "{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "vibrant", "vibrant\vibrant\vibrant.vcproj", "{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "vibrant", "vibrant\vibrant\vibrant.vcproj", "{25806259-F586-4AAC-BDD1-50C1B227147D}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "vibrant_ogl", "vibrant\vibrant_ogl\vibrant_ogl.vcproj", "{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "vibrant_ogl", "vibrant\vibrant_ogl\vibrant_ogl.vcproj", "{E2180D54-5F75-47B7-8D77-00D04A6BEF69}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "xconntest", "connect\test\xconntest.vcproj", "{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "xconntest", "connect\test\xconntest.vcproj", "{A9561C14-6DAF-4A28-9F59-297D39432D0B}"
 	ProjectSection(ProjectDependencies) = postProject
-		{CF596340-202E-4E79-B041-F4310A422C20} = {CF596340-202E-4E79-B041-F4310A422C20}
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214} = {74B970B2-6C7F-4AEE-9031-27CC087D7214}
 	EndProjectSection
 EndProject
 Global
@@ -1257,2038 +1305,2102 @@ Global
 		ReleaseDLL|x64 = ReleaseDLL|x64
 	EndGlobalSection
 	GlobalSection(ProjectConfigurationPlatforms) = postSolution
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.Debug|Win32.ActiveCfg = Debug|Win32
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.Debug|Win32.Build.0 = Debug|Win32
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.Debug|x64.ActiveCfg = Debug|x64
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.Debug|x64.Build.0 = Debug|x64
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.Release|Win32.ActiveCfg = Release|Win32
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.Release|Win32.Build.0 = Release|Win32
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.Release|x64.ActiveCfg = Release|x64
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.Release|x64.Build.0 = Release|x64
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{27665816-D337-4E8D-AA41-AEB7CA3C7FF1}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.Debug|Win32.Build.0 = Debug|Win32
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.Debug|x64.ActiveCfg = Debug|x64
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.Debug|x64.Build.0 = Debug|x64
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.Release|Win32.ActiveCfg = Release|Win32
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.Release|Win32.Build.0 = Release|Win32
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.Release|x64.ActiveCfg = Release|x64
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.Release|x64.Build.0 = Release|x64
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D786BB9A-FC43-4C02-B1F8-A7F96B2B6D1C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.Debug|Win32.ActiveCfg = Debug|Win32
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.Debug|Win32.Build.0 = Debug|Win32
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.Debug|x64.ActiveCfg = Debug|x64
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.Debug|x64.Build.0 = Debug|x64
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.Release|Win32.ActiveCfg = Release|Win32
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.Release|Win32.Build.0 = Release|Win32
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.Release|x64.ActiveCfg = Release|x64
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.Release|x64.Build.0 = Release|x64
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{4109D7F4-1D18-495F-B5C7-DFEA565DE9C6}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.Debug|Win32.ActiveCfg = Debug|Win32
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.Debug|Win32.Build.0 = Debug|Win32
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.Debug|x64.ActiveCfg = Debug|x64
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.Debug|x64.Build.0 = Debug|x64
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.Release|Win32.ActiveCfg = Release|Win32
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.Release|Win32.Build.0 = Release|Win32
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.Release|x64.ActiveCfg = Release|x64
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.Release|x64.Build.0 = Release|x64
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{FEA214E0-E333-43A5-BD15-E5902264A91A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.Debug|Win32.ActiveCfg = Debug|Win32
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.Debug|Win32.Build.0 = Debug|Win32
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.Debug|x64.ActiveCfg = Debug|x64
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.Debug|x64.Build.0 = Debug|x64
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.Release|Win32.ActiveCfg = Release|Win32
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.Release|Win32.Build.0 = Release|Win32
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.Release|x64.ActiveCfg = Release|x64
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.Release|x64.Build.0 = Release|x64
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{0204EA88-C175-4970-922F-6F2C4FDA52EE}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.Debug|Win32.ActiveCfg = Debug|Win32
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.Debug|Win32.Build.0 = Debug|Win32
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.Debug|x64.ActiveCfg = Debug|x64
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.Debug|x64.Build.0 = Debug|x64
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.Release|Win32.ActiveCfg = Release|Win32
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.Release|Win32.Build.0 = Release|Win32
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.Release|x64.ActiveCfg = Release|x64
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.Release|x64.Build.0 = Release|x64
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{04452BB8-39AC-4DC3-8C42-58384D285FED}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.Debug|Win32.ActiveCfg = Debug|Win32
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.Debug|Win32.Build.0 = Debug|Win32
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.Debug|x64.ActiveCfg = Debug|x64
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.Debug|x64.Build.0 = Debug|x64
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.Release|Win32.ActiveCfg = Release|Win32
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.Release|Win32.Build.0 = Release|Win32
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.Release|x64.ActiveCfg = Release|x64
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.Release|x64.Build.0 = Release|x64
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{CD41CEB1-4E2C-494B-86E8-E29AF398D7ED}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.Debug|Win32.ActiveCfg = Debug|Win32
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.Debug|Win32.Build.0 = Debug|Win32
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.Debug|x64.ActiveCfg = Debug|x64
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.Debug|x64.Build.0 = Debug|x64
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.Release|Win32.ActiveCfg = Release|Win32
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.Release|Win32.Build.0 = Release|Win32
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.Release|x64.ActiveCfg = Release|x64
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.Release|x64.Build.0 = Release|x64
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{96FC3702-E2ED-434F-BBA5-3DE1366FFA1F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.Debug|Win32.ActiveCfg = Debug|Win32
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.Debug|Win32.Build.0 = Debug|Win32
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.Debug|x64.ActiveCfg = Debug|x64
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.Debug|x64.Build.0 = Debug|x64
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.Release|Win32.ActiveCfg = Release|Win32
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.Release|Win32.Build.0 = Release|Win32
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.Release|x64.ActiveCfg = Release|x64
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.Release|x64.Build.0 = Release|x64
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{F7164C61-0D7C-4EC8-9209-88A760907B6B}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.Debug|Win32.ActiveCfg = Debug|Win32
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.Debug|Win32.Build.0 = Debug|Win32
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.Debug|x64.ActiveCfg = Debug|x64
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.Debug|x64.Build.0 = Debug|x64
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.Release|Win32.ActiveCfg = Release|Win32
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.Release|Win32.Build.0 = Release|Win32
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.Release|x64.ActiveCfg = Release|x64
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.Release|x64.Build.0 = Release|x64
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{3D2820CB-F5E6-4807-864C-2C751ADC556D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.Debug|Win32.ActiveCfg = Debug|Win32
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.Debug|Win32.Build.0 = Debug|Win32
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.Debug|x64.ActiveCfg = Debug|x64
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.Debug|x64.Build.0 = Debug|x64
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.Release|Win32.ActiveCfg = Release|Win32
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.Release|Win32.Build.0 = Release|Win32
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.Release|x64.ActiveCfg = Release|x64
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.Release|x64.Build.0 = Release|x64
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{C817F26E-4541-45D0-A6DA-59E58DB9DB7E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.Debug|Win32.Build.0 = Debug|Win32
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.Debug|x64.ActiveCfg = Debug|x64
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.Debug|x64.Build.0 = Debug|x64
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.Release|Win32.ActiveCfg = Release|Win32
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.Release|Win32.Build.0 = Release|Win32
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.Release|x64.ActiveCfg = Release|x64
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.Release|x64.Build.0 = Release|x64
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D3D92BB5-1C47-4797-8486-4441926F2A54}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.Debug|Win32.ActiveCfg = Debug|Win32
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.Debug|Win32.Build.0 = Debug|Win32
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.Debug|x64.ActiveCfg = Debug|x64
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.Debug|x64.Build.0 = Debug|x64
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.Release|Win32.ActiveCfg = Release|Win32
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.Release|Win32.Build.0 = Release|Win32
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.Release|x64.ActiveCfg = Release|x64
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.Release|x64.Build.0 = Release|x64
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{2675C4D0-0894-426B-B291-2807B4B79D3F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.Debug|Win32.ActiveCfg = Debug|Win32
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.Debug|Win32.Build.0 = Debug|Win32
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.Debug|x64.ActiveCfg = Debug|x64
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.Debug|x64.Build.0 = Debug|x64
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.Release|Win32.ActiveCfg = Release|Win32
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.Release|Win32.Build.0 = Release|Win32
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.Release|x64.ActiveCfg = Release|x64
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.Release|x64.Build.0 = Release|x64
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{9CC7403B-4370-4C93-9155-697EA11A8810}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.Debug|Win32.ActiveCfg = Debug|Win32
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.Debug|Win32.Build.0 = Debug|Win32
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.Debug|x64.ActiveCfg = Debug|x64
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.Debug|x64.Build.0 = Debug|x64
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.Release|Win32.ActiveCfg = Release|Win32
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.Release|Win32.Build.0 = Release|Win32
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.Release|x64.ActiveCfg = Release|x64
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.Release|x64.Build.0 = Release|x64
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{06636583-FBC6-4274-9BD8-B5956A23B5C8}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.Debug|Win32.ActiveCfg = Debug|Win32
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.Debug|Win32.Build.0 = Debug|Win32
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.Debug|x64.ActiveCfg = Debug|x64
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.Debug|x64.Build.0 = Debug|x64
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.Release|Win32.ActiveCfg = Release|Win32
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.Release|Win32.Build.0 = Release|Win32
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.Release|x64.ActiveCfg = Release|x64
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.Release|x64.Build.0 = Release|x64
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{CBF870AB-2EE6-4F12-9F0E-0D8CB207751D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{E95696E6-C316-4957-853A-547A1088D338}.Debug|Win32.ActiveCfg = Debug|Win32
-		{E95696E6-C316-4957-853A-547A1088D338}.Debug|Win32.Build.0 = Debug|Win32
-		{E95696E6-C316-4957-853A-547A1088D338}.Debug|x64.ActiveCfg = Debug|x64
-		{E95696E6-C316-4957-853A-547A1088D338}.Debug|x64.Build.0 = Debug|x64
-		{E95696E6-C316-4957-853A-547A1088D338}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{E95696E6-C316-4957-853A-547A1088D338}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{E95696E6-C316-4957-853A-547A1088D338}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{E95696E6-C316-4957-853A-547A1088D338}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{E95696E6-C316-4957-853A-547A1088D338}.Release|Win32.ActiveCfg = Release|Win32
-		{E95696E6-C316-4957-853A-547A1088D338}.Release|Win32.Build.0 = Release|Win32
-		{E95696E6-C316-4957-853A-547A1088D338}.Release|x64.ActiveCfg = Release|x64
-		{E95696E6-C316-4957-853A-547A1088D338}.Release|x64.Build.0 = Release|x64
-		{E95696E6-C316-4957-853A-547A1088D338}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{E95696E6-C316-4957-853A-547A1088D338}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{E95696E6-C316-4957-853A-547A1088D338}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{E95696E6-C316-4957-853A-547A1088D338}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.Debug|Win32.ActiveCfg = Debug|Win32
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.Debug|Win32.Build.0 = Debug|Win32
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.Debug|x64.ActiveCfg = Debug|x64
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.Debug|x64.Build.0 = Debug|x64
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.Release|Win32.ActiveCfg = Release|Win32
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.Release|Win32.Build.0 = Release|Win32
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.Release|x64.ActiveCfg = Release|x64
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.Release|x64.Build.0 = Release|x64
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{6E9207DA-5998-4B79-8850-D019EEA4251D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.Debug|Win32.Build.0 = Debug|Win32
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.Debug|x64.ActiveCfg = Debug|x64
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.Debug|x64.Build.0 = Debug|x64
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.Release|Win32.ActiveCfg = Release|Win32
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.Release|Win32.Build.0 = Release|Win32
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.Release|x64.ActiveCfg = Release|x64
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.Release|x64.Build.0 = Release|x64
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D1B78D4D-E0B1-4430-AA1A-20E870FBC038}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.Debug|Win32.ActiveCfg = Debug|Win32
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.Debug|Win32.Build.0 = Debug|Win32
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.Debug|x64.ActiveCfg = Debug|x64
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.Debug|x64.Build.0 = Debug|x64
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.Release|Win32.ActiveCfg = Release|Win32
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.Release|Win32.Build.0 = Release|Win32
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.Release|x64.ActiveCfg = Release|x64
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.Release|x64.Build.0 = Release|x64
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{049092E8-80F0-40F6-81F1-0AF99640134D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.Debug|Win32.Build.0 = Debug|Win32
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.Debug|x64.ActiveCfg = Debug|x64
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.Debug|x64.Build.0 = Debug|x64
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.Release|Win32.ActiveCfg = Release|Win32
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.Release|Win32.Build.0 = Release|Win32
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.Release|x64.ActiveCfg = Release|x64
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.Release|x64.Build.0 = Release|x64
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D13243FE-FD39-476C-BAB7-14C583B3BC9E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.Debug|Win32.ActiveCfg = Debug|Win32
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.Debug|Win32.Build.0 = Debug|Win32
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.Debug|x64.ActiveCfg = Debug|x64
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.Debug|x64.Build.0 = Debug|x64
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.Release|Win32.ActiveCfg = Release|Win32
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.Release|Win32.Build.0 = Release|Win32
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.Release|x64.ActiveCfg = Release|x64
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.Release|x64.Build.0 = Release|x64
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{E778C1FD-C2F7-47A9-A453-259F6F520B4A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.Debug|Win32.ActiveCfg = Debug|Win32
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.Debug|Win32.Build.0 = Debug|Win32
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.Debug|x64.ActiveCfg = Debug|x64
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.Debug|x64.Build.0 = Debug|x64
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.Release|Win32.ActiveCfg = Release|Win32
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.Release|Win32.Build.0 = Release|Win32
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.Release|x64.ActiveCfg = Release|x64
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.Release|x64.Build.0 = Release|x64
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{F832691F-2EF5-4937-BBB4-626EE814A383}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.Debug|Win32.ActiveCfg = Debug|Win32
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.Debug|Win32.Build.0 = Debug|Win32
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.Debug|x64.ActiveCfg = Debug|x64
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.Debug|x64.Build.0 = Debug|x64
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.Release|Win32.ActiveCfg = Release|Win32
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.Release|Win32.Build.0 = Release|Win32
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.Release|x64.ActiveCfg = Release|x64
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.Release|x64.Build.0 = Release|x64
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{3039EEDE-B503-4E9D-AAEF-79EF07DF3A9B}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.Debug|Win32.ActiveCfg = Debug|Win32
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.Debug|Win32.Build.0 = Debug|Win32
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.Debug|x64.ActiveCfg = Debug|x64
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.Debug|x64.Build.0 = Debug|x64
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.Release|Win32.ActiveCfg = Release|Win32
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.Release|Win32.Build.0 = Release|Win32
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.Release|x64.ActiveCfg = Release|x64
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.Release|x64.Build.0 = Release|x64
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{1C14632F-22E1-40D3-B0C8-1E53C72ED92F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.Debug|Win32.ActiveCfg = Debug|Win32
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.Debug|Win32.Build.0 = Debug|Win32
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.Debug|x64.ActiveCfg = Debug|x64
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.Debug|x64.Build.0 = Debug|x64
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.Release|Win32.ActiveCfg = Release|Win32
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.Release|Win32.Build.0 = Release|Win32
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.Release|x64.ActiveCfg = Release|x64
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.Release|x64.Build.0 = Release|x64
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{AA8B7736-A934-41FD-A1F2-92FA47FE518E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.Debug|Win32.ActiveCfg = Debug|Win32
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.Debug|Win32.Build.0 = Debug|Win32
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.Debug|x64.ActiveCfg = Debug|x64
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.Debug|x64.Build.0 = Debug|x64
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.Release|Win32.ActiveCfg = Release|Win32
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.Release|Win32.Build.0 = Release|Win32
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.Release|x64.ActiveCfg = Release|x64
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.Release|x64.Build.0 = Release|x64
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{1E7F80A2-A2F7-43C5-A5CD-D9A745A2D9BC}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.Debug|Win32.ActiveCfg = Debug|Win32
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.Debug|Win32.Build.0 = Debug|Win32
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.Debug|x64.ActiveCfg = Debug|x64
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.Debug|x64.Build.0 = Debug|x64
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.Release|Win32.ActiveCfg = Release|Win32
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.Release|Win32.Build.0 = Release|Win32
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.Release|x64.ActiveCfg = Release|x64
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.Release|x64.Build.0 = Release|x64
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{4C2CCC7D-3D19-4E13-9317-3927894F0F3B}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.Debug|Win32.Build.0 = Debug|Win32
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.Debug|x64.ActiveCfg = Debug|x64
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.Debug|x64.Build.0 = Debug|x64
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.Release|Win32.ActiveCfg = Release|Win32
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.Release|Win32.Build.0 = Release|Win32
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.Release|x64.ActiveCfg = Release|x64
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.Release|x64.Build.0 = Release|x64
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D221EDFA-64EB-479A-B15B-792A90ADE47D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.Debug|Win32.ActiveCfg = Debug|Win32
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.Debug|Win32.Build.0 = Debug|Win32
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.Debug|x64.ActiveCfg = Debug|x64
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.Debug|x64.Build.0 = Debug|x64
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.Release|Win32.ActiveCfg = Release|Win32
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.Release|Win32.Build.0 = Release|Win32
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.Release|x64.ActiveCfg = Release|x64
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.Release|x64.Build.0 = Release|x64
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{83D6FAB0-4A26-4EB6-9B0D-7E665CBE703C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.Debug|Win32.ActiveCfg = Debug|Win32
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.Debug|Win32.Build.0 = Debug|Win32
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.Debug|x64.ActiveCfg = Debug|x64
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.Debug|x64.Build.0 = Debug|x64
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.Release|Win32.ActiveCfg = Release|Win32
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.Release|Win32.Build.0 = Release|Win32
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.Release|x64.ActiveCfg = Release|x64
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.Release|x64.Build.0 = Release|x64
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{2874FAEF-31B3-4A57-9CD4-998089E73480}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.Debug|Win32.ActiveCfg = Debug|Win32
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.Debug|Win32.Build.0 = Debug|Win32
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.Debug|x64.ActiveCfg = Debug|x64
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.Debug|x64.Build.0 = Debug|x64
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.Release|Win32.ActiveCfg = Release|Win32
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.Release|Win32.Build.0 = Release|Win32
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.Release|x64.ActiveCfg = Release|x64
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.Release|x64.Build.0 = Release|x64
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{F97DC7EE-9AD3-48A6-8F68-2CFA84F4B38A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.Debug|Win32.ActiveCfg = Debug|Win32
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.Debug|Win32.Build.0 = Debug|Win32
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.Debug|x64.ActiveCfg = Debug|x64
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.Debug|x64.Build.0 = Debug|x64
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.Release|Win32.ActiveCfg = Release|Win32
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.Release|Win32.Build.0 = Release|Win32
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.Release|x64.ActiveCfg = Release|x64
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.Release|x64.Build.0 = Release|x64
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{487B891B-190D-4534-9B6F-120C53FB4BB9}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.Debug|Win32.ActiveCfg = Debug|Win32
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.Debug|Win32.Build.0 = Debug|Win32
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.Debug|x64.ActiveCfg = Debug|x64
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.Debug|x64.Build.0 = Debug|x64
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.Release|Win32.ActiveCfg = Release|Win32
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.Release|Win32.Build.0 = Release|Win32
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.Release|x64.ActiveCfg = Release|x64
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.Release|x64.Build.0 = Release|x64
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{750C92D0-CF2F-413E-8D46-CE2D01901322}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{1DC69786-C012-46C5-8B82-92C093434D05}.Debug|Win32.ActiveCfg = Debug|Win32
-		{1DC69786-C012-46C5-8B82-92C093434D05}.Debug|Win32.Build.0 = Debug|Win32
-		{1DC69786-C012-46C5-8B82-92C093434D05}.Debug|x64.ActiveCfg = Debug|x64
-		{1DC69786-C012-46C5-8B82-92C093434D05}.Debug|x64.Build.0 = Debug|x64
-		{1DC69786-C012-46C5-8B82-92C093434D05}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{1DC69786-C012-46C5-8B82-92C093434D05}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{1DC69786-C012-46C5-8B82-92C093434D05}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{1DC69786-C012-46C5-8B82-92C093434D05}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{1DC69786-C012-46C5-8B82-92C093434D05}.Release|Win32.ActiveCfg = Release|Win32
-		{1DC69786-C012-46C5-8B82-92C093434D05}.Release|Win32.Build.0 = Release|Win32
-		{1DC69786-C012-46C5-8B82-92C093434D05}.Release|x64.ActiveCfg = Release|x64
-		{1DC69786-C012-46C5-8B82-92C093434D05}.Release|x64.Build.0 = Release|x64
-		{1DC69786-C012-46C5-8B82-92C093434D05}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{1DC69786-C012-46C5-8B82-92C093434D05}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{1DC69786-C012-46C5-8B82-92C093434D05}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{1DC69786-C012-46C5-8B82-92C093434D05}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.Debug|Win32.ActiveCfg = Debug|Win32
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.Debug|Win32.Build.0 = Debug|Win32
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.Debug|x64.ActiveCfg = Debug|x64
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.Debug|x64.Build.0 = Debug|x64
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.Release|Win32.ActiveCfg = Release|Win32
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.Release|Win32.Build.0 = Release|Win32
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.Release|x64.ActiveCfg = Release|x64
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.Release|x64.Build.0 = Release|x64
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{4F4585B4-7710-4BCA-86CE-4766F0F905E8}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.Debug|Win32.ActiveCfg = Debug|Win32
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.Debug|Win32.Build.0 = Debug|Win32
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.Debug|x64.ActiveCfg = Debug|x64
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.Debug|x64.Build.0 = Debug|x64
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.Release|Win32.ActiveCfg = Release|Win32
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.Release|Win32.Build.0 = Release|Win32
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.Release|x64.ActiveCfg = Release|x64
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.Release|x64.Build.0 = Release|x64
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{EC823D54-D2D0-4E00-A831-2BA12DF2AD50}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.Debug|Win32.Build.0 = Debug|Win32
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.Debug|x64.ActiveCfg = Debug|x64
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.Debug|x64.Build.0 = Debug|x64
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.Release|Win32.ActiveCfg = Release|Win32
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.Release|Win32.Build.0 = Release|Win32
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.Release|x64.ActiveCfg = Release|x64
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.Release|x64.Build.0 = Release|x64
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D3DCCB97-8DA8-4F61-BE14-F7078635FE43}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.Debug|Win32.ActiveCfg = Debug|Win32
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.Debug|Win32.Build.0 = Debug|Win32
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.Debug|x64.ActiveCfg = Debug|x64
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.Debug|x64.Build.0 = Debug|x64
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.Release|Win32.ActiveCfg = Release|Win32
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.Release|Win32.Build.0 = Release|Win32
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.Release|x64.ActiveCfg = Release|x64
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.Release|x64.Build.0 = Release|x64
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{053F419B-7D93-4051-A624-C6753A0B1A43}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.Debug|Win32.ActiveCfg = Debug|Win32
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.Debug|Win32.Build.0 = Debug|Win32
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.Debug|x64.ActiveCfg = Debug|x64
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.Debug|x64.Build.0 = Debug|x64
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.Release|Win32.ActiveCfg = Release|Win32
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.Release|Win32.Build.0 = Release|Win32
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.Release|x64.ActiveCfg = Release|x64
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.Release|x64.Build.0 = Release|x64
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{DAF15754-B721-430A-A1B9-55D6D67C036D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.Debug|Win32.ActiveCfg = Debug|Win32
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.Debug|Win32.Build.0 = Debug|Win32
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.Debug|x64.ActiveCfg = Debug|x64
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.Debug|x64.Build.0 = Debug|x64
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.Release|Win32.ActiveCfg = Release|Win32
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.Release|Win32.Build.0 = Release|Win32
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.Release|x64.ActiveCfg = Release|x64
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.Release|x64.Build.0 = Release|x64
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{7ACBE6DC-0F7B-4071-B3EF-8DFD67CC4D13}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.Debug|Win32.ActiveCfg = Debug|Win32
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.Debug|Win32.Build.0 = Debug|Win32
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.Debug|x64.ActiveCfg = Debug|x64
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.Debug|x64.Build.0 = Debug|x64
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.Release|Win32.ActiveCfg = Release|Win32
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.Release|Win32.Build.0 = Release|Win32
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.Release|x64.ActiveCfg = Release|x64
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.Release|x64.Build.0 = Release|x64
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{0F815DB5-EFA3-482B-8E8C-3DEFFD34F614}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.Debug|Win32.ActiveCfg = Debug|Win32
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.Debug|Win32.Build.0 = Debug|Win32
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.Debug|x64.ActiveCfg = Debug|x64
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.Debug|x64.Build.0 = Debug|x64
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.Release|Win32.ActiveCfg = Release|Win32
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.Release|Win32.Build.0 = Release|Win32
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.Release|x64.ActiveCfg = Release|x64
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.Release|x64.Build.0 = Release|x64
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{C9D7C3C5-2568-46D9-A1C8-08305F90C6A0}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.Debug|Win32.ActiveCfg = Debug|Win32
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.Debug|Win32.Build.0 = Debug|Win32
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.Debug|x64.ActiveCfg = Debug|x64
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.Debug|x64.Build.0 = Debug|x64
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.Release|Win32.ActiveCfg = Release|Win32
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.Release|Win32.Build.0 = Release|Win32
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.Release|x64.ActiveCfg = Release|x64
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.Release|x64.Build.0 = Release|x64
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{3EFBB872-C18C-4F90-BA06-286C205E8A8A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.Debug|Win32.ActiveCfg = Debug|Win32
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.Debug|Win32.Build.0 = Debug|Win32
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.Debug|x64.ActiveCfg = Debug|x64
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.Debug|x64.Build.0 = Debug|x64
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.Release|Win32.ActiveCfg = Release|Win32
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.Release|Win32.Build.0 = Release|Win32
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.Release|x64.ActiveCfg = Release|x64
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.Release|x64.Build.0 = Release|x64
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{3218262E-1A52-4542-8F22-A49D06C334AC}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.Debug|Win32.ActiveCfg = Debug|Win32
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.Debug|Win32.Build.0 = Debug|Win32
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.Debug|x64.ActiveCfg = Debug|x64
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.Debug|x64.Build.0 = Debug|x64
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.Release|Win32.ActiveCfg = Release|Win32
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.Release|Win32.Build.0 = Release|Win32
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.Release|x64.ActiveCfg = Release|x64
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.Release|x64.Build.0 = Release|x64
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{1DF27097-97DB-4932-BD3B-6F14A92816A3}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.Debug|Win32.ActiveCfg = Debug|Win32
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.Debug|Win32.Build.0 = Debug|Win32
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.Debug|x64.ActiveCfg = Debug|x64
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.Debug|x64.Build.0 = Debug|x64
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.Release|Win32.ActiveCfg = Release|Win32
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.Release|Win32.Build.0 = Release|Win32
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.Release|x64.ActiveCfg = Release|x64
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.Release|x64.Build.0 = Release|x64
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{F2092248-A59C-4CC3-8571-F6F6809919A5}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.Debug|Win32.ActiveCfg = Debug|Win32
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.Debug|Win32.Build.0 = Debug|Win32
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.Debug|x64.ActiveCfg = Debug|x64
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.Debug|x64.Build.0 = Debug|x64
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.Release|Win32.ActiveCfg = Release|Win32
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.Release|Win32.Build.0 = Release|Win32
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.Release|x64.ActiveCfg = Release|x64
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.Release|x64.Build.0 = Release|x64
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{A276E338-0D0C-4A5C-88C7-531574422EBA}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.Debug|Win32.ActiveCfg = Debug|Win32
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.Debug|Win32.Build.0 = Debug|Win32
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.Debug|x64.ActiveCfg = Debug|x64
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.Debug|x64.Build.0 = Debug|x64
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.Release|Win32.ActiveCfg = Release|Win32
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.Release|Win32.Build.0 = Release|Win32
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.Release|x64.ActiveCfg = Release|x64
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.Release|x64.Build.0 = Release|x64
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{A250CCFC-47DA-4895-BC62-66CADA053A52}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.Debug|Win32.ActiveCfg = Debug|Win32
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.Debug|Win32.Build.0 = Debug|Win32
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.Debug|x64.ActiveCfg = Debug|x64
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.Debug|x64.Build.0 = Debug|x64
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.Release|Win32.ActiveCfg = Release|Win32
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.Release|Win32.Build.0 = Release|Win32
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.Release|x64.ActiveCfg = Release|x64
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.Release|x64.Build.0 = Release|x64
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{876560CC-AE03-49C7-9FA8-D1656CB7F040}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.Debug|Win32.ActiveCfg = Debug|Win32
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.Debug|Win32.Build.0 = Debug|Win32
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.Debug|x64.ActiveCfg = Debug|x64
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.Debug|x64.Build.0 = Debug|x64
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.Release|Win32.ActiveCfg = Release|Win32
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.Release|Win32.Build.0 = Release|Win32
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.Release|x64.ActiveCfg = Release|x64
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.Release|x64.Build.0 = Release|x64
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{FD45D87E-E729-4BA2-90A6-F42C1ACD2CA4}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.Debug|Win32.Build.0 = Debug|Win32
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.Debug|x64.ActiveCfg = Debug|x64
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.Debug|x64.Build.0 = Debug|x64
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.Release|Win32.ActiveCfg = Release|Win32
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.Release|Win32.Build.0 = Release|Win32
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.Release|x64.ActiveCfg = Release|x64
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.Release|x64.Build.0 = Release|x64
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D962509C-BBA8-43AC-BDB9-4D420B16D099}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.Debug|Win32.ActiveCfg = Debug|Win32
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.Debug|Win32.Build.0 = Debug|Win32
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.Debug|x64.ActiveCfg = Debug|x64
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.Debug|x64.Build.0 = Debug|x64
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.Release|Win32.ActiveCfg = Release|Win32
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.Release|Win32.Build.0 = Release|Win32
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.Release|x64.ActiveCfg = Release|x64
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.Release|x64.Build.0 = Release|x64
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{86E2DEFE-91A2-400B-A093-82B0DE4968C0}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D3399079-037C-4873-AB41-8535E0F5124E}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D3399079-037C-4873-AB41-8535E0F5124E}.Debug|Win32.Build.0 = Debug|Win32
-		{D3399079-037C-4873-AB41-8535E0F5124E}.Debug|x64.ActiveCfg = Debug|x64
-		{D3399079-037C-4873-AB41-8535E0F5124E}.Debug|x64.Build.0 = Debug|x64
-		{D3399079-037C-4873-AB41-8535E0F5124E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D3399079-037C-4873-AB41-8535E0F5124E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D3399079-037C-4873-AB41-8535E0F5124E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D3399079-037C-4873-AB41-8535E0F5124E}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D3399079-037C-4873-AB41-8535E0F5124E}.Release|Win32.ActiveCfg = Release|Win32
-		{D3399079-037C-4873-AB41-8535E0F5124E}.Release|Win32.Build.0 = Release|Win32
-		{D3399079-037C-4873-AB41-8535E0F5124E}.Release|x64.ActiveCfg = Release|x64
-		{D3399079-037C-4873-AB41-8535E0F5124E}.Release|x64.Build.0 = Release|x64
-		{D3399079-037C-4873-AB41-8535E0F5124E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D3399079-037C-4873-AB41-8535E0F5124E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D3399079-037C-4873-AB41-8535E0F5124E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D3399079-037C-4873-AB41-8535E0F5124E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{9B82B22D-3287-4512-9C61-054CF931C402}.Debug|Win32.ActiveCfg = Debug|Win32
-		{9B82B22D-3287-4512-9C61-054CF931C402}.Debug|Win32.Build.0 = Debug|Win32
-		{9B82B22D-3287-4512-9C61-054CF931C402}.Debug|x64.ActiveCfg = Debug|x64
-		{9B82B22D-3287-4512-9C61-054CF931C402}.Debug|x64.Build.0 = Debug|x64
-		{9B82B22D-3287-4512-9C61-054CF931C402}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{9B82B22D-3287-4512-9C61-054CF931C402}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{9B82B22D-3287-4512-9C61-054CF931C402}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{9B82B22D-3287-4512-9C61-054CF931C402}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{9B82B22D-3287-4512-9C61-054CF931C402}.Release|Win32.ActiveCfg = Release|Win32
-		{9B82B22D-3287-4512-9C61-054CF931C402}.Release|Win32.Build.0 = Release|Win32
-		{9B82B22D-3287-4512-9C61-054CF931C402}.Release|x64.ActiveCfg = Release|x64
-		{9B82B22D-3287-4512-9C61-054CF931C402}.Release|x64.Build.0 = Release|x64
-		{9B82B22D-3287-4512-9C61-054CF931C402}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{9B82B22D-3287-4512-9C61-054CF931C402}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{9B82B22D-3287-4512-9C61-054CF931C402}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{9B82B22D-3287-4512-9C61-054CF931C402}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.Debug|Win32.ActiveCfg = Debug|Win32
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.Debug|Win32.Build.0 = Debug|Win32
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.Debug|x64.ActiveCfg = Debug|x64
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.Debug|x64.Build.0 = Debug|x64
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.Release|Win32.ActiveCfg = Release|Win32
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.Release|Win32.Build.0 = Release|Win32
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.Release|x64.ActiveCfg = Release|x64
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.Release|x64.Build.0 = Release|x64
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{6B0FCA0A-B988-4994-9343-8860CABDD9D2}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.Debug|Win32.ActiveCfg = Debug|Win32
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.Debug|Win32.Build.0 = Debug|Win32
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.Debug|x64.ActiveCfg = Debug|x64
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.Debug|x64.Build.0 = Debug|x64
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.Release|Win32.ActiveCfg = Release|Win32
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.Release|Win32.Build.0 = Release|Win32
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.Release|x64.ActiveCfg = Release|x64
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.Release|x64.Build.0 = Release|x64
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{3657A377-E327-4B16-9EE9-16E0E1ECFCE9}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.Debug|Win32.ActiveCfg = Debug|Win32
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.Debug|Win32.Build.0 = Debug|Win32
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.Debug|x64.ActiveCfg = Debug|x64
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.Debug|x64.Build.0 = Debug|x64
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.Release|Win32.ActiveCfg = Release|Win32
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.Release|Win32.Build.0 = Release|Win32
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.Release|x64.ActiveCfg = Release|x64
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.Release|x64.Build.0 = Release|x64
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{0DF9D837-5184-4BB7-BFF0-FF679C5EB7AF}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.Debug|Win32.ActiveCfg = Debug|Win32
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.Debug|Win32.Build.0 = Debug|Win32
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.Debug|x64.ActiveCfg = Debug|x64
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.Debug|x64.Build.0 = Debug|x64
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.Release|Win32.ActiveCfg = Release|Win32
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.Release|Win32.Build.0 = Release|Win32
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.Release|x64.ActiveCfg = Release|x64
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.Release|x64.Build.0 = Release|x64
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{AD4D8660-5128-4DAA-9CC9-BB4ABE051C4E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.Debug|Win32.Build.0 = Debug|Win32
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.Debug|x64.ActiveCfg = Debug|x64
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.Debug|x64.Build.0 = Debug|x64
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.Release|Win32.ActiveCfg = Release|Win32
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.Release|Win32.Build.0 = Release|Win32
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.Release|x64.ActiveCfg = Release|x64
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.Release|x64.Build.0 = Release|x64
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D0B197BF-1409-4108-81C0-A2754CD97ADA}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.Debug|Win32.ActiveCfg = Debug|Win32
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.Debug|Win32.Build.0 = Debug|Win32
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.Debug|x64.ActiveCfg = Debug|x64
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.Debug|x64.Build.0 = Debug|x64
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.Release|Win32.ActiveCfg = Release|Win32
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.Release|Win32.Build.0 = Release|Win32
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.Release|x64.ActiveCfg = Release|x64
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.Release|x64.Build.0 = Release|x64
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.Debug|Win32.ActiveCfg = Debug|Win32
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.Debug|Win32.Build.0 = Debug|Win32
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.Debug|x64.ActiveCfg = Debug|x64
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.Debug|x64.Build.0 = Debug|x64
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.Release|Win32.ActiveCfg = Release|Win32
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.Release|Win32.Build.0 = Release|Win32
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.Release|x64.ActiveCfg = Release|x64
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.Release|x64.Build.0 = Release|x64
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{8DD4CBD4-79DB-433D-86D3-FF9C61DC86A3}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.Debug|Win32.ActiveCfg = Debug|Win32
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.Debug|Win32.Build.0 = Debug|Win32
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.Debug|x64.ActiveCfg = Debug|x64
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.Debug|x64.Build.0 = Debug|x64
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.Release|Win32.ActiveCfg = Release|Win32
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.Release|Win32.Build.0 = Release|Win32
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.Release|x64.ActiveCfg = Release|x64
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.Release|x64.Build.0 = Release|x64
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{8BA07548-3F40-4D95-8BF5-ED3F257ACB96}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.Debug|Win32.ActiveCfg = Debug|Win32
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.Debug|Win32.Build.0 = Debug|Win32
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.Debug|x64.ActiveCfg = Debug|x64
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.Debug|x64.Build.0 = Debug|x64
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.Release|Win32.ActiveCfg = Release|Win32
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.Release|Win32.Build.0 = Release|Win32
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.Release|x64.ActiveCfg = Release|x64
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.Release|x64.Build.0 = Release|x64
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{33854DD9-B6AE-4BBA-9188-0A6AF2B9F098}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.Debug|Win32.ActiveCfg = Debug|Win32
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.Debug|Win32.Build.0 = Debug|Win32
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.Debug|x64.ActiveCfg = Debug|x64
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.Debug|x64.Build.0 = Debug|x64
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.Release|Win32.ActiveCfg = Release|Win32
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.Release|Win32.Build.0 = Release|Win32
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.Release|x64.ActiveCfg = Release|x64
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.Release|x64.Build.0 = Release|x64
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{4B5696EE-C2E8-49D1-A0ED-4E54AF811221}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.Debug|Win32.ActiveCfg = Debug|Win32
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.Debug|Win32.Build.0 = Debug|Win32
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.Debug|x64.ActiveCfg = Debug|x64
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.Debug|x64.Build.0 = Debug|x64
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.Release|Win32.ActiveCfg = Release|Win32
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.Release|Win32.Build.0 = Release|Win32
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.Release|x64.ActiveCfg = Release|x64
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.Release|x64.Build.0 = Release|x64
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{6C98CBEC-6EEF-472F-9BD2-80CF04B58E84}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.Debug|Win32.ActiveCfg = Debug|Win32
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.Debug|Win32.Build.0 = Debug|Win32
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.Debug|x64.ActiveCfg = Debug|x64
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.Debug|x64.Build.0 = Debug|x64
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.Release|Win32.ActiveCfg = Release|Win32
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.Release|Win32.Build.0 = Release|Win32
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.Release|x64.ActiveCfg = Release|x64
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.Release|x64.Build.0 = Release|x64
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{AED09298-117B-4D01-8C01-45F820D3BDE8}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.Debug|Win32.ActiveCfg = Debug|Win32
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.Debug|Win32.Build.0 = Debug|Win32
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.Debug|x64.ActiveCfg = Debug|x64
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.Debug|x64.Build.0 = Debug|x64
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.Release|Win32.ActiveCfg = Release|Win32
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.Release|Win32.Build.0 = Release|Win32
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.Release|x64.ActiveCfg = Release|x64
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.Release|x64.Build.0 = Release|x64
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{E85FC734-1E47-413F-82E3-A83908FC3A77}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.Debug|Win32.ActiveCfg = Debug|Win32
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.Debug|Win32.Build.0 = Debug|Win32
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.Debug|x64.ActiveCfg = Debug|x64
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.Debug|x64.Build.0 = Debug|x64
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.Release|Win32.ActiveCfg = Release|Win32
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.Release|Win32.Build.0 = Release|Win32
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.Release|x64.ActiveCfg = Release|x64
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.Release|x64.Build.0 = Release|x64
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{D2928CA0-E664-4C71-9254-AD1B1CB9A201}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.Debug|Win32.ActiveCfg = Debug|Win32
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.Debug|Win32.Build.0 = Debug|Win32
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.Debug|x64.ActiveCfg = Debug|x64
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.Debug|x64.Build.0 = Debug|x64
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.Release|Win32.ActiveCfg = Release|Win32
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.Release|Win32.Build.0 = Release|Win32
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.Release|x64.ActiveCfg = Release|x64
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.Release|x64.Build.0 = Release|x64
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{924EF5EC-35C3-41A2-AB29-827D491DA574}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.Debug|Win32.ActiveCfg = Debug|Win32
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.Debug|Win32.Build.0 = Debug|Win32
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.Debug|x64.ActiveCfg = Debug|x64
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.Debug|x64.Build.0 = Debug|x64
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.Release|Win32.ActiveCfg = Release|Win32
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.Release|Win32.Build.0 = Release|Win32
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.Release|x64.ActiveCfg = Release|x64
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.Release|x64.Build.0 = Release|x64
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{42E5A984-7EA8-4DF0-9918-970247935C64}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.Debug|Win32.ActiveCfg = Debug|Win32
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.Debug|Win32.Build.0 = Debug|Win32
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.Debug|x64.ActiveCfg = Debug|x64
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.Debug|x64.Build.0 = Debug|x64
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.Release|Win32.ActiveCfg = Release|Win32
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.Release|Win32.Build.0 = Release|Win32
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.Release|x64.ActiveCfg = Release|x64
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.Release|x64.Build.0 = Release|x64
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{3684FA7A-0E39-4377-876F-17FA3C6869F2}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.Debug|Win32.ActiveCfg = Debug|Win32
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.Debug|Win32.Build.0 = Debug|Win32
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.Debug|x64.ActiveCfg = Debug|x64
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.Debug|x64.Build.0 = Debug|x64
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.Release|Win32.ActiveCfg = Release|Win32
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.Release|Win32.Build.0 = Release|Win32
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.Release|x64.ActiveCfg = Release|x64
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.Release|x64.Build.0 = Release|x64
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{69D59444-9FA8-41D4-82AC-1CA12A8F160F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.Debug|Win32.ActiveCfg = Debug|Win32
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.Debug|Win32.Build.0 = Debug|Win32
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.Debug|x64.ActiveCfg = Debug|x64
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.Debug|x64.Build.0 = Debug|x64
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.Release|Win32.ActiveCfg = Release|Win32
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.Release|Win32.Build.0 = Release|Win32
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.Release|x64.ActiveCfg = Release|x64
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.Release|x64.Build.0 = Release|x64
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{C015E441-C32E-4F5F-9DCA-9B9329E3B7C0}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.Debug|Win32.ActiveCfg = Debug|Win32
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.Debug|Win32.Build.0 = Debug|Win32
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.Debug|x64.ActiveCfg = Debug|x64
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.Debug|x64.Build.0 = Debug|x64
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.Release|Win32.ActiveCfg = Release|Win32
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.Release|Win32.Build.0 = Release|Win32
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.Release|x64.ActiveCfg = Release|x64
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.Release|x64.Build.0 = Release|x64
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{8C72F165-0AC2-4462-BAB9-8AE276273AC0}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.Debug|Win32.ActiveCfg = Debug|Win32
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.Debug|Win32.Build.0 = Debug|Win32
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.Debug|x64.ActiveCfg = Debug|x64
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.Debug|x64.Build.0 = Debug|x64
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.Release|Win32.ActiveCfg = Release|Win32
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.Release|Win32.Build.0 = Release|Win32
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.Release|x64.ActiveCfg = Release|x64
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.Release|x64.Build.0 = Release|x64
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{914A88CB-0667-40BC-8F0F-4594BA7B9D85}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.Debug|Win32.ActiveCfg = Debug|Win32
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.Debug|Win32.Build.0 = Debug|Win32
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.Debug|x64.ActiveCfg = Debug|x64
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.Debug|x64.Build.0 = Debug|x64
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.Release|Win32.ActiveCfg = Release|Win32
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.Release|Win32.Build.0 = Release|Win32
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.Release|x64.ActiveCfg = Release|x64
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.Release|x64.Build.0 = Release|x64
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{805D635B-FA95-4A2B-A5DD-1EC3667AE7B1}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.Debug|Win32.ActiveCfg = Debug|Win32
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.Debug|Win32.Build.0 = Debug|Win32
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.Debug|x64.ActiveCfg = Debug|x64
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.Debug|x64.Build.0 = Debug|x64
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.Release|Win32.ActiveCfg = Release|Win32
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.Release|Win32.Build.0 = Release|Win32
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.Release|x64.ActiveCfg = Release|x64
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.Release|x64.Build.0 = Release|x64
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{9AA6C9C9-1442-48CD-BD94-F134953418A9}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.Debug|Win32.ActiveCfg = Debug|Win32
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.Debug|Win32.Build.0 = Debug|Win32
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.Debug|x64.ActiveCfg = Debug|x64
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.Debug|x64.Build.0 = Debug|x64
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.Release|Win32.ActiveCfg = Release|Win32
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.Release|Win32.Build.0 = Release|Win32
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.Release|x64.ActiveCfg = Release|x64
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.Release|x64.Build.0 = Release|x64
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.Debug|Win32.ActiveCfg = Debug|Win32
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.Debug|Win32.Build.0 = Debug|Win32
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.Debug|x64.ActiveCfg = Debug|x64
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.Debug|x64.Build.0 = Debug|x64
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.Release|Win32.ActiveCfg = Release|Win32
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.Release|Win32.Build.0 = Release|Win32
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.Release|x64.ActiveCfg = Release|x64
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.Release|x64.Build.0 = Release|x64
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{3BF6CF52-B403-4F8A-8DD5-4F1CF619CCC9}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.Debug|Win32.ActiveCfg = Debug|Win32
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.Debug|Win32.Build.0 = Debug|Win32
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.Debug|x64.ActiveCfg = Debug|x64
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.Debug|x64.Build.0 = Debug|x64
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.Release|Win32.ActiveCfg = Release|Win32
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.Release|Win32.Build.0 = Release|Win32
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.Release|x64.ActiveCfg = Release|x64
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.Release|x64.Build.0 = Release|x64
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{BB120D1D-3A68-4107-A8A1-427E448DEA98}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.Debug|Win32.ActiveCfg = Debug|Win32
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.Debug|Win32.Build.0 = Debug|Win32
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.Debug|x64.ActiveCfg = Debug|x64
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.Debug|x64.Build.0 = Debug|x64
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.Release|Win32.ActiveCfg = Release|Win32
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.Release|Win32.Build.0 = Release|Win32
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.Release|x64.ActiveCfg = Release|x64
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.Release|x64.Build.0 = Release|x64
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.Debug|Win32.ActiveCfg = Debug|Win32
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.Debug|Win32.Build.0 = Debug|Win32
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.Debug|x64.ActiveCfg = Debug|x64
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.Debug|x64.Build.0 = Debug|x64
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.Release|Win32.ActiveCfg = Release|Win32
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.Release|Win32.Build.0 = Release|Win32
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.Release|x64.ActiveCfg = Release|x64
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.Release|x64.Build.0 = Release|x64
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{002CC81D-C6AF-4AED-8624-301D0E13ED46}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.Debug|Win32.ActiveCfg = Debug|Win32
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.Debug|Win32.Build.0 = Debug|Win32
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.Debug|x64.ActiveCfg = Debug|x64
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.Debug|x64.Build.0 = Debug|x64
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.Release|Win32.ActiveCfg = Release|Win32
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.Release|Win32.Build.0 = Release|Win32
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.Release|x64.ActiveCfg = Release|x64
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.Release|x64.Build.0 = Release|x64
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.Debug|Win32.ActiveCfg = Debug|Win32
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.Debug|Win32.Build.0 = Debug|Win32
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.Debug|x64.ActiveCfg = Debug|x64
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.Debug|x64.Build.0 = Debug|x64
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.Release|Win32.ActiveCfg = Release|Win32
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.Release|Win32.Build.0 = Release|Win32
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.Release|x64.ActiveCfg = Release|x64
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.Release|x64.Build.0 = Release|x64
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{A73BBA44-40FF-4306-AF50-94737CD49839}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.Debug|Win32.ActiveCfg = Debug|Win32
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.Debug|Win32.Build.0 = Debug|Win32
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.Debug|x64.ActiveCfg = Debug|x64
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.Debug|x64.Build.0 = Debug|x64
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.Release|Win32.ActiveCfg = Release|Win32
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.Release|Win32.Build.0 = Release|Win32
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.Release|x64.ActiveCfg = Release|x64
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.Release|x64.Build.0 = Release|x64
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.Debug|Win32.ActiveCfg = Debug|Win32
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.Debug|Win32.Build.0 = Debug|Win32
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.Debug|x64.ActiveCfg = Debug|x64
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.Debug|x64.Build.0 = Debug|x64
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.Release|Win32.ActiveCfg = Release|Win32
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.Release|Win32.Build.0 = Release|Win32
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.Release|x64.ActiveCfg = Release|x64
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.Release|x64.Build.0 = Release|x64
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{E29B255C-2B3A-4E74-85E1-6CD033DFA55D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.Debug|Win32.ActiveCfg = Debug|Win32
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.Debug|Win32.Build.0 = Debug|Win32
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.Debug|x64.ActiveCfg = Debug|x64
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.Debug|x64.Build.0 = Debug|x64
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.Release|Win32.ActiveCfg = Release|Win32
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.Release|Win32.Build.0 = Release|Win32
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.Release|x64.ActiveCfg = Release|x64
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.Release|x64.Build.0 = Release|x64
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{AFDEDE71-796D-4896-BEE6-AFFC4F77CC09}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.Debug|Win32.ActiveCfg = Debug|Win32
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.Debug|Win32.Build.0 = Debug|Win32
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.Debug|x64.ActiveCfg = Debug|x64
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.Debug|x64.Build.0 = Debug|x64
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.Release|Win32.ActiveCfg = Release|Win32
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.Release|Win32.Build.0 = Release|Win32
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.Release|x64.ActiveCfg = Release|x64
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.Release|x64.Build.0 = Release|x64
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{3C4476FB-5518-425A-9D4E-44DD91068776}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.Debug|Win32.ActiveCfg = Debug|Win32
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.Debug|Win32.Build.0 = Debug|Win32
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.Debug|x64.ActiveCfg = Debug|x64
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.Debug|x64.Build.0 = Debug|x64
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.Release|Win32.ActiveCfg = Release|Win32
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.Release|Win32.Build.0 = Release|Win32
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.Release|x64.ActiveCfg = Release|x64
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.Release|x64.Build.0 = Release|x64
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{0A01AD98-3A52-430A-A7A8-2A3E990D1BA2}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.Debug|Win32.ActiveCfg = Debug|Win32
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.Debug|Win32.Build.0 = Debug|Win32
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.Debug|x64.ActiveCfg = Debug|x64
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.Debug|x64.Build.0 = Debug|x64
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.Release|Win32.ActiveCfg = Release|Win32
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.Release|Win32.Build.0 = Release|Win32
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.Release|x64.ActiveCfg = Release|x64
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.Release|x64.Build.0 = Release|x64
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{B5934B23-8476-4D68-9769-2A65BF5C33A4}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{CF596340-202E-4E79-B041-F4310A422C20}.Debug|Win32.ActiveCfg = Debug|Win32
-		{CF596340-202E-4E79-B041-F4310A422C20}.Debug|Win32.Build.0 = Debug|Win32
-		{CF596340-202E-4E79-B041-F4310A422C20}.Debug|x64.ActiveCfg = Debug|x64
-		{CF596340-202E-4E79-B041-F4310A422C20}.Debug|x64.Build.0 = Debug|x64
-		{CF596340-202E-4E79-B041-F4310A422C20}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{CF596340-202E-4E79-B041-F4310A422C20}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{CF596340-202E-4E79-B041-F4310A422C20}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{CF596340-202E-4E79-B041-F4310A422C20}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{CF596340-202E-4E79-B041-F4310A422C20}.Release|Win32.ActiveCfg = Release|Win32
-		{CF596340-202E-4E79-B041-F4310A422C20}.Release|Win32.Build.0 = Release|Win32
-		{CF596340-202E-4E79-B041-F4310A422C20}.Release|x64.ActiveCfg = Release|x64
-		{CF596340-202E-4E79-B041-F4310A422C20}.Release|x64.Build.0 = Release|x64
-		{CF596340-202E-4E79-B041-F4310A422C20}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{CF596340-202E-4E79-B041-F4310A422C20}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{CF596340-202E-4E79-B041-F4310A422C20}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{CF596340-202E-4E79-B041-F4310A422C20}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.Debug|Win32.ActiveCfg = Debug|Win32
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.Debug|Win32.Build.0 = Debug|Win32
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.Debug|x64.ActiveCfg = Debug|x64
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.Debug|x64.Build.0 = Debug|x64
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.Release|Win32.ActiveCfg = Release|Win32
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.Release|Win32.Build.0 = Release|Win32
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.Release|x64.ActiveCfg = Release|x64
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.Release|x64.Build.0 = Release|x64
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{FD5A8225-8809-4FFB-9190-B6403A2AD467}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.Debug|Win32.ActiveCfg = Debug|Win32
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.Debug|Win32.Build.0 = Debug|Win32
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.Debug|x64.ActiveCfg = Debug|x64
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.Debug|x64.Build.0 = Debug|x64
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.Release|Win32.ActiveCfg = Release|Win32
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.Release|Win32.Build.0 = Release|Win32
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.Release|x64.ActiveCfg = Release|x64
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.Release|x64.Build.0 = Release|x64
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{707F859C-FE05-486E-BB82-A447A6CD5036}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{35C18E88-9F42-49EA-9881-C3128245490F}.Debug|Win32.ActiveCfg = Debug|Win32
-		{35C18E88-9F42-49EA-9881-C3128245490F}.Debug|Win32.Build.0 = Debug|Win32
-		{35C18E88-9F42-49EA-9881-C3128245490F}.Debug|x64.ActiveCfg = Debug|x64
-		{35C18E88-9F42-49EA-9881-C3128245490F}.Debug|x64.Build.0 = Debug|x64
-		{35C18E88-9F42-49EA-9881-C3128245490F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{35C18E88-9F42-49EA-9881-C3128245490F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{35C18E88-9F42-49EA-9881-C3128245490F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{35C18E88-9F42-49EA-9881-C3128245490F}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{35C18E88-9F42-49EA-9881-C3128245490F}.Release|Win32.ActiveCfg = Release|Win32
-		{35C18E88-9F42-49EA-9881-C3128245490F}.Release|Win32.Build.0 = Release|Win32
-		{35C18E88-9F42-49EA-9881-C3128245490F}.Release|x64.ActiveCfg = Release|x64
-		{35C18E88-9F42-49EA-9881-C3128245490F}.Release|x64.Build.0 = Release|x64
-		{35C18E88-9F42-49EA-9881-C3128245490F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{35C18E88-9F42-49EA-9881-C3128245490F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{35C18E88-9F42-49EA-9881-C3128245490F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{35C18E88-9F42-49EA-9881-C3128245490F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.Debug|Win32.ActiveCfg = Debug|Win32
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.Debug|Win32.Build.0 = Debug|Win32
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.Debug|x64.ActiveCfg = Debug|x64
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.Debug|x64.Build.0 = Debug|x64
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.Release|Win32.ActiveCfg = Release|Win32
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.Release|Win32.Build.0 = Release|Win32
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.Release|x64.ActiveCfg = Release|x64
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.Release|x64.Build.0 = Release|x64
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{98C1A680-89B6-4911-8C36-42D14F43B868}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.Debug|Win32.ActiveCfg = Debug|Win32
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.Debug|Win32.Build.0 = Debug|Win32
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.Debug|x64.ActiveCfg = Debug|x64
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.Debug|x64.Build.0 = Debug|x64
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.Release|Win32.ActiveCfg = Release|Win32
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.Release|Win32.Build.0 = Release|Win32
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.Release|x64.ActiveCfg = Release|x64
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.Release|x64.Build.0 = Release|x64
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{3E5CD700-5AE9-41CF-9A12-794A15EDE7D2}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.Debug|Win32.ActiveCfg = Debug|Win32
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.Debug|Win32.Build.0 = Debug|Win32
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.Debug|x64.ActiveCfg = Debug|x64
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.Debug|x64.Build.0 = Debug|x64
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.Release|Win32.ActiveCfg = Release|Win32
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.Release|Win32.Build.0 = Release|Win32
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.Release|x64.ActiveCfg = Release|x64
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.Release|x64.Build.0 = Release|x64
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.Debug|Win32.ActiveCfg = Debug|Win32
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.Debug|Win32.Build.0 = Debug|Win32
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.Debug|x64.ActiveCfg = Debug|x64
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.Debug|x64.Build.0 = Debug|x64
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.Release|Win32.ActiveCfg = Release|Win32
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.Release|Win32.Build.0 = Release|Win32
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.Release|x64.ActiveCfg = Release|x64
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.Release|x64.Build.0 = Release|x64
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.Debug|Win32.ActiveCfg = Debug|Win32
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.Debug|Win32.Build.0 = Debug|Win32
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.Debug|x64.ActiveCfg = Debug|x64
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.Debug|x64.Build.0 = Debug|x64
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.Release|Win32.ActiveCfg = Release|Win32
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.Release|Win32.Build.0 = Release|Win32
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.Release|x64.ActiveCfg = Release|x64
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.Release|x64.Build.0 = Release|x64
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{32AB53DD-66B1-4E17-B411-FEB804E62CF0}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.Debug|Win32.ActiveCfg = Debug|Win32
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.Debug|Win32.Build.0 = Debug|Win32
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.Debug|x64.ActiveCfg = Debug|x64
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.Debug|x64.Build.0 = Debug|x64
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.Release|Win32.ActiveCfg = Release|Win32
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.Release|Win32.Build.0 = Release|Win32
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.Release|x64.ActiveCfg = Release|x64
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.Release|x64.Build.0 = Release|x64
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.Debug|Win32.ActiveCfg = Debug|Win32
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.Debug|Win32.Build.0 = Debug|Win32
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.Debug|x64.ActiveCfg = Debug|x64
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.Debug|x64.Build.0 = Debug|x64
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.Release|Win32.ActiveCfg = Release|Win32
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.Release|Win32.Build.0 = Release|Win32
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.Release|x64.ActiveCfg = Release|x64
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.Release|x64.Build.0 = Release|x64
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{327A10DD-2251-4191-8425-17E535235D30}.Debug|Win32.ActiveCfg = Debug|Win32
-		{327A10DD-2251-4191-8425-17E535235D30}.Debug|Win32.Build.0 = Debug|Win32
-		{327A10DD-2251-4191-8425-17E535235D30}.Debug|x64.ActiveCfg = Debug|x64
-		{327A10DD-2251-4191-8425-17E535235D30}.Debug|x64.Build.0 = Debug|x64
-		{327A10DD-2251-4191-8425-17E535235D30}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{327A10DD-2251-4191-8425-17E535235D30}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{327A10DD-2251-4191-8425-17E535235D30}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{327A10DD-2251-4191-8425-17E535235D30}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{327A10DD-2251-4191-8425-17E535235D30}.Release|Win32.ActiveCfg = Release|Win32
-		{327A10DD-2251-4191-8425-17E535235D30}.Release|Win32.Build.0 = Release|Win32
-		{327A10DD-2251-4191-8425-17E535235D30}.Release|x64.ActiveCfg = Release|x64
-		{327A10DD-2251-4191-8425-17E535235D30}.Release|x64.Build.0 = Release|x64
-		{327A10DD-2251-4191-8425-17E535235D30}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{327A10DD-2251-4191-8425-17E535235D30}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{327A10DD-2251-4191-8425-17E535235D30}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{327A10DD-2251-4191-8425-17E535235D30}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.Debug|Win32.ActiveCfg = Debug|Win32
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.Debug|Win32.Build.0 = Debug|Win32
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.Debug|x64.ActiveCfg = Debug|x64
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.Debug|x64.Build.0 = Debug|x64
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.Release|Win32.ActiveCfg = Release|Win32
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.Release|Win32.Build.0 = Release|Win32
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.Release|x64.ActiveCfg = Release|x64
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.Release|x64.Build.0 = Release|x64
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{E2B932C9-4C8A-4922-9DFF-9FB646184223}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{21191422-314F-421D-93A8-EABF933C3065}.Debug|Win32.ActiveCfg = Debug|Win32
-		{21191422-314F-421D-93A8-EABF933C3065}.Debug|Win32.Build.0 = Debug|Win32
-		{21191422-314F-421D-93A8-EABF933C3065}.Debug|x64.ActiveCfg = Debug|x64
-		{21191422-314F-421D-93A8-EABF933C3065}.Debug|x64.Build.0 = Debug|x64
-		{21191422-314F-421D-93A8-EABF933C3065}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{21191422-314F-421D-93A8-EABF933C3065}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{21191422-314F-421D-93A8-EABF933C3065}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{21191422-314F-421D-93A8-EABF933C3065}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{21191422-314F-421D-93A8-EABF933C3065}.Release|Win32.ActiveCfg = Release|Win32
-		{21191422-314F-421D-93A8-EABF933C3065}.Release|Win32.Build.0 = Release|Win32
-		{21191422-314F-421D-93A8-EABF933C3065}.Release|x64.ActiveCfg = Release|x64
-		{21191422-314F-421D-93A8-EABF933C3065}.Release|x64.Build.0 = Release|x64
-		{21191422-314F-421D-93A8-EABF933C3065}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{21191422-314F-421D-93A8-EABF933C3065}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{21191422-314F-421D-93A8-EABF933C3065}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{21191422-314F-421D-93A8-EABF933C3065}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.Debug|Win32.ActiveCfg = Debug|Win32
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.Debug|Win32.Build.0 = Debug|Win32
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.Debug|x64.ActiveCfg = Debug|x64
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.Debug|x64.Build.0 = Debug|x64
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.Release|Win32.ActiveCfg = Release|Win32
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.Release|Win32.Build.0 = Release|Win32
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.Release|x64.ActiveCfg = Release|x64
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.Release|x64.Build.0 = Release|x64
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{2B743DB7-9F8B-4652-B45D-04E23AE2B547}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.Debug|Win32.ActiveCfg = Debug|Win32
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.Debug|Win32.Build.0 = Debug|Win32
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.Debug|x64.ActiveCfg = Debug|x64
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.Debug|x64.Build.0 = Debug|x64
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.Release|Win32.ActiveCfg = Release|Win32
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.Release|Win32.Build.0 = Release|Win32
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.Release|x64.ActiveCfg = Release|x64
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.Release|x64.Build.0 = Release|x64
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{1F10C6E1-3C88-4C78-9C18-05AC31B2421F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.Debug|Win32.ActiveCfg = Debug|Win32
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.Debug|Win32.Build.0 = Debug|Win32
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.Debug|x64.ActiveCfg = Debug|x64
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.Debug|x64.Build.0 = Debug|x64
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.Release|Win32.ActiveCfg = Release|Win32
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.Release|Win32.Build.0 = Release|Win32
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.Release|x64.ActiveCfg = Release|x64
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.Release|x64.Build.0 = Release|x64
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{9149ED1B-E896-4A64-A3D2-C42FC10A7F63}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.Debug|Win32.ActiveCfg = Debug|Win32
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.Debug|Win32.Build.0 = Debug|Win32
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.Debug|x64.ActiveCfg = Debug|x64
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.Debug|x64.Build.0 = Debug|x64
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.Release|Win32.ActiveCfg = Release|Win32
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.Release|Win32.Build.0 = Release|Win32
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.Release|x64.ActiveCfg = Release|x64
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.Release|x64.Build.0 = Release|x64
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{AD565A88-01DA-4401-8E8F-53CCF8C759B5}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{E85F8917-C596-477B-8D92-851E3726DE96}.Debug|Win32.ActiveCfg = Debug|Win32
-		{E85F8917-C596-477B-8D92-851E3726DE96}.Debug|Win32.Build.0 = Debug|Win32
-		{E85F8917-C596-477B-8D92-851E3726DE96}.Debug|x64.ActiveCfg = Debug|x64
-		{E85F8917-C596-477B-8D92-851E3726DE96}.Debug|x64.Build.0 = Debug|x64
-		{E85F8917-C596-477B-8D92-851E3726DE96}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{E85F8917-C596-477B-8D92-851E3726DE96}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{E85F8917-C596-477B-8D92-851E3726DE96}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{E85F8917-C596-477B-8D92-851E3726DE96}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{E85F8917-C596-477B-8D92-851E3726DE96}.Release|Win32.ActiveCfg = Release|Win32
-		{E85F8917-C596-477B-8D92-851E3726DE96}.Release|Win32.Build.0 = Release|Win32
-		{E85F8917-C596-477B-8D92-851E3726DE96}.Release|x64.ActiveCfg = Release|x64
-		{E85F8917-C596-477B-8D92-851E3726DE96}.Release|x64.Build.0 = Release|x64
-		{E85F8917-C596-477B-8D92-851E3726DE96}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{E85F8917-C596-477B-8D92-851E3726DE96}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{E85F8917-C596-477B-8D92-851E3726DE96}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{E85F8917-C596-477B-8D92-851E3726DE96}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.Debug|Win32.ActiveCfg = Debug|Win32
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.Debug|Win32.Build.0 = Debug|Win32
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.Debug|x64.ActiveCfg = Debug|x64
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.Debug|x64.Build.0 = Debug|x64
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.Release|Win32.ActiveCfg = Release|Win32
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.Release|Win32.Build.0 = Release|Win32
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.Release|x64.ActiveCfg = Release|x64
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.Release|x64.Build.0 = Release|x64
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{A6AC837C-8852-48B3-9232-57A2493AEDA4}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.Debug|Win32.ActiveCfg = Debug|Win32
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.Debug|Win32.Build.0 = Debug|Win32
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.Debug|x64.ActiveCfg = Debug|x64
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.Debug|x64.Build.0 = Debug|x64
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.Release|Win32.ActiveCfg = Release|Win32
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.Release|Win32.Build.0 = Release|Win32
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.Release|x64.ActiveCfg = Release|x64
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.Release|x64.Build.0 = Release|x64
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{AAD6BEB3-618D-492E-BFC8-D3892D9D26AB}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.Debug|Win32.ActiveCfg = Debug|Win32
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.Debug|Win32.Build.0 = Debug|Win32
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.Debug|x64.ActiveCfg = Debug|x64
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.Debug|x64.Build.0 = Debug|x64
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.Release|Win32.ActiveCfg = Release|Win32
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.Release|Win32.Build.0 = Release|Win32
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.Release|x64.ActiveCfg = Release|x64
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.Release|x64.Build.0 = Release|x64
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{032E43BB-816C-4BEE-9ABD-1E0B599C007A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.Debug|Win32.ActiveCfg = Debug|Win32
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.Debug|Win32.Build.0 = Debug|Win32
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.Debug|x64.ActiveCfg = Debug|x64
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.Debug|x64.Build.0 = Debug|x64
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.Release|Win32.ActiveCfg = Release|Win32
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.Release|Win32.Build.0 = Release|Win32
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.Release|x64.ActiveCfg = Release|x64
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.Release|x64.Build.0 = Release|x64
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{57BABFE8-331D-41A9-8776-314F2D8791E2}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.Debug|Win32.ActiveCfg = Debug|Win32
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.Debug|Win32.Build.0 = Debug|Win32
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.Debug|x64.ActiveCfg = Debug|x64
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.Debug|x64.Build.0 = Debug|x64
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.Release|Win32.ActiveCfg = Release|Win32
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.Release|Win32.Build.0 = Release|Win32
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.Release|x64.ActiveCfg = Release|x64
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.Release|x64.Build.0 = Release|x64
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{8B6B0E08-62BA-4E92-8672-06CCA7432096}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.Debug|Win32.ActiveCfg = Debug|Win32
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.Debug|Win32.Build.0 = Debug|Win32
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.Debug|x64.ActiveCfg = Debug|x64
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.Debug|x64.Build.0 = Debug|x64
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.Release|Win32.ActiveCfg = Release|Win32
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.Release|Win32.Build.0 = Release|Win32
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.Release|x64.ActiveCfg = Release|x64
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.Release|x64.Build.0 = Release|x64
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{C5FFDC7A-C2A7-49C0-9EED-92D987AC3AC9}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.Debug|Win32.ActiveCfg = Debug|Win32
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.Debug|Win32.Build.0 = Debug|Win32
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.Debug|x64.ActiveCfg = Debug|x64
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.Debug|x64.Build.0 = Debug|x64
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.Release|Win32.ActiveCfg = Release|Win32
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.Release|Win32.Build.0 = Release|Win32
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.Release|x64.ActiveCfg = Release|x64
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.Release|x64.Build.0 = Release|x64
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{42140DF3-03C5-4A99-9D7B-F4385733D694}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.Debug|Win32.ActiveCfg = Debug|Win32
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.Debug|Win32.Build.0 = Debug|Win32
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.Debug|x64.ActiveCfg = Debug|x64
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.Debug|x64.Build.0 = Debug|x64
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.Release|Win32.ActiveCfg = Release|Win32
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.Release|Win32.Build.0 = Release|Win32
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.Release|x64.ActiveCfg = Release|x64
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.Release|x64.Build.0 = Release|x64
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{AA4B7095-5FBB-41E5-AE2A-39247638EC14}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.Debug|Win32.ActiveCfg = Debug|Win32
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.Debug|Win32.Build.0 = Debug|Win32
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.Debug|x64.ActiveCfg = Debug|x64
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.Debug|x64.Build.0 = Debug|x64
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.Release|Win32.ActiveCfg = Release|Win32
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.Release|Win32.Build.0 = Release|Win32
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.Release|x64.ActiveCfg = Release|x64
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.Release|x64.Build.0 = Release|x64
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{A40959E8-B640-49F7-B2E0-806A03544AB5}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.Debug|Win32.ActiveCfg = Debug|Win32
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.Debug|Win32.Build.0 = Debug|Win32
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.Debug|x64.ActiveCfg = Debug|x64
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.Debug|x64.Build.0 = Debug|x64
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.Release|Win32.ActiveCfg = Release|Win32
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.Release|Win32.Build.0 = Release|Win32
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.Release|x64.ActiveCfg = Release|x64
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.Release|x64.Build.0 = Release|x64
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{67F5D600-6FE3-420E-B9F3-7EA1DD452FC9}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.Debug|Win32.ActiveCfg = Debug|Win32
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.Debug|Win32.Build.0 = Debug|Win32
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.Debug|x64.ActiveCfg = Debug|x64
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.Debug|x64.Build.0 = Debug|x64
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.Release|Win32.ActiveCfg = Release|Win32
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.Release|Win32.Build.0 = Release|Win32
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.Release|x64.ActiveCfg = Release|x64
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.Release|x64.Build.0 = Release|x64
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{BD7E75D1-DEDC-450E-A3E5-4823C06100D5}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.Debug|Win32.ActiveCfg = Debug|Win32
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.Debug|Win32.Build.0 = Debug|Win32
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.Debug|x64.ActiveCfg = Debug|x64
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.Debug|x64.Build.0 = Debug|x64
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.Release|Win32.ActiveCfg = Release|Win32
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.Release|Win32.Build.0 = Release|Win32
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.Release|x64.ActiveCfg = Release|x64
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.Release|x64.Build.0 = Release|x64
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.Debug|Win32.ActiveCfg = Debug|Win32
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.Debug|Win32.Build.0 = Debug|Win32
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.Debug|x64.ActiveCfg = Debug|x64
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.Debug|x64.Build.0 = Debug|x64
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.Release|Win32.ActiveCfg = Release|Win32
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.Release|Win32.Build.0 = Release|Win32
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.Release|x64.ActiveCfg = Release|x64
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.Release|x64.Build.0 = Release|x64
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{08C550B7-3DA6-46A6-96EB-A48806F1900C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.Debug|Win32.ActiveCfg = Debug|Win32
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.Debug|Win32.Build.0 = Debug|Win32
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.Debug|x64.ActiveCfg = Debug|x64
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.Debug|x64.Build.0 = Debug|x64
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.Release|Win32.ActiveCfg = Release|Win32
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.Release|Win32.Build.0 = Release|Win32
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.Release|x64.ActiveCfg = Release|x64
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.Release|x64.Build.0 = Release|x64
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{47BB9C01-3751-4E25-87AE-6B4BAAA00340}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.Debug|Win32.ActiveCfg = Debug|Win32
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.Debug|Win32.Build.0 = Debug|Win32
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.Debug|x64.ActiveCfg = Debug|x64
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.Debug|x64.Build.0 = Debug|x64
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.Release|Win32.ActiveCfg = Release|Win32
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.Release|Win32.Build.0 = Release|Win32
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.Release|x64.ActiveCfg = Release|x64
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.Release|x64.Build.0 = Release|x64
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.Debug|Win32.ActiveCfg = Debug|Win32
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.Debug|Win32.Build.0 = Debug|Win32
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.Debug|x64.ActiveCfg = Debug|x64
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.Debug|x64.Build.0 = Debug|x64
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.Release|Win32.ActiveCfg = Release|Win32
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.Release|Win32.Build.0 = Release|Win32
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.Release|x64.ActiveCfg = Release|x64
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.Release|x64.Build.0 = Release|x64
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.Debug|Win32.ActiveCfg = Debug|Win32
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.Debug|Win32.Build.0 = Debug|Win32
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.Debug|x64.ActiveCfg = Debug|x64
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.Debug|x64.Build.0 = Debug|x64
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.DebugDLL|x64.Build.0 = DebugDLL|x64
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.Release|Win32.ActiveCfg = Release|Win32
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.Release|Win32.Build.0 = Release|Win32
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.Release|x64.ActiveCfg = Release|x64
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.Release|x64.Build.0 = Release|x64
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
-		{8D0BB3E1-BFB0-4557-9DD0-A2E82D3D9C70}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.Debug|Win32.ActiveCfg = Debug|Win32
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.Debug|Win32.Build.0 = Debug|Win32
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.Debug|x64.ActiveCfg = Debug|x64
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.Debug|x64.Build.0 = Debug|x64
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.Release|Win32.ActiveCfg = Release|Win32
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.Release|Win32.Build.0 = Release|Win32
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.Release|x64.ActiveCfg = Release|x64
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.Release|x64.Build.0 = Release|x64
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{347672C9-B4CA-4B21-8281-51955A9C50AC}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.Debug|Win32.ActiveCfg = Debug|Win32
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.Debug|Win32.Build.0 = Debug|Win32
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.Debug|x64.ActiveCfg = Debug|x64
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.Debug|x64.Build.0 = Debug|x64
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.Release|Win32.ActiveCfg = Release|Win32
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.Release|Win32.Build.0 = Release|Win32
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.Release|x64.ActiveCfg = Release|x64
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.Release|x64.Build.0 = Release|x64
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{B2AEBA00-E619-4FD2-80DA-9F713DD0306E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.Debug|Win32.ActiveCfg = Debug|Win32
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.Debug|Win32.Build.0 = Debug|Win32
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.Debug|x64.ActiveCfg = Debug|x64
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.Debug|x64.Build.0 = Debug|x64
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.Release|Win32.ActiveCfg = Release|Win32
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.Release|Win32.Build.0 = Release|Win32
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.Release|x64.ActiveCfg = Release|x64
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.Release|x64.Build.0 = Release|x64
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{4DFAAB85-944C-4B34-A3C0-70370B655451}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.Debug|Win32.ActiveCfg = Debug|Win32
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.Debug|Win32.Build.0 = Debug|Win32
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.Debug|x64.ActiveCfg = Debug|x64
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.Debug|x64.Build.0 = Debug|x64
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.Release|Win32.ActiveCfg = Release|Win32
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.Release|Win32.Build.0 = Release|Win32
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.Release|x64.ActiveCfg = Release|x64
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.Release|x64.Build.0 = Release|x64
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{53EC88ED-74CA-4F01-8FDB-94989A896E22}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.Debug|Win32.ActiveCfg = Debug|Win32
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.Debug|Win32.Build.0 = Debug|Win32
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.Debug|x64.ActiveCfg = Debug|x64
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.Debug|x64.Build.0 = Debug|x64
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.Release|Win32.ActiveCfg = Release|Win32
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.Release|Win32.Build.0 = Release|Win32
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.Release|x64.ActiveCfg = Release|x64
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.Release|x64.Build.0 = Release|x64
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{4FDCF0D2-40AA-4856-98BE-A6FD3B7A443C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.Debug|Win32.ActiveCfg = Debug|Win32
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.Debug|Win32.Build.0 = Debug|Win32
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.Debug|x64.ActiveCfg = Debug|x64
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.Debug|x64.Build.0 = Debug|x64
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.Release|Win32.ActiveCfg = Release|Win32
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.Release|Win32.Build.0 = Release|Win32
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.Release|x64.ActiveCfg = Release|x64
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.Release|x64.Build.0 = Release|x64
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{CAD80EBF-2DAF-4091-B486-59D86D65A8AD}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.Debug|Win32.ActiveCfg = Debug|Win32
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.Debug|Win32.Build.0 = Debug|Win32
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.Debug|x64.ActiveCfg = Debug|x64
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.Debug|x64.Build.0 = Debug|x64
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.Release|Win32.ActiveCfg = Release|Win32
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.Release|Win32.Build.0 = Release|Win32
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.Release|x64.ActiveCfg = Release|x64
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.Release|x64.Build.0 = Release|x64
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{B8E40D4D-C20C-42BD-B5E4-6BEB9D08344A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.Debug|Win32.ActiveCfg = Debug|Win32
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.Debug|Win32.Build.0 = Debug|Win32
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.Debug|x64.ActiveCfg = Debug|x64
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.Debug|x64.Build.0 = Debug|x64
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.Release|Win32.ActiveCfg = Release|Win32
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.Release|Win32.Build.0 = Release|Win32
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.Release|x64.ActiveCfg = Release|x64
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.Release|x64.Build.0 = Release|x64
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{6058EDC4-453A-48B1-8E27-83820FFB7203}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.Debug|Win32.ActiveCfg = Debug|Win32
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.Debug|Win32.Build.0 = Debug|Win32
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.Debug|x64.ActiveCfg = Debug|x64
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.Debug|x64.Build.0 = Debug|x64
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.Release|Win32.ActiveCfg = Release|Win32
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.Release|Win32.Build.0 = Release|Win32
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.Release|x64.ActiveCfg = Release|x64
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.Release|x64.Build.0 = Release|x64
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{A2E2AE46-C7B9-4544-B138-6F7662DF2216}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.Debug|Win32.Build.0 = Debug|Win32
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.Debug|x64.ActiveCfg = Debug|x64
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.Debug|x64.Build.0 = Debug|x64
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.Release|Win32.ActiveCfg = Release|Win32
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.Release|Win32.Build.0 = Release|Win32
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.Release|x64.ActiveCfg = Release|x64
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.Release|x64.Build.0 = Release|x64
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{D2059A10-7A4D-471A-BAEA-76479FD2773D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.Debug|Win32.ActiveCfg = Debug|Win32
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.Debug|Win32.Build.0 = Debug|Win32
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.Debug|x64.ActiveCfg = Debug|x64
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.Debug|x64.Build.0 = Debug|x64
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.Release|Win32.ActiveCfg = Release|Win32
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.Release|Win32.Build.0 = Release|Win32
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.Release|x64.ActiveCfg = Release|x64
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.Release|x64.Build.0 = Release|x64
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{D3E7608D-BA37-41A8-8012-9DC2E44E2703}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.Debug|Win32.ActiveCfg = Debug|Win32
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.Debug|Win32.Build.0 = Debug|Win32
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.Debug|x64.ActiveCfg = Debug|x64
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.Debug|x64.Build.0 = Debug|x64
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.Release|Win32.ActiveCfg = Release|Win32
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.Release|Win32.Build.0 = Release|Win32
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.Release|x64.ActiveCfg = Release|x64
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.Release|x64.Build.0 = Release|x64
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{DD4C129E-9390-41EC-90E8-CEDF4C6F7152}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.Debug|Win32.ActiveCfg = Debug|Win32
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.Debug|Win32.Build.0 = Debug|Win32
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.Debug|x64.ActiveCfg = Debug|x64
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.Debug|x64.Build.0 = Debug|x64
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.Release|Win32.ActiveCfg = Release|Win32
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.Release|Win32.Build.0 = Release|Win32
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.Release|x64.ActiveCfg = Release|x64
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.Release|x64.Build.0 = Release|x64
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{A901D889-28AD-4B69-9F81-5817D0B7120F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.Debug|Win32.ActiveCfg = Debug|Win32
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.Debug|Win32.Build.0 = Debug|Win32
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.Debug|x64.ActiveCfg = Debug|x64
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.Debug|x64.Build.0 = Debug|x64
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.Release|Win32.ActiveCfg = Release|Win32
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.Release|Win32.Build.0 = Release|Win32
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.Release|x64.ActiveCfg = Release|x64
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.Release|x64.Build.0 = Release|x64
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{1DDF5590-54DA-48B9-9168-E970F443F224}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.Debug|Win32.ActiveCfg = Debug|Win32
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.Debug|Win32.Build.0 = Debug|Win32
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.Debug|x64.ActiveCfg = Debug|x64
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.Debug|x64.Build.0 = Debug|x64
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.Release|Win32.ActiveCfg = Release|Win32
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.Release|Win32.Build.0 = Release|Win32
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.Release|x64.ActiveCfg = Release|x64
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.Release|x64.Build.0 = Release|x64
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{A546FCD9-97BD-475F-975E-04AB9AC4E077}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.Debug|Win32.ActiveCfg = Debug|Win32
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.Debug|Win32.Build.0 = Debug|Win32
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.Debug|x64.ActiveCfg = Debug|x64
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.Debug|x64.Build.0 = Debug|x64
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.Release|Win32.ActiveCfg = Release|Win32
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.Release|Win32.Build.0 = Release|Win32
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.Release|x64.ActiveCfg = Release|x64
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.Release|x64.Build.0 = Release|x64
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{C17DDF84-6A2C-4801-85ED-04AD0B29CD0F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.Debug|Win32.ActiveCfg = Debug|Win32
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.Debug|Win32.Build.0 = Debug|Win32
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.Debug|x64.ActiveCfg = Debug|x64
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.Debug|x64.Build.0 = Debug|x64
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.Release|Win32.ActiveCfg = Release|Win32
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.Release|Win32.Build.0 = Release|Win32
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.Release|x64.ActiveCfg = Release|x64
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.Release|x64.Build.0 = Release|x64
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{1136C677-E611-42A1-8BBF-C68BBFE19470}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.Debug|Win32.ActiveCfg = Debug|Win32
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.Debug|Win32.Build.0 = Debug|Win32
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.Debug|x64.ActiveCfg = Debug|x64
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.Debug|x64.Build.0 = Debug|x64
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.Release|Win32.ActiveCfg = Release|Win32
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.Release|Win32.Build.0 = Release|Win32
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.Release|x64.ActiveCfg = Release|x64
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.Release|x64.Build.0 = Release|x64
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{95AE7147-09C4-4C87-A6AB-9B5714D51714}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.Debug|Win32.ActiveCfg = Debug|Win32
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.Debug|Win32.Build.0 = Debug|Win32
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.Debug|x64.ActiveCfg = Debug|x64
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.Debug|x64.Build.0 = Debug|x64
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.Release|Win32.ActiveCfg = Release|Win32
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.Release|Win32.Build.0 = Release|Win32
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.Release|x64.ActiveCfg = Release|x64
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.Release|x64.Build.0 = Release|x64
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{6171ABC9-E3CF-402A-A5A1-58FF5A6D3AB5}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.Debug|Win32.ActiveCfg = Debug|Win32
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.Debug|Win32.Build.0 = Debug|Win32
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.Debug|x64.ActiveCfg = Debug|x64
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.Debug|x64.Build.0 = Debug|x64
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.Release|Win32.ActiveCfg = Release|Win32
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.Release|Win32.Build.0 = Release|Win32
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.Release|x64.ActiveCfg = Release|x64
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.Release|x64.Build.0 = Release|x64
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{08AA84EC-97CC-4997-BFFF-7CDC535A5C25}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.Debug|Win32.ActiveCfg = Debug|Win32
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.Debug|Win32.Build.0 = Debug|Win32
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.Debug|x64.ActiveCfg = Debug|x64
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.Debug|x64.Build.0 = Debug|x64
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.Release|Win32.ActiveCfg = Release|Win32
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.Release|Win32.Build.0 = Release|Win32
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.Release|x64.ActiveCfg = Release|x64
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.Release|x64.Build.0 = Release|x64
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{24B6F0A3-B354-4089-B489-560DEF53C75C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.Debug|Win32.ActiveCfg = Debug|Win32
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.Debug|Win32.Build.0 = Debug|Win32
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.Debug|x64.ActiveCfg = Debug|x64
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.Debug|x64.Build.0 = Debug|x64
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.Release|Win32.ActiveCfg = Release|Win32
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.Release|Win32.Build.0 = Release|Win32
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.Release|x64.ActiveCfg = Release|x64
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.Release|x64.Build.0 = Release|x64
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{43D2CAEA-F7C5-43AB-9460-53229B1A8CCE}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.Debug|Win32.ActiveCfg = Debug|Win32
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.Debug|Win32.Build.0 = Debug|Win32
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.Debug|x64.ActiveCfg = Debug|x64
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.Debug|x64.Build.0 = Debug|x64
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.Release|Win32.ActiveCfg = Release|Win32
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.Release|Win32.Build.0 = Release|Win32
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.Release|x64.ActiveCfg = Release|x64
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.Release|x64.Build.0 = Release|x64
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{CFF41F73-FF0C-4EDF-94FD-5FDCB8D0D19F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{4E04088C-D796-4227-8227-2539E30F04BD}.Debug|Win32.ActiveCfg = Debug|Win32
+		{4E04088C-D796-4227-8227-2539E30F04BD}.Debug|Win32.Build.0 = Debug|Win32
+		{4E04088C-D796-4227-8227-2539E30F04BD}.Debug|x64.ActiveCfg = Debug|x64
+		{4E04088C-D796-4227-8227-2539E30F04BD}.Debug|x64.Build.0 = Debug|x64
+		{4E04088C-D796-4227-8227-2539E30F04BD}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{4E04088C-D796-4227-8227-2539E30F04BD}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{4E04088C-D796-4227-8227-2539E30F04BD}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{4E04088C-D796-4227-8227-2539E30F04BD}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{4E04088C-D796-4227-8227-2539E30F04BD}.Release|Win32.ActiveCfg = Release|Win32
+		{4E04088C-D796-4227-8227-2539E30F04BD}.Release|Win32.Build.0 = Release|Win32
+		{4E04088C-D796-4227-8227-2539E30F04BD}.Release|x64.ActiveCfg = Release|x64
+		{4E04088C-D796-4227-8227-2539E30F04BD}.Release|x64.Build.0 = Release|x64
+		{4E04088C-D796-4227-8227-2539E30F04BD}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{4E04088C-D796-4227-8227-2539E30F04BD}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{4E04088C-D796-4227-8227-2539E30F04BD}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{4E04088C-D796-4227-8227-2539E30F04BD}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.Debug|Win32.ActiveCfg = Debug|Win32
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.Debug|Win32.Build.0 = Debug|Win32
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.Debug|x64.ActiveCfg = Debug|x64
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.Debug|x64.Build.0 = Debug|x64
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.Release|Win32.ActiveCfg = Release|Win32
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.Release|Win32.Build.0 = Release|Win32
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.Release|x64.ActiveCfg = Release|x64
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.Release|x64.Build.0 = Release|x64
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{36A2447A-460B-4A29-9327-18BE2B7007CB}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.Debug|Win32.ActiveCfg = Debug|Win32
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.Debug|Win32.Build.0 = Debug|Win32
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.Debug|x64.ActiveCfg = Debug|x64
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.Debug|x64.Build.0 = Debug|x64
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.Release|Win32.ActiveCfg = Release|Win32
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.Release|Win32.Build.0 = Release|Win32
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.Release|x64.ActiveCfg = Release|x64
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.Release|x64.Build.0 = Release|x64
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{61F9752D-4AE9-4B68-8D20-FF5CF31631A9}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.Debug|Win32.ActiveCfg = Debug|Win32
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.Debug|Win32.Build.0 = Debug|Win32
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.Debug|x64.ActiveCfg = Debug|x64
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.Debug|x64.Build.0 = Debug|x64
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.Release|Win32.ActiveCfg = Release|Win32
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.Release|Win32.Build.0 = Release|Win32
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.Release|x64.ActiveCfg = Release|x64
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.Release|x64.Build.0 = Release|x64
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{9DC94AC5-FEA4-40B1-9F01-B08B899DE64E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.Debug|Win32.ActiveCfg = Debug|Win32
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.Debug|Win32.Build.0 = Debug|Win32
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.Debug|x64.ActiveCfg = Debug|x64
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.Debug|x64.Build.0 = Debug|x64
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.Release|Win32.ActiveCfg = Release|Win32
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.Release|Win32.Build.0 = Release|Win32
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.Release|x64.ActiveCfg = Release|x64
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.Release|x64.Build.0 = Release|x64
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{F8DA831A-6128-4FB6-A41F-D4051D736D81}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.Debug|Win32.ActiveCfg = Debug|Win32
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.Debug|Win32.Build.0 = Debug|Win32
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.Debug|x64.ActiveCfg = Debug|x64
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.Debug|x64.Build.0 = Debug|x64
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.Release|Win32.ActiveCfg = Release|Win32
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.Release|Win32.Build.0 = Release|Win32
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.Release|x64.ActiveCfg = Release|x64
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.Release|x64.Build.0 = Release|x64
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{3F5FD5F7-2FB9-477E-9011-F09EECEA56E3}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.Debug|Win32.ActiveCfg = Debug|Win32
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.Debug|Win32.Build.0 = Debug|Win32
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.Debug|x64.ActiveCfg = Debug|x64
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.Debug|x64.Build.0 = Debug|x64
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.Release|Win32.ActiveCfg = Release|Win32
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.Release|Win32.Build.0 = Release|Win32
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.Release|x64.ActiveCfg = Release|x64
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.Release|x64.Build.0 = Release|x64
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{A8DC9C13-504F-4ED7-B299-ED251D8D7D57}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.Debug|Win32.ActiveCfg = Debug|Win32
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.Debug|Win32.Build.0 = Debug|Win32
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.Debug|x64.ActiveCfg = Debug|x64
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.Debug|x64.Build.0 = Debug|x64
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.Release|Win32.ActiveCfg = Release|Win32
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.Release|Win32.Build.0 = Release|Win32
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.Release|x64.ActiveCfg = Release|x64
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.Release|x64.Build.0 = Release|x64
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{D6205067-CD94-494E-A553-C3706C7CFB3B}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.Debug|Win32.ActiveCfg = Debug|Win32
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.Debug|Win32.Build.0 = Debug|Win32
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.Debug|x64.ActiveCfg = Debug|x64
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.Debug|x64.Build.0 = Debug|x64
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.Release|Win32.ActiveCfg = Release|Win32
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.Release|Win32.Build.0 = Release|Win32
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.Release|x64.ActiveCfg = Release|x64
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.Release|x64.Build.0 = Release|x64
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{5F755177-01B3-44E5-BC77-6FCF825CE0C8}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.Debug|Win32.ActiveCfg = Debug|Win32
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.Debug|Win32.Build.0 = Debug|Win32
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.Debug|x64.ActiveCfg = Debug|x64
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.Debug|x64.Build.0 = Debug|x64
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.Release|Win32.ActiveCfg = Release|Win32
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.Release|Win32.Build.0 = Release|Win32
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.Release|x64.ActiveCfg = Release|x64
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.Release|x64.Build.0 = Release|x64
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{9BCA1F30-F3E2-4F16-8974-C0C2D3902292}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{27575CBA-8AD7-4999-995C-694483047B3C}.Debug|Win32.ActiveCfg = Debug|Win32
+		{27575CBA-8AD7-4999-995C-694483047B3C}.Debug|Win32.Build.0 = Debug|Win32
+		{27575CBA-8AD7-4999-995C-694483047B3C}.Debug|x64.ActiveCfg = Debug|x64
+		{27575CBA-8AD7-4999-995C-694483047B3C}.Debug|x64.Build.0 = Debug|x64
+		{27575CBA-8AD7-4999-995C-694483047B3C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{27575CBA-8AD7-4999-995C-694483047B3C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{27575CBA-8AD7-4999-995C-694483047B3C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{27575CBA-8AD7-4999-995C-694483047B3C}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{27575CBA-8AD7-4999-995C-694483047B3C}.Release|Win32.ActiveCfg = Release|Win32
+		{27575CBA-8AD7-4999-995C-694483047B3C}.Release|Win32.Build.0 = Release|Win32
+		{27575CBA-8AD7-4999-995C-694483047B3C}.Release|x64.ActiveCfg = Release|x64
+		{27575CBA-8AD7-4999-995C-694483047B3C}.Release|x64.Build.0 = Release|x64
+		{27575CBA-8AD7-4999-995C-694483047B3C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{27575CBA-8AD7-4999-995C-694483047B3C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{27575CBA-8AD7-4999-995C-694483047B3C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{27575CBA-8AD7-4999-995C-694483047B3C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.Debug|Win32.ActiveCfg = Debug|Win32
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.Debug|Win32.Build.0 = Debug|Win32
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.Debug|x64.ActiveCfg = Debug|x64
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.Debug|x64.Build.0 = Debug|x64
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.Release|Win32.ActiveCfg = Release|Win32
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.Release|Win32.Build.0 = Release|Win32
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.Release|x64.ActiveCfg = Release|x64
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.Release|x64.Build.0 = Release|x64
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{8D7875E5-8DC6-44CA-8B25-6501CC30C301}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.Debug|Win32.ActiveCfg = Debug|Win32
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.Debug|Win32.Build.0 = Debug|Win32
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.Debug|x64.ActiveCfg = Debug|x64
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.Debug|x64.Build.0 = Debug|x64
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.Release|Win32.ActiveCfg = Release|Win32
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.Release|Win32.Build.0 = Release|Win32
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.Release|x64.ActiveCfg = Release|x64
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.Release|x64.Build.0 = Release|x64
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{6A9781AB-D45C-4D85-971D-04ED02400001}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.Debug|Win32.ActiveCfg = Debug|Win32
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.Debug|Win32.Build.0 = Debug|Win32
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.Debug|x64.ActiveCfg = Debug|x64
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.Debug|x64.Build.0 = Debug|x64
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.Release|Win32.ActiveCfg = Release|Win32
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.Release|Win32.Build.0 = Release|Win32
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.Release|x64.ActiveCfg = Release|x64
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.Release|x64.Build.0 = Release|x64
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{090B589F-7704-4D2F-9778-F884AFFB2359}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.Debug|Win32.ActiveCfg = Debug|Win32
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.Debug|Win32.Build.0 = Debug|Win32
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.Debug|x64.ActiveCfg = Debug|x64
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.Debug|x64.Build.0 = Debug|x64
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.Release|Win32.ActiveCfg = Release|Win32
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.Release|Win32.Build.0 = Release|Win32
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.Release|x64.ActiveCfg = Release|x64
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.Release|x64.Build.0 = Release|x64
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{28B5A386-FA1C-4106-AB6E-5DA967D979E0}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.Debug|Win32.Build.0 = Debug|Win32
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.Debug|x64.ActiveCfg = Debug|x64
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.Debug|x64.Build.0 = Debug|x64
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.Release|Win32.ActiveCfg = Release|Win32
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.Release|Win32.Build.0 = Release|Win32
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.Release|x64.ActiveCfg = Release|x64
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.Release|x64.Build.0 = Release|x64
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{C6348B36-F5C4-43A9-8577-4F6646B3D78D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.Debug|Win32.ActiveCfg = Debug|Win32
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.Debug|Win32.Build.0 = Debug|Win32
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.Debug|x64.ActiveCfg = Debug|x64
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.Debug|x64.Build.0 = Debug|x64
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.Release|Win32.ActiveCfg = Release|Win32
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.Release|Win32.Build.0 = Release|Win32
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.Release|x64.ActiveCfg = Release|x64
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.Release|x64.Build.0 = Release|x64
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{7D38F129-EF19-4A07-8EDC-AED9E364E2CB}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.Debug|Win32.ActiveCfg = Debug|Win32
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.Debug|Win32.Build.0 = Debug|Win32
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.Debug|x64.ActiveCfg = Debug|x64
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.Debug|x64.Build.0 = Debug|x64
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.Release|Win32.ActiveCfg = Release|Win32
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.Release|Win32.Build.0 = Release|Win32
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.Release|x64.ActiveCfg = Release|x64
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.Release|x64.Build.0 = Release|x64
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{C19E4244-4CAD-40A7-900A-7942991DFB75}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.Debug|Win32.ActiveCfg = Debug|Win32
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.Debug|Win32.Build.0 = Debug|Win32
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.Debug|x64.ActiveCfg = Debug|x64
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.Debug|x64.Build.0 = Debug|x64
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.Release|Win32.ActiveCfg = Release|Win32
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.Release|Win32.Build.0 = Release|Win32
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.Release|x64.ActiveCfg = Release|x64
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.Release|x64.Build.0 = Release|x64
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{7BFFD010-510A-4C0C-BD77-5845016DABBA}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{B487568D-8168-46AC-80AA-86F955301F21}.Debug|Win32.ActiveCfg = Debug|Win32
+		{B487568D-8168-46AC-80AA-86F955301F21}.Debug|Win32.Build.0 = Debug|Win32
+		{B487568D-8168-46AC-80AA-86F955301F21}.Debug|x64.ActiveCfg = Debug|x64
+		{B487568D-8168-46AC-80AA-86F955301F21}.Debug|x64.Build.0 = Debug|x64
+		{B487568D-8168-46AC-80AA-86F955301F21}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{B487568D-8168-46AC-80AA-86F955301F21}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{B487568D-8168-46AC-80AA-86F955301F21}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{B487568D-8168-46AC-80AA-86F955301F21}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{B487568D-8168-46AC-80AA-86F955301F21}.Release|Win32.ActiveCfg = Release|Win32
+		{B487568D-8168-46AC-80AA-86F955301F21}.Release|Win32.Build.0 = Release|Win32
+		{B487568D-8168-46AC-80AA-86F955301F21}.Release|x64.ActiveCfg = Release|x64
+		{B487568D-8168-46AC-80AA-86F955301F21}.Release|x64.Build.0 = Release|x64
+		{B487568D-8168-46AC-80AA-86F955301F21}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{B487568D-8168-46AC-80AA-86F955301F21}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{B487568D-8168-46AC-80AA-86F955301F21}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{B487568D-8168-46AC-80AA-86F955301F21}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.Debug|Win32.ActiveCfg = Debug|Win32
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.Debug|Win32.Build.0 = Debug|Win32
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.Debug|x64.ActiveCfg = Debug|x64
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.Debug|x64.Build.0 = Debug|x64
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.Release|Win32.ActiveCfg = Release|Win32
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.Release|Win32.Build.0 = Release|Win32
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.Release|x64.ActiveCfg = Release|x64
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.Release|x64.Build.0 = Release|x64
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{CF28E0B7-FBC4-4850-98C7-0B2716D3A9BC}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.Debug|Win32.ActiveCfg = Debug|Win32
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.Debug|Win32.Build.0 = Debug|Win32
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.Debug|x64.ActiveCfg = Debug|x64
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.Debug|x64.Build.0 = Debug|x64
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.Release|Win32.ActiveCfg = Release|Win32
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.Release|Win32.Build.0 = Release|Win32
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.Release|x64.ActiveCfg = Release|x64
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.Release|x64.Build.0 = Release|x64
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{051B2ABA-EDD6-455D-8600-53B8EB79DF21}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.Debug|Win32.ActiveCfg = Debug|Win32
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.Debug|Win32.Build.0 = Debug|Win32
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.Debug|x64.ActiveCfg = Debug|x64
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.Debug|x64.Build.0 = Debug|x64
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.Release|Win32.ActiveCfg = Release|Win32
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.Release|Win32.Build.0 = Release|Win32
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.Release|x64.ActiveCfg = Release|x64
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.Release|x64.Build.0 = Release|x64
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{531E4D12-C794-4509-8160-A6B6FCB1FE0C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.Debug|Win32.ActiveCfg = Debug|Win32
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.Debug|Win32.Build.0 = Debug|Win32
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.Debug|x64.ActiveCfg = Debug|x64
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.Debug|x64.Build.0 = Debug|x64
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.Release|Win32.ActiveCfg = Release|Win32
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.Release|Win32.Build.0 = Release|Win32
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.Release|x64.ActiveCfg = Release|x64
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.Release|x64.Build.0 = Release|x64
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{00DEC39E-11F7-40B4-8840-0556F331A964}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.Debug|Win32.ActiveCfg = Debug|Win32
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.Debug|Win32.Build.0 = Debug|Win32
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.Debug|x64.ActiveCfg = Debug|x64
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.Debug|x64.Build.0 = Debug|x64
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.Release|Win32.ActiveCfg = Release|Win32
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.Release|Win32.Build.0 = Release|Win32
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.Release|x64.ActiveCfg = Release|x64
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.Release|x64.Build.0 = Release|x64
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{FE555145-82E8-4721-B2CB-A60B94658A65}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.Debug|Win32.ActiveCfg = Debug|Win32
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.Debug|Win32.Build.0 = Debug|Win32
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.Debug|x64.ActiveCfg = Debug|x64
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.Debug|x64.Build.0 = Debug|x64
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.Release|Win32.ActiveCfg = Release|Win32
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.Release|Win32.Build.0 = Release|Win32
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.Release|x64.ActiveCfg = Release|x64
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.Release|x64.Build.0 = Release|x64
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{C2B3A6D5-5498-4D73-826A-4A839EBA9571}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.Debug|Win32.ActiveCfg = Debug|Win32
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.Debug|Win32.Build.0 = Debug|Win32
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.Debug|x64.ActiveCfg = Debug|x64
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.Debug|x64.Build.0 = Debug|x64
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.Release|Win32.ActiveCfg = Release|Win32
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.Release|Win32.Build.0 = Release|Win32
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.Release|x64.ActiveCfg = Release|x64
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.Release|x64.Build.0 = Release|x64
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{D92CDEC8-1E56-4F1C-8563-04037BCCB9BD}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.Debug|Win32.ActiveCfg = Debug|Win32
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.Debug|Win32.Build.0 = Debug|Win32
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.Debug|x64.ActiveCfg = Debug|x64
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.Debug|x64.Build.0 = Debug|x64
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.Release|Win32.ActiveCfg = Release|Win32
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.Release|Win32.Build.0 = Release|Win32
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.Release|x64.ActiveCfg = Release|x64
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.Release|x64.Build.0 = Release|x64
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{CCEA00C6-F850-4BDA-B420-6214E40A3469}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.Debug|Win32.ActiveCfg = Debug|Win32
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.Debug|Win32.Build.0 = Debug|Win32
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.Debug|x64.ActiveCfg = Debug|x64
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.Debug|x64.Build.0 = Debug|x64
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.Release|Win32.ActiveCfg = Release|Win32
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.Release|Win32.Build.0 = Release|Win32
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.Release|x64.ActiveCfg = Release|x64
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.Release|x64.Build.0 = Release|x64
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{EB8FB82E-5466-4430-9BD2-17CF562E8349}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.Debug|Win32.ActiveCfg = Debug|Win32
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.Debug|Win32.Build.0 = Debug|Win32
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.Debug|x64.ActiveCfg = Debug|x64
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.Debug|x64.Build.0 = Debug|x64
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.Release|Win32.ActiveCfg = Release|Win32
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.Release|Win32.Build.0 = Release|Win32
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.Release|x64.ActiveCfg = Release|x64
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.Release|x64.Build.0 = Release|x64
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{1557FB61-9785-4955-ACB3-259F8695AA61}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.Debug|Win32.ActiveCfg = Debug|Win32
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.Debug|Win32.Build.0 = Debug|Win32
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.Debug|x64.ActiveCfg = Debug|x64
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.Debug|x64.Build.0 = Debug|x64
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.Release|Win32.ActiveCfg = Release|Win32
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.Release|Win32.Build.0 = Release|Win32
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.Release|x64.ActiveCfg = Release|x64
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.Release|x64.Build.0 = Release|x64
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{61AC31CE-6BF2-4C4A-97C7-7DE62A2A546E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.Debug|Win32.ActiveCfg = Debug|Win32
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.Debug|Win32.Build.0 = Debug|Win32
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.Debug|x64.ActiveCfg = Debug|x64
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.Debug|x64.Build.0 = Debug|x64
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.Release|Win32.ActiveCfg = Release|Win32
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.Release|Win32.Build.0 = Release|Win32
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.Release|x64.ActiveCfg = Release|x64
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.Release|x64.Build.0 = Release|x64
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{B641C7E0-F29C-422C-B3C0-BC3C103BC973}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.Debug|Win32.ActiveCfg = Debug|Win32
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.Debug|Win32.Build.0 = Debug|Win32
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.Debug|x64.ActiveCfg = Debug|x64
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.Debug|x64.Build.0 = Debug|x64
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.Release|Win32.ActiveCfg = Release|Win32
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.Release|Win32.Build.0 = Release|Win32
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.Release|x64.ActiveCfg = Release|x64
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.Release|x64.Build.0 = Release|x64
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{7FD62FF2-E65C-45F1-9BF3-12CD2D78C7A5}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.Debug|Win32.ActiveCfg = Debug|Win32
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.Debug|Win32.Build.0 = Debug|Win32
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.Debug|x64.ActiveCfg = Debug|x64
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.Debug|x64.Build.0 = Debug|x64
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.Release|Win32.ActiveCfg = Release|Win32
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.Release|Win32.Build.0 = Release|Win32
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.Release|x64.ActiveCfg = Release|x64
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.Release|x64.Build.0 = Release|x64
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{DF2DCFDD-1AFC-418A-80AC-EA2624BB534A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{939AD270-6758-4304-9B42-F776B03B2B30}.Debug|Win32.ActiveCfg = Debug|Win32
+		{939AD270-6758-4304-9B42-F776B03B2B30}.Debug|Win32.Build.0 = Debug|Win32
+		{939AD270-6758-4304-9B42-F776B03B2B30}.Debug|x64.ActiveCfg = Debug|x64
+		{939AD270-6758-4304-9B42-F776B03B2B30}.Debug|x64.Build.0 = Debug|x64
+		{939AD270-6758-4304-9B42-F776B03B2B30}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{939AD270-6758-4304-9B42-F776B03B2B30}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{939AD270-6758-4304-9B42-F776B03B2B30}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{939AD270-6758-4304-9B42-F776B03B2B30}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{939AD270-6758-4304-9B42-F776B03B2B30}.Release|Win32.ActiveCfg = Release|Win32
+		{939AD270-6758-4304-9B42-F776B03B2B30}.Release|Win32.Build.0 = Release|Win32
+		{939AD270-6758-4304-9B42-F776B03B2B30}.Release|x64.ActiveCfg = Release|x64
+		{939AD270-6758-4304-9B42-F776B03B2B30}.Release|x64.Build.0 = Release|x64
+		{939AD270-6758-4304-9B42-F776B03B2B30}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{939AD270-6758-4304-9B42-F776B03B2B30}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{939AD270-6758-4304-9B42-F776B03B2B30}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{939AD270-6758-4304-9B42-F776B03B2B30}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.Debug|Win32.ActiveCfg = Debug|Win32
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.Debug|Win32.Build.0 = Debug|Win32
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.Debug|x64.ActiveCfg = Debug|x64
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.Debug|x64.Build.0 = Debug|x64
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.Release|Win32.ActiveCfg = Release|Win32
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.Release|Win32.Build.0 = Release|Win32
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.Release|x64.ActiveCfg = Release|x64
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.Release|x64.Build.0 = Release|x64
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{7B92691D-13E1-400B-BFDA-1C085DB12DC7}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.Debug|Win32.ActiveCfg = Debug|Win32
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.Debug|Win32.Build.0 = Debug|Win32
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.Debug|x64.ActiveCfg = Debug|x64
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.Debug|x64.Build.0 = Debug|x64
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.Release|Win32.ActiveCfg = Release|Win32
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.Release|Win32.Build.0 = Release|Win32
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.Release|x64.ActiveCfg = Release|x64
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.Release|x64.Build.0 = Release|x64
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{02F5DB27-2C2D-4995-AE03-AE866FD0D726}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.Debug|Win32.ActiveCfg = Debug|Win32
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.Debug|Win32.Build.0 = Debug|Win32
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.Debug|x64.ActiveCfg = Debug|x64
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.Debug|x64.Build.0 = Debug|x64
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.Release|Win32.ActiveCfg = Release|Win32
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.Release|Win32.Build.0 = Release|Win32
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.Release|x64.ActiveCfg = Release|x64
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.Release|x64.Build.0 = Release|x64
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{13E51223-EDBF-46E1-A98A-895FB3685000}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.Debug|Win32.Build.0 = Debug|Win32
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.Debug|x64.ActiveCfg = Debug|x64
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.Debug|x64.Build.0 = Debug|x64
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.Release|Win32.ActiveCfg = Release|Win32
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.Release|Win32.Build.0 = Release|Win32
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.Release|x64.ActiveCfg = Release|x64
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.Release|x64.Build.0 = Release|x64
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{4BCEFEBE-22AD-4D8E-BE1F-19FF5925271D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.Debug|Win32.ActiveCfg = Debug|Win32
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.Debug|Win32.Build.0 = Debug|Win32
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.Debug|x64.ActiveCfg = Debug|x64
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.Debug|x64.Build.0 = Debug|x64
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.Release|Win32.ActiveCfg = Release|Win32
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.Release|Win32.Build.0 = Release|Win32
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.Release|x64.ActiveCfg = Release|x64
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.Release|x64.Build.0 = Release|x64
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{E6270A0D-B665-450E-BA6A-B9D648D5B145}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.Debug|Win32.ActiveCfg = Debug|Win32
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.Debug|Win32.Build.0 = Debug|Win32
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.Debug|x64.ActiveCfg = Debug|x64
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.Debug|x64.Build.0 = Debug|x64
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.Release|Win32.ActiveCfg = Release|Win32
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.Release|Win32.Build.0 = Release|Win32
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.Release|x64.ActiveCfg = Release|x64
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.Release|x64.Build.0 = Release|x64
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{82933EEE-EB79-486D-A8E2-B440D33D924A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.Debug|Win32.ActiveCfg = Debug|Win32
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.Debug|Win32.Build.0 = Debug|Win32
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.Debug|x64.ActiveCfg = Debug|x64
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.Debug|x64.Build.0 = Debug|x64
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.Release|Win32.ActiveCfg = Release|Win32
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.Release|Win32.Build.0 = Release|Win32
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.Release|x64.ActiveCfg = Release|x64
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.Release|x64.Build.0 = Release|x64
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{8EFB0853-50E8-4167-88A5-2C71DAB74098}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.Debug|Win32.ActiveCfg = Debug|Win32
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.Debug|Win32.Build.0 = Debug|Win32
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.Debug|x64.ActiveCfg = Debug|x64
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.Debug|x64.Build.0 = Debug|x64
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.Release|Win32.ActiveCfg = Release|Win32
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.Release|Win32.Build.0 = Release|Win32
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.Release|x64.ActiveCfg = Release|x64
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.Release|x64.Build.0 = Release|x64
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{84BE55F0-B6BE-4DFA-B387-4D09C24B4875}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.Debug|Win32.ActiveCfg = Debug|Win32
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.Debug|Win32.Build.0 = Debug|Win32
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.Debug|x64.ActiveCfg = Debug|x64
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.Debug|x64.Build.0 = Debug|x64
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.Release|Win32.ActiveCfg = Release|Win32
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.Release|Win32.Build.0 = Release|Win32
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.Release|x64.ActiveCfg = Release|x64
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.Release|x64.Build.0 = Release|x64
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{478B9CE3-2141-4C1C-A54C-984865DF5930}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.Debug|Win32.ActiveCfg = Debug|Win32
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.Debug|Win32.Build.0 = Debug|Win32
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.Debug|x64.ActiveCfg = Debug|x64
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.Debug|x64.Build.0 = Debug|x64
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.Release|Win32.ActiveCfg = Release|Win32
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.Release|Win32.Build.0 = Release|Win32
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.Release|x64.ActiveCfg = Release|x64
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.Release|x64.Build.0 = Release|x64
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{136554B9-6A33-46F2-9595-5B3E90A00553}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.Debug|Win32.ActiveCfg = Debug|Win32
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.Debug|Win32.Build.0 = Debug|Win32
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.Debug|x64.ActiveCfg = Debug|x64
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.Debug|x64.Build.0 = Debug|x64
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.Release|Win32.ActiveCfg = Release|Win32
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.Release|Win32.Build.0 = Release|Win32
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.Release|x64.ActiveCfg = Release|x64
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.Release|x64.Build.0 = Release|x64
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{05C7D1D5-557E-4868-90BB-2F7B1B0DB9C6}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.Debug|Win32.ActiveCfg = Debug|Win32
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.Debug|Win32.Build.0 = Debug|Win32
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.Debug|x64.ActiveCfg = Debug|x64
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.Debug|x64.Build.0 = Debug|x64
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.Release|Win32.ActiveCfg = Release|Win32
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.Release|Win32.Build.0 = Release|Win32
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.Release|x64.ActiveCfg = Release|x64
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.Release|x64.Build.0 = Release|x64
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{2861713F-5EA6-486E-AE98-55CC4200305E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.Debug|Win32.ActiveCfg = Debug|Win32
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.Debug|Win32.Build.0 = Debug|Win32
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.Debug|x64.ActiveCfg = Debug|x64
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.Debug|x64.Build.0 = Debug|x64
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.Release|Win32.ActiveCfg = Release|Win32
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.Release|Win32.Build.0 = Release|Win32
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.Release|x64.ActiveCfg = Release|x64
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.Release|x64.Build.0 = Release|x64
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{00EABCA8-578E-4BC9-A0DA-5006B5C28A3A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.Debug|Win32.ActiveCfg = Debug|Win32
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.Debug|Win32.Build.0 = Debug|Win32
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.Debug|x64.ActiveCfg = Debug|x64
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.Debug|x64.Build.0 = Debug|x64
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.Release|Win32.ActiveCfg = Release|Win32
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.Release|Win32.Build.0 = Release|Win32
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.Release|x64.ActiveCfg = Release|x64
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.Release|x64.Build.0 = Release|x64
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{931A5E4E-E25D-4895-B202-E1D1B3F37ED1}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.Debug|Win32.ActiveCfg = Debug|Win32
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.Debug|Win32.Build.0 = Debug|Win32
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.Debug|x64.ActiveCfg = Debug|x64
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.Debug|x64.Build.0 = Debug|x64
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.Release|Win32.ActiveCfg = Release|Win32
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.Release|Win32.Build.0 = Release|Win32
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.Release|x64.ActiveCfg = Release|x64
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.Release|x64.Build.0 = Release|x64
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{A40990ED-A5F2-4175-A8A5-DEE67FDFD64A}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.Debug|Win32.ActiveCfg = Debug|Win32
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.Debug|Win32.Build.0 = Debug|Win32
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.Debug|x64.ActiveCfg = Debug|x64
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.Debug|x64.Build.0 = Debug|x64
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.Release|Win32.ActiveCfg = Release|Win32
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.Release|Win32.Build.0 = Release|Win32
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.Release|x64.ActiveCfg = Release|x64
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.Release|x64.Build.0 = Release|x64
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{29EAEDFD-B486-433D-8809-7C4B298BFF17}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.Debug|Win32.ActiveCfg = Debug|Win32
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.Debug|Win32.Build.0 = Debug|Win32
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.Debug|x64.ActiveCfg = Debug|x64
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.Debug|x64.Build.0 = Debug|x64
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.Release|Win32.ActiveCfg = Release|Win32
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.Release|Win32.Build.0 = Release|Win32
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.Release|x64.ActiveCfg = Release|x64
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.Release|x64.Build.0 = Release|x64
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{F7125366-276A-455F-A1AA-80846F7BE09F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{986196FD-0900-451E-818F-7373FBAFF793}.Debug|Win32.ActiveCfg = Debug|Win32
+		{986196FD-0900-451E-818F-7373FBAFF793}.Debug|Win32.Build.0 = Debug|Win32
+		{986196FD-0900-451E-818F-7373FBAFF793}.Debug|x64.ActiveCfg = Debug|x64
+		{986196FD-0900-451E-818F-7373FBAFF793}.Debug|x64.Build.0 = Debug|x64
+		{986196FD-0900-451E-818F-7373FBAFF793}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{986196FD-0900-451E-818F-7373FBAFF793}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{986196FD-0900-451E-818F-7373FBAFF793}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{986196FD-0900-451E-818F-7373FBAFF793}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{986196FD-0900-451E-818F-7373FBAFF793}.Release|Win32.ActiveCfg = Release|Win32
+		{986196FD-0900-451E-818F-7373FBAFF793}.Release|Win32.Build.0 = Release|Win32
+		{986196FD-0900-451E-818F-7373FBAFF793}.Release|x64.ActiveCfg = Release|x64
+		{986196FD-0900-451E-818F-7373FBAFF793}.Release|x64.Build.0 = Release|x64
+		{986196FD-0900-451E-818F-7373FBAFF793}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{986196FD-0900-451E-818F-7373FBAFF793}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{986196FD-0900-451E-818F-7373FBAFF793}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{986196FD-0900-451E-818F-7373FBAFF793}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.Debug|Win32.ActiveCfg = Debug|Win32
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.Debug|Win32.Build.0 = Debug|Win32
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.Debug|x64.ActiveCfg = Debug|x64
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.Debug|x64.Build.0 = Debug|x64
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.Release|Win32.ActiveCfg = Release|Win32
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.Release|Win32.Build.0 = Release|Win32
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.Release|x64.ActiveCfg = Release|x64
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.Release|x64.Build.0 = Release|x64
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{09DBA8E7-7471-4D6D-B6EF-5B8B2B32A020}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.Debug|Win32.ActiveCfg = Debug|Win32
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.Debug|Win32.Build.0 = Debug|Win32
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.Debug|x64.ActiveCfg = Debug|x64
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.Debug|x64.Build.0 = Debug|x64
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.Release|Win32.ActiveCfg = Release|Win32
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.Release|Win32.Build.0 = Release|Win32
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.Release|x64.ActiveCfg = Release|x64
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.Release|x64.Build.0 = Release|x64
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{B592842F-6270-4C2E-8FBC-DBE1D5EF71D0}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.Debug|Win32.ActiveCfg = Debug|Win32
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.Debug|Win32.Build.0 = Debug|Win32
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.Debug|x64.ActiveCfg = Debug|x64
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.Debug|x64.Build.0 = Debug|x64
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.Release|Win32.ActiveCfg = Release|Win32
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.Release|Win32.Build.0 = Release|Win32
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.Release|x64.ActiveCfg = Release|x64
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.Release|x64.Build.0 = Release|x64
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{FAB79DB6-B9B5-4FDA-B2FB-17B4BEB6011F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.Debug|Win32.ActiveCfg = Debug|Win32
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.Debug|Win32.Build.0 = Debug|Win32
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.Debug|x64.ActiveCfg = Debug|x64
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.Debug|x64.Build.0 = Debug|x64
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.Release|Win32.ActiveCfg = Release|Win32
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.Release|Win32.Build.0 = Release|Win32
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.Release|x64.ActiveCfg = Release|x64
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.Release|x64.Build.0 = Release|x64
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{5E35A42F-8E72-4ED7-ABA3-469E86F14DB8}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.Debug|Win32.ActiveCfg = Debug|Win32
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.Debug|Win32.Build.0 = Debug|Win32
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.Debug|x64.ActiveCfg = Debug|x64
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.Debug|x64.Build.0 = Debug|x64
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.Release|Win32.ActiveCfg = Release|Win32
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.Release|Win32.Build.0 = Release|Win32
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.Release|x64.ActiveCfg = Release|x64
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.Release|x64.Build.0 = Release|x64
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{B9B3203E-0C07-46DB-BABE-3024B22F923C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.Debug|Win32.ActiveCfg = Debug|Win32
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.Debug|Win32.Build.0 = Debug|Win32
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.Debug|x64.ActiveCfg = Debug|x64
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.Debug|x64.Build.0 = Debug|x64
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.Release|Win32.ActiveCfg = Release|Win32
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.Release|Win32.Build.0 = Release|Win32
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.Release|x64.ActiveCfg = Release|x64
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.Release|x64.Build.0 = Release|x64
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{95BF266E-0195-4BEB-B306-B99489EE3991}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.Debug|Win32.Build.0 = Debug|Win32
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.Debug|x64.ActiveCfg = Debug|x64
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.Debug|x64.Build.0 = Debug|x64
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.Release|Win32.ActiveCfg = Release|Win32
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.Release|Win32.Build.0 = Release|Win32
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.Release|x64.ActiveCfg = Release|x64
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.Release|x64.Build.0 = Release|x64
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.Debug|Win32.ActiveCfg = Debug|Win32
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.Debug|Win32.Build.0 = Debug|Win32
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.Debug|x64.ActiveCfg = Debug|x64
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.Debug|x64.Build.0 = Debug|x64
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.Release|Win32.ActiveCfg = Release|Win32
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.Release|Win32.Build.0 = Release|Win32
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.Release|x64.ActiveCfg = Release|x64
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.Release|x64.Build.0 = Release|x64
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{49F50B13-96C8-44F1-9B8C-68197E0DBE7E}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.Debug|Win32.ActiveCfg = Debug|Win32
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.Debug|Win32.Build.0 = Debug|Win32
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.Debug|x64.ActiveCfg = Debug|x64
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.Debug|x64.Build.0 = Debug|x64
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.Release|Win32.ActiveCfg = Release|Win32
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.Release|Win32.Build.0 = Release|Win32
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.Release|x64.ActiveCfg = Release|x64
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.Release|x64.Build.0 = Release|x64
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{67436D24-0D70-48D5-B1AE-6E8DFA978983}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.Debug|Win32.ActiveCfg = Debug|Win32
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.Debug|Win32.Build.0 = Debug|Win32
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.Debug|x64.ActiveCfg = Debug|x64
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.Debug|x64.Build.0 = Debug|x64
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.Release|Win32.ActiveCfg = Release|Win32
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.Release|Win32.Build.0 = Release|Win32
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.Release|x64.ActiveCfg = Release|x64
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.Release|x64.Build.0 = Release|x64
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{028EEC3D-499E-453C-A1F4-5A4478BBB39F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.Debug|Win32.ActiveCfg = Debug|Win32
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.Debug|Win32.Build.0 = Debug|Win32
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.Debug|x64.ActiveCfg = Debug|x64
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.Debug|x64.Build.0 = Debug|x64
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.Release|Win32.ActiveCfg = Release|Win32
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.Release|Win32.Build.0 = Release|Win32
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.Release|x64.ActiveCfg = Release|x64
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.Release|x64.Build.0 = Release|x64
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{86F47145-3ABB-45BA-8D51-89C24997882F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.Debug|Win32.Build.0 = Debug|Win32
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.Debug|x64.ActiveCfg = Debug|x64
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.Debug|x64.Build.0 = Debug|x64
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.Release|Win32.ActiveCfg = Release|Win32
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.Release|Win32.Build.0 = Release|Win32
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.Release|x64.ActiveCfg = Release|x64
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.Release|x64.Build.0 = Release|x64
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.Debug|Win32.ActiveCfg = Debug|Win32
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.Debug|Win32.Build.0 = Debug|Win32
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.Debug|x64.ActiveCfg = Debug|x64
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.Debug|x64.Build.0 = Debug|x64
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.Release|Win32.ActiveCfg = Release|Win32
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.Release|Win32.Build.0 = Release|Win32
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.Release|x64.ActiveCfg = Release|x64
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.Release|x64.Build.0 = Release|x64
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{6266F193-8E41-4543-BB84-4DEA87146A44}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.Debug|Win32.ActiveCfg = Debug|Win32
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.Debug|Win32.Build.0 = Debug|Win32
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.Debug|x64.ActiveCfg = Debug|x64
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.Debug|x64.Build.0 = Debug|x64
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.Release|Win32.ActiveCfg = Release|Win32
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.Release|Win32.Build.0 = Release|Win32
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.Release|x64.ActiveCfg = Release|x64
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.Release|x64.Build.0 = Release|x64
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{2746DC43-68A9-42FE-80F0-1806679538FA}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.Debug|Win32.Build.0 = Debug|Win32
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.Debug|x64.ActiveCfg = Debug|x64
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.Debug|x64.Build.0 = Debug|x64
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.Release|Win32.ActiveCfg = Release|Win32
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.Release|Win32.Build.0 = Release|Win32
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.Release|x64.ActiveCfg = Release|x64
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.Release|x64.Build.0 = Release|x64
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{F6DB30E7-94C5-4760-92FA-449884953A9D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.Debug|Win32.ActiveCfg = Debug|Win32
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.Debug|Win32.Build.0 = Debug|Win32
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.Debug|x64.ActiveCfg = Debug|x64
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.Debug|x64.Build.0 = Debug|x64
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.Release|Win32.ActiveCfg = Release|Win32
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.Release|Win32.Build.0 = Release|Win32
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.Release|x64.ActiveCfg = Release|x64
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.Release|x64.Build.0 = Release|x64
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{8FB57DC4-F98A-4E0D-BDBA-5AB2F7405B58}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.Debug|Win32.Build.0 = Debug|Win32
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.Debug|x64.ActiveCfg = Debug|x64
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.Debug|x64.Build.0 = Debug|x64
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.Release|Win32.ActiveCfg = Release|Win32
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.Release|Win32.Build.0 = Release|Win32
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.Release|x64.ActiveCfg = Release|x64
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.Release|x64.Build.0 = Release|x64
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{F8832A8F-9EA0-4DFD-B181-FAA767F3B9AF}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.Debug|Win32.ActiveCfg = Debug|Win32
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.Debug|Win32.Build.0 = Debug|Win32
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.Debug|x64.ActiveCfg = Debug|x64
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.Debug|x64.Build.0 = Debug|x64
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.Release|Win32.ActiveCfg = Release|Win32
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.Release|Win32.Build.0 = Release|Win32
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.Release|x64.ActiveCfg = Release|x64
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.Release|x64.Build.0 = Release|x64
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{2F198E60-4B02-46C3-8FEF-CE86D69E2C59}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.Debug|Win32.Build.0 = Debug|Win32
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.Debug|x64.ActiveCfg = Debug|x64
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.Debug|x64.Build.0 = Debug|x64
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.Release|Win32.ActiveCfg = Release|Win32
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.Release|Win32.Build.0 = Release|Win32
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.Release|x64.ActiveCfg = Release|x64
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.Release|x64.Build.0 = Release|x64
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{DEBC32A0-A4F7-4C4C-9E93-62C1C4E6544D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.Debug|Win32.ActiveCfg = Debug|Win32
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.Debug|Win32.Build.0 = Debug|Win32
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.Debug|x64.ActiveCfg = Debug|x64
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.Debug|x64.Build.0 = Debug|x64
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.Release|Win32.ActiveCfg = Release|Win32
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.Release|Win32.Build.0 = Release|Win32
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.Release|x64.ActiveCfg = Release|x64
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.Release|x64.Build.0 = Release|x64
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{74B970B2-6C7F-4AEE-9031-27CC087D7214}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.Debug|Win32.Build.0 = Debug|Win32
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.Debug|x64.ActiveCfg = Debug|x64
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.Debug|x64.Build.0 = Debug|x64
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.Release|Win32.ActiveCfg = Release|Win32
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.Release|Win32.Build.0 = Release|Win32
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.Release|x64.ActiveCfg = Release|x64
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.Release|x64.Build.0 = Release|x64
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{BDDE8ABD-4E45-49DA-B499-131BD6FCABBD}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.Debug|Win32.ActiveCfg = Debug|Win32
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.Debug|Win32.Build.0 = Debug|Win32
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.Debug|x64.ActiveCfg = Debug|x64
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.Debug|x64.Build.0 = Debug|x64
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.Release|Win32.ActiveCfg = Release|Win32
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.Release|Win32.Build.0 = Release|Win32
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.Release|x64.ActiveCfg = Release|x64
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.Release|x64.Build.0 = Release|x64
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{85E82D79-6144-4151-A3E7-8140E9ED01CF}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.Debug|Win32.ActiveCfg = Debug|Win32
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.Debug|Win32.Build.0 = Debug|Win32
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.Debug|x64.ActiveCfg = Debug|x64
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.Debug|x64.Build.0 = Debug|x64
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.Release|Win32.ActiveCfg = Release|Win32
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.Release|Win32.Build.0 = Release|Win32
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.Release|x64.ActiveCfg = Release|x64
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.Release|x64.Build.0 = Release|x64
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{610E62DA-4DD6-479E-8D85-1FB87126D750}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.Debug|Win32.ActiveCfg = Debug|Win32
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.Debug|Win32.Build.0 = Debug|Win32
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.Debug|x64.ActiveCfg = Debug|x64
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.Debug|x64.Build.0 = Debug|x64
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.Release|Win32.ActiveCfg = Release|Win32
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.Release|Win32.Build.0 = Release|Win32
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.Release|x64.ActiveCfg = Release|x64
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.Release|x64.Build.0 = Release|x64
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{2DD94017-2F95-470D-94F5-9F10AD650BDC}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.Debug|Win32.ActiveCfg = Debug|Win32
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.Debug|Win32.Build.0 = Debug|Win32
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.Debug|x64.ActiveCfg = Debug|x64
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.Debug|x64.Build.0 = Debug|x64
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.Release|Win32.ActiveCfg = Release|Win32
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.Release|Win32.Build.0 = Release|Win32
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.Release|x64.ActiveCfg = Release|x64
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.Release|x64.Build.0 = Release|x64
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{7C0D1F06-0B97-49A1-A25D-93D5E7A96786}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.Debug|Win32.ActiveCfg = Debug|Win32
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.Debug|Win32.Build.0 = Debug|Win32
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.Debug|x64.ActiveCfg = Debug|x64
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.Debug|x64.Build.0 = Debug|x64
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.Release|Win32.ActiveCfg = Release|Win32
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.Release|Win32.Build.0 = Release|Win32
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.Release|x64.ActiveCfg = Release|x64
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.Release|x64.Build.0 = Release|x64
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.Debug|Win32.Build.0 = Debug|Win32
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.Debug|x64.ActiveCfg = Debug|x64
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.Debug|x64.Build.0 = Debug|x64
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.Release|Win32.ActiveCfg = Release|Win32
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.Release|Win32.Build.0 = Release|Win32
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.Release|x64.ActiveCfg = Release|x64
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.Release|x64.Build.0 = Release|x64
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{8B58713F-B6F4-4A76-9888-309FDDFB985D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.Debug|Win32.ActiveCfg = Debug|Win32
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.Debug|Win32.Build.0 = Debug|Win32
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.Debug|x64.ActiveCfg = Debug|x64
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.Debug|x64.Build.0 = Debug|x64
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.Release|Win32.ActiveCfg = Release|Win32
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.Release|Win32.Build.0 = Release|Win32
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.Release|x64.ActiveCfg = Release|x64
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.Release|x64.Build.0 = Release|x64
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{C2857848-3327-46C6-929C-192629A21F60}.Debug|Win32.ActiveCfg = Debug|Win32
+		{C2857848-3327-46C6-929C-192629A21F60}.Debug|Win32.Build.0 = Debug|Win32
+		{C2857848-3327-46C6-929C-192629A21F60}.Debug|x64.ActiveCfg = Debug|x64
+		{C2857848-3327-46C6-929C-192629A21F60}.Debug|x64.Build.0 = Debug|x64
+		{C2857848-3327-46C6-929C-192629A21F60}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{C2857848-3327-46C6-929C-192629A21F60}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{C2857848-3327-46C6-929C-192629A21F60}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{C2857848-3327-46C6-929C-192629A21F60}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{C2857848-3327-46C6-929C-192629A21F60}.Release|Win32.ActiveCfg = Release|Win32
+		{C2857848-3327-46C6-929C-192629A21F60}.Release|Win32.Build.0 = Release|Win32
+		{C2857848-3327-46C6-929C-192629A21F60}.Release|x64.ActiveCfg = Release|x64
+		{C2857848-3327-46C6-929C-192629A21F60}.Release|x64.Build.0 = Release|x64
+		{C2857848-3327-46C6-929C-192629A21F60}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{C2857848-3327-46C6-929C-192629A21F60}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{C2857848-3327-46C6-929C-192629A21F60}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{C2857848-3327-46C6-929C-192629A21F60}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{759991FD-441C-4267-A364-1BB2236C67B8}.Debug|Win32.ActiveCfg = Debug|Win32
+		{759991FD-441C-4267-A364-1BB2236C67B8}.Debug|Win32.Build.0 = Debug|Win32
+		{759991FD-441C-4267-A364-1BB2236C67B8}.Debug|x64.ActiveCfg = Debug|x64
+		{759991FD-441C-4267-A364-1BB2236C67B8}.Debug|x64.Build.0 = Debug|x64
+		{759991FD-441C-4267-A364-1BB2236C67B8}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{759991FD-441C-4267-A364-1BB2236C67B8}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{759991FD-441C-4267-A364-1BB2236C67B8}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{759991FD-441C-4267-A364-1BB2236C67B8}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{759991FD-441C-4267-A364-1BB2236C67B8}.Release|Win32.ActiveCfg = Release|Win32
+		{759991FD-441C-4267-A364-1BB2236C67B8}.Release|Win32.Build.0 = Release|Win32
+		{759991FD-441C-4267-A364-1BB2236C67B8}.Release|x64.ActiveCfg = Release|x64
+		{759991FD-441C-4267-A364-1BB2236C67B8}.Release|x64.Build.0 = Release|x64
+		{759991FD-441C-4267-A364-1BB2236C67B8}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{759991FD-441C-4267-A364-1BB2236C67B8}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{759991FD-441C-4267-A364-1BB2236C67B8}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{759991FD-441C-4267-A364-1BB2236C67B8}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.Debug|Win32.ActiveCfg = Debug|Win32
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.Debug|Win32.Build.0 = Debug|Win32
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.Debug|x64.ActiveCfg = Debug|x64
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.Debug|x64.Build.0 = Debug|x64
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.Release|Win32.ActiveCfg = Release|Win32
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.Release|Win32.Build.0 = Release|Win32
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.Release|x64.ActiveCfg = Release|x64
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.Release|x64.Build.0 = Release|x64
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.Debug|Win32.ActiveCfg = Debug|Win32
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.Debug|Win32.Build.0 = Debug|Win32
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.Debug|x64.ActiveCfg = Debug|x64
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.Debug|x64.Build.0 = Debug|x64
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.Release|Win32.ActiveCfg = Release|Win32
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.Release|Win32.Build.0 = Release|Win32
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.Release|x64.ActiveCfg = Release|x64
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.Release|x64.Build.0 = Release|x64
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{AB9DEE32-64FD-4700-84DF-485166A3E367}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.Debug|Win32.ActiveCfg = Debug|Win32
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.Debug|Win32.Build.0 = Debug|Win32
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.Debug|x64.ActiveCfg = Debug|x64
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.Debug|x64.Build.0 = Debug|x64
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.Release|Win32.ActiveCfg = Release|Win32
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.Release|Win32.Build.0 = Release|Win32
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.Release|x64.ActiveCfg = Release|x64
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.Release|x64.Build.0 = Release|x64
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{C0B91754-0757-42BD-8F53-C05964FFFB66}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.Debug|Win32.ActiveCfg = Debug|Win32
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.Debug|Win32.Build.0 = Debug|Win32
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.Debug|x64.ActiveCfg = Debug|x64
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.Debug|x64.Build.0 = Debug|x64
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.Release|Win32.ActiveCfg = Release|Win32
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.Release|Win32.Build.0 = Release|Win32
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.Release|x64.ActiveCfg = Release|x64
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.Release|x64.Build.0 = Release|x64
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{43337FCD-B171-4441-B44E-D1C90C2700EE}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.Debug|Win32.ActiveCfg = Debug|Win32
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.Debug|Win32.Build.0 = Debug|Win32
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.Debug|x64.ActiveCfg = Debug|x64
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.Debug|x64.Build.0 = Debug|x64
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.Release|Win32.ActiveCfg = Release|Win32
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.Release|Win32.Build.0 = Release|Win32
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.Release|x64.ActiveCfg = Release|x64
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.Release|x64.Build.0 = Release|x64
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{BC50422E-D841-4EDF-B987-5135EC4D8F11}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.Debug|Win32.ActiveCfg = Debug|Win32
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.Debug|Win32.Build.0 = Debug|Win32
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.Debug|x64.ActiveCfg = Debug|x64
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.Debug|x64.Build.0 = Debug|x64
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.Release|Win32.ActiveCfg = Release|Win32
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.Release|Win32.Build.0 = Release|Win32
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.Release|x64.ActiveCfg = Release|x64
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.Release|x64.Build.0 = Release|x64
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{2EDD4E60-025D-4167-B827-9A700DFA6D72}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.Debug|Win32.ActiveCfg = Debug|Win32
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.Debug|Win32.Build.0 = Debug|Win32
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.Debug|x64.ActiveCfg = Debug|x64
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.Debug|x64.Build.0 = Debug|x64
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.Release|Win32.ActiveCfg = Release|Win32
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.Release|Win32.Build.0 = Release|Win32
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.Release|x64.ActiveCfg = Release|x64
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.Release|x64.Build.0 = Release|x64
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{760EA748-5473-48CE-8BE0-76538A0CE1B2}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.Debug|Win32.ActiveCfg = Debug|Win32
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.Debug|Win32.Build.0 = Debug|Win32
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.Debug|x64.ActiveCfg = Debug|x64
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.Debug|x64.Build.0 = Debug|x64
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.Release|Win32.ActiveCfg = Release|Win32
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.Release|Win32.Build.0 = Release|Win32
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.Release|x64.ActiveCfg = Release|x64
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.Release|x64.Build.0 = Release|x64
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{9218C976-8194-4AD4-BC5C-7CBC456C2475}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.Debug|Win32.ActiveCfg = Debug|Win32
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.Debug|Win32.Build.0 = Debug|Win32
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.Debug|x64.ActiveCfg = Debug|x64
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.Debug|x64.Build.0 = Debug|x64
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.Release|Win32.ActiveCfg = Release|Win32
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.Release|Win32.Build.0 = Release|Win32
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.Release|x64.ActiveCfg = Release|x64
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.Release|x64.Build.0 = Release|x64
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{167BDE33-267C-49EE-9AC5-6177D283D799}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.Debug|Win32.ActiveCfg = Debug|Win32
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.Debug|Win32.Build.0 = Debug|Win32
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.Debug|x64.ActiveCfg = Debug|x64
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.Debug|x64.Build.0 = Debug|x64
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.Release|Win32.ActiveCfg = Release|Win32
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.Release|Win32.Build.0 = Release|Win32
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.Release|x64.ActiveCfg = Release|x64
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.Release|x64.Build.0 = Release|x64
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{087A2516-3C90-4D46-AEA9-670592894CB4}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.Debug|Win32.ActiveCfg = Debug|Win32
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.Debug|Win32.Build.0 = Debug|Win32
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.Debug|x64.ActiveCfg = Debug|x64
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.Debug|x64.Build.0 = Debug|x64
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.Release|Win32.ActiveCfg = Release|Win32
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.Release|Win32.Build.0 = Release|Win32
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.Release|x64.ActiveCfg = Release|x64
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.Release|x64.Build.0 = Release|x64
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{3B976840-4F3F-46A9-832D-4AB79417F712}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.Debug|Win32.ActiveCfg = Debug|Win32
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.Debug|Win32.Build.0 = Debug|Win32
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.Debug|x64.ActiveCfg = Debug|x64
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.Debug|x64.Build.0 = Debug|x64
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.Release|Win32.ActiveCfg = Release|Win32
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.Release|Win32.Build.0 = Release|Win32
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.Release|x64.ActiveCfg = Release|x64
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.Release|x64.Build.0 = Release|x64
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{F171E3D9-FC0B-4404-B96F-AD98C055CD8B}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.Debug|Win32.ActiveCfg = Debug|Win32
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.Debug|Win32.Build.0 = Debug|Win32
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.Debug|x64.ActiveCfg = Debug|x64
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.Debug|x64.Build.0 = Debug|x64
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.Release|Win32.ActiveCfg = Release|Win32
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.Release|Win32.Build.0 = Release|Win32
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.Release|x64.ActiveCfg = Release|x64
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.Release|x64.Build.0 = Release|x64
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{862D2BCD-67ED-4398-A811-7E247C2029E5}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.Debug|Win32.ActiveCfg = Debug|Win32
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.Debug|Win32.Build.0 = Debug|Win32
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.Debug|x64.ActiveCfg = Debug|x64
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.Debug|x64.Build.0 = Debug|x64
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.Release|Win32.ActiveCfg = Release|Win32
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.Release|Win32.Build.0 = Release|Win32
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.Release|x64.ActiveCfg = Release|x64
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.Release|x64.Build.0 = Release|x64
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{DD51F357-26FE-46F2-9AC9-5B682DBC198C}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.Debug|Win32.ActiveCfg = Debug|Win32
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.Debug|Win32.Build.0 = Debug|Win32
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.Debug|x64.ActiveCfg = Debug|x64
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.Debug|x64.Build.0 = Debug|x64
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.Release|Win32.ActiveCfg = Release|Win32
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.Release|Win32.Build.0 = Release|Win32
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.Release|x64.ActiveCfg = Release|x64
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.Release|x64.Build.0 = Release|x64
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{6F8036D0-9AEE-4B60-A65A-5A51A9D8725F}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.Debug|Win32.ActiveCfg = Debug|Win32
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.Debug|Win32.Build.0 = Debug|Win32
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.Debug|x64.ActiveCfg = Debug|x64
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.Debug|x64.Build.0 = Debug|x64
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.Release|Win32.ActiveCfg = Release|Win32
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.Release|Win32.Build.0 = Release|Win32
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.Release|x64.ActiveCfg = Release|x64
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.Release|x64.Build.0 = Release|x64
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{E459338E-39A8-49C9-9DFC-612E47863CE3}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{7719A61E-FAE1-4564-AD24-416318E48967}.Debug|Win32.ActiveCfg = Debug|Win32
+		{7719A61E-FAE1-4564-AD24-416318E48967}.Debug|Win32.Build.0 = Debug|Win32
+		{7719A61E-FAE1-4564-AD24-416318E48967}.Debug|x64.ActiveCfg = Debug|x64
+		{7719A61E-FAE1-4564-AD24-416318E48967}.Debug|x64.Build.0 = Debug|x64
+		{7719A61E-FAE1-4564-AD24-416318E48967}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{7719A61E-FAE1-4564-AD24-416318E48967}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{7719A61E-FAE1-4564-AD24-416318E48967}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{7719A61E-FAE1-4564-AD24-416318E48967}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{7719A61E-FAE1-4564-AD24-416318E48967}.Release|Win32.ActiveCfg = Release|Win32
+		{7719A61E-FAE1-4564-AD24-416318E48967}.Release|Win32.Build.0 = Release|Win32
+		{7719A61E-FAE1-4564-AD24-416318E48967}.Release|x64.ActiveCfg = Release|x64
+		{7719A61E-FAE1-4564-AD24-416318E48967}.Release|x64.Build.0 = Release|x64
+		{7719A61E-FAE1-4564-AD24-416318E48967}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{7719A61E-FAE1-4564-AD24-416318E48967}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{7719A61E-FAE1-4564-AD24-416318E48967}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{7719A61E-FAE1-4564-AD24-416318E48967}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.Debug|Win32.ActiveCfg = Debug|Win32
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.Debug|Win32.Build.0 = Debug|Win32
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.Debug|x64.ActiveCfg = Debug|x64
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.Debug|x64.Build.0 = Debug|x64
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.Release|Win32.ActiveCfg = Release|Win32
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.Release|Win32.Build.0 = Release|Win32
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.Release|x64.ActiveCfg = Release|x64
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.Release|x64.Build.0 = Release|x64
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{E6CE793E-7882-4E77-9D26-22C950DE0AFE}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.Debug|Win32.ActiveCfg = Debug|Win32
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.Debug|Win32.Build.0 = Debug|Win32
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.Debug|x64.ActiveCfg = Debug|x64
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.Debug|x64.Build.0 = Debug|x64
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.Release|Win32.ActiveCfg = Release|Win32
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.Release|Win32.Build.0 = Release|Win32
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.Release|x64.ActiveCfg = Release|x64
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.Release|x64.Build.0 = Release|x64
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{9AAE2D3F-4D37-43B6-96EB-593DE7679811}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{B6875C47-6809-4972-A89D-0085058670C9}.Debug|Win32.ActiveCfg = Debug|Win32
+		{B6875C47-6809-4972-A89D-0085058670C9}.Debug|Win32.Build.0 = Debug|Win32
+		{B6875C47-6809-4972-A89D-0085058670C9}.Debug|x64.ActiveCfg = Debug|x64
+		{B6875C47-6809-4972-A89D-0085058670C9}.Debug|x64.Build.0 = Debug|x64
+		{B6875C47-6809-4972-A89D-0085058670C9}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{B6875C47-6809-4972-A89D-0085058670C9}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{B6875C47-6809-4972-A89D-0085058670C9}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{B6875C47-6809-4972-A89D-0085058670C9}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{B6875C47-6809-4972-A89D-0085058670C9}.Release|Win32.ActiveCfg = Release|Win32
+		{B6875C47-6809-4972-A89D-0085058670C9}.Release|Win32.Build.0 = Release|Win32
+		{B6875C47-6809-4972-A89D-0085058670C9}.Release|x64.ActiveCfg = Release|x64
+		{B6875C47-6809-4972-A89D-0085058670C9}.Release|x64.Build.0 = Release|x64
+		{B6875C47-6809-4972-A89D-0085058670C9}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{B6875C47-6809-4972-A89D-0085058670C9}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{B6875C47-6809-4972-A89D-0085058670C9}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{B6875C47-6809-4972-A89D-0085058670C9}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.Debug|Win32.ActiveCfg = Debug|Win32
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.Debug|Win32.Build.0 = Debug|Win32
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.Debug|x64.ActiveCfg = Debug|x64
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.Debug|x64.Build.0 = Debug|x64
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.Release|Win32.ActiveCfg = Release|Win32
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.Release|Win32.Build.0 = Release|Win32
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.Release|x64.ActiveCfg = Release|x64
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.Release|x64.Build.0 = Release|x64
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{A0F67E98-8A07-4319-A3E8-B983D522D8CA}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.Debug|Win32.ActiveCfg = Debug|Win32
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.Debug|Win32.Build.0 = Debug|Win32
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.Debug|x64.ActiveCfg = Debug|x64
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.Debug|x64.Build.0 = Debug|x64
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.Release|Win32.ActiveCfg = Release|Win32
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.Release|Win32.Build.0 = Release|Win32
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.Release|x64.ActiveCfg = Release|x64
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.Release|x64.Build.0 = Release|x64
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.Debug|Win32.ActiveCfg = Debug|Win32
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.Debug|Win32.Build.0 = Debug|Win32
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.Debug|x64.ActiveCfg = Debug|x64
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.Debug|x64.Build.0 = Debug|x64
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.Release|Win32.ActiveCfg = Release|Win32
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.Release|Win32.Build.0 = Release|Win32
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.Release|x64.ActiveCfg = Release|x64
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.Release|x64.Build.0 = Release|x64
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{25806259-F586-4AAC-BDD1-50C1B227147D}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.Debug|Win32.ActiveCfg = Debug|Win32
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.Debug|Win32.Build.0 = Debug|Win32
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.Debug|x64.ActiveCfg = Debug|x64
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.Debug|x64.Build.0 = Debug|x64
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.Release|Win32.ActiveCfg = Release|Win32
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.Release|Win32.Build.0 = Release|Win32
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.Release|x64.ActiveCfg = Release|x64
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.Release|x64.Build.0 = Release|x64
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{E2180D54-5F75-47B7-8D77-00D04A6BEF69}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.Debug|Win32.ActiveCfg = Debug|Win32
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.Debug|Win32.Build.0 = Debug|Win32
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.Debug|x64.ActiveCfg = Debug|x64
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.Debug|x64.Build.0 = Debug|x64
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.DebugDLL|Win32.ActiveCfg = DebugDLL|Win32
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.DebugDLL|Win32.Build.0 = DebugDLL|Win32
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.DebugDLL|x64.ActiveCfg = DebugDLL|x64
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.DebugDLL|x64.Build.0 = DebugDLL|x64
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.Release|Win32.ActiveCfg = Release|Win32
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.Release|Win32.Build.0 = Release|Win32
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.Release|x64.ActiveCfg = Release|x64
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.Release|x64.Build.0 = Release|x64
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.ReleaseDLL|Win32.ActiveCfg = ReleaseDLL|Win32
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.ReleaseDLL|Win32.Build.0 = ReleaseDLL|Win32
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.ReleaseDLL|x64.ActiveCfg = ReleaseDLL|x64
+		{A9561C14-6DAF-4A28-9F59-297D39432D0B}.ReleaseDLL|x64.Build.0 = ReleaseDLL|x64
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
diff --git a/make/msvc800_prj/network/blast3/blastcl3/exe_blastcl3.vcproj b/make/msvc800_prj/network/blast3/blastcl3/exe_blastcl3.vcproj
index a819dd24..83ba8601 100644
--- a/make/msvc800_prj/network/blast3/blastcl3/exe_blastcl3.vcproj
+++ b/make/msvc800_prj/network/blast3/blastcl3/exe_blastcl3.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="exe_blastcl3"
-	ProjectGUID="{74C9A79B-EAE3-46B3-848E-73C3B5F679B9}"
+	ProjectGUID="{0516C2CE-F3B1-476B-AECC-9E2A02D40D8D}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/network/blast3/netblast/netblast.vcproj b/make/msvc800_prj/network/blast3/netblast/netblast.vcproj
index 2d1f6a06..b0a6e77f 100644
--- a/make/msvc800_prj/network/blast3/netblast/netblast.vcproj
+++ b/make/msvc800_prj/network/blast3/netblast/netblast.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="netblast"
-	ProjectGUID="{45CF24A4-E238-4E5C-BACC-5F0D6556A8EC}"
+	ProjectGUID="{759991FD-441C-4267-A364-1BB2236C67B8}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/network/entrez/client/netentr.vcproj b/make/msvc800_prj/network/entrez/client/netentr.vcproj
index 0025b09d..79be0b8b 100644
--- a/make/msvc800_prj/network/entrez/client/netentr.vcproj
+++ b/make/msvc800_prj/network/entrez/client/netentr.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="netentr"
-	ProjectGUID="{E2B932C9-4C8A-4922-9DFF-9FB646184223}"
+	ProjectGUID="{AB9DEE32-64FD-4700-84DF-485166A3E367}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/network/id1arch/ncbiid1.vcproj b/make/msvc800_prj/network/id1arch/ncbiid1.vcproj
index 4bb1b158..f6994c4b 100644
--- a/make/msvc800_prj/network/id1arch/ncbiid1.vcproj
+++ b/make/msvc800_prj/network/id1arch/ncbiid1.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbiid1"
-	ProjectGUID="{707F859C-FE05-486E-BB82-A447A6CD5036}"
+	ProjectGUID="{85E82D79-6144-4151-A3E7-8140E9ED01CF}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/network/idfetch/exe_idfetch.vcproj b/make/msvc800_prj/network/idfetch/exe_idfetch.vcproj
index b0ad2c6c..69fc407f 100644
--- a/make/msvc800_prj/network/idfetch/exe_idfetch.vcproj
+++ b/make/msvc800_prj/network/idfetch/exe_idfetch.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="exe_idfetch"
-	ProjectGUID="{BB120D1D-3A68-4107-A8A1-427E448DEA98}"
+	ProjectGUID="{67436D24-0D70-48D5-B1AE-6E8DFA978983}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/network/medarch/client/medarch.vcproj b/make/msvc800_prj/network/medarch/client/medarch.vcproj
index 4f84b498..727f002c 100644
--- a/make/msvc800_prj/network/medarch/client/medarch.vcproj
+++ b/make/msvc800_prj/network/medarch/client/medarch.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="medarch"
-	ProjectGUID="{4502FEB5-256A-4E4E-A8EF-34F7C7FC09DB}"
+	ProjectGUID="{2746DC43-68A9-42FE-80F0-1806679538FA}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/network/nsclilib/netcli.vcproj b/make/msvc800_prj/network/nsclilib/netcli.vcproj
index 07fd39a8..f68a94c2 100644
--- a/make/msvc800_prj/network/nsclilib/netcli.vcproj
+++ b/make/msvc800_prj/network/nsclilib/netcli.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="netcli"
-	ProjectGUID="{327A10DD-2251-4191-8425-17E535235D30}"
+	ProjectGUID="{14D69C18-0E8E-4816-8CC6-FC22AEA3E1C7}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/network/spell/client/ncbispel.vcproj b/make/msvc800_prj/network/spell/client/ncbispel.vcproj
index db5b37c7..45faa29e 100644
--- a/make/msvc800_prj/network/spell/client/ncbispel.vcproj
+++ b/make/msvc800_prj/network/spell/client/ncbispel.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbispel"
-	ProjectGUID="{ACB6E56A-AA8C-43C8-B9C4-A8E1E10E496C}"
+	ProjectGUID="{8B58713F-B6F4-4A76-9888-309FDDFB985D}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/network/taxon1/taxon2/ncbitxc2.vcproj b/make/msvc800_prj/network/taxon1/taxon2/ncbitxc2.vcproj
index 8281cd67..f8067df7 100644
--- a/make/msvc800_prj/network/taxon1/taxon2/ncbitxc2.vcproj
+++ b/make/msvc800_prj/network/taxon1/taxon2/ncbitxc2.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbitxc2"
-	ProjectGUID="{A9FD8A3D-345F-4F7B-B8D6-9032E1884F94}"
+	ProjectGUID="{C2857848-3327-46C6-929C-192629A21F60}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/network/vibnet/vibnet.vcproj b/make/msvc800_prj/network/vibnet/vibnet.vcproj
index afd03908..35bce4b5 100644
--- a/make/msvc800_prj/network/vibnet/vibnet.vcproj
+++ b/make/msvc800_prj/network/vibnet/vibnet.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="vibnet"
-	ProjectGUID="{47BB9C01-3751-4E25-87AE-6B4BAAA00340}"
+	ProjectGUID="{DE96F5AB-AC39-44FF-9BAB-36805FE07A86}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/object/ncbiobj.vcproj b/make/msvc800_prj/object/ncbiobj.vcproj
index 759ea42d..1b67231b 100644
--- a/make/msvc800_prj/object/ncbiobj.vcproj
+++ b/make/msvc800_prj/object/ncbiobj.vcproj
@@ -3,7 +3,8 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbiobj"
-	ProjectGUID="{F8CD481D-462C-40ED-98FA-C6EEF477B5CF}"
+	ProjectGUID="{7B5BF3BF-33A5-4830-A9CC-78EBD3F368E0}"
+	RootNamespace="ncbiobj"
 	>
 	<Platforms>
 		<Platform
@@ -92,9 +93,9 @@
 			/>
 		</Configuration>
 		<Configuration
-			Name="Debug|Win32"
-			OutputDirectory=".\Debug"
-			IntermediateDirectory=".\Debug"
+			Name="ReleaseDLL|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
 			ConfigurationType="4"
 			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
 			UseOfMFC="0"
@@ -114,14 +115,17 @@
 			/>
 			<Tool
 				Name="VCMIDLTool"
+				TargetEnvironment="3"
 			/>
 			<Tool
 				Name="VCCLCompilerTool"
-				Optimization="0"
+				Optimization="2"
+				InlineFunctionExpansion="1"
 				AdditionalIncludeDirectories="..\..\..,..\..\..\corelib,..\..\..\asnstat,..\..\..\asnlib,..\..\..\object,..\..\..\api,..\..\..\cdromlib,..\..\..\biostruc,..\..\..\ddv,..\..\..\access,..\..\..\connect,..\..\..\tools"
-				PreprocessorDefinitions="WIN32;_DEBUG"
-				BasicRuntimeChecks="3"
-				RuntimeLibrary="1"
+				PreprocessorDefinitions="WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="true"
 				RuntimeTypeInfo="true"
 				PrecompiledHeaderFile="$(IntDir)/ncbiobj.pch"
 				AssemblerListingLocation="$(IntDir)/"
@@ -129,14 +133,13 @@
 				ProgramDataBaseFileName="$(IntDir)/"
 				WarningLevel="3"
 				SuppressStartupBanner="true"
-				DebugInformationFormat="1"
 			/>
 			<Tool
 				Name="VCManagedResourceCompilerTool"
 			/>
 			<Tool
 				Name="VCResourceCompilerTool"
-				PreprocessorDefinitions="_DEBUG"
+				PreprocessorDefinitions="NDEBUG"
 				Culture="1033"
 			/>
 			<Tool
@@ -166,9 +169,9 @@
 			/>
 		</Configuration>
 		<Configuration
-			Name="Release|Win32"
-			OutputDirectory=".\Release"
-			IntermediateDirectory=".\Release"
+			Name="Debug|Win32"
+			OutputDirectory=".\Debug"
+			IntermediateDirectory=".\Debug"
 			ConfigurationType="4"
 			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
 			UseOfMFC="0"
@@ -191,13 +194,11 @@
 			/>
 			<Tool
 				Name="VCCLCompilerTool"
-				Optimization="2"
-				InlineFunctionExpansion="1"
+				Optimization="0"
 				AdditionalIncludeDirectories="..\..\..,..\..\..\corelib,..\..\..\asnstat,..\..\..\asnlib,..\..\..\object,..\..\..\api,..\..\..\cdromlib,..\..\..\biostruc,..\..\..\ddv,..\..\..\access,..\..\..\connect,..\..\..\tools"
-				PreprocessorDefinitions="WIN32;NDEBUG"
-				StringPooling="true"
-				RuntimeLibrary="0"
-				EnableFunctionLevelLinking="true"
+				PreprocessorDefinitions="WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="1"
 				RuntimeTypeInfo="true"
 				PrecompiledHeaderFile="$(IntDir)/ncbiobj.pch"
 				AssemblerListingLocation="$(IntDir)/"
@@ -205,13 +206,14 @@
 				ProgramDataBaseFileName="$(IntDir)/"
 				WarningLevel="3"
 				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
 			/>
 			<Tool
 				Name="VCManagedResourceCompilerTool"
 			/>
 			<Tool
 				Name="VCResourceCompilerTool"
-				PreprocessorDefinitions="NDEBUG"
+				PreprocessorDefinitions="_DEBUG"
 				Culture="1033"
 			/>
 			<Tool
@@ -241,9 +243,9 @@
 			/>
 		</Configuration>
 		<Configuration
-			Name="DebugDLL|Win32"
-			OutputDirectory=".\DebugDLL"
-			IntermediateDirectory=".\DebugDLL"
+			Name="Debug|x64"
+			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
+			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
 			ConfigurationType="4"
 			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
 			UseOfMFC="0"
@@ -263,6 +265,7 @@
 			/>
 			<Tool
 				Name="VCMIDLTool"
+				TargetEnvironment="3"
 			/>
 			<Tool
 				Name="VCCLCompilerTool"
@@ -270,7 +273,7 @@
 				AdditionalIncludeDirectories="..\..\..,..\..\..\corelib,..\..\..\asnstat,..\..\..\asnlib,..\..\..\object,..\..\..\api,..\..\..\cdromlib,..\..\..\biostruc,..\..\..\ddv,..\..\..\access,..\..\..\connect,..\..\..\tools"
 				PreprocessorDefinitions="WIN32;_DEBUG"
 				BasicRuntimeChecks="3"
-				RuntimeLibrary="3"
+				RuntimeLibrary="1"
 				RuntimeTypeInfo="true"
 				PrecompiledHeaderFile="$(IntDir)/ncbiobj.pch"
 				AssemblerListingLocation="$(IntDir)/"
@@ -315,9 +318,9 @@
 			/>
 		</Configuration>
 		<Configuration
-			Name="ReleaseDLL|x64"
-			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
-			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			Name="Release|Win32"
+			OutputDirectory=".\Release"
+			IntermediateDirectory=".\Release"
 			ConfigurationType="4"
 			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
 			UseOfMFC="0"
@@ -337,7 +340,6 @@
 			/>
 			<Tool
 				Name="VCMIDLTool"
-				TargetEnvironment="3"
 			/>
 			<Tool
 				Name="VCCLCompilerTool"
@@ -346,7 +348,7 @@
 				AdditionalIncludeDirectories="..\..\..,..\..\..\corelib,..\..\..\asnstat,..\..\..\asnlib,..\..\..\object,..\..\..\api,..\..\..\cdromlib,..\..\..\biostruc,..\..\..\ddv,..\..\..\access,..\..\..\connect,..\..\..\tools"
 				PreprocessorDefinitions="WIN32;NDEBUG"
 				StringPooling="true"
-				RuntimeLibrary="2"
+				RuntimeLibrary="0"
 				EnableFunctionLevelLinking="true"
 				RuntimeTypeInfo="true"
 				PrecompiledHeaderFile="$(IntDir)/ncbiobj.pch"
@@ -391,7 +393,7 @@
 			/>
 		</Configuration>
 		<Configuration
-			Name="Debug|x64"
+			Name="Release|x64"
 			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
 			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
 			ConfigurationType="4"
@@ -417,11 +419,13 @@
 			/>
 			<Tool
 				Name="VCCLCompilerTool"
-				Optimization="0"
+				Optimization="2"
+				InlineFunctionExpansion="1"
 				AdditionalIncludeDirectories="..\..\..,..\..\..\corelib,..\..\..\asnstat,..\..\..\asnlib,..\..\..\object,..\..\..\api,..\..\..\cdromlib,..\..\..\biostruc,..\..\..\ddv,..\..\..\access,..\..\..\connect,..\..\..\tools"
-				PreprocessorDefinitions="WIN32;_DEBUG"
-				BasicRuntimeChecks="3"
-				RuntimeLibrary="1"
+				PreprocessorDefinitions="WIN32;NDEBUG"
+				StringPooling="true"
+				RuntimeLibrary="0"
+				EnableFunctionLevelLinking="true"
 				RuntimeTypeInfo="true"
 				PrecompiledHeaderFile="$(IntDir)/ncbiobj.pch"
 				AssemblerListingLocation="$(IntDir)/"
@@ -429,14 +433,13 @@
 				ProgramDataBaseFileName="$(IntDir)/"
 				WarningLevel="3"
 				SuppressStartupBanner="true"
-				DebugInformationFormat="1"
 			/>
 			<Tool
 				Name="VCManagedResourceCompilerTool"
 			/>
 			<Tool
 				Name="VCResourceCompilerTool"
-				PreprocessorDefinitions="_DEBUG"
+				PreprocessorDefinitions="NDEBUG"
 				Culture="1033"
 			/>
 			<Tool
@@ -466,9 +469,9 @@
 			/>
 		</Configuration>
 		<Configuration
-			Name="Release|x64"
-			OutputDirectory="$(PlatformName)\$(ConfigurationName)"
-			IntermediateDirectory="$(PlatformName)\$(ConfigurationName)"
+			Name="DebugDLL|Win32"
+			OutputDirectory=".\DebugDLL"
+			IntermediateDirectory=".\DebugDLL"
 			ConfigurationType="4"
 			InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC60.vsprops"
 			UseOfMFC="0"
@@ -488,17 +491,14 @@
 			/>
 			<Tool
 				Name="VCMIDLTool"
-				TargetEnvironment="3"
 			/>
 			<Tool
 				Name="VCCLCompilerTool"
-				Optimization="2"
-				InlineFunctionExpansion="1"
+				Optimization="0"
 				AdditionalIncludeDirectories="..\..\..,..\..\..\corelib,..\..\..\asnstat,..\..\..\asnlib,..\..\..\object,..\..\..\api,..\..\..\cdromlib,..\..\..\biostruc,..\..\..\ddv,..\..\..\access,..\..\..\connect,..\..\..\tools"
-				PreprocessorDefinitions="WIN32;NDEBUG"
-				StringPooling="true"
-				RuntimeLibrary="0"
-				EnableFunctionLevelLinking="true"
+				PreprocessorDefinitions="WIN32;_DEBUG"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
 				RuntimeTypeInfo="true"
 				PrecompiledHeaderFile="$(IntDir)/ncbiobj.pch"
 				AssemblerListingLocation="$(IntDir)/"
@@ -506,13 +506,14 @@
 				ProgramDataBaseFileName="$(IntDir)/"
 				WarningLevel="3"
 				SuppressStartupBanner="true"
+				DebugInformationFormat="1"
 			/>
 			<Tool
 				Name="VCManagedResourceCompilerTool"
 			/>
 			<Tool
 				Name="VCResourceCompilerTool"
-				PreprocessorDefinitions="NDEBUG"
+				PreprocessorDefinitions="_DEBUG"
 				Culture="1033"
 			/>
 			<Tool
@@ -637,7 +638,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -646,7 +647,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -655,7 +656,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -664,7 +665,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -673,7 +674,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -682,7 +683,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -713,7 +714,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -722,7 +723,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -731,7 +732,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -740,7 +741,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -749,7 +750,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -758,7 +759,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -789,7 +790,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -798,7 +799,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -807,7 +808,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -816,7 +817,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -825,7 +826,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -834,7 +835,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -865,7 +866,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -874,7 +875,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -883,7 +884,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -892,7 +893,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -901,7 +902,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -910,7 +911,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -941,7 +942,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -950,7 +951,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -959,7 +960,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -968,7 +969,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -977,7 +978,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -986,7 +987,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1017,7 +1018,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1026,7 +1027,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1035,7 +1036,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1044,7 +1045,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1053,7 +1054,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1062,7 +1063,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1093,7 +1094,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1102,7 +1103,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1111,7 +1112,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1120,7 +1121,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1129,7 +1130,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1138,7 +1139,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1169,7 +1170,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1178,7 +1179,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1187,7 +1188,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1196,7 +1197,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1205,7 +1206,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1214,7 +1215,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1245,7 +1246,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1254,7 +1255,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1263,7 +1264,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1272,7 +1273,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1281,7 +1282,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1290,7 +1291,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1321,7 +1322,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1330,7 +1331,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1339,7 +1340,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1348,7 +1349,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1357,7 +1358,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1366,7 +1367,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1397,7 +1398,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1406,7 +1407,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1415,7 +1416,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1424,7 +1425,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1433,7 +1434,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1442,7 +1443,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1473,7 +1474,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1482,7 +1483,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1491,7 +1492,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1500,7 +1501,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1509,7 +1510,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1518,7 +1519,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1549,7 +1550,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1558,7 +1559,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1567,7 +1568,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1576,7 +1577,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1585,7 +1586,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1594,7 +1595,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1625,7 +1626,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1634,7 +1635,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1643,7 +1644,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1652,7 +1653,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1661,7 +1662,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1670,7 +1671,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1701,7 +1702,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1710,7 +1711,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1719,7 +1720,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1728,7 +1729,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1737,7 +1738,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1746,7 +1747,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1777,7 +1778,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1786,7 +1787,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1795,7 +1796,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1804,7 +1805,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1813,7 +1814,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1822,7 +1823,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1853,7 +1854,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1862,7 +1863,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1871,7 +1872,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1880,7 +1881,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1889,7 +1890,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1898,7 +1899,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1929,7 +1930,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1938,7 +1939,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1947,7 +1948,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1956,7 +1957,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1965,7 +1966,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -1974,7 +1975,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2005,7 +2006,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2014,7 +2015,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2023,7 +2024,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2032,7 +2033,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2041,7 +2042,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2050,7 +2051,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2081,7 +2082,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2090,7 +2091,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2099,7 +2100,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2108,7 +2109,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2117,7 +2118,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2126,7 +2127,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2157,7 +2158,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2166,7 +2167,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2175,7 +2176,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2184,7 +2185,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2193,7 +2194,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2202,7 +2203,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2233,7 +2234,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2242,7 +2243,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2251,7 +2252,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2260,7 +2261,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2269,7 +2270,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2278,7 +2279,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2309,7 +2310,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2318,7 +2319,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2327,7 +2328,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2336,7 +2337,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2345,7 +2346,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2354,7 +2355,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2385,7 +2386,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2394,7 +2395,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2403,7 +2404,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2412,7 +2413,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2421,7 +2422,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2430,7 +2431,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2461,7 +2462,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2470,7 +2471,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2479,7 +2480,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2488,7 +2489,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2497,7 +2498,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2506,7 +2507,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2537,7 +2538,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2546,7 +2547,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2555,7 +2556,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2564,7 +2565,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2573,7 +2574,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2582,7 +2583,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2613,7 +2614,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2622,7 +2623,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2631,7 +2632,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2640,7 +2641,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2649,7 +2650,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2658,7 +2659,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2689,7 +2690,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2698,7 +2699,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2707,7 +2708,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2716,7 +2717,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2725,7 +2726,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2734,7 +2735,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2765,7 +2766,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2774,7 +2775,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2783,7 +2784,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2792,7 +2793,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2801,7 +2802,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2810,7 +2811,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2841,7 +2842,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2850,7 +2851,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2859,7 +2860,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2868,7 +2869,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2877,7 +2878,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2886,7 +2887,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2917,7 +2918,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2926,7 +2927,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2935,7 +2936,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2944,7 +2945,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2953,7 +2954,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2962,7 +2963,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -2993,7 +2994,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3002,7 +3003,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3011,7 +3012,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3020,7 +3021,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3029,7 +3030,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3038,7 +3039,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3069,7 +3070,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3078,7 +3079,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3087,7 +3088,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3096,7 +3097,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3105,7 +3106,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3114,7 +3115,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3145,7 +3146,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3154,7 +3155,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3163,7 +3164,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3172,7 +3173,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3181,7 +3182,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3190,7 +3191,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3221,7 +3222,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3230,7 +3231,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3239,7 +3240,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3248,7 +3249,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3257,7 +3258,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3266,7 +3267,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3297,7 +3298,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3306,7 +3307,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3315,7 +3316,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3324,7 +3325,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3333,7 +3334,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3342,7 +3343,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3373,7 +3374,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3382,7 +3383,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3391,7 +3392,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3400,7 +3401,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3409,7 +3410,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3418,7 +3419,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3449,6 +3450,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Debug|Win32"
 					>
 					<Tool
@@ -3458,6 +3468,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Release|Win32"
 					>
 					<Tool
@@ -3467,6 +3486,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="DebugDLL|Win32"
 					>
 					<Tool
@@ -3476,6 +3504,28 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="..\..\..\api\macroapi.c"
+				>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="ReleaseDLL|x64"
 					>
 					<Tool
@@ -3485,6 +3535,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Debug|x64"
 					>
 					<Tool
@@ -3494,6 +3553,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Release|x64"
 					>
 					<Tool
@@ -3503,6 +3571,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="DebugDLL|x64"
 					>
 					<Tool
@@ -3525,7 +3602,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3534,7 +3611,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3543,7 +3620,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3552,7 +3629,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3561,7 +3638,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3570,7 +3647,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3601,7 +3678,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3610,7 +3687,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3619,7 +3696,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3628,7 +3705,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3637,7 +3714,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3646,7 +3723,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3677,7 +3754,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3686,7 +3763,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3695,7 +3772,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3704,7 +3781,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3713,7 +3790,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3722,7 +3799,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3753,7 +3830,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3762,7 +3839,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3771,7 +3848,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3780,7 +3857,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3789,7 +3866,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3798,7 +3875,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3829,7 +3906,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3838,7 +3915,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3847,7 +3924,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3856,7 +3933,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3865,7 +3942,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3874,7 +3951,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3905,7 +3982,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3914,7 +3991,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3923,7 +4000,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3932,7 +4009,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3941,7 +4018,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3950,7 +4027,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3981,7 +4058,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3990,7 +4067,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -3999,7 +4076,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4008,7 +4085,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4017,7 +4094,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4026,7 +4103,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4057,7 +4134,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4066,7 +4143,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4075,7 +4152,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4084,7 +4161,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4093,7 +4170,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4102,7 +4179,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4133,7 +4210,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4142,7 +4219,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4151,7 +4228,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4160,7 +4237,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4169,7 +4246,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4178,7 +4255,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4209,7 +4286,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4218,7 +4295,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4227,7 +4304,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4236,7 +4313,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4245,7 +4322,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4254,7 +4331,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4285,7 +4362,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4294,7 +4371,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4303,7 +4380,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4312,7 +4389,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4321,7 +4398,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4330,7 +4407,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4361,7 +4438,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4370,7 +4447,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4379,7 +4456,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4388,7 +4465,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4397,7 +4474,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4406,7 +4483,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4437,7 +4514,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4446,7 +4523,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4455,7 +4532,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4464,7 +4541,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4473,7 +4550,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4482,7 +4559,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4513,7 +4590,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4522,7 +4599,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4531,7 +4608,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4540,7 +4617,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4549,7 +4626,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4558,7 +4635,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4589,7 +4666,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4598,7 +4675,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4607,7 +4684,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4616,7 +4693,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4625,7 +4702,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4634,7 +4711,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4665,7 +4742,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4674,7 +4751,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4683,7 +4760,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4692,7 +4769,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4701,7 +4778,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4710,7 +4787,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4741,7 +4818,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4750,7 +4827,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4759,7 +4836,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4768,7 +4845,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4777,7 +4854,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4786,7 +4863,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4817,7 +4894,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4826,7 +4903,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4835,7 +4912,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4844,7 +4921,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4853,7 +4930,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4862,7 +4939,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4893,7 +4970,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4902,7 +4979,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4911,7 +4988,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4920,7 +4997,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4929,7 +5006,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4938,7 +5015,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4969,7 +5046,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4978,7 +5055,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4987,7 +5064,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -4996,7 +5073,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5005,7 +5082,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5014,7 +5091,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5045,6 +5122,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Debug|Win32"
 					>
 					<Tool
@@ -5054,6 +5140,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Release|Win32"
 					>
 					<Tool
@@ -5063,6 +5158,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="DebugDLL|Win32"
 					>
 					<Tool
@@ -5072,6 +5176,28 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="..\..\..\object\objmacro.c"
+				>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="ReleaseDLL|x64"
 					>
 					<Tool
@@ -5081,6 +5207,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Debug|x64"
 					>
 					<Tool
@@ -5090,6 +5225,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Release|x64"
 					>
 					<Tool
@@ -5099,6 +5243,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="DebugDLL|x64"
 					>
 					<Tool
@@ -5121,7 +5274,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5130,7 +5283,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5139,7 +5292,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5148,7 +5301,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5157,7 +5310,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5166,7 +5319,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5197,7 +5350,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5206,7 +5359,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5215,7 +5368,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5224,7 +5377,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5233,7 +5386,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5242,7 +5395,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5273,7 +5426,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5282,7 +5435,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5291,7 +5444,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5300,7 +5453,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5309,7 +5462,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5318,7 +5471,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5349,7 +5502,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5358,7 +5511,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5367,7 +5520,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5376,7 +5529,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5385,7 +5538,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5394,7 +5547,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5425,7 +5578,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5434,7 +5587,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5443,7 +5596,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5452,7 +5605,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5461,7 +5614,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5470,7 +5623,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5501,7 +5654,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5510,7 +5663,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5519,7 +5672,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5528,7 +5681,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5537,7 +5690,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5546,7 +5699,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5577,7 +5730,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5586,7 +5739,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5595,7 +5748,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5604,7 +5757,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5613,7 +5766,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5622,7 +5775,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5653,7 +5806,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5662,7 +5815,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5671,7 +5824,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5680,7 +5833,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5689,7 +5842,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5698,7 +5851,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5729,7 +5882,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5738,7 +5891,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5747,7 +5900,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5756,7 +5909,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5765,7 +5918,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5774,7 +5927,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5805,7 +5958,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5814,7 +5967,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5823,7 +5976,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5832,7 +5985,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5841,7 +5994,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5850,7 +6003,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5881,7 +6034,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5890,7 +6043,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5899,7 +6052,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5908,7 +6061,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5917,7 +6070,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5926,7 +6079,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5957,7 +6110,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5966,7 +6119,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5975,7 +6128,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5984,7 +6137,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -5993,7 +6146,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6002,7 +6155,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6033,7 +6186,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6042,7 +6195,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6051,7 +6204,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6060,7 +6213,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6069,7 +6222,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6078,7 +6231,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6109,6 +6262,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="ReleaseDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Debug|Win32"
 					>
 					<Tool
@@ -6118,6 +6280,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Debug|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Release|Win32"
 					>
 					<Tool
@@ -6127,6 +6298,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Release|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="DebugDLL|Win32"
 					>
 					<Tool
@@ -6136,6 +6316,28 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="DebugDLL|x64"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="..\..\..\object\objtable.c"
+				>
+				<FileConfiguration
+					Name="ReleaseDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="ReleaseDLL|x64"
 					>
 					<Tool
@@ -6145,6 +6347,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Debug|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Debug|x64"
 					>
 					<Tool
@@ -6154,6 +6365,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="Release|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="Release|x64"
 					>
 					<Tool
@@ -6163,6 +6383,15 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
+					Name="DebugDLL|Win32"
+					>
+					<Tool
+						Name="VCCLCompilerTool"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+					/>
+				</FileConfiguration>
+				<FileConfiguration
 					Name="DebugDLL|x64"
 					>
 					<Tool
@@ -6185,7 +6414,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6194,7 +6423,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6203,7 +6432,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6212,7 +6441,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6221,7 +6450,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6230,7 +6459,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6261,7 +6490,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6270,7 +6499,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6279,7 +6508,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6288,7 +6517,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6297,7 +6526,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6306,7 +6535,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6337,7 +6566,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6346,7 +6575,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6355,7 +6584,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6364,7 +6593,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6373,7 +6602,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6382,7 +6611,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6413,7 +6642,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6422,7 +6651,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6431,7 +6660,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6440,7 +6669,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6449,7 +6678,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6458,7 +6687,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6489,7 +6718,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6498,7 +6727,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6507,7 +6736,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6516,7 +6745,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6525,7 +6754,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6534,7 +6763,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6565,7 +6794,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6574,7 +6803,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6583,7 +6812,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6592,7 +6821,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6601,7 +6830,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6610,7 +6839,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6641,7 +6870,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6650,7 +6879,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6659,7 +6888,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6668,7 +6897,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6677,7 +6906,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6686,7 +6915,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6717,7 +6946,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6726,7 +6955,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6735,7 +6964,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6744,7 +6973,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6753,7 +6982,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6762,7 +6991,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6793,7 +7022,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6802,7 +7031,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6811,7 +7040,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6820,7 +7049,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6829,7 +7058,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6838,7 +7067,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6869,7 +7098,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6878,7 +7107,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6887,7 +7116,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6896,7 +7125,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6905,7 +7134,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6914,7 +7143,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6945,7 +7174,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6954,7 +7183,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6963,7 +7192,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6972,7 +7201,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6981,7 +7210,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -6990,7 +7219,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7021,7 +7250,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7030,7 +7259,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7039,7 +7268,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7048,7 +7277,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7057,7 +7286,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7066,7 +7295,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7097,7 +7326,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7106,7 +7335,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7115,7 +7344,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7124,7 +7353,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7133,7 +7362,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7142,7 +7371,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7173,7 +7402,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7182,7 +7411,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7191,7 +7420,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7200,7 +7429,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7209,7 +7438,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7218,7 +7447,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7249,7 +7478,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7258,7 +7487,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7267,7 +7496,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7276,7 +7505,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7285,7 +7514,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7294,7 +7523,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7325,7 +7554,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7334,7 +7563,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7343,7 +7572,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7352,7 +7581,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7361,7 +7590,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7370,7 +7599,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7401,7 +7630,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7410,7 +7639,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7419,7 +7648,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7428,7 +7657,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7437,7 +7666,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7446,7 +7675,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7477,7 +7706,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7486,7 +7715,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7495,7 +7724,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7504,7 +7733,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7513,7 +7742,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7522,7 +7751,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7553,7 +7782,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7562,7 +7791,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7571,7 +7800,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7580,7 +7809,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7589,7 +7818,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7598,7 +7827,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7629,7 +7858,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7638,7 +7867,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7647,7 +7876,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7656,7 +7885,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7665,7 +7894,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7674,7 +7903,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7705,7 +7934,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7714,7 +7943,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7723,7 +7952,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7732,7 +7961,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7741,7 +7970,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7750,7 +7979,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7781,7 +8010,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7790,7 +8019,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7799,7 +8028,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7808,7 +8037,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7817,7 +8046,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7826,7 +8055,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7845,6 +8074,10 @@
 				</FileConfiguration>
 			</File>
 			<File
+				RelativePath="..\..\..\api\sqnutil4.c"
+				>
+			</File>
+			<File
 				RelativePath="..\..\..\access\strucapi.c"
 				>
 				<FileConfiguration
@@ -7857,7 +8090,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7866,7 +8099,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7875,7 +8108,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7884,7 +8117,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7893,7 +8126,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7902,7 +8135,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7933,7 +8166,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7942,7 +8175,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7951,7 +8184,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7960,7 +8193,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7969,7 +8202,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -7978,7 +8211,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8009,7 +8242,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8018,7 +8251,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8027,7 +8260,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8036,7 +8269,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8045,7 +8278,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8054,7 +8287,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8085,7 +8318,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8094,7 +8327,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8103,7 +8336,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8112,7 +8345,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8121,7 +8354,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8130,7 +8363,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8161,7 +8394,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8170,7 +8403,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8179,7 +8412,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8188,7 +8421,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8197,7 +8430,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8206,7 +8439,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8237,7 +8470,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8246,7 +8479,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8255,7 +8488,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8264,7 +8497,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8273,7 +8506,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8282,7 +8515,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8313,7 +8546,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8322,7 +8555,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8331,7 +8564,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8340,7 +8573,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8349,7 +8582,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8358,7 +8591,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8389,7 +8622,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8398,7 +8631,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8407,7 +8640,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8416,7 +8649,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8425,7 +8658,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8434,7 +8667,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8465,7 +8698,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8474,7 +8707,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8483,7 +8716,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8492,7 +8725,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8501,7 +8734,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8510,7 +8743,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8541,7 +8774,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8550,7 +8783,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8559,7 +8792,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8568,7 +8801,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8577,7 +8810,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8586,7 +8819,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8617,7 +8850,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8626,7 +8859,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8635,7 +8868,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8644,7 +8877,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8653,7 +8886,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8662,7 +8895,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8693,7 +8926,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8702,7 +8935,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8711,7 +8944,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8720,7 +8953,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8729,7 +8962,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8738,7 +8971,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8769,7 +9002,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8778,7 +9011,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8787,7 +9020,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8796,7 +9029,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8805,7 +9038,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8814,7 +9047,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8845,7 +9078,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|Win32"
+					Name="ReleaseDLL|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8854,7 +9087,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|Win32"
+					Name="Debug|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8863,7 +9096,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="DebugDLL|Win32"
+					Name="Debug|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8872,7 +9105,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="ReleaseDLL|x64"
+					Name="Release|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8881,7 +9114,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Debug|x64"
+					Name="Release|x64"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -8890,7 +9123,7 @@
 					/>
 				</FileConfiguration>
 				<FileConfiguration
-					Name="Release|x64"
+					Name="DebugDLL|Win32"
 					>
 					<Tool
 						Name="VCCLCompilerTool"
@@ -9182,6 +9415,10 @@
 				>
 			</File>
 			<File
+				RelativePath="..\..\..\api\macroapi.h"
+				>
+			</File>
+			<File
 				RelativePath="..\..\..\object\mapmime.h"
 				>
 			</File>
@@ -9294,6 +9531,10 @@
 				>
 			</File>
 			<File
+				RelativePath="..\..\..\object\objmacro.h"
+				>
+			</File>
+			<File
 				RelativePath="..\..\..\object\objmdrs.h"
 				>
 			</File>
@@ -9354,6 +9595,10 @@
 				>
 			</File>
 			<File
+				RelativePath="..\..\..\object\objtable.h"
+				>
+			</File>
+			<File
 				RelativePath="..\..\..\access\objtax3.h"
 				>
 			</File>
@@ -9510,4 +9755,3 @@
 	<Globals>
 	</Globals>
 </VisualStudioProject>
-
diff --git a/make/msvc800_prj/regexp/demo/demo_regexp.vcproj b/make/msvc800_prj/regexp/demo/demo_regexp.vcproj
index 53ed4287..ef92424c 100644
--- a/make/msvc800_prj/regexp/demo/demo_regexp.vcproj
+++ b/make/msvc800_prj/regexp/demo/demo_regexp.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_regexp"
-	ProjectGUID="{D0B197BF-1409-4108-81C0-A2754CD97ADA}"
+	ProjectGUID="{82933EEE-EB79-486D-A8E2-B440D33D924A}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/regexp/demo/demo_regexp_grep.vcproj b/make/msvc800_prj/regexp/demo/demo_regexp_grep.vcproj
index cbe18d53..7fc83fdf 100644
--- a/make/msvc800_prj/regexp/demo/demo_regexp_grep.vcproj
+++ b/make/msvc800_prj/regexp/demo/demo_regexp_grep.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="demo_regexp_grep"
-	ProjectGUID="{CCA73A4F-96E8-48BE-A1B6-77EC3697584C}"
+	ProjectGUID="{8EFB0853-50E8-4167-88A5-2C71DAB74098}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/regexp/regexp.vcproj b/make/msvc800_prj/regexp/regexp.vcproj
index a543519f..87d3adc0 100644
--- a/make/msvc800_prj/regexp/regexp.vcproj
+++ b/make/msvc800_prj/regexp/regexp.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="regexp"
-	ProjectGUID="{21191422-314F-421D-93A8-EABF933C3065}"
+	ProjectGUID="{C0B91754-0757-42BD-8F53-C05964FFFB66}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/regexp/test/test_regexp.vcproj b/make/msvc800_prj/regexp/test/test_regexp.vcproj
index 44d29f3d..1b87eb4c 100644
--- a/make/msvc800_prj/regexp/test/test_regexp.vcproj
+++ b/make/msvc800_prj/regexp/test/test_regexp.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="test_regexp"
-	ProjectGUID="{8FBFAE5E-50CA-42EF-B614-BEA3252064BD}"
+	ProjectGUID="{B6875C47-6809-4972-A89D-0085058670C9}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/sequin/sbtedit/exe_sbtedit.vcproj b/make/msvc800_prj/sequin/sbtedit/exe_sbtedit.vcproj
index d32ff173..8c0930e2 100644
--- a/make/msvc800_prj/sequin/sbtedit/exe_sbtedit.vcproj
+++ b/make/msvc800_prj/sequin/sbtedit/exe_sbtedit.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="exe_sbtedit"
-	ProjectGUID="{6F58FEBB-1C0A-4C28-B0D4-82629AC0E1C6}"
+	ProjectGUID="{028EEC3D-499E-453C-A1F4-5A4478BBB39F}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/sequin/sequin/exe_sequin.vcproj b/make/msvc800_prj/sequin/sequin/exe_sequin.vcproj
index 3d33676c..2841db6f 100644
--- a/make/msvc800_prj/sequin/sequin/exe_sequin.vcproj
+++ b/make/msvc800_prj/sequin/sequin/exe_sequin.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="exe_sequin"
-	ProjectGUID="{002CC81D-C6AF-4AED-8624-301D0E13ED46}"
+	ProjectGUID="{86F47145-3ABB-45BA-8D51-89C24997882F}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/sequin/ssequin/exe_ssequin.vcproj b/make/msvc800_prj/sequin/ssequin/exe_ssequin.vcproj
index 37bca95e..c315605c 100644
--- a/make/msvc800_prj/sequin/ssequin/exe_ssequin.vcproj
+++ b/make/msvc800_prj/sequin/ssequin/exe_ssequin.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="exe_ssequin"
-	ProjectGUID="{808F70AF-6AA9-49CB-A7AE-28E85C1D22FE}"
+	ProjectGUID="{7469FFC1-059F-45B2-A9B8-B17CD881CA8D}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/tools/ncbitool.vcproj b/make/msvc800_prj/tools/ncbitool.vcproj
index 3ce5267c..b665dfb1 100644
--- a/make/msvc800_prj/tools/ncbitool.vcproj
+++ b/make/msvc800_prj/tools/ncbitool.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="ncbitool"
-	ProjectGUID="{32AB53DD-66B1-4E17-B411-FEB804E62CF0}"
+	ProjectGUID="{19DB0E0E-BB30-4A19-93A8-7B67FBB0C937}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/vibrant/vibrant/vibrant.vcproj b/make/msvc800_prj/vibrant/vibrant/vibrant.vcproj
index 22ca0377..2aa60673 100644
--- a/make/msvc800_prj/vibrant/vibrant/vibrant.vcproj
+++ b/make/msvc800_prj/vibrant/vibrant/vibrant.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="vibrant"
-	ProjectGUID="{F2107221-7687-4F18-AEAC-FAA7C4EFCC16}"
+	ProjectGUID="{25806259-F586-4AAC-BDD1-50C1B227147D}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc800_prj/vibrant/vibrant_ogl/vibrant_ogl.vcproj b/make/msvc800_prj/vibrant/vibrant_ogl/vibrant_ogl.vcproj
index f0656114..08812286 100644
--- a/make/msvc800_prj/vibrant/vibrant_ogl/vibrant_ogl.vcproj
+++ b/make/msvc800_prj/vibrant/vibrant_ogl/vibrant_ogl.vcproj
@@ -3,7 +3,7 @@
 	ProjectType="Visual C++"
 	Version="8.00"
 	Name="vibrant_ogl"
-	ProjectGUID="{94B3883E-2A1C-4B7C-A98F-6ED6343F0D8B}"
+	ProjectGUID="{E2180D54-5F75-47B7-8D77-00D04A6BEF69}"
 	>
 	<Platforms>
 		<Platform
diff --git a/make/msvc_prj/demo/asnmacro/demo_asnmacro.dsp b/make/msvc_prj/demo/asnmacro/demo_asnmacro.dsp
new file mode 100644
index 00000000..a503a0dc
--- /dev/null
+++ b/make/msvc_prj/demo/asnmacro/demo_asnmacro.dsp
@@ -0,0 +1,75 @@
+# Microsoft Developer Studio Project File - Name="demo_asnmacro" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Application" 0x0101
+
+CFG=demo_asnmacro - Win32 DebugDLL
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "demo_asnmacro.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "demo_asnmacro.mak" CFG="demo_asnmacro - Win32 DebugDLL"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "demo_asnmacro - Win32 DebugDLL" (based on "Win32 (x86) Application")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "DebugDLL"
+# PROP BASE Intermediate_Dir "DebugDLL"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "DebugDLL"
+# PROP Intermediate_Dir "DebugDLL"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+LIB32=link.exe -lib
+# ADD BASE CPP /nologo /MDd /W3 /GX /Z7 /Od /D "WIN32" /D "_DEBUG" /D "_NETENT_" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# ADD CPP /nologo /MDd /W3 /GR /Z7 /Od /I "..\..\..\.." /I "..\..\..\..\corelib" /I "..\..\..\..\connect" /I "..\..\..\..\api" /I "..\..\..\..\asnstat" /I "..\..\..\..\asnlib" /I "..\..\..\..\access" /I "..\..\..\..\object" /I "..\..\..\..\cdromlib" /I "..\..\..\..\biostruc" /I "..\..\..\..\tools" /D "_CONSOLE" /D "WIN32" /D "_DEBUG" /YX /FD /GZ /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /pdb:none /debug /machine:I386
+# ADD LINK32 oldnames.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib wsock32.lib /nologo /subsystem:console /debug /machine:I386 /out:"DebugDLL/asnmacro.exe" /pdbtype:sept
+# SUBTRACT LINK32 /pdb:none
+# Begin Target
+
+# Name "demo_asnmacro - Win32 DebugDLL"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=..\..\..\..\demo\asnmacro.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\link\mswin\asnmacro.rc
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# End Group
+# End Target
+# End Project
diff --git a/make/msvc_prj/demo/cleanasn/demo_cleanasn.dsp b/make/msvc_prj/demo/cleanasn/demo_cleanasn.dsp
new file mode 100644
index 00000000..9a374b1e
--- /dev/null
+++ b/make/msvc_prj/demo/cleanasn/demo_cleanasn.dsp
@@ -0,0 +1,75 @@
+# Microsoft Developer Studio Project File - Name="demo_cleanasn" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Application" 0x0101
+
+CFG=demo_cleanasn - Win32 DebugDLL
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "demo_cleanasn.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "demo_cleanasn.mak" CFG="demo_cleanasn - Win32 DebugDLL"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "demo_cleanasn - Win32 DebugDLL" (based on "Win32 (x86) Application")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "DebugDLL"
+# PROP BASE Intermediate_Dir "DebugDLL"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "DebugDLL"
+# PROP Intermediate_Dir "DebugDLL"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+LIB32=link.exe -lib
+# ADD BASE CPP /nologo /MDd /W3 /GX /Z7 /Od /D "WIN32" /D "_DEBUG" /D "_NETENT_" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# ADD CPP /nologo /MDd /W3 /GR /Z7 /Od /I "..\..\..\.." /I "..\..\..\..\corelib" /I "..\..\..\..\connect" /I "..\..\..\..\api" /I "..\..\..\..\asnstat" /I "..\..\..\..\asnlib" /I "..\..\..\..\access" /I "..\..\..\..\object" /I "..\..\..\..\cdromlib" /I "..\..\..\..\biostruc" /I "..\..\..\..\tools" /D "_CONSOLE" /D "WIN32" /D "_DEBUG" /YX /FD /GZ /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /pdb:none /debug /machine:I386
+# ADD LINK32 oldnames.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib  wsock32.lib /nologo /subsystem:console /debug /machine:I386 /out:"DebugDLL/cleanasn.exe" /pdbtype:sept
+# SUBTRACT LINK32 /pdb:none
+# Begin Target
+
+# Name "demo_cleanasn - Win32 DebugDLL"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=..\..\..\..\demo\cleanasn.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\link\mswin\cleanasn.rc
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# End Group
+# End Target
+# End Project
diff --git a/make/msvc_prj/demo/cspeedtest/demo_cspeedtest.dsp b/make/msvc_prj/demo/cspeedtest/demo_cspeedtest.dsp
new file mode 100644
index 00000000..cf9765d8
--- /dev/null
+++ b/make/msvc_prj/demo/cspeedtest/demo_cspeedtest.dsp
@@ -0,0 +1,75 @@
+# Microsoft Developer Studio Project File - Name="demo_cspeedtest" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Application" 0x0101
+
+CFG=demo_cspeedtest - Win32 DebugDLL
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "demo_cspeedtest.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "demo_cspeedtest.mak" CFG="demo_cspeedtest - Win32 DebugDLL"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "demo_cspeedtest - Win32 DebugDLL" (based on "Win32 (x86) Application")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "DebugDLL"
+# PROP BASE Intermediate_Dir "DebugDLL"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "DebugDLL"
+# PROP Intermediate_Dir "DebugDLL"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+LIB32=link.exe -lib
+# ADD BASE CPP /nologo /MDd /W3 /GX /Z7 /Od /D "WIN32" /D "_DEBUG" /D "_NETENT_" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# ADD CPP /nologo /MDd /W3 /GR /Z7 /Od /I "..\..\..\.." /I "..\..\..\..\corelib" /I "..\..\..\..\connect" /I "..\..\..\..\api" /I "..\..\..\..\asnstat" /I "..\..\..\..\asnlib" /I "..\..\..\..\access" /I "..\..\..\..\object" /I "..\..\..\..\cdromlib" /I "..\..\..\..\biostruc" /I "..\..\..\..\tools" /D "_CONSOLE" /D "WIN32" /D "_DEBUG" /YX /FD /GZ /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /pdb:none /debug /machine:I386
+# ADD LINK32 oldnames.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib  wsock32.lib /nologo /subsystem:console /debug /machine:I386 /out:"DebugDLL/cspeedtest.exe" /pdbtype:sept
+# SUBTRACT LINK32 /pdb:none
+# Begin Target
+
+# Name "demo_cspeedtest - Win32 DebugDLL"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=..\..\..\..\demo\cspeedtest.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\link\mswin\cspeedtest.rc
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# End Group
+# End Target
+# End Project
diff --git a/make/msvc_prj/demo/raw2delt/demo_raw2delt.dsp b/make/msvc_prj/demo/raw2delt/demo_raw2delt.dsp
new file mode 100644
index 00000000..2461fb32
--- /dev/null
+++ b/make/msvc_prj/demo/raw2delt/demo_raw2delt.dsp
@@ -0,0 +1,75 @@
+# Microsoft Developer Studio Project File - Name="demo_raw2delt" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Application" 0x0101
+
+CFG=demo_raw2delt - Win32 DebugDLL
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "demo_raw2delt.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "demo_raw2delt.mak" CFG="demo_raw2delt - Win32 DebugDLL"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "demo_raw2delt - Win32 DebugDLL" (based on "Win32 (x86) Application")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "DebugDLL"
+# PROP BASE Intermediate_Dir "DebugDLL"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "DebugDLL"
+# PROP Intermediate_Dir "DebugDLL"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+LIB32=link.exe -lib
+# ADD BASE CPP /nologo /MDd /W3 /GX /Z7 /Od /D "WIN32" /D "_DEBUG" /D "_NETENT_" /D "_WINDOWS" /D "_MBCS" /YX /FD /GZ /c
+# ADD CPP /nologo /MDd /W3 /GR /Z7 /Od /I "..\..\..\.." /I "..\..\..\..\corelib" /I "..\..\..\..\api" /I "..\..\..\..\asnstat" /I "..\..\..\..\asnlib" /I "..\..\..\..\access" /I "..\..\..\..\object" /D "_CONSOLE" /D "WIN32" /D "_DEBUG" /YX /FD /GZ /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /pdb:none /debug /machine:I386
+# ADD LINK32 oldnames.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib wsock32.lib /nologo /subsystem:console /debug /machine:I386 /out:"DebugDLL/raw2delt.exe" /pdbtype:sept
+# SUBTRACT LINK32 /pdb:none
+# Begin Target
+
+# Name "demo_raw2delt - Win32 DebugDLL"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=..\..\..\..\demo\raw2delt.c
+# End Source File
+# Begin Source File
+
+SOURCE=..\..\..\..\link\mswin\raw2delt.rc
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# End Group
+# End Target
+# End Project
diff --git a/make/msvc_prj/desktop/ncbidesk.dsp b/make/msvc_prj/desktop/ncbidesk.dsp
index 93abda1f..f51b52d9 100644
--- a/make/msvc_prj/desktop/ncbidesk.dsp
+++ b/make/msvc_prj/desktop/ncbidesk.dsp
@@ -165,6 +165,10 @@ SOURCE=..\..\..\desktop\layout.c
 # End Source File
 # Begin Source File
 
+SOURCE=..\..\..\desktop\macrodlg.c
+# End Source File
+# Begin Source File
+
 SOURCE=..\..\..\desktop\mapgene.c
 # End Source File
 # Begin Source File
@@ -385,6 +389,10 @@ SOURCE=..\..\..\desktop\legend.h
 # End Source File
 # Begin Source File
 
+SOURCE=..\..\..\desktop\macrodlg.h
+# End Source File
+# Begin Source File
+
 SOURCE=..\..\..\desktop\mapgene.h
 # End Source File
 # Begin Source File
diff --git a/make/msvc_prj/ncbi.dsw b/make/msvc_prj/ncbi.dsw
index 670b4705..64ef146b 100644
--- a/make/msvc_prj/ncbi.dsw
+++ b/make/msvc_prj/ncbi.dsw
@@ -90,6 +90,9 @@ Package=<4>
     Project_Dep_Name demo_checksub
     End Project Dependency
     Begin Project Dependency
+    Project_Dep_Name demo_cleanasn
+    End Project Dependency
+    Begin Project Dependency
     Project_Dep_Name demo_cnsgn
     End Project Dependency
     Begin Project Dependency
@@ -105,6 +108,9 @@ Package=<4>
     Project_Dep_Name demo_copymat
     End Project Dependency
     Begin Project Dependency
+    Project_Dep_Name demo_cspeedtest
+    End Project Dependency
+    Begin Project Dependency
     Project_Dep_Name demo_dosimple
     End Project Dependency
     Begin Project Dependency
@@ -284,6 +290,15 @@ Package=<4>
     Begin Project Dependency
     Project_Dep_Name test_regexp
     End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name demo_asnbarval
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name demo_raw2delt
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name demo_asnmacro
+    End Project Dependency
 }}}
 
 ###############################################################################
@@ -425,6 +440,12 @@ Package=<4>
     Begin Project Dependency
     Project_Dep_Name blastcompadj
     End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbimain
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name xconntest
+    End Project Dependency
 }}}
 
 ###############################################################################
@@ -783,6 +804,48 @@ Package=<4>
 
 ###############################################################################
 
+Project: "demo_asnmacro"=.\demo\asnmacro\demo_asnmacro.dsp - Package Owner=<4>
+
+Package=<5>
+{{{
+}}}
+
+Package=<4>
+{{{
+    Begin Project Dependency
+    Project_Dep_Name blast
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name blastapi
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name blastcompadj
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name netblast
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbitool
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbiobj
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name netcli
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbinacc
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbi
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbimain
+    End Project Dependency
+}}}
+
+###############################################################################
+
 Project: "demo_asnstrip"=.\demo\asnstrip\demo_asnstrip.dsp - Package Owner=<4>
 
 Package=<5>
@@ -1161,6 +1224,33 @@ Package=<4>
 
 ###############################################################################
 
+Project: "demo_cleanasn"=.\demo\cleanasn\demo_cleanasn.dsp - Package Owner=<4>
+
+Package=<5>
+{{{
+}}}
+
+Package=<4>
+{{{
+    Begin Project Dependency
+    Project_Dep_Name ncbitool
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbinacc
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbiobj
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbi
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbimain
+    End Project Dependency
+}}}
+
+###############################################################################
+
 Project: "demo_cnsgn"=.\demo\cnsgn\demo_cnsgn.dsp - Package Owner=<4>
 
 Package=<5>
@@ -1362,6 +1452,33 @@ Package=<4>
 
 ###############################################################################
 
+Project: "demo_cspeedtest"=.\demo\cspeedtest\demo_cspeedtest.dsp - Package Owner=<4>
+
+Package=<5>
+{{{
+}}}
+
+Package=<4>
+{{{
+    Begin Project Dependency
+    Project_Dep_Name ncbitool
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbinacc
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbiobj
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbi
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbimain
+    End Project Dependency
+}}}
+
+###############################################################################
+
 Project: "demo_dosimple"=.\demo\dosimple\demo_dosimple.dsp - Package Owner=<4>
 
 Package=<5>
@@ -2175,6 +2292,30 @@ Package=<4>
 
 ###############################################################################
 
+Project: "demo_raw2delt"=.\demo\raw2delt\demo_raw2delt.dsp - Package Owner=<4>
+
+Package=<5>
+{{{
+}}}
+
+Package=<4>
+{{{
+    Begin Project Dependency
+    Project_Dep_Name ncbimmdb
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbiobj
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbi
+    End Project Dependency
+    Begin Project Dependency
+    Project_Dep_Name ncbimain
+    End Project Dependency
+}}}
+
+###############################################################################
+
 Project: "demo_regexp"=.\regexp\demo\demo_regexp.dsp - Package Owner=<4>
 
 Package=<5>
@@ -2979,6 +3120,9 @@ Package=<4>
     Project_Dep_Name blastapi
     End Project Dependency
     Begin Project Dependency
+    Project_Dep_Name blastcompadj
+    End Project Dependency
+    Begin Project Dependency
     Project_Dep_Name ncbi
     End Project Dependency
 }}}
diff --git a/make/msvc_prj/object/ncbiobj.dsp b/make/msvc_prj/object/ncbiobj.dsp
index 6cb57bf1..cd60d2c5 100644
--- a/make/msvc_prj/object/ncbiobj.dsp
+++ b/make/msvc_prj/object/ncbiobj.dsp
@@ -207,6 +207,10 @@ SOURCE=..\..\..\api\lsqfetch.c
 # End Source File
 # Begin Source File
 
+SOURCE=..\..\..\api\macroapi.c
+# End Source File
+# Begin Source File
+
 SOURCE=..\..\..\api\maputil.c
 # End Source File
 # Begin Source File
@@ -291,6 +295,10 @@ SOURCE=..\..\..\object\objloc.c
 # End Source File
 # Begin Source File
 
+SOURCE=..\..\..\object\objmacro.c
+# End Source File
+# Begin Source File
+
 SOURCE=..\..\..\object\objmdrs.c
 # End Source File
 # Begin Source File
@@ -347,6 +355,10 @@ SOURCE=..\..\..\object\objsub.c
 # End Source File
 # Begin Source File
 
+SOURCE=..\..\..\object\objtable.c
+# End Source File
+# Begin Source File
+
 SOURCE=..\..\..\access\objtax3.c
 # End Source File
 # Begin Source File
@@ -435,6 +447,10 @@ SOURCE=..\..\..\api\sqnutil3.c
 # End Source File
 # Begin Source File
 
+SOURCE=..\..\..\api\sqnutil4.c
+# End Source File
+# Begin Source File
+
 SOURCE=..\..\..\access\strucapi.c
 # End Source File
 # Begin Source File
@@ -763,6 +779,10 @@ SOURCE=..\..\..\api\lsqfetch.h
 # End Source File
 # Begin Source File
 
+SOURCE=..\..\..\api\macroapi.h
+# End Source File
+# Begin Source File
+
 SOURCE=..\..\..\object\mapmime.h
 # End Source File
 # Begin Source File
@@ -875,6 +895,10 @@ SOURCE=..\..\..\object\objloc.h
 # End Source File
 # Begin Source File
 
+SOURCE=..\..\..\object\objmacro.h
+# End Source File
+# Begin Source File
+
 SOURCE=..\..\..\object\objmdrs.h
 # End Source File
 # Begin Source File
@@ -935,6 +959,10 @@ SOURCE=..\..\..\object\objsub.h
 # End Source File
 # Begin Source File
 
+SOURCE=..\..\..\object\objtable.h
+# End Source File
+# Begin Source File
+
 SOURCE=..\..\..\access\objtax3.h
 # End Source File
 # Begin Source File
diff --git a/make/xCode/ncbictoolkit/ncbictoolkit.xcodeproj/project.pbxproj b/make/xCode/ncbictoolkit/ncbictoolkit.xcodeproj/project.pbxproj
index 5b8c9cd0..d9d6fd01 100644
--- a/make/xCode/ncbictoolkit/ncbictoolkit.xcodeproj/project.pbxproj
+++ b/make/xCode/ncbictoolkit/ncbictoolkit.xcodeproj/project.pbxproj
@@ -7,6 +7,14 @@
 	objects = {
 
 /* Begin PBXBuildFile section */
+		3701072D0CCD3D410030B936 /* objtable.c in Sources */ = {isa = PBXBuildFile; fileRef = 3701072B0CCD3D410030B936 /* objtable.c */; };
+		3701072E0CCD3D410030B936 /* objtable.h in Headers */ = {isa = PBXBuildFile; fileRef = 3701072C0CCD3D410030B936 /* objtable.h */; };
+		371D8D6A0CFB6E3800170BF6 /* objmacro.c in Sources */ = {isa = PBXBuildFile; fileRef = 371D8D680CFB6E3800170BF6 /* objmacro.c */; };
+		371D8D6B0CFB6E3800170BF6 /* objmacro.h in Headers */ = {isa = PBXBuildFile; fileRef = 371D8D690CFB6E3800170BF6 /* objmacro.h */; };
+		371D8D6E0CFB6E7B00170BF6 /* macroapi.c in Sources */ = {isa = PBXBuildFile; fileRef = 371D8D6C0CFB6E7B00170BF6 /* macroapi.c */; };
+		371D8D6F0CFB6E7B00170BF6 /* macroapi.h in Headers */ = {isa = PBXBuildFile; fileRef = 371D8D6D0CFB6E7B00170BF6 /* macroapi.h */; };
+		371D8D720CFB6EBD00170BF6 /* macrodlg.c in Sources */ = {isa = PBXBuildFile; fileRef = 371D8D700CFB6EBD00170BF6 /* macrodlg.c */; };
+		371D8D730CFB6EBD00170BF6 /* macrodlg.h in Headers */ = {isa = PBXBuildFile; fileRef = 371D8D710CFB6EBD00170BF6 /* macrodlg.h */; };
 		373A56D80BA5EE190055ED6F /* split_query.c in Sources */ = {isa = PBXBuildFile; fileRef = 373A56D60BA5EE190055ED6F /* split_query.c */; };
 		373A56D90BA5EE190055ED6F /* split_query.h in Headers */ = {isa = PBXBuildFile; fileRef = 373A56D70BA5EE190055ED6F /* split_query.h */; };
 		37569ACC0B9E06AA00AD4AB8 /* objscoremat.c in Sources */ = {isa = PBXBuildFile; fileRef = 37569ACB0B9E06AA00AD4AB8 /* objscoremat.c */; };
@@ -16,6 +24,7 @@
 		377925DF0BBD631100A61171 /* index_ungapped.h in Headers */ = {isa = PBXBuildFile; fileRef = 377925DD0BBD631100A61171 /* index_ungapped.h */; };
 		377B18A50BA7302000CFED28 /* gencode_singleton.c in Sources */ = {isa = PBXBuildFile; fileRef = 377B18A30BA7302000CFED28 /* gencode_singleton.c */; };
 		377B18A60BA7302000CFED28 /* gencode_singleton.h in Headers */ = {isa = PBXBuildFile; fileRef = 377B18A40BA7302000CFED28 /* gencode_singleton.h */; };
+		379194780D2ED0700013E717 /* sqnutil4.c in Sources */ = {isa = PBXBuildFile; fileRef = 379194770D2ED0700013E717 /* sqnutil4.c */; };
 		379C4E2A0B4D973B0013063F /* netcnfg.c in Sources */ = {isa = PBXBuildFile; fileRef = 379C4E250B4D973B0013063F /* netcnfg.c */; };
 		379C4E2B0B4D973B0013063F /* netcnfg.h in Headers */ = {isa = PBXBuildFile; fileRef = 379C4E260B4D973B0013063F /* netcnfg.h */; };
 		37B126A90B6FF73000C686CA /* mla2api.c in Sources */ = {isa = PBXBuildFile; fileRef = 37B126A80B6FF73000C686CA /* mla2api.c */; };
@@ -1017,6 +1026,14 @@
 /* Begin PBXFileReference section */
 		089C1667FE841158C02AAC07 /* English */ = {isa = PBXFileReference; fileEncoding = 10; lastKnownFileType = text.plist.strings; name = English; path = English.lproj/InfoPlist.strings; sourceTree = "<group>"; };
 		08FB77AAFE841565C02AAC07 /* Carbon.framework */ = {isa = PBXFileReference; lastKnownFileType = wrapper.framework; name = Carbon.framework; path = /System/Library/Frameworks/Carbon.framework; sourceTree = "<absolute>"; };
+		3701072B0CCD3D410030B936 /* objtable.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = objtable.c; path = ../../../object/objtable.c; sourceTree = SOURCE_ROOT; };
+		3701072C0CCD3D410030B936 /* objtable.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = objtable.h; path = ../../../object/objtable.h; sourceTree = SOURCE_ROOT; };
+		371D8D680CFB6E3800170BF6 /* objmacro.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = objmacro.c; path = ../../../object/objmacro.c; sourceTree = SOURCE_ROOT; };
+		371D8D690CFB6E3800170BF6 /* objmacro.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = objmacro.h; path = ../../../object/objmacro.h; sourceTree = SOURCE_ROOT; };
+		371D8D6C0CFB6E7B00170BF6 /* macroapi.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = macroapi.c; path = ../../../api/macroapi.c; sourceTree = SOURCE_ROOT; };
+		371D8D6D0CFB6E7B00170BF6 /* macroapi.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = macroapi.h; path = ../../../api/macroapi.h; sourceTree = SOURCE_ROOT; };
+		371D8D700CFB6EBD00170BF6 /* macrodlg.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = macrodlg.c; path = ../../../desktop/macrodlg.c; sourceTree = SOURCE_ROOT; };
+		371D8D710CFB6EBD00170BF6 /* macrodlg.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = macrodlg.h; path = ../../../desktop/macrodlg.h; sourceTree = SOURCE_ROOT; };
 		373A56D60BA5EE190055ED6F /* split_query.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = split_query.c; path = ../../../algo/blast/core/split_query.c; sourceTree = SOURCE_ROOT; };
 		373A56D70BA5EE190055ED6F /* split_query.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = split_query.h; path = ../../../algo/blast/core/split_query.h; sourceTree = SOURCE_ROOT; };
 		37569ACB0B9E06AA00AD4AB8 /* objscoremat.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = objscoremat.c; path = ../../../object/objscoremat.c; sourceTree = SOURCE_ROOT; };
@@ -1026,6 +1043,7 @@
 		377925DD0BBD631100A61171 /* index_ungapped.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = index_ungapped.h; path = ../../../algo/blast/core/index_ungapped.h; sourceTree = SOURCE_ROOT; };
 		377B18A30BA7302000CFED28 /* gencode_singleton.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = gencode_singleton.c; path = ../../../algo/blast/core/gencode_singleton.c; sourceTree = SOURCE_ROOT; };
 		377B18A40BA7302000CFED28 /* gencode_singleton.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = gencode_singleton.h; path = ../../../algo/blast/core/gencode_singleton.h; sourceTree = SOURCE_ROOT; };
+		379194770D2ED0700013E717 /* sqnutil4.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = sqnutil4.c; path = ../../../api/sqnutil4.c; sourceTree = SOURCE_ROOT; };
 		379C4E250B4D973B0013063F /* netcnfg.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = netcnfg.c; path = ../../../network/vibnet/netcnfg.c; sourceTree = SOURCE_ROOT; };
 		379C4E260B4D973B0013063F /* netcnfg.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = netcnfg.h; path = ../../../network/vibnet/netcnfg.h; sourceTree = SOURCE_ROOT; };
 		37B126A80B6FF73000C686CA /* mla2api.c */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.c; name = mla2api.c; path = ../../../access/mla2api.c; sourceTree = SOURCE_ROOT; };
@@ -2303,6 +2321,8 @@
 				37ED9A2B0B41B49B00BA3806 /* lookup_util.h */,
 				37ED9A2D0B41B49B00BA3806 /* lookup_wrap.h */,
 				37ED9A860B41B49B00BA3806 /* lsqfetch.h */,
+				371D8D6D0CFB6E7B00170BF6 /* macroapi.h */,
+				371D8D710CFB6EBD00170BF6 /* macrodlg.h */,
 				37ED9B170B41B49C00BA3806 /* mapcn3d.h */,
 				37ED9CBF0B41B49D00BA3806 /* mapgene.h */,
 				37ED9D7B0B41B49D00BA3806 /* mapmime.h */,
@@ -2427,6 +2447,7 @@
 				37ED9D930B41B49D00BA3806 /* objgen.h */,
 				37ED9D950B41B49D00BA3806 /* objinsdseq.h */,
 				37ED9D970B41B49D00BA3806 /* objloc.h */,
+				371D8D690CFB6E3800170BF6 /* objmacro.h */,
 				37ED9D990B41B49D00BA3806 /* objmdrs.h */,
 				37ED9D9B0B41B49D00BA3806 /* objmedli.h */,
 				37ED9A8E0B41B49B00BA3806 /* objmgr.h */,
@@ -2447,6 +2468,7 @@
 				37ED9D590B41B49D00BA3806 /* objspell.h */,
 				37ED9DAC0B41B49D00BA3806 /* objsset.h */,
 				37ED9DAE0B41B49D00BA3806 /* objsub.h */,
+				3701072C0CCD3D410030B936 /* objtable.h */,
 				37ED9D620B41B49D00BA3806 /* objtax1.h */,
 				37ED99910B41B49B00BA3806 /* objtax3.h */,
 				37ED9DB00B41B49D00BA3806 /* objtseq.h */,
@@ -2802,6 +2824,7 @@
 				37ED9A810B41B49B00BA3806 /* jzcoll.c */,
 				37ED9A830B41B49B00BA3806 /* jzmisc.c */,
 				37ED9A850B41B49B00BA3806 /* lsqfetch.c */,
+				371D8D6C0CFB6E7B00170BF6 /* macroapi.c */,
 				37ED9A870B41B49B00BA3806 /* maputil.c */,
 				37ED9A890B41B49B00BA3806 /* mconsist.c */,
 				37ED9A8B0B41B49B00BA3806 /* needleman.c */,
@@ -2824,6 +2847,7 @@
 				37ED9AB00B41B49C00BA3806 /* sqnutil1.c */,
 				37ED9AB10B41B49C00BA3806 /* sqnutil2.c */,
 				37ED9AB20B41B49C00BA3806 /* sqnutil3.c */,
+				379194770D2ED0700013E717 /* sqnutil4.c */,
 				37ED9AB40B41B49C00BA3806 /* subutil.c */,
 				37ED9AB60B41B49C00BA3806 /* tofasta.c */,
 				37ED9AB80B41B49C00BA3806 /* tofile.c */,
@@ -3046,6 +3070,7 @@
 				37ED9CB70B41B49D00BA3806 /* ingengraph.c */,
 				37ED9CB90B41B49D00BA3806 /* ingenwin.c */,
 				37ED9CBB0B41B49D00BA3806 /* layout.c */,
+				371D8D700CFB6EBD00170BF6 /* macrodlg.c */,
 				37ED9CBE0B41B49D00BA3806 /* mapgene.c */,
 				37ED9CC00B41B49D00BA3806 /* medview.c */,
 				37ED9CC20B41B49D00BA3806 /* prtgene.c */,
@@ -3257,6 +3282,7 @@
 				37ED9D920B41B49D00BA3806 /* objgen.c */,
 				37ED9D940B41B49D00BA3806 /* objinsdseq.c */,
 				37ED9D960B41B49D00BA3806 /* objloc.c */,
+				371D8D680CFB6E3800170BF6 /* objmacro.c */,
 				37ED9D980B41B49D00BA3806 /* objmdrs.c */,
 				37ED9D9A0B41B49D00BA3806 /* objmedli.c */,
 				37ED9D9C0B41B49D00BA3806 /* objmime.c */,
@@ -3269,6 +3295,7 @@
 				37ED9DA90B41B49D00BA3806 /* objseq.c */,
 				37ED9DAB0B41B49D00BA3806 /* objsset.c */,
 				37ED9DAD0B41B49D00BA3806 /* objsub.c */,
+				3701072B0CCD3D410030B936 /* objtable.c */,
 				37ED9DAF0B41B49D00BA3806 /* objtseq.c */,
 			);
 			name = object;
@@ -3941,6 +3968,10 @@
 				373A56D90BA5EE190055ED6F /* split_query.h in Headers */,
 				377B18A60BA7302000CFED28 /* gencode_singleton.h in Headers */,
 				377925DF0BBD631100A61171 /* index_ungapped.h in Headers */,
+				3701072E0CCD3D410030B936 /* objtable.h in Headers */,
+				371D8D6B0CFB6E3800170BF6 /* objmacro.h in Headers */,
+				371D8D6F0CFB6E7B00170BF6 /* macroapi.h in Headers */,
+				371D8D730CFB6EBD00170BF6 /* macrodlg.h in Headers */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -4167,6 +4198,7 @@
 				37ED9FF10B41B4A000BA3806 /* sqnutil1.c in Sources */,
 				37ED9FF20B41B4A000BA3806 /* sqnutil2.c in Sources */,
 				37ED9FF30B41B4A000BA3806 /* sqnutil3.c in Sources */,
+				379194780D2ED0700013E717 /* sqnutil4.c in Sources */,
 				37ED9FF50B41B4A000BA3806 /* subutil.c in Sources */,
 				37ED9FF70B41B4A000BA3806 /* tofasta.c in Sources */,
 				37ED9FF90B41B4A000BA3806 /* tofile.c in Sources */,
@@ -4520,6 +4552,10 @@
 				377B18A50BA7302000CFED28 /* gencode_singleton.c in Sources */,
 				377925DE0BBD631100A61171 /* index_ungapped.c in Sources */,
 				37DA1FCF0C639E5700223E99 /* ncbi_types.c in Sources */,
+				3701072D0CCD3D410030B936 /* objtable.c in Sources */,
+				371D8D6A0CFB6E3800170BF6 /* objmacro.c in Sources */,
+				371D8D6E0CFB6E7B00170BF6 /* macroapi.c in Sources */,
+				371D8D720CFB6EBD00170BF6 /* macrodlg.c in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
diff --git a/network/id2arch/id2.asn b/network/id2arch/id2.asn
index 00db0250..f2bf2950 100644
--- a/network/id2arch/id2.asn
+++ b/network/id2arch/id2.asn
@@ -1,4 +1,4 @@
---$Revision: 1.20 $
+--$Revision: 1.21 $
 --********************************************************************
 --
 --  Network Id server network access
@@ -69,7 +69,8 @@ ID2-Request-Get-Seq-id ::= SEQUENCE {
                 gi      (1),    -- gi is preferred
                 text    (2),    -- text Seq-id (accession etc) is preferred
                 general (4),    -- general Seq-id is preferred
-                all     (127)   -- return all qualified Seq-ids of the sequence
+                all     (127),  -- return all qualified Seq-ids of the sequence
+                label   (128)   -- return a sequence string label as general id
         } DEFAULT any
 }
 
diff --git a/network/id2arch/id2.h b/network/id2arch/id2.h
index a76dd7ba..2092afb5 100644
--- a/network/id2arch/id2.h
+++ b/network/id2arch/id2.h
@@ -9,8 +9,8 @@
 #include <asn.h>
 #endif
 
-static char * asnfilename = "id2.h19";
-static AsnValxNode avnx[62] = {
+static char * asnfilename = "id2.h20";
+static AsnValxNode avnx[63] = {
     {20,"set-value" ,1,0.0,&avnx[1] } ,
     {20,"get-value" ,2,0.0,&avnx[2] } ,
     {20,"force-value" ,3,0.0,&avnx[3] } ,
@@ -29,49 +29,50 @@ static AsnValxNode avnx[62] = {
     {20,"mgc" ,16,0.0,&avnx[16] } ,
     {20,"hprd" ,32,0.0,&avnx[17] } ,
     {20,"sts" ,64,0.0,&avnx[18] } ,
-    {20,"trna" ,128,0.0,NULL } ,
+    {20,"trna" ,128,0.0,&avnx[19] } ,
+    {20,"exon" ,512,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
     {3,NULL,1,0.0,NULL } ,
     {3,NULL,1,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"none" ,0,0.0,&avnx[26] } ,
-    {20,"seq-map" ,1,0.0,&avnx[27] } ,
+    {20,"none" ,0,0.0,&avnx[27] } ,
+    {20,"seq-map" ,1,0.0,&avnx[28] } ,
     {20,"seq-data" ,2,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"warning" ,1,0.0,&avnx[30] } ,
-    {20,"failed-command" ,2,0.0,&avnx[31] } ,
-    {20,"failed-connection" ,3,0.0,&avnx[32] } ,
-    {20,"failed-server" ,4,0.0,&avnx[33] } ,
-    {20,"no-data" ,5,0.0,&avnx[34] } ,
-    {20,"restricted-data" ,6,0.0,&avnx[35] } ,
-    {20,"unsupported-command" ,7,0.0,&avnx[36] } ,
+    {20,"warning" ,1,0.0,&avnx[31] } ,
+    {20,"failed-command" ,2,0.0,&avnx[32] } ,
+    {20,"failed-connection" ,3,0.0,&avnx[33] } ,
+    {20,"failed-server" ,4,0.0,&avnx[34] } ,
+    {20,"no-data" ,5,0.0,&avnx[35] } ,
+    {20,"restricted-data" ,6,0.0,&avnx[36] } ,
+    {20,"unsupported-command" ,7,0.0,&avnx[37] } ,
     {20,"invalid-arguments" ,8,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"live" ,0,0.0,&avnx[39] } ,
-    {20,"suppressed-temp" ,1,0.0,&avnx[40] } ,
-    {20,"suppressed" ,2,0.0,&avnx[41] } ,
-    {20,"dead" ,3,0.0,&avnx[42] } ,
-    {20,"protected" ,4,0.0,&avnx[43] } ,
+    {20,"live" ,0,0.0,&avnx[40] } ,
+    {20,"suppressed-temp" ,1,0.0,&avnx[41] } ,
+    {20,"suppressed" ,2,0.0,&avnx[42] } ,
+    {20,"dead" ,3,0.0,&avnx[43] } ,
+    {20,"protected" ,4,0.0,&avnx[44] } ,
     {20,"withdrawn" ,5,0.0,NULL } ,
-    {20,"seq-entry" ,0,0.0,&avnx[45] } ,
-    {20,"seq-annot" ,1,0.0,&avnx[46] } ,
-    {20,"id2s-split-info" ,2,0.0,&avnx[47] } ,
+    {20,"seq-entry" ,0,0.0,&avnx[46] } ,
+    {20,"seq-annot" ,1,0.0,&avnx[47] } ,
+    {20,"id2s-split-info" ,2,0.0,&avnx[48] } ,
     {20,"id2s-chunk" ,3,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"asn-binary" ,0,0.0,&avnx[50] } ,
-    {20,"asn-text" ,1,0.0,&avnx[51] } ,
+    {20,"asn-binary" ,0,0.0,&avnx[51] } ,
+    {20,"asn-text" ,1,0.0,&avnx[52] } ,
     {20,"xml" ,2,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"none" ,0,0.0,&avnx[54] } ,
-    {20,"gzip" ,1,0.0,&avnx[55] } ,
-    {20,"nlmzip" ,2,0.0,&avnx[56] } ,
+    {20,"none" ,0,0.0,&avnx[55] } ,
+    {20,"gzip" ,1,0.0,&avnx[56] } ,
+    {20,"nlmzip" ,2,0.0,&avnx[57] } ,
     {20,"bzip2" ,3,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
     {3,NULL,0,0.0,NULL } ,
-    {20,"reply" ,0,0.0,&avnx[60] } ,
-    {20,"last-octet-string" ,1,0.0,&avnx[61] } ,
+    {20,"reply" ,0,0.0,&avnx[61] } ,
+    {20,"last-octet-string" ,1,0.0,&avnx[62] } ,
     {20,"nothing" ,2,0.0,NULL } };
 
 static AsnType atx[148] = {
@@ -124,7 +125,7 @@ static AsnType atx[148] = {
   {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[52]} ,
   {415, "ID2-Blob-Id" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[48],0,&atx[58]} ,
   {0, "sat" ,128,0,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[49]} ,
-  {0, "sub-sat" ,128,1,0,0,1,0,0,0,&avnx[19],&atx[8],&avnx[11],0,&atx[50]} ,
+  {0, "sub-sat" ,128,1,0,0,1,0,0,0,&avnx[20],&atx[8],&avnx[11],0,&atx[50]} ,
   {0, "sat-key" ,128,2,0,0,0,0,0,0,NULL,&atx[8],NULL,0,&atx[51]} ,
   {0, "version" ,128,3,0,1,0,0,0,0,NULL,&atx[8],NULL,0,NULL} ,
   {0, "resolve" ,128,1,0,0,0,0,0,0,NULL,&atx[20],&atx[53],0,NULL} ,
@@ -135,12 +136,12 @@ static AsnType atx[148] = {
   {0, "get-data" ,128,2,0,1,0,0,0,0,NULL,&atx[58],NULL,0,NULL} ,
   {416, "ID2-Get-Blob-Details" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[59],0,&atx[77]} ,
   {0, "location" ,128,0,0,1,0,0,0,0,NULL,&atx[1],NULL,0,&atx[60]} ,
-  {0, "seq-class-level" ,128,1,0,0,1,0,0,0,&avnx[20],&atx[8],NULL,0,&atx[61]} ,
-  {0, "descr-level" ,128,2,0,0,1,0,0,0,&avnx[21],&atx[8],NULL,0,&atx[62]} ,
-  {0, "descr-type-mask" ,128,3,0,0,1,0,0,0,&avnx[22],&atx[8],NULL,0,&atx[63]} ,
-  {0, "annot-type-mask" ,128,4,0,0,1,0,0,0,&avnx[23],&atx[8],NULL,0,&atx[64]} ,
-  {0, "feat-type-mask" ,128,5,0,0,1,0,0,0,&avnx[24],&atx[8],NULL,0,&atx[65]} ,
-  {0, "sequence-level" ,128,6,0,0,1,0,0,0,&avnx[28],&atx[19],&avnx[25],0,NULL} ,
+  {0, "seq-class-level" ,128,1,0,0,1,0,0,0,&avnx[21],&atx[8],NULL,0,&atx[61]} ,
+  {0, "descr-level" ,128,2,0,0,1,0,0,0,&avnx[22],&atx[8],NULL,0,&atx[62]} ,
+  {0, "descr-type-mask" ,128,3,0,0,1,0,0,0,&avnx[23],&atx[8],NULL,0,&atx[63]} ,
+  {0, "annot-type-mask" ,128,4,0,0,1,0,0,0,&avnx[24],&atx[8],NULL,0,&atx[64]} ,
+  {0, "feat-type-mask" ,128,5,0,0,1,0,0,0,&avnx[25],&atx[8],NULL,0,&atx[65]} ,
+  {0, "sequence-level" ,128,6,0,0,1,0,0,0,&avnx[29],&atx[19],&avnx[26],0,NULL} ,
   {0, "reget-blob" ,128,5,0,0,0,0,0,0,NULL,&atx[67],NULL,0,&atx[71]} ,
   {412, "ID2-Request-ReGet-Blob" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[68],0,&atx[72]} ,
   {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[69]} ,
@@ -158,7 +159,7 @@ static AsnType atx[148] = {
   {0, "error" ,128,2,0,1,0,0,0,0,NULL,&atx[17],&atx[81],0,&atx[86]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[82],NULL,0,NULL} ,
   {418, "ID2-Error" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[83],0,&atx[91]} ,
-  {0, "severity" ,128,0,0,0,0,0,0,0,NULL,&atx[19],&avnx[29],0,&atx[84]} ,
+  {0, "severity" ,128,0,0,0,0,0,0,0,NULL,&atx[19],&avnx[30],0,&atx[84]} ,
   {0, "retry-delay" ,128,1,0,1,0,0,0,0,NULL,&atx[8],NULL,0,&atx[85]} ,
   {0, "message" ,128,2,0,1,0,0,0,0,NULL,&atx[14],NULL,0,NULL} ,
   {0, "end-of-reply" ,128,3,0,1,0,0,0,0,NULL,&atx[23],NULL,0,&atx[87]} ,
@@ -179,27 +180,27 @@ static AsnType atx[148] = {
   {421, "ID2-Reply-Get-Blob-Id" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[102],0,&atx[111]} ,
   {0, "seq-id" ,128,0,0,0,0,0,0,0,NULL,&atx[0],NULL,0,&atx[103]} ,
   {0, "blob-id" ,128,1,0,1,0,0,0,0,NULL,&atx[47],NULL,0,&atx[104]} ,
-  {0, "split-version" ,128,2,0,0,1,0,0,0,&avnx[37],&atx[8],NULL,0,&atx[105]} ,
+  {0, "split-version" ,128,2,0,0,1,0,0,0,&avnx[38],&atx[8],NULL,0,&atx[105]} ,
   {0, "annot-info" ,128,3,0,1,0,0,0,0,NULL,&atx[17],&atx[106],0,&atx[107]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[3],NULL,0,NULL} ,
   {0, "end-of-reply" ,128,4,0,1,0,0,0,0,NULL,&atx[23],NULL,0,&atx[108]} ,
   {0, "blob-state" ,128,5,0,1,0,0,0,0,NULL,&atx[109],NULL,0,NULL} ,
-  {427, "ID2-Blob-State" ,1,0,0,0,0,0,0,0,NULL,&atx[19],&avnx[38],0,&atx[114]} ,
+  {427, "ID2-Blob-State" ,1,0,0,0,0,0,0,0,NULL,&atx[19],&avnx[39],0,&atx[114]} ,
   {0, "get-blob-seq-ids" ,128,5,0,0,0,0,0,0,NULL,&atx[111],NULL,0,&atx[121]} ,
   {422, "ID2-Reply-Get-Blob-Seq-ids" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[112],0,&atx[122]} ,
   {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[113]} ,
   {0, "ids" ,128,1,0,1,0,0,0,0,NULL,&atx[114],NULL,0,NULL} ,
   {428, "ID2-Reply-Data" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[115],0,&atx[143]} ,
-  {0, "data-type" ,128,0,0,0,1,0,0,0,&avnx[48],&atx[8],&avnx[44],0,&atx[116]} ,
-  {0, "data-format" ,128,1,0,0,1,0,0,0,&avnx[52],&atx[8],&avnx[49],0,&atx[117]} ,
-  {0, "data-compression" ,128,2,0,0,1,0,0,0,&avnx[57],&atx[8],&avnx[53],0,&atx[118]} ,
+  {0, "data-type" ,128,0,0,0,1,0,0,0,&avnx[49],&atx[8],&avnx[45],0,&atx[116]} ,
+  {0, "data-format" ,128,1,0,0,1,0,0,0,&avnx[53],&atx[8],&avnx[50],0,&atx[117]} ,
+  {0, "data-compression" ,128,2,0,0,1,0,0,0,&avnx[58],&atx[8],&avnx[54],0,&atx[118]} ,
   {0, "data" ,128,3,0,0,0,0,0,0,NULL,&atx[17],&atx[119],0,NULL} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[120],NULL,0,NULL} ,
   {304, "OCTET STRING" ,0,4,0,0,0,0,0,0,NULL,NULL,NULL,0,NULL} ,
   {0, "get-blob" ,128,6,0,0,0,0,0,0,NULL,&atx[122],NULL,0,&atx[126]} ,
   {423, "ID2-Reply-Get-Blob" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[123],0,&atx[127]} ,
   {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[124]} ,
-  {0, "split-version" ,128,1,0,0,1,0,0,0,&avnx[58],&atx[8],NULL,0,&atx[125]} ,
+  {0, "split-version" ,128,1,0,0,1,0,0,0,&avnx[59],&atx[8],NULL,0,&atx[125]} ,
   {0, "data" ,128,2,0,1,0,0,0,0,NULL,&atx[114],NULL,0,NULL} ,
   {0, "reget-blob" ,128,7,0,0,0,0,0,0,NULL,&atx[127],NULL,0,&atx[132]} ,
   {424, "ID2-Reply-ReGet-Blob" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[128],0,&atx[133]} ,
@@ -217,7 +218,7 @@ static AsnType atx[148] = {
   {0, "blob-id" ,128,0,0,0,0,0,0,0,NULL,&atx[47],NULL,0,&atx[140]} ,
   {0, "chunk-id" ,128,1,0,0,0,0,0,0,NULL,&atx[2],NULL,0,&atx[141]} ,
   {0, "data" ,128,2,0,1,0,0,0,0,NULL,&atx[114],NULL,0,NULL} ,
-  {0, "discard" ,128,5,0,1,0,0,0,0,NULL,&atx[19],&avnx[59],0,NULL} ,
+  {0, "discard" ,128,5,0,1,0,0,0,0,NULL,&atx[19],&avnx[60],0,NULL} ,
   {429, "ID2-Blob-Seq-ids" ,1,0,0,0,0,0,0,0,NULL,&atx[17],&atx[144],0,&atx[145]} ,
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[145],NULL,0,NULL} ,
   {430, "ID2-Blob-Seq-id" ,1,0,0,0,0,0,0,0,NULL,&atx[20],&atx[146],0,&atx[12]} ,
@@ -225,7 +226,7 @@ static AsnType atx[148] = {
   {0, "replaced" ,128,1,0,1,0,0,0,0,NULL,&atx[23],NULL,0,NULL} };
 
 static AsnModule ampx[1] = {
-  { "NCBI-ID2Access" , "id2.h19",&atx[0],NULL,NULL,0,0} };
+  { "NCBI-ID2Access" , "id2.h20",&atx[0],NULL,NULL,0,0} };
 
 static AsnValxNodePtr avn = avnx;
 static AsnTypePtr at = atx;
diff --git a/network/medarch/client/medutil.c b/network/medarch/client/medutil.c
index 0b81a201..ff59c9fd 100644
--- a/network/medarch/client/medutil.c
+++ b/network/medarch/client/medutil.c
@@ -28,7 +28,7 @@
 *   
 * Version Creation Date: 8/31/93
 *
-* $Revision: 6.21 $
+* $Revision: 6.23 $
 *
 * File Description:  Medline Utilities for MedArch
 *   Assumes user calls MedArchInit and Fini
@@ -44,6 +44,13 @@
 *
 * RCS Modification History:
 * $Log: medutil.c,v $
+* Revision 6.23  2007/12/04 23:29:22  bazhin
+* MergePubIds() renamed to MergeNonPubmedPubIds(). Merging is
+* limited to types DOI and OTHER only.
+*
+* Revision 6.22  2007/12/04 20:07:02  bazhin
+* Added ability to merge input article ids with ones from med server.
+*
 * Revision 6.21  2005/02/15 17:45:32  bazhin
 * Modified MedlineToISO() function: now in addition to Cit-art.Auth-list.ml
 * slot it also looks at Cit-art.Auth-list.Author.Person-id.ml one
@@ -587,6 +594,59 @@ void FindPub(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent)
     }
 }
 
+/**********************************************************/
+static void MergeNonPubmedPubIds(CitArtPtr new, CitArtPtr old)
+{
+    ValNodePtr vnpnew;
+    ValNodePtr vnpold;
+    ValNodePtr vnpoldprev;
+    ValNodePtr vnpoldnext;
+    DbtagPtr   dpnew;
+    DbtagPtr   dpold;
+
+    if(old->ids == NULL)
+        return;
+
+    vnpoldprev = NULL;
+    for(vnpold = old->ids; vnpold != NULL; vnpold = vnpoldnext)
+    {
+        vnpoldnext = vnpold->next;
+
+        if(vnpold->choice != ARTICLEID_DOI &&
+           vnpold->choice != ARTICLEID_OTHER)
+        {
+            vnpoldprev = vnpold;
+            continue;
+        }
+
+        for(vnpnew = new->ids; vnpnew != NULL; vnpnew = vnpnew->next)
+        {
+            if(vnpnew->choice != vnpold->choice)
+                continue;
+
+            if(vnpnew->choice != ARTICLEID_OTHER)
+                break;
+            dpnew = vnpnew->data.ptrvalue;
+            dpold = vnpold->data.ptrvalue;
+            if(StringCmp(dpold->db, dpnew->db) == 0)
+                break;
+        }
+
+        if(vnpnew != NULL)
+        {
+            vnpoldprev = vnpold;
+            continue;
+        }
+
+        vnpold->next = new->ids;
+        new->ids = vnpold;
+        if(vnpoldprev == NULL)
+            old->ids = vnpoldnext;
+        else
+            vnpoldprev->next = vnpoldnext;
+    }
+}
+
 /*****************************************************************************
 *
 *   FixPub(pub, fpop)
@@ -637,6 +697,9 @@ ValNodePtr FixPub(ValNodePtr pub, FindPubOptionPtr fpop)
                         if(ten_authors(pub->data.ptrvalue, tmp->data.ptrvalue))
                         {
                             fpop->fetches_succeeded++;
+                            if(fpop->merge_ids != FALSE)
+                                MergeNonPubmedPubIds(tmp->data.ptrvalue,
+                                                     pub->data.ptrvalue);
                             PubFree(pub);
                             pub = ValNodeNew(tmp);
                             pub->choice = PUB_PMid;
@@ -996,6 +1059,10 @@ ValNodePtr FixPubEquiv(ValNodePtr pube, FindPubOptionPtr fpop)
                         pube = FixPubEquivAppend(pube, tmp2, tmp);
                         tmp->next = new;
 
+                        if(fpop->merge_ids != FALSE)
+                            MergeNonPubmedPubIds(new->data.ptrvalue,
+                                                 citartptr->data.ptrvalue);
+
                         PubFree(citartptr);
                         citartptr = new;
                     }
diff --git a/network/medarch/client/medutil.h b/network/medarch/client/medutil.h
index daf20b22..88a2d90a 100644
--- a/network/medarch/client/medutil.h
+++ b/network/medarch/client/medutil.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 8/31/93
 *
-* $Revision: 6.2 $
+* $Revision: 6.3 $
 *
 * File Description:  * File Description:  Medline Utilities for MedArch
 *   Assumes user calls MedArchInit and Fini
@@ -45,6 +45,10 @@
 *
 * RCS Modification History:
 * $Log: medutil.h,v $
+* Revision 6.3  2007/12/04 20:06:35  bazhin
+* Added Boolean variable "merge_ids" to merge input article
+* ids with ones from med server.
+*
 * Revision 6.2  2003/03/25 19:14:50  bazhin
 * Function "ten_authors()" became public (from static).
 *
@@ -93,6 +97,9 @@ typedef struct findpubstr {
 		lookups_succeeded,  /* citartmatch worked */
 		fetches_attempted,  /* FetchPubs tried */
 		fetches_succeeded;  /* FetchPubs that worked */
+	Boolean merge_ids;	    /* If TRUE then merges Cit-art.ids from
+				       input Cit-sub and one gotten from
+				       med server. */
 } FindPubOption, PNTR FindPubOptionPtr;
 
                               /* SeqEntryExplore callback to fix all Pubs */
diff --git a/network/taxon1/taxon2/txcdproc.c b/network/taxon1/taxon2/txcdproc.c
index b7a11b97..98df8b42 100644
--- a/network/taxon1/taxon2/txcdproc.c
+++ b/network/taxon1/taxon2/txcdproc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   07/15/97
 *
-* $Revision: 1.17 $
+* $Revision: 1.18 $
 *
 * File Description: 
 *       API for Taxonomy service
@@ -44,6 +44,9 @@
 *
 * RCS Modification History:
 * $Log: txcdproc.c,v $
+* Revision 1.18  2007/09/14 18:28:47  soussov
+* fixes bug in init function (it now calls NetFini instead of TaxArchFini
+*
 * Revision 1.17  2006/07/13 17:14:49  bollin
 * use Uint4 instead of Uint2 for itemID values
 *
@@ -199,7 +202,7 @@ static Boolean TaxServInit(void)
 
     if (svcp == NULL) {
         ErrPostEx(SEV_ERROR, 0, 0, "NI_ServiceGet [%s] (%s)", ni_errlist[ni_errno], ni_errtext);
-        TaxServFini();
+        NetFini();
         return FALSE;
     }
 
diff --git a/object/objalign.c b/object/objalign.c
index b455e527..4f32cc5a 100644
--- a/object/objalign.c
+++ b/object/objalign.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.14 $
+* $Revision: 6.15 $
 *
 * File Description:  Object manager for module NCBI-Seqalign
 *
@@ -332,6 +332,7 @@ NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignFree (SeqAlignPtr sap)
 {
 	DenseDiagPtr ddp, ddpnext;
 	StdSegPtr ssp, sspnext;
+	ValNodePtr anp, next;
 	
     if (sap == NULL)
         return (SeqAlignPtr)NULL;
@@ -373,7 +374,16 @@ NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignFree (SeqAlignPtr sap)
             break;
     }
     ScoreSetFree(sap->score);
+    anp = sap->id;
+    while (anp != NULL) {
+        next = anp->next;
+        ObjectIdFree((ObjectIdPtr)anp->data.ptrvalue);
+        MemFree(anp);
+        anp = next;
+    }
+    /*
     AsnGenericChoiceSeqOfFree(sap -> id, (AsnOptFreeFunc) ObjectIdFree);
+    */
     AsnGenericUserSeqOfFree(sap -> ext, (AsnOptFreeFunc) UserObjectFree);
 	SeqLocSetFree(sap->bounds);
     SeqIdFree(sap->master);
@@ -397,6 +407,7 @@ NLM_EXTERN Boolean LIBCALL SeqAlignAsnWrite (SeqAlignPtr sap, AsnIoPtr aip, AsnT
     DenseDiagPtr ddp;
     StdSegPtr ssp;
     Boolean retval = FALSE;
+    ValNodePtr anp;
 
 	if (! loaded)
 	{
@@ -509,8 +520,18 @@ NLM_EXTERN Boolean LIBCALL SeqAlignAsnWrite (SeqAlignPtr sap, AsnIoPtr aip, AsnT
 	   {
 	   	ErrPostEx(SEV_ERROR,0,0,"ASN3: SeqAlign.id stripped");
 	   }
-	   else
-	    AsnGenericChoiceSeqOfAsnWrite(sap -> id, (AsnWriteFunc) ObjectIdAsnWrite, aip, SEQ_ALIGN_id, SEQ_ALIGN_id_E);
+	   else {
+			if (! AsnOpenStruct(aip, SEQ_ALIGN_id, (Pointer)sap->id)) goto erret;
+			anp = sap->id;
+			while (anp != NULL) {
+		        if (! ObjectIdAsnWrite((ObjectIdPtr)anp->data.ptrvalue, aip, SEQ_ALIGN_id_E)) goto erret;
+		        anp = anp->next;
+			}
+			if (! AsnCloseStruct(aip, SEQ_ALIGN_id, (Pointer)sap->id)) goto erret;
+			/*
+			AsnGenericChoiceSeqOfAsnWrite(sap -> id, (AsnWriteFunc) ObjectIdAsnWrite, aip, SEQ_ALIGN_id, SEQ_ALIGN_id_E);
+			*/
+	   }
 	}
 
 	if (sap->ext != NULL)
@@ -548,6 +569,8 @@ NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignAsnRead (AsnIoPtr aip, AsnTypePtr orig)
     DenseDiagPtr currddp = NULL, ddp;
     StdSegPtr currssp = NULL, ssp;
     Boolean isError = FALSE;
+	ValNodePtr anp, prev = NULL;
+	ObjectIdPtr oip;
 
 	if (! loaded)
 	{
@@ -669,7 +692,25 @@ NLM_EXTERN SeqAlignPtr LIBCALL SeqAlignAsnRead (AsnIoPtr aip, AsnTypePtr orig)
         }
         else if (atp == SEQ_ALIGN_id)
         {
+            if (AsnReadVal (aip, atp, &av) <= 0) goto erret;  /* START_STRUCT */
+            while ((atp = AsnReadId(aip, amp, atp)) == SEQ_ALIGN_id_E) {
+                oip = ObjectIdAsnRead (aip, atp);
+                if (oip == NULL) goto erret;
+                anp = ValNodeNew (NULL);
+                if (anp == NULL) goto erret;
+                anp->data.ptrvalue = (Pointer) oip;
+                if (sap->id == NULL) {
+                    sap->id = anp;
+                }
+                if (prev != NULL) {
+                    prev->next = anp;
+                }
+                prev = anp;
+            }
+            if (AsnReadVal (aip, atp, &av) <= 0) goto erret;  /* END_STRUCT */
+            /*
             sap->id = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ObjectIdAsnRead, (AsnOptFreeFunc) ObjectIdFree);
+            */
             if (sap->id == NULL)
                 goto erret;
         }
diff --git a/object/objfdef.c b/object/objfdef.c
index 586a2e6d..f3a2f62b 100644
--- a/object/objfdef.c
+++ b/object/objfdef.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 9/94
 *
-* $Revision: 6.32 $
+* $Revision: 6.36 $
 *
 * File Description:  Object manager for feature definitions
 *
@@ -613,8 +613,8 @@ static CharPtr featDefSetMemStr = "FeatDefGroupSet ::= {\n" \
 "{ typelabel \"mRNA\" , menulabel \"Mature Messenger RNA\" , featdef-key 6 , seqfeat-key 5 , entrygroup 2 , displaygroup 2 , molgroup na } ,\n" \
 "{ typelabel \"tRNA\" , menulabel \"Transfer RNA\" , featdef-key 7 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \
 "{ typelabel \"rRNA\" , menulabel \"Ribosomal RNA\" , featdef-key 8 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \
-"{ typelabel \"snRNA\" , menulabel \"Small Nuclear RNA\" , featdef-key 9 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \
-"{ typelabel \"scRNA\" , menulabel \"Small Cytoplasmic RNA\" , featdef-key 10 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \
+"{ typelabel \"snRNA\" , menulabel \"Small Nuclear RNA\" , featdef-key 9 , seqfeat-key 5 , entrygroup 0 , displaygroup 3 , molgroup na } ,\n" \
+"{ typelabel \"scRNA\" , menulabel \"Small Cytoplasmic RNA\" , featdef-key 10 , seqfeat-key 5 , entrygroup 0 , displaygroup 3 , molgroup na } ,\n" \
 "{ typelabel \"RNA\" , menulabel \"Other Types of RNA\" , featdef-key 11 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \
 "{ typelabel \"Cit\" , menulabel \"Bibliographic Citations\" , featdef-key 12 , seqfeat-key 6 , entrygroup 4 , displaygroup 4 , molgroup both } ,\n" \
 "{ typelabel \"Xref\" , menulabel \"Reference to Another Sequence\" , featdef-key 13 , seqfeat-key 7 , entrygroup 4 , displaygroup 4 , molgroup both } ,\n" \
@@ -694,10 +694,12 @@ static CharPtr featDefSetMemStr = "FeatDefGroupSet ::= {\n" \
 "{ typelabel \"mat_peptide\" , menulabel \"Mature Peptide\" , featdef-key 87 , seqfeat-key 4 , entrygroup 1 , displaygroup 1 , molgroup aa } ,\n" \
 "{ typelabel \"sig_peptide\" , menulabel \"Signal Peptide\" , featdef-key 88 , seqfeat-key 4 , entrygroup 1 , displaygroup 1 , molgroup aa } ,\n" \
 "{ typelabel \"transit_peptide\" , menulabel \"Transit Peptide\" , featdef-key 89 , seqfeat-key 4 , entrygroup 1 , displaygroup 1 , molgroup aa } ,\n" \
-"{ typelabel \"snoRNA\" , menulabel \"Small Nucleolar RNA\" , featdef-key 90 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \
+"{ typelabel \"snoRNA\" , menulabel \"Small Nucleolar RNA\" , featdef-key 90 , seqfeat-key 5 , entrygroup 0 , displaygroup 3 , molgroup na } ,\n" \
 "{ typelabel \"gap\" , menulabel \"Gap\" , featdef-key 91 , seqfeat-key 8 , entrygroup 0 , displaygroup 4 , molgroup na } ,\n" \
 "{ typelabel \"operon\" , menulabel \"Operon\" , featdef-key 92 , seqfeat-key 8 , entrygroup 1 , displaygroup 1 , molgroup na } ,\n" \
-"{ typelabel \"oriT\" , menulabel \"Origin of Transcription\" , featdef-key 93 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na  } } };\n";
+"{ typelabel \"oriT\" , menulabel \"Origin of Transcription\" , featdef-key 93 , seqfeat-key 8 , entrygroup 5 , displaygroup 5 , molgroup na } ,\n" \
+"{ typelabel \"ncRNA\" , menulabel \"Non-coding RNA\" , featdef-key 94 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na } ,\n" \
+"{ typelabel \"tmRNA\" , menulabel \"Transfer-messenger RNA\" , featdef-key 95 , seqfeat-key 5 , entrygroup 3 , displaygroup 3 , molgroup na  } } };\n";
 #endif
 
 /*****************************************************************************
@@ -930,8 +932,8 @@ NLM_EXTERN Uint1 LIBCALL FindFeatDefType(SeqFeatPtr sfp)
 				    if (rrp->ext.choice == 1) {
 				      name = (CharPtr) rrp->ext.value.ptrvalue;
 				      if (StringICmp (name, "misc_RNA") == 0) return FEATDEF_otherRNA;
-				      if (StringICmp (name, "ncRNA") == 0) return FEATDEF_otherRNA; /* FEATDEF_ncRNA */
-				      if (StringICmp (name, "tmRNA") == 0) return FEATDEF_otherRNA; /* FEATDEF_tmRNA */
+				      if (StringICmp (name, "ncRNA") == 0) return FEATDEF_ncRNA;
+				      if (StringICmp (name, "tmRNA") == 0) return FEATDEF_tmRNA;
 				    }
 					return FEATDEF_otherRNA;
 			}
@@ -1132,7 +1134,15 @@ protref:    if (prp->name != NULL)
 					}
 					break;
 				case 1:
-					label = (CharPtr)(trrp->ext.value.ptrvalue);
+          label = (CharPtr)(trrp->ext.value.ptrvalue);
+          if (StringCmp (label, "ncRNA") == 0 || StringCmp (label, "tmRNA") == 0 || StringCmp (label, "misc_RNA") == 0) {
+            for (gbp = sfp->qual; gbp != NULL; gbp = gbp->next) {
+              if (StringICmp ("product", gbp->qual) == 0) {
+						  	label = gbp->val;
+                break;
+              }
+            }
+          }
 					if (label != NULL) {
 					  if (StringStr(label, typelabel) != NULL)
 					  	prefix = NULL;
@@ -1415,7 +1425,6 @@ NLM_EXTERN Int2 LIBCALL FeatDefLabel (SeqFeatPtr sfp, CharPtr buf, Int2 buflen,
 {
 	Int2 len, i, diff;
 	CharPtr curr, typelabel, tmp;
-	Uint1 extras = 0;
 	Char tbuf[40];
 	ImpFeatPtr ifp;
 	FeatDefPtr fdp;
diff --git a/object/objgen.c b/object/objgen.c
index c32da8b2..2c2b5f61 100644
--- a/object/objgen.c
+++ b/object/objgen.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 1/1/91
 *
-* $Revision: 6.12 $
+* $Revision: 6.14 $
 *
 * File Description:  Object manager for module NCBI-General
 *
@@ -43,6 +43,12 @@
 *                      it is linked as a DLL).
 *
 * $Log: objgen.c,v $
+* Revision 6.14  2008/01/25 15:24:21  kans
+* in UserFieldAsnRead, finished implementing ints, reals, oss as list, does not need num in advance
+*
+* Revision 6.13  2008/01/24 23:05:55  kans
+*  User-field.strs stores strings as list, does not need num supplied in advance - have not done ints, reals, oss yet
+*
 * Revision 6.12  2005/05/18 17:30:16  bollin
 * added NameStdMatch and PersonIdMatch functions
 *
@@ -1849,6 +1855,7 @@ NLM_EXTERN UserFieldPtr LIBCALL UserFieldAsnRead (AsnIoPtr aip, AsnTypePtr orig)
     FloatHiPtr fp;
     UserFieldPtr ufpa, ufpb = NULL;
     UserObjectPtr uopa, uopb = NULL;
+    ValNodePtr vnp, first = NULL, last = NULL;
     static char * emsg1 = "Too many %s in UserField. line %ld",
         * emsg2 = "Too few %s in UserField. line %ld";
 
@@ -1901,108 +1908,174 @@ NLM_EXTERN UserFieldPtr LIBCALL UserFieldAsnRead (AsnIoPtr aip, AsnTypePtr orig)
     {
         ufp->choice = 7;
         if (AsnReadVal(aip, atp, &av) <= 0) goto erret;   /* start SEQUENCE OF */
-        ufp->data.ptrvalue = MemNew((size_t)(sizeof(CharPtr) * num));
-        if (ufp->data.ptrvalue == NULL)
-            goto erret;
-        cpp = (CharPtr PNTR) ufp->data.ptrvalue;
+
         while ((atp = AsnReadId(aip, amp, atp)) == USER_FIELD_data_strs_E)
         {
-            if (i >= num)
+            if (num > 0 && i >= num)
             {
                 ErrPost(CTX_NCBIOBJ,1, emsg1, "strs", aip->linenumber);
                 goto erret;
             }
             if (AsnReadVal(aip, atp, &av) <= 0) goto erret;
+            /*
             cpp[i] = (CharPtr)av.ptrvalue;
+            */
+            vnp = ValNodeAddStr (&last, 0, (CharPtr)av.ptrvalue);
+            if (first == NULL) {
+                first = vnp;
+            }
+            last = vnp;
             i++;
         }
         if (atp == NULL) goto erret;
-        if (i != num)
+        if (num > 0 && i != num)
         {
             ErrPost(CTX_NCBIOBJ,1, emsg2, "strs", aip->linenumber);
             goto erret;
         }
         if (AsnReadVal(aip, atp, &av) <= 0) goto erret;   /* end SEQUENCE OF */
+
+        num = i;
+        ufp->num = num;
+
+        ufp->data.ptrvalue = MemNew((size_t)(sizeof(CharPtr) * num));
+        cpp = (CharPtr PNTR) ufp->data.ptrvalue;
+        if (cpp == NULL) goto erret;
+        for (vnp = first, i = 0; vnp != NULL && i < num; vnp = vnp->next, i++) {
+            cpp [i] = (CharPtr) vnp->data.ptrvalue;
+        }
+
+        ValNodeFree (first);
     }
     else if (atp == USER_FIELD_data_ints)
     {
         ufp->choice = 8;
         if (AsnReadVal(aip, atp, &av) <= 0) goto erret;   /* start SEQUENCE OF */
-        ufp->data.ptrvalue = MemNew((size_t)(sizeof(Int4) * num));
-        ip = (Int4Ptr) ufp->data.ptrvalue;
-        if (ip == NULL) goto erret;
+
         while ((atp = AsnReadId(aip, amp, atp)) == USER_FIELD_data_ints_E)
         {
-            if (i >= num)
+            if (num > 0 && i >= num)
             {
                 ErrPost(CTX_NCBIOBJ,1, emsg1, "ints", aip->linenumber);
                 goto erret;
             }
             if (AsnReadVal(aip, atp, &av) <= 0) goto erret;
+            /*
             ip[i] = av.intvalue;
+            */
+            vnp = ValNodeAddInt (&last, 0, (Int4)av.intvalue);
+            if (first == NULL) {
+                first = vnp;
+            }
+            last = vnp;
             i++;
         }
         if (atp == NULL) goto erret;
-        if (i != num)
+        if (num > 0 && i != num)
         {
             ErrPost(CTX_NCBIOBJ,1, emsg2, "ints", aip->linenumber);
             goto erret;
         }
         if (AsnReadVal(aip, atp, &av) <= 0) goto erret;   /* end SEQUENCE OF */
+
+        num = i;
+        ufp->num = num;
+
+        ufp->data.ptrvalue = MemNew((size_t)(sizeof(Int4) * num));
+        ip = (Int4Ptr) ufp->data.ptrvalue;
+        if (ip == NULL) goto erret;
+        for (vnp = first, i = 0; vnp != NULL && i < num; vnp = vnp->next, i++) {
+            ip [i] = (Int4) vnp->data.intvalue;
+        }
+
+        ValNodeFree (first);
     }
     else if (atp == USER_FIELD_data_reals)
     {
         ufp->choice = 9;
         if (AsnReadVal(aip, atp, &av) <= 0) goto erret;   /* start SEQUENCE OF */
-        ufp->data.ptrvalue = MemNew((size_t)(sizeof(FloatHi) * num));
-        fp = (FloatHiPtr) ufp->data.ptrvalue;
-        if (fp == NULL)
-            goto erret;
+
         while ((atp = AsnReadId(aip, amp, atp)) == USER_FIELD_data_reals_E)
         {
-            if (i >= num)
+            if (num > 0 && i >= num)
             {
                 ErrPost(CTX_NCBIOBJ,1, emsg1, "reals", aip->linenumber);
                 goto erret;
             }
             if (AsnReadVal(aip, atp, &av) <= 0) goto erret;
+            /*
             fp[i] = av.realvalue;
+            */
+            vnp = ValNodeAddFloat (&last, 0, (FloatHi)av.realvalue);
+            if (first == NULL) {
+                first = vnp;
+            }
+            last = vnp;
             i++;
         }
         if (atp == NULL) goto erret;
-        if (i != num)
+        if (num > 0 && i != num)
         {
             ErrPost(CTX_NCBIOBJ,1, emsg2, "reals", aip->linenumber);
             goto erret;
         }
         if (AsnReadVal(aip, atp, &av) <= 0) goto erret;   /* end SEQUENCE OF */
+
+        num = i;
+        ufp->num = num;
+
+        ufp->data.ptrvalue = MemNew((size_t)(sizeof(FloatHi) * num));
+        fp = (FloatHiPtr) ufp->data.ptrvalue;
+        if (fp == NULL) goto erret;
+        for (vnp = first, i = 0; vnp != NULL && i < num; vnp = vnp->next, i++) {
+            fp [i] = (FloatHi) vnp->data.realvalue;
+        }
+
+        ValNodeFree (first);
     }
     else if (atp == USER_FIELD_data_oss)
     {
         ufp->choice = 10;
         if (AsnReadVal(aip, atp, &av) <= 0) goto erret;   /* start SEQUENCE OF */
-        ufp->data.ptrvalue = MemNew((size_t)(sizeof(ByteStorePtr) * num));
-        bpp = (ByteStorePtr PNTR) ufp->data.ptrvalue;
-        if (bpp == NULL)
-            goto erret;
+
         while ((atp = AsnReadId(aip, amp, atp)) == USER_FIELD_data_oss_E)
         {
-            if (i >= num)
+            if (num > 0 && i >= num)
             {
                 ErrPost(CTX_NCBIOBJ,1, emsg1, "oss", aip->linenumber);
                 goto erret;
             }
             if (AsnReadVal(aip, atp, &av) <= 0) goto erret;
+            /*
             bpp[i] = (ByteStorePtr)av.ptrvalue;
+            */
+            vnp = ValNodeAddPointer (&last, 0, (Pointer)av.ptrvalue);
+            if (first == NULL) {
+                first = vnp;
+            }
+            last = vnp;
             i++;
         }
         if (atp == NULL) goto erret;
-        if (i != num)
+        if (num > 0 && i != num)
         {
             ErrPost(CTX_NCBIOBJ,1, emsg2, "oss", aip->linenumber);
             goto erret;
         }
         if (AsnReadVal(aip, atp, &av) <= 0) goto erret;   /* end SEQUENCE OF */
+
+        num = i;
+        ufp->num = num;
+
+        ufp->data.ptrvalue = MemNew((size_t)(sizeof(ByteStorePtr) * num));
+        bpp = (ByteStorePtr PNTR) ufp->data.ptrvalue;
+        if (bpp == NULL) goto erret;
+
+        for (vnp = first, i = 0; vnp != NULL && i < num; vnp = vnp->next, i++) {
+            bpp [i] = (ByteStorePtr) vnp->data.ptrvalue;
+        }
+
+        ValNodeFree (first);
     }
     else if (atp == USER_FIELD_data_fields)
     {
diff --git a/object/objloc.c b/object/objloc.c
index a30f65be..1a9acc4c 100644
--- a/object/objloc.c
+++ b/object/objloc.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.10 $
+* $Revision: 6.11 $
 *
 * File Description:  Object manager for module NCBI-Seqloc
 *
@@ -41,6 +41,9 @@
 *
 *
 * $Log: objloc.c,v $
+* Revision 6.11  2007/10/04 14:30:35  madden
+* Fix typo in SeqIdDup
+*
 * Revision 6.10  2005/04/26 21:33:00  kans
 * added SEQID_GPIPE
 *
@@ -709,7 +712,7 @@ NLM_EXTERN SeqIdPtr LIBCALL SeqIdDup (SeqIdPtr oldid)
 			if (bt == NULL) return NULL;
 			bt->name = StringSave(at->name);
 			bt->accession = StringSave(at->accession);
-			bt->release = StringSave(bt->release);
+			bt->release = StringSave(at->release);
 			bt->version = at->version;
 			newid->data.ptrvalue = bt;
 			break;
diff --git a/object/objmacro.c b/object/objmacro.c
new file mode 100755
index 00000000..1e95379c
--- /dev/null
+++ b/object/objmacro.c
@@ -0,0 +1,10615 @@
+#include <asn.h>
+
+#define NLM_GENERATED_CODE_PROTO
+
+#include <objmacro.h>
+
+static Boolean loaded = FALSE;
+
+#include <asnmacro.h>
+
+#ifndef NLM_EXTERN_LOADS
+#define NLM_EXTERN_LOADS {}
+#endif
+
+NLM_EXTERN Boolean LIBCALL
+objmacroAsnLoad(void)
+{
+
+   if ( ! loaded) {
+      NLM_EXTERN_LOADS
+
+      if ( ! AsnLoad ())
+      return FALSE;
+      loaded = TRUE;
+   }
+
+   return TRUE;
+}
+
+
+
+/**************************************************
+*    Generated object loaders for Module NCBI-Macro
+*    Generated using ASNCODE Revision: 6.16 at Feb 22, 2008 12:57 PM
+*
+**************************************************/
+
+
+/**************************************************
+*
+*    AECRActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+AECRActionPtr LIBCALL
+AECRActionNew(void)
+{
+   AECRActionPtr ptr = MemNew((size_t) sizeof(AECRAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    AECRActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+AECRActionPtr LIBCALL
+AECRActionFree(AECRActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ActionChoiceFree(ptr -> action);
+   ConstraintChoiceSetFree(ptr -> constraint);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    AECRActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+AECRActionPtr LIBCALL
+AECRActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   AECRActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* AECRAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, AECR_ACTION);
+   } else {
+      atp = AsnLinkType(orig, AECR_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = AECRActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == AECR_ACTION_action) {
+      ptr -> action = ActionChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == AECR_ACTION_constraint) {
+      ptr -> constraint = ConstraintChoiceSetAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = AECRActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    AECRActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+AECRActionAsnWrite(AECRActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, AECR_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> action != NULL) {
+      if ( ! ActionChoiceAsnWrite(ptr -> action, aip, AECR_ACTION_action)) {
+         goto erret;
+      }
+   }
+   if (ptr -> constraint != NULL) {
+      if ( ! ConstraintChoiceSetAsnWrite(ptr -> constraint, aip, AECR_ACTION_constraint)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ParseActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+ParseActionPtr LIBCALL
+ParseActionNew(void)
+{
+   ParseActionPtr ptr = MemNew((size_t) sizeof(ParseAction));
+
+   ptr -> capitalization = 0;
+   ptr -> remove_from_parsed = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ParseActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+ParseActionPtr LIBCALL
+ParseActionFree(ParseActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   TextPortionFree(ptr -> portion);
+   ParseSrcFree(ptr -> src);
+   ParseDestFree(ptr -> dest);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ParseActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ParseActionPtr LIBCALL
+ParseActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ParseActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ParseAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, PARSE_ACTION);
+   } else {
+      atp = AsnLinkType(orig, PARSE_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ParseActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == PARSE_ACTION_portion) {
+      ptr -> portion = TextPortionAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PARSE_ACTION_src) {
+      ptr -> src = ParseSrcAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PARSE_ACTION_dest) {
+      ptr -> dest = ParseDestAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PARSE_ACTION_capitalization) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> capitalization = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PARSE_ACTION_remove_from_parsed) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> remove_from_parsed = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PARSE_ACTION_existing_text) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> existing_text = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ParseActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ParseActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ParseActionAsnWrite(ParseActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, PARSE_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> portion != NULL) {
+      if ( ! TextPortionAsnWrite(ptr -> portion, aip, PARSE_ACTION_portion)) {
+         goto erret;
+      }
+   }
+   if (ptr -> src != NULL) {
+      if ( ! ParseSrcAsnWrite(ptr -> src, aip, PARSE_ACTION_src)) {
+         goto erret;
+      }
+   }
+   if (ptr -> dest != NULL) {
+      if ( ! ParseDestAsnWrite(ptr -> dest, aip, PARSE_ACTION_dest)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> capitalization;
+   retval = AsnWrite(aip, PARSE_ACTION_capitalization,  &av);
+   av.boolvalue = ptr -> remove_from_parsed;
+   retval = AsnWrite(aip, PARSE_ACTION_remove_from_parsed,  &av);
+   av.intvalue = ptr -> existing_text;
+   retval = AsnWrite(aip, PARSE_ACTION_existing_text,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    MacroActionListFree()
+*
+**************************************************/
+NLM_EXTERN 
+MacroActionListPtr LIBCALL
+MacroActionListFree(MacroActionListPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericChoiceSeqOfFree(ptr, (AsnOptFreeFunc) MacroActionChoiceFree);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    MacroActionListAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MacroActionListPtr LIBCALL
+MacroActionListAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   MacroActionListPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MacroActionList ::= (self contained) */
+      atp = AsnReadId(aip, amp, MACRO_ACTION_LIST);
+   } else {
+      atp = AsnLinkType(orig, MACRO_ACTION_LIST);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) MacroActionChoiceAsnRead, (AsnOptFreeFunc) MacroActionChoiceFree);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = MacroActionListFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    MacroActionListAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MacroActionListAsnWrite(MacroActionListPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, MACRO_ACTION_LIST);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericChoiceSeqOfAsnWrite(ptr , (AsnWriteFunc) MacroActionChoiceAsnWrite, aip, atp, MACRO_ACTION_LIST_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    StringConstraintNew()
+*
+**************************************************/
+NLM_EXTERN 
+StringConstraintPtr LIBCALL
+StringConstraintNew(void)
+{
+   StringConstraintPtr ptr = MemNew((size_t) sizeof(StringConstraint));
+
+   ptr -> match_location = 1;
+   ptr -> case_sensitive = 0;
+   ptr -> whole_word = 0;
+   ptr -> not_present = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    StringConstraintFree()
+*
+**************************************************/
+NLM_EXTERN 
+StringConstraintPtr LIBCALL
+StringConstraintFree(StringConstraintPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> match_text);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    StringConstraintAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+StringConstraintPtr LIBCALL
+StringConstraintAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   StringConstraintPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* StringConstraint ::= (self contained) */
+      atp = AsnReadId(aip, amp, STRING_CONSTRAINT);
+   } else {
+      atp = AsnLinkType(orig, STRING_CONSTRAINT);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = StringConstraintNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == STRING_CONSTRAINT_match_text) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> match_text = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == CONSTRAINT_match_location) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> match_location = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == CONSTRAINT_case_sensitive) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> case_sensitive = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == STRING_CONSTRAINT_whole_word) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> whole_word = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == STRING_CONSTRAINT_not_present) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> not_present = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = StringConstraintFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    StringConstraintAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+StringConstraintAsnWrite(StringConstraintPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, STRING_CONSTRAINT);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> match_text != NULL) {
+      av.ptrvalue = ptr -> match_text;
+      retval = AsnWrite(aip, STRING_CONSTRAINT_match_text,  &av);
+   }
+   av.intvalue = ptr -> match_location;
+   retval = AsnWrite(aip, CONSTRAINT_match_location,  &av);
+   av.boolvalue = ptr -> case_sensitive;
+   retval = AsnWrite(aip, CONSTRAINT_case_sensitive,  &av);
+   av.boolvalue = ptr -> whole_word;
+   retval = AsnWrite(aip, STRING_CONSTRAINT_whole_word,  &av);
+   av.boolvalue = ptr -> not_present;
+   retval = AsnWrite(aip, STRING_CONSTRAINT_not_present,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    LocationConstraintNew()
+*
+**************************************************/
+NLM_EXTERN 
+LocationConstraintPtr LIBCALL
+LocationConstraintNew(void)
+{
+   LocationConstraintPtr ptr = MemNew((size_t) sizeof(LocationConstraint));
+
+   ptr -> strand = 0;
+   ptr -> seq_type = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    LocationConstraintFree()
+*
+**************************************************/
+NLM_EXTERN 
+LocationConstraintPtr LIBCALL
+LocationConstraintFree(LocationConstraintPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    LocationConstraintAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+LocationConstraintPtr LIBCALL
+LocationConstraintAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   LocationConstraintPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* LocationConstraint ::= (self contained) */
+      atp = AsnReadId(aip, amp, LOCATION_CONSTRAINT);
+   } else {
+      atp = AsnLinkType(orig, LOCATION_CONSTRAINT);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = LocationConstraintNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == LOCATION_CONSTRAINT_strand) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> strand = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == LOCATION_CONSTRAINT_seq_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> seq_type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = LocationConstraintFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    LocationConstraintAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+LocationConstraintAsnWrite(LocationConstraintPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, LOCATION_CONSTRAINT);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> strand;
+   retval = AsnWrite(aip, LOCATION_CONSTRAINT_strand,  &av);
+   av.intvalue = ptr -> seq_type;
+   retval = AsnWrite(aip, LOCATION_CONSTRAINT_seq_type,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    FeatQualLegalValNew()
+*
+**************************************************/
+NLM_EXTERN 
+FeatQualLegalValPtr LIBCALL
+FeatQualLegalValNew(void)
+{
+   FeatQualLegalValPtr ptr = MemNew((size_t) sizeof(FeatQualLegalVal));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    FeatQualLegalValFree()
+*
+**************************************************/
+NLM_EXTERN 
+FeatQualLegalValPtr LIBCALL
+FeatQualLegalValFree(FeatQualLegalValPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> val);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    FeatQualLegalValAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FeatQualLegalValPtr LIBCALL
+FeatQualLegalValAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   FeatQualLegalValPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FeatQualLegalVal ::= (self contained) */
+      atp = AsnReadId(aip, amp, FEAT_QUAL_LEGAL_VAL);
+   } else {
+      atp = AsnLinkType(orig, FEAT_QUAL_LEGAL_VAL);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = FeatQualLegalValNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == FEAT_QUAL_LEGAL_VAL_qual) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> qual = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEAT_QUAL_LEGAL_VAL_val) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> val = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = FeatQualLegalValFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    FeatQualLegalValAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FeatQualLegalValAsnWrite(FeatQualLegalValPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, FEAT_QUAL_LEGAL_VAL);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> qual;
+   retval = AsnWrite(aip, FEAT_QUAL_LEGAL_VAL_qual,  &av);
+   if (ptr -> val != NULL) {
+      av.ptrvalue = ptr -> val;
+      retval = AsnWrite(aip, FEAT_QUAL_LEGAL_VAL_val,  &av);
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    FeatQualLegalValChoiceFree()
+*
+**************************************************/
+NLM_EXTERN 
+FeatQualLegalValChoicePtr LIBCALL
+FeatQualLegalValChoiceFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case FeatQualLegalValChoice_qual:
+      FeatQualLegalValFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    FeatQualLegalValChoiceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FeatQualLegalValChoicePtr LIBCALL
+FeatQualLegalValChoiceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FeatQualLegalValChoice ::= (self contained) */
+      atp = AsnReadId(aip, amp, FEAT_QUAL_LEGAL_VAL_CHOICE);
+   } else {
+      atp = AsnLinkType(orig, FEAT_QUAL_LEGAL_VAL_CHOICE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == FEAT_QUAL_LEGAL_VAL_CHOICE_qual) {
+      choice = FeatQualLegalValChoice_qual;
+      func = (AsnReadFunc) FeatQualLegalValAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    FeatQualLegalValChoiceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FeatQualLegalValChoiceAsnWrite(FeatQualLegalValChoicePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, FEAT_QUAL_LEGAL_VAL_CHOICE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case FeatQualLegalValChoice_qual:
+      writetype = FEAT_QUAL_LEGAL_VAL_CHOICE_qual;
+      func = (AsnWriteFunc) FeatQualLegalValAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    FeatQualLegalSetFree()
+*
+**************************************************/
+NLM_EXTERN 
+FeatQualLegalSetPtr LIBCALL
+FeatQualLegalSetFree(FeatQualLegalSetPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericChoiceSeqOfFree(ptr, (AsnOptFreeFunc) FeatQualLegalValChoiceFree);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    FeatQualLegalSetAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FeatQualLegalSetPtr LIBCALL
+FeatQualLegalSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   FeatQualLegalSetPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FeatQualLegalSet ::= (self contained) */
+      atp = AsnReadId(aip, amp, FEAT_QUAL_LEGAL_SET);
+   } else {
+      atp = AsnLinkType(orig, FEAT_QUAL_LEGAL_SET);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) FeatQualLegalValChoiceAsnRead, (AsnOptFreeFunc) FeatQualLegalValChoiceFree);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = FeatQualLegalSetFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    FeatQualLegalSetAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FeatQualLegalSetAsnWrite(FeatQualLegalSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, FEAT_QUAL_LEGAL_SET);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericChoiceSeqOfAsnWrite(ptr , (AsnWriteFunc) FeatQualLegalValChoiceAsnWrite, aip, atp, FEAT_QUAL_LEGAL_SET_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    FeatQualChoiceFree()
+*
+**************************************************/
+NLM_EXTERN 
+FeatQualChoicePtr LIBCALL
+FeatQualChoiceFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case FeatQualChoice_illegal_qual:
+      StringConstraintFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    FeatQualChoiceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FeatQualChoicePtr LIBCALL
+FeatQualChoiceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FeatQualChoice ::= (self contained) */
+      atp = AsnReadId(aip, amp, FEAT_QUAL_CHOICE);
+   } else {
+      atp = AsnLinkType(orig, FEAT_QUAL_CHOICE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == FEAT_QUAL_CHOICE_legal_qual) {
+      choice = FeatQualChoice_legal_qual;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == FEAT_QUAL_CHOICE_illegal_qual) {
+      choice = FeatQualChoice_illegal_qual;
+      func = (AsnReadFunc) StringConstraintAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    FeatQualChoiceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FeatQualChoiceAsnWrite(FeatQualChoicePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, FEAT_QUAL_CHOICE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case FeatQualChoice_legal_qual:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, FEAT_QUAL_CHOICE_legal_qual, &av);
+      break;
+   case FeatQualChoice_illegal_qual:
+      writetype = FEAT_QUAL_CHOICE_illegal_qual;
+      func = (AsnWriteFunc) StringConstraintAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    FeatureFieldNew()
+*
+**************************************************/
+NLM_EXTERN 
+FeatureFieldPtr LIBCALL
+FeatureFieldNew(void)
+{
+   FeatureFieldPtr ptr = MemNew((size_t) sizeof(FeatureField));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    FeatureFieldFree()
+*
+**************************************************/
+NLM_EXTERN 
+FeatureFieldPtr LIBCALL
+FeatureFieldFree(FeatureFieldPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   FeatQualChoiceFree(ptr -> field);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    FeatureFieldAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FeatureFieldPtr LIBCALL
+FeatureFieldAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   FeatureFieldPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FeatureField ::= (self contained) */
+      atp = AsnReadId(aip, amp, FEATURE_FIELD);
+   } else {
+      atp = AsnLinkType(orig, FEATURE_FIELD);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = FeatureFieldNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == FEATURE_FIELD_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_FIELD_field) {
+      ptr -> field = FeatQualChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = FeatureFieldFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    FeatureFieldAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FeatureFieldAsnWrite(FeatureFieldPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, FEATURE_FIELD);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, FEATURE_FIELD_type,  &av);
+   if (ptr -> field != NULL) {
+      if ( ! FeatQualChoiceAsnWrite(ptr -> field, aip, FEATURE_FIELD_field)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    FeatureFieldLegalNew()
+*
+**************************************************/
+NLM_EXTERN 
+FeatureFieldLegalPtr LIBCALL
+FeatureFieldLegalNew(void)
+{
+   FeatureFieldLegalPtr ptr = MemNew((size_t) sizeof(FeatureFieldLegal));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    FeatureFieldLegalFree()
+*
+**************************************************/
+NLM_EXTERN 
+FeatureFieldLegalPtr LIBCALL
+FeatureFieldLegalFree(FeatureFieldLegalPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    FeatureFieldLegalAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FeatureFieldLegalPtr LIBCALL
+FeatureFieldLegalAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   FeatureFieldLegalPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FeatureFieldLegal ::= (self contained) */
+      atp = AsnReadId(aip, amp, FEATURE_FIELD_LEGAL);
+   } else {
+      atp = AsnLinkType(orig, FEATURE_FIELD_LEGAL);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = FeatureFieldLegalNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == FEATURE_FIELD_LEGAL_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_FIELD_LEGAL_field) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> field = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = FeatureFieldLegalFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    FeatureFieldLegalAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FeatureFieldLegalAsnWrite(FeatureFieldLegalPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, FEATURE_FIELD_LEGAL);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, FEATURE_FIELD_LEGAL_type,  &av);
+   av.intvalue = ptr -> field;
+   retval = AsnWrite(aip, FEATURE_FIELD_LEGAL_field,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    FeatureFieldPairNew()
+*
+**************************************************/
+NLM_EXTERN 
+FeatureFieldPairPtr LIBCALL
+FeatureFieldPairNew(void)
+{
+   FeatureFieldPairPtr ptr = MemNew((size_t) sizeof(FeatureFieldPair));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    FeatureFieldPairFree()
+*
+**************************************************/
+NLM_EXTERN 
+FeatureFieldPairPtr LIBCALL
+FeatureFieldPairFree(FeatureFieldPairPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   FeatQualChoiceFree(ptr -> field_from);
+   FeatQualChoiceFree(ptr -> field_to);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    FeatureFieldPairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FeatureFieldPairPtr LIBCALL
+FeatureFieldPairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   FeatureFieldPairPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FeatureFieldPair ::= (self contained) */
+      atp = AsnReadId(aip, amp, FEATURE_FIELD_PAIR);
+   } else {
+      atp = AsnLinkType(orig, FEATURE_FIELD_PAIR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = FeatureFieldPairNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == FEATURE_FIELD_PAIR_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_FIELD_PAIR_field_from) {
+      ptr -> field_from = FeatQualChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_FIELD_PAIR_field_to) {
+      ptr -> field_to = FeatQualChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = FeatureFieldPairFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    FeatureFieldPairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FeatureFieldPairAsnWrite(FeatureFieldPairPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, FEATURE_FIELD_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, FEATURE_FIELD_PAIR_type,  &av);
+   if (ptr -> field_from != NULL) {
+      if ( ! FeatQualChoiceAsnWrite(ptr -> field_from, aip, FEATURE_FIELD_PAIR_field_from)) {
+         goto erret;
+      }
+   }
+   if (ptr -> field_to != NULL) {
+      if ( ! FeatQualChoiceAsnWrite(ptr -> field_to, aip, FEATURE_FIELD_PAIR_field_to)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    SourceQualPairNew()
+*
+**************************************************/
+NLM_EXTERN 
+SourceQualPairPtr LIBCALL
+SourceQualPairNew(void)
+{
+   SourceQualPairPtr ptr = MemNew((size_t) sizeof(SourceQualPair));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    SourceQualPairFree()
+*
+**************************************************/
+NLM_EXTERN 
+SourceQualPairPtr LIBCALL
+SourceQualPairFree(SourceQualPairPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    SourceQualPairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SourceQualPairPtr LIBCALL
+SourceQualPairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   SourceQualPairPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SourceQualPair ::= (self contained) */
+      atp = AsnReadId(aip, amp, SOURCE_QUAL_PAIR);
+   } else {
+      atp = AsnLinkType(orig, SOURCE_QUAL_PAIR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = SourceQualPairNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == SOURCE_QUAL_PAIR_field_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> field_from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SOURCE_QUAL_PAIR_field_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> field_to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = SourceQualPairFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    SourceQualPairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SourceQualPairAsnWrite(SourceQualPairPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, SOURCE_QUAL_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> field_from;
+   retval = AsnWrite(aip, SOURCE_QUAL_PAIR_field_from,  &av);
+   av.intvalue = ptr -> field_to;
+   retval = AsnWrite(aip, SOURCE_QUAL_PAIR_field_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    SourceQualChoiceFree()
+*
+**************************************************/
+NLM_EXTERN 
+SourceQualChoicePtr LIBCALL
+SourceQualChoiceFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    SourceQualChoiceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SourceQualChoicePtr LIBCALL
+SourceQualChoiceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SourceQualChoice ::= (self contained) */
+      atp = AsnReadId(aip, amp, SOURCE_QUAL_CHOICE);
+   } else {
+      atp = AsnLinkType(orig, SOURCE_QUAL_CHOICE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == SOURCE_QUAL_CHOICE_textqual) {
+      choice = SourceQualChoice_textqual;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == SOURCE_QUAL_CHOICE_location) {
+      choice = SourceQualChoice_location;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == SOURCE_QUAL_CHOICE_origin) {
+      choice = SourceQualChoice_origin;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    SourceQualChoiceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SourceQualChoiceAsnWrite(SourceQualChoicePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, SOURCE_QUAL_CHOICE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case SourceQualChoice_textqual:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, SOURCE_QUAL_CHOICE_textqual, &av);
+      break;
+   case SourceQualChoice_location:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, SOURCE_QUAL_CHOICE_location, &av);
+      break;
+   case SourceQualChoice_origin:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, SOURCE_QUAL_CHOICE_origin, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtFieldPairNew()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtFieldPairPtr LIBCALL
+CDSGeneProtFieldPairNew(void)
+{
+   CDSGeneProtFieldPairPtr ptr = MemNew((size_t) sizeof(CDSGeneProtFieldPair));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtFieldPairFree()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtFieldPairPtr LIBCALL
+CDSGeneProtFieldPairFree(CDSGeneProtFieldPairPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtFieldPairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtFieldPairPtr LIBCALL
+CDSGeneProtFieldPairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CDSGeneProtFieldPairPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CDSGeneProtFieldPair ::= (self contained) */
+      atp = AsnReadId(aip, amp, CDSGENEPROT_FIELD_PAIR);
+   } else {
+      atp = AsnLinkType(orig, CDSGENEPROT_FIELD_PAIR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = CDSGeneProtFieldPairNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == FIELD_PAIR_field_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> field_from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == CDSGENEPROT_FIELD_PAIR_field_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> field_to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CDSGeneProtFieldPairFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CDSGeneProtFieldPairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CDSGeneProtFieldPairAsnWrite(CDSGeneProtFieldPairPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, CDSGENEPROT_FIELD_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> field_from;
+   retval = AsnWrite(aip, FIELD_PAIR_field_from,  &av);
+   av.intvalue = ptr -> field_to;
+   retval = AsnWrite(aip, CDSGENEPROT_FIELD_PAIR_field_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoFieldFree()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoFieldPtr LIBCALL
+MolinfoFieldFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    MolinfoFieldAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoFieldPtr LIBCALL
+MolinfoFieldAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MolinfoField ::= (self contained) */
+      atp = AsnReadId(aip, amp, MOLINFO_FIELD);
+   } else {
+      atp = AsnLinkType(orig, MOLINFO_FIELD);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == MOLINFO_FIELD_molecule) {
+      choice = MolinfoField_molecule;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == MOLINFO_FIELD_technique) {
+      choice = MolinfoField_technique;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == MOLINFO_FIELD_completedness) {
+      choice = MolinfoField_completedness;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == MOLINFO_FIELD_mol_class) {
+      choice = MolinfoField_mol_class;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == MOLINFO_FIELD_topology) {
+      choice = MolinfoField_topology;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == MOLINFO_FIELD_strand) {
+      choice = MolinfoField_strand;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    MolinfoFieldAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MolinfoFieldAsnWrite(MolinfoFieldPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, MOLINFO_FIELD);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case MolinfoField_molecule:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, MOLINFO_FIELD_molecule, &av);
+      break;
+   case MolinfoField_technique:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, MOLINFO_FIELD_technique, &av);
+      break;
+   case MolinfoField_completedness:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, MOLINFO_FIELD_completedness, &av);
+      break;
+   case MolinfoField_mol_class:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, MOLINFO_FIELD_mol_class, &av);
+      break;
+   case MolinfoField_topology:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, MOLINFO_FIELD_topology, &av);
+      break;
+   case MolinfoField_strand:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, MOLINFO_FIELD_strand, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    MolinfoMoleculePairNew()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoMoleculePairPtr LIBCALL
+MolinfoMoleculePairNew(void)
+{
+   MolinfoMoleculePairPtr ptr = MemNew((size_t) sizeof(MolinfoMoleculePair));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    MolinfoMoleculePairFree()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoMoleculePairPtr LIBCALL
+MolinfoMoleculePairFree(MolinfoMoleculePairPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    MolinfoMoleculePairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoMoleculePairPtr LIBCALL
+MolinfoMoleculePairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   MolinfoMoleculePairPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MolinfoMoleculePair ::= (self contained) */
+      atp = AsnReadId(aip, amp, MOLINFO_MOLECULE_PAIR);
+   } else {
+      atp = AsnLinkType(orig, MOLINFO_MOLECULE_PAIR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = MolinfoMoleculePairNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == MOLINFO_MOLECULE_PAIR_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == MOLINFO_MOLECULE_PAIR_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = MolinfoMoleculePairFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoMoleculePairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MolinfoMoleculePairAsnWrite(MolinfoMoleculePairPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, MOLINFO_MOLECULE_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> from;
+   retval = AsnWrite(aip, MOLINFO_MOLECULE_PAIR_from,  &av);
+   av.intvalue = ptr -> to;
+   retval = AsnWrite(aip, MOLINFO_MOLECULE_PAIR_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoTechniquePairNew()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoTechniquePairPtr LIBCALL
+MolinfoTechniquePairNew(void)
+{
+   MolinfoTechniquePairPtr ptr = MemNew((size_t) sizeof(MolinfoTechniquePair));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    MolinfoTechniquePairFree()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoTechniquePairPtr LIBCALL
+MolinfoTechniquePairFree(MolinfoTechniquePairPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    MolinfoTechniquePairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoTechniquePairPtr LIBCALL
+MolinfoTechniquePairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   MolinfoTechniquePairPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MolinfoTechniquePair ::= (self contained) */
+      atp = AsnReadId(aip, amp, MOLINFO_TECHNIQUE_PAIR);
+   } else {
+      atp = AsnLinkType(orig, MOLINFO_TECHNIQUE_PAIR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = MolinfoTechniquePairNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == MOLINFO_TECHNIQUE_PAIR_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == MOLINFO_TECHNIQUE_PAIR_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = MolinfoTechniquePairFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoTechniquePairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MolinfoTechniquePairAsnWrite(MolinfoTechniquePairPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, MOLINFO_TECHNIQUE_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> from;
+   retval = AsnWrite(aip, MOLINFO_TECHNIQUE_PAIR_from,  &av);
+   av.intvalue = ptr -> to;
+   retval = AsnWrite(aip, MOLINFO_TECHNIQUE_PAIR_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoCompletednessPairNew()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoCompletednessPairPtr LIBCALL
+MolinfoCompletednessPairNew(void)
+{
+   MolinfoCompletednessPairPtr ptr = MemNew((size_t) sizeof(MolinfoCompletednessPair));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    MolinfoCompletednessPairFree()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoCompletednessPairPtr LIBCALL
+MolinfoCompletednessPairFree(MolinfoCompletednessPairPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    MolinfoCompletednessPairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoCompletednessPairPtr LIBCALL
+MolinfoCompletednessPairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   MolinfoCompletednessPairPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MolinfoCompletednessPair ::= (self contained) */
+      atp = AsnReadId(aip, amp, MOLINFO_COMPLETEDNESS_PAIR);
+   } else {
+      atp = AsnLinkType(orig, MOLINFO_COMPLETEDNESS_PAIR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = MolinfoCompletednessPairNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == MOLINFO_COMPLETEDNESS_PAIR_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == MOLINFO_COMPLETEDNESS_PAIR_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = MolinfoCompletednessPairFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoCompletednessPairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MolinfoCompletednessPairAsnWrite(MolinfoCompletednessPairPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, MOLINFO_COMPLETEDNESS_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> from;
+   retval = AsnWrite(aip, MOLINFO_COMPLETEDNESS_PAIR_from,  &av);
+   av.intvalue = ptr -> to;
+   retval = AsnWrite(aip, MOLINFO_COMPLETEDNESS_PAIR_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoMolClassPairNew()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoMolClassPairPtr LIBCALL
+MolinfoMolClassPairNew(void)
+{
+   MolinfoMolClassPairPtr ptr = MemNew((size_t) sizeof(MolinfoMolClassPair));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    MolinfoMolClassPairFree()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoMolClassPairPtr LIBCALL
+MolinfoMolClassPairFree(MolinfoMolClassPairPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    MolinfoMolClassPairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoMolClassPairPtr LIBCALL
+MolinfoMolClassPairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   MolinfoMolClassPairPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MolinfoMolClassPair ::= (self contained) */
+      atp = AsnReadId(aip, amp, MOLINFO_MOL_CLASS_PAIR);
+   } else {
+      atp = AsnLinkType(orig, MOLINFO_MOL_CLASS_PAIR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = MolinfoMolClassPairNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == MOLINFO_MOL_CLASS_PAIR_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == MOLINFO_MOL_CLASS_PAIR_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = MolinfoMolClassPairFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoMolClassPairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MolinfoMolClassPairAsnWrite(MolinfoMolClassPairPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, MOLINFO_MOL_CLASS_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> from;
+   retval = AsnWrite(aip, MOLINFO_MOL_CLASS_PAIR_from,  &av);
+   av.intvalue = ptr -> to;
+   retval = AsnWrite(aip, MOLINFO_MOL_CLASS_PAIR_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoTopologyPairNew()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoTopologyPairPtr LIBCALL
+MolinfoTopologyPairNew(void)
+{
+   MolinfoTopologyPairPtr ptr = MemNew((size_t) sizeof(MolinfoTopologyPair));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    MolinfoTopologyPairFree()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoTopologyPairPtr LIBCALL
+MolinfoTopologyPairFree(MolinfoTopologyPairPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    MolinfoTopologyPairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoTopologyPairPtr LIBCALL
+MolinfoTopologyPairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   MolinfoTopologyPairPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MolinfoTopologyPair ::= (self contained) */
+      atp = AsnReadId(aip, amp, MOLINFO_TOPOLOGY_PAIR);
+   } else {
+      atp = AsnLinkType(orig, MOLINFO_TOPOLOGY_PAIR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = MolinfoTopologyPairNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == MOLINFO_TOPOLOGY_PAIR_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == MOLINFO_TOPOLOGY_PAIR_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = MolinfoTopologyPairFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoTopologyPairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MolinfoTopologyPairAsnWrite(MolinfoTopologyPairPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, MOLINFO_TOPOLOGY_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> from;
+   retval = AsnWrite(aip, MOLINFO_TOPOLOGY_PAIR_from,  &av);
+   av.intvalue = ptr -> to;
+   retval = AsnWrite(aip, MOLINFO_TOPOLOGY_PAIR_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoStrandPairNew()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoStrandPairPtr LIBCALL
+MolinfoStrandPairNew(void)
+{
+   MolinfoStrandPairPtr ptr = MemNew((size_t) sizeof(MolinfoStrandPair));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    MolinfoStrandPairFree()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoStrandPairPtr LIBCALL
+MolinfoStrandPairFree(MolinfoStrandPairPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    MolinfoStrandPairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoStrandPairPtr LIBCALL
+MolinfoStrandPairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   MolinfoStrandPairPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MolinfoStrandPair ::= (self contained) */
+      atp = AsnReadId(aip, amp, MOLINFO_STRAND_PAIR);
+   } else {
+      atp = AsnLinkType(orig, MOLINFO_STRAND_PAIR);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = MolinfoStrandPairNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == MOLINFO_STRAND_PAIR_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == MOLINFO_STRAND_PAIR_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = MolinfoStrandPairFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoStrandPairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MolinfoStrandPairAsnWrite(MolinfoStrandPairPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, MOLINFO_STRAND_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> from;
+   retval = AsnWrite(aip, MOLINFO_STRAND_PAIR_from,  &av);
+   av.intvalue = ptr -> to;
+   retval = AsnWrite(aip, MOLINFO_STRAND_PAIR_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    MolinfoFieldPairFree()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoFieldPairPtr LIBCALL
+MolinfoFieldPairFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case MolinfoFieldPair_molecule:
+      MolinfoMoleculePairFree(anp -> data.ptrvalue);
+      break;
+   case MolinfoFieldPair_technique:
+      MolinfoTechniquePairFree(anp -> data.ptrvalue);
+      break;
+   case MolinfoFieldPair_completedness:
+      MolinfoCompletednessPairFree(anp -> data.ptrvalue);
+      break;
+   case MolinfoFieldPair_mol_class:
+      MolinfoMolClassPairFree(anp -> data.ptrvalue);
+      break;
+   case MolinfoFieldPair_topology:
+      MolinfoTopologyPairFree(anp -> data.ptrvalue);
+      break;
+   case MolinfoFieldPair_strand:
+      MolinfoStrandPairFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    MolinfoFieldPairAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MolinfoFieldPairPtr LIBCALL
+MolinfoFieldPairAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MolinfoFieldPair ::= (self contained) */
+      atp = AsnReadId(aip, amp, MOLINFO_FIELD_PAIR);
+   } else {
+      atp = AsnLinkType(orig, MOLINFO_FIELD_PAIR);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == MOLINFO_FIELD_PAIR_molecule) {
+      choice = MolinfoFieldPair_molecule;
+      func = (AsnReadFunc) MolinfoMoleculePairAsnRead;
+   }
+   else if (atp == MOLINFO_FIELD_PAIR_technique) {
+      choice = MolinfoFieldPair_technique;
+      func = (AsnReadFunc) MolinfoTechniquePairAsnRead;
+   }
+   else if (atp == FIELD_PAIR_completedness) {
+      choice = MolinfoFieldPair_completedness;
+      func = (AsnReadFunc) MolinfoCompletednessPairAsnRead;
+   }
+   else if (atp == MOLINFO_FIELD_PAIR_mol_class) {
+      choice = MolinfoFieldPair_mol_class;
+      func = (AsnReadFunc) MolinfoMolClassPairAsnRead;
+   }
+   else if (atp == MOLINFO_FIELD_PAIR_topology) {
+      choice = MolinfoFieldPair_topology;
+      func = (AsnReadFunc) MolinfoTopologyPairAsnRead;
+   }
+   else if (atp == MOLINFO_FIELD_PAIR_strand) {
+      choice = MolinfoFieldPair_strand;
+      func = (AsnReadFunc) MolinfoStrandPairAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    MolinfoFieldPairAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MolinfoFieldPairAsnWrite(MolinfoFieldPairPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, MOLINFO_FIELD_PAIR);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case MolinfoFieldPair_molecule:
+      writetype = MOLINFO_FIELD_PAIR_molecule;
+      func = (AsnWriteFunc) MolinfoMoleculePairAsnWrite;
+      break;
+   case MolinfoFieldPair_technique:
+      writetype = MOLINFO_FIELD_PAIR_technique;
+      func = (AsnWriteFunc) MolinfoTechniquePairAsnWrite;
+      break;
+   case MolinfoFieldPair_completedness:
+      writetype = FIELD_PAIR_completedness;
+      func = (AsnWriteFunc) MolinfoCompletednessPairAsnWrite;
+      break;
+   case MolinfoFieldPair_mol_class:
+      writetype = MOLINFO_FIELD_PAIR_mol_class;
+      func = (AsnWriteFunc) MolinfoMolClassPairAsnWrite;
+      break;
+   case MolinfoFieldPair_topology:
+      writetype = MOLINFO_FIELD_PAIR_topology;
+      func = (AsnWriteFunc) MolinfoTopologyPairAsnWrite;
+      break;
+   case MolinfoFieldPair_strand:
+      writetype = MOLINFO_FIELD_PAIR_strand;
+      func = (AsnWriteFunc) MolinfoStrandPairAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    SourceConstraintNew()
+*
+**************************************************/
+NLM_EXTERN 
+SourceConstraintPtr LIBCALL
+SourceConstraintNew(void)
+{
+   SourceConstraintPtr ptr = MemNew((size_t) sizeof(SourceConstraint));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    SourceConstraintFree()
+*
+**************************************************/
+NLM_EXTERN 
+SourceConstraintPtr LIBCALL
+SourceConstraintFree(SourceConstraintPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   SourceQualChoiceFree(ptr -> field1);
+   SourceQualChoiceFree(ptr -> field2);
+   StringConstraintFree(ptr -> constraint);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    SourceConstraintAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SourceConstraintPtr LIBCALL
+SourceConstraintAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   SourceConstraintPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SourceConstraint ::= (self contained) */
+      atp = AsnReadId(aip, amp, SOURCE_CONSTRAINT);
+   } else {
+      atp = AsnLinkType(orig, SOURCE_CONSTRAINT);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = SourceConstraintNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == SOURCE_CONSTRAINT_field1) {
+      ptr -> field1 = SourceQualChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SOURCE_CONSTRAINT_field2) {
+      ptr -> field2 = SourceQualChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SOURCE_CONSTRAINT_constraint) {
+      ptr -> constraint = StringConstraintAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == CONSTRAINT_type_constraint) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type_constraint = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = SourceConstraintFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    SourceConstraintAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SourceConstraintAsnWrite(SourceConstraintPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, SOURCE_CONSTRAINT);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> field1 != NULL) {
+      if ( ! SourceQualChoiceAsnWrite(ptr -> field1, aip, SOURCE_CONSTRAINT_field1)) {
+         goto erret;
+      }
+   }
+   if (ptr -> field2 != NULL) {
+      if ( ! SourceQualChoiceAsnWrite(ptr -> field2, aip, SOURCE_CONSTRAINT_field2)) {
+         goto erret;
+      }
+   }
+   if (ptr -> constraint != NULL) {
+      if ( ! StringConstraintAsnWrite(ptr -> constraint, aip, SOURCE_CONSTRAINT_constraint)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> type_constraint;
+   retval = AsnWrite(aip, CONSTRAINT_type_constraint,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    CDSGeneProtPseudoConstraintNew()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtPseudoConstraintPtr LIBCALL
+CDSGeneProtPseudoConstraintNew(void)
+{
+   CDSGeneProtPseudoConstraintPtr ptr = MemNew((size_t) sizeof(CDSGeneProtPseudoConstraint));
+
+   ptr -> is_pseudo = 1;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtPseudoConstraintFree()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtPseudoConstraintPtr LIBCALL
+CDSGeneProtPseudoConstraintFree(CDSGeneProtPseudoConstraintPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtPseudoConstraintAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtPseudoConstraintPtr LIBCALL
+CDSGeneProtPseudoConstraintAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CDSGeneProtPseudoConstraintPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CDSGeneProtPseudoConstraint ::= (self contained) */
+      atp = AsnReadId(aip, amp, CDSGENEPROT_PSEUDO_CONSTRAINT);
+   } else {
+      atp = AsnLinkType(orig, CDSGENEPROT_PSEUDO_CONSTRAINT);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = CDSGeneProtPseudoConstraintNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == PSEUDO_CONSTRAINT_feature) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> feature = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PSEUDO_CONSTRAINT_is_pseudo) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> is_pseudo = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CDSGeneProtPseudoConstraintFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CDSGeneProtPseudoConstraintAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CDSGeneProtPseudoConstraintAsnWrite(CDSGeneProtPseudoConstraintPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, CDSGENEPROT_PSEUDO_CONSTRAINT);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> feature;
+   retval = AsnWrite(aip, PSEUDO_CONSTRAINT_feature,  &av);
+   av.boolvalue = ptr -> is_pseudo;
+   retval = AsnWrite(aip, PSEUDO_CONSTRAINT_is_pseudo,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    CDSGeneProtConstraintFieldFree()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtConstraintFieldPtr LIBCALL
+CDSGeneProtConstraintFieldFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtConstraintFieldAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtConstraintFieldPtr LIBCALL
+CDSGeneProtConstraintFieldAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CDSGeneProtConstraintField ::= (self contained) */
+      atp = AsnReadId(aip, amp, CDSGENEPROT_CONSTRAINT_FIELD);
+   } else {
+      atp = AsnLinkType(orig, CDSGENEPROT_CONSTRAINT_FIELD);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == CONSTRAINT_FIELD_field) {
+      choice = CDSGeneProtConstraintField_field;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtConstraintFieldAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CDSGeneProtConstraintFieldAsnWrite(CDSGeneProtConstraintFieldPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, CDSGENEPROT_CONSTRAINT_FIELD);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case CDSGeneProtConstraintField_field:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, CONSTRAINT_FIELD_field, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtQualConstraintNew()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtQualConstraintPtr LIBCALL
+CDSGeneProtQualConstraintNew(void)
+{
+   CDSGeneProtQualConstraintPtr ptr = MemNew((size_t) sizeof(CDSGeneProtQualConstraint));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtQualConstraintFree()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtQualConstraintPtr LIBCALL
+CDSGeneProtQualConstraintFree(CDSGeneProtQualConstraintPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   CDSGeneProtConstraintFieldFree(ptr -> field1);
+   CDSGeneProtConstraintFieldFree(ptr -> field2);
+   StringConstraintFree(ptr -> constraint);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    CDSGeneProtQualConstraintAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CDSGeneProtQualConstraintPtr LIBCALL
+CDSGeneProtQualConstraintAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CDSGeneProtQualConstraintPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CDSGeneProtQualConstraint ::= (self contained) */
+      atp = AsnReadId(aip, amp, CDSGENEPROT_QUAL_CONSTRAINT);
+   } else {
+      atp = AsnLinkType(orig, CDSGENEPROT_QUAL_CONSTRAINT);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = CDSGeneProtQualConstraintNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == QUAL_CONSTRAINT_field1) {
+      ptr -> field1 = CDSGeneProtConstraintFieldAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == QUAL_CONSTRAINT_field2) {
+      ptr -> field2 = CDSGeneProtConstraintFieldAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == QUAL_CONSTRAINT_constraint) {
+      ptr -> constraint = StringConstraintAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CDSGeneProtQualConstraintFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CDSGeneProtQualConstraintAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CDSGeneProtQualConstraintAsnWrite(CDSGeneProtQualConstraintPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, CDSGENEPROT_QUAL_CONSTRAINT);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> field1 != NULL) {
+      if ( ! CDSGeneProtConstraintFieldAsnWrite(ptr -> field1, aip, QUAL_CONSTRAINT_field1)) {
+         goto erret;
+      }
+   }
+   if (ptr -> field2 != NULL) {
+      if ( ! CDSGeneProtConstraintFieldAsnWrite(ptr -> field2, aip, QUAL_CONSTRAINT_field2)) {
+         goto erret;
+      }
+   }
+   if (ptr -> constraint != NULL) {
+      if ( ! StringConstraintAsnWrite(ptr -> constraint, aip, QUAL_CONSTRAINT_constraint)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    SequenceConstraintMolTypeConstraintFree()
+*
+**************************************************/
+NLM_EXTERN 
+SequenceConstraintMolTypeConstraintPtr LIBCALL
+SequenceConstraintMolTypeConstraintFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    SequenceConstraintMolTypeConstraintAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SequenceConstraintMolTypeConstraintPtr LIBCALL
+SequenceConstraintMolTypeConstraintAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SequenceConstraintMolTypeConstraint ::= (self contained) */
+      atp = AsnReadId(aip, amp, CONSTRAINT_MOL_TYPE_CONSTRAINT);
+   } else {
+      atp = AsnLinkType(orig, CONSTRAINT_MOL_TYPE_CONSTRAINT);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == MOL_TYPE_CONSTRAINT_any) {
+      choice = SequenceConstraintMolTypeConstraint_any;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == MOL_TYPE_CONSTRAINT_nucleotide) {
+      choice = SequenceConstraintMolTypeConstraint_nucleotide;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == MOL_TYPE_CONSTRAINT_dna) {
+      choice = SequenceConstraintMolTypeConstraint_dna;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == MOL_TYPE_CONSTRAINT_rna) {
+      choice = SequenceConstraintMolTypeConstraint_rna;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == MOL_TYPE_CONSTRAINT_protein) {
+      choice = SequenceConstraintMolTypeConstraint_protein;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    SequenceConstraintMolTypeConstraintAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SequenceConstraintMolTypeConstraintAsnWrite(SequenceConstraintMolTypeConstraintPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, CONSTRAINT_MOL_TYPE_CONSTRAINT);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case SequenceConstraintMolTypeConstraint_any:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, MOL_TYPE_CONSTRAINT_any, &av);
+      break;
+   case SequenceConstraintMolTypeConstraint_nucleotide:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, MOL_TYPE_CONSTRAINT_nucleotide, &av);
+      break;
+   case SequenceConstraintMolTypeConstraint_dna:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, MOL_TYPE_CONSTRAINT_dna, &av);
+      break;
+   case SequenceConstraintMolTypeConstraint_rna:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, MOL_TYPE_CONSTRAINT_rna, &av);
+      break;
+   case SequenceConstraintMolTypeConstraint_protein:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, MOL_TYPE_CONSTRAINT_protein, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    SequenceConstraintNew()
+*
+**************************************************/
+NLM_EXTERN 
+SequenceConstraintPtr LIBCALL
+SequenceConstraintNew(void)
+{
+   SequenceConstraintPtr ptr = MemNew((size_t) sizeof(SequenceConstraint));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    SequenceConstraintFree()
+*
+**************************************************/
+NLM_EXTERN 
+SequenceConstraintPtr LIBCALL
+SequenceConstraintFree(SequenceConstraintPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   SequenceConstraintMolTypeConstraintFree(ptr -> seqtype);
+   StringConstraintFree(ptr -> id);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    SequenceConstraintAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SequenceConstraintPtr LIBCALL
+SequenceConstraintAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   SequenceConstraintPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SequenceConstraint ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQUENCE_CONSTRAINT);
+   } else {
+      atp = AsnLinkType(orig, SEQUENCE_CONSTRAINT);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = SequenceConstraintNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == SEQUENCE_CONSTRAINT_seqtype) {
+      ptr -> seqtype = SequenceConstraintMolTypeConstraintAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQUENCE_CONSTRAINT_id) {
+      ptr -> id = StringConstraintAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQUENCE_CONSTRAINT_feature) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> feature = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = SequenceConstraintFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    SequenceConstraintAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SequenceConstraintAsnWrite(SequenceConstraintPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, SEQUENCE_CONSTRAINT);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> seqtype != NULL) {
+      if ( ! SequenceConstraintMolTypeConstraintAsnWrite(ptr -> seqtype, aip, SEQUENCE_CONSTRAINT_seqtype)) {
+         goto erret;
+      }
+   }
+   if (ptr -> id != NULL) {
+      if ( ! StringConstraintAsnWrite(ptr -> id, aip, SEQUENCE_CONSTRAINT_id)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> feature;
+   retval = AsnWrite(aip, SEQUENCE_CONSTRAINT_feature,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ConstraintChoiceFree()
+*
+**************************************************/
+NLM_EXTERN 
+ConstraintChoicePtr LIBCALL
+ConstraintChoiceFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case ConstraintChoice_string:
+      StringConstraintFree(anp -> data.ptrvalue);
+      break;
+   case ConstraintChoice_location:
+      LocationConstraintFree(anp -> data.ptrvalue);
+      break;
+   case ConstraintChoice_source:
+      SourceConstraintFree(anp -> data.ptrvalue);
+      break;
+   case ConstraintChoice_cdsgeneprot_qual:
+      CDSGeneProtQualConstraintFree(anp -> data.ptrvalue);
+      break;
+   case ConstraintChoice_cdsgeneprot_pseudo:
+      CDSGeneProtPseudoConstraintFree(anp -> data.ptrvalue);
+      break;
+   case ConstraintChoice_sequence:
+      SequenceConstraintFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ConstraintChoiceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ConstraintChoicePtr LIBCALL
+ConstraintChoiceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ConstraintChoice ::= (self contained) */
+      atp = AsnReadId(aip, amp, CONSTRAINT_CHOICE);
+   } else {
+      atp = AsnLinkType(orig, CONSTRAINT_CHOICE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == CONSTRAINT_CHOICE_string) {
+      choice = ConstraintChoice_string;
+      func = (AsnReadFunc) StringConstraintAsnRead;
+   }
+   else if (atp == CONSTRAINT_CHOICE_location) {
+      choice = ConstraintChoice_location;
+      func = (AsnReadFunc) LocationConstraintAsnRead;
+   }
+   else if (atp == CONSTRAINT_CHOICE_source) {
+      choice = ConstraintChoice_source;
+      func = (AsnReadFunc) SourceConstraintAsnRead;
+   }
+   else if (atp == CHOICE_cdsgeneprot_qual) {
+      choice = ConstraintChoice_cdsgeneprot_qual;
+      func = (AsnReadFunc) CDSGeneProtQualConstraintAsnRead;
+   }
+   else if (atp == CHOICE_cdsgeneprot_pseudo) {
+      choice = ConstraintChoice_cdsgeneprot_pseudo;
+      func = (AsnReadFunc) CDSGeneProtPseudoConstraintAsnRead;
+   }
+   else if (atp == CONSTRAINT_CHOICE_sequence) {
+      choice = ConstraintChoice_sequence;
+      func = (AsnReadFunc) SequenceConstraintAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ConstraintChoiceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ConstraintChoiceAsnWrite(ConstraintChoicePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, CONSTRAINT_CHOICE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case ConstraintChoice_string:
+      writetype = CONSTRAINT_CHOICE_string;
+      func = (AsnWriteFunc) StringConstraintAsnWrite;
+      break;
+   case ConstraintChoice_location:
+      writetype = CONSTRAINT_CHOICE_location;
+      func = (AsnWriteFunc) LocationConstraintAsnWrite;
+      break;
+   case ConstraintChoice_source:
+      writetype = CONSTRAINT_CHOICE_source;
+      func = (AsnWriteFunc) SourceConstraintAsnWrite;
+      break;
+   case ConstraintChoice_cdsgeneprot_qual:
+      writetype = CHOICE_cdsgeneprot_qual;
+      func = (AsnWriteFunc) CDSGeneProtQualConstraintAsnWrite;
+      break;
+   case ConstraintChoice_cdsgeneprot_pseudo:
+      writetype = CHOICE_cdsgeneprot_pseudo;
+      func = (AsnWriteFunc) CDSGeneProtPseudoConstraintAsnWrite;
+      break;
+   case ConstraintChoice_sequence:
+      writetype = CONSTRAINT_CHOICE_sequence;
+      func = (AsnWriteFunc) SequenceConstraintAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ConstraintChoiceSetFree()
+*
+**************************************************/
+NLM_EXTERN 
+ConstraintChoiceSetPtr LIBCALL
+ConstraintChoiceSetFree(ConstraintChoiceSetPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericChoiceSeqOfFree(ptr, (AsnOptFreeFunc) ConstraintChoiceFree);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    ConstraintChoiceSetAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ConstraintChoiceSetPtr LIBCALL
+ConstraintChoiceSetAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ConstraintChoiceSetPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ConstraintChoiceSet ::= (self contained) */
+      atp = AsnReadId(aip, amp, CONSTRAINT_CHOICE_SET);
+   } else {
+      atp = AsnLinkType(orig, CONSTRAINT_CHOICE_SET);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) ConstraintChoiceAsnRead, (AsnOptFreeFunc) ConstraintChoiceFree);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ConstraintChoiceSetFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ConstraintChoiceSetAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ConstraintChoiceSetAsnWrite(ConstraintChoiceSetPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, CONSTRAINT_CHOICE_SET);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericChoiceSeqOfAsnWrite(ptr , (AsnWriteFunc) ConstraintChoiceAsnWrite, aip, atp, CONSTRAINT_CHOICE_SET_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    TextPortionNew()
+*
+**************************************************/
+NLM_EXTERN 
+TextPortionPtr LIBCALL
+TextPortionNew(void)
+{
+   TextPortionPtr ptr = MemNew((size_t) sizeof(TextPortion));
+
+   ptr -> case_sensitive = 0;
+   ptr -> whole_word = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    TextPortionFree()
+*
+**************************************************/
+NLM_EXTERN 
+TextPortionPtr LIBCALL
+TextPortionFree(TextPortionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> left_text);
+   MemFree(ptr -> right_text);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    TextPortionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+TextPortionPtr LIBCALL
+TextPortionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   TextPortionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* TextPortion ::= (self contained) */
+      atp = AsnReadId(aip, amp, TEXT_PORTION);
+   } else {
+      atp = AsnLinkType(orig, TEXT_PORTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = TextPortionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == TEXT_PORTION_left_text) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> left_text = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == TEXT_PORTION_include_left) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> include_left = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == TEXT_PORTION_right_text) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> right_text = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == TEXT_PORTION_include_right) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> include_right = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == TEXT_PORTION_inside) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> inside = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == TEXT_PORTION_case_sensitive) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> case_sensitive = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == TEXT_PORTION_whole_word) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> whole_word = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = TextPortionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    TextPortionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+TextPortionAsnWrite(TextPortionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, TEXT_PORTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> left_text != NULL) {
+      av.ptrvalue = ptr -> left_text;
+      retval = AsnWrite(aip, TEXT_PORTION_left_text,  &av);
+   }
+   av.boolvalue = ptr -> include_left;
+   retval = AsnWrite(aip, TEXT_PORTION_include_left,  &av);
+   if (ptr -> right_text != NULL) {
+      av.ptrvalue = ptr -> right_text;
+      retval = AsnWrite(aip, TEXT_PORTION_right_text,  &av);
+   }
+   av.boolvalue = ptr -> include_right;
+   retval = AsnWrite(aip, TEXT_PORTION_include_right,  &av);
+   av.boolvalue = ptr -> inside;
+   retval = AsnWrite(aip, TEXT_PORTION_inside,  &av);
+   av.boolvalue = ptr -> case_sensitive;
+   retval = AsnWrite(aip, TEXT_PORTION_case_sensitive,  &av);
+   av.boolvalue = ptr -> whole_word;
+   retval = AsnWrite(aip, TEXT_PORTION_whole_word,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    FieldEditNew()
+*
+**************************************************/
+NLM_EXTERN 
+FieldEditPtr LIBCALL
+FieldEditNew(void)
+{
+   FieldEditPtr ptr = MemNew((size_t) sizeof(FieldEdit));
+
+   ptr -> location = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    FieldEditFree()
+*
+**************************************************/
+NLM_EXTERN 
+FieldEditPtr LIBCALL
+FieldEditFree(FieldEditPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> find_txt);
+   MemFree(ptr -> repl_txt);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    FieldEditAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FieldEditPtr LIBCALL
+FieldEditAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   FieldEditPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FieldEdit ::= (self contained) */
+      atp = AsnReadId(aip, amp, FIELD_EDIT);
+   } else {
+      atp = AsnLinkType(orig, FIELD_EDIT);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = FieldEditNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == FIELD_EDIT_find_txt) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> find_txt = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FIELD_EDIT_repl_txt) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> repl_txt = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FIELD_EDIT_location) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> location = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = FieldEditFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    FieldEditAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FieldEditAsnWrite(FieldEditPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, FIELD_EDIT);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> find_txt != NULL) {
+      av.ptrvalue = ptr -> find_txt;
+      retval = AsnWrite(aip, FIELD_EDIT_find_txt,  &av);
+   }
+   if (ptr -> repl_txt != NULL) {
+      av.ptrvalue = ptr -> repl_txt;
+      retval = AsnWrite(aip, FIELD_EDIT_repl_txt,  &av);
+   }
+   av.intvalue = ptr -> location;
+   retval = AsnWrite(aip, FIELD_EDIT_location,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    FieldTypeFree()
+*
+**************************************************/
+NLM_EXTERN 
+FieldTypePtr LIBCALL
+FieldTypeFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case FieldType_source_qual:
+      SourceQualChoiceFree(anp -> data.ptrvalue);
+      break;
+   case FieldType_feature_field:
+      FeatureFieldFree(anp -> data.ptrvalue);
+      break;
+   case FieldType_molinfo_field:
+      MolinfoFieldFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    FieldTypeAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FieldTypePtr LIBCALL
+FieldTypeAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FieldType ::= (self contained) */
+      atp = AsnReadId(aip, amp, FIELD_TYPE);
+   } else {
+      atp = AsnLinkType(orig, FIELD_TYPE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == FIELD_TYPE_source_qual) {
+      choice = FieldType_source_qual;
+      func = (AsnReadFunc) SourceQualChoiceAsnRead;
+   }
+   else if (atp == FIELD_TYPE_feature_field) {
+      choice = FieldType_feature_field;
+      func = (AsnReadFunc) FeatureFieldAsnRead;
+   }
+   else if (atp == FIELD_TYPE_cds_gene_prot) {
+      choice = FieldType_cds_gene_prot;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == FIELD_TYPE_molinfo_field) {
+      choice = FieldType_molinfo_field;
+      func = (AsnReadFunc) MolinfoFieldAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    FieldTypeAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FieldTypeAsnWrite(FieldTypePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, FIELD_TYPE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case FieldType_source_qual:
+      writetype = FIELD_TYPE_source_qual;
+      func = (AsnWriteFunc) SourceQualChoiceAsnWrite;
+      break;
+   case FieldType_feature_field:
+      writetype = FIELD_TYPE_feature_field;
+      func = (AsnWriteFunc) FeatureFieldAsnWrite;
+      break;
+   case FieldType_cds_gene_prot:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, FIELD_TYPE_cds_gene_prot, &av);
+      break;
+   case FieldType_molinfo_field:
+      writetype = FIELD_TYPE_molinfo_field;
+      func = (AsnWriteFunc) MolinfoFieldAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    FieldPairTypeFree()
+*
+**************************************************/
+NLM_EXTERN 
+FieldPairTypePtr LIBCALL
+FieldPairTypeFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case FieldPairType_source_qual:
+      SourceQualPairFree(anp -> data.ptrvalue);
+      break;
+   case FieldPairType_feature_field:
+      FeatureFieldPairFree(anp -> data.ptrvalue);
+      break;
+   case FieldPairType_cds_gene_prot:
+      CDSGeneProtFieldPairFree(anp -> data.ptrvalue);
+      break;
+   case FieldPairType_molinfo_field:
+      MolinfoFieldPairFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    FieldPairTypeAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+FieldPairTypePtr LIBCALL
+FieldPairTypeAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* FieldPairType ::= (self contained) */
+      atp = AsnReadId(aip, amp, FIELD_PAIR_TYPE);
+   } else {
+      atp = AsnLinkType(orig, FIELD_PAIR_TYPE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == FIELD_PAIR_TYPE_source_qual) {
+      choice = FieldPairType_source_qual;
+      func = (AsnReadFunc) SourceQualPairAsnRead;
+   }
+   else if (atp == FIELD_PAIR_TYPE_feature_field) {
+      choice = FieldPairType_feature_field;
+      func = (AsnReadFunc) FeatureFieldPairAsnRead;
+   }
+   else if (atp == FIELD_PAIR_TYPE_cds_gene_prot) {
+      choice = FieldPairType_cds_gene_prot;
+      func = (AsnReadFunc) CDSGeneProtFieldPairAsnRead;
+   }
+   else if (atp == FIELD_PAIR_TYPE_molinfo_field) {
+      choice = FieldPairType_molinfo_field;
+      func = (AsnReadFunc) MolinfoFieldPairAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    FieldPairTypeAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+FieldPairTypeAsnWrite(FieldPairTypePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, FIELD_PAIR_TYPE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case FieldPairType_source_qual:
+      writetype = FIELD_PAIR_TYPE_source_qual;
+      func = (AsnWriteFunc) SourceQualPairAsnWrite;
+      break;
+   case FieldPairType_feature_field:
+      writetype = FIELD_PAIR_TYPE_feature_field;
+      func = (AsnWriteFunc) FeatureFieldPairAsnWrite;
+      break;
+   case FieldPairType_cds_gene_prot:
+      writetype = FIELD_PAIR_TYPE_cds_gene_prot;
+      func = (AsnWriteFunc) CDSGeneProtFieldPairAsnWrite;
+      break;
+   case FieldPairType_molinfo_field:
+      writetype = FIELD_PAIR_TYPE_molinfo_field;
+      func = (AsnWriteFunc) MolinfoFieldPairAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ApplyActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+ApplyActionPtr LIBCALL
+ApplyActionNew(void)
+{
+   ApplyActionPtr ptr = MemNew((size_t) sizeof(ApplyAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ApplyActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+ApplyActionPtr LIBCALL
+ApplyActionFree(ApplyActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   FieldTypeFree(ptr -> field);
+   MemFree(ptr -> value);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ApplyActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ApplyActionPtr LIBCALL
+ApplyActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ApplyActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ApplyAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, APPLY_ACTION);
+   } else {
+      atp = AsnLinkType(orig, APPLY_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ApplyActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == APPLY_ACTION_field) {
+      ptr -> field = FieldTypeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == APPLY_ACTION_value) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> value = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == APPLY_ACTION_existing_text) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> existing_text = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ApplyActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ApplyActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ApplyActionAsnWrite(ApplyActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, APPLY_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> field != NULL) {
+      if ( ! FieldTypeAsnWrite(ptr -> field, aip, APPLY_ACTION_field)) {
+         goto erret;
+      }
+   }
+   if (ptr -> value != NULL) {
+      av.ptrvalue = ptr -> value;
+      retval = AsnWrite(aip, APPLY_ACTION_value,  &av);
+   }
+   av.intvalue = ptr -> existing_text;
+   retval = AsnWrite(aip, APPLY_ACTION_existing_text,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    EditActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+EditActionPtr LIBCALL
+EditActionNew(void)
+{
+   EditActionPtr ptr = MemNew((size_t) sizeof(EditAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    EditActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+EditActionPtr LIBCALL
+EditActionFree(EditActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   FieldEditFree(ptr -> edit);
+   FieldTypeFree(ptr -> field);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    EditActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+EditActionPtr LIBCALL
+EditActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   EditActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* EditAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, EDIT_ACTION);
+   } else {
+      atp = AsnLinkType(orig, EDIT_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = EditActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == EDIT_ACTION_edit) {
+      ptr -> edit = FieldEditAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == EDIT_ACTION_field) {
+      ptr -> field = FieldTypeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = EditActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    EditActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+EditActionAsnWrite(EditActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, EDIT_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> edit != NULL) {
+      if ( ! FieldEditAsnWrite(ptr -> edit, aip, EDIT_ACTION_edit)) {
+         goto erret;
+      }
+   }
+   if (ptr -> field != NULL) {
+      if ( ! FieldTypeAsnWrite(ptr -> field, aip, EDIT_ACTION_field)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ConvertActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+ConvertActionPtr LIBCALL
+ConvertActionNew(void)
+{
+   ConvertActionPtr ptr = MemNew((size_t) sizeof(ConvertAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ConvertActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+ConvertActionPtr LIBCALL
+ConvertActionFree(ConvertActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   FieldPairTypeFree(ptr -> fields);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ConvertActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ConvertActionPtr LIBCALL
+ConvertActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ConvertActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ConvertAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, CONVERT_ACTION);
+   } else {
+      atp = AsnLinkType(orig, CONVERT_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ConvertActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == CONVERT_ACTION_fields) {
+      ptr -> fields = FieldPairTypeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == CONVERT_ACTION_existing_text) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> existing_text = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ConvertActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ConvertActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ConvertActionAsnWrite(ConvertActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, CONVERT_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> fields != NULL) {
+      if ( ! FieldPairTypeAsnWrite(ptr -> fields, aip, CONVERT_ACTION_fields)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> existing_text;
+   retval = AsnWrite(aip, CONVERT_ACTION_existing_text,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    CopyActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+CopyActionPtr LIBCALL
+CopyActionNew(void)
+{
+   CopyActionPtr ptr = MemNew((size_t) sizeof(CopyAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    CopyActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+CopyActionPtr LIBCALL
+CopyActionFree(CopyActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   FieldPairTypeFree(ptr -> fields);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    CopyActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CopyActionPtr LIBCALL
+CopyActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CopyActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CopyAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, COPY_ACTION);
+   } else {
+      atp = AsnLinkType(orig, COPY_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = CopyActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == COPY_ACTION_fields) {
+      ptr -> fields = FieldPairTypeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == COPY_ACTION_existing_text) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> existing_text = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CopyActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CopyActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CopyActionAsnWrite(CopyActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, COPY_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> fields != NULL) {
+      if ( ! FieldPairTypeAsnWrite(ptr -> fields, aip, COPY_ACTION_fields)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> existing_text;
+   retval = AsnWrite(aip, COPY_ACTION_existing_text,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    SwapActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+SwapActionPtr LIBCALL
+SwapActionNew(void)
+{
+   SwapActionPtr ptr = MemNew((size_t) sizeof(SwapAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    SwapActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+SwapActionPtr LIBCALL
+SwapActionFree(SwapActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   FieldPairTypeFree(ptr -> fields);
+   FieldTypeFree(ptr -> field_to);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    SwapActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SwapActionPtr LIBCALL
+SwapActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   SwapActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SwapAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, SWAP_ACTION);
+   } else {
+      atp = AsnLinkType(orig, SWAP_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = SwapActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == SWAP_ACTION_fields) {
+      ptr -> fields = FieldPairTypeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SWAP_ACTION_field_to) {
+      ptr -> field_to = FieldTypeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = SwapActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    SwapActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SwapActionAsnWrite(SwapActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, SWAP_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> fields != NULL) {
+      if ( ! FieldPairTypeAsnWrite(ptr -> fields, aip, SWAP_ACTION_fields)) {
+         goto erret;
+      }
+   }
+   if (ptr -> field_to != NULL) {
+      if ( ! FieldTypeAsnWrite(ptr -> field_to, aip, SWAP_ACTION_field_to)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    AECRParseActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+AECRParseActionPtr LIBCALL
+AECRParseActionNew(void)
+{
+   AECRParseActionPtr ptr = MemNew((size_t) sizeof(AECRParseAction));
+
+   ptr -> remove_from_parsed = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    AECRParseActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+AECRParseActionPtr LIBCALL
+AECRParseActionFree(AECRParseActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   TextPortionFree(ptr -> portion);
+   FieldPairTypeFree(ptr -> fields);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    AECRParseActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+AECRParseActionPtr LIBCALL
+AECRParseActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   AECRParseActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* AECRParseAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, AECRPARSE_ACTION);
+   } else {
+      atp = AsnLinkType(orig, AECRPARSE_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = AECRParseActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == AECRPARSE_ACTION_portion) {
+      ptr -> portion = TextPortionAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == AECRPARSE_ACTION_fields) {
+      ptr -> fields = FieldPairTypeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == ACTION_remove_from_parsed) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> remove_from_parsed = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == AECRPARSE_ACTION_existing_text) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> existing_text = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = AECRParseActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    AECRParseActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+AECRParseActionAsnWrite(AECRParseActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, AECRPARSE_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> portion != NULL) {
+      if ( ! TextPortionAsnWrite(ptr -> portion, aip, AECRPARSE_ACTION_portion)) {
+         goto erret;
+      }
+   }
+   if (ptr -> fields != NULL) {
+      if ( ! FieldPairTypeAsnWrite(ptr -> fields, aip, AECRPARSE_ACTION_fields)) {
+         goto erret;
+      }
+   }
+   av.boolvalue = ptr -> remove_from_parsed;
+   retval = AsnWrite(aip, ACTION_remove_from_parsed,  &av);
+   av.intvalue = ptr -> existing_text;
+   retval = AsnWrite(aip, AECRPARSE_ACTION_existing_text,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    RemoveActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+RemoveActionPtr LIBCALL
+RemoveActionNew(void)
+{
+   RemoveActionPtr ptr = MemNew((size_t) sizeof(RemoveAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    RemoveActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+RemoveActionPtr LIBCALL
+RemoveActionFree(RemoveActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   FieldTypeFree(ptr -> field);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    RemoveActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+RemoveActionPtr LIBCALL
+RemoveActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   RemoveActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* RemoveAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, REMOVE_ACTION);
+   } else {
+      atp = AsnLinkType(orig, REMOVE_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = RemoveActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == REMOVE_ACTION_field) {
+      ptr -> field = FieldTypeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = RemoveActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    RemoveActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+RemoveActionAsnWrite(RemoveActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, REMOVE_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> field != NULL) {
+      if ( ! FieldTypeAsnWrite(ptr -> field, aip, REMOVE_ACTION_field)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ActionChoiceFree()
+*
+**************************************************/
+NLM_EXTERN 
+ActionChoicePtr LIBCALL
+ActionChoiceFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case ActionChoice_apply:
+      ApplyActionFree(anp -> data.ptrvalue);
+      break;
+   case ActionChoice_edit:
+      EditActionFree(anp -> data.ptrvalue);
+      break;
+   case ActionChoice_convert:
+      ConvertActionFree(anp -> data.ptrvalue);
+      break;
+   case ActionChoice_copy:
+      CopyActionFree(anp -> data.ptrvalue);
+      break;
+   case ActionChoice_swap:
+      SwapActionFree(anp -> data.ptrvalue);
+      break;
+   case ActionChoice_remove:
+      RemoveActionFree(anp -> data.ptrvalue);
+      break;
+   case ActionChoice_parse:
+      AECRParseActionFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ActionChoiceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ActionChoicePtr LIBCALL
+ActionChoiceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ActionChoice ::= (self contained) */
+      atp = AsnReadId(aip, amp, ACTION_CHOICE);
+   } else {
+      atp = AsnLinkType(orig, ACTION_CHOICE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == ACTION_CHOICE_apply) {
+      choice = ActionChoice_apply;
+      func = (AsnReadFunc) ApplyActionAsnRead;
+   }
+   else if (atp == ACTION_CHOICE_edit) {
+      choice = ActionChoice_edit;
+      func = (AsnReadFunc) EditActionAsnRead;
+   }
+   else if (atp == ACTION_CHOICE_convert) {
+      choice = ActionChoice_convert;
+      func = (AsnReadFunc) ConvertActionAsnRead;
+   }
+   else if (atp == ACTION_CHOICE_copy) {
+      choice = ActionChoice_copy;
+      func = (AsnReadFunc) CopyActionAsnRead;
+   }
+   else if (atp == ACTION_CHOICE_swap) {
+      choice = ActionChoice_swap;
+      func = (AsnReadFunc) SwapActionAsnRead;
+   }
+   else if (atp == ACTION_CHOICE_remove) {
+      choice = ActionChoice_remove;
+      func = (AsnReadFunc) RemoveActionAsnRead;
+   }
+   else if (atp == ACTION_CHOICE_parse) {
+      choice = ActionChoice_parse;
+      func = (AsnReadFunc) AECRParseActionAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ActionChoiceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ActionChoiceAsnWrite(ActionChoicePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, ACTION_CHOICE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case ActionChoice_apply:
+      writetype = ACTION_CHOICE_apply;
+      func = (AsnWriteFunc) ApplyActionAsnWrite;
+      break;
+   case ActionChoice_edit:
+      writetype = ACTION_CHOICE_edit;
+      func = (AsnWriteFunc) EditActionAsnWrite;
+      break;
+   case ActionChoice_convert:
+      writetype = ACTION_CHOICE_convert;
+      func = (AsnWriteFunc) ConvertActionAsnWrite;
+      break;
+   case ActionChoice_copy:
+      writetype = ACTION_CHOICE_copy;
+      func = (AsnWriteFunc) CopyActionAsnWrite;
+      break;
+   case ActionChoice_swap:
+      writetype = ACTION_CHOICE_swap;
+      func = (AsnWriteFunc) SwapActionAsnWrite;
+      break;
+   case ActionChoice_remove:
+      writetype = ACTION_CHOICE_remove;
+      func = (AsnWriteFunc) RemoveActionAsnWrite;
+      break;
+   case ActionChoice_parse:
+      writetype = ACTION_CHOICE_parse;
+      func = (AsnWriteFunc) AECRParseActionAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ParseSrcOrgChoiceFree()
+*
+**************************************************/
+NLM_EXTERN 
+ParseSrcOrgChoicePtr LIBCALL
+ParseSrcOrgChoiceFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ParseSrcOrgChoiceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ParseSrcOrgChoicePtr LIBCALL
+ParseSrcOrgChoiceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ParseSrcOrgChoice ::= (self contained) */
+      atp = AsnReadId(aip, amp, PARSE_SRC_ORG_CHOICE);
+   } else {
+      atp = AsnLinkType(orig, PARSE_SRC_ORG_CHOICE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == SRC_ORG_CHOICE_source_qual) {
+      choice = ParseSrcOrgChoice_source_qual;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == CHOICE_taxname_after_binomial) {
+      choice = ParseSrcOrgChoice_taxname_after_binomial;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ParseSrcOrgChoiceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ParseSrcOrgChoiceAsnWrite(ParseSrcOrgChoicePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, PARSE_SRC_ORG_CHOICE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case ParseSrcOrgChoice_source_qual:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, SRC_ORG_CHOICE_source_qual, &av);
+      break;
+   case ParseSrcOrgChoice_taxname_after_binomial:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, CHOICE_taxname_after_binomial, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ParseSrcOrgNew()
+*
+**************************************************/
+NLM_EXTERN 
+ParseSrcOrgPtr LIBCALL
+ParseSrcOrgNew(void)
+{
+   ParseSrcOrgPtr ptr = MemNew((size_t) sizeof(ParseSrcOrg));
+
+   ptr -> type = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ParseSrcOrgFree()
+*
+**************************************************/
+NLM_EXTERN 
+ParseSrcOrgPtr LIBCALL
+ParseSrcOrgFree(ParseSrcOrgPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ParseSrcOrgChoiceFree(ptr -> field);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ParseSrcOrgAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ParseSrcOrgPtr LIBCALL
+ParseSrcOrgAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ParseSrcOrgPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ParseSrcOrg ::= (self contained) */
+      atp = AsnReadId(aip, amp, PARSE_SRC_ORG);
+   } else {
+      atp = AsnLinkType(orig, PARSE_SRC_ORG);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ParseSrcOrgNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == PARSE_SRC_ORG_field) {
+      ptr -> field = ParseSrcOrgChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PARSE_SRC_ORG_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ParseSrcOrgFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ParseSrcOrgAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ParseSrcOrgAsnWrite(ParseSrcOrgPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, PARSE_SRC_ORG);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> field != NULL) {
+      if ( ! ParseSrcOrgChoiceAsnWrite(ptr -> field, aip, PARSE_SRC_ORG_field)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, PARSE_SRC_ORG_type,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ParseSrcFree()
+*
+**************************************************/
+NLM_EXTERN 
+ParseSrcPtr LIBCALL
+ParseSrcFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case ParseSrc_org:
+      ParseSrcOrgFree(anp -> data.ptrvalue);
+      break;
+   case ParseSrc_structured_comment:
+      MemFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ParseSrcAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ParseSrcPtr LIBCALL
+ParseSrcAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ParseSrc ::= (self contained) */
+      atp = AsnReadId(aip, amp, PARSE_SRC);
+   } else {
+      atp = AsnLinkType(orig, PARSE_SRC);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == PARSE_SRC_defline) {
+      choice = ParseSrc_defline;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == PARSE_SRC_flatfile) {
+      choice = ParseSrc_flatfile;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == PARSE_SRC_local_id) {
+      choice = ParseSrc_local_id;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == PARSE_SRC_org) {
+      choice = ParseSrc_org;
+      func = (AsnReadFunc) ParseSrcOrgAsnRead;
+   }
+   else if (atp == PARSE_SRC_comment) {
+      choice = ParseSrc_comment;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == PARSE_SRC_bankit_comment) {
+      choice = ParseSrc_bankit_comment;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == PARSE_SRC_structured_comment) {
+      choice = ParseSrc_structured_comment;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.ptrvalue = av.ptrvalue;
+   }
+   else if (atp == PARSE_SRC_file_id) {
+      choice = ParseSrc_file_id;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ParseSrcAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ParseSrcAsnWrite(ParseSrcPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, PARSE_SRC);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case ParseSrc_defline:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, PARSE_SRC_defline, &av);
+      break;
+   case ParseSrc_flatfile:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, PARSE_SRC_flatfile, &av);
+      break;
+   case ParseSrc_local_id:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, PARSE_SRC_local_id, &av);
+      break;
+   case ParseSrc_org:
+      writetype = PARSE_SRC_org;
+      func = (AsnWriteFunc) ParseSrcOrgAsnWrite;
+      break;
+   case ParseSrc_comment:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, PARSE_SRC_comment, &av);
+      break;
+   case ParseSrc_bankit_comment:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, PARSE_SRC_bankit_comment, &av);
+      break;
+   case ParseSrc_structured_comment:
+      av.ptrvalue = anp->data.ptrvalue;
+      retval = AsnWrite(aip, PARSE_SRC_structured_comment, &av);
+      break;
+   case ParseSrc_file_id:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, PARSE_SRC_file_id, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ParseDstOrgNew()
+*
+**************************************************/
+NLM_EXTERN 
+ParseDstOrgPtr LIBCALL
+ParseDstOrgNew(void)
+{
+   ParseDstOrgPtr ptr = MemNew((size_t) sizeof(ParseDstOrg));
+
+   ptr -> type = 0;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ParseDstOrgFree()
+*
+**************************************************/
+NLM_EXTERN 
+ParseDstOrgPtr LIBCALL
+ParseDstOrgFree(ParseDstOrgPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   SourceQualChoiceFree(ptr -> field);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ParseDstOrgAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ParseDstOrgPtr LIBCALL
+ParseDstOrgAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ParseDstOrgPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ParseDstOrg ::= (self contained) */
+      atp = AsnReadId(aip, amp, PARSE_DST_ORG);
+   } else {
+      atp = AsnLinkType(orig, PARSE_DST_ORG);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ParseDstOrgNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == PARSE_DST_ORG_field) {
+      ptr -> field = SourceQualChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PARSE_DST_ORG_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ParseDstOrgFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ParseDstOrgAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ParseDstOrgAsnWrite(ParseDstOrgPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, PARSE_DST_ORG);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> field != NULL) {
+      if ( ! SourceQualChoiceAsnWrite(ptr -> field, aip, PARSE_DST_ORG_field)) {
+         goto erret;
+      }
+   }
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, PARSE_DST_ORG_type,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    ParseDestFree()
+*
+**************************************************/
+NLM_EXTERN 
+ParseDestPtr LIBCALL
+ParseDestFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case ParseDest_org:
+      ParseDstOrgFree(anp -> data.ptrvalue);
+      break;
+   case ParseDest_featqual:
+      FeatureFieldLegalFree(anp -> data.ptrvalue);
+      break;
+   case ParseDest_dbxref:
+      MemFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    ParseDestAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ParseDestPtr LIBCALL
+ParseDestAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ParseDest ::= (self contained) */
+      atp = AsnReadId(aip, amp, PARSE_DEST);
+   } else {
+      atp = AsnLinkType(orig, PARSE_DEST);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == PARSE_DEST_defline) {
+      choice = ParseDest_defline;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == PARSE_DEST_org) {
+      choice = ParseDest_org;
+      func = (AsnReadFunc) ParseDstOrgAsnRead;
+   }
+   else if (atp == PARSE_DEST_featqual) {
+      choice = ParseDest_featqual;
+      func = (AsnReadFunc) FeatureFieldLegalAsnRead;
+   }
+   else if (atp == PARSE_DEST_dbxref) {
+      choice = ParseDest_dbxref;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.ptrvalue = av.ptrvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    ParseDestAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ParseDestAsnWrite(ParseDestPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, PARSE_DEST);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case ParseDest_defline:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, PARSE_DEST_defline, &av);
+      break;
+   case ParseDest_org:
+      writetype = PARSE_DEST_org;
+      func = (AsnWriteFunc) ParseDstOrgAsnWrite;
+      break;
+   case ParseDest_featqual:
+      writetype = PARSE_DEST_featqual;
+      func = (AsnWriteFunc) FeatureFieldLegalAsnWrite;
+      break;
+   case ParseDest_dbxref:
+      av.ptrvalue = anp->data.ptrvalue;
+      retval = AsnWrite(aip, PARSE_DEST_dbxref, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    LocationIntervalNew()
+*
+**************************************************/
+NLM_EXTERN 
+LocationIntervalPtr LIBCALL
+LocationIntervalNew(void)
+{
+   LocationIntervalPtr ptr = MemNew((size_t) sizeof(LocationInterval));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    LocationIntervalFree()
+*
+**************************************************/
+NLM_EXTERN 
+LocationIntervalPtr LIBCALL
+LocationIntervalFree(LocationIntervalPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    LocationIntervalAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+LocationIntervalPtr LIBCALL
+LocationIntervalAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   LocationIntervalPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* LocationInterval ::= (self contained) */
+      atp = AsnReadId(aip, amp, LOCATION_INTERVAL);
+   } else {
+      atp = AsnLinkType(orig, LOCATION_INTERVAL);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = LocationIntervalNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == LOCATION_INTERVAL_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == LOCATION_INTERVAL_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = LocationIntervalFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    LocationIntervalAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+LocationIntervalAsnWrite(LocationIntervalPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, LOCATION_INTERVAL);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> from;
+   retval = AsnWrite(aip, LOCATION_INTERVAL_from,  &av);
+   av.intvalue = ptr -> to;
+   retval = AsnWrite(aip, LOCATION_INTERVAL_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    LocationChoiceFree()
+*
+**************************************************/
+NLM_EXTERN 
+LocationChoicePtr LIBCALL
+LocationChoiceFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case LocationChoice_interval:
+      LocationIntervalFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    LocationChoiceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+LocationChoicePtr LIBCALL
+LocationChoiceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* LocationChoice ::= (self contained) */
+      atp = AsnReadId(aip, amp, LOCATION_CHOICE);
+   } else {
+      atp = AsnLinkType(orig, LOCATION_CHOICE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == LOCATION_CHOICE_interval) {
+      choice = LocationChoice_interval;
+      func = (AsnReadFunc) LocationIntervalAsnRead;
+   }
+   else if (atp == LOCATION_CHOICE_whole_sequence) {
+      choice = LocationChoice_whole_sequence;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    LocationChoiceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+LocationChoiceAsnWrite(LocationChoicePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, LOCATION_CHOICE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case LocationChoice_interval:
+      writetype = LOCATION_CHOICE_interval;
+      func = (AsnWriteFunc) LocationIntervalAsnWrite;
+      break;
+   case LocationChoice_whole_sequence:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, LOCATION_CHOICE_whole_sequence, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    SequenceListFree()
+*
+**************************************************/
+NLM_EXTERN 
+SequenceListPtr LIBCALL
+SequenceListFree(SequenceListPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericBaseSeqOfFree(ptr,ASNCODE_PTRVAL_SLOT);
+   return NULL;
+}
+
+
+/**************************************************
+*
+*    SequenceListAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SequenceListPtr LIBCALL
+SequenceListAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   SequenceListPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SequenceList ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQUENCE_LIST);
+   } else {
+      atp = AsnLinkType(orig, SEQUENCE_LIST);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   func = NULL;
+
+   ptr  = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_PTRVAL_SLOT, &isError);
+   if (isError && ptr  == NULL) {
+      goto erret;
+   }
+
+
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = SequenceListFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    SequenceListAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SequenceListAsnWrite(SequenceListPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, SEQUENCE_LIST);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr, ASNCODE_PTRVAL_SLOT, aip, atp, SEQUENCE_LIST_E);
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    SequenceListChoiceFree()
+*
+**************************************************/
+NLM_EXTERN 
+SequenceListChoicePtr LIBCALL
+SequenceListChoiceFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case SequenceListChoice_list:
+      SequenceListFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    SequenceListChoiceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SequenceListChoicePtr LIBCALL
+SequenceListChoiceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SequenceListChoice ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQUENCE_LIST_CHOICE);
+   } else {
+      atp = AsnLinkType(orig, SEQUENCE_LIST_CHOICE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == SEQUENCE_LIST_CHOICE_list) {
+      choice = SequenceListChoice_list;
+      func = (AsnReadFunc) SequenceListAsnRead;
+   }
+   else if (atp == SEQUENCE_LIST_CHOICE_all) {
+      choice = SequenceListChoice_all;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    SequenceListChoiceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SequenceListChoiceAsnWrite(SequenceListChoicePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, SEQUENCE_LIST_CHOICE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case SequenceListChoice_list:
+      writetype = SEQUENCE_LIST_CHOICE_list;
+      func = (AsnWriteFunc) SequenceListAsnWrite;
+      break;
+   case SequenceListChoice_all:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, SEQUENCE_LIST_CHOICE_all, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    ApplyFeatureActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+ApplyFeatureActionPtr LIBCALL
+ApplyFeatureActionNew(void)
+{
+   ApplyFeatureActionPtr ptr = MemNew((size_t) sizeof(ApplyFeatureAction));
+
+   ptr -> partial5 = 0;
+   ptr -> partial3 = 0;
+   ptr -> plus_strand = 1;
+   ptr -> add_redundant = 1;
+   ptr -> add_mrna = 0;
+   ptr -> apply_to_parts = 0;
+   ptr -> only_seg_num = -1;
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    ApplyFeatureActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+ApplyFeatureActionPtr LIBCALL
+ApplyFeatureActionFree(ApplyFeatureActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   LocationChoiceFree(ptr -> location);
+   SequenceListChoiceFree(ptr -> seq_list);
+   FeatQualLegalSetFree(ptr -> fields);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    ApplyFeatureActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+ApplyFeatureActionPtr LIBCALL
+ApplyFeatureActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   ApplyFeatureActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* ApplyFeatureAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, APPLY_FEATURE_ACTION);
+   } else {
+      atp = AsnLinkType(orig, APPLY_FEATURE_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = ApplyFeatureActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == APPLY_FEATURE_ACTION_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == APPLY_FEATURE_ACTION_partial5) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> partial5 = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == APPLY_FEATURE_ACTION_partial3) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> partial3 = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_ACTION_plus_strand) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> plus_strand = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == APPLY_FEATURE_ACTION_location) {
+      ptr -> location = LocationChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == APPLY_FEATURE_ACTION_seq_list) {
+      ptr -> seq_list = SequenceListChoiceAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_ACTION_add_redundant) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> add_redundant = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == APPLY_FEATURE_ACTION_add_mrna) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> add_mrna = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_ACTION_apply_to_parts) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> apply_to_parts = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_ACTION_only_seg_num) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> only_seg_num = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == APPLY_FEATURE_ACTION_fields) {
+      ptr -> fields = FeatQualLegalSetAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = ApplyFeatureActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    ApplyFeatureActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+ApplyFeatureActionAsnWrite(ApplyFeatureActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, APPLY_FEATURE_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, APPLY_FEATURE_ACTION_type,  &av);
+   av.boolvalue = ptr -> partial5;
+   retval = AsnWrite(aip, APPLY_FEATURE_ACTION_partial5,  &av);
+   av.boolvalue = ptr -> partial3;
+   retval = AsnWrite(aip, APPLY_FEATURE_ACTION_partial3,  &av);
+   av.boolvalue = ptr -> plus_strand;
+   retval = AsnWrite(aip, FEATURE_ACTION_plus_strand,  &av);
+   if (ptr -> location != NULL) {
+      if ( ! LocationChoiceAsnWrite(ptr -> location, aip, APPLY_FEATURE_ACTION_location)) {
+         goto erret;
+      }
+   }
+   if (ptr -> seq_list != NULL) {
+      if ( ! SequenceListChoiceAsnWrite(ptr -> seq_list, aip, APPLY_FEATURE_ACTION_seq_list)) {
+         goto erret;
+      }
+   }
+   av.boolvalue = ptr -> add_redundant;
+   retval = AsnWrite(aip, FEATURE_ACTION_add_redundant,  &av);
+   av.boolvalue = ptr -> add_mrna;
+   retval = AsnWrite(aip, APPLY_FEATURE_ACTION_add_mrna,  &av);
+   av.boolvalue = ptr -> apply_to_parts;
+   retval = AsnWrite(aip, FEATURE_ACTION_apply_to_parts,  &av);
+   av.intvalue = ptr -> only_seg_num;
+   retval = AsnWrite(aip, FEATURE_ACTION_only_seg_num,  &av);
+   if (ptr -> fields != NULL) {
+      if ( ! FeatQualLegalSetAsnWrite(ptr -> fields, aip, APPLY_FEATURE_ACTION_fields)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    RemoveFeatureActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+RemoveFeatureActionPtr LIBCALL
+RemoveFeatureActionNew(void)
+{
+   RemoveFeatureActionPtr ptr = MemNew((size_t) sizeof(RemoveFeatureAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    RemoveFeatureActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+RemoveFeatureActionPtr LIBCALL
+RemoveFeatureActionFree(RemoveFeatureActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   ConstraintChoiceSetFree(ptr -> constraint);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    RemoveFeatureActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+RemoveFeatureActionPtr LIBCALL
+RemoveFeatureActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   RemoveFeatureActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* RemoveFeatureAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, REMOVE_FEATURE_ACTION);
+   } else {
+      atp = AsnLinkType(orig, REMOVE_FEATURE_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = RemoveFeatureActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == REMOVE_FEATURE_ACTION_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_ACTION_constraint) {
+      ptr -> constraint = ConstraintChoiceSetAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = RemoveFeatureActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    RemoveFeatureActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+RemoveFeatureActionAsnWrite(RemoveFeatureActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, REMOVE_FEATURE_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, REMOVE_FEATURE_ACTION_type,  &av);
+   if (ptr -> constraint != NULL) {
+      if ( ! ConstraintChoiceSetAsnWrite(ptr -> constraint, aip, FEATURE_ACTION_constraint)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    EditLocationStrandNew()
+*
+**************************************************/
+NLM_EXTERN 
+EditLocationStrandPtr LIBCALL
+EditLocationStrandNew(void)
+{
+   EditLocationStrandPtr ptr = MemNew((size_t) sizeof(EditLocationStrand));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    EditLocationStrandFree()
+*
+**************************************************/
+NLM_EXTERN 
+EditLocationStrandPtr LIBCALL
+EditLocationStrandFree(EditLocationStrandPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    EditLocationStrandAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+EditLocationStrandPtr LIBCALL
+EditLocationStrandAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   EditLocationStrandPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* EditLocationStrand ::= (self contained) */
+      atp = AsnReadId(aip, amp, EDIT_LOCATION_STRAND);
+   } else {
+      atp = AsnLinkType(orig, EDIT_LOCATION_STRAND);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = EditLocationStrandNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == LOCATION_STRAND_strand_from) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> strand_from = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == EDIT_LOCATION_STRAND_strand_to) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> strand_to = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = EditLocationStrandFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    EditLocationStrandAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+EditLocationStrandAsnWrite(EditLocationStrandPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, EDIT_LOCATION_STRAND);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> strand_from;
+   retval = AsnWrite(aip, LOCATION_STRAND_strand_from,  &av);
+   av.intvalue = ptr -> strand_to;
+   retval = AsnWrite(aip, EDIT_LOCATION_STRAND_strand_to,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    Partial5SetActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+Partial5SetActionPtr LIBCALL
+Partial5SetActionNew(void)
+{
+   Partial5SetActionPtr ptr = MemNew((size_t) sizeof(Partial5SetAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    Partial5SetActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+Partial5SetActionPtr LIBCALL
+Partial5SetActionFree(Partial5SetActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    Partial5SetActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+Partial5SetActionPtr LIBCALL
+Partial5SetActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   Partial5SetActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* Partial5SetAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, PARTIAL_5_SET_ACTION);
+   } else {
+      atp = AsnLinkType(orig, PARTIAL_5_SET_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = Partial5SetActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == PARTIAL_5_SET_ACTION_constraint) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> constraint = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PARTIAL_5_SET_ACTION_extend) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> extend = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = Partial5SetActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    Partial5SetActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+Partial5SetActionAsnWrite(Partial5SetActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, PARTIAL_5_SET_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> constraint;
+   retval = AsnWrite(aip, PARTIAL_5_SET_ACTION_constraint,  &av);
+   av.boolvalue = ptr -> extend;
+   retval = AsnWrite(aip, PARTIAL_5_SET_ACTION_extend,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    Partial3SetActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+Partial3SetActionPtr LIBCALL
+Partial3SetActionNew(void)
+{
+   Partial3SetActionPtr ptr = MemNew((size_t) sizeof(Partial3SetAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    Partial3SetActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+Partial3SetActionPtr LIBCALL
+Partial3SetActionFree(Partial3SetActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    Partial3SetActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+Partial3SetActionPtr LIBCALL
+Partial3SetActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   Partial3SetActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* Partial3SetAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, PARTIAL_3_SET_ACTION);
+   } else {
+      atp = AsnLinkType(orig, PARTIAL_3_SET_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = Partial3SetActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == PARTIAL_3_SET_ACTION_constraint) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> constraint = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == PARTIAL_3_SET_ACTION_extend) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> extend = av.boolvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = Partial3SetActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    Partial3SetActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+Partial3SetActionAsnWrite(Partial3SetActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, PARTIAL_3_SET_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> constraint;
+   retval = AsnWrite(aip, PARTIAL_3_SET_ACTION_constraint,  &av);
+   av.boolvalue = ptr -> extend;
+   retval = AsnWrite(aip, PARTIAL_3_SET_ACTION_extend,  &av);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    LocationEditTypeFree()
+*
+**************************************************/
+NLM_EXTERN 
+LocationEditTypePtr LIBCALL
+LocationEditTypeFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case LocationEditType_strand:
+      EditLocationStrandFree(anp -> data.ptrvalue);
+      break;
+   case LocationEditType_set_5_partial:
+      Partial5SetActionFree(anp -> data.ptrvalue);
+      break;
+   case LocationEditType_set_3_partial:
+      Partial3SetActionFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    LocationEditTypeAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+LocationEditTypePtr LIBCALL
+LocationEditTypeAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* LocationEditType ::= (self contained) */
+      atp = AsnReadId(aip, amp, LOCATION_EDIT_TYPE);
+   } else {
+      atp = AsnLinkType(orig, LOCATION_EDIT_TYPE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == LOCATION_EDIT_TYPE_strand) {
+      choice = LocationEditType_strand;
+      func = (AsnReadFunc) EditLocationStrandAsnRead;
+   }
+   else if (atp == EDIT_TYPE_set_5_partial) {
+      choice = LocationEditType_set_5_partial;
+      func = (AsnReadFunc) Partial5SetActionAsnRead;
+   }
+   else if (atp == EDIT_TYPE_clear_5_partial) {
+      choice = LocationEditType_clear_5_partial;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == EDIT_TYPE_set_3_partial) {
+      choice = LocationEditType_set_3_partial;
+      func = (AsnReadFunc) Partial3SetActionAsnRead;
+   }
+   else if (atp == EDIT_TYPE_clear_3_partial) {
+      choice = LocationEditType_clear_3_partial;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == LOCATION_EDIT_TYPE_convert) {
+      choice = LocationEditType_convert;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    LocationEditTypeAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+LocationEditTypeAsnWrite(LocationEditTypePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, LOCATION_EDIT_TYPE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case LocationEditType_strand:
+      writetype = LOCATION_EDIT_TYPE_strand;
+      func = (AsnWriteFunc) EditLocationStrandAsnWrite;
+      break;
+   case LocationEditType_set_5_partial:
+      writetype = EDIT_TYPE_set_5_partial;
+      func = (AsnWriteFunc) Partial5SetActionAsnWrite;
+      break;
+   case LocationEditType_clear_5_partial:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, EDIT_TYPE_clear_5_partial, &av);
+      break;
+   case LocationEditType_set_3_partial:
+      writetype = EDIT_TYPE_set_3_partial;
+      func = (AsnWriteFunc) Partial3SetActionAsnWrite;
+      break;
+   case LocationEditType_clear_3_partial:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, EDIT_TYPE_clear_3_partial, &av);
+      break;
+   case LocationEditType_convert:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, LOCATION_EDIT_TYPE_convert, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    EditFeatureLocationActionNew()
+*
+**************************************************/
+NLM_EXTERN 
+EditFeatureLocationActionPtr LIBCALL
+EditFeatureLocationActionNew(void)
+{
+   EditFeatureLocationActionPtr ptr = MemNew((size_t) sizeof(EditFeatureLocationAction));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    EditFeatureLocationActionFree()
+*
+**************************************************/
+NLM_EXTERN 
+EditFeatureLocationActionPtr LIBCALL
+EditFeatureLocationActionFree(EditFeatureLocationActionPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   LocationEditTypeFree(ptr -> action);
+   ConstraintChoiceSetFree(ptr -> constraint);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    EditFeatureLocationActionAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+EditFeatureLocationActionPtr LIBCALL
+EditFeatureLocationActionAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   EditFeatureLocationActionPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* EditFeatureLocationAction ::= (self contained) */
+      atp = AsnReadId(aip, amp, EDIT_FEATURE_LOCATION_ACTION);
+   } else {
+      atp = AsnLinkType(orig, EDIT_FEATURE_LOCATION_ACTION);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = EditFeatureLocationActionNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == FEATURE_LOCATION_ACTION_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == FEATURE_LOCATION_ACTION_action) {
+      ptr -> action = LocationEditTypeAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == LOCATION_ACTION_constraint) {
+      ptr -> constraint = ConstraintChoiceSetAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = EditFeatureLocationActionFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    EditFeatureLocationActionAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+EditFeatureLocationActionAsnWrite(EditFeatureLocationActionPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, EDIT_FEATURE_LOCATION_ACTION);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> type;
+   retval = AsnWrite(aip, FEATURE_LOCATION_ACTION_type,  &av);
+   if (ptr -> action != NULL) {
+      if ( ! LocationEditTypeAsnWrite(ptr -> action, aip, FEATURE_LOCATION_ACTION_action)) {
+         goto erret;
+      }
+   }
+   if (ptr -> constraint != NULL) {
+      if ( ! ConstraintChoiceSetAsnWrite(ptr -> constraint, aip, LOCATION_ACTION_constraint)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    MacroActionChoiceFree()
+*
+**************************************************/
+NLM_EXTERN 
+MacroActionChoicePtr LIBCALL
+MacroActionChoiceFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case MacroActionChoice_aecr:
+      AECRActionFree(anp -> data.ptrvalue);
+      break;
+   case MacroActionChoice_parse:
+      ParseActionFree(anp -> data.ptrvalue);
+      break;
+   case MacroActionChoice_add_feature:
+      ApplyFeatureActionFree(anp -> data.ptrvalue);
+      break;
+   case MacroActionChoice_remove_feature:
+      RemoveFeatureActionFree(anp -> data.ptrvalue);
+      break;
+   case MacroActionChoice_edit_location:
+      EditFeatureLocationActionFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    MacroActionChoiceAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+MacroActionChoicePtr LIBCALL
+MacroActionChoiceAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* MacroActionChoice ::= (self contained) */
+      atp = AsnReadId(aip, amp, MACRO_ACTION_CHOICE);
+   } else {
+      atp = AsnLinkType(orig, MACRO_ACTION_CHOICE);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == MACRO_ACTION_CHOICE_aecr) {
+      choice = MacroActionChoice_aecr;
+      func = (AsnReadFunc) AECRActionAsnRead;
+   }
+   else if (atp == MACRO_ACTION_CHOICE_parse) {
+      choice = MacroActionChoice_parse;
+      func = (AsnReadFunc) ParseActionAsnRead;
+   }
+   else if (atp == MACRO_ACTION_CHOICE_add_feature) {
+      choice = MacroActionChoice_add_feature;
+      func = (AsnReadFunc) ApplyFeatureActionAsnRead;
+   }
+   else if (atp == ACTION_CHOICE_remove_feature) {
+      choice = MacroActionChoice_remove_feature;
+      func = (AsnReadFunc) RemoveFeatureActionAsnRead;
+   }
+   else if (atp == ACTION_CHOICE_edit_location) {
+      choice = MacroActionChoice_edit_location;
+      func = (AsnReadFunc) EditFeatureLocationActionAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    MacroActionChoiceAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+MacroActionChoiceAsnWrite(MacroActionChoicePtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objmacroAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, MACRO_ACTION_CHOICE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case MacroActionChoice_aecr:
+      writetype = MACRO_ACTION_CHOICE_aecr;
+      func = (AsnWriteFunc) AECRActionAsnWrite;
+      break;
+   case MacroActionChoice_parse:
+      writetype = MACRO_ACTION_CHOICE_parse;
+      func = (AsnWriteFunc) ParseActionAsnWrite;
+      break;
+   case MacroActionChoice_add_feature:
+      writetype = MACRO_ACTION_CHOICE_add_feature;
+      func = (AsnWriteFunc) ApplyFeatureActionAsnWrite;
+      break;
+   case MacroActionChoice_remove_feature:
+      writetype = ACTION_CHOICE_remove_feature;
+      func = (AsnWriteFunc) RemoveFeatureActionAsnWrite;
+      break;
+   case MacroActionChoice_edit_location:
+      writetype = ACTION_CHOICE_edit_location;
+      func = (AsnWriteFunc) EditFeatureLocationActionAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
diff --git a/object/objmacro.h b/object/objmacro.h
new file mode 100755
index 00000000..647f34c7
--- /dev/null
+++ b/object/objmacro.h
@@ -0,0 +1,1538 @@
+#ifndef _objmacro_ 
+#define _objmacro_ 
+
+#undef NLM_EXTERN
+#ifdef NLM_IMPORT
+#define NLM_EXTERN NLM_IMPORT
+#else
+#define NLM_EXTERN extern
+#endif
+
+
+#ifdef __cplusplus
+extern "C" { /* } */
+#endif
+
+
+/**************************************************
+*
+*    Generated objects for Module NCBI-Macro
+*    Generated using ASNCODE Revision: 6.16 at Feb 22, 2008 12:57 PM
+*
+**************************************************/
+
+NLM_EXTERN Boolean LIBCALL
+objmacroAsnLoad PROTO((void));
+
+
+/**************************************************
+*
+*    AECRAction
+*
+**************************************************/
+typedef struct struct_AECR_action {
+   ValNodePtr   action;
+   ValNodePtr   constraint;
+} AECRAction, PNTR AECRActionPtr;
+
+
+NLM_EXTERN AECRActionPtr LIBCALL AECRActionFree PROTO ((AECRActionPtr ));
+NLM_EXTERN AECRActionPtr LIBCALL AECRActionNew PROTO (( void ));
+NLM_EXTERN AECRActionPtr LIBCALL AECRActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL AECRActionAsnWrite PROTO (( AECRActionPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ParseAction
+*
+**************************************************/
+typedef struct struct_Parse_action {
+   struct struct_Text_portion PNTR   portion;
+   ValNodePtr   src;
+   ValNodePtr   dest;
+   Uint2   capitalization;
+   Uint1   remove_from_parsed;
+   Uint2   existing_text;
+} ParseAction, PNTR ParseActionPtr;
+
+
+NLM_EXTERN ParseActionPtr LIBCALL ParseActionFree PROTO ((ParseActionPtr ));
+NLM_EXTERN ParseActionPtr LIBCALL ParseActionNew PROTO (( void ));
+NLM_EXTERN ParseActionPtr LIBCALL ParseActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ParseActionAsnWrite PROTO (( ParseActionPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    MacroActionList
+*
+**************************************************/
+typedef ValNode MacroActionList;
+typedef ValNodePtr MacroActionListPtr;
+#define MacroActionListNew() ValNodeNew(NULL) 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN MacroActionListPtr LIBCALL MacroActionListFree PROTO ((MacroActionListPtr ));
+NLM_EXTERN MacroActionListPtr LIBCALL MacroActionListNew PROTO (( void ));
+NLM_EXTERN MacroActionListPtr LIBCALL MacroActionListAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MacroActionListAsnWrite PROTO (( MacroActionListPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define String_location_contains 1
+#define String_location_equals 2
+#define String_location_starts 3
+#define String_location_ends 4
+#define String_location_inlist 5
+
+
+
+/**************************************************
+*
+*    StringConstraint
+*
+**************************************************/
+typedef struct struct_String_constraint {
+   CharPtr   match_text;
+   Uint2   match_location;
+   Uint1   case_sensitive;
+   Uint1   whole_word;
+   Uint1   not_present;
+} StringConstraint, PNTR StringConstraintPtr;
+
+
+NLM_EXTERN StringConstraintPtr LIBCALL StringConstraintFree PROTO ((StringConstraintPtr ));
+NLM_EXTERN StringConstraintPtr LIBCALL StringConstraintNew PROTO (( void ));
+NLM_EXTERN StringConstraintPtr LIBCALL StringConstraintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL StringConstraintAsnWrite PROTO (( StringConstraintPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Strand_constraint_any 0
+#define Strand_constraint_plus 1
+#define Strand_constraint_minus 2
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Seqtype_constraint_any 0
+#define Seqtype_constraint_nuc 1
+#define Seqtype_constraint_prot 2
+
+
+
+/**************************************************
+*
+*    LocationConstraint
+*
+**************************************************/
+typedef struct struct_Location_constraint {
+   Uint2   strand;
+   Uint2   seq_type;
+} LocationConstraint, PNTR LocationConstraintPtr;
+
+
+NLM_EXTERN LocationConstraintPtr LIBCALL LocationConstraintFree PROTO ((LocationConstraintPtr ));
+NLM_EXTERN LocationConstraintPtr LIBCALL LocationConstraintNew PROTO (( void ));
+NLM_EXTERN LocationConstraintPtr LIBCALL LocationConstraintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL LocationConstraintAsnWrite PROTO (( LocationConstraintPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Object_type_constraint_any 0
+#define Object_type_constraint_feature 1
+#define Object_type_constraint_descriptor 2
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Feature_type_any 0
+#define Feature_type_gene 1
+#define Feature_type_org 2
+#define Feature_type_cds 3
+#define Feature_type_prot 4
+#define Feature_type_preRNA 5
+#define Feature_type_mRNA 6
+#define Feature_type_tRNA 7
+#define Feature_type_rRNA 8
+#define Feature_type_snRNA 9
+#define Feature_type_scRNA 10
+#define Feature_type_otherRNA 11
+#define Feature_type_pub 12
+#define Feature_type_seq 13
+#define Feature_type_imp 14
+#define Feature_type_allele 15
+#define Feature_type_attenuator 16
+#define Feature_type_c_region 17
+#define Feature_type_caat_signal 18
+#define Feature_type_imp_CDS 19
+#define Feature_type_conflict 20
+#define Feature_type_d_loop 21
+#define Feature_type_d_segment 22
+#define Feature_type_enhancer 23
+#define Feature_type_exon 24
+#define Feature_type_gC_signal 25
+#define Feature_type_iDNA 26
+#define Feature_type_intron 27
+#define Feature_type_j_segment 28
+#define Feature_type_ltr 29
+#define Feature_type_mat_peptide 30
+#define Feature_type_misc_binding 31
+#define Feature_type_misc_difference 32
+#define Feature_type_misc_feature 33
+#define Feature_type_misc_recomb 34
+#define Feature_type_misc_RNA 35
+#define Feature_type_misc_signal 36
+#define Feature_type_misc_structure 37
+#define Feature_type_modified_base 38
+#define Feature_type_mutation 39
+#define Feature_type_n_region 40
+#define Feature_type_old_sequence 41
+#define Feature_type_polyA_signal 42
+#define Feature_type_polyA_site 43
+#define Feature_type_precursor_RNA 44
+#define Feature_type_prim_transcript 45
+#define Feature_type_primer_bind 46
+#define Feature_type_promoter 47
+#define Feature_type_protein_bind 48
+#define Feature_type_rbs 49
+#define Feature_type_repeat_region 50
+#define Feature_type_repeat_unit 51
+#define Feature_type_rep_origin 52
+#define Feature_type_s_region 53
+#define Feature_type_satellite 54
+#define Feature_type_sig_peptide 55
+#define Feature_type_source 56
+#define Feature_type_stem_loop 57
+#define Feature_type_sts 58
+#define Feature_type_tata_signal 59
+#define Feature_type_terminator 60
+#define Feature_type_transit_peptide 61
+#define Feature_type_unsure 62
+#define Feature_type_v_region 63
+#define Feature_type_v_segment 64
+#define Feature_type_variation 65
+#define Feature_type_virion 66
+#define Feature_type_n3clip 67
+#define Feature_type_n3UTR 68
+#define Feature_type_n5clip 69
+#define Feature_type_n5UTR 70
+#define Feature_type_n10_signal 71
+#define Feature_type_n35_signal 72
+#define Feature_type_site_ref 73
+#define Feature_type_region 74
+#define Feature_type_comment 75
+#define Feature_type_bond 76
+#define Feature_type_site 77
+#define Feature_type_rsite 78
+#define Feature_type_user 79
+#define Feature_type_txinit 80
+#define Feature_type_num 81
+#define Feature_type_psec_str 82
+#define Feature_type_non_std_residue 83
+#define Feature_type_het 84
+#define Feature_type_biosrc 85
+#define Feature_type_preprotein 86
+#define Feature_type_mat_peptide_aa 87
+#define Feature_type_sig_peptide_aa 88
+#define Feature_type_transit_peptide_aa 89
+#define Feature_type_snoRNA 90
+#define Feature_type_gap 91
+#define Feature_type_operon 92
+#define Feature_type_oriT 93
+#define Feature_type_ncRNA 94
+#define Feature_type_tmRNA 95
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Feat_qual_legal_allele 1
+#define Feat_qual_legal_activity 2
+#define Feat_qual_legal_anticodon 3
+#define Feat_qual_legal_bound_moiety 4
+#define Feat_qual_legal_chromosome 5
+#define Feat_qual_legal_citation 6
+#define Feat_qual_legal_codon 7
+#define Feat_qual_legal_codon_start 8
+#define Feat_qual_legal_codons_recognized 9
+#define Feat_qual_legal_compare 10
+#define Feat_qual_legal_cons_splice 11
+#define Feat_qual_legal_db_xref 12
+#define Feat_qual_legal_description 13
+#define Feat_qual_legal_direction 14
+#define Feat_qual_legal_ec_number 15
+#define Feat_qual_legal_environmental_sample 16
+#define Feat_qual_legal_evidence 17
+#define Feat_qual_legal_exception 18
+#define Feat_qual_legal_experiment 19
+#define Feat_qual_legal_focus 20
+#define Feat_qual_legal_frequency 21
+#define Feat_qual_legal_function 22
+#define Feat_qual_legal_gene 23
+#define Feat_qual_legal_gene_description 24
+#define Feat_qual_legal_inference 25
+#define Feat_qual_legal_label 26
+#define Feat_qual_legal_locus_tag 27
+#define Feat_qual_legal_map 28
+#define Feat_qual_legal_mobile_element 29
+#define Feat_qual_legal_mod_base 30
+#define Feat_qual_legal_mol_type 31
+#define Feat_qual_legal_ncRNA_class 32
+#define Feat_qual_legal_note 33
+#define Feat_qual_legal_number 34
+#define Feat_qual_legal_old_locus_tag 35
+#define Feat_qual_legal_operon 36
+#define Feat_qual_legal_organism 37
+#define Feat_qual_legal_organelle 38
+#define Feat_qual_legal_partial 39
+#define Feat_qual_legal_phenotype 40
+#define Feat_qual_legal_plasmid 41
+#define Feat_qual_legal_product 42
+#define Feat_qual_legal_protein_id 43
+#define Feat_qual_legal_pseudo 44
+#define Feat_qual_legal_rearranged 45
+#define Feat_qual_legal_replace 46
+#define Feat_qual_legal_rpt_family 47
+#define Feat_qual_legal_rpt_type 48
+#define Feat_qual_legal_rpt_unit 49
+#define Feat_qual_legal_rpt_unit_seq 50
+#define Feat_qual_legal_rpt_unit_range 51
+#define Feat_qual_legal_segment 52
+#define Feat_qual_legal_sequenced_mol 53
+#define Feat_qual_legal_standard_name 54
+#define Feat_qual_legal_synonym 55
+#define Feat_qual_legal_transcript_id 56
+#define Feat_qual_legal_transgenic 57
+#define Feat_qual_legal_translation 58
+#define Feat_qual_legal_transl_except 59
+#define Feat_qual_legal_transl_table 60
+#define Feat_qual_legal_usedin 61
+
+
+
+/**************************************************
+*
+*    FeatQualLegalVal
+*
+**************************************************/
+typedef struct struct_Feat_qual_legal_val {
+   Uint2   qual;
+   CharPtr   val;
+} FeatQualLegalVal, PNTR FeatQualLegalValPtr;
+
+
+NLM_EXTERN FeatQualLegalValPtr LIBCALL FeatQualLegalValFree PROTO ((FeatQualLegalValPtr ));
+NLM_EXTERN FeatQualLegalValPtr LIBCALL FeatQualLegalValNew PROTO (( void ));
+NLM_EXTERN FeatQualLegalValPtr LIBCALL FeatQualLegalValAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FeatQualLegalValAsnWrite PROTO (( FeatQualLegalValPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr FeatQualLegalValChoicePtr;
+typedef ValNode FeatQualLegalValChoice;
+#define FeatQualLegalValChoice_qual 1
+
+
+NLM_EXTERN FeatQualLegalValChoicePtr LIBCALL FeatQualLegalValChoiceFree PROTO ((FeatQualLegalValChoicePtr ));
+NLM_EXTERN FeatQualLegalValChoicePtr LIBCALL FeatQualLegalValChoiceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FeatQualLegalValChoiceAsnWrite PROTO (( FeatQualLegalValChoicePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    FeatQualLegalSet
+*
+**************************************************/
+typedef ValNode FeatQualLegalSet;
+typedef ValNodePtr FeatQualLegalSetPtr;
+#define FeatQualLegalSetNew() ValNodeNew(NULL) 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN FeatQualLegalSetPtr LIBCALL FeatQualLegalSetFree PROTO ((FeatQualLegalSetPtr ));
+NLM_EXTERN FeatQualLegalSetPtr LIBCALL FeatQualLegalSetNew PROTO (( void ));
+NLM_EXTERN FeatQualLegalSetPtr LIBCALL FeatQualLegalSetAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FeatQualLegalSetAsnWrite PROTO (( FeatQualLegalSetPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+typedef ValNodePtr FeatQualChoicePtr;
+typedef ValNode FeatQualChoice;
+#define FeatQualChoice_legal_qual 1
+#define FeatQualChoice_illegal_qual 2
+
+
+NLM_EXTERN FeatQualChoicePtr LIBCALL FeatQualChoiceFree PROTO ((FeatQualChoicePtr ));
+NLM_EXTERN FeatQualChoicePtr LIBCALL FeatQualChoiceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FeatQualChoiceAsnWrite PROTO (( FeatQualChoicePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    FeatureField
+*
+**************************************************/
+typedef struct struct_Feature_field {
+   Uint2   type;
+   ValNodePtr   field;
+} FeatureField, PNTR FeatureFieldPtr;
+
+
+NLM_EXTERN FeatureFieldPtr LIBCALL FeatureFieldFree PROTO ((FeatureFieldPtr ));
+NLM_EXTERN FeatureFieldPtr LIBCALL FeatureFieldNew PROTO (( void ));
+NLM_EXTERN FeatureFieldPtr LIBCALL FeatureFieldAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FeatureFieldAsnWrite PROTO (( FeatureFieldPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    FeatureFieldLegal
+*
+**************************************************/
+typedef struct struct_Feature_field_legal {
+   Uint2   type;
+   Uint2   field;
+} FeatureFieldLegal, PNTR FeatureFieldLegalPtr;
+
+
+NLM_EXTERN FeatureFieldLegalPtr LIBCALL FeatureFieldLegalFree PROTO ((FeatureFieldLegalPtr ));
+NLM_EXTERN FeatureFieldLegalPtr LIBCALL FeatureFieldLegalNew PROTO (( void ));
+NLM_EXTERN FeatureFieldLegalPtr LIBCALL FeatureFieldLegalAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FeatureFieldLegalAsnWrite PROTO (( FeatureFieldLegalPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    FeatureFieldPair
+*
+**************************************************/
+typedef struct struct_Feature_field_pair {
+   Uint2   type;
+   ValNodePtr   field_from;
+   ValNodePtr   field_to;
+} FeatureFieldPair, PNTR FeatureFieldPairPtr;
+
+
+NLM_EXTERN FeatureFieldPairPtr LIBCALL FeatureFieldPairFree PROTO ((FeatureFieldPairPtr ));
+NLM_EXTERN FeatureFieldPairPtr LIBCALL FeatureFieldPairNew PROTO (( void ));
+NLM_EXTERN FeatureFieldPairPtr LIBCALL FeatureFieldPairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FeatureFieldPairAsnWrite PROTO (( FeatureFieldPairPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Source_qual_acronym 1
+#define Source_qual_anamorph 2
+#define Source_qual_authority 3
+#define Source_qual_bio_material 4
+#define Source_qual_biotype 5
+#define Source_qual_biovar 6
+#define Source_qual_breed 7
+#define Source_qual_cell_line 8
+#define Source_qual_cell_type 9
+#define Source_qual_chemovar 10
+#define Source_qual_chromosome 11
+#define Source_qual_clone 12
+#define Source_qual_clone_lib 13
+#define Source_qual_collected_by 14
+#define Source_qual_collection_date 15
+#define Source_qual_common 16
+#define Source_qual_common_name 17
+#define Source_qual_country 18
+#define Source_qual_cultivar 19
+#define Source_qual_culture_collection 20
+#define Source_qual_dev_stage 21
+#define Source_qual_division 22
+#define Source_qual_dosage 23
+#define Source_qual_ecotype 24
+#define Source_qual_endogenous_virus_name 25
+#define Source_qual_environmental_sample 26
+#define Source_qual_forma 27
+#define Source_qual_forma_specialis 28
+#define Source_qual_frequency 29
+#define Source_qual_fwd_primer_name 30
+#define Source_qual_fwd_primer_seq 31
+#define Source_qual_gb_acronym 32
+#define Source_qual_gb_anamorph 33
+#define Source_qual_gb_synonym 34
+#define Source_qual_genotype 35
+#define Source_qual_germline 36
+#define Source_qual_group 37
+#define Source_qual_haplotype 38
+#define Source_qual_identified_by 39
+#define Source_qual_insertion_seq_name 40
+#define Source_qual_isolate 41
+#define Source_qual_isolation_source 42
+#define Source_qual_lab_host 43
+#define Source_qual_lat_lon 44
+#define Source_qual_lineage 45
+#define Source_qual_map 46
+#define Source_qual_metagenome_source 47
+#define Source_qual_metagenomic 48
+#define Source_qual_old_lineage 49
+#define Source_qual_old_name 50
+#define Source_qual_orgmod_note 51
+#define Source_qual_nat_host 52
+#define Source_qual_pathovar 53
+#define Source_qual_plasmid_name 54
+#define Source_qual_plastid_name 55
+#define Source_qual_pop_variant 56
+#define Source_qual_rearranged 57
+#define Source_qual_rev_primer_name 58
+#define Source_qual_rev_primer_seq 59
+#define Source_qual_segment 60
+#define Source_qual_serogroup 61
+#define Source_qual_serotype 62
+#define Source_qual_serovar 63
+#define Source_qual_sex 64
+#define Source_qual_specimen_voucher 65
+#define Source_qual_strain 66
+#define Source_qual_subclone 67
+#define Source_qual_subgroup 68
+#define Source_qual_subsource_note 69
+#define Source_qual_sub_species 70
+#define Source_qual_substrain 71
+#define Source_qual_subtype 72
+#define Source_qual_synonym 73
+#define Source_qual_taxname 74
+#define Source_qual_teleomorph 75
+#define Source_qual_tissue_lib 76
+#define Source_qual_tissue_type 77
+#define Source_qual_transgenic 78
+#define Source_qual_transposon_name 79
+#define Source_qual_type 80
+#define Source_qual_variety 81
+
+
+
+/**************************************************
+*
+*    SourceQualPair
+*
+**************************************************/
+typedef struct struct_Source_qual_pair {
+   Uint2   field_from;
+   Uint2   field_to;
+} SourceQualPair, PNTR SourceQualPairPtr;
+
+
+NLM_EXTERN SourceQualPairPtr LIBCALL SourceQualPairFree PROTO ((SourceQualPairPtr ));
+NLM_EXTERN SourceQualPairPtr LIBCALL SourceQualPairNew PROTO (( void ));
+NLM_EXTERN SourceQualPairPtr LIBCALL SourceQualPairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SourceQualPairAsnWrite PROTO (( SourceQualPairPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Source_location_unknown 0
+#define Source_location_genomic 1
+#define Source_location_chloroplast 2
+#define Source_location_chromoplast 3
+#define Source_location_kinetoplast 4
+#define Source_location_mitochondrion 5
+#define Source_location_plastid 6
+#define Source_location_macronuclear 7
+#define Source_location_extrachrom 8
+#define Source_location_plasmid 9
+#define Source_location_transposon 10
+#define Source_location_insertion_seq 11
+#define Source_location_cyanelle 12
+#define Source_location_proviral 13
+#define Source_location_virion 14
+#define Source_location_nucleomorph 15
+#define Source_location_apicoplast 16
+#define Source_location_leucoplast 17
+#define Source_location_proplastid 18
+#define Source_location_endogenous_virus 19
+#define Source_location_hydrogenosome 20
+#define Source_location_chromosome 21
+#define Source_location_chromatophore 22
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Source_origin_unknown 0
+#define Source_origin_natural 1
+#define Source_origin_natmut 2
+#define Source_origin_mut 3
+#define Source_origin_artificial 4
+#define Source_origin_synthetic 5
+#define Source_origin_other 255
+
+typedef ValNodePtr SourceQualChoicePtr;
+typedef ValNode SourceQualChoice;
+#define SourceQualChoice_textqual 1
+#define SourceQualChoice_location 2
+#define SourceQualChoice_origin 3
+
+
+NLM_EXTERN SourceQualChoicePtr LIBCALL SourceQualChoiceFree PROTO ((SourceQualChoicePtr ));
+NLM_EXTERN SourceQualChoicePtr LIBCALL SourceQualChoiceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SourceQualChoiceAsnWrite PROTO (( SourceQualChoicePtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define CDSGeneProt_field_cds_comment 1
+#define CDSGeneProt_field_gene_locus 2
+#define CDSGeneProt_field_gene_description 3
+#define CDSGeneProt_field_gene_comment 4
+#define CDSGeneProt_field_gene_allele 5
+#define CDSGeneProt_field_gene_maploc 6
+#define CDSGeneProt_field_gene_locus_tag 7
+#define CDSGeneProt_field_gene_synonym 8
+#define CDSGeneProt_field_gene_old_locus_tag 9
+#define CDSGeneProt_field_mrna_product 10
+#define CDSGeneProt_field_mrna_comment 11
+#define CDSGeneProt_field_prot_name 12
+#define CDSGeneProt_field_prot_description 13
+#define CDSGeneProt_field_prot_ec_number 14
+#define CDSGeneProt_field_prot_activity 15
+#define CDSGeneProt_field_prot_comment 16
+#define CDSGeneProt_field_mat_peptide_name 17
+#define CDSGeneProt_field_mat_peptide_description 18
+#define CDSGeneProt_field_mat_peptide_ec_number 19
+#define CDSGeneProt_field_mat_peptide_activity 20
+#define CDSGeneProt_field_mat_peptide_comment 21
+
+
+
+/**************************************************
+*
+*    CDSGeneProtFieldPair
+*
+**************************************************/
+typedef struct struct_CDSGeneProt_field_pair {
+   Uint2   field_from;
+   Uint2   field_to;
+} CDSGeneProtFieldPair, PNTR CDSGeneProtFieldPairPtr;
+
+
+NLM_EXTERN CDSGeneProtFieldPairPtr LIBCALL CDSGeneProtFieldPairFree PROTO ((CDSGeneProtFieldPairPtr ));
+NLM_EXTERN CDSGeneProtFieldPairPtr LIBCALL CDSGeneProtFieldPairNew PROTO (( void ));
+NLM_EXTERN CDSGeneProtFieldPairPtr LIBCALL CDSGeneProtFieldPairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CDSGeneProtFieldPairAsnWrite PROTO (( CDSGeneProtFieldPairPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Molecule_type_unknown 0
+#define Molecule_type_genomic 1
+#define Molecule_type_precursor_RNA 2
+#define Molecule_type_mRNA 3
+#define Molecule_type_rRNA 4
+#define Molecule_type_tRNA 5
+#define Molecule_type_snRNA 6
+#define Molecule_type_scRNA 7
+#define Molecule_type_genomic_mRNA 8
+#define Molecule_type_cRNA 9
+#define Molecule_type_snoRNA 10
+#define Molecule_type_transcribed_RNA 11
+#define Molecule_type_ncRNA 12
+#define Molecule_type_transfer_messenger_RNA 13
+#define Molecule_type_other 14
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Technique_type_unknown 0
+#define Technique_type_standard 1
+#define Technique_type_est 2
+#define Technique_type_sts 3
+#define Technique_type_survey 4
+#define Technique_type_genetic_map 5
+#define Technique_type_physical_map 6
+#define Technique_type_derived 7
+#define Technique_type_concept_trans 8
+#define Technique_type_seq_pept 9
+#define Technique_type_both 10
+#define Technique_type_seq_pept_overlap 11
+#define Technique_type_seq_pept_homol 12
+#define Technique_type_concept_trans_a 13
+#define Technique_type_htgs_1 14
+#define Technique_type_htgs_2 15
+#define Technique_type_htgs_3 16
+#define Technique_type_fli_cDNA 17
+#define Technique_type_htgs_0 18
+#define Technique_type_htc 19
+#define Technique_type_wgs 20
+#define Technique_type_barcode 21
+#define Technique_type_composite_wgs_htgs 22
+#define Technique_type_tsa 23
+#define Technique_type_other 24
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Completedness_type_unknown 0
+#define Completedness_type_complete 1
+#define Completedness_type_partial 2
+#define Completedness_type_no_left 3
+#define Completedness_type_no_right 4
+#define Completedness_type_no_ends 5
+#define Completedness_type_has_left 6
+#define Completedness_type_has_right 7
+#define Completedness_type_other 6
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Molecule_class_type_unknown 0
+#define Molecule_class_type_dna 1
+#define Molecule_class_type_rna 2
+#define Molecule_class_type_protein 3
+#define Molecule_class_type_nucleotide 4
+#define Molecule_class_type_other 5
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Topology_type_unknown 0
+#define Topology_type_linear 1
+#define Topology_type_circular 2
+#define Topology_type_tandem 3
+#define Topology_type_other 4
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Strand_type_unknown 0
+#define Strand_type_single 1
+#define Strand_type_double__ 2
+#define Strand_type_mixed 3
+#define Strand_type_mixed_rev 4
+#define Strand_type_other 5
+
+typedef ValNodePtr MolinfoFieldPtr;
+typedef ValNode MolinfoField;
+#define MolinfoField_molecule 1
+#define MolinfoField_technique 2
+#define MolinfoField_completedness 3
+#define MolinfoField_mol_class 4
+#define MolinfoField_topology 5
+#define MolinfoField_strand 6
+
+
+NLM_EXTERN MolinfoFieldPtr LIBCALL MolinfoFieldFree PROTO ((MolinfoFieldPtr ));
+NLM_EXTERN MolinfoFieldPtr LIBCALL MolinfoFieldAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MolinfoFieldAsnWrite PROTO (( MolinfoFieldPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    MolinfoMoleculePair
+*
+**************************************************/
+typedef struct struct_Molinfo_molecule_pair {
+   Uint2   from;
+   Uint2   to;
+} MolinfoMoleculePair, PNTR MolinfoMoleculePairPtr;
+
+
+NLM_EXTERN MolinfoMoleculePairPtr LIBCALL MolinfoMoleculePairFree PROTO ((MolinfoMoleculePairPtr ));
+NLM_EXTERN MolinfoMoleculePairPtr LIBCALL MolinfoMoleculePairNew PROTO (( void ));
+NLM_EXTERN MolinfoMoleculePairPtr LIBCALL MolinfoMoleculePairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MolinfoMoleculePairAsnWrite PROTO (( MolinfoMoleculePairPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    MolinfoTechniquePair
+*
+**************************************************/
+typedef struct struct_Molinfo_technique_pair {
+   Uint2   from;
+   Uint2   to;
+} MolinfoTechniquePair, PNTR MolinfoTechniquePairPtr;
+
+
+NLM_EXTERN MolinfoTechniquePairPtr LIBCALL MolinfoTechniquePairFree PROTO ((MolinfoTechniquePairPtr ));
+NLM_EXTERN MolinfoTechniquePairPtr LIBCALL MolinfoTechniquePairNew PROTO (( void ));
+NLM_EXTERN MolinfoTechniquePairPtr LIBCALL MolinfoTechniquePairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MolinfoTechniquePairAsnWrite PROTO (( MolinfoTechniquePairPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    MolinfoCompletednessPair
+*
+**************************************************/
+typedef struct struct_Molinfo_completedness_pair {
+   Uint2   from;
+   Uint2   to;
+} MolinfoCompletednessPair, PNTR MolinfoCompletednessPairPtr;
+
+
+NLM_EXTERN MolinfoCompletednessPairPtr LIBCALL MolinfoCompletednessPairFree PROTO ((MolinfoCompletednessPairPtr ));
+NLM_EXTERN MolinfoCompletednessPairPtr LIBCALL MolinfoCompletednessPairNew PROTO (( void ));
+NLM_EXTERN MolinfoCompletednessPairPtr LIBCALL MolinfoCompletednessPairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MolinfoCompletednessPairAsnWrite PROTO (( MolinfoCompletednessPairPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    MolinfoMolClassPair
+*
+**************************************************/
+typedef struct struct_Molinfo_mol_class_pair {
+   Uint2   from;
+   Uint2   to;
+} MolinfoMolClassPair, PNTR MolinfoMolClassPairPtr;
+
+
+NLM_EXTERN MolinfoMolClassPairPtr LIBCALL MolinfoMolClassPairFree PROTO ((MolinfoMolClassPairPtr ));
+NLM_EXTERN MolinfoMolClassPairPtr LIBCALL MolinfoMolClassPairNew PROTO (( void ));
+NLM_EXTERN MolinfoMolClassPairPtr LIBCALL MolinfoMolClassPairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MolinfoMolClassPairAsnWrite PROTO (( MolinfoMolClassPairPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    MolinfoTopologyPair
+*
+**************************************************/
+typedef struct struct_Molinfo_topology_pair {
+   Uint2   from;
+   Uint2   to;
+} MolinfoTopologyPair, PNTR MolinfoTopologyPairPtr;
+
+
+NLM_EXTERN MolinfoTopologyPairPtr LIBCALL MolinfoTopologyPairFree PROTO ((MolinfoTopologyPairPtr ));
+NLM_EXTERN MolinfoTopologyPairPtr LIBCALL MolinfoTopologyPairNew PROTO (( void ));
+NLM_EXTERN MolinfoTopologyPairPtr LIBCALL MolinfoTopologyPairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MolinfoTopologyPairAsnWrite PROTO (( MolinfoTopologyPairPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    MolinfoStrandPair
+*
+**************************************************/
+typedef struct struct_Molinfo_strand_pair {
+   Uint2   from;
+   Uint2   to;
+} MolinfoStrandPair, PNTR MolinfoStrandPairPtr;
+
+
+NLM_EXTERN MolinfoStrandPairPtr LIBCALL MolinfoStrandPairFree PROTO ((MolinfoStrandPairPtr ));
+NLM_EXTERN MolinfoStrandPairPtr LIBCALL MolinfoStrandPairNew PROTO (( void ));
+NLM_EXTERN MolinfoStrandPairPtr LIBCALL MolinfoStrandPairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MolinfoStrandPairAsnWrite PROTO (( MolinfoStrandPairPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr MolinfoFieldPairPtr;
+typedef ValNode MolinfoFieldPair;
+#define MolinfoFieldPair_molecule 1
+#define MolinfoFieldPair_technique 2
+#define MolinfoFieldPair_completedness 3
+#define MolinfoFieldPair_mol_class 4
+#define MolinfoFieldPair_topology 5
+#define MolinfoFieldPair_strand 6
+
+
+NLM_EXTERN MolinfoFieldPairPtr LIBCALL MolinfoFieldPairFree PROTO ((MolinfoFieldPairPtr ));
+NLM_EXTERN MolinfoFieldPairPtr LIBCALL MolinfoFieldPairAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MolinfoFieldPairAsnWrite PROTO (( MolinfoFieldPairPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    SourceConstraint
+*
+**************************************************/
+typedef struct struct_Source_constraint {
+   ValNodePtr   field1;
+   ValNodePtr   field2;
+   struct struct_String_constraint PNTR   constraint;
+   Uint2   type_constraint;
+} SourceConstraint, PNTR SourceConstraintPtr;
+
+
+NLM_EXTERN SourceConstraintPtr LIBCALL SourceConstraintFree PROTO ((SourceConstraintPtr ));
+NLM_EXTERN SourceConstraintPtr LIBCALL SourceConstraintNew PROTO (( void ));
+NLM_EXTERN SourceConstraintPtr LIBCALL SourceConstraintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SourceConstraintAsnWrite PROTO (( SourceConstraintPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define CDSGeneProt_feature_type_constraint_gene 1
+#define CDSGeneProt_feature_type_constraint_mRNA 2
+#define CDSGeneProt_feature_type_constraint_cds 3
+#define CDSGeneProt_feature_type_constraint_prot 4
+#define CDSGeneProt_feature_type_constraint_exon 5
+#define CDSGeneProt_feature_type_constraint_mat_peptide 6
+
+
+
+/**************************************************
+*
+*    CDSGeneProtPseudoConstraint
+*
+**************************************************/
+typedef struct struct_CDSGeneProt_pseudo_constraint {
+   Uint2   feature;
+   Uint1   is_pseudo;
+} CDSGeneProtPseudoConstraint, PNTR CDSGeneProtPseudoConstraintPtr;
+
+
+NLM_EXTERN CDSGeneProtPseudoConstraintPtr LIBCALL CDSGeneProtPseudoConstraintFree PROTO ((CDSGeneProtPseudoConstraintPtr ));
+NLM_EXTERN CDSGeneProtPseudoConstraintPtr LIBCALL CDSGeneProtPseudoConstraintNew PROTO (( void ));
+NLM_EXTERN CDSGeneProtPseudoConstraintPtr LIBCALL CDSGeneProtPseudoConstraintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CDSGeneProtPseudoConstraintAsnWrite PROTO (( CDSGeneProtPseudoConstraintPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr CDSGeneProtConstraintFieldPtr;
+typedef ValNode CDSGeneProtConstraintField;
+#define CDSGeneProtConstraintField_field 1
+
+
+NLM_EXTERN CDSGeneProtConstraintFieldPtr LIBCALL CDSGeneProtConstraintFieldFree PROTO ((CDSGeneProtConstraintFieldPtr ));
+NLM_EXTERN CDSGeneProtConstraintFieldPtr LIBCALL CDSGeneProtConstraintFieldAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CDSGeneProtConstraintFieldAsnWrite PROTO (( CDSGeneProtConstraintFieldPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    CDSGeneProtQualConstraint
+*
+**************************************************/
+typedef struct struct_CDSGeneProt_qual_constraint {
+   ValNodePtr   field1;
+   ValNodePtr   field2;
+   struct struct_String_constraint PNTR   constraint;
+} CDSGeneProtQualConstraint, PNTR CDSGeneProtQualConstraintPtr;
+
+
+NLM_EXTERN CDSGeneProtQualConstraintPtr LIBCALL CDSGeneProtQualConstraintFree PROTO ((CDSGeneProtQualConstraintPtr ));
+NLM_EXTERN CDSGeneProtQualConstraintPtr LIBCALL CDSGeneProtQualConstraintNew PROTO (( void ));
+NLM_EXTERN CDSGeneProtQualConstraintPtr LIBCALL CDSGeneProtQualConstraintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CDSGeneProtQualConstraintAsnWrite PROTO (( CDSGeneProtQualConstraintPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Sequence_constraint_rnamol_any 0
+#define Sequence_constraint_rnamol_genomic 1
+#define Sequence_constraint_rnamol_precursor_RNA 2
+#define Sequence_constraint_rnamol_mRNA 3
+#define Sequence_constraint_rnamol_rRNA 4
+#define Sequence_constraint_rnamol_tRNA 5
+#define Sequence_constraint_rnamol_snRNA 6
+#define Sequence_constraint_rnamol_scRNA 7
+#define Sequence_constraint_rnamol_genomic_mRNA 8
+#define Sequence_constraint_rnamol_cRNA 9
+#define Sequence_constraint_rnamol_snoRNA 10
+#define Sequence_constraint_rnamol_transcribed_RNA 11
+#define Sequence_constraint_rnamol_ncRNA 12
+#define Sequence_constraint_rnamol_transfer_messenger_RNA 13
+
+typedef ValNodePtr SequenceConstraintMolTypeConstraintPtr;
+typedef ValNode SequenceConstraintMolTypeConstraint;
+#define SequenceConstraintMolTypeConstraint_any 1
+#define SequenceConstraintMolTypeConstraint_nucleotide 2
+#define SequenceConstraintMolTypeConstraint_dna 3
+#define SequenceConstraintMolTypeConstraint_rna 4
+#define SequenceConstraintMolTypeConstraint_protein 5
+
+
+NLM_EXTERN SequenceConstraintMolTypeConstraintPtr LIBCALL SequenceConstraintMolTypeConstraintFree PROTO ((SequenceConstraintMolTypeConstraintPtr ));
+NLM_EXTERN SequenceConstraintMolTypeConstraintPtr LIBCALL SequenceConstraintMolTypeConstraintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SequenceConstraintMolTypeConstraintAsnWrite PROTO (( SequenceConstraintMolTypeConstraintPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    SequenceConstraint
+*
+**************************************************/
+typedef struct struct_Sequence_constraint {
+   ValNodePtr   seqtype;
+   struct struct_String_constraint PNTR   id;
+   Uint2   feature;
+} SequenceConstraint, PNTR SequenceConstraintPtr;
+
+
+NLM_EXTERN SequenceConstraintPtr LIBCALL SequenceConstraintFree PROTO ((SequenceConstraintPtr ));
+NLM_EXTERN SequenceConstraintPtr LIBCALL SequenceConstraintNew PROTO (( void ));
+NLM_EXTERN SequenceConstraintPtr LIBCALL SequenceConstraintAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SequenceConstraintAsnWrite PROTO (( SequenceConstraintPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr ConstraintChoicePtr;
+typedef ValNode ConstraintChoice;
+#define ConstraintChoice_string 1
+#define ConstraintChoice_location 2
+#define ConstraintChoice_source 3
+#define ConstraintChoice_cdsgeneprot_qual 4
+#define ConstraintChoice_cdsgeneprot_pseudo 5
+#define ConstraintChoice_sequence 6
+
+
+NLM_EXTERN ConstraintChoicePtr LIBCALL ConstraintChoiceFree PROTO ((ConstraintChoicePtr ));
+NLM_EXTERN ConstraintChoicePtr LIBCALL ConstraintChoiceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ConstraintChoiceAsnWrite PROTO (( ConstraintChoicePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ConstraintChoiceSet
+*
+**************************************************/
+typedef ValNode ConstraintChoiceSet;
+typedef ValNodePtr ConstraintChoiceSetPtr;
+#define ConstraintChoiceSetNew() ValNodeNew(NULL) 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN ConstraintChoiceSetPtr LIBCALL ConstraintChoiceSetFree PROTO ((ConstraintChoiceSetPtr ));
+NLM_EXTERN ConstraintChoiceSetPtr LIBCALL ConstraintChoiceSetNew PROTO (( void ));
+NLM_EXTERN ConstraintChoiceSetPtr LIBCALL ConstraintChoiceSetAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ConstraintChoiceSetAsnWrite PROTO (( ConstraintChoiceSetPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+
+
+/**************************************************
+*
+*    TextPortion
+*
+**************************************************/
+typedef struct struct_Text_portion {
+   CharPtr   left_text;
+   Uint1   include_left;
+   CharPtr   right_text;
+   Uint1   include_right;
+   Uint1   inside;
+   Uint1   case_sensitive;
+   Uint1   whole_word;
+} TextPortion, PNTR TextPortionPtr;
+
+
+NLM_EXTERN TextPortionPtr LIBCALL TextPortionFree PROTO ((TextPortionPtr ));
+NLM_EXTERN TextPortionPtr LIBCALL TextPortionNew PROTO (( void ));
+NLM_EXTERN TextPortionPtr LIBCALL TextPortionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL TextPortionAsnWrite PROTO (( TextPortionPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Field_edit_location_anywhere 0
+#define Field_edit_location_beginning 1
+#define Field_edit_location_end 2
+
+
+
+/**************************************************
+*
+*    FieldEdit
+*
+**************************************************/
+typedef struct struct_Field_edit {
+   CharPtr   find_txt;
+   CharPtr   repl_txt;
+   Uint2   location;
+} FieldEdit, PNTR FieldEditPtr;
+
+
+NLM_EXTERN FieldEditPtr LIBCALL FieldEditFree PROTO ((FieldEditPtr ));
+NLM_EXTERN FieldEditPtr LIBCALL FieldEditNew PROTO (( void ));
+NLM_EXTERN FieldEditPtr LIBCALL FieldEditAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FieldEditAsnWrite PROTO (( FieldEditPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr FieldTypePtr;
+typedef ValNode FieldType;
+#define FieldType_source_qual 1
+#define FieldType_feature_field 2
+#define FieldType_cds_gene_prot 3
+#define FieldType_molinfo_field 4
+
+
+NLM_EXTERN FieldTypePtr LIBCALL FieldTypeFree PROTO ((FieldTypePtr ));
+NLM_EXTERN FieldTypePtr LIBCALL FieldTypeAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FieldTypeAsnWrite PROTO (( FieldTypePtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr FieldPairTypePtr;
+typedef ValNode FieldPairType;
+#define FieldPairType_source_qual 1
+#define FieldPairType_feature_field 2
+#define FieldPairType_cds_gene_prot 3
+#define FieldPairType_molinfo_field 4
+
+
+NLM_EXTERN FieldPairTypePtr LIBCALL FieldPairTypeFree PROTO ((FieldPairTypePtr ));
+NLM_EXTERN FieldPairTypePtr LIBCALL FieldPairTypeAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL FieldPairTypeAsnWrite PROTO (( FieldPairTypePtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define ExistingTextOption_replace_old 1
+#define ExistingTextOption_append_semi 2
+#define ExistingTextOption_append_space 3
+#define ExistingTextOption_append_colon 4
+#define ExistingTextOption_append_none 5
+#define ExistingTextOption_prefix_semi 6
+#define ExistingTextOption_prefix_space 7
+#define ExistingTextOption_prefix_colon 8
+#define ExistingTextOption_prefix_none 9
+#define ExistingTextOption_leave_old 10
+
+
+
+/**************************************************
+*
+*    ApplyAction
+*
+**************************************************/
+typedef struct struct_Apply_action {
+   ValNodePtr   field;
+   CharPtr   value;
+   Uint2   existing_text;
+} ApplyAction, PNTR ApplyActionPtr;
+
+
+NLM_EXTERN ApplyActionPtr LIBCALL ApplyActionFree PROTO ((ApplyActionPtr ));
+NLM_EXTERN ApplyActionPtr LIBCALL ApplyActionNew PROTO (( void ));
+NLM_EXTERN ApplyActionPtr LIBCALL ApplyActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ApplyActionAsnWrite PROTO (( ApplyActionPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    EditAction
+*
+**************************************************/
+typedef struct struct_Edit_action {
+   struct struct_Field_edit PNTR   edit;
+   ValNodePtr   field;
+} EditAction, PNTR EditActionPtr;
+
+
+NLM_EXTERN EditActionPtr LIBCALL EditActionFree PROTO ((EditActionPtr ));
+NLM_EXTERN EditActionPtr LIBCALL EditActionNew PROTO (( void ));
+NLM_EXTERN EditActionPtr LIBCALL EditActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL EditActionAsnWrite PROTO (( EditActionPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ConvertAction
+*
+**************************************************/
+typedef struct struct_Convert_action {
+   ValNodePtr   fields;
+   Uint2   existing_text;
+} ConvertAction, PNTR ConvertActionPtr;
+
+
+NLM_EXTERN ConvertActionPtr LIBCALL ConvertActionFree PROTO ((ConvertActionPtr ));
+NLM_EXTERN ConvertActionPtr LIBCALL ConvertActionNew PROTO (( void ));
+NLM_EXTERN ConvertActionPtr LIBCALL ConvertActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ConvertActionAsnWrite PROTO (( ConvertActionPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    CopyAction
+*
+**************************************************/
+typedef struct struct_Copy_action {
+   ValNodePtr   fields;
+   Uint2   existing_text;
+} CopyAction, PNTR CopyActionPtr;
+
+
+NLM_EXTERN CopyActionPtr LIBCALL CopyActionFree PROTO ((CopyActionPtr ));
+NLM_EXTERN CopyActionPtr LIBCALL CopyActionNew PROTO (( void ));
+NLM_EXTERN CopyActionPtr LIBCALL CopyActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CopyActionAsnWrite PROTO (( CopyActionPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    SwapAction
+*
+**************************************************/
+typedef struct struct_Swap_action {
+   ValNodePtr   fields;
+   ValNodePtr   field_to;
+} SwapAction, PNTR SwapActionPtr;
+
+
+NLM_EXTERN SwapActionPtr LIBCALL SwapActionFree PROTO ((SwapActionPtr ));
+NLM_EXTERN SwapActionPtr LIBCALL SwapActionNew PROTO (( void ));
+NLM_EXTERN SwapActionPtr LIBCALL SwapActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SwapActionAsnWrite PROTO (( SwapActionPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    AECRParseAction
+*
+**************************************************/
+typedef struct struct_AECRParse_action {
+   struct struct_Text_portion PNTR   portion;
+   ValNodePtr   fields;
+   Uint1   remove_from_parsed;
+   Uint2   existing_text;
+} AECRParseAction, PNTR AECRParseActionPtr;
+
+
+NLM_EXTERN AECRParseActionPtr LIBCALL AECRParseActionFree PROTO ((AECRParseActionPtr ));
+NLM_EXTERN AECRParseActionPtr LIBCALL AECRParseActionNew PROTO (( void ));
+NLM_EXTERN AECRParseActionPtr LIBCALL AECRParseActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL AECRParseActionAsnWrite PROTO (( AECRParseActionPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    RemoveAction
+*
+**************************************************/
+typedef struct struct_Remove_action {
+   ValNodePtr   field;
+} RemoveAction, PNTR RemoveActionPtr;
+
+
+NLM_EXTERN RemoveActionPtr LIBCALL RemoveActionFree PROTO ((RemoveActionPtr ));
+NLM_EXTERN RemoveActionPtr LIBCALL RemoveActionNew PROTO (( void ));
+NLM_EXTERN RemoveActionPtr LIBCALL RemoveActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL RemoveActionAsnWrite PROTO (( RemoveActionPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr ActionChoicePtr;
+typedef ValNode ActionChoice;
+#define ActionChoice_apply 1
+#define ActionChoice_edit 2
+#define ActionChoice_convert 3
+#define ActionChoice_copy 4
+#define ActionChoice_swap 5
+#define ActionChoice_remove 6
+#define ActionChoice_parse 7
+
+
+NLM_EXTERN ActionChoicePtr LIBCALL ActionChoiceFree PROTO ((ActionChoicePtr ));
+NLM_EXTERN ActionChoicePtr LIBCALL ActionChoiceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ActionChoiceAsnWrite PROTO (( ActionChoicePtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Cap_change_none 0
+#define Cap_change_tolower 1
+#define Cap_change_toupper 2
+#define Cap_change_firstcap 3
+
+typedef ValNodePtr ParseSrcOrgChoicePtr;
+typedef ValNode ParseSrcOrgChoice;
+#define ParseSrcOrgChoice_source_qual 1
+#define ParseSrcOrgChoice_taxname_after_binomial 2
+
+
+NLM_EXTERN ParseSrcOrgChoicePtr LIBCALL ParseSrcOrgChoiceFree PROTO ((ParseSrcOrgChoicePtr ));
+NLM_EXTERN ParseSrcOrgChoicePtr LIBCALL ParseSrcOrgChoiceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ParseSrcOrgChoiceAsnWrite PROTO (( ParseSrcOrgChoicePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ParseSrcOrg
+*
+**************************************************/
+typedef struct struct_Parse_src_org {
+   ValNodePtr   field;
+   Uint2   type;
+} ParseSrcOrg, PNTR ParseSrcOrgPtr;
+
+
+NLM_EXTERN ParseSrcOrgPtr LIBCALL ParseSrcOrgFree PROTO ((ParseSrcOrgPtr ));
+NLM_EXTERN ParseSrcOrgPtr LIBCALL ParseSrcOrgNew PROTO (( void ));
+NLM_EXTERN ParseSrcOrgPtr LIBCALL ParseSrcOrgAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ParseSrcOrgAsnWrite PROTO (( ParseSrcOrgPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr ParseSrcPtr;
+typedef ValNode ParseSrc;
+#define ParseSrc_defline 1
+#define ParseSrc_flatfile 2
+#define ParseSrc_local_id 3
+#define ParseSrc_org 4
+#define ParseSrc_comment 5
+#define ParseSrc_bankit_comment 6
+#define ParseSrc_structured_comment 7
+#define ParseSrc_file_id 8
+
+
+NLM_EXTERN ParseSrcPtr LIBCALL ParseSrcFree PROTO ((ParseSrcPtr ));
+NLM_EXTERN ParseSrcPtr LIBCALL ParseSrcAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ParseSrcAsnWrite PROTO (( ParseSrcPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ParseDstOrg
+*
+**************************************************/
+typedef struct struct_Parse_dst_org {
+   ValNodePtr   field;
+   Uint2   type;
+} ParseDstOrg, PNTR ParseDstOrgPtr;
+
+
+NLM_EXTERN ParseDstOrgPtr LIBCALL ParseDstOrgFree PROTO ((ParseDstOrgPtr ));
+NLM_EXTERN ParseDstOrgPtr LIBCALL ParseDstOrgNew PROTO (( void ));
+NLM_EXTERN ParseDstOrgPtr LIBCALL ParseDstOrgAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ParseDstOrgAsnWrite PROTO (( ParseDstOrgPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr ParseDestPtr;
+typedef ValNode ParseDest;
+#define ParseDest_defline 1
+#define ParseDest_org 2
+#define ParseDest_featqual 3
+#define ParseDest_dbxref 4
+
+
+NLM_EXTERN ParseDestPtr LIBCALL ParseDestFree PROTO ((ParseDestPtr ));
+NLM_EXTERN ParseDestPtr LIBCALL ParseDestAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ParseDestAsnWrite PROTO (( ParseDestPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    LocationInterval
+*
+**************************************************/
+typedef struct struct_Location_interval {
+   Int4   from;
+   Int4   to;
+} LocationInterval, PNTR LocationIntervalPtr;
+
+
+NLM_EXTERN LocationIntervalPtr LIBCALL LocationIntervalFree PROTO ((LocationIntervalPtr ));
+NLM_EXTERN LocationIntervalPtr LIBCALL LocationIntervalNew PROTO (( void ));
+NLM_EXTERN LocationIntervalPtr LIBCALL LocationIntervalAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL LocationIntervalAsnWrite PROTO (( LocationIntervalPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr LocationChoicePtr;
+typedef ValNode LocationChoice;
+#define LocationChoice_interval 1
+#define LocationChoice_whole_sequence 2
+
+
+NLM_EXTERN LocationChoicePtr LIBCALL LocationChoiceFree PROTO ((LocationChoicePtr ));
+NLM_EXTERN LocationChoicePtr LIBCALL LocationChoiceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL LocationChoiceAsnWrite PROTO (( LocationChoicePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    SequenceList
+*
+**************************************************/
+typedef ValNode SequenceList;
+typedef ValNodePtr SequenceListPtr;
+#define SequenceListNew() ValNodeNew(NULL) 
+
+#ifdef NLM_GENERATED_CODE_PROTO
+
+NLM_EXTERN SequenceListPtr LIBCALL SequenceListFree PROTO ((SequenceListPtr ));
+NLM_EXTERN SequenceListPtr LIBCALL SequenceListNew PROTO (( void ));
+NLM_EXTERN SequenceListPtr LIBCALL SequenceListAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SequenceListAsnWrite PROTO (( SequenceListPtr , AsnIoPtr, AsnTypePtr));
+
+#endif /* NLM_GENERATED_CODE_PROTO */
+
+typedef ValNodePtr SequenceListChoicePtr;
+typedef ValNode SequenceListChoice;
+#define SequenceListChoice_list 1
+#define SequenceListChoice_all 2
+
+
+NLM_EXTERN SequenceListChoicePtr LIBCALL SequenceListChoiceFree PROTO ((SequenceListChoicePtr ));
+NLM_EXTERN SequenceListChoicePtr LIBCALL SequenceListChoiceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SequenceListChoiceAsnWrite PROTO (( SequenceListChoicePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    ApplyFeatureAction
+*
+**************************************************/
+typedef struct struct_Apply_feature_action {
+   Uint2   type;
+   Uint1   partial5;
+   Uint1   partial3;
+   Uint1   plus_strand;
+   ValNodePtr   location;
+   ValNodePtr   seq_list;
+   Uint1   add_redundant;
+   Uint1   add_mrna;
+   Uint1   apply_to_parts;
+   Int4   only_seg_num;
+   ValNodePtr   fields;
+} ApplyFeatureAction, PNTR ApplyFeatureActionPtr;
+
+
+NLM_EXTERN ApplyFeatureActionPtr LIBCALL ApplyFeatureActionFree PROTO ((ApplyFeatureActionPtr ));
+NLM_EXTERN ApplyFeatureActionPtr LIBCALL ApplyFeatureActionNew PROTO (( void ));
+NLM_EXTERN ApplyFeatureActionPtr LIBCALL ApplyFeatureActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL ApplyFeatureActionAsnWrite PROTO (( ApplyFeatureActionPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    RemoveFeatureAction
+*
+**************************************************/
+typedef struct struct_Remove_feature_action {
+   Uint2   type;
+   ValNodePtr   constraint;
+} RemoveFeatureAction, PNTR RemoveFeatureActionPtr;
+
+
+NLM_EXTERN RemoveFeatureActionPtr LIBCALL RemoveFeatureActionFree PROTO ((RemoveFeatureActionPtr ));
+NLM_EXTERN RemoveFeatureActionPtr LIBCALL RemoveFeatureActionNew PROTO (( void ));
+NLM_EXTERN RemoveFeatureActionPtr LIBCALL RemoveFeatureActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL RemoveFeatureActionAsnWrite PROTO (( RemoveFeatureActionPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Feature_location_strand_from_any 0
+#define Feature_location_strand_from_plus 1
+#define Feature_location_strand_from_minus 2
+#define Feature_location_strand_from_unknown 3
+#define Feature_location_strand_from_both 4
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Feature_location_strand_to_plus 1
+#define Feature_location_strand_to_minus 2
+#define Feature_location_strand_to_unknown 3
+#define Feature_location_strand_to_both 4
+#define Feature_location_strand_to_reverse 5
+
+
+
+/**************************************************
+*
+*    EditLocationStrand
+*
+**************************************************/
+typedef struct struct_Edit_location_strand {
+   Uint2   strand_from;
+   Uint2   strand_to;
+} EditLocationStrand, PNTR EditLocationStrandPtr;
+
+
+NLM_EXTERN EditLocationStrandPtr LIBCALL EditLocationStrandFree PROTO ((EditLocationStrandPtr ));
+NLM_EXTERN EditLocationStrandPtr LIBCALL EditLocationStrandNew PROTO (( void ));
+NLM_EXTERN EditLocationStrandPtr LIBCALL EditLocationStrandAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL EditLocationStrandAsnWrite PROTO (( EditLocationStrandPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Partial_5_set_constraint_all 0
+#define Partial_5_set_constraint_at_end 1
+#define Partial_5_set_constraint_bad_start 2
+#define Partial_5_set_constraint_frame_not_one 3
+
+
+
+/**************************************************
+*
+*    Partial5SetAction
+*
+**************************************************/
+typedef struct struct_Partial_5_set_action {
+   Uint2   constraint;
+   Uint1   extend;
+} Partial5SetAction, PNTR Partial5SetActionPtr;
+
+
+NLM_EXTERN Partial5SetActionPtr LIBCALL Partial5SetActionFree PROTO ((Partial5SetActionPtr ));
+NLM_EXTERN Partial5SetActionPtr LIBCALL Partial5SetActionNew PROTO (( void ));
+NLM_EXTERN Partial5SetActionPtr LIBCALL Partial5SetActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL Partial5SetActionAsnWrite PROTO (( Partial5SetActionPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Partial_5_clear_constraint_all 0
+#define Partial_5_clear_constraint_not_at_end 1
+#define Partial_5_clear_constraint_good_start 2
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Partial_3_set_constraint_all 0
+#define Partial_3_set_constraint_at_end 1
+#define Partial_3_set_constraint_bad_end 2
+
+
+
+/**************************************************
+*
+*    Partial3SetAction
+*
+**************************************************/
+typedef struct struct_Partial_3_set_action {
+   Uint2   constraint;
+   Uint1   extend;
+} Partial3SetAction, PNTR Partial3SetActionPtr;
+
+
+NLM_EXTERN Partial3SetActionPtr LIBCALL Partial3SetActionFree PROTO ((Partial3SetActionPtr ));
+NLM_EXTERN Partial3SetActionPtr LIBCALL Partial3SetActionNew PROTO (( void ));
+NLM_EXTERN Partial3SetActionPtr LIBCALL Partial3SetActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL Partial3SetActionAsnWrite PROTO (( Partial3SetActionPtr , AsnIoPtr, AsnTypePtr));
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Partial_3_clear_constraint_all 0
+#define Partial_3_clear_constraint_not_at_end 1
+#define Partial_3_clear_constraint_good_end 2
+
+/* following #defines are for enumerated type, not used by object loaders */
+#define Convert_location_type_join 1
+#define Convert_location_type_order 2
+#define Convert_location_type_merge 3
+
+typedef ValNodePtr LocationEditTypePtr;
+typedef ValNode LocationEditType;
+#define LocationEditType_strand 1
+#define LocationEditType_set_5_partial 2
+#define LocationEditType_clear_5_partial 3
+#define LocationEditType_set_3_partial 4
+#define LocationEditType_clear_3_partial 5
+#define LocationEditType_convert 6
+
+
+NLM_EXTERN LocationEditTypePtr LIBCALL LocationEditTypeFree PROTO ((LocationEditTypePtr ));
+NLM_EXTERN LocationEditTypePtr LIBCALL LocationEditTypeAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL LocationEditTypeAsnWrite PROTO (( LocationEditTypePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    EditFeatureLocationAction
+*
+**************************************************/
+typedef struct struct_Edit_feature_location_action {
+   Uint2   type;
+   ValNodePtr   action;
+   ValNodePtr   constraint;
+} EditFeatureLocationAction, PNTR EditFeatureLocationActionPtr;
+
+
+NLM_EXTERN EditFeatureLocationActionPtr LIBCALL EditFeatureLocationActionFree PROTO ((EditFeatureLocationActionPtr ));
+NLM_EXTERN EditFeatureLocationActionPtr LIBCALL EditFeatureLocationActionNew PROTO (( void ));
+NLM_EXTERN EditFeatureLocationActionPtr LIBCALL EditFeatureLocationActionAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL EditFeatureLocationActionAsnWrite PROTO (( EditFeatureLocationActionPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr MacroActionChoicePtr;
+typedef ValNode MacroActionChoice;
+#define MacroActionChoice_aecr 1
+#define MacroActionChoice_parse 2
+#define MacroActionChoice_add_feature 3
+#define MacroActionChoice_remove_feature 4
+#define MacroActionChoice_edit_location 5
+
+
+NLM_EXTERN MacroActionChoicePtr LIBCALL MacroActionChoiceFree PROTO ((MacroActionChoicePtr ));
+NLM_EXTERN MacroActionChoicePtr LIBCALL MacroActionChoiceAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL MacroActionChoiceAsnWrite PROTO (( MacroActionChoicePtr , AsnIoPtr, AsnTypePtr));
+
+#ifdef __cplusplus
+/* { */ }
+#endif
+
+#endif /* _objmacro_ */
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
diff --git a/object/objpubd.h b/object/objpubd.h
index 0c73e100..05e0ef02 100644
--- a/object/objpubd.h
+++ b/object/objpubd.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.11 $
+* $Revision: 6.12 $
 *
 * File Description:  Object manager interface for type Pubdesc from
 *                    NCBI-Sequence.  This is separate to avoid typedef
@@ -45,6 +45,9 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: objpubd.h,v $
+* Revision 6.12  2007/12/04 17:50:55  kans
+* added MI_TECH_tsa
+*
 * Revision 6.11  2005/12/29 13:46:18  bollin
 * added PubdescContentMatch function
 *
@@ -256,6 +259,7 @@ typedef struct molinfo {
 #define MI_TECH_wgs 20       /* Whole Genome Shotgun */
 #define MI_TECH_barcode 21   /* Barcode of Life Project */
 #define MI_TECH_composite_wgs_htgs 22   /* Assembly/Scaffold composite of techniques */
+#define MI_TECH_tsa 23       /* Transcriptome Shotgun Assembly */
 #define MI_TECH_other 255           /* doesnt' fit anything */
 
 NLM_EXTERN MolInfoPtr LIBCALL MolInfoNew PROTO((void));
diff --git a/object/objseq.c b/object/objseq.c
index 282dfc37..6ed3b04d 100644
--- a/object/objseq.c
+++ b/object/objseq.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.29 $
+* $Revision: 6.30 $
 *
 * File Description:  Object manager for module NCBI-Seq
 *
@@ -60,6 +60,7 @@ static char *this_file = __FILE__;
 #include <objgbseq.h>
 #include <objinsdseq.h>
 #include <objtseq.h>
+#include <objtable.h>
 
 static Boolean SeqDescrAsnWriteExtra (ValNodePtr anp, AsnIoPtr aip, AsnTypePtr orig,
 					Boolean anp_not_null);
@@ -3115,6 +3116,7 @@ NLM_EXTERN SeqAnnotPtr LIBCALL SeqAnnotFree (SeqAnnotPtr sap)
     SeqGraphPtr sgp, sgpnext;
 	SeqIdPtr sip;
 	SeqLocPtr slp;
+	SeqTablePtr stp;
 
     if (sap == NULL)
         return sap;
@@ -3161,6 +3163,10 @@ NLM_EXTERN SeqAnnotPtr LIBCALL SeqAnnotFree (SeqAnnotPtr sap)
 			slp = (SeqLocPtr)sap->data;
 			SeqLocSetFree(slp);
 			break;
+		case 6:   /* SeqTable */
+			stp = (SeqTablePtr)sap->data;
+			SeqTableFree(stp);
+			break;
 
     }
 	return (SeqAnnotPtr)MemFree(sap);
@@ -3269,6 +3275,9 @@ static Boolean SeqAnnotAsnWriteExtra (SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr
         case 5:
             if (! SeqLocSetAsnWrite((SeqLocPtr)sap->data, aip, SEQ_ANNOT_data_locs, SEQ_ANNOT_data_locs_E)) goto erret;
             break;
+        case 6:
+            if (! SeqTableAsnWrite((SeqTablePtr)sap->data, aip, SEQ_ANNOT_data_seq_table)) goto erret;
+            break;
     }
 
     if (! AsnCloseStruct(aip, atp, (Pointer)sap)) goto erret;
@@ -3385,6 +3394,11 @@ NLM_EXTERN SeqAnnotPtr LIBCALL SeqAnnotAsnRead (AsnIoPtr aip, AsnTypePtr orig)
 			sap->type = 3;
 		}
     }
+    else if (atp == SEQ_ANNOT_data_seq_table)
+    {
+        sap->type = 6;
+        sap->data = (Pointer) SeqTableAsnRead(aip, atp);
+    }
 
     atp = AsnReadId(aip, amp, atp); if (atp == NULL) goto erret;   /* end struct */
     if (AsnReadVal(aip, atp, &av) <= 0) goto erret;
diff --git a/object/objtable.c b/object/objtable.c
new file mode 100644
index 00000000..38162741
--- /dev/null
+++ b/object/objtable.c
@@ -0,0 +1,1633 @@
+#include <asn.h>
+
+#define NLM_GENERATED_CODE_PROTO
+
+#include <objtable.h>
+
+static Boolean loaded = FALSE;
+
+#include <asntable.h>
+#include <objloc.h>
+
+#ifndef NLM_EXTERN_LOADS
+#define NLM_EXTERN_LOADS {}
+#endif
+
+NLM_EXTERN Boolean LIBCALL
+objtableAsnLoad(void)
+{
+
+   if ( ! loaded) {
+      NLM_EXTERN_LOADS
+
+      if ( ! AsnLoad ())
+      return FALSE;
+      loaded = TRUE;
+   }
+
+   return TRUE;
+}
+
+
+
+/**************************************************
+*    Generated object loaders for Module NCBI-SeqTable
+*    Generated using ASNCODE Revision: 6.16 at Dec 12, 2007  3:30 PM
+*
+**************************************************/
+
+
+/**************************************************
+*
+*    SeqTableColumnInfoNew()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableColumnInfoPtr LIBCALL
+SeqTableColumnInfoNew(void)
+{
+   SeqTableColumnInfoPtr ptr = MemNew((size_t) sizeof(SeqTableColumnInfo));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    SeqTableColumnInfoFree()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableColumnInfoPtr LIBCALL
+SeqTableColumnInfoFree(SeqTableColumnInfoPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   MemFree(ptr -> title);
+   MemFree(ptr -> field_name);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    SeqTableColumnInfoAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableColumnInfoPtr LIBCALL
+SeqTableColumnInfoAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   SeqTableColumnInfoPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SeqTableColumnInfo ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQTABLE_COLUMN_INFO);
+   } else {
+      atp = AsnLinkType(orig, SEQTABLE_COLUMN_INFO);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = SeqTableColumnInfoNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == SEQTABLE_COLUMN_INFO_title) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> title = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQTABLE_COLUMN_INFO_field_id) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> field_id = av.intvalue;
+      ptr -> OBbits__ |= 1<<0;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQTABLE_COLUMN_INFO_field_name) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> field_name = av.ptrvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = SeqTableColumnInfoFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    SeqTableColumnInfoAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SeqTableColumnInfoAsnWrite(SeqTableColumnInfoPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, SEQTABLE_COLUMN_INFO);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> title != NULL) {
+      av.ptrvalue = ptr -> title;
+      retval = AsnWrite(aip, SEQTABLE_COLUMN_INFO_title,  &av);
+   }
+   if (ptr -> field_id || (ptr -> OBbits__ & (1<<0) )){   av.intvalue = ptr -> field_id;
+      retval = AsnWrite(aip, SEQTABLE_COLUMN_INFO_field_id,  &av);
+   }
+   if (ptr -> field_name != NULL) {
+      av.ptrvalue = ptr -> field_name;
+      retval = AsnWrite(aip, SEQTABLE_COLUMN_INFO_field_name,  &av);
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    SeqTableColumnNew()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableColumnPtr LIBCALL
+SeqTableColumnNew(void)
+{
+   SeqTableColumnPtr ptr = MemNew((size_t) sizeof(SeqTableColumn));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    SeqTableColumnFree()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableColumnPtr LIBCALL
+SeqTableColumnFree(SeqTableColumnPtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   SeqTableColumnInfoFree(ptr -> header);
+   SeqTableMultiDataFree(ptr -> data);
+   SeqTableSparseIndexFree(ptr -> sparse);
+   SeqTableSingleDataFree(ptr -> default__);
+   SeqTableSingleDataFree(ptr -> sparse_other);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    SeqTableColumnAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableColumnPtr LIBCALL
+SeqTableColumnAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   SeqTableColumnPtr ptr;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SeqTableColumn ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQTABLE_COLUMN);
+   } else {
+      atp = AsnLinkType(orig, SEQTABLE_COLUMN);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = SeqTableColumnNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == SEQTABLE_COLUMN_header) {
+      ptr -> header = SeqTableColumnInfoAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQTABLE_COLUMN_data) {
+      ptr -> data = SeqTableMultiDataAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQTABLE_COLUMN_sparse) {
+      ptr -> sparse = SeqTableSparseIndexAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQTABLE_COLUMN_default) {
+      ptr -> default__ = SeqTableSingleDataAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQTABLE_COLUMN_sparse_other) {
+      ptr -> sparse_other = SeqTableSingleDataAsnRead(aip, atp);
+      if (aip -> io_failure) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = SeqTableColumnFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    SeqTableColumnAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SeqTableColumnAsnWrite(SeqTableColumnPtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, SEQTABLE_COLUMN);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   if (ptr -> header != NULL) {
+      if ( ! SeqTableColumnInfoAsnWrite(ptr -> header, aip, SEQTABLE_COLUMN_header)) {
+         goto erret;
+      }
+   }
+   if (ptr -> data != NULL) {
+      if ( ! SeqTableMultiDataAsnWrite(ptr -> data, aip, SEQTABLE_COLUMN_data)) {
+         goto erret;
+      }
+   }
+   if (ptr -> sparse != NULL) {
+      if ( ! SeqTableSparseIndexAsnWrite(ptr -> sparse, aip, SEQTABLE_COLUMN_sparse)) {
+         goto erret;
+      }
+   }
+   if (ptr -> default__ != NULL) {
+      if ( ! SeqTableSingleDataAsnWrite(ptr -> default__, aip, SEQTABLE_COLUMN_default)) {
+         goto erret;
+      }
+   }
+   if (ptr -> sparse_other != NULL) {
+      if ( ! SeqTableSingleDataAsnWrite(ptr -> sparse_other, aip, SEQTABLE_COLUMN_sparse_other)) {
+         goto erret;
+      }
+   }
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    SeqTableNew()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTablePtr LIBCALL
+SeqTableNew(void)
+{
+   SeqTablePtr ptr = MemNew((size_t) sizeof(SeqTable));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    SeqTableFree()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTablePtr LIBCALL
+SeqTableFree(SeqTablePtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericUserSeqOfFree(ptr -> columns, (AsnOptFreeFunc) SeqTableColumnFree);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    SeqTableAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTablePtr LIBCALL
+SeqTableAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   SeqTablePtr ptr;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SeqTable ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQ_TABLE);
+   } else {
+      atp = AsnLinkType(orig, SEQ_TABLE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = SeqTableNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == SEQ_TABLE_feat_type) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> feat_type = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQ_TABLE_feat_subtype) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> feat_subtype = av.intvalue;
+      ptr -> OBbits__ |= 1<<0;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQ_TABLE_num_rows) {
+      if ( AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      ptr -> num_rows = av.intvalue;
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == SEQ_TABLE_columns) {
+      ptr -> columns = AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqTableColumnAsnRead, (AsnOptFreeFunc) SeqTableColumnFree);
+      if (isError && ptr -> columns == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = SeqTableFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    SeqTableAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SeqTableAsnWrite(SeqTablePtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, SEQ_TABLE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   av.intvalue = ptr -> feat_type;
+   retval = AsnWrite(aip, SEQ_TABLE_feat_type,  &av);
+   if (ptr -> feat_subtype || (ptr -> OBbits__ & (1<<0) )){   av.intvalue = ptr -> feat_subtype;
+      retval = AsnWrite(aip, SEQ_TABLE_feat_subtype,  &av);
+   }
+   av.intvalue = ptr -> num_rows;
+   retval = AsnWrite(aip, SEQ_TABLE_num_rows,  &av);
+   AsnGenericUserSeqOfAsnWrite(ptr -> columns, (AsnWriteFunc) SeqTableColumnAsnWrite, aip, SEQ_TABLE_columns, SEQ_TABLE_columns_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    CommonStringTableNew()
+*
+**************************************************/
+NLM_EXTERN 
+CommonStringTablePtr LIBCALL
+CommonStringTableNew(void)
+{
+   CommonStringTablePtr ptr = MemNew((size_t) sizeof(CommonStringTable));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    CommonStringTableFree()
+*
+**************************************************/
+NLM_EXTERN 
+CommonStringTablePtr LIBCALL
+CommonStringTableFree(CommonStringTablePtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericBaseSeqOfFree(ptr -> strings ,ASNCODE_PTRVAL_SLOT);
+   AsnGenericBaseSeqOfFree(ptr -> indexes ,ASNCODE_INTVAL_SLOT);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    CommonStringTableAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CommonStringTablePtr LIBCALL
+CommonStringTableAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CommonStringTablePtr ptr;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CommonStringTable ::= (self contained) */
+      atp = AsnReadId(aip, amp, COMMONSTRING_TABLE);
+   } else {
+      atp = AsnLinkType(orig, COMMONSTRING_TABLE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = CommonStringTableNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == COMMONSTRING_TABLE_strings) {
+      ptr -> strings = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_PTRVAL_SLOT, &isError);
+      if (isError && ptr -> strings == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == COMMONSTRING_TABLE_indexes) {
+      ptr -> indexes = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_INTVAL_SLOT, &isError);
+      if (isError && ptr -> indexes == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CommonStringTableFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CommonStringTableAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CommonStringTableAsnWrite(CommonStringTablePtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, COMMONSTRING_TABLE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> strings ,ASNCODE_PTRVAL_SLOT, aip, COMMONSTRING_TABLE_strings, COMMONSTRING_TABLE_strings_E);
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> indexes ,ASNCODE_INTVAL_SLOT, aip, COMMONSTRING_TABLE_indexes, COMMONSTRING_TABLE_indexes_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    CommonBytesTableNew()
+*
+**************************************************/
+NLM_EXTERN 
+CommonBytesTablePtr LIBCALL
+CommonBytesTableNew(void)
+{
+   CommonBytesTablePtr ptr = MemNew((size_t) sizeof(CommonBytesTable));
+
+   return ptr;
+
+}
+
+
+/**************************************************
+*
+*    CommonBytesTableFree()
+*
+**************************************************/
+NLM_EXTERN 
+CommonBytesTablePtr LIBCALL
+CommonBytesTableFree(CommonBytesTablePtr ptr)
+{
+
+   if(ptr == NULL) {
+      return NULL;
+   }
+   AsnGenericBaseSeqOfFree(ptr -> bytes ,ASNCODE_BYTEVAL_SLOT);
+   AsnGenericBaseSeqOfFree(ptr -> indexes ,ASNCODE_INTVAL_SLOT);
+   return MemFree(ptr);
+}
+
+
+/**************************************************
+*
+*    CommonBytesTableAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+CommonBytesTablePtr LIBCALL
+CommonBytesTableAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean isError = FALSE;
+   AsnReadFunc func;
+   CommonBytesTablePtr ptr;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* CommonBytesTable ::= (self contained) */
+      atp = AsnReadId(aip, amp, COMMONBYTES_TABLE);
+   } else {
+      atp = AsnLinkType(orig, COMMONBYTES_TABLE);
+   }
+   /* link in local tree */
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   ptr = CommonBytesTableNew();
+   if (ptr == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the start struct */
+      goto erret;
+   }
+
+   atp = AsnReadId(aip,amp, atp);
+   func = NULL;
+
+   if (atp == COMMONBYTES_TABLE_bytes) {
+      ptr -> bytes = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_BYTEVAL_SLOT, &isError);
+      if (isError && ptr -> bytes == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+   if (atp == COMMONBYTES_TABLE_indexes) {
+      ptr -> indexes = AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_INTVAL_SLOT, &isError);
+      if (isError && ptr -> indexes == NULL) {
+         goto erret;
+      }
+      atp = AsnReadId(aip,amp, atp);
+   }
+
+   if (AsnReadVal(aip, atp, &av) <= 0) {
+      goto erret;
+   }
+   /* end struct */
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return ptr;
+
+erret:
+   aip -> io_failure = TRUE;
+   ptr = CommonBytesTableFree(ptr);
+   goto ret;
+}
+
+
+
+/**************************************************
+*
+*    CommonBytesTableAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+CommonBytesTableAsnWrite(CommonBytesTablePtr ptr, AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return FALSE;
+      }
+   }
+
+   if (aip == NULL) {
+      return FALSE;
+   }
+
+   atp = AsnLinkType(orig, COMMONBYTES_TABLE);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (ptr == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+   if (! AsnOpenStruct(aip, atp, (Pointer) ptr)) {
+      goto erret;
+   }
+
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> bytes ,ASNCODE_BYTEVAL_SLOT, aip, COMMONBYTES_TABLE_bytes, COMMONBYTES_TABLE_bytes_E);
+   retval = AsnGenericBaseSeqOfAsnWrite(ptr -> indexes ,ASNCODE_INTVAL_SLOT, aip, COMMONBYTES_TABLE_indexes, COMMONBYTES_TABLE_indexes_E);
+   if (! AsnCloseStruct(aip, atp, (Pointer)ptr)) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+
+/**************************************************
+*
+*    SeqTableMultiDataFree()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableMultiDataPtr LIBCALL
+SeqTableMultiDataFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case SeqTableMultiData_int__:
+      AsnGenericBaseSeqOfFree((ValNodePtr) pnt,ASNCODE_INTVAL_SLOT);
+      break;
+   case SeqTableMultiData_real:
+      AsnGenericBaseSeqOfFree((ValNodePtr) pnt,ASNCODE_REALVAL_SLOT);
+      break;
+   case SeqTableMultiData_string:
+      AsnGenericBaseSeqOfFree((ValNodePtr) pnt,ASNCODE_PTRVAL_SLOT);
+      break;
+   case SeqTableMultiData_bytes:
+      AsnGenericBaseSeqOfFree((ValNodePtr) pnt,ASNCODE_BYTEVAL_SLOT);
+      break;
+   case SeqTableMultiData_common_string:
+      CommonStringTableFree(anp -> data.ptrvalue);
+      break;
+   case SeqTableMultiData_common_bytes:
+      CommonBytesTableFree(anp -> data.ptrvalue);
+      break;
+   case SeqTableMultiData_bit:
+      BSFree(anp -> data.ptrvalue);
+      break;
+   case SeqTableMultiData_loc:
+      AsnGenericChoiceSeqOfFree((Pointer) pnt, (AsnOptFreeFunc) SeqLocFree);
+      break;
+   case SeqTableMultiData_id:
+      AsnGenericChoiceSeqOfFree((Pointer) pnt, (AsnOptFreeFunc) SeqIdFree);
+      break;
+   case SeqTableMultiData_interval:
+      AsnGenericUserSeqOfFree((Pointer) pnt, (AsnOptFreeFunc) SeqIntFree);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    SeqTableMultiDataAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableMultiDataPtr LIBCALL
+SeqTableMultiDataAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SeqTableMultiData ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQTABLE_MULTI_DATA);
+   } else {
+      atp = AsnLinkType(orig, SEQTABLE_MULTI_DATA);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == SEQTABLE_MULTI_DATA_int) {
+      choice = SeqTableMultiData_int__;
+      anp -> data.ptrvalue = 
+      AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_INTVAL_SLOT, &isError);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   else if (atp == SEQTABLE_MULTI_DATA_real) {
+      choice = SeqTableMultiData_real;
+      anp -> data.ptrvalue = 
+      AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_REALVAL_SLOT, &isError);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   else if (atp == SEQTABLE_MULTI_DATA_string) {
+      choice = SeqTableMultiData_string;
+      anp -> data.ptrvalue = 
+      AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_PTRVAL_SLOT, &isError);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   else if (atp == SEQTABLE_MULTI_DATA_bytes) {
+      choice = SeqTableMultiData_bytes;
+      anp -> data.ptrvalue = 
+      AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_BYTEVAL_SLOT, &isError);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   else if (atp == MULTI_DATA_common_string) {
+      choice = SeqTableMultiData_common_string;
+      func = (AsnReadFunc) CommonStringTableAsnRead;
+   }
+   else if (atp == MULTI_DATA_common_bytes) {
+      choice = SeqTableMultiData_common_bytes;
+      func = (AsnReadFunc) CommonBytesTableAsnRead;
+   }
+   else if (atp == SEQTABLE_MULTI_DATA_bit) {
+      choice = SeqTableMultiData_bit;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.ptrvalue = av.ptrvalue;
+   }
+   else if (atp == SEQTABLE_MULTI_DATA_loc) {
+      choice = SeqTableMultiData_loc;
+      anp -> data.ptrvalue =
+      AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqLocAsnRead,             (AsnOptFreeFunc) SeqLocFree);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   else if (atp == SEQTABLE_MULTI_DATA_id) {
+      choice = SeqTableMultiData_id;
+      anp -> data.ptrvalue =
+      AsnGenericChoiceSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqIdAsnRead,             (AsnOptFreeFunc) SeqIdFree);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   else if (atp == SEQTABLE_MULTI_DATA_interval) {
+      choice = SeqTableMultiData_interval;
+      anp -> data.ptrvalue =
+      AsnGenericUserSeqOfAsnRead(aip, amp, atp, &isError, (AsnReadFunc) SeqIntAsnRead,             (AsnOptFreeFunc) SeqIntFree);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    SeqTableMultiDataAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SeqTableMultiDataAsnWrite(SeqTableMultiDataPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, SEQTABLE_MULTI_DATA);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case SeqTableMultiData_int__:
+      retval = AsnGenericBaseSeqOfAsnWrite((Pointer) pnt,ASNCODE_INTVAL_SLOT, aip, SEQTABLE_MULTI_DATA_int, SEQTABLE_MULTI_DATA_int_E);            break;
+   case SeqTableMultiData_real:
+      retval = AsnGenericBaseSeqOfAsnWrite((Pointer) pnt,ASNCODE_REALVAL_SLOT, aip, SEQTABLE_MULTI_DATA_real, SEQTABLE_MULTI_DATA_real_E);            break;
+   case SeqTableMultiData_string:
+      retval = AsnGenericBaseSeqOfAsnWrite((Pointer) pnt,ASNCODE_PTRVAL_SLOT, aip, SEQTABLE_MULTI_DATA_string, SEQTABLE_MULTI_DATA_string_E);            break;
+   case SeqTableMultiData_bytes:
+      retval = AsnGenericBaseSeqOfAsnWrite((Pointer) pnt,ASNCODE_BYTEVAL_SLOT, aip, SEQTABLE_MULTI_DATA_bytes, SEQTABLE_MULTI_DATA_bytes_E);            break;
+   case SeqTableMultiData_common_string:
+      writetype = MULTI_DATA_common_string;
+      func = (AsnWriteFunc) CommonStringTableAsnWrite;
+      break;
+   case SeqTableMultiData_common_bytes:
+      writetype = MULTI_DATA_common_bytes;
+      func = (AsnWriteFunc) CommonBytesTableAsnWrite;
+      break;
+   case SeqTableMultiData_bit:
+      av.ptrvalue = anp->data.ptrvalue;
+      retval = AsnWrite(aip, SEQTABLE_MULTI_DATA_bit, &av);
+      break;
+   case SeqTableMultiData_loc:
+      retval = AsnGenericChoiceSeqOfAsnWrite((Pointer) pnt, (AsnWriteFunc) SeqLocAsnWrite, aip, SEQTABLE_MULTI_DATA_loc, SEQTABLE_MULTI_DATA_loc_E);
+      break;
+   case SeqTableMultiData_id:
+      retval = AsnGenericChoiceSeqOfAsnWrite((Pointer) pnt, (AsnWriteFunc) SeqIdAsnWrite, aip, SEQTABLE_MULTI_DATA_id, SEQTABLE_MULTI_DATA_id_E);
+      break;
+   case SeqTableMultiData_interval:
+      retval = AsnGenericUserSeqOfAsnWrite((Pointer) pnt, (AsnWriteFunc) SeqIntAsnWrite, aip, SEQTABLE_MULTI_DATA_interval, SEQTABLE_MULTI_DATA_interval_E);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    SeqTableSingleDataFree()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableSingleDataPtr LIBCALL
+SeqTableSingleDataFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case SeqTableSingleData_string:
+      MemFree(anp -> data.ptrvalue);
+      break;
+   case SeqTableSingleData_bytes:
+      BSFree(anp -> data.ptrvalue);
+      break;
+   case SeqTableSingleData_loc:
+      SeqLocFree(anp -> data.ptrvalue);
+      break;
+   case SeqTableSingleData_id:
+      SeqIdFree(anp -> data.ptrvalue);
+      break;
+   case SeqTableSingleData_interval:
+      SeqIntFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    SeqTableSingleDataAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableSingleDataPtr LIBCALL
+SeqTableSingleDataAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SeqTableSingleData ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQTABLE_SINGLE_DATA);
+   } else {
+      atp = AsnLinkType(orig, SEQTABLE_SINGLE_DATA);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == SEQTABLE_SINGLE_DATA_int) {
+      choice = SeqTableSingleData_int__;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.intvalue = av.intvalue;
+   }
+   else if (atp == SEQTABLE_SINGLE_DATA_real) {
+      choice = SeqTableSingleData_real;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.realvalue = av.realvalue;
+   }
+   else if (atp == SEQTABLE_SINGLE_DATA_string) {
+      choice = SeqTableSingleData_string;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.ptrvalue = av.ptrvalue;
+   }
+   else if (atp == SEQTABLE_SINGLE_DATA_bytes) {
+      choice = SeqTableSingleData_bytes;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.ptrvalue = av.ptrvalue;
+   }
+   else if (atp == SEQTABLE_SINGLE_DATA_bit) {
+      choice = SeqTableSingleData_bit;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.boolvalue = av.boolvalue;
+   }
+   else if (atp == SEQTABLE_SINGLE_DATA_loc) {
+      choice = SeqTableSingleData_loc;
+      func = (AsnReadFunc) SeqLocAsnRead;
+   }
+   else if (atp == SEQTABLE_SINGLE_DATA_id) {
+      choice = SeqTableSingleData_id;
+      func = (AsnReadFunc) SeqIdAsnRead;
+   }
+   else if (atp == SEQTABLE_SINGLE_DATA_interval) {
+      choice = SeqTableSingleData_interval;
+      func = (AsnReadFunc) SeqIntAsnRead;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    SeqTableSingleDataAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SeqTableSingleDataAsnWrite(SeqTableSingleDataPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, SEQTABLE_SINGLE_DATA);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case SeqTableSingleData_int__:
+      av.intvalue = anp->data.intvalue;
+      retval = AsnWrite(aip, SEQTABLE_SINGLE_DATA_int, &av);
+      break;
+   case SeqTableSingleData_real:
+      av.realvalue = anp->data.realvalue;
+      retval = AsnWrite(aip, SEQTABLE_SINGLE_DATA_real, &av);
+      break;
+   case SeqTableSingleData_string:
+      av.ptrvalue = anp->data.ptrvalue;
+      retval = AsnWrite(aip, SEQTABLE_SINGLE_DATA_string, &av);
+      break;
+   case SeqTableSingleData_bytes:
+      av.ptrvalue = anp->data.ptrvalue;
+      retval = AsnWrite(aip, SEQTABLE_SINGLE_DATA_bytes, &av);
+      break;
+   case SeqTableSingleData_bit:
+      av.boolvalue = anp->data.boolvalue;
+      retval = AsnWrite(aip, SEQTABLE_SINGLE_DATA_bit, &av);
+      break;
+   case SeqTableSingleData_loc:
+      writetype = SEQTABLE_SINGLE_DATA_loc;
+      func = (AsnWriteFunc) SeqLocAsnWrite;
+      break;
+   case SeqTableSingleData_id:
+      writetype = SEQTABLE_SINGLE_DATA_id;
+      func = (AsnWriteFunc) SeqIdAsnWrite;
+      break;
+   case SeqTableSingleData_interval:
+      writetype = SEQTABLE_SINGLE_DATA_interval;
+      func = (AsnWriteFunc) SeqIntAsnWrite;
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
+
+
+/**************************************************
+*
+*    SeqTableSparseIndexFree()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableSparseIndexPtr LIBCALL
+SeqTableSparseIndexFree(ValNodePtr anp)
+{
+   Pointer pnt;
+
+   if (anp == NULL) {
+      return NULL;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   default:
+      break;
+   case SeqTableSparseIndex_indexes:
+      AsnGenericBaseSeqOfFree((ValNodePtr) pnt,ASNCODE_INTVAL_SLOT);
+      break;
+   case SeqTableSparseIndex_bit_set:
+      BSFree(anp -> data.ptrvalue);
+      break;
+   }
+   return MemFree(anp);
+}
+
+
+/**************************************************
+*
+*    SeqTableSparseIndexAsnRead()
+*
+**************************************************/
+NLM_EXTERN 
+SeqTableSparseIndexPtr LIBCALL
+SeqTableSparseIndexAsnRead(AsnIoPtr aip, AsnTypePtr orig)
+{
+   DataVal av;
+   AsnTypePtr atp;
+   ValNodePtr anp;
+   Uint1 choice;
+   Boolean isError = FALSE;
+   Boolean nullIsError = FALSE;
+   AsnReadFunc func;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad()) {
+         return NULL;
+      }
+   }
+
+   if (aip == NULL) {
+      return NULL;
+   }
+
+   if (orig == NULL) {         /* SeqTableSparseIndex ::= (self contained) */
+      atp = AsnReadId(aip, amp, SEQTABLE_SPARSE_INDEX);
+   } else {
+      atp = AsnLinkType(orig, SEQTABLE_SPARSE_INDEX);    /* link in local tree */
+   }
+   if (atp == NULL) {
+      return NULL;
+   }
+
+   anp = ValNodeNew(NULL);
+   if (anp == NULL) {
+      goto erret;
+   }
+   if (AsnReadVal(aip, atp, &av) <= 0) { /* read the CHOICE or OpenStruct value (nothing) */
+      goto erret;
+   }
+
+   func = NULL;
+
+   atp = AsnReadId(aip, amp, atp);  /* find the choice */
+   if (atp == NULL) {
+      goto erret;
+   }
+   if (atp == SEQTABLE_SPARSE_INDEX_indexes) {
+      choice = SeqTableSparseIndex_indexes;
+      anp -> data.ptrvalue = 
+      AsnGenericBaseSeqOfAsnRead(aip, amp, atp, ASNCODE_INTVAL_SLOT, &isError);
+      if (isError && anp -> data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+   else if (atp == SEQTABLE_SPARSE_INDEX_bit_set) {
+      choice = SeqTableSparseIndex_bit_set;
+      if (AsnReadVal(aip, atp, &av) <= 0) {
+         goto erret;
+      }
+      anp->data.ptrvalue = av.ptrvalue;
+   }
+   anp->choice = choice;
+   if (func != NULL)
+   {
+      anp->data.ptrvalue = (* func)(aip, atp);
+      if (aip -> io_failure) goto erret;
+
+      if (nullIsError && anp->data.ptrvalue == NULL) {
+         goto erret;
+      }
+   }
+
+ret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return anp;
+
+erret:
+   anp = MemFree(anp);
+   aip -> io_failure = TRUE;
+   goto ret;
+}
+
+
+/**************************************************
+*
+*    SeqTableSparseIndexAsnWrite()
+*
+**************************************************/
+NLM_EXTERN Boolean LIBCALL 
+SeqTableSparseIndexAsnWrite(SeqTableSparseIndexPtr anp, AsnIoPtr aip, AsnTypePtr orig)
+
+{
+   DataVal av;
+   AsnTypePtr atp, writetype = NULL;
+   Pointer pnt;
+   AsnWriteFunc func = NULL;
+   Boolean retval = FALSE;
+
+   if (! loaded)
+   {
+      if (! objtableAsnLoad())
+      return FALSE;
+   }
+
+   if (aip == NULL)
+   return FALSE;
+
+   atp = AsnLinkType(orig, SEQTABLE_SPARSE_INDEX);   /* link local tree */
+   if (atp == NULL) {
+      return FALSE;
+   }
+
+   if (anp == NULL) { AsnNullValueMsg(aip, atp); goto erret; }
+
+   av.ptrvalue = (Pointer)anp;
+   if (! AsnWriteChoice(aip, atp, (Int2)anp->choice, &av)) {
+      goto erret;
+   }
+
+   pnt = anp->data.ptrvalue;
+   switch (anp->choice)
+   {
+   case SeqTableSparseIndex_indexes:
+      retval = AsnGenericBaseSeqOfAsnWrite((Pointer) pnt,ASNCODE_INTVAL_SLOT, aip, SEQTABLE_SPARSE_INDEX_indexes, SEQTABLE_SPARSE_INDEX_indexes_E);            break;
+   case SeqTableSparseIndex_bit_set:
+      av.ptrvalue = anp->data.ptrvalue;
+      retval = AsnWrite(aip, SEQTABLE_SPARSE_INDEX_bit_set, &av);
+      break;
+   }
+   if (writetype != NULL) {
+      retval = (* func)(pnt, aip, writetype);   /* write it out */
+   }
+   if (!retval) {
+      goto erret;
+   }
+   retval = TRUE;
+
+erret:
+   AsnUnlinkType(orig);       /* unlink local tree */
+   return retval;
+}
diff --git a/object/objtable.h b/object/objtable.h
new file mode 100644
index 00000000..5cb49023
--- /dev/null
+++ b/object/objtable.h
@@ -0,0 +1,188 @@
+#ifndef _objtable_ 
+#define _objtable_ 
+
+#undef NLM_EXTERN
+#ifdef NLM_IMPORT
+#define NLM_EXTERN NLM_IMPORT
+#else
+#define NLM_EXTERN extern
+#endif
+
+
+#ifdef __cplusplus
+extern "C" { /* } */
+#endif
+
+
+/**************************************************
+*
+*    Generated objects for Module NCBI-SeqTable
+*    Generated using ASNCODE Revision: 6.16 at Dec 12, 2007  3:30 PM
+*
+**************************************************/
+
+NLM_EXTERN Boolean LIBCALL
+objtableAsnLoad PROTO((void));
+
+
+/**************************************************
+*
+*    SeqTableColumnInfo
+*
+**************************************************/
+typedef struct struct_SeqTable_column_info {
+   Uint4 OBbits__;
+   CharPtr   title;
+#define OB__SeqTable_column_info_field_id 0
+
+   Int4   field_id;
+   CharPtr   field_name;
+} SeqTableColumnInfo, PNTR SeqTableColumnInfoPtr;
+
+
+NLM_EXTERN SeqTableColumnInfoPtr LIBCALL SeqTableColumnInfoFree PROTO ((SeqTableColumnInfoPtr ));
+NLM_EXTERN SeqTableColumnInfoPtr LIBCALL SeqTableColumnInfoNew PROTO (( void ));
+NLM_EXTERN SeqTableColumnInfoPtr LIBCALL SeqTableColumnInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SeqTableColumnInfoAsnWrite PROTO (( SeqTableColumnInfoPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    SeqTableColumn
+*
+**************************************************/
+typedef struct struct_SeqTable_column {
+   struct struct_SeqTable_column PNTR next;
+   Uint4 OBbits__;
+   struct struct_SeqTable_column_info PNTR   header;
+   ValNodePtr   data;
+   ValNodePtr   sparse;
+   ValNodePtr   default__;
+   ValNodePtr   sparse_other;
+} SeqTableColumn, PNTR SeqTableColumnPtr;
+
+
+NLM_EXTERN SeqTableColumnPtr LIBCALL SeqTableColumnFree PROTO ((SeqTableColumnPtr ));
+NLM_EXTERN SeqTableColumnPtr LIBCALL SeqTableColumnNew PROTO (( void ));
+NLM_EXTERN SeqTableColumnPtr LIBCALL SeqTableColumnAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SeqTableColumnAsnWrite PROTO (( SeqTableColumnPtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    SeqTable
+*
+**************************************************/
+typedef struct struct_Seq_table {
+   Uint4 OBbits__;
+   Int4   feat_type;
+#define OB__Seq_table_feat_subtype 0
+
+   Int4   feat_subtype;
+   Int4   num_rows;
+   struct struct_SeqTable_column PNTR   columns;
+} SeqTable, PNTR SeqTablePtr;
+
+
+NLM_EXTERN SeqTablePtr LIBCALL SeqTableFree PROTO ((SeqTablePtr ));
+NLM_EXTERN SeqTablePtr LIBCALL SeqTableNew PROTO (( void ));
+NLM_EXTERN SeqTablePtr LIBCALL SeqTableAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SeqTableAsnWrite PROTO (( SeqTablePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    CommonStringTable
+*
+**************************************************/
+typedef struct struct_CommonString_table {
+   Uint4 OBbits__;
+   ValNodePtr   strings;
+   ValNodePtr   indexes;
+} CommonStringTable, PNTR CommonStringTablePtr;
+
+
+NLM_EXTERN CommonStringTablePtr LIBCALL CommonStringTableFree PROTO ((CommonStringTablePtr ));
+NLM_EXTERN CommonStringTablePtr LIBCALL CommonStringTableNew PROTO (( void ));
+NLM_EXTERN CommonStringTablePtr LIBCALL CommonStringTableAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CommonStringTableAsnWrite PROTO (( CommonStringTablePtr , AsnIoPtr, AsnTypePtr));
+
+
+
+/**************************************************
+*
+*    CommonBytesTable
+*
+**************************************************/
+typedef struct struct_CommonBytes_table {
+   Uint4 OBbits__;
+   ValNodePtr   bytes;
+   ValNodePtr   indexes;
+} CommonBytesTable, PNTR CommonBytesTablePtr;
+
+
+NLM_EXTERN CommonBytesTablePtr LIBCALL CommonBytesTableFree PROTO ((CommonBytesTablePtr ));
+NLM_EXTERN CommonBytesTablePtr LIBCALL CommonBytesTableNew PROTO (( void ));
+NLM_EXTERN CommonBytesTablePtr LIBCALL CommonBytesTableAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL CommonBytesTableAsnWrite PROTO (( CommonBytesTablePtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr SeqTableMultiDataPtr;
+typedef ValNode SeqTableMultiData;
+#define SeqTableMultiData_int__ 1
+#define SeqTableMultiData_real 2
+#define SeqTableMultiData_string 3
+#define SeqTableMultiData_bytes 4
+#define SeqTableMultiData_common_string 5
+#define SeqTableMultiData_common_bytes 6
+#define SeqTableMultiData_bit 7
+#define SeqTableMultiData_loc 8
+#define SeqTableMultiData_id 9
+#define SeqTableMultiData_interval 10
+
+
+NLM_EXTERN SeqTableMultiDataPtr LIBCALL SeqTableMultiDataFree PROTO ((SeqTableMultiDataPtr ));
+NLM_EXTERN SeqTableMultiDataPtr LIBCALL SeqTableMultiDataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SeqTableMultiDataAsnWrite PROTO (( SeqTableMultiDataPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr SeqTableSingleDataPtr;
+typedef ValNode SeqTableSingleData;
+#define SeqTableSingleData_int__ 1
+#define SeqTableSingleData_real 2
+#define SeqTableSingleData_string 3
+#define SeqTableSingleData_bytes 4
+#define SeqTableSingleData_bit 5
+#define SeqTableSingleData_loc 6
+#define SeqTableSingleData_id 7
+#define SeqTableSingleData_interval 8
+
+
+NLM_EXTERN SeqTableSingleDataPtr LIBCALL SeqTableSingleDataFree PROTO ((SeqTableSingleDataPtr ));
+NLM_EXTERN SeqTableSingleDataPtr LIBCALL SeqTableSingleDataAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SeqTableSingleDataAsnWrite PROTO (( SeqTableSingleDataPtr , AsnIoPtr, AsnTypePtr));
+
+typedef ValNodePtr SeqTableSparseIndexPtr;
+typedef ValNode SeqTableSparseIndex;
+#define SeqTableSparseIndex_indexes 1
+#define SeqTableSparseIndex_bit_set 2
+
+
+NLM_EXTERN SeqTableSparseIndexPtr LIBCALL SeqTableSparseIndexFree PROTO ((SeqTableSparseIndexPtr ));
+NLM_EXTERN SeqTableSparseIndexPtr LIBCALL SeqTableSparseIndexAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
+NLM_EXTERN Boolean LIBCALL SeqTableSparseIndexAsnWrite PROTO (( SeqTableSparseIndexPtr , AsnIoPtr, AsnTypePtr));
+
+#ifdef __cplusplus
+/* { */ }
+#endif
+
+#endif /* _objtable_ */
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
diff --git a/sequin/macro.asn b/sequin/macro.asn
new file mode 100755
index 00000000..06589618
--- /dev/null
+++ b/sequin/macro.asn
@@ -0,0 +1,814 @@
+--$Revision: 1.13 $
+--**********************************************************************
+--
+--  NCBI ASN.1 macro editing language specifications
+--
+--  by Colleen Bollin, 2007
+--
+--**********************************************************************
+
+NCBI-Macro DEFINITIONS ::=
+BEGIN
+
+EXPORTS AECR-action, Parse-action, Macro-action-list;
+
+-- simple constraints --
+
+String-location ::= ENUMERATED {
+    contains (1) ,
+    equals (2) ,
+    starts (3) ,
+    ends (4) ,
+    inlist (5) }
+
+String-constraint ::= SEQUENCE {
+    match-text VisibleString ,
+    match-location String-location DEFAULT contains ,
+    case-sensitive BOOLEAN DEFAULT FALSE ,
+    whole-word BOOLEAN DEFAULT FALSE ,
+    not-present BOOLEAN DEFAULT FALSE }
+
+Strand-constraint ::= ENUMERATED {
+    any (0) ,
+    plus (1) ,
+    minus (2) }
+
+Seqtype-constraint ::= ENUMERATED {
+    any (0) ,
+    nuc (1) ,
+    prot (2) }
+
+Location-constraint ::= SEQUENCE {
+    strand Strand-constraint DEFAULT any ,
+    seq-type Seqtype-constraint DEFAULT any }
+
+Object-type-constraint ::= ENUMERATED {
+    any (0) ,
+    feature (1) ,
+    descriptor (2) }
+
+
+-- feature values --
+
+Feature-type ::= ENUMERATED {
+    any (0) ,
+    gene (1) ,
+    org (2) ,
+    cds (3) ,
+    prot (4) ,
+    preRNA (5) ,
+    mRNA (6) ,
+    tRNA (7) ,
+    rRNA (8) ,
+    snRNA (9) ,
+    scRNA (10) ,
+    otherRNA (11) ,
+    pub (12) ,
+    seq (13) ,
+    imp (14) ,
+    allele (15) ,
+    attenuator (16) ,
+    c-region (17) ,
+    caat-signal (18) ,
+    imp-CDS (19) ,
+    conflict (20) ,
+    d-loop (21) ,
+    d-segment (22) ,
+    enhancer (23) ,
+    exon (24) ,
+    gC-signal (25) ,
+    iDNA (26) ,
+    intron (27) ,
+    j-segment (28) ,
+    ltr (29) ,
+    mat-peptide (30) ,
+    misc-binding (31) ,
+    misc-difference (32) ,
+    misc-feature (33) ,
+    misc-recomb (34) ,
+    misc-RNA (35) ,
+    misc-signal (36) ,
+    misc-structure (37) ,
+    modified-base (38) ,
+    mutation (39) ,
+    n-region (40) ,
+    old-sequence (41) ,
+    polyA-signal (42) ,
+    polyA-site (43) ,
+    precursor-RNA (44) ,
+    prim-transcript (45) ,
+    primer-bind (46) ,
+    promoter (47) ,
+    protein-bind (48) ,
+    rbs (49) ,
+    repeat-region (50) ,
+    repeat-unit (51) ,
+    rep-origin (52) ,
+    s-region (53) ,
+    satellite (54) ,
+    sig-peptide (55) ,
+    source (56) ,
+    stem-loop (57) ,
+    sts (58) ,
+    tata-signal (59) ,
+    terminator (60) ,
+    transit-peptide (61) ,
+    unsure (62) ,
+    v-region (63) ,
+    v-segment (64) ,
+    variation (65) ,
+    virion (66) ,
+    n3clip (67) ,
+    n3UTR (68) ,
+    n5clip (69) ,
+    n5UTR (70) ,
+    n10-signal (71) ,
+    n35-signal (72) ,
+    site-ref (73) ,
+    region (74) ,
+    comment (75) ,
+    bond (76) ,
+    site (77) ,
+    rsite (78) ,
+    user (79) ,
+    txinit (80) ,
+    num (81) ,
+    psec-str (82) ,
+    non-std-residue (83) ,
+    het (84) ,
+    biosrc (85) ,
+    preprotein (86) ,
+    mat-peptide-aa (87) ,
+    sig-peptide-aa (88) ,
+    transit-peptide-aa (89) ,
+    snoRNA (90) ,
+    gap (91) ,
+    operon (92) ,
+    oriT (93) ,
+    ncRNA (94) ,
+    tmRNA (95) }
+
+Feat-qual-legal ::= ENUMERATED {
+    allele (1) ,
+    activity (2) ,
+    anticodon (3) ,
+    bound-moiety (4) ,
+    chromosome (5),
+    citation (6),
+    codon (7) ,
+    codon-start (8) ,
+    codons-recognized (9) ,
+    compare (10) ,
+    cons-splice (11) ,
+    db-xref (12) ,
+    description (13) ,
+    direction (14) ,
+    ec-number (15) ,
+    environmental-sample (16) ,
+    evidence (17) ,
+    exception (18) ,
+    experiment (19) ,
+    focus (20) ,
+    frequency (21) ,
+    function (22) ,
+    gene (23) ,
+    gene-description (24) ,
+    inference (25) ,
+    label (26) ,
+    locus-tag (27) ,
+    map (28) ,
+    mobile-element (29) ,
+    mod-base (30) ,
+    mol-type (31) ,
+    ncRNA-class (32) ,
+    note (33) ,
+    number (34) ,
+    old-locus-tag (35) ,
+    operon (36) ,
+    organism (37) ,
+    organelle (38) ,
+    partial (39) ,
+    phenotype (40) ,
+    plasmid (41) ,
+    product (42) ,
+    protein-id (43) ,
+    pseudo (44) ,
+    rearranged (45) ,
+    replace (46) ,
+    rpt-family (47) ,
+    rpt-type (48) ,
+    rpt-unit (49) ,
+    rpt-unit-seq (50) ,
+    rpt-unit-range (51) ,
+    segment (52) ,
+    sequenced-mol (53) ,
+    standard-name (54) ,
+    synonym (55) ,
+    transcript-id (56) ,
+    transgenic (57) ,
+    translation (58) ,
+    transl-except (59) ,
+    transl-table (60) ,
+    usedin (61) }
+
+Feat-qual-legal-val ::= SEQUENCE {
+    qual Feat-qual-legal ,
+    val  VisibleString }
+
+Feat-qual-legal-val-choice ::= CHOICE {
+    qual Feat-qual-legal-val }
+
+Feat-qual-legal-set ::= SET OF Feat-qual-legal-val-choice
+
+Feat-qual-choice ::= CHOICE {
+    legal-qual Feat-qual-legal ,
+    illegal-qual String-constraint }
+
+Feature-field ::= SEQUENCE {
+    type Feature-type ,
+    field Feat-qual-choice }
+
+Feature-field-legal ::= SEQUENCE {
+    type Feature-type ,
+    field Feat-qual-legal }
+
+Feature-field-pair ::= SEQUENCE {
+    type Feature-type ,
+    field-from Feat-qual-choice ,
+    field-to Feat-qual-choice }
+
+Source-qual ::= ENUMERATED {
+    acronym (1) ,
+    anamorph (2) ,
+    authority (3) ,
+    bio-material (4) ,
+    biotype (5) ,
+    biovar (6) ,
+    breed (7) ,
+    cell-line (8) ,
+    cell-type (9) ,
+    chemovar (10) ,
+    chromosome (11) ,
+    clone (12) ,
+    clone-lib (13) ,
+    collected-by (14) ,
+    collection-date (15) ,
+    common (16) ,
+    common-name (17) ,
+    country (18) ,
+    cultivar (19) ,
+    culture-collection (20) ,
+    dev-stage (21) ,
+    division (22) ,
+    dosage (23) ,
+    ecotype (24) ,
+    endogenous-virus-name (25) ,
+    environmental-sample (26) ,
+    forma (27) ,
+    forma-specialis (28) ,
+    frequency (29) ,
+    fwd-primer-name (30) ,
+    fwd-primer-seq (31) ,
+    gb-acronym (32) ,
+    gb-anamorph (33) ,
+    gb-synonym (34) ,
+    genotype (35) ,
+    germline (36) ,
+    group (37) ,
+    haplotype (38) ,
+    identified-by (39) ,
+    insertion-seq-name (40) ,
+    isolate (41) ,
+    isolation-source (42) ,
+    lab-host (43) ,
+    lat-lon (44) ,
+    lineage (45) ,
+    map (46) ,
+    metagenome-source (47) ,
+    metagenomic (48) ,
+    old-lineage (49) ,
+    old-name (50) ,
+    orgmod-note (51) ,
+    nat-host (52) ,
+    pathovar (53) ,
+    plasmid-name (54) ,
+    plastid-name (55) ,
+    pop-variant (56) ,
+    rearranged (57) ,
+    rev-primer-name (58) ,
+    rev-primer-seq (59) ,
+    segment (60) ,
+    serogroup (61) ,
+    serotype (62) ,
+    serovar (63) ,
+    sex (64) ,
+    specimen-voucher (65) ,
+    strain (66) ,
+    subclone (67) ,
+    subgroup (68) ,
+    subsource-note (69),
+    sub-species (70) ,
+    substrain (71) ,
+    subtype (72) ,
+    synonym (73) ,
+    taxname (74) ,
+    teleomorph (75) ,
+    tissue-lib (76) ,
+    tissue-type (77) ,
+    transgenic (78) ,
+    transposon-name (79) ,
+    type (80) ,
+    variety (81) }
+
+Source-qual-pair ::= SEQUENCE {
+    field-from Source-qual ,
+    field-to Source-qual }
+
+Source-location ::= ENUMERATED {
+    unknown (0) ,
+    genomic (1) ,
+    chloroplast (2) ,
+    chromoplast (3) ,
+    kinetoplast (4) ,
+    mitochondrion (5) ,
+    plastid (6) ,
+    macronuclear (7) ,
+    extrachrom (8) ,
+    plasmid (9) ,
+    transposon (10) ,
+    insertion-seq (11) ,
+    cyanelle (12) ,
+    proviral (13) ,
+    virion (14) ,
+    nucleomorph (15) ,
+    apicoplast (16) ,
+    leucoplast (17) ,
+    proplastid (18) ,
+    endogenous-virus (19) ,
+    hydrogenosome (20) ,
+    chromosome (21) ,
+    chromatophore (22) }
+
+Source-origin ::= ENUMERATED {
+    unknown (0) ,
+    natural (1) ,
+    natmut (2) ,
+    mut (3) ,
+    artificial (4) ,
+    synthetic (5) ,
+    other (255) }
+
+Source-qual-choice ::= CHOICE {
+    textqual Source-qual ,
+    location Source-location,
+    origin Source-origin }
+    
+
+CDSGeneProt-field ::= ENUMERATED {
+    cds-comment (1) ,
+    gene-locus (2) ,
+    gene-description (3) ,
+    gene-comment (4) ,
+    gene-allele (5) ,
+    gene-maploc (6) ,
+    gene-locus-tag (7) ,
+    gene-synonym (8) ,
+    gene-old-locus-tag (9) ,
+    mrna-product (10) ,
+    mrna-comment (11) ,
+    prot-name (12) ,
+    prot-description (13) ,
+    prot-ec-number (14) ,
+    prot-activity (15) ,
+    prot-comment (16) ,
+    mat-peptide-name (17) ,
+    mat-peptide-description (18) ,
+    mat-peptide-ec-number (19) ,
+    mat-peptide-activity (20) ,
+    mat-peptide-comment (21) }
+
+CDSGeneProt-field-pair ::= SEQUENCE {
+    field-from CDSGeneProt-field ,
+    field-to CDSGeneProt-field }
+
+Molecule-type ::= ENUMERATED {
+  unknown (0) ,
+  genomic (1) ,
+  precursor-RNA (2) ,
+  mRNA (3) ,
+  rRNA (4) ,
+  tRNA (5) ,
+  snRNA (6) ,
+  scRNA (7) ,
+  genomic-mRNA (8) ,
+  cRNA (9) ,
+  snoRNA (10) ,
+  transcribed-RNA (11) ,
+  ncRNA (12) ,
+  transfer-messenger-RNA (13) ,
+  other (14) }
+
+Technique-type ::= ENUMERATED {
+  unknown (0) , 
+  standard (1) ,
+  est (2) ,
+  sts (3) ,
+  survey (4) ,
+  genetic-map (5) ,
+  physical-map (6) ,
+  derived (7) ,
+  concept-trans (8) ,
+  seq-pept (9) ,
+  both (10) ,
+  seq-pept-overlap (11) ,
+  seq-pept-homol (12) , 
+  concept-trans-a (13) ,
+  htgs-1 (14) ,
+  htgs-2 (15) ,
+  htgs-3 (16) ,
+  fli-cDNA (17) ,
+  htgs-0 (18) ,
+  htc (19) ,
+  wgs (20) ,
+  barcode (21) ,
+  composite-wgs-htgs (22) ,
+  tsa (23) ,
+  other (24) }
+
+Completedness-type ::= ENUMERATED {
+  unknown (0) ,
+  complete (1) ,
+  partial (2) ,
+  no-left (3) ,
+  no-right (4) ,
+  no-ends (5) ,
+  has-left (6) ,
+  has-right (7) ,
+  other (6) }
+
+Molecule-class-type ::= ENUMERATED {
+  unknown (0) ,
+  dna (1) ,
+  rna (2) ,
+  protein (3) ,
+  nucleotide (4),
+  other (5) }
+
+Topology-type ::= ENUMERATED {
+  unknown (0) ,
+  linear (1) ,
+  circular (2) ,
+  tandem (3) ,
+  other (4) }
+
+Strand-type ::= ENUMERATED {
+  unknown (0) ,
+  single (1) ,
+  double (2) ,
+  mixed (3) ,
+  mixed-rev (4) ,
+  other (5) }
+
+Molinfo-field ::= CHOICE {
+    molecule Molecule-type ,
+    technique Technique-type ,
+    completedness Completedness-type ,
+    mol-class Molecule-class-type ,
+    topology Topology-type ,
+    strand Strand-type }
+
+Molinfo-molecule-pair ::= SEQUENCE {
+    from Molecule-type ,
+    to Molecule-type }
+
+Molinfo-technique-pair ::= SEQUENCE {
+    from Technique-type ,
+    to Technique-type }
+
+Molinfo-completedness-pair ::= SEQUENCE {
+    from Completedness-type ,
+    to Completedness-type }
+
+Molinfo-mol-class-pair ::= SEQUENCE {
+    from Molecule-class-type ,
+    to Molecule-class-type }
+
+Molinfo-topology-pair ::= SEQUENCE {
+    from Topology-type ,
+    to Topology-type }
+
+Molinfo-strand-pair ::= SEQUENCE {
+    from Strand-type ,
+    to Strand-type }
+
+Molinfo-field-pair ::= CHOICE {
+    molecule Molinfo-molecule-pair ,
+    technique Molinfo-technique-pair ,
+    completedness Molinfo-completedness-pair ,
+    mol-class Molinfo-mol-class-pair ,
+    topology Molinfo-topology-pair ,
+    strand Molinfo-strand-pair }
+   
+    
+-- complex constraints --
+
+Source-constraint ::= SEQUENCE {
+  field1 Source-qual-choice OPTIONAL ,
+  field2 Source-qual-choice OPTIONAL ,
+  constraint String-constraint OPTIONAL ,
+  type-constraint Object-type-constraint OPTIONAL }
+
+CDSGeneProt-feature-type-constraint ::= ENUMERATED {
+    gene (1) ,
+    mRNA (2) ,
+    cds (3) ,
+    prot (4) ,
+    exon (5) ,
+    mat-peptide (6) }
+
+CDSGeneProt-pseudo-constraint ::= SEQUENCE {
+    feature CDSGeneProt-feature-type-constraint ,
+    is-pseudo BOOLEAN DEFAULT TRUE }
+
+CDSGeneProt-constraint-field ::= CHOICE {
+  field CDSGeneProt-field }
+
+CDSGeneProt-qual-constraint ::= SEQUENCE {
+  field1 CDSGeneProt-constraint-field OPTIONAL ,
+  field2 CDSGeneProt-constraint-field OPTIONAL ,
+  constraint String-constraint OPTIONAL }
+  
+Sequence-constraint-rnamol ::= ENUMERATED {
+  any (0) ,
+  genomic (1) ,
+  precursor-RNA (2) ,
+  mRNA (3) ,
+  rRNA (4) ,
+  tRNA (5) ,
+  snRNA (6) ,
+  scRNA (7) ,
+  genomic-mRNA (8) ,
+  cRNA (9) ,
+  snoRNA (10) ,
+  transcribed-RNA (11) ,
+  ncRNA (12) ,
+  transfer-messenger-RNA (13) }
+
+Sequence-constraint-mol-type-constraint ::= CHOICE {
+  any NULL ,
+  nucleotide NULL ,
+  dna NULL ,
+  rna Sequence-constraint-rnamol ,
+  protein NULL }
+
+Sequence-constraint ::= SEQUENCE {
+    seqtype Sequence-constraint-mol-type-constraint OPTIONAL ,
+    id String-constraint OPTIONAL ,
+    feature Feature-type }
+
+Constraint-choice ::= CHOICE {
+    string String-constraint ,
+    location Location-constraint ,
+    source Source-constraint,
+    cdsgeneprot-qual CDSGeneProt-qual-constraint ,
+    cdsgeneprot-pseudo CDSGeneProt-pseudo-constraint ,
+    sequence Sequence-constraint }
+
+Constraint-choice-set ::= SET OF Constraint-choice
+
+Text-portion ::= SEQUENCE {
+    left-text VisibleString OPTIONAL ,
+    include-left BOOLEAN ,
+    right-text VisibleString OPTIONAL ,
+    include-right BOOLEAN ,
+    inside BOOLEAN ,
+    case-sensitive BOOLEAN DEFAULT FALSE ,
+    whole-word BOOLEAN DEFAULT FALSE }
+
+Field-edit-location ::= ENUMERATED {
+    anywhere (0) ,
+    beginning (1) ,
+    end (2) }
+
+Field-edit ::= SEQUENCE {
+    find-txt VisibleString ,
+    repl-txt VisibleString OPTIONAL ,
+    location Field-edit-location DEFAULT anywhere }
+
+Field-type ::= CHOICE {
+    source-qual Source-qual-choice ,
+    feature-field Feature-field ,
+    cds-gene-prot CDSGeneProt-field ,
+    molinfo-field Molinfo-field }
+
+Field-pair-type ::= CHOICE {
+    source-qual Source-qual-pair ,
+    feature-field Feature-field-pair ,
+    cds-gene-prot CDSGeneProt-field-pair ,
+    molinfo-field Molinfo-field-pair } 
+
+ExistingTextOption ::= ENUMERATED {
+  replace-old (1) ,
+  append-semi (2) ,
+  append-space (3) ,
+  append-colon (4) ,
+  append-none (5) ,
+  prefix-semi (6) ,
+  prefix-space (7) ,
+  prefix-colon (8) ,
+  prefix-none (9) ,
+  leave-old (10) }
+
+
+Apply-action ::= SEQUENCE {
+    field Field-type ,
+    value VisibleString ,
+    existing-text ExistingTextOption }
+
+Edit-action ::= SEQUENCE {
+    edit Field-edit ,
+    field Field-type }
+
+Convert-action ::= SEQUENCE {
+    fields Field-pair-type ,
+    existing-text ExistingTextOption }
+
+Copy-action ::= SEQUENCE {
+    fields Field-pair-type ,
+    existing-text ExistingTextOption }
+
+Swap-action ::= SEQUENCE {
+    fields Field-pair-type ,
+    field-to Field-type }
+
+AECRParse-action ::= SEQUENCE {
+    portion Text-portion ,
+    fields Field-pair-type ,
+    remove-from-parsed BOOLEAN DEFAULT FALSE ,
+    existing-text ExistingTextOption }
+
+Remove-action ::= SEQUENCE {
+    field Field-type }
+
+Action-choice ::= CHOICE {
+    apply Apply-action ,
+    edit Edit-action ,
+    convert Convert-action ,
+    copy Copy-action ,
+    swap Swap-action ,
+    remove Remove-action ,
+    parse AECRParse-action }
+
+AECR-action ::= SEQUENCE {
+    action Action-choice ,
+    constraint Constraint-choice-set OPTIONAL }
+
+Cap-change ::= ENUMERATED {
+    none (0) ,
+    tolower (1) ,
+    toupper (2) ,
+    firstcap (3) }
+
+Parse-src-org-choice ::= CHOICE {
+    source-qual Source-qual ,
+    taxname-after-binomial NULL }
+
+Parse-src-org ::= SEQUENCE {
+    field Parse-src-org-choice ,
+    type Object-type-constraint DEFAULT any }
+
+Parse-src ::= CHOICE {
+    defline NULL ,
+    flatfile NULL ,
+    local-id NULL ,
+    org Parse-src-org ,
+    comment NULL ,
+    bankit-comment NULL ,
+    structured-comment VisibleString ,
+    file-id NULL }
+
+Parse-dst-org ::= SEQUENCE {
+    field Source-qual-choice ,
+    type Object-type-constraint DEFAULT any }
+
+Parse-dest ::= CHOICE {
+    defline NULL ,
+    org Parse-dst-org ,
+    featqual Feature-field-legal ,
+    dbxref VisibleString }
+
+Parse-action ::= SEQUENCE {
+    portion Text-portion ,
+    src Parse-src ,
+    dest Parse-dest ,
+    capitalization Cap-change DEFAULT none ,
+    remove-from-parsed BOOLEAN DEFAULT FALSE ,
+    existing-text ExistingTextOption }
+
+
+Location-interval ::= SEQUENCE {
+    from INTEGER ,
+    to INTEGER  }
+
+Location-choice ::= CHOICE {
+    interval Location-interval ,
+    whole-sequence NULL }
+
+Sequence-list ::= SET OF VisibleString
+Sequence-list-choice ::= CHOICE {
+    list Sequence-list ,
+    all NULL }
+    
+Apply-feature-action ::= SEQUENCE {
+    type Feature-type ,
+    partial5 BOOLEAN DEFAULT FALSE ,
+    partial3 BOOLEAN DEFAULT FALSE ,
+    plus-strand BOOLEAN DEFAULT TRUE ,
+    location Location-choice ,
+    seq-list Sequence-list-choice ,
+    add-redundant BOOLEAN DEFAULT TRUE ,
+    add-mrna BOOLEAN DEFAULT FALSE ,
+    apply-to-parts BOOLEAN DEFAULT FALSE ,
+    only-seg-num INTEGER DEFAULT -1 ,
+    fields Feat-qual-legal-set OPTIONAL }
+
+Remove-feature-action ::= SEQUENCE {
+    type Feature-type ,
+    constraint Constraint-choice-set OPTIONAL }
+
+Feature-location-strand-from ::= ENUMERATED {
+  any (0) ,
+  plus (1) ,
+  minus (2) ,
+  unknown (3) ,
+  both (4) }
+
+Feature-location-strand-to ::= ENUMERATED {
+  plus (1) ,
+  minus (2) ,
+  unknown (3) ,
+  both (4) ,
+  reverse (5) }
+
+Edit-location-strand ::= SEQUENCE {
+  strand-from Feature-location-strand-from ,
+  strand-to   Feature-location-strand-to } 
+
+Partial-5-set-constraint ::= ENUMERATED {
+  all (0) ,
+  at-end (1) ,
+  bad-start (2) ,
+  frame-not-one (3) }
+
+Partial-5-set-action ::= SEQUENCE {
+  constraint Partial-5-set-constraint ,
+  extend BOOLEAN }
+
+Partial-5-clear-constraint ::= ENUMERATED {
+  all (0) ,
+  not-at-end (1) ,
+  good-start (2) }
+
+Partial-3-set-constraint ::= ENUMERATED {
+  all (0) ,
+  at-end (1) ,
+  bad-end (2) }
+
+Partial-3-set-action ::= SEQUENCE {
+  constraint Partial-3-set-constraint ,
+  extend BOOLEAN }
+
+Partial-3-clear-constraint ::= ENUMERATED {
+  all (0) ,
+  not-at-end (1) ,
+  good-end (2) }
+
+Convert-location-type ::= ENUMERATED {
+  join (1) ,
+  order (2) ,
+  merge (3) }
+
+Location-edit-type ::= CHOICE {
+  strand Edit-location-strand ,
+  set-5-partial Partial-5-set-action ,
+  clear-5-partial Partial-5-clear-constraint ,
+  set-3-partial Partial-3-set-action ,
+  clear-3-partial Partial-3-clear-constraint ,
+  convert Convert-location-type }
+
+Edit-feature-location-action ::= SEQUENCE {
+  type Feature-type ,
+  action Location-edit-type ,
+  constraint Constraint-choice-set OPTIONAL }
+
+Macro-action-choice ::= CHOICE {
+  aecr AECR-action ,
+  parse Parse-action ,
+  add-feature Apply-feature-action ,
+  remove-feature Remove-feature-action ,
+  edit-location Edit-feature-location-action }
+
+
+Macro-action-list ::= SET OF Macro-action-choice
+
+END
diff --git a/sequin/sequin.h b/sequin/sequin.h
index b27516a2..aa5bff85 100644
--- a/sequin/sequin.h
+++ b/sequin/sequin.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.477 $
+* $Revision: 6.513 $
 *
 * File Description: 
 *
@@ -167,7 +167,6 @@ extern void ExtendFastaSet (IteM i);
 extern void ExtendAllSequencesInSet (IteM i);
 extern void SeqLocAdjustByOffset (SeqLocPtr slp, Int4 offset);
 extern void SplitSegmentedFeatsMenuItem (IteM i);
-extern SeqLocPtr SeqLocWholeNew (BioseqPtr bsp);
 extern SeqFeatPtr SeqFeatCopy (SeqFeatPtr sfp);
 extern SeqLocPtr SeqLocReplaceLocalID (SeqLocPtr slp,
 				       SeqIdPtr  new_sip);
@@ -248,6 +247,7 @@ extern void EditPubsEx (BaseFormPtr bfp);
 extern void RemovePubConsortiums (IteM i);
 
 extern void ExtendPartialFeatures (IteM i);
+extern void ExtendPartialFeaturesWithConstraint (IteM i);
 extern void TrimOrganismName (IteM i);
 extern void SUCSubmitterProc (IteM i);
 
@@ -348,7 +348,6 @@ extern Uint2 PackageFormResults (SequinBlockPtr sbp, SeqEntryPtr sep,
 extern void EnableFeaturesPerTarget (BaseFormPtr bfp);
 extern void EnableAnalysisItems (BaseFormPtr bfp, Boolean isDocSum);
 
-extern Int4 ExtendSeqLocToEnd (SeqLocPtr slp, BioseqPtr bsp, Boolean end5);
 extern void ExtendSeqLocToPosition (SeqLocPtr slp, Boolean end5, Int4 pos);
 
 #define REGISTER_BIOSEQ_SEG_EDIT ObjMgrProcLoad(OMPROC_EDIT,"Edit Bioseq Seg","BioseqSegEditor",OBJ_BIOSEQ_SEG,0,OBJ_BIOSEQ_SEG,0,NULL,BioseqSegEditFunc,PROC_PRIORITY_DEFAULT)
@@ -435,7 +434,6 @@ extern void CombineMultipleCDS (IteM i);
 
 extern void NewDescriptorMenuFunc (ObjMgrProcPtr ompp, BaseFormPtr bfp, Uint2 descsubtype);
 extern Boolean PropagateFromGenBankBioseqSet (SeqEntryPtr sep, Boolean ask);
-extern CharPtr MergeValNodeStrings (ValNodePtr list, Boolean useReturn);
 extern int LIBCALLBACK SortByVnpChoice (VoidPtr ptr1, VoidPtr ptr2);
 extern void PrepareToConvertToCDS (SeqEntryPtr sep, Uint2 entityID,
                                    Uint2 subtype, CharPtr findthis);
@@ -449,23 +447,21 @@ extern void ChangeGenBankNameToLocal (IteM i);
 extern void RemoveGBIDsFromBioseqs (IteM i);
 extern void RemoveGBIDsFromProteins (IteM i);
 extern void RemoveGIsFromBioseqs (IteM i);
-extern CharPtr MergeValNodeStrings (ValNodePtr list, Boolean useReturn);
 
 extern void CommonApplyToAllProc (BaseFormPtr bfp, Int2 type);
 extern void ApplyTitle (IteM i);
 extern void ApplyCDS (IteM i);
 extern void ApplyRRNA (IteM i);
 extern void ApplyImpFeat (IteM i);
-extern void AdjustCDSLocationsForUnknownGapsCallback (SeqFeatPtr sfp, Pointer userdata);
 extern void AdjustCDSLocationsForKnownAndUnknownGapsCallback (SeqFeatPtr sfp, Pointer userdata);
 extern void AdjustFeaturesForGaps (IteM i);
 extern void LoadTPAAccessionNumbersFromFile (IteM i);
 extern void LoadSecondaryAccessionNumbersFromFile (IteM i);
 extern void LoadHistoryAccessionNumbersFromFile (IteM i);
 extern void LoadOrganismModifierTable (IteM i);
+extern void LoadTaxConsult (IteM i);
 extern void ExportOrganismTable (IteM i);
 extern void LoadFeatureQualifierTable (IteM i);
-extern CharPtr GetModifierPopupPositionName (Int2 val);
 
 extern void AddCodonListTotRNA (tRNAPtr trna, ValNodePtr codons);
 
@@ -807,13 +803,6 @@ extern void LogCDSAmbiguousFrame (LogInfoPtr lip, SeqFeatPtr sfp);
 extern void LoadGenomeProjectIDsFromFile (IteM i);
 extern void RemoveEmptyGenomeProjectIDs (IteM i);
 
-typedef struct sourcequaldesc
-{
-  CharPtr       name;
-  Boolean       isOrgMod;
-  Uint1         subtype;
-} SourceQualDescData, PNTR SourceQualDescPtr;
-
 extern CharPtr SourceQualValNodeName (ValNodePtr vnp);
 extern ValNodePtr SourceQualValNodeDataCopy (ValNodePtr vnp);
 extern Boolean SourceQualValNodeMatch (ValNodePtr vnp1, ValNodePtr vnp2);
@@ -888,7 +877,7 @@ extern void ExportLastLineage (IteM i);
 #define LOCATION_CONSTRAINT_NUC_SEQ      2
 #define LOCATION_CONSTRAINT_PROT_SEQ     3
 
-typedef struct locationconstraint
+typedef struct LocationConstraintX
 {
   Int4      left;
   Int4      right;
@@ -896,7 +885,7 @@ typedef struct locationconstraint
   Int4      match_choice;
   Int4      strand;
   Int4      sequence_type;
-} LocationConstraintData, PNTR LocationConstraintPtr;
+} LocationConstraintXData, PNTR LocationConstraintXPtr;
 
 typedef enum
 {
@@ -914,9 +903,9 @@ typedef struct stringconstraint
   Boolean insensitive;
   Boolean whole_word;
   Boolean not_present;
-} StringConstraintData, PNTR StringConstraintPtr;
+} StringConstraintData, PNTR StringConstraintXPtr;
 
-extern StringConstraintPtr StringConstraintFree (StringConstraintPtr scp);
+extern StringConstraintXPtr StringConstraintXFree (StringConstraintXPtr scp);
 
 typedef struct pseudoconstraint
 {
@@ -935,7 +924,7 @@ typedef struct choiceconstraint
   Int4                constraint_type;
   ValNodePtr          qual_choice;
   ValNodePtr          qual_choice_match;
-  StringConstraintPtr string_constraint;
+  StringConstraintXPtr string_constraint;
   PseudoConstraintPtr pseudo_constraint;
   FreeValNodeProc     free_vn_proc;
   CopyValNodeDataProc copy_vn_proc;
@@ -943,20 +932,38 @@ typedef struct choiceconstraint
 
 extern ChoiceConstraintPtr ChoiceConstraintFree (ChoiceConstraintPtr scp);
 
+typedef struct sequenceconstraint 
+{
+  Boolean nucs_ok;
+  Boolean prots_ok;
+  
+  Int4                other_constraint_type;
+  StringConstraintXPtr string_constraint;
+  ChoiceConstraintPtr source_constraint;
+  ValNodePtr          feature_list;
+  
+} SequenceConstraintXData, PNTR SequenceConstraintXPtr;
+
+extern SequenceConstraintXPtr SequenceConstraintXFree (SequenceConstraintXPtr scp);
+extern DialoG SequenceConstraintXDialog (GrouP g);
+extern Boolean DoesSequenceMatchSequenceConstraintX (BioseqPtr bsp, SequenceConstraintXPtr scp);
+
+
+
 typedef struct filterset 
 {
-  StringConstraintPtr   scp;
+  StringConstraintXPtr   scp;
   ChoiceConstraintPtr   ccp;
-  LocationConstraintPtr lcp;
+  LocationConstraintXPtr lcp;
   ChoiceConstraintPtr   cgp;
-  StringConstraintPtr   id_list;
+  StringConstraintXPtr   id_list;
 } FilterSetData, PNTR FilterSetPtr;
 
 extern void FilterSetClearText (FilterSetPtr fsp);
 extern FilterSetPtr FilterSetNew (void);
 extern FilterSetPtr FilterSetFree (FilterSetPtr fsp);
 
-extern Boolean DoesStringMatchConstraint (CharPtr pchSource, StringConstraintPtr scp);
+extern Boolean DoesStringMatchConstraintX (CharPtr pchSource, StringConstraintXPtr scp);
 
 typedef CharPtr (*GetFeatureFieldString) PROTO ((SeqFeatPtr, ValNodePtr, FilterSetPtr));
 typedef void (*SetFeatureFieldString) PROTO ((SeqFeatPtr, Pointer, FilterSetPtr));
@@ -999,18 +1006,18 @@ typedef struct textportion
   CharPtr end_text;
   Boolean insensitive;
   Boolean whole_word;
-} TextPortionData, PNTR TextPortionPtr;
+} TextPortionXData, PNTR TextPortionXPtr;
 
-extern TextPortionPtr TextPortionFree (TextPortionPtr tp);
+extern TextPortionXPtr TextPortionXFree (TextPortionXPtr tp);
 extern void 
-FindTextPortionInString 
+FindTextPortionXInString 
 (CharPtr        str, 
- TextPortionPtr tp, 
+ TextPortionXPtr tp, 
  CharPtr PNTR   ploc, 
  Int4Ptr        plen);
 
-extern DialoG TextPortionDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
-extern DialoG TextPortionDialog (GrouP h);
+extern DialoG TextPortionXDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
+extern DialoG TextPortionXDialog (GrouP h);
 
 #define CONVERT_TYPE_MOVE  0
 #define CONVERT_TYPE_COPY  1
@@ -1031,13 +1038,13 @@ typedef struct convertfield
   RemoveDescriptorFieldString remove_d_str_func;
   NameFromValNodeProc         name_field_func;
   FilterSetPtr                fsp;
-  TextPortionPtr              text_portion;
+  TextPortionXPtr              text_portion;
   Boolean                     strip_name_from_text;
   Boolean                     remove_parsed;
 } ConvertFieldData, PNTR ConvertFieldPtr;
 
-extern DialoG StringConstraintDialog (GrouP h, CharPtr label, Boolean clear_btn);
-extern DialoG LocationConstraintDialog (GrouP h, Boolean show_interval_controls, Boolean clear_btn);
+extern DialoG StringConstraintDialogX (GrouP h, CharPtr label, Boolean clear_btn);
+extern DialoG LocationConstraintXDialog (GrouP h, Boolean show_interval_controls, Boolean clear_btn);
 
 enum pub_field_nums 
 {
@@ -1235,7 +1242,7 @@ ConstraintChoiceDialog
  CharPtr                   text_name,
  Boolean                   clear_btn,
  Boolean                   use_pseudo);
-extern DialoG SourceConstraintDialog (GrouP h, Boolean clear_btn);
+extern DialoG SourceConstraintDialogX (GrouP h, Boolean clear_btn);
 extern Boolean DoesOneSourceMatchConstraint (BioSourcePtr biop, ChoiceConstraintPtr scp);
 extern DialoG CDSGeneProtConstraintDialog (GrouP h, Boolean clear_btn);
 extern DialoG 
@@ -1259,6 +1266,12 @@ typedef struct parsefield
 
 extern ParseFieldPtr ParseFieldFree (ParseFieldPtr pfp);
  
+extern DialoG ParseFieldDestDialogEx 
+(GrouP                    h,
+ Nlm_ChangeNotifyProc     change_notify,
+ Pointer                  change_userdata,
+ Boolean                  is_search_field,
+ Boolean                  include_dbxref);
 extern DialoG ParseFieldDestDialog 
 (GrouP                    h, 
  Nlm_ChangeNotifyProc     change_notify,
@@ -1452,7 +1465,7 @@ extern void ConvertCodingRegionsWithInternalKnownGapToMiscFeat (IteM i);
 extern void FixOneAlignmentOverGaps (SeqAlignPtr salp, Uint2 entityID);
 extern void ConsolidateSegmentsOverKnownLengthGaps (SeqAlignPtr salp);
 
-extern void CreateDiscrepancyReportWindow ();
+extern void CreateDiscrepancyReportWindow (void);
 extern void ScrollToDiscrepancyItem (ValNodePtr vnp, Pointer userdata);
 extern void EditDiscrepancyItem (ValNodePtr vnp, Pointer userdata);
 extern void WriteClickableListReport (FILE *fp, ValNodePtr discrepancy_list, Boolean show_all, Boolean use_feature_table_fmt);
@@ -1462,9 +1475,8 @@ extern void ChangeKnownGapLength (IteM i);
 extern void AddFlankingNsToKnownLengthGaps (IteM i);
 
 extern Int2 GetSequinAppParam (CharPtr section, CharPtr type, CharPtr dflt, CharPtr buf, Int2 buflen);
-extern Boolean DoBioseqFeaturesMatchSequenceConstraint (BioseqPtr bsp, ValNodePtr feat_list, StringConstraintPtr scp);
-extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr string_constraint);
-extern void ResetCapitalization (Boolean first_is_upper, CharPtr pString);
+extern Boolean DoBioseqFeaturesMatchSequenceConstraintX (BioseqPtr bsp, ValNodePtr feat_list, StringConstraintXPtr scp);
+extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintXPtr string_constraint);
 extern Int2 LIBCALLBACK ReorderSetByAccession (Pointer data);
 
 extern Int2 LIBCALLBACK CopyDescriptorToList (Pointer data);
@@ -1516,7 +1528,7 @@ extern void MakeGeneralIDsFromLocusTags (IteM i);
 extern void ShowClickableItemList (ValNodePtr clickable_list, BaseFormPtr bfp, CharPtr win_title, CharPtr label1, CharPtr label2);
 
 extern Int4 CountChosenDiscrepancies (ValNodePtr discrepancy_list, Boolean count_all);
-extern void AddTranslExcept (SeqFeatPtr sfp, CharPtr cds_comment, Boolean use_strict);
+extern void AddTranslExcept (SeqFeatPtr sfp, CharPtr cds_comment, Boolean use_strict, Boolean extend);
 
 enum table_data_errors 
 {
@@ -1603,17 +1615,20 @@ ConvertOneCDSToMiscFeat
 
 extern void SuppressGenesOnFeaturesInsideMobileElements (IteM i);
 
-extern Int4 GetDeltaSeqLen (DeltaSeqPtr dsp);
 extern BaseFormPtr GetBaseFormForEntityID (Uint2 entityID);
 
 extern ValNodePtr ParseAccessionNumberListFromString (CharPtr list_str, SeqEntryPtr sep);
-extern SeqIdPtr CreateSeqIdFromText (CharPtr id_str, SeqEntryPtr sep);
 
 extern SubSourcePtr FindBadLatLon (BioSourcePtr biop);
 extern DialoG LatLonTestResultsDisplay (GrouP h);
 extern void LatLonTool (IteM i);
 extern DialoG SpecificHostResultsDisplay (GrouP h);
 extern void FixSpecificHostValues (IteM i);
+extern DialoG LatLonCountryResultsDisplay (GrouP h);
+extern Pointer GetLatLonCountryCorrection (Uint1 data_choice, Pointer data, Pointer metadata);
+extern void LatLonCountryTool (IteM i);
+extern DialoG CountryTestResultsDisplay (GrouP h, Pointer metadata);
+extern void CountryFixupTool (IteM i);
 
 extern void SetTransgenicOnSourceDescWhenSourceFeatPresent (IteM i);
 extern void SetFocusOnSourceDescWhenSourceFeatPresent (IteM i);
@@ -1624,7 +1639,7 @@ extern const char *nucleotide_alphabet;
 extern const char *protein_alphabet;
 
 extern DialoG AlnSettingsDlg (GrouP h, Boolean allow_sequence_type);
-extern TSequenceInfoPtr GetDefaultSequenceInfo ();
+extern TSequenceInfoPtr GetDefaultSequenceInfo (void);
 extern TSequenceInfoPtr GetAlignmentOptions (Uint1Ptr moltype, TSequenceInfoPtr sequence_info);
 
 
@@ -1634,6 +1649,85 @@ extern SeqFeatPtr GetGeneForFeature (SeqFeatPtr sfp);
 
 extern void LoadFeatureFieldTable (IteM i);
 
+/* structure used for taxname options for loading values froma table or the Apply/Edit/Convert/Remove dialogs */
+typedef struct taxnameoptions {
+ Boolean remove_taxref;
+ Boolean remove_old_name;
+ Boolean remove_common;
+} TaxnameOptionsData, PNTR TaxnameOptionsPtr;
+
+extern void ApplyTaxnameOptionsToBioSource (BioSourcePtr biop, TaxnameOptionsPtr top);
+extern DialoG TaxnameOptionsDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
+
+extern void CleanTableLine (CharPtr line);
+
+extern void ApplyTagToCodingRegionsInSourceFeatures (IteM i);
+extern Boolean EntityIDAlreadyInList (Uint2 entityID, ValNodePtr entityIDList);
+
+extern void ResolveFeatureOverlaps (IteM i);
+extern void ConvertGeneralIdToLocalID (IteM i);
+
+extern void UpdateFeatures (IteM i);
+
+extern void AbbreviateCitSubAffilStates (IteM i);
+extern void RemoveQualityScores (BioseqPtr bsp, FILE *log_fp, BoolPtr data_in_log);
+extern void NewLoadFeatureQualifierTable (IteM i);
+extern void ListAllSequences (BioseqPtr bsp, Pointer userdata);
+extern void ChooseCategories (ValNodePtr value_list, Boolean do_choose);
+extern void ChooseCategoriesByStringConstraint (ValNodePtr value_list, StringConstraintXPtr scp, Boolean do_choose);
+extern void CapitalizeFirstLetterOfEveryWord (CharPtr pString);
+
+typedef void (*BulkSetFieldFunc) PROTO ((Pointer, Pointer));
+typedef Pointer (*BulkSetFieldStringFunc) PROTO ((Pointer, ApplyValuePtr));
+typedef Pointer (*BulkGetFieldFunc) PROTO ((Uint1, Pointer, Pointer));
+typedef CharPtr (*BulkDisplayFieldFunc) PROTO ((Pointer));
+typedef void (*BulkFreeFieldFunc) PROTO ((Pointer));
+typedef DialoG (*BulkCreateDlgFunc) PROTO ((GrouP, CharPtr, SeqEntryPtr));
+typedef Int4 (*BulkFormatColumnFunc) PROTO ((ColPtr, CharPtr));
+typedef void (*BulkDrawColumnFunc) PROTO ((Pointer, RectPtr));
+typedef Pointer (*BulkReleaseCellFunc) PROTO ((Pointer));
+typedef Pointer (*BulkCopyFieldFunc) PROTO ((Pointer));
+
+typedef struct bulkedfield {
+  CharPtr name;
+  BulkSetFieldFunc set_func;
+  BulkSetFieldStringFunc set_str_func;
+  BulkGetFieldFunc get_func;
+  BulkDisplayFieldFunc display_func;
+  BulkFreeFieldFunc free_func;
+  BulkCreateDlgFunc create_dlg_func;
+  BulkFormatColumnFunc format_col_func;
+  BulkDrawColumnFunc  draw_col_func;
+  BulkReleaseCellFunc release_cell_func;
+  BulkCopyFieldFunc   copy_func;
+} BulkEdFieldData, PNTR BulkEdFieldPtr;
+
+NLM_EXTERN Pointer BulkSetSimpleTextString (Pointer curr_val, ApplyValuePtr avp);
+NLM_EXTERN CharPtr BulkDisplaySimpleText (Pointer data);
+NLM_EXTERN void BulkFreeSimpleText (Pointer data);
+NLM_EXTERN Int4 BulkFormatSimpleText (ColPtr col, CharPtr name);
+NLM_EXTERN Pointer BulkSimpleTextCopy (Pointer data);
+NLM_EXTERN DialoG BulkSimpleTextDialog (GrouP g, CharPtr name, SeqEntryPtr sep);
+
+NLM_EXTERN void BulkEditorObjectList (Uint2 entityID, CharPtr title, ValNodePtr feat_list, BulkEdFieldPtr field_list);
+NLM_EXTERN DialoG 
+CreateBulkEditorDialog 
+(GrouP               h,
+ BulkEdFieldPtr      field_list,
+ ValNodePtr          feat_list,
+ SeqEntryPtr         sep, 
+ Boolean             collapse_by_default,
+ ClickableCallback   single_click_func,
+ ClickableCallback   double_click_func);
+
+NLM_EXTERN void RevCompOneFeatForBioseq (SeqFeatPtr sfp, BioseqPtr bsp);
+NLM_EXTERN void FlipSequenceIntervals (IteM i);
+
+#ifdef OS_MSWIN
+NLM_EXTERN Int4 RunSilent(const char *cmdline);
+#endif
+
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/sequin/sequin1.c b/sequin/sequin1.c
index 06cffe29..387f6d33 100644
--- a/sequin/sequin1.c
+++ b/sequin/sequin1.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.622 $
+* $Revision: 6.653 $
 *
 * File Description: 
 *
@@ -92,6 +92,7 @@ static char *time_of_compilation = "now";
 #include <tax3api.h>
 #include <validerr.h>
 #include <algo/blast/api/blast_api.h>
+#include <findrepl.h>
 
 /* USE_SMARTNET */
 #ifdef USE_SMARTNET
@@ -130,7 +131,7 @@ static char *time_of_compilation = "now";
 #include <Gestalt.h>
 #endif
 
-#define SEQ_APP_VER "7.70"
+#define SEQ_APP_VER "8.03"
 
 #ifndef CODECENTER
 static char* sequin_version_binary = "Sequin Indexer Services Version " SEQ_APP_VER " " __DATE__ " " __TIME__;
@@ -147,6 +148,7 @@ extern EnumFieldAssoc  biosource_genome_simple_alist [];
 Boolean  useDesktop = FALSE;
 Boolean  useEntrez = FALSE;
 Boolean  useSeqFetch = FALSE;
+Boolean  useIdLookup = FALSE;
 Boolean  useLocal = FALSE;
 Boolean  useBlast = FALSE;
 Boolean  useMedarch = FALSE;
@@ -306,7 +308,7 @@ static Boolean  strictLatLonCountry = FALSE;
 static Int4 SMWriteBioseqObj(VoidPtr bio_data, SMUserDataPtr sm_usr_data, 
                              VoidPtr data);
 static Int4 SMReadBioseqObj(VoidPtr data, CharPtr buffer, 
-                            Int4 length, Int4 fd);
+                            Int4 length, void* fd);
 #define SMART_KEY 1313
 #define DUMB_KEY 1314
 #endif
@@ -391,6 +393,9 @@ static void CheckForCookedBioseqs (SeqEntryPtr sep, Pointer mydata, Int4 index,
   }
 }
 
+static void TaxonValidate (SeqEntryPtr sep, ValidStructPtr vsp);
+
+
 static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f)
 
 {
@@ -406,6 +411,9 @@ static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f)
   if (entityID < 1) return FALSE;
   sep = GetTopSeqEntryForEntityID (entityID);
   if (sep == NULL) return FALSE;
+
+  if (!FixSpecialCharacters (entityID)) return FALSE;
+
   if (GetSequinAppParam ("PREFERENCES", "ASKBEFOREVALIDATE", NULL, str, sizeof (str))) {
     if (StringICmp (str, "TRUE") == 0) {
       if (! (subtoolMode ||smartnetMode || backupMode) ) {
@@ -424,15 +432,34 @@ static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f)
     }
     if (indexerVersion) {
       vsp->alwaysRequireIsoJTA = TRUE;
+      if (smartnetMode) {
+        vsp->farFetchCDSproducts = TRUE;
+        vsp->farFetchMRNAproducts = TRUE;
+      }
     }
     oldErrSev = ErrSetMessageLevel (SEV_MAX);
     vsp->validateAlignments = TRUE;
     vsp->alignFindRemoteBsp = TRUE;
     vsp->doSeqHistAssembly = FALSE;
+    if (smartnetMode) {
+      vsp->doSeqHistAssembly = TRUE;
+      vsp->farIDsInAlignments = TRUE;
+      if (useEntrez) {
+        /*
+        LookupFarSeqIDs (sep, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE);
+        vsp->inferenceAccnCheck = TRUE;
+        */
+      }
+      vsp->testLatLonSubregion = testLatLonSubregion;
+      vsp->strictLatLonCountry = strictLatLonCountry;
+    }
     for (j = 0; j < 6; j++) {
       vsp->errors [j] = 0;
     }
     ValidateSeqEntry (sep, vsp);
+    if (indexerVersion && useEntrez) {
+      TaxonValidate (sep, vsp);
+    }
     ErrSetMessageLevel (oldErrSev);
     ErrClear ();
     ErrShow ();
@@ -1269,6 +1296,10 @@ static void SmartnetDoneFunc (BaseFormPtr bfp)
         
         omudp = ObjMgrGetUserData(bfp->input_entityID, 0, 0, SMART_KEY);
         if (omudp == NULL) return;
+
+        /* for now set dirty flag to force validation in OkayToWriteTheEntity */
+        ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+
         omdp = ObjMgrGetData (bfp->input_entityID);
 
         sm_usr_data = (SMUserDataPtr) omudp->userdata.ptrvalue;
@@ -1558,6 +1589,9 @@ static void ProcessDoneButton (ForM f)
       vsp->errors [j] = 0;
     }
     ValidateSeqEntry (sep, vsp);
+    if (indexerVersion && useEntrez) {
+      TaxonValidate (sep, vsp);
+    }
     ErrSetMessageLevel (oldErrSev);
     ErrClear ();
     ErrShow ();
@@ -1603,6 +1637,9 @@ static void ProcessDoneButton (ForM f)
           }
           vsp->errfunc = ValidErrCallback;
           ValidateSeqEntry (sep, vsp);
+          if (indexerVersion && useEntrez) {
+            TaxonValidate (sep, vsp);
+          }
           ErrSetMessageLevel (oldErrSev);
           ErrSetHandler (oldErrHook);
           ErrClear ();
@@ -1828,8 +1865,10 @@ static void ReportBadSpecificHostValues (SeqEntryPtr sep, ValidStructPtr vsp)
 {
   ValNodePtr  bad_biop_list, vnp;
   ObjValNodePtr ovp;
+  BioSourcePtr  biop;
+  OrgModPtr     mod;
 
-  bad_biop_list = Taxon3CheckSpecificHostInSeqEntry (sep, TRUE);
+  bad_biop_list = Taxon3CheckSpecificHostInSeqEntry (sep, TRUE, FALSE);
 
   for (vnp = bad_biop_list; vnp != NULL; vnp = vnp->next)
   {
@@ -1837,6 +1876,8 @@ static void ReportBadSpecificHostValues (SeqEntryPtr sep, ValidStructPtr vsp)
     vsp->descr = NULL;
     vsp->bsp = NULL;
     vsp->bssp = NULL;
+    biop = NULL;
+    mod = NULL;
 
     if (vnp->choice == OBJ_SEQFEAT)
     {
@@ -1852,6 +1893,7 @@ static void ReportBadSpecificHostValues (SeqEntryPtr sep, ValidStructPtr vsp)
       {
         vsp->bssp = vsp->sfp->idx.parentptr;        
       }
+      biop = (BioSourcePtr) vsp->sfp->data.value.ptrvalue;
     } 
     else if (vnp->choice == OBJ_SEQDESC)
     {
@@ -1872,13 +1914,27 @@ static void ReportBadSpecificHostValues (SeqEntryPtr sep, ValidStructPtr vsp)
           vsp->bssp = ovp->idx.parentptr;        
         }
       }
+      biop = vsp->descr->data.ptrvalue;
     }
     
-    ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_TaxonomyLookupProblem, "Invalid value for specific host");
+    if (biop != NULL && biop->org != NULL && biop->org->orgname != NULL)
+    {
+      mod = biop->org->orgname->mod;
+      while (mod != NULL && mod->subtype != ORGMOD_nat_host)
+      {
+        mod = mod->next;
+      }
+      if (mod != NULL)
+      {      
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadSpecificHost, "Invalid value for specific host: %s", mod->subname);
+      }
+    }
   }
   bad_biop_list = ValNodeFree (bad_biop_list);
 }
 
+static Boolean log_tax_asn = FALSE;
+static Boolean log_tax_set = FALSE;
 
 static void TaxonValidate (SeqEntryPtr sep, ValidStructPtr vsp)
 
@@ -1930,11 +1986,29 @@ static void TaxonValidate (SeqEntryPtr sep, ValidStructPtr vsp)
     last = vnp2;
   }
 
+#ifdef OS_UNIX
+  if (! log_tax_set) {
+    str = (CharPtr) getenv ("LOG_TAX_ASN");
+    if (StringDoesHaveText (str)) {
+      if (StringICmp (str, "TRUE") == 0) {
+        log_tax_asn = TRUE;
+      }
+    }
+    log_tax_set = TRUE;
+  }
+#endif
+
   sev = ErrSetMessageLevel (SEV_WARNING);
+  if (log_tax_asn) {
+    LaunchAsnTextViewer ((Pointer) t3rq, (AsnWriteFunc) Taxon3RequestAsnWrite, "tax3 request");
+  }
   t3ry = Tax3SynchronousQuery (t3rq);
   ErrSetMessageLevel (sev);
   Taxon3RequestFree (t3rq);
   if (t3ry == NULL) return;
+  if (log_tax_asn) {
+    LaunchAsnTextViewer ((Pointer) t3ry, (AsnWriteFunc) Taxon3ReplyAsnWrite, "tax3 result");
+  }
 
   for (trp = t3ry->reply, vnp = srclist.head;
        trp != NULL && vnp != NULL;
@@ -2038,7 +2112,7 @@ static void TaxonValidate (SeqEntryPtr sep, ValidStructPtr vsp)
   ReportBadSpecificHostValues (sep, vsp);
 }
 
-static void ValSeqEntryFormEx (ForM f, Boolean doAligns, Int2 limit)
+static void ValSeqEntryFormEx (ForM f, Boolean doAligns, Int2 limit, Boolean inferenceAccnCheck)
 
 {
   Boolean         allRawOrSeg = TRUE;
@@ -2102,7 +2176,7 @@ static void ValSeqEntryFormEx (ForM f, Boolean doAligns, Int2 limit)
             }
           }
         }
-        if (useEntrez) {
+        if (useEntrez && inferenceAccnCheck) {
           LookupFarSeqIDs (sep, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE);
           vsp->inferenceAccnCheck = TRUE;
         }
@@ -2142,16 +2216,61 @@ static void ValSeqEntryFormEx (ForM f, Boolean doAligns, Int2 limit)
   }
 }
 
+static void CountInfAccnVer (SeqFeatPtr sfp, Pointer userdata)
+
+{
+  Int4Ptr    countP;
+  GBQualPtr  gbq;
+
+  if (sfp == NULL || userdata == NULL) return;
+  countP = (Int4Ptr) userdata;
+
+  for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
+    if (StringICmp (gbq->qual, "inference") == 0) {
+      (*countP)++;
+    }
+  }
+}
+
+static Boolean SmallInferenceAccnVer (ForM f)
+
+{
+  BaseFormPtr  bfp;
+  Int4         count = 0;
+  SeqEntryPtr  sep;
+
+  bfp = (BaseFormPtr) GetObjectExtra (f);
+  if (bfp == NULL) return FALSE;
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return FALSE;
+
+  VisitFeaturesInSep (sep, (Pointer) &count, CountInfAccnVer);
+
+  if (count < 100) return TRUE;
+
+  if (indexerVersion) {
+    Message (MSG_POST, "Validation skipping %ld inference accession.version tests",
+             (long) count);
+  }
+
+  return FALSE;
+}
+
 extern void ValSeqEntryForm (ForM f)
 
 {
-  ValSeqEntryFormEx (f, TRUE, VALIDATE_ALL);
+  Boolean  inferenceAccnCheck;
+
+  inferenceAccnCheck = SmallInferenceAccnVer (f);
+  ValSeqEntryFormEx (f, TRUE, VALIDATE_ALL, inferenceAccnCheck);
 }
 
 static void ValSeqEntryProc (IteM i)
 
 {
   BaseFormPtr  bfp;
+  Boolean      inferenceAccnCheck;
 
 #ifdef WIN_MAC
   bfp = (BaseFormPtr) currentFormDataPtr;
@@ -2159,7 +2278,8 @@ static void ValSeqEntryProc (IteM i)
   bfp = (BaseFormPtr) GetObjectExtra (i);
 #endif
   if (bfp != NULL) {
-    ValSeqEntryForm (bfp->form);
+    inferenceAccnCheck = SmallInferenceAccnVer (bfp->form);
+    ValSeqEntryFormEx (bfp->form, TRUE, VALIDATE_ALL, inferenceAccnCheck);
   }
 }
 
@@ -2174,7 +2294,22 @@ static void ValSeqEntryProcNoAln (IteM i)
   bfp = (BaseFormPtr) GetObjectExtra (i);
 #endif
   if (bfp != NULL) {
-    ValSeqEntryFormEx (bfp->form, FALSE, VALIDATE_ALL);
+    ValSeqEntryFormEx (bfp->form, FALSE, VALIDATE_ALL, FALSE);
+  }
+}
+
+static void ValSeqEntryProcInfAccn (IteM i)
+
+{
+  BaseFormPtr  bfp;
+
+#ifdef WIN_MAC
+  bfp = (BaseFormPtr) currentFormDataPtr;
+#else
+  bfp = (BaseFormPtr) GetObjectExtra (i);
+#endif
+  if (bfp != NULL) {
+    ValSeqEntryFormEx (bfp->form, FALSE, VALIDATE_ALL, TRUE);
   }
 }
 
@@ -2189,7 +2324,7 @@ static void ValSeqEntryProcSpec (IteM i, Int2 limit)
   bfp = (BaseFormPtr) GetObjectExtra (i);
 #endif
   if (bfp != NULL) {
-    ValSeqEntryFormEx (bfp->form, FALSE, limit);
+    ValSeqEntryFormEx (bfp->form, FALSE, limit, FALSE);
   }
 }
 
@@ -4021,7 +4156,7 @@ replaced by the actual characters from the first sequence.";
 const char *nucleotide_alphabet = "ABCDGHKMRSTUVWYabcdghkmrstuvwy";
 const char *protein_alphabet = "ABCDEFGHIKLMPQRSTUVWXYZabcdefghiklmpqrstuvwxyz";
 
-extern TSequenceInfoPtr GetDefaultSequenceInfo ()
+extern TSequenceInfoPtr GetDefaultSequenceInfo (void)
 {
   TSequenceInfoPtr sequence_info = SequenceInfoNew();
 
@@ -5661,76 +5796,13 @@ static void DuplicateViewProc (IteM i)
   }
 }
 
-extern SeqEntryPtr RestoreFromFile (CharPtr path);
-extern SeqEntryPtr RestoreFromFile (CharPtr path)
-
-{
-  BioseqPtr     bsp;
-  BioseqSetPtr  bssp;
-  Pointer       dataptr;
-  Uint2         datatype;
-  Uint2         entityID;
-  SeqEntryPtr   rsult;
-  SeqEntryPtr   sep;
-
-  rsult = NULL;
-  if (path != NULL && path [0] != '\0') {
-    dataptr = ObjMgrGenericAsnTextFileRead (path, &datatype, &entityID);
-    if (dataptr != NULL && entityID > 0) {
-      if (datatype == OBJ_SEQSUB || datatype == OBJ_SEQENTRY ||
-          datatype == OBJ_BIOSEQ || datatype == OBJ_BIOSEQSET) {
-        WatchCursor ();
-        sep = GetTopSeqEntryForEntityID (entityID);
-        if (sep == NULL) {
-          sep = SeqEntryNew ();
-          if (sep != NULL) {
-            if (datatype == OBJ_BIOSEQ) {
-              bsp = (BioseqPtr) dataptr;
-              sep->choice = 1;
-              sep->data.ptrvalue = bsp;
-              SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep);
-            } else if (datatype == OBJ_BIOSEQSET) {
-              bssp = (BioseqSetPtr) dataptr;
-              sep->choice = 2;
-              sep->data.ptrvalue = bssp;
-              SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) bssp, sep);
-            } else {
-              sep = SeqEntryFree (sep);
-            }
-          }
-          sep = GetTopSeqEntryForEntityID (entityID);
-        }
-        if (sep != NULL) {
-          rsult = SeqEntryNew ();
-          if (rsult != NULL) {
-            rsult->choice = sep->choice;
-            rsult->data.ptrvalue = sep->data.ptrvalue;
-            sep->data.ptrvalue = NULL;
-            if (datatype == OBJ_SEQSUB) {
-              SeqSubmitFree ((SeqSubmitPtr) dataptr);
-            } else {
-              SeqEntryFree (sep);
-            }
-            /*Message (MSG_OK, "Call new object manager free function");*/
-          }
-        }
-        ArrowCursor ();
-      }
-      /*
-      ObjMgrDelete (entityID);
-      */
-    }
-  }
-  return rsult;
-}
 
 static void RestoreSeqEntryProc (IteM i)
 
 {
-  SeqEntryPtr  currsep;
   BaseFormPtr  bfp;
-  SeqEntryPtr  oldsep;
   Char         path [PATH_MAX];
+  Uint2        new_entityID;
 
 #ifdef WIN_MAC
   bfp = currentFormDataPtr;
@@ -5739,14 +5811,12 @@ static void RestoreSeqEntryProc (IteM i)
 #endif
   if (bfp != NULL && bfp->input_itemtype == OBJ_BIOSEQ) {
     if (GetInputFileName (path, sizeof (path), "", "TEXT")) {
-      SeqEntrySetScope (NULL);
-      oldsep = RestoreFromFile (path);
-      currsep = GetTopSeqEntryForEntityID (bfp->input_entityID);
-      ReplaceSeqEntryWithSeqEntry (currsep, oldsep, TRUE);
-      SeqEntrySetScope (NULL);
-      bfp->input_entityID = ObjMgrGetEntityIDForChoice (currsep);
-      ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
-      ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+      new_entityID = RestoreEntityIDFromFile (path, bfp->input_entityID);
+      if (new_entityID != 0) {
+        bfp->input_entityID = new_entityID;
+        ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+        ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+      }
     }
   }
 }
@@ -6686,6 +6756,8 @@ static void BioseqViewFormMenus (WindoW w)
       SetObjectExtra (i, bfp, NULL);
       i = CommandItem (sub, "Validate no Alignments/ A", ValSeqEntryProcNoAln);
       SetObjectExtra (i, bfp, NULL);
+      i = CommandItem (sub, "Validate check Inference", ValSeqEntryProcInfAccn);
+      SetObjectExtra (i, bfp, NULL);
       SeparatorItem (sub);
       i = CommandItem (sub, "Validate Inst", ValSeqEntryProcInst);
       SetObjectExtra (i, bfp, NULL);
@@ -7378,10 +7450,16 @@ static void SequinSeqViewFormMessage (ForM f, Int2 mssg)
   if (bfp != NULL) {
     switch (mssg) {
       case VIB_MSG_SAVE :
-        SaveSeqSubmitProc (bfp, FALSE);
+        if (FixSpecialCharacters (bfp->input_entityID))
+        {
+          SaveSeqSubmitProc (bfp, FALSE);
+        }
         break;
       case VIB_MSG_SAVE_AS :
-        SaveSeqSubmitProc (bfp, TRUE);
+        if (FixSpecialCharacters (bfp->input_entityID))
+        {
+          SaveSeqSubmitProc (bfp, TRUE);
+        }
         break;
       case VIB_MSG_CLOSE :
         CloseProc (bfp);
@@ -9077,6 +9155,7 @@ static void SetupMacMenus (void)
     validateMenu = SubMenu (m, "Validate");
     CommandItem (validateMenu, "Validate Record/ V", ValSeqEntryProc);
     CommandItem (validateMenu, "Validate no Alignments", ValSeqEntryProcNoAln);
+    CommandItem (validateMenu, "Validate check Inference", ValSeqEntryProcInfAccn);
     SeparatorItem (validateMenu);
     CommandItem (validateMenu, "Validate Inst", ValSeqEntryProcInst);
     CommandItem (validateMenu, "Validate Hist", ValSeqEntryProcHist);
@@ -9804,6 +9883,7 @@ static void ReadSettings (void)
   useDesktop = FALSE;
   useEntrez = FALSE;
   useLocal = FALSE;
+  useIdLookup = FALSE;
   useBlast = FALSE;
   useMedarch = FALSE;
   newMedarch = FALSE;
@@ -9820,6 +9900,7 @@ static void ReadSettings (void)
   useDesktop = TRUE;
   useEntrez = TRUE;
   useLocal = TRUE;
+  useIdLookup = TRUE;
   useBlast = TRUE;
   useMedarch = TRUE;
   newMedarch = TRUE;
@@ -9833,6 +9914,7 @@ static void ReadSettings (void)
       useDesktop = TRUE;
       useEntrez = TRUE;
       useLocal = TRUE;
+      useIdLookup = TRUE;
       useBlast = TRUE;
       useMedarch = TRUE;
       newMedarch = TRUE;
@@ -9845,6 +9927,7 @@ static void ReadSettings (void)
   useDesktop = TRUE;
   useEntrez = TRUE;
   useLocal = TRUE;
+  useIdLookup = TRUE;
   useBlast = TRUE;
   useMedarch = TRUE;
   newMedarch = TRUE;
@@ -9856,6 +9939,7 @@ static void ReadSettings (void)
       useDesktop = TRUE;
       useEntrez = TRUE;
       useLocal = TRUE;
+      useIdLookup = TRUE;
       useBlast = TRUE;
       useMedarch = TRUE;
       newMedarch = TRUE;
@@ -9939,6 +10023,22 @@ static void ReadSettings (void)
     if (StringICmp (str, "TRUE") == 0) {
       allowDownload = FALSE;
       useEntrez = FALSE;
+      useMedarch = FALSE;
+      useTaxon = FALSE;
+    }
+  }
+
+  useSeqFetch = useEntrez;
+
+  if (GetSequinAppParam ("SETTINGS", "SUPPRESSSEQFETCH", NULL, str, sizeof (str))) {
+    if (StringICmp (str, "TRUE") == 0) {
+      useSeqFetch = FALSE;
+    }
+  }
+
+  if (GetSequinAppParam ("SETTINGS", "SUPPRESSIDLOOKUP", NULL, str, sizeof (str))) {
+    if (StringICmp (str, "TRUE") == 0) {
+      useIdLookup = FALSE;
     }
   }
 
@@ -9953,6 +10053,12 @@ static void ReadSettings (void)
     }
   }
 
+  if (GetSequinAppParam ("SETTINGS", "SUPPRESSLOCAL", NULL, str, sizeof (str))) {
+    if (StringICmp (str, "TRUE") == 0) {
+      useLocal = FALSE;
+    }
+  }
+
   if (GetSequinAppParam ("SETTINGS", "GENOMETAG", NULL, str, sizeof (str))) {
     TrimSpacesAroundString (str);
     if (! StringHasNoText (str)) {
@@ -10140,7 +10246,7 @@ extern Pointer ReadFromDirSub (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityI
 #endif
 #ifdef OS_MSWIN
   sprintf (cmmd, "%s %s -o %s", dirsubfetchcmd, accn, path);
-  system (cmmd);
+  RunSilent (cmmd);
 #endif
 
   fp = FileOpen (path, "r");
@@ -10197,7 +10303,7 @@ static Int2 LIBCALLBACK DirSubBioseqFetchFunc (Pointer data)
 #endif
 #ifdef OS_MSWIN
   sprintf (cmmd, "%s %s -o %s", dirsubfetchcmd, tsip->accession, path);
-  system (cmmd);
+  RunSilent (cmmd);
 #endif
 
   fp = FileOpen (path, "r");
@@ -10265,7 +10371,7 @@ extern Pointer ReadFromSmart (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityID
 #endif
 #ifdef OS_MSWIN
   sprintf (cmmd, "%s %s -o %s", smartfetchcmd, accn, path);
-  system (cmmd);
+  RunSilent (cmmd);
 #endif
 
   fp = FileOpen (path, "r");
@@ -10323,7 +10429,7 @@ static Int2 LIBCALLBACK SmartBioseqFetchFunc (Pointer data)
 #endif
 #ifdef OS_MSWIN
   sprintf (cmmd, "%s %s -o %s", smartfetchcmd, tsip->accession, path);
-  system (cmmd);
+  RunSilent (cmmd);
 #endif
 
   fp = FileOpen (path, "r");
@@ -10358,6 +10464,136 @@ static Boolean SmartFetchEnable (void)
   return TRUE;
 }
 
+static CharPtr hupfetchproc = "HUPBioseqFetch";
+
+static CharPtr hupfetchcmd = NULL;
+
+extern Pointer ReadFromHUP (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityID);
+extern Pointer ReadFromHUP (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityID)
+
+{
+  Char     cmmd [256];
+  Pointer  dataptr;
+  FILE*    fp;
+  Char     path [PATH_MAX];
+
+  if (datatype != NULL) {
+    *datatype = 0;
+  }
+  if (entityID != NULL) {
+    *entityID = 0;
+  }
+  if (! dirsubMode) return NULL;
+  if (StringHasNoText (accn)) return NULL;
+
+  if (hupfetchcmd == NULL) {
+    if (GetAppParam ("SEQUIN", "HUP", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
+    	hupfetchcmd = StringSaveNoNull (cmmd);
+    }
+  }
+  if (hupfetchcmd == NULL) return NULL;
+
+  TmpNam (path);
+
+#ifdef OS_UNIX
+  sprintf (cmmd, "csh %s %s > %s", hupfetchcmd, accn, path);
+  system (cmmd);
+#endif
+#ifdef OS_MSWIN
+  sprintf (cmmd, "%s %s -o %s", hupfetchcmd, accn, path);
+  RunSilent (cmmd);
+#endif
+
+  fp = FileOpen (path, "r");
+  if (fp == NULL) {
+    FileRemove (path);
+    return NULL;
+  }
+  dataptr = ReadAsnFastaOrFlatFile (fp, datatype, entityID, FALSE, FALSE, TRUE, FALSE);
+  FileClose (fp);
+  FileRemove (path);
+  return dataptr;
+}
+
+
+static Int2 LIBCALLBACK HUPBioseqFetchFunc (Pointer data)
+
+{
+  BioseqPtr         bsp;
+  Char              cmmd [256];
+  Pointer           dataptr;
+  Uint2             datatype;
+  Uint2             entityID;
+  FILE*             fp;
+  OMProcControlPtr  ompcp;
+  ObjMgrProcPtr     ompp;
+  Char              path [PATH_MAX];
+  SeqEntryPtr       sep = NULL;
+  SeqIdPtr          sip;
+  TextSeqIdPtr      tsip;
+  OMUserDataPtr     omudp;
+
+  ompcp = (OMProcControlPtr) data;
+  if (ompcp == NULL) return OM_MSG_RET_ERROR;
+  ompp = ompcp->proc;
+  if (ompp == NULL) return OM_MSG_RET_ERROR;
+  sip = (SeqIdPtr) ompcp->input_data;
+  if (sip == NULL) return OM_MSG_RET_ERROR;
+
+  if (sip->choice != SEQID_GENBANK) return OM_MSG_RET_ERROR;
+  tsip = (TextSeqIdPtr) sip->data.ptrvalue;
+  if (tsip == NULL || StringHasNoText (tsip->accession)) return OM_MSG_RET_ERROR;
+
+  if (hupfetchcmd == NULL) {
+    if (GetAppParam ("SEQUIN", "HUP", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
+    	hupfetchcmd = StringSaveNoNull (cmmd);
+    }
+  }
+  if (hupfetchcmd == NULL) return OM_MSG_RET_ERROR;
+
+  TmpNam (path);
+
+#ifdef OS_UNIX
+  sprintf (cmmd, "csh %s %s > %s", hupfetchcmd, tsip->accession, path);
+  system (cmmd);
+#endif
+#ifdef OS_MSWIN
+  sprintf (cmmd, "%s %s -o %s", hupfetchcmd, tsip->accession, path);
+  RunSilent (cmmd);
+#endif
+
+  fp = FileOpen (path, "r");
+  if (fp == NULL) {
+    FileRemove (path);
+    return OM_MSG_RET_ERROR;
+  }
+  dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, FALSE, FALSE, TRUE, FALSE);
+  FileClose (fp);
+  FileRemove (path);
+
+  if (dataptr == NULL) return OM_MSG_RET_OK;
+
+  sep = GetTopSeqEntryForEntityID (entityID);
+  if (sep == NULL) return OM_MSG_RET_ERROR;
+  bsp = BioseqFindInSeqEntry (sip, sep);
+  ompcp->output_data = (Pointer) bsp;
+  ompcp->output_entityID = ObjMgrGetEntityIDForChoice (sep);
+
+  omudp = ObjMgrAddUserData(ompcp->output_entityID, ompp->procid, OMPROC_FETCH, 0);
+  
+
+  return OM_MSG_RET_DONE;
+}
+
+static Boolean HUPFetchEnable (void)
+
+{
+  ObjMgrProcLoad (OMPROC_FETCH, hupfetchproc, hupfetchproc,
+                  OBJ_SEQID, 0, OBJ_BIOSEQ, 0, NULL,
+                  HUPBioseqFetchFunc, PROC_PRIORITY_DEFAULT);
+  return TRUE;
+}
+
 static CharPtr tpasmartfetchproc = "TPASmartBioseqFetch";
 
 static CharPtr tpasmartfetchcmd = NULL;
@@ -10395,7 +10631,7 @@ extern Pointer ReadFromTPASmart (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entit
 #endif
 #ifdef OS_MSWIN
   sprintf (cmmd, "%s %s -o %s", tpasmartfetchcmd, accn, path);
-  system (cmmd);
+  RunSilent (cmmd);
 #endif
 
   fp = FileOpen (path, "r");
@@ -10452,7 +10688,7 @@ static Int2 LIBCALLBACK TPASmartBioseqFetchFunc (Pointer data)
 #endif
 #ifdef OS_MSWIN
   sprintf (cmmd, "%s %s -o %s", tpasmartfetchcmd, tsip->accession, path);
-  system (cmmd);
+  RunSilent (cmmd);
 #endif
 
   fp = FileOpen (path, "r");
@@ -10547,7 +10783,7 @@ static void CountBioSources (BioSourcePtr biop, Pointer userdata)
   (*count)++;
 }
 
-static Int4 SMReadBioseqObj(VoidPtr data, CharPtr buffer, Int4 length, Int4 fd)
+static Int4 SMReadBioseqObj(VoidPtr data, CharPtr buffer, Int4 length, void* fd)
 {
     AsnIoMemPtr    aimp;
     BaseFormPtr    bfp;
@@ -10668,7 +10904,7 @@ static Int4 SMReadBioseqObj(VoidPtr data, CharPtr buffer, Int4 length, Int4 fd)
     }
     
     sm_user_data = MemNew(sizeof(SMUserData));
-    sm_user_data->fd = fd;
+    sm_user_data->fd = (void*) fd;
     sm_user_data->header = header;
 
     if(bio_data == NULL) {
@@ -11038,8 +11274,6 @@ Int2 Main (void)
   subtoolEntityID = 0;
   leaveAsOldAsn = FALSE;
 
-  useSeqFetch = useEntrez;
-
 #if defined(OS_UNIX) || defined(WIN_MOTIF)
   {{
     Nlm_Int4         argc = GetArgc();
@@ -11090,6 +11324,10 @@ Int2 Main (void)
           backupMode = TRUE;
         } else if (StringCmp (argv[i], "-noseqfetch") == 0) {
           useSeqFetch = FALSE;
+        } else if (StringCmp (argv[i], "-nolocalfetch") == 0) {
+          useLocal = FALSE;
+        } else if (StringCmp (argv[i], "-noseqidlookup") == 0) {
+          useIdLookup = FALSE;
         }
 #ifdef USE_SMARTNET
         else if (StringCmp (argv[i], "-ds") == 0) {
@@ -11127,6 +11365,10 @@ Int2 Main (void)
           nohelpMode = TRUE;
         else if (StringCmp (argv[i], "-noseqfetch") == 0)
           useSeqFetch = FALSE;
+        else if (StringCmp (argv[i], "-nolocalfetch") == 0)
+          useLocal = FALSE;
+        else if (StringCmp (argv[i], "-noseqidlookup") == 0)
+          useIdLookup = FALSE;
 #ifdef USE_SMARTNET
         else if (StringNCmp (argv[i], "-z", 2) == 0) {
           smartnetMode = TRUE;
@@ -11253,33 +11495,64 @@ Int2 Main (void)
   VSeqMgrInit (FALSE);
   WatchCursor ();
 
-#ifdef USE_SMARTNET
-  if (dirsubMode) {
-    DirSubFetchEnable ();
-    SmartFetchEnable ();
-    TPASmartFetchEnable ();
-  }
-#endif
+  /* register fetch functions */
 
-/*#ifdef USE_ENTREZ*/
   if (useEntrez) {
     /* EntrezBioseqFetchEnable ("Sequin", FALSE); */
     if (useSeqFetch) {
       /* ID1BioseqFetchEnable ("Sequin", FALSE); */
       PubSeqFetchEnable ();
       PubMedFetchEnable ();
-    } else {
+    } else if (useIdLookup) {
       PubSeqFetchEnableEx (FALSE, TRUE, TRUE, TRUE, TRUE);
       PubMedFetchEnable ();
     }
   }
-/*#endif*/
 
-/*#ifdef USE_LOCAL*/
+#ifdef USE_SMARTNET
+  if (dirsubMode) {
+    if (useSeqFetch) {
+      /* DirSubFetchEnable (); */
+      TPASmartFetchEnable ();
+      SmartFetchEnable ();
+      HUPFetchEnable ();
+    }
+  }
+#endif
+
   if (useLocal) {
     LocalSeqFetchInit (FALSE);
   }
-/*#endif*/
+
+/*
+#ifdef USE_SMARTNET
+  if (dirsubMode) {
+    if (only_use_smart) {
+      SmartFetchEnable ();
+    } else {
+      DirSubFetchEnable ();
+      SmartFetchEnable ();
+      TPASmartFetchEnable ();
+    }
+  }
+#endif
+
+  if (! only_use_smart) {
+    if (useEntrez) {
+      if (useSeqFetch) {
+        PubSeqFetchEnable ();
+        PubMedFetchEnable ();
+      } else {
+        PubSeqFetchEnableEx (FALSE, TRUE, TRUE, TRUE, TRUE);
+        PubMedFetchEnable ();
+      }
+    }
+
+    if (useLocal) {
+      LocalSeqFetchInit (FALSE);
+    }
+  }
+*/
 
 #ifdef WIN_MAC
   SetDeactivate (NULL, MacDeactProc);
@@ -11639,6 +11912,9 @@ Int2 Main (void)
   Remove (initSubmitForm);
   Remove (formatForm);
   Remove (helpForm);
+
+  FreeSqnTempFiles ();
+
   ArrowCursor ();
   Update ();
 
@@ -11732,7 +12008,7 @@ extern void MakeBadSpecificHostValueTable (IteM i)
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
 
-  bad_biop_list = Taxon3CheckSpecificHostInSeqEntry (sep, TRUE);
+  bad_biop_list = Taxon3CheckSpecificHostInSeqEntry (sep, TRUE, FALSE);
 
   if (bad_biop_list == NULL)
   {
@@ -11747,3 +12023,300 @@ extern void MakeBadSpecificHostValueTable (IteM i)
   CloseLog (lip);
   lip = FreeLog (lip);
 }
+
+
+typedef struct updatefeaturesform {
+  FORM_MESSAGE_BLOCK
+  DialoG new_features;
+  ValNodePtr feat_list;
+  SeqAnnotPtr sap;
+} UpdateFeaturesFormData, PNTR UpdateFeaturesFormPtr;
+
+
+static void CleanupUpdateFeaturesForm (GraphiC g, VoidPtr data)
+{
+    UpdateFeaturesFormPtr f;
+
+    f = (UpdateFeaturesFormPtr) data;
+    if (f != NULL) {
+      f->feat_list = FreeClickableList (f->feat_list);
+      f->sap = SeqAnnotFree (f->sap);
+    }
+    StdCleanupFormProc (g, data);
+}
+
+
+
+static CharPtr GetNewItemDescription (SeqFeatPtr sfp)
+{
+  CharPtr location, label, row_text;
+  Char buf[129];
+  
+  location = SeqLocPrintUseBestID (sfp->location);
+  label = (CharPtr) FeatDefTypeLabel(sfp);
+
+  FeatDefLabel (sfp, buf, sizeof (buf) - 1, OM_LABEL_CONTENT);
+
+  row_text = (CharPtr) MemNew (sizeof (Char) * 
+                              (StringLen (label) 
+                              + StringLen (buf) 
+                              + StringLen (location) 
+                              + 6));
+  sprintf (row_text, "%s:%s:%s\n", label, buf, location);
+  location = MemFree (location);
+  return row_text;
+}
+
+
+static ClickableItemPtr PutFeaturesInOldItem (ValNodePtr item_list)
+{
+  ClickableItemPtr cip_olditems, cip;
+  ValNodePtr       vnp;
+
+  cip_olditems = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+  if (item_list == NULL) {
+    cip_olditems->description = StringSave ("No old features found");
+    cip_olditems->chosen = FALSE;
+  } else {
+    for (vnp = item_list; vnp != NULL; vnp = vnp->next) {
+      cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+      cip->description = GetNewItemDescription (vnp->data.ptrvalue);
+      cip->chosen = TRUE;
+      ValNodeAddPointer (&(cip->item_list), OBJ_SEQFEAT, vnp->data.ptrvalue);
+      ValNodeAddPointer (&(cip_olditems->subcategories), 0, cip);
+    }
+    cip_olditems->description = StringSave ("Old Features (check to delete)");
+    cip_olditems->chosen = TRUE;
+  }
+  return cip_olditems;
+}
+
+
+static void MarkChosenFeatures (ValNodePtr item_list, Boolean delete_marked)
+{
+  ClickableItemPtr cip;
+  ValNodePtr vnp;
+  SeqFeatPtr sfp;
+
+  while (item_list != NULL) {
+    cip = (ClickableItemPtr) item_list->data.ptrvalue;
+    if (cip != NULL) {
+      for (vnp = cip->item_list; vnp != NULL; vnp = vnp->next) {
+        if (vnp->choice == OBJ_SEQFEAT) {
+          sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+          if ((cip->chosen && delete_marked) || (!cip->chosen && !delete_marked)) {
+            sfp->idx.deleteme = TRUE;
+          }
+        }
+      }
+    }
+    item_list = item_list->next;
+  }
+}
+
+
+static void MarkChosenFeaturesForBioseqs (ValNodePtr feat_list)
+{
+  ClickableItemPtr cip, cip_new, cip_old;
+
+  if (feat_list == NULL) return;
+  cip = (ClickableItemPtr) feat_list->data.ptrvalue;
+  if (cip->item_list != NULL && cip->item_list->choice == OBJ_BIOSEQ) {
+    if (cip->subcategories != NULL) {
+      cip_new = (ClickableItemPtr) cip->subcategories->data.ptrvalue;
+      MarkChosenFeatures (cip_new->subcategories, FALSE);
+      if (cip->subcategories->next != NULL) {
+        cip_old = (ClickableItemPtr) cip->subcategories->next->data.ptrvalue;
+        MarkChosenFeatures (cip_old->subcategories, TRUE);
+      }
+    }
+    MarkChosenFeaturesForBioseqs (feat_list->next);
+  } else if (feat_list->next != NULL && feat_list->next->next == NULL && cip->item_list == NULL) {
+    cip_new = (ClickableItemPtr) feat_list->data.ptrvalue;
+    cip_old = (ClickableItemPtr) feat_list->next->data.ptrvalue;
+    MarkChosenFeatures (cip_new->subcategories, FALSE);
+    MarkChosenFeatures (cip_old->subcategories, TRUE);
+  }
+}
+
+
+static void DoUpdateFeatures (ButtoN b)
+{
+  UpdateFeaturesFormPtr f;
+
+  f = (UpdateFeaturesFormPtr) GetObjectExtra (b);
+  if (f == NULL) return;
+
+  MarkChosenFeaturesForBioseqs (f->feat_list);
+  
+  SmartAttachSeqAnnotToSeqEntry (f->input_entityID, f->sap, NULL);
+  f->sap = NULL;
+
+  DeleteMarkedObjects (f->input_entityID, 0, NULL);
+  ObjMgrSetDirtyFlag (f->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, f->input_entityID, 0, 0);
+
+  Remove (f->form);
+}
+
+
+extern void UpdateFeatures (IteM i)
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+  Pointer        dataptr;
+  Uint2          datatype;
+  FILE           *fp;
+  Char           path [PATH_MAX];
+  SeqAnnotPtr    sap;
+  SeqFeatPtr     sfp;
+  ValNodePtr     new_feat_list = NULL, no_bsp_list = NULL, old_item_list;
+  Int4           leftmost = -1, rightmost = -1, new_left, new_right, tmp;
+  BioseqPtr      bsp, last_bsp = NULL;
+  ClickableItemPtr cip = NULL, cip_newitems = NULL, cip_olditems, cip_newfeat;
+  SeqLocPtr        slp;
+  WindoW           w;
+  GrouP            h, g, c;
+  ButtoN           b;
+  UpdateFeaturesFormPtr f;
+  Char             id [42];
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+
+  path [0] = '\0';
+  if (!GetInputFileName (path, sizeof (path), "", "TEXT")) {
+    return;
+  }
+
+  fp = FileOpen (path, "r");
+  if (fp == NULL) {
+    Message (MSG_ERROR, "Unable to open file!");
+    return;
+  }
+  dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, FALSE,
+                                    TRUE, TRUE);
+  FileClose (fp);
+  if (dataptr == NULL || datatype != OBJ_SEQANNOT) {
+    Message (MSG_ERROR, "File does not contain feature table!");
+    return;
+  }
+
+  sap = (SeqAnnotPtr) dataptr;
+  if (sap->type != 1) {
+    Message (MSG_ERROR, "File does not contain feature table!");
+    sap = SeqAnnotFree (sap);
+    return;
+  }
+
+  // list features for each bioseq
+  for (sfp = sap->data; sfp != NULL; sfp = sfp->next) {
+    bsp = BioseqFindFromSeqLoc (sfp->location);
+    if (bsp == NULL) {    
+      ValNodeAddPointer (&no_bsp_list, OBJ_SEQFEAT, sfp);
+    } else {
+      if (bsp != last_bsp) {   
+        if (last_bsp != NULL) {
+          slp = SeqLocIntNew (leftmost, rightmost, Seq_strand_plus, SeqIdDup (SeqIdFindWorst (bsp->id)));
+          old_item_list = ListFeaturesOverlappingLocation (last_bsp, slp, 0, 0);
+          slp = SeqLocFree (slp);
+          cip_olditems = PutFeaturesInOldItem (old_item_list);
+          old_item_list = ValNodeFree (old_item_list);
+          ValNodeAddPointer (&(cip->subcategories), 0, cip_olditems);
+        }   
+        cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+        ValNodeAddPointer (&(cip->item_list), OBJ_BIOSEQ, bsp);
+
+        SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id, PRINTID_FASTA_LONG, sizeof (id) - 1);
+        cip->description = StringSave (id);
+        cip_newitems = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+        cip_newitems->description = StringSave ("New Features (check to import)");
+        cip_newitems->chosen = TRUE;
+        ValNodeAddPointer (&(cip->subcategories), 0, cip_newitems);
+        last_bsp = bsp;
+        ValNodeAddPointer (&new_feat_list, 0, cip);
+        leftmost = -1;
+        rightmost = -1;
+      }
+      cip_newfeat = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+      cip_newfeat->description = GetNewItemDescription (sfp);      
+      cip_newfeat->chosen = TRUE;
+      ValNodeAddPointer (&(cip_newfeat->item_list), OBJ_SEQFEAT, sfp);
+      ValNodeAddPointer (&(cip_newitems->subcategories), 0, cip_newfeat);
+      new_left = SeqLocStart (sfp->location);
+      new_right = SeqLocStop (sfp->location);
+      if (new_left > new_right) {
+        tmp = new_left;
+        new_left = new_right;
+        new_right = tmp;
+      }
+      if (leftmost == -1 || new_left < leftmost) {
+        leftmost = new_left;
+      }
+      if (rightmost == -1 || new_right > rightmost) {
+        rightmost = new_right;
+      }
+    }
+  }
+  if (last_bsp != NULL) {
+    slp = SeqLocIntNew (leftmost, rightmost, Seq_strand_plus, SeqIdDup (SeqIdFindWorst (bsp->id)));
+    old_item_list = ListFeaturesOverlappingLocation (last_bsp, slp, 0, 0);
+    slp = SeqLocFree (slp);
+    cip_olditems = PutFeaturesInOldItem (old_item_list);
+    old_item_list = ValNodeFree (old_item_list);
+    ValNodeAddPointer (&(cip->subcategories), 0, cip_olditems);
+  }
+
+  if (no_bsp_list != NULL) {
+    Message (MSG_ERROR, "%d features in table are not found on a Bioseq in this record!", ValNodeLen (no_bsp_list));
+    no_bsp_list = ValNodeFree (no_bsp_list);
+  }
+ 
+  if (new_feat_list == NULL) {
+    Message (MSG_ERROR, "No features found!");
+    sap = SeqAnnotFree (sap);
+    return;
+  }
+  if (new_feat_list->next == NULL) {
+    no_bsp_list = new_feat_list;
+    cip = (ClickableItemPtr) new_feat_list->data.ptrvalue;
+    new_feat_list = cip->subcategories;
+    cip->subcategories = NULL;
+    no_bsp_list = FreeClickableList (no_bsp_list);
+  }  
+   
+
+  /* Now create dialog to allow user to select new features to import and existing features to delete */
+  f = (UpdateFeaturesFormPtr) MemNew (sizeof (UpdateFeaturesFormData));
+  w = FixedWindow (-50, -33, -10, -10, "Update Features", StdCloseWindowProc);
+  SetObjectExtra (w, f, CleanupUpdateFeaturesForm);
+  f->form = (ForM) w;
+  f->input_entityID = bfp->input_entityID;
+  f->feat_list = new_feat_list;
+  f->sap = sap;
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+  g = HiddenGroup (h, 2, 0, NULL);
+  f->new_features = CreateClickableListDialog (g, "New Features (check to import)", "label1", NULL, NULL, NULL, GetDiscrepancyItemText);
+  PointerToDialog (f->new_features, new_feat_list);
+/*  f->old_features = CreateClickableListDialog (g, "Old Features", "label1",
+                                               ScrollToDiscrepancyItem, EditDiscrepancyItem, bfp,
+                                               GetDiscrepancyItemText); */
+  c = HiddenGroup (h, 4, 0, NULL);
+  b = PushButton (c, "Accept", DoUpdateFeatures);
+  SetObjectExtra (b, f, NULL);
+  PushButton (c, "Cancel", StdCancelButtonProc);
+  
+  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
+  Show (w);
+  Select (w);
+
+
+}
+
diff --git a/sequin/sequin10.c b/sequin/sequin10.c
index 3b6ebb6f..c61c7338 100644
--- a/sequin/sequin10.c
+++ b/sequin/sequin10.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/3/2003
 *
-* $Revision: 1.366 $
+* $Revision: 1.405 $
 *
 * File Description: 
 *
@@ -51,9987 +51,20 @@
 #include <gbftdef.h>
 #include <gbfeat.h>
 #include <biosrc.h>
+#include <findrepl.h>
+#include <asnenbin.h>
+#include <cdrgn.h>
+#include <macrodlg.h>
+#include <macroapi.h>
 
-/* The matchFunction functions are used to identify features that meet
- * specific requirements, usually that the feature is of a particular type.
- * This function is used instead of simply using the subtype for the feature
- * because some features are identified based on the contents or presence of
- * certain modifiers.
- * Functions of this type should always return FALSE if handed a NULL argument.
- */
-typedef Boolean (LIBCALLBACK *matchFunction) (
-  SeqFeatPtr sfp
-);
-
-static void ListClauses (
-  ValNodePtr clauselist,
-  ValNodePtr PNTR strings,
-  Boolean    allow_semicolons,
-  Boolean    suppress_final_and
-);
-
-static void LabelClauses 
-( ValNodePtr clause_list,
-  Uint1      biomol,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag);
-
-static CharPtr GetProductName 
-( SeqFeatPtr cds,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag);
-
-#define DEFLINE_FEATLIST    1
-#define DEFLINE_CLAUSEPLUS  2
-#define DEFLINE_REMOVEFEAT  3
-
-typedef struct featurelabeldata {
-  Boolean pluralizable;
-  Boolean is_typeword_first;
-  CharPtr typeword;
-  CharPtr description;
-  CharPtr productname;
-} FeatureLabelData, PNTR FeatureLabelPtr;
-
-
-typedef struct featureclause {
-  ValNodePtr       featlist;
-  FeatureLabelData feature_label_data;
-  CharPtr          allelename;
-  CharPtr          interval;
-  Boolean          is_alt_spliced;
-  Boolean          has_mrna;
-  SeqLocPtr        slp;
-  GeneRefPtr       grp;
-  Boolean          clause_info_only;
-  Boolean          is_unknown;
-  Boolean          make_plural;
-  Boolean          delete_me;
-  /* this information used only for segments */
-  Int2             numivals;
-  Int4Ptr          ivals;
-} FeatureClauseData, PNTR FeatureClausePtr;
-
-FeatureClausePtr NewFeatureClause (
-  SeqFeatPtr sfp,
-  BioseqPtr bsp,
-  Boolean   suppress_locus_tag);
-
-static void PluralizeConsolidatedClauseDescription (
-  FeatureClausePtr fcp
-);
-
-typedef Boolean (LIBCALLBACK *ShouldRemoveFunction) (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr        bsp,
-  Boolean          isLonely,
-  Boolean          isRequested,
-  Boolean          isSegment,
-  Boolean          suppress_locus_tag
-);
-
-/* This section of the code contains some functions for dealing with
- * linked lists of strings */
-
-/* This function finds the first occurrence of "search" in one of the
- * strings in list "strings".
- * "search" could be part of the string or could be the entire string.
- */
-static ValNodePtr FindStringInStrings (
-  ValNodePtr strings,
-  CharPtr search
-)
-{
-  while (strings != NULL)
-  {
-    if (StringStr (strings->data.ptrvalue, search))
-    {
-      return strings;
-    }
-    strings = strings->next;
-  }
-  return NULL;
-}
-
-/* This function finds the first item in "strings" that is identical to
- * "value".
- */
-extern ValNodePtr FindExactStringInStrings (
-  ValNodePtr strings,
-  CharPtr    value
-)
-{
-  ValNodePtr    string_match;
-
-  for (string_match = FindStringInStrings (strings, value);
-       string_match != NULL
-         && StringCmp (string_match->data.ptrvalue, value) != 0;
-       string_match = FindStringInStrings (string_match->next, value))
-  {}
-  return string_match;
-}
-
-/* This function creates a new linked list of strings with copies of
- * contents of orig.
- */
-static ValNodePtr CopyStrings (
-  ValNodePtr orig
-)
-{
-  ValNodePtr new_string_start = NULL;
-
-  while (orig != NULL)
-  {
-    ValNodeAddStr (&new_string_start, 0,
-      StringSave (orig->data.ptrvalue));
-    orig = orig->next;
-  }
-  return new_string_start;
-}
-
-/*
- * This section of the code contains functions and structures for obtaining a
- * description of the organism in the record, including functions for finding
- * the combination of modifiers that will make each organism description 
- * unique.
- * The method used for determining the best combination of modifiers involves
- * creating a list of required modifiers, and then creating a list of
- * combinations of modifiers by adding modifiers one at a time
- * to see if the additional modifiers provide any more differentiation in
- * the list.
- * In order to do this, I start with a list of required modifiers, and 
- * then create copies of this list.  For each copy I add one of the modifiers
- * that are present in the bio sources and not already on the list.
- * If adding the modifier increases the differentiation, I add that copy to
- * the list of possible combinations, otherwise I discard it.
- * I then make copies of all of the new items I added to the list and
- * add another modifier to each list, keeping the combinations that increase
- * the differentiation and discarding the rest.
- * This process continues until I have a combination that produces completely
- * differentiated bio sources, or I run out of possible combinations.
- * If I run out of possible combinations, I select the best combination from
- * the list.
- * This search process occurs in FindBestCombo.  The majority of the functions
- * in this section are here to support FindBestCombo, specifically to create,
- * copy, and grow lists of combinations. 
- */
-
-/* BioSrcDescData is used to calculate the best possible combination of
- * source and organism modifiers for uniqueness.
- * biop contains the BioSourcePtr from a sequence in the record.
- * strings contains a list of string representations of the modifiers
- * for this combination for this organism.
- */
-typedef struct biosrcdescdata {
-  BioSourcePtr  biop;
-  ValNodePtr    strings;
-  Pointer       next;
-} BioSrcDescData, PNTR BioSrcDescPtr;
-
-/* OrgGroupData is used to calculate the best possible combination of
- * source and organism modifiers for uniqueness.
- * org_list is a list of all organisms that have identical descriptions
- * using the current set of modifiers.
- * num_organisms contains the number of organisms with identical descriptions.
- */
-typedef struct orggroupdata {
-  BioSrcDescPtr org_list;
-  Int4          num_organisms;
-  Pointer       next;
-} OrgGroupData, PNTR OrgGroupPtr;
-
-/* ModifierCombinationData is used to calculate the best possible combination
- * of source and organism modifiers for uniqueness.
- * num_groups is the number of groups of organisms with identical descriptions
- *           using the modifiers specified in modifier_indices.
- * num_mods is the number of modifiers specified in modifier_indices.
- * max_orgs_in_group is the maximum number of organisms in any one group.
- * num_unique_orgs is the number of organisms that are alone in their groups
- *           i.e., their description is unique.
- * modifier_indices is the list of modifier indices for this combination.
- * group_list is the list of groups of organisms with identical descriptions
- *           using the modifiers specified in modifier_indices.
- */
-typedef struct modifiercombination {
-  Int4         num_groups;
-  Int4         num_mods;
-  Int4         max_orgs_in_group;
-  Int4         num_unique_orgs;
-  ValNodePtr   modifier_indices;
-  OrgGroupPtr  group_list;
-  Pointer      next;
-} ModifierCombinationData, PNTR ModifierCombinationPtr;
-
-/* ModifierItemGlobalData is used to store information about the available
- * modifiers - the name to use when displaying a list of checkboxes, whether
- * the modifier is an Organism modifier or a Source modifier, the subtype
- * to use when looking for the modifier in the organism qualifier list,
- * and whether this modifier is required by default.
- */
-typedef struct modifieritemglobal {
-  CharPtr       name;
-  Boolean       isOrgMod;
-  Uint1         subtype;
-} ModifierItemGlobalData, PNTR ModifierItemGlobalPtr;
-
-/* ModifierItemLocalData is used to store information about the results of
- * a search of the set of organisms in a record and the results of user
- * input to a dialog for deciding which modifiers should be used in the
- * organism description.
- */
-typedef struct modifieritemlocal {
-  ButtoN        button;
-  Boolean       any_present;
-  Boolean       all_present;
-  Boolean       is_unique;
-  CharPtr       first_value_seen;
-  ValNodePtr    values_seen;
-  Boolean       all_unique;
-  CharPtr       status;
-  Boolean       required;
-} ModifierItemLocalData, PNTR ModifierItemLocalPtr;
-
-/* OrganismDescriptionModifiers is used to apply specific user preferences
- * for how to construct the organism descriptions - whether or not to use
- * labels for the modifiers, whether and how to limit the number of modifiers
- * used in any one organism description, whether to keep or remove modifier
- * information in parentheses in the organism taxonomy name, and whether or
- * not to apply modifiers to organisms with "sp." in the middle of the
- * taxonomy name.
- */
-typedef struct organismdescriptionmodifiers {
-  Boolean  use_labels;
-  Int2     max_mods;
-  Boolean  keep_paren;
-  Boolean  exclude_sp;
-  Boolean  exclude_cf;
-  Boolean  exclude_aff;
-  Boolean  include_country_extra;
-  Int4     clone_isolate_HIV_rule_num;
-  Boolean  use_modifiers;
-  Boolean  allow_semicolon_in_modifier;
-} OrganismDescriptionModifiers, PNTR OrganismDescriptionModifiersPtr;
-/* This is a list of the modifiers that are of interest */
-/* Note that if you modify the DefLineModifiers array, */ 
-/* you should make the corresponding change to the DefLinePos enum. */
-
-static ModifierItemGlobalData DefLineModifiers[] = {
-  { "Acronym"              , TRUE , ORGMOD_acronym              },
-  { "Anamorph"             , TRUE , ORGMOD_anamorph             },
-  { "Authority"            , TRUE , ORGMOD_authority            },
-  { "Biotype"              , TRUE , ORGMOD_biotype              },
-  { "Biovar"               , TRUE , ORGMOD_biovar               },
-  { "Breed"                , TRUE , ORGMOD_breed                },
-  { "Cell-line"            , FALSE, SUBSRC_cell_line            },
-  { "Cell-type"            , FALSE, SUBSRC_cell_type            },
-  { "Chemovar"             , TRUE , ORGMOD_chemovar             },
-  { "Chromosome"           , FALSE, SUBSRC_chromosome           },
-  { "Clone"                , FALSE, SUBSRC_clone                },
-  { "Clone-lib"            , FALSE, SUBSRC_clone_lib            },
-  { "Collected-by"         , FALSE, SUBSRC_collected_by         },
-  { "Collection-date"      , FALSE, SUBSRC_collection_date      },
-  { "Common"               , TRUE , ORGMOD_common               },
-  { "Country"              , FALSE, SUBSRC_country              },
-  { "Cultivar"             , TRUE , ORGMOD_cultivar             },
-  { "Dev-stage"            , FALSE, SUBSRC_dev_stage            },
-  { "Ecotype"              , TRUE , ORGMOD_ecotype              },
-  { "Endogenous-virus-name", FALSE, SUBSRC_endogenous_virus_name},
-  { "Environmental-sample" , FALSE, SUBSRC_environmental_sample },
-  { "Forma"                , TRUE , ORGMOD_forma                },
-  { "Forma-specialis"      , TRUE , ORGMOD_forma_specialis      },
-  { "Frequency"            , FALSE, SUBSRC_frequency            },
-  { "Genotype"             , FALSE, SUBSRC_genotype             },
-  { "Germline"             , FALSE, SUBSRC_germline             },
-  { "Group"                , TRUE , ORGMOD_group                },
-  { "Haplotype"            , FALSE, SUBSRC_haplotype            },
-  { "Identified-by"        , FALSE, SUBSRC_identified_by        },
-  { "Isolate"              , TRUE , ORGMOD_isolate              },
-  { "Isolation-source"     , FALSE, SUBSRC_isolation_source     },
-  { "Lab-host"             , FALSE, SUBSRC_lab_host             },
-  { "Lat-lon"              , FALSE, SUBSRC_lat_lon              },
-  { "Map"                  , FALSE, SUBSRC_map                  },
-  { "Metagenomic"          , FALSE, SUBSRC_metagenomic          },
-  {	"Note-OrgMod"          , TRUE,  ORGMOD_other                },
-  {	"Note-SubSrc"          , FALSE, SUBSRC_other                },
-  { "Pathovar"             , TRUE , ORGMOD_pathovar             },
-  { "Plasmid-name"         , FALSE, SUBSRC_plasmid_name         },
-  { "Plastid-name"         , FALSE, SUBSRC_plastid_name         },
-  { "Pop-variant"          , FALSE, SUBSRC_pop_variant          },
-  { "Rearranged"           , FALSE, SUBSRC_rearranged           },
-  { "Segment"              , FALSE, SUBSRC_segment              },
-  { "Serogroup"            , TRUE , ORGMOD_serogroup            },
-  { "Serotype"             , TRUE , ORGMOD_serotype             },
-  { "Serovar"              , TRUE , ORGMOD_serovar              },
-  { "Sex"                  , FALSE, SUBSRC_sex                  },
-  { "Specific-host"        , TRUE , ORGMOD_nat_host             },
-  { "Specimen voucher"     , TRUE , ORGMOD_specimen_voucher     },
-  { "Strain"               , TRUE , ORGMOD_strain               },
-  { "Subclone"             , FALSE, SUBSRC_subclone             },
-  { "Subgroup"             , TRUE , ORGMOD_subgroup             },
-  { "Sub-species"          , TRUE , ORGMOD_sub_species          },
-  { "Substrain"            , TRUE , ORGMOD_substrain            },
-  { "Subtype"              , TRUE , ORGMOD_subtype              },
-  { "Synonym"              , TRUE , ORGMOD_synonym              },
-  { "Teleomorph"           , TRUE , ORGMOD_teleomorph           },
-  { "Tissue-lib"           , FALSE, SUBSRC_tissue_lib           },
-  { "Tissue-type"          , FALSE, SUBSRC_tissue_type          },
-  { "Transgenic"           , FALSE, SUBSRC_transgenic           },
-  { "Type"                 , TRUE , ORGMOD_type                 },
-  { "Variety"              , TRUE , ORGMOD_variety              }
-};
-
-static Boolean IsDeflineModifierRequiredByDefault (Boolean is_orgmod, Int2 index)
-{
-  if (!is_orgmod
-      && (index == SUBSRC_endogenous_virus_name
-          || index == SUBSRC_plasmid_name
-          || index == SUBSRC_transgenic)) {
-    return TRUE;
-  } else {
-    return FALSE;
-  }
-}
-
-typedef enum {
-  DEFLINE_POS_Acronym = 0,
-  DEFLINE_POS_Anamorph,
-  DEFLINE_POS_Authority,
-  DEFLINE_POS_Biotype,
-  DEFLINE_POS_Biovar,
-  DEFLINE_POS_Breed,
-  DEFLINE_POS_Cell_line,
-  DEFLINE_POS_Cell_type,
-  DEFLINE_POS_Chemovar,
-  DEFLINE_POS_Chromosome,
-  DEFLINE_POS_Clone,
-  DEFLINE_POS_Clone_lib,
-  DEFLINE_POS_Collected_by,
-  DEFLINE_POS_Collection_date,
-  DEFLINE_POS_Common,
-  DEFLINE_POS_Country,
-  DEFLINE_POS_Cultivar,
-  DEFLINE_POS_Dev_stage,
-  DEFLINE_POS_Ecotype,
-  DEFLINE_POS_Endogenous_virus_name,
-  DEFLINE_POS_Environmental_sample,
-  DEFLINE_POS_Forma,
-  DEFLINE_POS_Forma_specialis,
-  DEFLINE_POS_Frequency,
-  DEFLINE_POS_Genotype,
-  DEFLINE_POS_Germline,
-  DEFLINE_POS_Group,
-  DEFLINE_POS_Haplotype,
-  DEFLINE_POS_Identified_by,
-  DEFLINE_POS_Isolate,
-  DEFLINE_POS_Isolation_source,
-  DEFLINE_POS_Lab_host,
-  DEFLINE_POS_Lat_lon,
-  DEFLINE_POS_Map,
-  DEFLINE_POS_Metagenomic,
-  DEFLINE_POS_Note_orgmod,
-  DEFLINE_POS_Note_subsrc,
-  DEFLINE_POS_Pathovar,
-  DEFLINE_POS_Plasmid_name,
-  DEFLINE_POS_Plastid_name,
-  DEFLINE_POS_Pop_variant,
-  DEFLINE_POS_Rearranged,
-  DEFLINE_POS_Segment,
-  DEFLINE_POS_Serogroup,
-  DEFLINE_POS_Serotype,
-  DEFLINE_POS_Serovar,
-  DEFLINE_POS_Sex,
-  DEFLINE_POS_Specific_host,
-  DEFLINE_POS_Specimen_voucher,
-  DEFLINE_POS_Strain,
-  DEFLINE_POS_Subclone,
-  DEFLINE_POS_Subgroup,
-  DEFLINE_POS_Sub_species,
-  DEFLINE_POS_Substrain,
-  DEFLINE_POS_Subtype,
-  DEFLINE_POS_Synonym,
-  DEFLINE_POS_Teleomorph,
-  DEFLINE_POS_Tissue_lib,
-  DEFLINE_POS_Tissue_type,
-  DEFLINE_POS_Transgenic,
-  DEFLINE_POS_Type,
-  DEFLINE_POS_Variety
-} DefLinePos;
-
-#define NumDefLineModifiers (sizeof (DefLineModifiers) / sizeof (ModifierItemGlobalData))
-
-extern ValNodePtr GetSourceQualDescList (Boolean get_subsrc, Boolean get_orgmod, Boolean get_discouraged, Boolean get_discontinued)
-{
-  Int4              index;
-  ValNodePtr        source_qual_list = NULL;
-  SourceQualDescPtr sqdp;
-  EnumFieldAssocPtr eap;
-  Uint2             subtype;
-  Boolean           isOrgMod;
-  
-  eap = GetSubSourceAndOrgModEnum (get_discouraged, get_discontinued);
-  for (index = 0; eap[index].name != NULL; index++)
-  {
-    if (StringHasNoText (eap[index].name)) {
-      continue;
-    }
-    subtype = eap[index].value;
-    if (subtype > 1000) {
-      isOrgMod = FALSE;
-      subtype -= 1000;
-    } else {
-      isOrgMod = TRUE;
-    }
-
-    /* create sqdp */
-    if (isOrgMod && !get_orgmod) continue;
-    if (!isOrgMod && !get_subsrc) continue;
-    sqdp = (SourceQualDescPtr) MemNew (sizeof (SourceQualDescData));
-    if (sqdp != NULL)
-    {
-      sqdp->name = eap [index].name;
-      sqdp->isOrgMod = isOrgMod;
-      sqdp->subtype = (Uint1) subtype;
-      ValNodeAddPointer (&source_qual_list, 0, sqdp);
-    }
-  }
-  eap = MemFree (eap);
-
-  return source_qual_list;
-}
-
-typedef enum {
-  clone_isolate_HIV_rule_prefer_clone = 1,
-  clone_isolate_HIV_rule_prefer_isolate,
-  clone_isolate_HIV_rule_want_both
-} clone_isolate_HIV_rule_values;
-  
-/*
- * The CountModifiersProc is used as the callback function for
- * VisitBioSourcesInSep when we are getting a list of all the modifiers
- * that appear in the sources.  We also obtain, for each modifier class,
- * the first value seen, whether or not each value seen is unique for
- * for the modifier, and whether or not the modifier is present for all
- * sources.
- */
-static void CountModifiersProc (
-  BioSourcePtr biop,
-  Pointer userdata
-)
-{
-  ModifierItemLocalPtr ItemList;
-  OrgModPtr     mod;
-  SubSourcePtr  ssp;
-  Int2 i;
-  Boolean       found_this_modifier;
-
-  if (biop == NULL) return;
-  ItemList = (ModifierItemLocalPtr) userdata;
-
-  for (i=0; i < NumDefLineModifiers; i++)
-  {
-    found_this_modifier = FALSE;
-    if (DefLineModifiers[i].isOrgMod)
-    {
-      if ( biop->org != NULL && biop->org->orgname != NULL) 
-      {
-        mod = biop->org->orgname->mod;
-        while (mod != NULL
-          && mod->subtype != DefLineModifiers[i].subtype)
-        {
-          mod = mod->next;
-        }
-        if (mod != NULL && mod->subname != NULL)
-        {
-          found_this_modifier = TRUE;
-          if (ItemList[i].first_value_seen != NULL)
-          {
-            if (StringCmp (ItemList[i].first_value_seen, mod->subname) != 0)
-            {
-              ItemList[i].is_unique = FALSE;
-            }
-          }
-          else
-          {
-            ItemList[i].first_value_seen = mod->subname;
-          }
-          if ( FindExactStringInStrings (ItemList[i].values_seen, mod->subname)
-            == NULL)
-          {
-            ValNodeAddStr (&ItemList[i].values_seen, 0, mod->subname);
-          }
-          else
-          {
-            ItemList[i].all_unique = FALSE;
-          }
-        }
-      }
-    } else {
-      ssp = biop->subtype;
-      while (ssp != NULL && ssp->subtype != DefLineModifiers[i].subtype)
-      {
-        ssp = ssp->next;
-      }
-      if (ssp != NULL && ssp->name != NULL)
-      {
-        found_this_modifier = TRUE;
-        if (ItemList[i].first_value_seen != NULL)
-        {
-          if (StringCmp (ItemList[i].first_value_seen, ssp->name) != 0)
-          {
-            ItemList[i].is_unique = FALSE;
-          }
-        }
-        else
-        {
-          ItemList[i].first_value_seen = ssp->name;
-        }
-        if ( FindExactStringInStrings (ItemList[i].values_seen, ssp->name)
-          == NULL)
-        {
-          ValNodeAddStr (&ItemList[i].values_seen, 0, ssp->name);
-        }
-        else
-        {
-          ItemList[i].all_unique = FALSE;
-        }
-      }
-    }
-    if (found_this_modifier)
-    {
-      ItemList[i].any_present = TRUE;
-    } else {
-      ItemList[i].all_present = FALSE;
-    }
-  }
-} 
-
-/* The CountModifiers function visits all of the bio sources, determining
- * which modifiers are present, which modifiers have only one value,
- * which modifiers have all different values, and which modifiers are
- * present in all sources.
- * After this survey is complete, the function prepares a short summary
- * of the above information for each modifier, which is used in the 
- * definition line options dialog.
- */ 
-static void CountModifiers (
-  ModifierItemLocalPtr ItemList,
-  SeqEntryPtr sep
-)
-{
-  Int2 i;
-
-  for (i=0; i < NumDefLineModifiers; i++)
-  {
-    ItemList[i].all_present = TRUE;
-    ItemList[i].is_unique = TRUE;
-    ItemList[i].first_value_seen = NULL;
-    ItemList[i].values_seen = NULL;
-    ItemList[i].all_unique = TRUE;
-  }
-
-  VisitBioSourcesInSep (sep, ItemList, CountModifiersProc);
- 
-  for (i=0; i < NumDefLineModifiers; i++)
-  {
-    if (ItemList[i].all_present && ItemList[i].all_unique)
-    {
-      ItemList[i].status = "All present, all unique";
-    }
-    else if (ItemList[i].all_present && ItemList[i].is_unique)
-    {
-      ItemList[i].status = "All present, one unique";
-    }
-    else if (ItemList[i].all_present && ! ItemList[i].is_unique)
-    {
-      ItemList[i].status = "All present, mixed";
-    }
-    else if (! ItemList[i].all_present && ItemList[i].all_unique)
-    {
-      ItemList[i].status = "Some missing, all unique";
-    }
-    else if (! ItemList[i].all_present && ItemList[i].is_unique)
-    {
-      ItemList[i].status = "Some missing, one unique";
-    }
-    else if (! ItemList[i].all_present && ! ItemList[i].is_unique)
-    {
-      ItemList[i].status = "Some missing, mixed";
-    }
-  }
-}
-
-/* The BioSrcDescData structure is used to hold a BioSourcePtr, a list
- * of strings used to describe the biosource, including the taxonomy name
- * and the values of all of the modifiers selected so far for this bio
- * source, and a pointer to the next BioSrcDescData structure in the list.
- */
-
-/* The CopyBioSrcDescPtr function creates a copy of the linked list of
- * BioSrcDescData structures.
- */
-static BioSrcDescPtr CopyBioSrcDescPtr (
-  BioSrcDescPtr orig
-)
-{
-  BioSrcDescPtr new_bsdp_start;
-
-  if (orig == NULL) return NULL;
-
-  new_bsdp_start = (BioSrcDescPtr) MemNew (sizeof (BioSrcDescData));
-  if (new_bsdp_start == NULL) return NULL;
-
-  new_bsdp_start->biop = orig->biop;
-  new_bsdp_start->strings = CopyStrings (orig->strings);
-  new_bsdp_start->next = CopyBioSrcDescPtr (orig->next);
-  return new_bsdp_start;
-}
-
-/* The FreeBioSrcDescPtr function frees the memory associated with a
- * linked list of BioSrcDescData structures.
- */
-static void FreeBioSrcDescPtr (
-  BioSrcDescPtr bsdp
-)
-{
-  if (bsdp == NULL) return;
-  FreeBioSrcDescPtr (bsdp->next);
-  bsdp->biop = NULL;
-  ValNodeFreeData (bsdp->strings);
-  MemFree (bsdp);
-}
-
-/* The AddQualToBioSrcDescPtr function finds the qualifier at the
- * feature_index position in the DefLineModifiers array in the
- * BioSourcePtr and adds the value for that modifier to the array
- * of strings describing the bio source.
- */
-static void AddQualToBioSrcDescPtr (
-  BioSrcDescPtr bsdp,
-  ModifierItemLocalPtr qual,
-  Int2 feature_index
-)
-{
-  OrgModPtr          mod;
-  SubSourcePtr       ssp;
-
-  if (bsdp == NULL) return;
-  if (bsdp->biop == NULL) return;
-
-  if (DefLineModifiers[feature_index].isOrgMod)
-  {
-    if (bsdp->biop->org == NULL || bsdp->biop->org->orgname == NULL) return;
-    mod = bsdp->biop->org->orgname->mod;
-    while (mod != NULL
-        && mod->subtype != DefLineModifiers[feature_index].subtype)
-    {
-      mod = mod->next;
-    }
-    if (mod != NULL && mod->subname != NULL)
-    {
-      ValNodeCopyStr( &(bsdp->strings), 0, mod->subname);
-    }
-  } else {
-    ssp = bsdp->biop->subtype;
-    while (ssp != NULL
-        && ssp->subtype != DefLineModifiers[feature_index].subtype)
-    {
-      ssp = ssp->next;
-    }
-    if (ssp != NULL)
-    {
-      if (ssp->subtype == SUBSRC_transgenic)
-      {
-        ValNodeCopyStr( &(bsdp->strings), 0, "transgenic");
-      }
-      else if (ssp->name != NULL)
-      {
-        ValNodeCopyStr( &(bsdp->strings), 0, ssp->name);
-      }
-    }
-  }
-}
- 
-/* The CompareOrganismDescriptors function compares the contents of the
- * lists of strings for each BioSrcDesc item.
- * The function returns:
- *     -1 if org1 < org2
- *      0 if org1 = org2
- *      1 if org1 > org2
- */
-static int CompareOrganismDescriptors (
-  BioSrcDescPtr org1,
-  BioSrcDescPtr org2
-)
-{
-  ValNodePtr vnp1, vnp2;
-  int cmpval;
-
-  vnp1 = org1->strings;
-  vnp2 = org2->strings;
-
-  while (vnp1 != NULL && vnp2 != NULL)
-  {
-    cmpval = StringCmp (vnp1->data.ptrvalue, vnp2->data.ptrvalue);
-    if (cmpval != 0) return cmpval;
-
-    vnp1 = vnp1->next;
-    vnp2 = vnp2->next;
-  }
-  if (vnp1 == NULL && vnp2 == NULL)
-  {
-    return 0;
-  }
-  else if (vnp1 != NULL && vnp2 == NULL)
-  {
-    return 1;
-  }
-  else
-  {
-    return -1;
-  }
-}
-
-/* The OrgGroupData structure contains a list of BioSrcDescData items
- * for which the contents of the descriptive strings list are identical,
- * i.e., all the organisms in the group would have the same description
- * if you used the modifiers used to generate this list of strings.
- * The structure also contains the number of organisms in the list
- * so that it will be easy to tell that the OrgGroup now contains a
- * single organism with a unique description.
- */
-
-/* The CopyOrgGroupList function creates a copy of the list of OrgGroups */
-static OrgGroupPtr CopyOrgGroupList (
-  OrgGroupPtr orig
-)
-{
-  OrgGroupPtr new_ogp_start;
-
-  if (orig == NULL) return NULL;
-
-  new_ogp_start = (OrgGroupPtr) MemNew (sizeof (OrgGroupData));
-  if (new_ogp_start == NULL) return NULL;
-
-  new_ogp_start->num_organisms = orig->num_organisms;
-  new_ogp_start->org_list = CopyBioSrcDescPtr (orig->org_list);
-  new_ogp_start->next = CopyOrgGroupList (orig->next);
-  return new_ogp_start;
-}
-
-/* The FreeOrgGroupPtr function frees the memory associated with a
- * list of OrgGroups */
-static void FreeOrgGroupPtr (
-  OrgGroupPtr ogp
-)
-{
-  if (ogp == NULL) return;
-  FreeOrgGroupPtr (ogp->next);
-  FreeBioSrcDescPtr (ogp->org_list);
-  MemFree (ogp);
-  return;
-}
-
-/* The ReorderGroupOrgs function sorts the OrgGroup list based on the results
- * of the CompareOrganismDescriptors function.
- */
-static void ReorderGroupOrgs (
-  OrgGroupPtr this_group
-)
-{
-  BioSrcDescPtr bsdp;
-  BioSrcDescPtr nextBsdp;
-  BioSrcDescPtr prevBsdp;
-  Boolean swap_needed = TRUE;
-
-  if (this_group->org_list == NULL) return;
-  if (this_group->org_list->next == NULL) return;
-
-  while (swap_needed)
-  {
-    swap_needed = FALSE;
-    bsdp = this_group->org_list;
-    prevBsdp = NULL;
-    while (bsdp->next != NULL)
-    {
-      nextBsdp = bsdp->next;
-      if (CompareOrganismDescriptors (bsdp, nextBsdp) > 0)
-      {
-        swap_needed = TRUE;
-        bsdp->next = nextBsdp->next;
-        nextBsdp->next = bsdp;
-        if (prevBsdp == NULL)
-        {
-          this_group->org_list = nextBsdp;
-        }
-        else
-        {
-          prevBsdp->next = nextBsdp;
-        }
-        prevBsdp = nextBsdp;
-      }
-      else
-      {
-        prevBsdp = bsdp;
-        bsdp = bsdp->next;
-      }
-    }
-  }
-}
-
-/* The ReGroupOrgs function operates on a single OrgGroup item.
- * If any of the BioSrcDesc items in the group now have different
- * descriptions, the function breaks it up into smaller, homogenous OrgGroups.
- */
-static void ReGroupOrgs (
-  OrgGroupPtr this_group
-)
-{
-  BioSrcDescPtr bsdp;
-  OrgGroupPtr new_group;
-  int num_organisms;
-
-  if (this_group == NULL) return;
-  bsdp = this_group->org_list;
-  if (bsdp == NULL) return;
-  num_organisms = 0;
-  while (bsdp->next != NULL)
-  {
-    num_organisms ++;
-    if (CompareOrganismDescriptors (bsdp, bsdp->next) != 0)
-    {
-      /* create new group to hold next set of organisms */
-      new_group = (OrgGroupPtr) MemNew (sizeof (OrgGroupData));
-      if (new_group == NULL) return;
-      new_group->org_list = bsdp->next;
-      new_group->num_organisms = this_group->num_organisms - num_organisms;
-      new_group->next = this_group->next;
-      this_group->next = new_group;
-      this_group->num_organisms = num_organisms;
-      bsdp->next = NULL;
-      ReGroupOrgs (new_group);
-    }
-    else
-    {
-      bsdp = bsdp->next;
-    }
-  }
-}
-
-/* The AddQualToGroup function operates on a single OrgGroup item.
- * The function adds a qualifier to each BioSrcDesc item in the OrgGroup,
- * breaks the group into multiple groups if the group is no longer
- * homogenous, and sorts the new list.
- */
-static void AddQualToGroup (
-  OrgGroupPtr this_group,
-  ModifierItemLocalPtr qual,
-  Int2 feature_index
-)
-{
-  BioSrcDescPtr bsdp;
-
-  if (this_group == NULL) return;
-
-  bsdp = this_group->org_list;
-  while (bsdp != NULL)
-  {
-    AddQualToBioSrcDescPtr (bsdp, qual, feature_index);
-    bsdp= bsdp->next;
-  }
-
-  /* now reorder organisms and break up group */
-  ReorderGroupOrgs (this_group);
-
-  ReGroupOrgs (this_group);
-}
-
-/* The AddQualToGroupList function operates on a list of OrgGroup items.
- * It calls AddQualToGroup for each item in the list.
- */
-static void AddQualToGroupList (
-  OrgGroupPtr group_list,
-  ModifierItemLocalPtr qual,
-  Int2 feature_index
-)
-{
-  OrgGroupPtr ogp;
-
-  ogp = group_list;
-  while (ogp != NULL)
-  {
-    AddQualToGroup (ogp, qual, feature_index);
-    ogp = ogp->next;
-  }
-}
-
-/* The CopyModifierIndices function creates a new ValNode list with the
- * same data.intvalue values for each node as the original modifier_indices
- * ValNode list.
- */
-static ValNodePtr CopyModifierIndices (
-  ValNodePtr modifier_indices
-)
-{
-  ValNodePtr new_indices;
-
-  if (modifier_indices == NULL) return NULL;
-  new_indices = ValNodeNew (NULL);
-  if (new_indices == NULL) return NULL;
-  new_indices->choice = modifier_indices->choice;
-  new_indices->data.intvalue = modifier_indices->data.intvalue;
-  new_indices->next = CopyModifierIndices (modifier_indices->next);
-  return new_indices;
-}
- 
-/* The CopyModifierCombo creates a copy of a ModificationCombination item.
- * This includes creating a copy of the number and list of modifiers
- * and a copy of the number and list of OrgGroups, as well as copying the
- * maximum number of organisms in any one group and the number of unique
- * organism descriptions produced by this combination of modifiers.
- */
-static ModifierCombinationPtr CopyModifierCombo (
-  ModifierCombinationPtr m
-)
-{
-  ModifierCombinationPtr newm;
-  ValNodePtr  vnp;
-  ValNodePtr  newval;
-
-  newm = (ModifierCombinationPtr) MemNew (sizeof (ModifierCombinationData));
-  if (newm == NULL) return NULL;
-
-  newm->next = NULL;
-
-  /* copy list of modifier indices */
-  newm->num_mods = m->num_mods;
-  newm->modifier_indices = NULL;
-  vnp = m->modifier_indices;
-  if (vnp != NULL)
-  {
-    newm->modifier_indices = ValNodeNew (NULL);
-    if (newm->modifier_indices == NULL) return NULL;
-    newm->modifier_indices->data.intvalue = vnp->data.intvalue;
-    vnp = vnp->next;
-    while (vnp != NULL)
-    {
-      newval = ValNodeNew (newm->modifier_indices);
-      if (newval == NULL) return NULL;
-      newval->data.intvalue = vnp->data.intvalue;
-      vnp = vnp->next;
-    }
-  }
-  
-  /* copy groups */
-  newm->num_groups = m->num_groups;
-  newm->group_list = CopyOrgGroupList (m->group_list);
- 
-  return newm; 
-}
-
-/* This function creates a new ModifierCombination item using the supplied
- * OrgGroup list.  It calculates the number of groups, maximum number of 
- * organisms in any one group, and number of unique organisms.
- * Initially there are no modifiers.
- */
-static ModifierCombinationPtr NewModifierCombo (
-  OrgGroupPtr group_list
-)
-{
-  ModifierCombinationPtr newm;
-  OrgGroupPtr  ogp;
-
-  newm = (ModifierCombinationPtr) MemNew (sizeof (ModifierCombinationData));
-  if (newm == NULL) return NULL;
-
-  newm->num_mods = 0;
-  newm->modifier_indices = NULL;
-  newm->num_unique_orgs = 0;
-  
-  /* copy groups */
-  newm->group_list = CopyOrgGroupList (group_list);
- 
-  ogp = newm->group_list;
-  newm->max_orgs_in_group = 0;
-  newm->num_groups = 0;
-  while (ogp != NULL)
-  {
-    if (newm->max_orgs_in_group < ogp->num_organisms)
-      newm->max_orgs_in_group = ogp->num_organisms;
-    if (ogp->num_organisms == 1)
-      newm->num_unique_orgs ++;
-    newm->num_groups ++;
-    ogp = ogp->next;
-  }
-
-  newm->next = NULL;
-  return newm; 
-}
-
-/* This function frees the memory associated with a list of
- * ModifierCombination items.
- */
-static void FreeModifierCombo (
-  ModifierCombinationPtr m
-)
-{
-  if (m == NULL) return;
-  FreeModifierCombo (m->next);
-  ValNodeFree (m->modifier_indices);
-  FreeOrgGroupPtr (m->group_list);
-  MemFree (m);
-}
-
-/* This function adds the qualifier at the feature_index position in the
- * DefLineModifiers array to each OrgGroup in the list and recalculates
- * the maximum number of organisms in any one group and the number of
- * unique organism descriptions generated by this new combination of 
- * modifiers.
- */
-static void AddQualToModifierCombo (
-  ModifierCombinationPtr m,
-  ModifierItemLocalPtr qual,
-  Int2 feature_index
-)
-{
-  OrgGroupPtr ogp;
-  ValNodePtr vnp;
-
-  if (m == NULL) return;
-
-  /* now try adding the modifier, see if the number of groups goes up */
-  /* if the number of organisms in each group is one, we can stop */
-  vnp = ValNodeNew (m->modifier_indices);
-  if (vnp == NULL) return;
-  if (m->modifier_indices == NULL)
-  {
-    m->modifier_indices = vnp;
-  }
-  vnp->data.intvalue = feature_index;
-  m->num_mods ++;
-  AddQualToGroupList (m->group_list, qual, feature_index);
-  ogp = m->group_list;
-  m->max_orgs_in_group = 0;
-  m->num_unique_orgs = 0;
-  m->num_groups = 0;
-  while (ogp != NULL)
-  {
-    if (m->max_orgs_in_group < ogp->num_organisms)
-      m->max_orgs_in_group = ogp->num_organisms;
-    if (ogp->num_organisms == 1)
-      m->num_unique_orgs ++;
-    m->num_groups ++;
-    ogp = ogp->next;
-  }
-}
-
-/* This function creates the initial OrgGroup list that is copied for every
- * ModifierCombination item.
- */
-static void BuildTaxOrgGroupList (
-  BioSourcePtr biop,
-  Pointer userdata
-)
-{
-  OrgGroupPtr   ogp;
-  OrgGroupPtr   prevOgp;
-  OrgGroupPtr PNTR pogp;
-  BioSrcDescPtr newBsdp;
-  OrgRefPtr     orp;
-  int cmpval;
-
-  pogp = (OrgGroupPtr PNTR) userdata;
-  ogp = *pogp;
-
-  newBsdp = (BioSrcDescPtr) MemNew (sizeof (BioSrcDescData));
-  if (newBsdp == NULL) return;
-  newBsdp->biop = biop;
-  newBsdp->next = NULL;
-  newBsdp->strings = NULL;
-
-  /* add tax name as first string */
-  /* later, move this into a separate function and add special handling */
-  orp = biop->org;
-  if (orp != NULL && orp->taxname != NULL)
-  {
-    ValNodeCopyStr (&(newBsdp->strings), 0, orp->taxname);
-  }
-
-  prevOgp = NULL;
-  cmpval = -1;
-  while (ogp != NULL && cmpval < 0)
-  {
-    if (ogp->org_list != NULL)
-    {
-      cmpval = CompareOrganismDescriptors (ogp->org_list, newBsdp);
-      if (cmpval == 0)
-      {
-        newBsdp->next = ogp->org_list;
-        ogp->org_list = newBsdp;
-        ogp->num_organisms ++;
-      }
-    }
-    if (cmpval < 0)
-    {
-      prevOgp = ogp;
-      ogp = ogp->next;
-    }
-  }
-  if (cmpval != 0)
-  {
-    /* create new group */
-    ogp = (OrgGroupPtr) MemNew (sizeof (OrgGroupData));
-    if (ogp == NULL) return;
-    ogp->org_list = newBsdp;
-    ogp->num_organisms = 1;
-    ogp->next = NULL;
-    if (prevOgp == NULL)
-    {
-      ogp->next = *pogp;
-      *pogp = ogp;
-    }
-    else
-    {
-      ogp->next = prevOgp->next;
-      prevOgp->next = ogp;
-    }
-  }
-}
-
-typedef struct bestsortdata {
-  Int4    feature_index;
-  Boolean all_unique;
-  Boolean all_present;
-  Boolean is_unique;
-} BestSortData, PNTR BestSortPtr;
-
-static Boolean Index1FoundBeforeIndex2 (
-  Int4 index1,
-  Int4 index2,
-  ValNodePtr list
-)
-{
-  ValNodePtr  vnp;
-  BestSortPtr bsp;
-  for (vnp = list; vnp != NULL; vnp = vnp->next)
-  {
-    if ((bsp = vnp->data.ptrvalue) == NULL)
-    {
-      continue;
-    }
-    if (bsp->feature_index == index1) return TRUE;
-    if (bsp->feature_index == index2) return FALSE;
-  }
-  return FALSE;
-}
-
-/* This function determines whether or not we should try adding this modifier
- * to our combination.  If we've already tried it and not added it to the list,
- * there's no reason to try adding it again.
- */
-static Boolean OkToTryAddingQual (
-  ModifierCombinationPtr m,
-  ModifierItemLocalPtr ItemList,
-  ValNodePtr           available_modifiers_list,
-  Int2 feature_index
-)
-{
-  ValNodePtr vnp;
-
-  /* if feature_index indicates a value we don't use for best combos, skip */
-  if (feature_index == DEFLINE_POS_Map)
-  {
-    return FALSE;
-  }
-
-  if (m == NULL) return TRUE;
-
-  /* if feature_index is lower than anything else on list (other than */
-  /* a required value, this is a repeat combination, so skip it */
-  vnp = m->modifier_indices;
-  while (vnp != NULL)
-  {
-    if (feature_index == m->modifier_indices->data.intvalue)
-      return FALSE;
-    if (! ItemList[m->modifier_indices->data.intvalue].required &&
-      Index1FoundBeforeIndex2 (feature_index,
-                               m->modifier_indices->data.intvalue, 
-                               available_modifiers_list))
-    {
-      return FALSE;
-    }
-    vnp = vnp->next;
-  }
-  return TRUE;
-}
-
-static ValNodePtr GetListOfAvailableModifiers ( ModifierItemLocalPtr ItemList)
-{
-  ValNodePtr  vnp, head;
-  Int2        feature_index;
-  BestSortPtr bsp;
-
-  head = NULL;
-  for (feature_index = 0; feature_index < NumDefLineModifiers; feature_index++)
-  {
-    if ( ItemList[feature_index].any_present)
-    {
-      bsp = (BestSortPtr) MemNew (sizeof (BestSortData));
-      if (bsp == NULL) return NULL;
-      bsp->feature_index = feature_index;
-      bsp->all_unique = ItemList[feature_index].all_unique;
-      bsp->all_present = ItemList[feature_index].all_present;
-      bsp->is_unique = ItemList[feature_index].is_unique;
-      vnp = ValNodeNew (head);
-      if (vnp == NULL) return NULL;
-      vnp->data.ptrvalue = bsp;
-      if (head == NULL) head = vnp;
-    }
-  }
-  return head;
-}
-
-static Int4 DefLineQualSortOrder [] = {
-  DEFLINE_POS_Transgenic,
-  DEFLINE_POS_Plasmid_name,
-  DEFLINE_POS_Endogenous_virus_name,
-  DEFLINE_POS_Strain,
-  DEFLINE_POS_Clone,
-  DEFLINE_POS_Isolate,
-  DEFLINE_POS_Haplotype,
-  DEFLINE_POS_Cultivar,
-  DEFLINE_POS_Specimen_voucher,
-  DEFLINE_POS_Ecotype,
-  DEFLINE_POS_Type,
-  DEFLINE_POS_Serotype,
-  DEFLINE_POS_Authority,
-  DEFLINE_POS_Breed
-};
-
-static int LIBCALLBACK SortByImportanceAndPresence (
-  VoidPtr ptr1,
-  VoidPtr ptr2
-)
-{
-  ValNodePtr  vnp1;
-  ValNodePtr  vnp2;
-  BestSortPtr bsp1, bsp2; 
-  Int4       num_defline_qual_sort_order, index;
-
-  if (ptr1 == NULL && ptr2 == NULL) return 0;
-  
-  if (ptr1 == NULL && ptr2 != NULL) return -1;
-  if (ptr1 != NULL && ptr2 == NULL) return 1;
- 
-  vnp1 = *((ValNodePtr PNTR) ptr1);
-  vnp2 = *((ValNodePtr PNTR) ptr2);
-  if (vnp1 == NULL || vnp2 == NULL) return 0;
-  if (vnp1->data.ptrvalue == NULL || vnp2->data.ptrvalue == NULL) return 0;
-
-  bsp1 = vnp1->data.ptrvalue;
-  bsp2 = vnp2->data.ptrvalue;
-  if (bsp1->feature_index == bsp2->feature_index) return 0;
-
-  if (bsp1->all_present && bsp1->all_unique
-    && (! bsp2->all_present || ! bsp2->all_unique))
-  {
-    return -1;
-  }
-  if (bsp2->all_present && bsp2->all_unique
-    && (! bsp1->all_present || ! bsp1->all_unique))
-  {
-    return 1;
-  }
-
-  if ( ! bsp1->is_unique && bsp2->is_unique) return -1;
-  if ( ! bsp2->is_unique && bsp1->is_unique) return 1;
-
-  num_defline_qual_sort_order = sizeof (DefLineQualSortOrder) / sizeof (Int4);
-  for (index = 0; index < num_defline_qual_sort_order; index++)
-  {
-    if (bsp1->feature_index == DefLineQualSortOrder [ index ]) return -1;
-    if (bsp2->feature_index == DefLineQualSortOrder [ index ]) return 1;
-  }
-
-  if (bsp1->feature_index > bsp2->feature_index) return 1;
-  if (bsp1->feature_index < bsp2->feature_index) return -1;
-  return 0;
-}
-
-
-/* The function FindBestCombo tries to find the best combination of modifiers
- * to create unique organism descriptions.  This is accomplished by
- * creating a list of required modifiers, and then creating a list of
- * combinations of modifiers by adding modifiers one at a time
- * to see if the additional modifiers provide any more differentiation in
- * the list.
- * In order to do this, I start with a list of required modifiers, and 
- * then create copies of this list.  For each copy I add one of the modifiers
- * that are present in the bio sources and not already on the list.
- * If adding the modifier increases the differentiation, I add that copy to
- * the list of possible combinations, otherwise I discard it.
- * The function then makes copies of all of the new items added to the list,
- * starting with the item pointed to by start_of_expand, and adds another
- * modifier to each combination, keeping the combinations that increase
- * the differentiation and discarding the rest.
- * This process continues until I have a combination that produces completely
- * differentiated bio sources, or I run out of possible combinations.
- * If the list of possible combinations is exhausted before each organism
- * has a unique description, the function selects the combination from the
- * list with the largest number of unique organism descriptions.  If more 
- * than one combination produces the largest number of unique organisms,
- * the combination with the largest number of unique organisms and the
- * largest number of groups will be selected.
- */
-static ModifierCombinationPtr FindBestCombo(
-  SeqEntryPtr sep,
-  ModifierItemLocalPtr ItemList
-)
-{
-  OrgGroupPtr group_list;
-  ModifierCombinationPtr mc_list, start_of_expand, best_found, end_of_list;
-  ModifierCombinationPtr next_start_of_expand, m, newm;
-  Int4 num_to_expand, next_num_to_expand;
-  Int2 i;
-  ValNodePtr available_modifier_list, vnp;
-  BestSortPtr bsp;
-
-  best_found = NULL;
-
-  /* first, get list of organisms */
-  group_list = NULL;
-  VisitBioSourcesInSep (sep, &group_list, BuildTaxOrgGroupList);
-
-  /* create combo with just the org groups */
-  mc_list = NewModifierCombo (group_list);
-  if (mc_list == NULL) return NULL;
-
-  available_modifier_list = GetListOfAvailableModifiers (ItemList);
-
-  /* next, add in any required qualifiers */
-  for (vnp = available_modifier_list; vnp != NULL; vnp = vnp->next)
-  {
-    bsp = vnp->data.ptrvalue;
-    if (bsp == NULL) return NULL;
-    if (ItemList[bsp->feature_index].required)
-    {
-      AddQualToModifierCombo (mc_list, ItemList + bsp->feature_index,
-                                       bsp->feature_index);
-    }
-  }
-  if (mc_list->max_orgs_in_group == 1)
-  {
-    /* we're done - they're all unique */
-    best_found = mc_list;
-    return best_found;
-  }
-
-  available_modifier_list = SortValNode (available_modifier_list,
-                                         SortByImportanceAndPresence);
-  start_of_expand = mc_list;
-  end_of_list = mc_list;
-  num_to_expand = 1;
-  while (best_found == NULL && start_of_expand != NULL)
-  {
-    next_num_to_expand = 0;
-    next_start_of_expand = NULL;
-    for (i=0; i < num_to_expand && start_of_expand != NULL; i++)
-    {
-      /* try adding qualifiers */ 
-      for (vnp = available_modifier_list;
-           vnp != NULL && best_found == NULL;
-           vnp = vnp->next)
-      {
-        bsp = vnp->data.ptrvalue;
-        if (bsp == NULL) return NULL;
-        if (OkToTryAddingQual (start_of_expand, ItemList,
-                               available_modifier_list,
-                               bsp->feature_index))
-        {
-          newm = CopyModifierCombo (start_of_expand);
-          AddQualToModifierCombo (newm, ItemList + bsp->feature_index,
-                                  bsp->feature_index);
-          if (start_of_expand->num_groups >= newm->num_groups)
-          {
-            /* situation didn't get better, don't bother to add this one */
-            FreeModifierCombo (newm);
-            newm = NULL;
-          }
-          else if (newm->max_orgs_in_group == 1)
-          {
-            best_found = newm;
-          }
-          else
-          {
-            end_of_list->next = newm;
-            end_of_list = end_of_list->next;
-            if (next_start_of_expand == NULL)
-              next_start_of_expand = newm;
-            next_num_to_expand++;
-          }
-        }
-      }
-      if (start_of_expand != NULL)
-      {
-        start_of_expand = start_of_expand->next;
-      }
-    }
-    num_to_expand = next_num_to_expand;
-    if (start_of_expand != NULL)
-    {
-      start_of_expand = start_of_expand->next;
-    }
-  }
-
-  if (best_found != NULL)
-  {
-    FreeModifierCombo (mc_list);
-    return best_found;
-  }
-  
-  /* we want to find the one with the highest number of unique organisms */
-  best_found = mc_list;
-  m = mc_list->next;
-  while (m!= NULL)
-  {
-    if (m->num_unique_orgs > best_found->num_unique_orgs)
-    {
-      best_found = m;
-    }
-    else if (m->num_unique_orgs == best_found->num_unique_orgs
-           && m->num_groups > best_found->num_groups)
-    {
-      best_found = m;
-    }
-    else if (m->num_unique_orgs == best_found->num_unique_orgs
-           && m->num_groups == best_found->num_groups
-           && m->num_mods < best_found->num_mods)
-    {
-      best_found = m;
-    }
-    m = m->next;
-  }
-
-  m = mc_list;
-  while (m != NULL)
-  {
-    if (m != best_found)
-    {
-      newm = m->next;
-      m->next = NULL;
-      FreeModifierCombo (m);
-      m = newm;
-    }
-    else
-    {
-      FreeModifierCombo (m->next);
-      m->next = NULL;
-      m = NULL;
-    }
-  }
-  return best_found;
-}
-
-/* create combo with the specified modifiers */
-static ModifierCombinationPtr CreateComboFromModList (
-  ModifierItemLocalPtr modList
-)
-{
-  ModifierCombinationPtr m;
-  Int4                   feature_index;
-
-  m = NewModifierCombo (NULL);
-  if (m == NULL) return NULL;
-  for (feature_index = 0; feature_index < NumDefLineModifiers; feature_index++)
-  {
-    if (modList[feature_index].any_present && modList [feature_index].required)
-    {
-      AddQualToModifierCombo (m, modList + feature_index, feature_index);
-    }
-  }
-  return m;
-}
-
-
-/* This is the callback function for sorting the modifier list.  It 
- * implements an order specified by the indexers.
- */
-static Int4 DefLineQualPresentationOrder [] = {
-  DEFLINE_POS_Transgenic,
-  DEFLINE_POS_Strain,
-  DEFLINE_POS_Isolate,
-  DEFLINE_POS_Cultivar,
-  DEFLINE_POS_Specimen_voucher,
-  DEFLINE_POS_Ecotype,
-  DEFLINE_POS_Type,
-  DEFLINE_POS_Serotype,
-  DEFLINE_POS_Authority,
-  DEFLINE_POS_Breed
-};
-
-static int LIBCALLBACK SortByImportance (
-  VoidPtr ptr1,
-  VoidPtr ptr2
-)
-{
-  ValNodePtr vnp1;
-  ValNodePtr vnp2;
-  Int4       num_defline_qual_sort_order, index;
-
-  if (ptr1 == NULL && ptr2 == NULL) return 0;
-  
-  if (ptr1 == NULL && ptr2 != NULL) return -1;
-  if (ptr1 != NULL && ptr2 == NULL) return 1;
- 
-  vnp1 = *((ValNodePtr PNTR) ptr1);
-  vnp2 = *((ValNodePtr PNTR) ptr2);
-  if (vnp1 == NULL || vnp2 == NULL) return 0;
-  if (vnp1->data.intvalue == vnp2->data.intvalue) return 0;
-
-  num_defline_qual_sort_order = sizeof (DefLineQualPresentationOrder) / sizeof (Int4);
-  for (index = 0; index < num_defline_qual_sort_order; index++)
-  {
-    if (vnp1->data.intvalue == DefLineQualPresentationOrder [ index ]) return -1;
-    if (vnp2->data.intvalue == DefLineQualPresentationOrder [ index ]) return 1;
-  }
-
-  if ((vnp1->data.intvalue < 0 || vnp1->data.intvalue > NumDefLineModifiers)
-    && (vnp2->data.intvalue < 0 || vnp2->data.intvalue > NumDefLineModifiers))
-  {
-    return 0;
-  }
-  if (vnp1->data.intvalue < 0 || vnp1->data.intvalue > NumDefLineModifiers)
-  {
-    return 1;
-  }
-  if (vnp2->data.intvalue < 0 || vnp2->data.intvalue > NumDefLineModifiers)
-  {
-    return -1;
-  }
-
-  if (DefLineModifiers [ vnp1->data.intvalue].isOrgMod
-    && (! DefLineModifiers [ vnp2->data.intvalue].isOrgMod
-      || vnp2->data.intvalue == DEFLINE_POS_Plasmid_name
-      || vnp2->data.intvalue == DEFLINE_POS_Endogenous_virus_name))
-  {
-    return -1;
-  }
-  if (DefLineModifiers [ vnp2->data.intvalue].isOrgMod
-    && (! DefLineModifiers [ vnp1->data.intvalue].isOrgMod
-      || vnp1->data.intvalue == DEFLINE_POS_Plasmid_name
-      || vnp1->data.intvalue == DEFLINE_POS_Endogenous_virus_name))
-  {
-    return 1;
-  }
-  
-  if (vnp1->data.intvalue == DEFLINE_POS_Plasmid_name)
-  {
-    return -1;
-  }
-  if (vnp2->data.intvalue == DEFLINE_POS_Plasmid_name)
-  {
-    return 1;
-  }
-    
-  if (vnp1->data.intvalue == DEFLINE_POS_Endogenous_virus_name)
-  {
-    return -1;
-  }
-  if (vnp2->data.intvalue == DEFLINE_POS_Endogenous_virus_name)
-  {
-    return 1;
-  }
-
-  if (! DefLineModifiers [ vnp1->data.intvalue].isOrgMod
-     && vnp2->data.intvalue == DEFLINE_POS_Clone)
-  {
-    return 1;
-  }
-  if (! DefLineModifiers [ vnp2->data.intvalue].isOrgMod
-     && vnp1->data.intvalue == DEFLINE_POS_Clone)
-  {
-    return -1;
-  }
-
-  if (! DefLineModifiers [ vnp1->data.intvalue].isOrgMod
-     && vnp2->data.intvalue == DEFLINE_POS_Haplotype)
-  {
-    return 1;
-  }
-  if (! DefLineModifiers [ vnp2->data.intvalue].isOrgMod
-     && vnp1->data.intvalue == DEFLINE_POS_Haplotype)
-  {
-    return -1;
-  }
-
-  if (vnp1->data.intvalue > vnp2->data.intvalue) return 1;
-  if (vnp1->data.intvalue < vnp2->data.intvalue) return -1;
-  return 0;
-}
-
-static Boolean RecordHasModifier (
-  BioSourcePtr biop,
-  Int4         modifier_index
-)
-{
-  OrgModPtr     mod;
-  OrgNamePtr    onp;
-  SubSourcePtr  ssp;
-
-  if (biop == NULL
-    || modifier_index < 0
-    || modifier_index >= NumDefLineModifiers)
-  {
-    return FALSE;
-  }
-  if (DefLineModifiers[modifier_index].isOrgMod)
-  {
-    if (biop->org == NULL || (onp = biop->org->orgname) == NULL)
-    {
-      return FALSE;
-    }
-    mod = onp->mod;
-    while (mod != NULL
-        && mod->subtype != DefLineModifiers[modifier_index].subtype)
-    {
-      mod = mod->next;
-    }
-    if (mod != NULL && mod->subname != NULL)
-    {
-      return TRUE;
-    }
-  } else {
-    ssp = biop->subtype;
-    while (ssp != NULL && ssp->subtype != DefLineModifiers[modifier_index].subtype)
-    {
-      ssp = ssp->next;
-    }
-    if (ssp != NULL && ssp->name != NULL)
-    {
-      return TRUE;
-    }
-  }
-  return FALSE;
-}
-  
-/* This function adds in required modifiers for HIV sequences */
-static void AddHIVModifierIndices (
-  ValNodePtr PNTR modifier_indices,
-  BioSourcePtr biop,
-  ModifierItemLocalPtr modList,
-  CharPtr taxName,
-  Int4    clone_isolate_HIV_rule_num
-)
-{
-  ValNodePtr  vnp;
-  Boolean have_country_in_list;
-  Boolean have_isolate_in_list;
-  Boolean have_clone_in_list;
-  Boolean have_country_mod;
-  Boolean have_isolate_mod;
-  Boolean have_clone_mod;
-
-  /* special handling for HIV */
-  if (StringICmp (taxName, "HIV-1") != 0
-    && StringICmp (taxName, "HIV-2") != 0)
-  {
-    return;
-  }
-
-  have_country_in_list = FALSE;
-  have_isolate_in_list = FALSE;
-  have_clone_in_list = FALSE;
-  have_country_mod = RecordHasModifier (biop, DEFLINE_POS_Country);
-  have_isolate_mod = RecordHasModifier (biop, DEFLINE_POS_Isolate);
-  have_clone_mod = RecordHasModifier (biop, DEFLINE_POS_Clone);
-
-  if (modifier_indices != NULL)
-  {
-    for (vnp = *modifier_indices;
-         vnp != NULL
-           && (! have_country_in_list
-             || ! have_isolate_in_list
-             || ! have_clone_in_list);
-         vnp = vnp->next)
-    {
-      if (vnp->data.intvalue == DEFLINE_POS_Country)
-      {
-        have_country_in_list = TRUE;
-      }
-      else if (vnp->data.intvalue == DEFLINE_POS_Isolate)
-      {
-        have_isolate_in_list = TRUE;
-      }
-      else if (vnp->data.intvalue == DEFLINE_POS_Clone)
-      {
-        have_clone_in_list = TRUE;
-      }
-    }
-  }
-
-  if ( ! have_country_in_list && have_country_mod)
-  {
-    vnp = ValNodeNew (*modifier_indices);
-    vnp->data.intvalue = DEFLINE_POS_Country;
-    if (*modifier_indices == NULL) *modifier_indices = vnp;
-  }
-
-  if ((have_clone_in_list && have_clone_mod)
-      || (have_isolate_in_list && have_isolate_mod))
-  {
-    /* don't need HIV rule */
-  }
-  else
-  {
-    if ( ! have_isolate_in_list
-        && have_isolate_mod
-        && ( clone_isolate_HIV_rule_num == clone_isolate_HIV_rule_prefer_isolate
-          || clone_isolate_HIV_rule_num == clone_isolate_HIV_rule_want_both
-          || ! have_clone_mod))
-    {
-      vnp = ValNodeNew (*modifier_indices);
-      vnp->data.intvalue = DEFLINE_POS_Isolate;
-      if (*modifier_indices == NULL) *modifier_indices = vnp;
-    }
-    
-    if ( ! have_clone_in_list
-        && have_clone_mod
-        && ( clone_isolate_HIV_rule_num == clone_isolate_HIV_rule_prefer_clone
-          || clone_isolate_HIV_rule_num == clone_isolate_HIV_rule_want_both
-          || ! have_isolate_mod))
-    {
-      vnp = ValNodeNew (*modifier_indices);
-      vnp->data.intvalue = DEFLINE_POS_Clone;
-      if (*modifier_indices == NULL) *modifier_indices = vnp;
-    }
-  }
-}
-
-static Boolean UseOrgModifier (OrgModPtr mod, CharPtr taxName);
-
-/* This function looks for an OrgMod note that contains the phrase
- * "type strain of".  This function is used to determine whether
- * strain is a required modifier for the defline for this source.
- */
-static Boolean HasTypeStrainComment (BioSourcePtr biop)
-{
-  OrgModPtr mod;
-  
-  if (biop == NULL || biop->org == NULL || biop->org->orgname == NULL)
-  {
-    return FALSE;
-  }
-  
-  mod = biop->org->orgname->mod;
-  while (mod != NULL && mod->subtype != ORGMOD_strain)
-  {
-    mod = mod->next;
-  }
-  
-  if (mod == NULL)
-  {
-    return FALSE;
-  }
-  
-  if (!UseOrgModifier (mod, biop->org->taxname))
-  {
-    return FALSE;
-  }
-  
-  mod = biop->org->orgname->mod;
-  while (mod != NULL)
-  {
-    if (mod->subtype == 255
-        && StringISearch (mod->subname, "type strain of") != NULL)
-    {
-      return TRUE;
-    }
-    mod = mod->next;
-  }
-  return FALSE;
-}
-
-/* This function checks to see if there is a type strain comment on
- * the bio source.  If there is one, it checks to see whether strain
- * is already in the list of modifiers for the definition line.
- * If strain is not already in the list, it is added.
- */
-static void 
-AddTypeStrainModifierIndices 
-(ValNodePtr PNTR modifier_indices,
- BioSourcePtr    biop)
-{
-  ValNodePtr vnp;
-  
-  if (modifier_indices == NULL || biop == NULL || ! HasTypeStrainComment (biop))
-  {
-    return;
-  }
-
-  for (vnp = *modifier_indices;
-       vnp != NULL && vnp->data.intvalue != DEFLINE_POS_Strain;
-       vnp = vnp->next)
-  {
-  }
-  
-  if (vnp == NULL)
-  {
-    ValNodeAddInt (modifier_indices, 0, DEFLINE_POS_Strain);
-  }
-}
-
-static Boolean SpecialHandlingForSpecialTechniques (
-  BioseqPtr bsp
-);
-
-/* This function checks to see if the Bioseq has a WGS technique.
- * If so, and if the strain text is not present in the taxname,
- * and strain is not already in the list of modifiers for the 
- * definition line, add strain.
- */
-static void 
-AddWGSModifierIndices 
-(ValNodePtr PNTR modifier_indices,
- BioSourcePtr    biop,
- BioseqPtr       bsp)
-{
-  ValNodePtr vnp;
-  OrgModPtr  omp;
-  
-  if (modifier_indices == NULL || biop == NULL 
-      || biop->org == NULL
-      || biop->org->orgname == NULL
-      || biop->org->orgname->mod == NULL
-      || ! SpecialHandlingForSpecialTechniques (bsp))
-  {
-    return;
-  }
-
-  for (vnp = *modifier_indices;
-       vnp != NULL && vnp->data.intvalue != DEFLINE_POS_Strain;
-       vnp = vnp->next)
-  {
-  }
-  
-  if (vnp == NULL)
-  {
-    omp = biop->org->orgname->mod;
-    while (omp != NULL && omp->subtype != ORGMOD_strain) 
-    {
-      omp = omp->next;
-    }
-    if (omp != NULL) 
-    {
-      if (StringStr (biop->org->taxname, omp->subname) != NULL) 
-      {
-        /* don't add, present already */
-      } else {
-        /* add strain modifier */
-        ValNodeAddInt (modifier_indices, 0, DEFLINE_POS_Strain);
-      }
-    }
-  }
-}
-
-/* This function provides a label to be used in the definition line for
- * each modifier that requires one.  Most modifiers use a label that is 
- * similar to the name of the modifier displayed in the definition line
- * options dialog.
- */
-static void AddModifierLabel (
-  Boolean use_labels,
-  Boolean is_orgmod,
-  Uint1   subtype,
-  CharPtr modifier_text
-)
-{
-  CharPtr cp;
-  if (!is_orgmod && subtype == SUBSRC_endogenous_virus_name)
-  {
-    StringCpy (modifier_text, "endogenous virus");
-  }
-  else if (is_orgmod && subtype == ORGMOD_specimen_voucher)
-  {
-    if (use_labels)
-    {
-      StringCpy (modifier_text, "voucher");
-    } 
-    else
-    {
-      modifier_text [0] = 0;
-    }
-  }
-  else if (use_labels 
-           || (!is_orgmod 
-               && (subtype == SUBSRC_transgenic
-                   || subtype == SUBSRC_plasmid_name)))
-  {
-    if (is_orgmod) 
-    {
-      StringCpy (modifier_text, GetOrgModQualName (subtype));
-    } else {
-      StringCpy (modifier_text, GetSubsourceQualName (subtype));
-    }
-    modifier_text[0] = tolower(modifier_text[0]);
-    cp = StringStr (modifier_text, "-name");
-    if (cp != NULL) *cp = 0;
-  }
-  else
-  {
-    modifier_text[0] = 0;
-  }
-}
-
-typedef struct orgmodabbrevdata {
-  Int2    subtype;
-  CharPtr abbrev;
-} OrgModAbbrevData, PNTR OrgModAbbrevPtr;
-
-static OrgModAbbrevData orgmod_abbrevs[] = {
-  { ORGMOD_variety, "var." },
-  { ORGMOD_forma, "f." },
-  { ORGMOD_forma_specialis, "f. sp." },
-  { ORGMOD_pathovar, "pv." }
-};
-
-/* The UseOrgModifier function looks for the values of certain kinds of 
- * modifiers in the taxonomy name, so that they will not be added to the
- * definition line as modifiers if they are already present in the
- * taxonomy name.
- */
-static Boolean UseOrgModifier (
-  OrgModPtr mod,
-  CharPtr   taxName
-)
-{
-  CharPtr value_found;
-  Int4    value_len;
-  Int4    num_abbrevs, i;
-  CharPtr abbrev_start;
-  Boolean other_abbrev_found;
-
-  if (mod == NULL || mod->subname == NULL) return FALSE;
-
-  num_abbrevs = sizeof (orgmod_abbrevs) / sizeof (OrgModAbbrevData);
-
-  /* If selected modifiers already appear in the tax Name, */
-  /* don't use them in the organism description again */
-  if (mod->subtype == ORGMOD_strain
-    || mod->subtype == ORGMOD_variety
-    || mod->subtype == ORGMOD_sub_species
-    || mod->subtype == ORGMOD_forma
-    || mod->subtype == ORGMOD_forma_specialis
-    || mod->subtype == ORGMOD_pathovar)
-  {
-    value_found = StringStr (taxName, mod->subname);
-    value_len = StringLen (mod->subname);
-    while (value_found != NULL)
-    {
-      if (value_found == taxName)
-      {
-        value_found = StringStr (value_found + 1, mod->subname);
-        continue;
-      }
-      if (*(value_found - 1) != ' ' && *(value_found - 1) != '(')
-      {
-        value_found = StringStr (value_found + 1, mod->subname);
-        continue;
-      }
-      if (*(value_found - 1) == ')' && *(value_found + value_len) != ')')
-      {
-        value_found = StringStr (value_found + 1, mod->subname);
-        continue;
-      }
-      if (*(value_found + value_len) != ' ' && *(value_found + value_len) != 0)
-      {
-        value_found = StringStr (value_found + 1, mod->subname);
-        continue;
-      }
-      other_abbrev_found = FALSE;
-      for (i = 0; i < num_abbrevs; i++)
-      {
-        abbrev_start = value_found - StringLen (orgmod_abbrevs[i].abbrev) - 1;
-        if (abbrev_start > taxName
-          && StringNCmp (abbrev_start,
-                         orgmod_abbrevs[i].abbrev,
-                         StringLen (orgmod_abbrevs[i].abbrev)) == 0)
-        {
-          if (mod->subtype == orgmod_abbrevs[i].subtype)
-          {
-            return FALSE;
-          }
-          else
-          {
-            other_abbrev_found = TRUE;
-          }
-        }
-      }
-      if ( ! other_abbrev_found 
-        && ( mod->subtype == ORGMOD_strain
-          || mod->subtype == ORGMOD_sub_species))
-      {
-        return FALSE;
-      }
-      value_found = StringStr (value_found + 1, mod->subname);
-    }
-  }
-  return TRUE;
-}
-
-/* The SetRequiredModifiers function copies the default required values from
- * the global DefLineModifiers array into the local list of modifier
- * information.
- */
-static void SetRequiredModifiers (
-  ModifierItemLocalPtr modList
-)
-{
-  Int4  item_index;
-
-  for (item_index = 0; item_index < NumDefLineModifiers; item_index++)
-  {
-    modList[item_index].required = IsDeflineModifierRequiredByDefault(DefLineModifiers[item_index].isOrgMod,
-                                                                      DefLineModifiers[item_index].subtype);
-  }
-  
-}
-
-/* The AddBestComboModifiersToModList function sets the modifiers
- * selected by the FindBestCombo process as selected.
- */
-static void AddBestComboModifiersToModList (
-  ModifierCombinationPtr m,
-  ModifierItemLocalPtr modList
-)
-{
-  ValNodePtr vnp;
-
-  for (vnp = m->modifier_indices; vnp != NULL; vnp = vnp->next)
-  {
-    modList[vnp->data.intvalue].required = TRUE;
-  }
-}
-
-/* This function fixes HIV abbreviations, removes items in parentheses,
- * and trims spaces around the taxonomy name.
- */
-static void CleanUpTaxName (
-  CharPtr taxName,
-  Boolean keep_in_paren
-)
-{
-  CharPtr ptr;
-
-  if (StringICmp (taxName, "Human immunodeficiency virus type 1") == 0
-    || StringICmp (taxName, "Human immunodeficiency virus 1") == 0)
-  {
-    StringCpy (taxName, "HIV-1");
-  }
-  else if (StringICmp (taxName, "Human immunodeficiency virus type 2") == 0
-    || StringICmp (taxName, "Human immunodeficiency virus 2") == 0)
-  {
-    StringCpy (taxName, "HIV-2");
-  }
-  else
-  {
-    if (! keep_in_paren)
-    {
-      ptr = StringStr (taxName, "(");
-      if (ptr != NULL)
-        *ptr = '\0';
-    }
-    TrimSpacesAroundString (taxName);
-  }
-}
-
-/* This function gets the BioSource descriptor for the BioSeq. */
-static BioSourcePtr GetBiopForBsp (
-  BioseqPtr bsp
-)
-{
-  SeqMgrDescContext  dcontext;
-  SeqDescrPtr    sdp;
-  BioSourcePtr    biop;
-
-  if (bsp == NULL) return NULL;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
-  if (sdp != NULL) {
-    biop = (BioSourcePtr) sdp->data.ptrvalue;
-    return biop;
-  }
-  
-  return NULL;
-}
-
-/* This function generates a string describing the organism based on the
- * modifiers selected and other organism description options.
- */
-static CharPtr GetOrganismDescription (
-  BioseqPtr bsp, 
-  ModifierItemLocalPtr modList,
-  ModifierCombinationPtr m,
-  OrganismDescriptionModifiersPtr odmp
-)
-{
-  Char         taxName [196];
-  Char         modifier_text [256];
-  ValNodePtr   strings;
-  BioSourcePtr biop;
-  OrgModPtr    mod;
-  SubSourcePtr ssp;
-  ValNodePtr   modifier_indices;
-  ValNodePtr   vnp;
-  Int2         feature_index;
-  CharPtr      org_desc;
-  CharPtr      cp;
-  Uint4        no_semicolon_len, label_len;
-
-  biop = NULL;
-  strings = NULL;
-  taxName [0] = '\0';
-
-  biop = GetBiopForBsp (bsp);
-  if (biop == NULL) return NULL;
-  if (biop->org == NULL) return NULL;
-  if (biop->org->taxname == NULL) return NULL;
-  StringNCpy (taxName, biop->org->taxname, sizeof (taxName) - 1);
-  taxName [ sizeof (taxName) - 1] = 0;
-
-  CleanUpTaxName (taxName, odmp->keep_paren);
-
-  if (odmp->exclude_sp)
-  {
-    cp = StringStr (taxName, " sp.");
-    /* check to make sure not "f. sp." */
-    if (cp != NULL && cp[4] == ' '
-      && (cp - taxName < 2 || *(cp - 2) != 'f' || *(cp - 1) != '.'))
-    {
-      return StringSave (taxName);
-    }
-  }
-
-  if (odmp->exclude_cf)
-  {
-    cp = StringStr (taxName, " cf.");
-    if (cp != NULL)
-    {
-      return StringSave (taxName);
-    }
-  }
-  
-  if (odmp->exclude_aff)
-  {
-    cp = StringStr (taxName, " aff.");
-    if (cp != NULL)
-    {
-      return StringSave (taxName);
-    }
-  }
-  
-  if (biop->origin == ORG_MUT)
-  {
-    ValNodeAddStr (&strings, 0, StringSave ("Mutant"));
-  }
-
-  ValNodeAddStr (&strings, 0, StringSave (taxName));
-
-  if (HasTypeStrainComment (biop))
-  {
-    
-  } 
-
-  modifier_indices = CopyModifierIndices (m->modifier_indices);
-  AddHIVModifierIndices (&modifier_indices, biop, modList, taxName,
-                         odmp->clone_isolate_HIV_rule_num);
-  AddTypeStrainModifierIndices (&modifier_indices, biop);
-  AddWGSModifierIndices (&modifier_indices, biop, bsp);
-  
-  modifier_indices = SortValNode (modifier_indices, SortByImportance);
-  for (vnp = modifier_indices;
-       vnp != NULL && (odmp->max_mods == -99 || odmp->max_mods > 0);
-       vnp = vnp->next)
-  {
-    feature_index = vnp->data.intvalue;
-    if (! odmp->use_modifiers && !IsDeflineModifierRequiredByDefault(DefLineModifiers[feature_index].isOrgMod,
-                                                                     DefLineModifiers[feature_index].subtype))
-    {
-      /* do nothing */
-    }
-    else if (DefLineModifiers[feature_index].isOrgMod)
-    {
-      if (biop->org == NULL || biop->org->orgname == NULL) continue;
-      mod = biop->org->orgname->mod;
-      while (mod != NULL
-        && mod->subtype != DefLineModifiers[feature_index].subtype)
-      {
-        mod = mod->next;
-      }
-      if ( UseOrgModifier (mod, taxName))
-      {
-        if (odmp->allow_semicolon_in_modifier) {
-          no_semicolon_len = StringLen (mod->subname);
-        } else {
-          no_semicolon_len = StringCSpn (mod->subname, ";");
-        }
-
-        if (mod->subtype == ORGMOD_nat_host)
-        {
-          sprintf (modifier_text, "from ");
-          if (no_semicolon_len > sizeof (modifier_text) - 6)
-          {
-            no_semicolon_len = sizeof (modifier_text) - 6;
-          }
-          StringNCpy (modifier_text + 5, mod->subname,
-                      no_semicolon_len);
-          modifier_text[no_semicolon_len + 5] = 0;
-        }
-        else
-        {
-          AddModifierLabel (odmp->use_labels, TRUE, mod->subtype, modifier_text);
-          if (modifier_text[0] != 0)
-            StringCat (modifier_text, " ");
-          label_len = StringLen (modifier_text);
-          if (no_semicolon_len > (Int4) sizeof (modifier_text) - label_len - 1)
-          {
-            no_semicolon_len = (Int4) sizeof (modifier_text) - label_len - 1;
-          } 
-          StringNCat (modifier_text, mod->subname,
-                      no_semicolon_len);
-          modifier_text [ no_semicolon_len + label_len] = 0;
-        }
-        ValNodeCopyStr( &strings, 0, modifier_text);
-        if (odmp->max_mods != -99)
-          odmp->max_mods --;
-      }
-    } else {
-      ssp = biop->subtype;
-      while (ssp != NULL
-          && ssp->subtype != DefLineModifiers[feature_index].subtype)
-      {
-        ssp = ssp->next;
-      }
-      if (ssp != NULL)
-      {
-        if (odmp->include_country_extra || odmp->allow_semicolon_in_modifier)
-        {
-          no_semicolon_len = StringLen (ssp->name);
-        }
-        else
-        {
-          no_semicolon_len = StringCSpn (ssp->name, ";");
-        }
-        AddModifierLabel (odmp->use_labels, FALSE, ssp->subtype, modifier_text);
-        if (ssp->subtype == SUBSRC_transgenic)
-        {
-          /* do nothing, transgenic already captured from label */
-        }
-        else if (ssp->subtype == SUBSRC_country)
-        {
-          sprintf (modifier_text, "from ");
-          if (no_semicolon_len > sizeof (modifier_text) - 6)
-          {
-            no_semicolon_len = sizeof (modifier_text) - 6;
-          }
-          StringNCpy (modifier_text + 5, ssp->name, no_semicolon_len);
-          modifier_text[5 + no_semicolon_len] = 0;
-          if (!odmp->include_country_extra)
-          {
-            cp = StringChr (modifier_text, ':');
-            if (cp != NULL) *cp = 0;
-          }
-        }
-        else if (ssp->name != NULL && ssp->name[0] != 0
-          && (ssp->subtype != SUBSRC_plasmid_name
-            || StringCmp (ssp->name, "unnamed") != 0))
-        {
-          if (modifier_text[0] != 0)
-            StringCat (modifier_text, " ");
-          label_len = StringLen (modifier_text);
-          if (no_semicolon_len > sizeof (modifier_text) - 1 - label_len)
-          {
-            no_semicolon_len = sizeof (modifier_text) - 1 - label_len;
-          }
-          StringNCat (modifier_text, ssp->name, no_semicolon_len);
-          modifier_text [ no_semicolon_len + label_len ] = 0;
-        }
-        ValNodeCopyStr( &strings, 0, modifier_text);
-        if (odmp->max_mods != -99)
-          odmp->max_mods --;
-      }
-    }
-  }
-  
-  org_desc = MergeValNodeStrings (strings, FALSE);
-  ValNodeFreeData (strings);
-  ValNodeFree (modifier_indices);
-  return org_desc;
-
-}
-
-/* end of organism description section */
-
-/* This section of code contains functions which are useful for dealing
- * with locations of features (SeqLocPtr objects).
- */
-
-/* This function determines whether location A is on the same strand as
- * location B
- */
-static Boolean AreAAndBOnSameStrand (
-  SeqLocPtr slp1,
-  SeqLocPtr slp2
-)
-{
-  Uint1 strand1;
-  Uint2 strand2;
-
-  strand1 = SeqLocStrand (slp1);
-  strand2 = SeqLocStrand (slp2);
-  if (strand1 == Seq_strand_minus && strand2 != Seq_strand_minus)
-    return FALSE;
-  else if (strand1 != Seq_strand_minus && strand2 == Seq_strand_minus)
-    return FALSE;
-  else
-    return TRUE;
-}
-
-/* This function determines whether location A is contained in or equal to
- * location B and on the same strand as location B.
- */
-static Boolean IsLocAInBonSameStrand (
-  SeqLocPtr slp1,
-  SeqLocPtr slp2
-)
-{
-  if (! AreAAndBOnSameStrand ( slp1, slp2))
-  {
-    return FALSE;
-  }
-  else if ( SeqLocAinB (slp1, slp2) < 0)
-  {
-    return FALSE;
-  }
-  else
-  {
-    return TRUE;
-  }
-}
-
-/* This function calculates the intersection between two locations.
- */
-static SeqLocPtr SeqLocIntersection (
-  SeqLocPtr slp1,
-  SeqLocPtr slp2,
-  BioseqPtr bsp
-)
-{
-  SeqLocPtr diff1, diff2, result;
-
-  diff1 = SeqLocMerge ( bsp, slp1, NULL, FALSE, TRUE, FALSE);
-  diff1 = SeqLocSubtract (diff1, slp2);
-  diff2 = SeqLocMerge ( bsp, slp2, NULL, FALSE, TRUE, FALSE);
-  diff2 = SeqLocSubtract (diff2, slp1);
-  result = SeqLocMerge ( bsp, slp1, slp2, FALSE, TRUE, FALSE);
-  
-  if (diff1 != NULL)
-  {
-    result = SeqLocSubtract (result, diff1);
-    SeqLocFree (diff1);
-    if (result == NULL) return NULL;
-  }
-  if (diff2 != NULL)
-  {
-    result = SeqLocSubtract (result, diff2);
-    SeqLocFree (diff2);
-    if (result == NULL) return NULL;
-  }
-  return result;
-}
-
-#define ADJACENT_TYPE_ANY        0
-#define ADJACENT_TYPE_UPSTREAM   1
-#define ADJACENT_TYPE_DOWNSTREAM 2
-
-/* This function determines whether A is "next to" B and upstream or downstream
- * from B.  A cannot overlap B.  If allow_interval is TRUE, there can be
- * space between A and B.
- */
-static Boolean IsAAdjacentToB (
-  SeqLocPtr a,
-  SeqLocPtr b,
-  BioseqPtr bsp,
-  Int2      adjacent_type,
-  Boolean   allow_interval
-)
-{
-  Int4      a_end, b_end;
-  Uint2     strand;
- 
-  if (adjacent_type != ADJACENT_TYPE_ANY
-    && adjacent_type != ADJACENT_TYPE_UPSTREAM
-    && adjacent_type != ADJACENT_TYPE_DOWNSTREAM)
-  {
-    return FALSE;
-  }
-  
-  if ( ! AreAAndBOnSameStrand (a, b))
-  {
-    return FALSE;
-  }
-
-  strand = SeqLocStrand (a);
-  if ( adjacent_type == ADJACENT_TYPE_ANY)
-  {
-    a_end = GetOffsetInBioseq (a, bsp, SEQLOC_RIGHT_END);
-    b_end = GetOffsetInBioseq (b, bsp, SEQLOC_LEFT_END);
-    if ((allow_interval && b_end < a_end)
-      || b_end == a_end + 1)
-    {
-      return TRUE;
-    }
-    a_end = GetOffsetInBioseq (a, bsp, SEQLOC_LEFT_END);
-    b_end = GetOffsetInBioseq (b, bsp, SEQLOC_RIGHT_END);
-    if ((allow_interval && b_end > a_end)
-      || a_end == b_end + 1)
-    {
-      return TRUE;
-    }
-    return FALSE;
-  }
-  else if ( (strand == Seq_strand_minus
-      && adjacent_type == ADJACENT_TYPE_UPSTREAM)
-    || (strand != Seq_strand_minus
-      && adjacent_type == ADJACENT_TYPE_DOWNSTREAM))
-  {
-    a_end = GetOffsetInBioseq (a, bsp, SEQLOC_RIGHT_END);
-    b_end = GetOffsetInBioseq (b, bsp, SEQLOC_LEFT_END);
-    if ((allow_interval && b_end < a_end)
-      || b_end == a_end + 1)
-    {
-      return TRUE;
-    }
-    else
-    {
-      return FALSE;
-    }
-  }
-  else
-  {
-    a_end = GetOffsetInBioseq (a, bsp, SEQLOC_LEFT_END);
-    b_end = GetOffsetInBioseq (b, bsp, SEQLOC_RIGHT_END);
-    if ((allow_interval && b_end > a_end)
-      || a_end == b_end + 1)
-    {
-      return TRUE;
-    }
-    else
-    {
-      return FALSE;
-    }
-  }
-}
-
-static Boolean IsAEmptyIntervalOfB (SeqLocPtr a, SeqLocPtr b, BioseqPtr bsp)
-{
-  Int4 a_right, a_left, b_right, b_left, prev_right, prev_left;
-  SeqLocPtr slp;
-  Uint1 a_strand, b_strand;
-  
-  if (a == NULL || b == NULL || bsp == NULL) return FALSE;
-  
-  a_strand = SeqLocStrand (a);
-  b_strand = SeqLocStrand (b);
-  if ((a_strand == Seq_strand_minus && b_strand != Seq_strand_minus)
-      || (a_strand != Seq_strand_minus && b_strand == Seq_strand_minus)) {
-      return FALSE;
-  }
-  
-  a_right = GetOffsetInBioseq (a, bsp, SEQLOC_RIGHT_END);
-  a_left = GetOffsetInBioseq (a, bsp, SEQLOC_LEFT_END);
-  
-  slp = SeqLocFindNext (b, NULL);
-  prev_right = GetOffsetInBioseq (slp, bsp, SEQLOC_RIGHT_END);
-  prev_left = GetOffsetInBioseq (slp, bsp, SEQLOC_LEFT_END);
-  slp = SeqLocFindNext (b, slp);
-  while (slp != NULL) {
-    b_right = GetOffsetInBioseq (slp, bsp, SEQLOC_RIGHT_END);
-    b_left = GetOffsetInBioseq (slp, bsp, SEQLOC_LEFT_END);
-    if (a_left == prev_right + 1 && a_right == b_left - 1) {
-      return TRUE;
-    } else if (a_left == b_right + 1 && a_right == prev_left - 1) {
-      return TRUE;
-    } else {
-      prev_right = b_right;
-      prev_left = b_left;
-      slp = SeqLocFindNext (b, slp);
-    }
-  }
-  return FALSE;
-}
-
-
-static Boolean LocAContainsIntervalOfB (SeqLocPtr a, SeqLocPtr b)
-{
-  SeqLocPtr interval;
-  Boolean   rval = FALSE;
-
-  if (a == NULL || b == NULL) return FALSE;
-
-  interval = SeqLocFindNext (b, NULL);
-  while (interval != NULL && !rval) {
-    if (IsLocAInBonSameStrand (interval, a)) {
-      rval = TRUE;
-    } else {
-      interval = SeqLocFindNext (b, interval);
-    }
-  }
-  return rval;
-}
-
-
-/* This section of code deals with identifying and labeling features
- * for the definition line.
- * The features currently handled are:
- *     genes
- *     exons
- *     introns
- *     LTRs
- *     3' UTRs
- *     5' UTRs
- *     CDSs
- *     rRNA
- *     mRNA
- *     misc RNA
- *     snRNA
- *     snoRNA
- *     insertion sequences
- *     integrons
- *     D-loops
- *     mRNA
- *     tRNA
- *     control regions
- *     misc feature listed as intergenic spacer in comment
- *     satellite sequences
- *     promoter regions
- *     endogenous virus source features
- *     transposons
- */
-
-static Boolean LIBCALLBACK IsGene (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->data.choice != SEQFEAT_GENE) return FALSE;
-  return TRUE;
-}
-
-static CharPtr GetGeneName (GeneRefPtr grp, Boolean suppress_locus_tag)
-{
-  ValNodePtr syn;
-
-  if (grp == NULL) return NULL;
-  if (SeqMgrGeneIsSuppressed (grp)) return NULL;
-  if (StringDoesHaveText (grp->locus)) return grp->locus;
-  if (! suppress_locus_tag && StringDoesHaveText (grp->locus_tag)) 
-      return grp->locus_tag;
-  if (StringDoesHaveText (grp->desc)) return grp->desc;
-  for (syn = grp->syn; syn != NULL; syn = syn->next)
-  {
-    if (syn != NULL && syn->data.ptrvalue != NULL)
-      return syn->data.ptrvalue;
-  }
-  return NULL;
-}
-
-static CharPtr GetAlleleName (GeneRefPtr grp, Boolean suppress_locus_tag)
-{
-  size_t  lenallele;
-  size_t  lengenename;
-  CharPtr  gene_name;
-  CharPtr  buffer;
-
-  if (grp == NULL) return NULL;
-  if (StringHasNoText (grp->allele)) return NULL;
-  gene_name = GetGeneName (grp, suppress_locus_tag);
-  if (StringHasNoText (gene_name)) return NULL;
-  lenallele = StringLen (grp->allele);
-  lengenename = StringLen (gene_name);
-  
-  if (lenallele > lengenename
-    && StringNICmp (gene_name, grp->allele, lengenename) == 0)
-  {
-    return StringSave (grp->allele);
-  }
-  else if (grp->allele[0] == '-')
-  {
-    buffer = MemNew (lenallele + lengenename + 1);
-    if (buffer == NULL) return NULL;
-    StringCpy (buffer, gene_name);
-    StringCat (buffer, grp->allele);
-  }
-  else
-  {
-    buffer = MemNew (lenallele + lengenename + 2);
-    if (buffer == NULL) return NULL;
-    StringCpy (buffer, gene_name);
-    StringCat (buffer, "-");
-    StringCat (buffer, grp->allele);
-  }
-
-  return buffer;
-}
-
-/* This function compares the gene names and allele names of the gene
- * to see if they match.
- */
-static Boolean DoGenesMatch 
-(GeneRefPtr grp1,
- GeneRefPtr grp2,
- Boolean suppress_locus_tag)
-{
-  CharPtr name1;
-  CharPtr name2;
-
-  name1 = GetGeneName (grp1, suppress_locus_tag);
-  name2 = GetGeneName (grp2, suppress_locus_tag);
-  if (StringCmp (name1, name2) != 0) return FALSE;
-  
-  name1 = GetAlleleName (grp1, suppress_locus_tag);
-  name2 = GetAlleleName (grp2, suppress_locus_tag);
-  if ((name1 == NULL && name2 != NULL)
-    || (name1 != NULL && name2 == NULL))
-  {
-    if (name1 != NULL) MemFree (name1);
-    if (name2 != NULL) MemFree (name2);
-    return FALSE;
-  }
-
-  if ((name1 == NULL && name2 == NULL)
-           || (StringCmp (name1, name2) == 0))
-  {
-    if (name1 != NULL) MemFree (name1);
-    if (name2 != NULL) MemFree (name2);
-    return TRUE;
-  }
-  
-  if (name1 != NULL) MemFree (name1);
-  if (name2 != NULL) MemFree (name2);
-  return  FALSE;
-}
-
-/* This function looks at the pseudo flag on the object itself as well as
- * the pseudo flag on the gene reference for the object (if one is present).
- */
-static Boolean IsPseudo (
-  SeqFeatPtr sfp
-)
-{
-  GeneRefPtr grp;
-  SeqMgrFeatContext context;
-
-  if (sfp == NULL) return FALSE;
-  if (sfp->pseudo) return TRUE;
-  if (sfp->data.choice == SEQFEAT_GENE)
-  {
-    grp = sfp->data.value.ptrvalue;
-  }
-  else
-  { 
-    grp = SeqMgrGetGeneXref (sfp);
-  }
-  if (grp == NULL) 
-  {
-    if (sfp->data.choice != SEQFEAT_GENE) {
-      sfp = SeqMgrGetOverlappingGene(sfp->location, &context);
-      return IsPseudo(sfp);
-    } else {
-      return FALSE;
-    }
-  } else {
-    return grp->pseudo;
-  }
-}
-
-static Boolean LIBCALLBACK IsExon (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_exon) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsIntron (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_intron) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsExonOrIntron (SeqFeatPtr sfp)
-{
-  return IsExon(sfp) || IsIntron(sfp);
-}
-
-static Boolean LIBCALLBACK IsLTR (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_LTR) return FALSE;
-  return TRUE;
-}
-
-static CharPtr GetLTRDescription (
-  SeqFeatPtr sfp
-)
-{
-  CharPtr description;
-  size_t comment_len;
-  if (sfp == NULL) return NULL;
-  if (sfp->comment == NULL) return NULL;
-  comment_len = StringLen (sfp->comment);
-  if (comment_len > 3 && StringCmp (sfp->comment + comment_len - 3, "LTR") == 0)
-  {
-    description = (CharPtr) MemNew (comment_len - 3);
-    if (description == NULL) return NULL;
-    StringNCpy (description, sfp->comment, comment_len - 4);
-    description[comment_len - 4] = 0;
-  }
-  else
-  {
-    description = StringSave (sfp->comment);
-  }
-  return description;
-}
-
-static Boolean LIBCALLBACK Is3UTR (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_3UTR) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK Is5UTR (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_5UTR) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsCDS (SeqFeatPtr sfp)
-{
-  if (sfp == NULL) return FALSE;
-  if (sfp->data.choice == SEQFEAT_CDREGION)
-    return TRUE;
-  return FALSE;
-}
-
-static Boolean LIBCALLBACK IsrRNA (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_rRNA) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsMiscRNA (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL 
-    || (sfp->idx.subtype != FEATDEF_misc_RNA
-      && sfp->idx.subtype != FEATDEF_otherRNA)) 
-  {
-    return FALSE;
-  }
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IssnoRNA (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_snoRNA) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IssnRNA (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_snRNA) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsscRNA (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_scRNA) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsPrecursorRNA (SeqFeatPtr sfp)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_preRNA) return FALSE;
-  return TRUE;
-}
-
-
-static CharPtr mobile_element_keywords [] = {
-  "insertion sequence",
-  "retrotransposon",
-  "non-LTR retrotransposon",
-  "transposon",
-  "integron",
-  "other",
-  "SINE",
-  "MITE",
-  "LINE"
-};
-
-enum mobile_element_keyword_nums 
-{
-  eMobileElementInsertionSequence = 0,
-  eMobileElementRetrotransposon,
-  eMobileElementNonLTRRetrotransposon,
-  eMobileElementTransposon,
-  eMobileElementIntegron,
-  eMobileElementOther,
-  eMobileElementSINE,
-  eMobileElementMITE,
-  eMobileElementLINE
-};
-
-static Int4 StartsWithMobileElementKeyword (CharPtr txt)
-{
-  Int4 i, keyword_len;
-    
-  for (i=0; i < sizeof (mobile_element_keywords) / sizeof (CharPtr); i++) {
-    keyword_len = StringLen (mobile_element_keywords[i]);
-    if (StringNCmp (txt, mobile_element_keywords[i], keyword_len) == 0
-        && (*(txt + keyword_len) == ':' || *(txt + keyword_len) == 0)) {      
-      return i;
-    }
-  }
-  return -1;
-}
-
-static Int4 IsMobileElementGBQual (GBQualPtr gbqual)
-{
-  Int4 keyword_idx;
-  if (gbqual == NULL || gbqual->qual == NULL || gbqual->val == NULL) return -1;
-  if (StringCmp (gbqual->qual, "mobile_element") != 0) return -1;
-  keyword_idx = StartsWithMobileElementKeyword (gbqual->val);
-  if (keyword_idx < 0) return -1;
-  if (keyword_idx == eMobileElementOther
-      && StringStr (gbqual->val, "transposable element") == NULL) {
-    return -1;
-  } else {
-    return keyword_idx;
-  }
-}
-
-
-static Boolean FeatureDoesNotGetPartialComplete (SeqFeatPtr sfp)
-{
-  GBQualPtr gbqual;
-  Int4 keyword_idx;
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_repeat_region) return FALSE;
-  
-  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
-  {
-    keyword_idx = IsMobileElementGBQual(gbqual);
-    if (keyword_idx == eMobileElementSINE
-        || keyword_idx == eMobileElementLINE) {
-      return TRUE;
-    }
-  }
-  return FALSE;
-}
-
-
-static Boolean LIBCALLBACK IsMobileElement (SeqFeatPtr sfp)
-{
-  GBQualPtr gbqual;
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_repeat_region) return FALSE;
-  
-  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
-  {
-    if (IsMobileElementGBQual(gbqual) > -1) {
-      return TRUE;
-    }
-  }
-  return FALSE;
-}
-
-static Boolean LIBCALLBACK IsRemovableMobileElement (SeqFeatPtr sfp)
-{
-  GBQualPtr gbqual;
-  Int4 keyword_idx;
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_repeat_region) return FALSE;
-  
-  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
-  {
-    keyword_idx = IsMobileElementGBQual(gbqual);
-    if (keyword_idx >= eMobileElementSINE
-        && keyword_idx <= eMobileElementLINE) {
-      return TRUE;
-    }
-  }
-  return FALSE;
-}
-
-static CharPtr GetMobileElementTypeword (CharPtr desc_start, Int4 keyword_idx)
-{
-  if (keyword_idx < 0) return NULL;
-  if (StringHasNoText (desc_start)) {
-    return mobile_element_keywords[keyword_idx];
-  }
-  switch (keyword_idx) {
-    case eMobileElementTransposon:
-      if (StringStr (desc_start, "P-element") != NULL) {
-        return "P-element";
-      } else if (StringStr (desc_start, "MITE") != NULL) {
-        return "MITE";
-      } else {
-        return mobile_element_keywords[keyword_idx];
-      }
-      break;
-    case eMobileElementOther:
-      return "transposable element";
-      break;
-    case eMobileElementIntegron:
-      if (StringStr (desc_start, "superintegron") != NULL) {
-        return "superintegron";
-      } else {
-        return mobile_element_keywords[keyword_idx];
-      }
-      break;
-    default:
-      return mobile_element_keywords[keyword_idx];
-      break;
-  }      
-}
-
-
-static void LIBCALLBACK GetMobileElementFeatureLabel (
-  ValNodePtr      featlist,
-  BioseqPtr       bsp,
-  Uint1           biomol,
-  FeatureLabelPtr flp
-)
-{
-  GBQualPtr  gbqual;
-  Int4    keyword_idx = -1;
-  Int4    keyword_len;
-  Int4    val_len;
-  SeqFeatPtr      sfp;
-  CharPtr         desc_start = NULL, typeword, cp;
-
-  flp->pluralizable = TRUE;
-  flp->is_typeword_first = FALSE;
-  flp->typeword = NULL;
-  flp->description = NULL;
-
-  if (featlist == NULL) return;
-  sfp = featlist->data.ptrvalue;
-  if (sfp == NULL) return;
-
-  gbqual = sfp->qual;
-  while (gbqual != NULL 
-         && (keyword_idx = IsMobileElementGBQual(gbqual)) < 0)
-  {
-    gbqual = gbqual->next;
-  }
-  if (gbqual == NULL) return;
-    
-  keyword_len = StringLen (mobile_element_keywords[keyword_idx]);
-  desc_start = gbqual->val + keyword_len;
-  while (isspace (*desc_start) || *desc_start == ':') {
-    desc_start++;
-  }
-
-  /* find alternate typewords */
-  typeword = GetMobileElementTypeword(desc_start, keyword_idx);
-  if (typeword == NULL) return;
-  keyword_len = StringLen (typeword);
-
-  flp->typeword = StringSave (typeword);
-  val_len = StringLen (desc_start);
-  
-  if (StringHasNoText (desc_start))
-  {
-    flp->is_typeword_first = FALSE;
-    flp->description = NULL;
-  } else if (StringCmp (desc_start, typeword) == 0) {
-    /* just the keyword */
-    flp->is_typeword_first = FALSE;
-    flp->description = NULL;
-    return;
-  } else if (StringNCmp (desc_start, typeword, keyword_len) == 0) {
-    /* starts with keyword */
-    /* if keyword is hyphenated portion of name, no pluralization */
-    if (desc_start[keyword_len] == '-') {
-      flp->description = StringSave (desc_start);
-      flp->typeword = MemFree (flp->typeword);
-      flp->typeword = StringSave ("");
-      flp->pluralizable = FALSE;
-    } else {
-      flp->is_typeword_first = TRUE;
-      flp->description = StringSave (desc_start + keyword_len + 1);
-    }
-    return;
-  } else if (val_len > 8 && StringCmp (desc_start + val_len - keyword_len, typeword) == 0
-             && val_len - keyword_len - 1 >= 0
-             && isspace (*(desc_start + val_len - keyword_len - 1))) {
-    /* ends with keyword */
-    flp->is_typeword_first = FALSE;
-    flp->description = MemNew (val_len - keyword_len);
-    if (flp->description == NULL) return;
-    StringNCpy (flp->description, desc_start, val_len - keyword_len - 1);
-    flp->description[val_len - keyword_len -1] = 0;
-  } else if ((cp = StringStr (desc_start, typeword)) != NULL
-             && cp != desc_start
-             && isspace (*(cp -1))) {
-    /* keyword in the middle */
-    flp->description = StringSave (desc_start);
-    flp->typeword = MemFree (flp->typeword);
-    flp->typeword = StringSave ("");
-    flp->pluralizable = FALSE;
-  } else {
-    /* keyword not in description */
-    if (StringICmp (flp->typeword, "integron") == 0) {
-      flp->is_typeword_first = FALSE;
-    } else {
-      flp->is_typeword_first = TRUE;
-    }
-    flp->description = StringSave (desc_start);
-    if (StringCmp (flp->description, "") == 0) {
-      flp->is_typeword_first = FALSE;
-    }
-  }
-  if (StringCmp (flp->description, "unnamed") == 0) {
-    flp->description = MemFree (flp->description);
-  }
-}
-
-
-static Boolean LIBCALLBACK IsEndogenousVirusSequence (
-  SeqFeatPtr sfp
-)
-{
-  GBQualPtr gbqual;
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_repeat_region) return FALSE;
-  
-  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
-  {
-    if (StringCmp (gbqual->qual, "endogenous_virus") == 0)
-      return TRUE;
-  }
-  return FALSE;
-}
-
-static CharPtr GetEndogenousVirusSequenceDescription (
-  SeqFeatPtr sfp
-)
-{
-  GBQualPtr gbqual;
-
-  if (sfp == NULL) return NULL;
-  
-  gbqual = sfp->qual;
-  while (gbqual != NULL && StringCmp (gbqual->qual, "endogenous_virus") != 0)
-  {
-    gbqual = gbqual->next;
-  }
-  if (gbqual != NULL)
-  {
-    if (StringDoesHaveText (gbqual->val)
-      && StringCmp (gbqual->val, "unnamed") != 0)
-    {
-      return StringSave (gbqual->val);
-    }
-  }
-  return NULL;
-}
-
-static Boolean LIBCALLBACK IsDloop (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_D_loop) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsmRNA (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_mRNA) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IstRNA (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_tRNA) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsControlRegion (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL
-    || sfp->idx.subtype != FEATDEF_misc_feature
-    || sfp->comment == NULL
-    || StringNCmp (sfp->comment, "control region", StringLen ("control region")) != 0)
-  {
-    return FALSE;
-  }
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsGeneCluster (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL
-    || sfp->idx.subtype != FEATDEF_misc_feature
-    || sfp->comment == NULL
-    || (StringStr (sfp->comment, "gene cluster") == NULL
-        && StringStr (sfp->comment, "gene locus") == NULL))
-  {
-    return FALSE;
-  }
-  return TRUE;
-}
-
-
-static void LIBCALLBACK GetGeneClusterFeatureLabel (
-  ValNodePtr      featlist,
-  BioseqPtr       bsp,
-  Uint1           biomol,
-  FeatureLabelPtr flp
-)
-{
-  SeqFeatPtr main_feat;
-  CharPtr    cp;
-  Int4       datalen;
-
-  if (featlist == NULL || featlist->data.ptrvalue == NULL) return;
-  main_feat = featlist->data.ptrvalue;
-  if (StringHasNoText (main_feat->comment)) return;
-  cp = StringStr (main_feat->comment, "gene cluster");
-  if (cp == NULL)
-  {
-    cp = StringStr (main_feat->comment, "gene locus");
-    if (cp == NULL) return;
-    flp->typeword = StringSave ("gene locus");
-  }
-  else
-  {
-    flp->typeword = StringSave ("gene cluster");
-  }
-  flp->pluralizable = FALSE;
-  flp->is_typeword_first = FALSE;
-  datalen = cp - main_feat->comment;
-  if (datalen > 0)
-  {
-    flp->description = (CharPtr) MemNew ((datalen + 1) * sizeof (Char));
-    StringNCpy (flp->description, main_feat->comment, datalen);
-    flp->description [datalen] = 0;
-    TrimSpacesAroundString (flp->description);
-  }
-  else
-  {
-    flp->description = NULL;
-  }
-}
-
-
-static Boolean LIBCALLBACK IsIntergenicSpacer (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL
-    || sfp->idx.subtype != FEATDEF_misc_feature
-    || sfp->comment == NULL
-    || StringStr (sfp->comment, "intergenic spacer") == NULL)
-  {
-    return FALSE;
-  }
-  return TRUE;
-}
-
-/* This function produces the default definition line label for a misc_feature 
- * that has the word "intergenic spacer" in the comment.  If the comment starts
- * with the word "contains", "contains" is ignored.  If "intergenic spacer"
- * appears first in the comment (or first after the word "contains", the text
- * after the words "intergenic spacer" but before the first semicolon (if any)
- * appear after the words "intergenic spacer" in the definition line.  If there
- * are words after "contains" or at the beginning of the comment before the words
- * "intergenic spacer", this text will appear in the definition line before the words
- * "intergenic spacer".
- */
-static void LIBCALLBACK GetIntergenicSpacerFeatureLabel (
-  ValNodePtr      featlist,
-  BioseqPtr       bsp,
-  Uint1           biomol,
-  FeatureLabelPtr flp
-)
-{
-  SeqFeatPtr main_feat;
-  CharPtr    cp, buffer;
-  Int4       datalen, offset;
-
-  if (featlist == NULL || featlist->data.ptrvalue == NULL) return;
-  main_feat = featlist->data.ptrvalue;
-  if (StringHasNoText (main_feat->comment)) return;
-  if (StringNCmp (main_feat->comment, "contains ", 9) == 0)
-  {
-    buffer = main_feat->comment + 9;
-  }
-  else
-  {
-    buffer = main_feat->comment;
-  }
-  cp = StringStr (buffer, "intergenic spacer");
-  if (cp == NULL) return;
-  flp->typeword = StringSave ("intergenic spacer");
-  flp->pluralizable = FALSE;
-  if (cp == buffer)
-  {
-    flp->is_typeword_first = TRUE;
-    offset = StringLen ("intergenic spacer") + 1;
-    if (StringNCmp (cp + offset, "and ", 4) == 0
-        || *(cp + StringLen("intergenic spacer")) == 0)
-    {
-      flp->description = NULL;
-    }
-    else
-    {
-      flp->description = StringSave (cp + StringLen ("intergenic spacer") + 1);
-      cp = StringChr (flp->description, ';');
-      if (cp != NULL)
-      {
-        *cp = 0;
-      }
-    }
-  }
-  else
-  {
-    flp->is_typeword_first = FALSE;
-    datalen = cp - buffer;
-    flp->description = MemNew ( datalen + 1);
-    if (flp->description == NULL) return;
-    StringNCpy (flp->description, buffer, datalen);
-    flp->description [datalen] = 0;
-    TrimSpacesAroundString (flp->description);
-  }
-}
-
-/* These structures are used for parsing tRNA and intergenic spacer information
- * from misc_feature comments. 
- */
-typedef struct trnadef
-{
-  Char product_name [9];
-  Char gene_name [5];
-} tRNADefData, PNTR tRNADefPtr;
-
-typedef struct intergenicspacerdef
-{
-  Char first_gene [5];
-  Char second_gene [5];
-} IntergenicSpacerDefData, PNTR IntergenicSpacerDefPtr;
-
-static Boolean IsUpperCaseChar (Char ch)
-{
-  if (StringChr("ABCDEFGHIJKLMNOPQRSTUVWXYZ",ch) != NULL)
-    return TRUE;
-  else
-    return FALSE;
-}
-
-static Boolean IsLowerCaseChar (Char ch)
-{
-  if (StringChr("abcdefghijklmnopqrstuvwxyz",ch) != NULL)
-    return TRUE;
-  else
-    return FALSE;
-}
-
-static tRNADefPtr ParsetRNAFromNoteForDefLine (CharPtr PNTR defline)
-{
-  tRNADefPtr tdp;
-  CharPtr    cp, gene_start;
-  
-  if (defline == NULL || *defline == NULL)
-  {
-    return NULL;
-  }
-  
-  /* tRNA name must start with "tRNA-" and be followed by one uppercase letter and
-   * two lowercase letters.
-   */
-  cp = *defline;
-  if (StringNCmp (cp, "tRNA-", 5) != 0
-      || ! IsUpperCaseChar (*(cp + 5))
-      || ! IsLowerCaseChar (*(cp + 6))
-      || ! IsLowerCaseChar (*(cp + 7)))
-  {
-    return NULL;
-  }
-  
-  gene_start = cp + 8;
-  /* gene name is required */
-  if (*gene_start == 0 || *gene_start == ',')
-  {
-    return NULL;
-  }
-  /* skip over spaces */
-  while (isspace (*gene_start))
-  {
-    gene_start ++;
-  }
-  
-  /* gene name must be in parentheses, start with letters "trn",
-   * and end with one uppercase letter.
-   */
-  if (StringNCmp (gene_start, "(trn", 4) != 0
-      || ! IsUpperCaseChar (*(gene_start + 4))
-      || * (gene_start + 5) != ')')
-  {
-    return NULL;
-  }
-
-  tdp = (tRNADefPtr) MemNew (sizeof (tRNADefData));
-  if (tdp == NULL)
-  {
-    return NULL;
-  }
-  StringNCpy (tdp->product_name, cp, 8);
-  tdp->product_name [8] = 0;
-  StringNCpy (tdp->gene_name, gene_start + 1, 4);
-  tdp->gene_name [4] = 0;
-  *defline = gene_start + 6;
-  return tdp;
-}
-
-static IntergenicSpacerDefPtr ParseIntergenicSpacerFromNoteForDef (CharPtr PNTR defline)
-{
-  IntergenicSpacerDefPtr idp;
-  CharPtr                cp;
-  
-  if (defline == NULL || *defline == NULL)
-  {
-    return NULL;
-  }
-  
-  /* description must start with "trn" and be followed by one uppercase letter, followed
-   * by a dash, followed by "trn", followed by one uppercase letter, followed by whitespace,
-   * followed by the phrase "intergenic spacer".
-   */
-  cp = *defline;
-  if (StringNCmp (cp, "trn", 3) != 0
-      || ! IsUpperCaseChar (*(cp + 3))
-      || *(cp + 4) != '-'
-      || StringNCmp (cp + 5, "trn", 3) != 0
-      || ! IsUpperCaseChar (*(cp + 8))
-      || *(cp + 9) != ' '
-      || StringNCmp (cp + 10 + StringSpn (cp + 10, " "), "intergenic spacer", 17) != 0)
-  {
-    return NULL;
-  }
-  
-  idp = (IntergenicSpacerDefPtr) MemNew (sizeof (IntergenicSpacerDefData));
-  if (idp == NULL)
-  {
-    return NULL;
-  }
-  
-  StringNCpy (idp->first_gene, cp, 4);
-  idp->first_gene [4] = 0;
-  StringNCpy (idp->second_gene, cp + 5, 4);
-  idp->second_gene [4] = 0;
-  *defline = cp + 27;
-  return idp;
-}
-
-/* This creates a feature clause from a tRNADef structure. */
-static FeatureClausePtr 
-FeatureClauseFromParsedtRNA 
-(tRNADefPtr tdp,
- SeqFeatPtr misc_feat,
- Boolean    is_partial,
- BioseqPtr  bsp,
- Boolean    suppress_locus_tag)
-{
-  FeatureClausePtr fcp;
-  
-  if (tdp == NULL)
-  {
-    return NULL;
-  }
-  
-  fcp = NewFeatureClause ( misc_feat, bsp, suppress_locus_tag);
-  if (fcp != NULL)
-  {
-    fcp->feature_label_data.is_typeword_first = FALSE;
-    fcp->feature_label_data.typeword = StringSave ("gene");
-    fcp->feature_label_data.description = (CharPtr) MemNew (16 * sizeof (Char));
-    if (fcp->feature_label_data.description != NULL)
-    {
-      sprintf (fcp->feature_label_data.description, "%s (%s)",
-               tdp->product_name, tdp->gene_name);
-    }
-    if (is_partial)
-    {
-      fcp->interval = StringSave ("partial sequence");
-    }
-    else
-    {
-      fcp->interval = StringSave ("complete sequence");
-    }
-  }
-  return fcp;
-}
-
-/* This function produces a feature clause list that should replace the original
- * single clause for a misc_feat that contains a note with one or more tRNAs and
- * an intergenic spacer.
- */
-static ValNodePtr 
-ParsetRNAIntergenicSpacerElements 
-(SeqFeatPtr misc_feat,
-BioseqPtr   bsp,
-Boolean     suppress_locus_tag)
-{
-  FeatureClausePtr fcp;
-  ValNodePtr head, vnp;
-  Boolean partial5, partial3;
-  CharPtr                cp;
-  IntergenicSpacerDefPtr spacer = NULL;
-  tRNADefPtr             trna1 = NULL, trna2 = NULL;
-  Boolean                parse_list = TRUE;
-  
-
-  if (misc_feat == NULL 
-      || StringHasNoText (misc_feat->comment)) 
-  {
-    return NULL;
-  }
-  
-  /* for list, must start with the word "contains" */
-  if (StringNICmp (misc_feat->comment, "contains ", 9) == 0)
-  {
-    cp = misc_feat->comment + 9;
-  }
-  else
-  {
-    return NULL;
-  }
-  
-  while (isspace (*cp))
-  {
-    cp ++;
-  }
-  
-  trna1 = ParsetRNAFromNoteForDefLine (&cp);
-  if (trna1 != NULL)
-  {
-    if (*cp == ',')
-    {
-      *cp++;
-    }
-    if (StringNCmp (cp, " and", 4) == 0)
-    {
-      cp += 4;
-    }
-    while (isspace (*cp))
-    {
-      cp++;
-    }
-  }
- 
-  spacer = ParseIntergenicSpacerFromNoteForDef (&cp);
-  if (spacer != NULL)
-  {
-    if (*cp == ',')
-    {
-      *cp++;
-    }
-    if (StringNCmp (cp, " and", 4) == 0)
-    {
-      cp += 4;
-    }
-    while (isspace (*cp))
-    {
-      cp++;
-    }
-  }
-  
-  trna2 = ParsetRNAFromNoteForDefLine (&cp);
-  
-  while (isspace (*cp))
-  {
-    cp++;
-  }
-  
-  head = NULL;
-  CheckSeqLocForPartial (misc_feat->location, &partial5, &partial3);
-
-  if ((*cp != 0 && *cp != ';') /* this must be the complete note or be separated from 
-                                * the rest of the note by a semicolon
-                                */
-      || ! parse_list /* didn't start with "contains" */
-      || spacer == NULL /* no spacer */
-      /* don't parse if genes don't match up */
-      || (trna1 != NULL && StringCmp (trna1->gene_name, spacer->first_gene) != 0)
-      || (trna2 != NULL && StringCmp (trna2->gene_name, spacer->second_gene) != 0))
-  {
-    /* do nothing - special parse conditions not met */
-    trna1 = MemFree (trna1);
-    trna2 = MemFree (trna2);
-    spacer = MemFree (spacer);
-    return NULL;
-  }
-  
-  /* add clause for tRNA before spacer (if any) */
-  fcp = FeatureClauseFromParsedtRNA (trna1, misc_feat, partial5, bsp, suppress_locus_tag);
-  if (fcp != NULL)
-  {   
-    vnp = ValNodeNew (head);
-    if (head == NULL) head = vnp;
-    if (vnp == NULL) return NULL;
-    vnp->data.ptrvalue = fcp;
-    vnp->choice = DEFLINE_CLAUSEPLUS;
-  }
-  
-  /* spacer was already checked, so we know it is not NULL */
-  fcp = NewFeatureClause ( misc_feat, bsp, suppress_locus_tag);
-  if (fcp != NULL)
-  {
-    fcp->feature_label_data.is_typeword_first = FALSE;
-    fcp->feature_label_data.typeword = StringSave ("intergenic spacer");
-    fcp->feature_label_data.description = (CharPtr) MemNew (10 * sizeof (Char));
-    if (fcp->feature_label_data.description != NULL)
-    {
-      sprintf (fcp->feature_label_data.description, "%s-%s",
-               spacer->first_gene, spacer->second_gene);
-    }
-    if ((trna1 == NULL && partial5) || (trna2 == NULL && partial3))
-    {
-      fcp->interval = StringSave ("partial sequence");
-    }
-    else
-    {
-      fcp->interval = StringSave ("complete sequence");
-    }
-      
-    vnp = ValNodeNew (head);
-    if (head == NULL) head = vnp;
-    if (vnp == NULL) return NULL;
-    vnp->data.ptrvalue = fcp;
-    vnp->choice = DEFLINE_CLAUSEPLUS;
-  }
-
-  /* add clause for tRNA after spacer (if any) */
-  fcp = FeatureClauseFromParsedtRNA (trna2, misc_feat, partial3, bsp, suppress_locus_tag);
-  if (fcp != NULL)
-  {   
-    vnp = ValNodeNew (head);
-    if (head == NULL) head = vnp;
-    if (vnp == NULL) return NULL;
-    vnp->data.ptrvalue = fcp;
-    vnp->choice = DEFLINE_CLAUSEPLUS;
-  }
-  
-  return head;
-}
-
-static Boolean LIBCALLBACK IsSatelliteSequence (
-  SeqFeatPtr sfp
-)
-{
-  GBQualPtr gbqual;
-  if (sfp == NULL
-    || sfp->idx.subtype != FEATDEF_repeat_region
-    || StringHasNoText (sfp->comment)
-    || (StringNCmp (sfp->comment, "microsatellite", 14) != 0
-      && StringNCmp (sfp->comment, "satellite", 9) != 0))
-  {
-    return FALSE;
-  }
-
-  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next)
-  {
-    if (StringCmp (gbqual->qual, "rpt_type") == 0
-      && StringCmp (gbqual->val, "tandem") == 0)
-    {
-      return TRUE;
-    }
-  }
-  return FALSE;
-}
-
-static Boolean LIBCALLBACK IsPromoter (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_promoter) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsEndogenousVirusSourceFeature (
-  SeqFeatPtr sfp
-)
-{
-  BioSourcePtr biop;
-  SubSourcePtr  ssp;
-
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_BIOSRC) return FALSE;
-  if ((biop = sfp->data.value.ptrvalue) == NULL) return FALSE;
-  ssp = biop->subtype;
-  while (ssp != NULL && ssp->subtype != SUBSRC_endogenous_virus_name)
-  {
-    ssp = ssp->next;
-  }
-  if (ssp != NULL) return TRUE;
-  return FALSE;
-}
-
-static CharPtr GetEndogenousVirusSourceFeatureDescription (
-  SeqFeatPtr sfp
-)
-{
-  BioSourcePtr biop;
-  SubSourcePtr  ssp;
-
-  if (sfp == NULL || sfp->idx.subtype != FEATDEF_BIOSRC) return NULL;
-  if ((biop = sfp->data.value.ptrvalue) == NULL) return NULL;
-  ssp = biop->subtype;
-  while (ssp != NULL && ssp->subtype != SUBSRC_endogenous_virus_name)
-  {
-    ssp = ssp->next;
-  }
-  if (ssp != NULL && ssp->name != NULL)
-  {
-    return StringSave (ssp->name);
-  }
-  return NULL;
-}
-
-
-static CharPtr noncoding_feature_keywords[] = {
-  "similar to ",
-  "contains "
-};
-
-static CharPtr find_noncoding_feature_keyword (
-  CharPtr comment
-)
-{
-  Int4 i, num_noncoding_feature_keywords, keywordlen;
-  CharPtr cp, buffer;
-
-  if (comment == NULL) return NULL;
-  num_noncoding_feature_keywords = sizeof (noncoding_feature_keywords) / sizeof (CharPtr);
-  for (i=0; i < num_noncoding_feature_keywords; i++)
-  {
-    keywordlen = StringLen (noncoding_feature_keywords [i]);
-    buffer = comment;
-    while ((cp = StringStr (buffer, noncoding_feature_keywords [i])) != NULL)
-    {
-      if ( StringNCmp (cp + keywordlen,
-                       "GenBank Accession Number",
-                       StringLen ("GenBank Accession Number")) != 0)
-      {
-        return cp + keywordlen;
-      }
-      else
-      {
-        buffer = cp + 1;
-      }
-    }
-  }
-  return NULL;
-}
-
-static Boolean LIBCALLBACK IsNoncodingProductFeat (
-  SeqFeatPtr sfp
-)
-{
-  if ( sfp == NULL
-    || sfp->idx.subtype != FEATDEF_misc_feature
-    || sfp->comment == NULL
-    || StringStr (sfp->comment, "intergenic") != NULL
-    || (find_noncoding_feature_keyword (sfp->comment) == NULL
-      && (StringStr (sfp->comment, "nonfunctional ") == NULL
-        || StringStr (sfp->comment, " due to ") == NULL)))
-  {
-    return FALSE;
-  }
-
-  return TRUE;
-}
-
-static CharPtr GetNoncodingProductFeatProduct (
-  SeqFeatPtr sfp
-)
-{
-  CharPtr productname;
-  Int4    namelen, compare_len;
-  CharPtr name_start, sep;
-
-  if (sfp == NULL || sfp->comment == NULL) return NULL;
-
-  if ((name_start = StringStr (sfp->comment, "nonfunctional ")) != NULL
-    && (sep = StringStr (sfp->comment, " due to ")) != NULL
-    && sep > name_start)
-  {
-    productname = StringSave (name_start);
-    productname [ sep - name_start] = 0;
-    return productname;
-  }
-
-  name_start = find_noncoding_feature_keyword (sfp->comment);
-  if (name_start == NULL) return NULL;
-
-  sep = StringStr (name_start, ";");
-  if (sep == NULL)
-  {
-    namelen = StringLen (name_start);
-  }
-  else
-  {
-    namelen = sep - name_start;
-  }
-
-  productname = MemNew (namelen + 6);
-  if (productname == NULL) return NULL;
-
-  StringNCpy (productname, name_start, namelen);
-  productname [namelen] = 0;
-  
-  /* remove sequence from end of name if present */
-  compare_len = StringLen (" sequence");
-  if (StringCmp (productname + namelen - compare_len, " sequence") == 0)
-  {
-    productname [ namelen - compare_len] = 0;
-    namelen = StringLen (productname);
-  }
-  /* add "-like" if not present */
-  compare_len = StringLen ("-like");
-  if (StringCmp (productname + namelen - compare_len, "-like") != 0)
-  {
-    StringCat (productname, "-like");
-    namelen = StringLen (productname);
-  }
-  return productname;
-}
-
-static Boolean LIBCALLBACK IsMiscFeat (
-  SeqFeatPtr sfp
-)
-{
-  if ( sfp == NULL
-    || sfp->idx.subtype != FEATDEF_misc_feature
-    || sfp->comment == NULL)
-  {
-    return FALSE;
-  }
-
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK IsOperon (
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL 
-    || sfp->idx.subtype != FEATDEF_operon)
-  {
-    return FALSE;
-  }
-
-  return TRUE;
-}
-
-static Boolean IsRecognizedFeature (
-  SeqFeatPtr sfp
-)
-{
-  if (IsGene (sfp)
-    || IsCDS (sfp)
-    || IsExon (sfp)
-    || IsIntron (sfp)
-    || IsLTR (sfp)
-    || IsrRNA (sfp)
-    || IstRNA (sfp)
-    || IsmRNA (sfp)
-    || IsMiscRNA (sfp)
-    || IssnoRNA (sfp)
-    || IssnRNA (sfp)
-    || IsscRNA (sfp)
-    || IsPrecursorRNA (sfp)
-    || Is3UTR (sfp)
-    || Is5UTR (sfp)
-    || IsMobileElement (sfp)
-    || IsEndogenousVirusSequence (sfp)
-    || IsEndogenousVirusSourceFeature (sfp)
-    || IsDloop (sfp)
-    || IsSatelliteSequence (sfp)
-    || IsControlRegion (sfp)
-    || IsIntergenicSpacer (sfp)
-    || IsGeneCluster (sfp)
-    || IsNoncodingProductFeat (sfp)
-    || IsPromoter (sfp)
-    || IsMiscFeat (sfp)
-    || IsOperon (sfp))
-  {
-    return TRUE;
-  }
-  else
-  {
-    return FALSE;
-  }
-}
-
-/* The following section of code contains functions for dealing with lists of
- * clauses.
- */
-
-/* The functions for freeing the memory associated with lists of clauses 
- * are recursive.
- */
-static void FreeListElement (ValNodePtr element);
-
-/* This function simply frees the ValNodePtr, since there is no extra
- * memory associated with a DEFLINE_FEATLIST item - the sfp that is
- * pointed to by data.ptrvalue came from the sequence indexing functions
- * and should under no circumstances be freed.
- */
-static void FreeFeatlist (
-  ValNodePtr featlist
-)
-{
-
-  if (featlist == NULL) return;
-  ValNodeFree (featlist);
-}
- 
-/* This function frees the memory associated with a FeatureClause, including
- * the memory associated with any subclauses.
- */
-static void FreeClausePlusData (
-  FeatureClausePtr fcp
-)
-{
-  if (fcp->interval != NULL)
-  {
-    MemFree (fcp->interval);
-    fcp->interval = NULL;
-  }
-  if (fcp->allelename != NULL)
-  {
-    MemFree (fcp->allelename);
-    fcp->allelename = NULL;
-  }
-  if (fcp->feature_label_data.typeword != NULL)
-  {
-    MemFree (fcp->feature_label_data.typeword);
-    fcp->feature_label_data.typeword = NULL;
-  }
-  if (fcp->feature_label_data.description != NULL)
-  {
-    MemFree (fcp->feature_label_data.description);
-    fcp->feature_label_data.description = NULL;
-  }
-  if (fcp->feature_label_data.productname != NULL)
-  {
-    MemFree (fcp->feature_label_data.productname);
-    fcp->feature_label_data.productname = NULL;
-  }
-  if (fcp->featlist != NULL)
-  {
-    FreeListElement (fcp->featlist);
-    fcp->featlist = NULL;
-  }
-  if (fcp->slp != NULL)
-  {
-    SeqLocFree (fcp->slp);
-  }
-}
-    
-/* This function frees the data associated with the FeatureClause
- * and then frees the ValNode.
- */
-static void FreeClausePlus (
-  ValNodePtr clauseplus
-)
-{
-  FeatureClausePtr data_struct;
-
-  if (clauseplus == NULL) return;
-  data_struct = (FeatureClausePtr) clauseplus->data.ptrvalue;
-  if (data_struct != NULL)
-  {
-    FreeClausePlusData (data_struct); 
-    MemFree (data_struct);
-    clauseplus->data.ptrvalue = NULL;
-  }
-  ValNodeFree (clauseplus);
-}
- 
-/* This function frees a list of DEFLINE_FEATLIST, DEFLINE_REMOVEFEAT,
- * and DEFLINE_CLAUSEPLUS items, starting with the last item in the list.
- * It recursively frees memory associated with subclauses.
- */ 
-static void FreeListElement (
-  ValNodePtr element
-)
-{
-  if (element == NULL) return;
-
-  FreeListElement (element->next);
-  element->next = NULL;
-  if (element->choice == DEFLINE_FEATLIST 
-    || element->choice == DEFLINE_REMOVEFEAT)
-  {
-    FreeFeatlist (element);
-  }
-  else if (element->choice == DEFLINE_CLAUSEPLUS)
-  {
-    FreeClausePlus (element);
-  }
-}
-
-/* This function excises from the list pointed to by head all of the clauses
- * with the delete_me flag set to TRUE and all of the ValNodes with a choice
- * of DEFLINE_REMOVEFEAT.
- */
-static void DeleteFeatureClauses (
-  ValNodePtr PNTR head
-)
-{
-  ValNodePtr vnp, prev;
-  FeatureClausePtr fcp;
-  Boolean          delete_this_one;
-
-  if (head == NULL) return;
-
-  prev = NULL;
-  vnp = *head;
-  while (vnp != NULL)
-  {
-    delete_this_one = FALSE;
-
-    if (vnp->choice == DEFLINE_CLAUSEPLUS)
-    {
-      fcp = vnp->data.ptrvalue;
-      if (fcp == NULL || fcp->delete_me || fcp->featlist == NULL) 
-      {
-        delete_this_one = TRUE;
-      }
-      else
-      {
-        DeleteFeatureClauses (&fcp->featlist);
-        if (fcp->featlist == NULL) delete_this_one = TRUE;
-      }
-    }
-    else if (vnp->choice == DEFLINE_REMOVEFEAT)
-    {
-      delete_this_one = TRUE;
-    }
-
-    if (delete_this_one)
-    {
-      if (prev == NULL)
-      {
-        *head = vnp->next;
-        vnp->next = NULL;
-        FreeListElement (vnp);
-        if (*head == NULL) return;
-        vnp = *head;
-      }
-      else
-      {
-        prev->next = vnp->next;
-        vnp->next = NULL;
-        FreeListElement (vnp);
-        vnp = prev->next;
-      }
-    }
-    else
-    {
-      prev = vnp;
-      vnp = vnp->next;
-    }
-  }
-}
-
-/* This function counts the number of features in the feature list that
- * satisfy the itemmatch function (or all of them, if itemmatch is NULL).
- * If recurse_past_found_item, the function will not count features in
- * subclauses of features that satisfy itemmatch.
- */
-static Int4 CountFeatures (
-  ValNodePtr clause_list,
-  matchFunction  itemmatch,
-  Boolean    recurse_past_found_item
-)
-{
-  ValNodePtr       vnp;
-  Int4             num_features;
-  FeatureClausePtr fcp;
-
-  num_features = 0;
-  for (vnp = clause_list;
-       vnp != NULL;
-       vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_FEATLIST 
-      && (itemmatch == NULL || itemmatch (vnp->data.ptrvalue)))
-    {
-      num_features++;
-      if (! recurse_past_found_item)
-      {
-        return num_features;
-      }
-    }
-    else if (vnp->choice == DEFLINE_CLAUSEPLUS
-      && (fcp = vnp->data.ptrvalue) != NULL)
-    {
-      num_features += CountFeatures (fcp->featlist,
-                                     itemmatch,
-                                     recurse_past_found_item);   
-    }
-  }
-  return num_features;
-}
-
-/* The following section of code contains functions for grouping features. */
-
-typedef struct matchruledata {
-  matchFunction is_item;
-  Int4          num_match_rules;
-  matchFunction *match_rules;
-} MatchRuleData, PNTR MatchRulePtr;
-
-static void InitRuleForTopLevelClauses (MatchRulePtr mrp)
-{
-  if (mrp == NULL)
-  {
-    return;
-  }
-  mrp->num_match_rules = 4;
-  mrp->match_rules = MemNew (mrp->num_match_rules
-                                    * sizeof (matchFunction));
-  if (mrp->match_rules == NULL) return;
-  mrp->match_rules[0] = IsMobileElement;
-  mrp->match_rules[1] = IsEndogenousVirusSourceFeature;
-  mrp->match_rules[2] = IsOperon;
-  mrp->match_rules[3] = IsGeneCluster;
-}
-
-static void InitRuleForBottomLevelClauses (MatchRulePtr mrp)
-{
-  if (mrp == NULL)
-  {
-    return;
-  }
-  mrp->num_match_rules = 6;
-  mrp->match_rules = MemNew (mrp->num_match_rules
-                                    * sizeof (matchFunction));
-  if (mrp->match_rules == NULL) return;
-  mrp->match_rules[0] = IsCDS;
-  mrp->match_rules[1] = IsmRNA;
-  mrp->match_rules[2] = IsGene;
-  mrp->match_rules[3] = IsEndogenousVirusSourceFeature;
-  mrp->match_rules[4] = IsOperon;
-  mrp->match_rules[5] = IsGeneCluster;
-}
-
-/* NumGroupingRules is the number of features for which there is a list of
- * features to group under.
- * When grouping features, each feature in the list is examined sequentially.
- * If there is a rule set that applies to that feature, the entire feature 
- * list is searched for each feature type that this feature might group
- * beneath.  This preserves the biological order that was generated by the
- * original listing of features by sequence indexing.
- */
-#define  NumGroupingRules 13
-static MatchRulePtr InitializeGroupingRules()
-{
-  MatchRulePtr grouping_rules;
-
-  grouping_rules = MemNew (NumGroupingRules * sizeof (MatchRuleData));
-  if (grouping_rules == NULL) return NULL;
-
-  grouping_rules[0].is_item = IsExon;
-  grouping_rules[0].num_match_rules = 8;
-  grouping_rules[0].match_rules = MemNew (grouping_rules[0].num_match_rules
-                                    * sizeof (matchFunction));
-  if (grouping_rules[0].match_rules == NULL) return NULL;
-  grouping_rules[0].match_rules[0] = IsCDS;
-  grouping_rules[0].match_rules[1] = IsNoncodingProductFeat;
-  grouping_rules[0].match_rules[2] = IsDloop;
-  grouping_rules[0].match_rules[3] = IsmRNA;
-  grouping_rules[0].match_rules[4] = IsGene;
-  grouping_rules[0].match_rules[5] = IsEndogenousVirusSourceFeature;
-  grouping_rules[0].match_rules[6] = IsOperon;
-  grouping_rules[0].match_rules[7] = IsGeneCluster;
-
-  grouping_rules[1].is_item = IsIntron;
-  grouping_rules[1].num_match_rules = 8;
-  grouping_rules[1].match_rules = MemNew (grouping_rules[1].num_match_rules
-                                    * sizeof (matchFunction));
-  if (grouping_rules[1].match_rules == NULL) return NULL;
-  grouping_rules[1].match_rules[0] = IsCDS;
-  grouping_rules[1].match_rules[1] = IsNoncodingProductFeat;
-  grouping_rules[1].match_rules[2] = IstRNA;
-  grouping_rules[1].match_rules[3] = IsDloop;
-  grouping_rules[1].match_rules[4] = IsGene;
-  grouping_rules[1].match_rules[5] = IsEndogenousVirusSourceFeature;
-  grouping_rules[1].match_rules[6] = IsOperon;
-  grouping_rules[1].match_rules[7] = IsGeneCluster;
-  
-  grouping_rules[2].is_item = IsPromoter;
-  InitRuleForBottomLevelClauses (grouping_rules + 2);
- 
-  grouping_rules[3].is_item = IsCDS;
-  grouping_rules[3].num_match_rules = 5;
-  grouping_rules[3].match_rules = MemNew (grouping_rules[3].num_match_rules
-                                    * sizeof (matchFunction));
-  if (grouping_rules[3].match_rules == NULL) return NULL;
-  grouping_rules[3].match_rules[0] = IsmRNA;
-  grouping_rules[3].match_rules[1] = IsMobileElement;
-  grouping_rules[3].match_rules[2] = IsEndogenousVirusSourceFeature;
-  grouping_rules[3].match_rules[3] = IsOperon;
-  grouping_rules[3].match_rules[4] = IsGeneCluster;
-  
-  grouping_rules[4].is_item = IsMobileElement;
-  InitRuleForTopLevelClauses (grouping_rules + 4);
- 
-  grouping_rules[5].is_item = Is3UTR;
-  InitRuleForBottomLevelClauses (grouping_rules + 5);
- 
-  grouping_rules[6].is_item = Is5UTR;
-  InitRuleForBottomLevelClauses (grouping_rules + 6);
- 
-  grouping_rules[7].is_item = IsLTR;
-  InitRuleForBottomLevelClauses (grouping_rules + 7);
- 
-  grouping_rules[8].is_item = IsGene;
-  InitRuleForTopLevelClauses (grouping_rules + 8);
-  
-  grouping_rules[9].is_item = IsIntergenicSpacer;
-  InitRuleForTopLevelClauses (grouping_rules + 9);
-
-  grouping_rules[10].is_item = IsNoncodingProductFeat;
-  InitRuleForTopLevelClauses (grouping_rules + 10);
- 
-  grouping_rules[11].is_item = IsOperon;
-  InitRuleForTopLevelClauses (grouping_rules + 11);
- 
-  grouping_rules[12].is_item = IsGeneCluster;
-  InitRuleForTopLevelClauses (grouping_rules + 12);
-
-  return grouping_rules; 
-}
-
-static void FreeGroupingRules(
-  MatchRulePtr grouping_rules
-)
-{
-  Int4 i;
-
-  if (grouping_rules == NULL) return;
-
-  for (i = 0; i < NumGroupingRules; i++)
-  {
-    if (grouping_rules[i].match_rules != NULL)
-    MemFree (grouping_rules[i].match_rules);
-    grouping_rules[i].match_rules = NULL;
-  }
-  MemFree (grouping_rules);
-}
-
-static Boolean IsmRNASequence (BioseqPtr bsp)
-{
-  SeqDescrPtr sdp;
-  MolInfoPtr  mip;
-  
-  if (bsp == NULL || bsp->mol != Seq_mol_rna || bsp->descr == NULL)
-  {
-    return FALSE;
-  }
-  sdp = bsp->descr;
-  while (sdp != NULL && sdp->choice != Seq_descr_molinfo)
-  {
-    sdp = sdp->next;
-  }
-  if (sdp == NULL || sdp->data.ptrvalue == NULL)
-  {
-    return FALSE;
-  }
-  mip = (MolInfoPtr) sdp->data.ptrvalue;
-  
-  if (mip->biomol == 3)
-  {
-    return TRUE;
-  }
-  else
-  {
-    return FALSE;
-  }
-}
-
-typedef struct matchcandidate 
-{
-  ValNodePtr matched_clause;
-  SeqLocPtr  slp;
-} MatchCandidateData, PNTR MatchCandidatePtr;
-
-/* This function searches the search_list for features that satisfy the
- * match function and satisfy locational requirements relative to the
- * clause.
- * If more than one clause meets the match requirements, the smallest one
- * is chosen.
- */
-static void FindBestMatchCandidate 
-(FeatureClausePtr  clause,
- ValNodePtr        search_list,
- FeatureClausePtr  search_parent,
- matchFunction     match,
- Boolean           gene_cluster_opp_strand,
- BioseqPtr         bsp,
- MatchCandidatePtr current_candidate)
-{
-  ValNodePtr       search_clause;
-  SeqFeatPtr       addsfp, clause_sfp;
-  FeatureClausePtr searchfcp;
-  SeqLocPtr        slp;
-
-  if (clause == NULL || clause->slp == NULL || current_candidate == NULL) return;
-  
-  clause_sfp = (SeqFeatPtr) (clause->featlist->data.ptrvalue);
-
-  for (search_clause = search_list;
-       search_clause != NULL;
-       search_clause = search_clause->next)
-  {
-    if (search_clause->data.ptrvalue == clause)
-      continue;
-    if (search_clause->choice == DEFLINE_FEATLIST
-      && search_clause->data.ptrvalue != NULL)
-    {
-      addsfp = search_clause->data.ptrvalue;
-      /* slp is the location of the feature we are trying to
-       * group this feature with
-       */ 
-      if (search_parent != NULL)
-      {
-        slp = search_parent->slp;
-      }
-      else
-      {
-        slp = addsfp->location;
-      }
-      if (match (search_clause->data.ptrvalue))
-      { 
-        /* Transposons, insertion sequences, integrons, and endogenous virii
-         * take subfeatures regardless of whether the subfeature is
-         * on the same strand.
-         * Gene Clusters can optionally take subfeatures on either
-         * strand (gene_cluster_opp_strand is flag).
-         * Promoters will match up to features that are adjacent.
-         * Introns will match up to coding regions whose intervals
-         * are adjacent to the endpoints of the intron, or to other
-         * features if the intron location is inside the other feature.
-         * All other feature matches must be that the feature to
-         * go into the clause must fit inside the location of the
-         * other clause.
-         */
-        if (((match == IsMobileElement
-             || match == IsEndogenousVirusSourceFeature
-             || (match == IsGeneCluster && gene_cluster_opp_strand))
-            && SeqLocAinB (clause->slp, slp) > -1)
-          || IsLocAInBonSameStrand (clause->slp, slp)
-          || ( IsPromoter (clause_sfp)
-            && IsAAdjacentToB (clause->slp, search_parent->slp, bsp,
-                               ADJACENT_TYPE_UPSTREAM, TRUE))
-          || IsmRNASequence (bsp)
-          || (match == IsCDS 
-              && IsIntron (clause_sfp)
-              && IsAEmptyIntervalOfB (clause->slp, slp, bsp))
-          || (match == IsCDS
-              && IsExon (clause_sfp)
-              && LocAContainsIntervalOfB (clause->slp, slp)))
-        {
-          /* if we don't already have a candidate, or if this
-           * candidate's location is inside the current candidate,
-           * take this candidate.
-           */
-          if (current_candidate->matched_clause == NULL
-              || SeqLocAinB (slp, current_candidate->slp) > 0)
-          {
-            current_candidate->matched_clause = search_clause;
-            current_candidate->slp = slp;
-          }
-        }
-      }
-    }
-    else if (search_clause->choice == DEFLINE_CLAUSEPLUS 
-      && search_clause->data.ptrvalue != NULL)
-    {
-      searchfcp = search_clause->data.ptrvalue;
-      FindBestMatchCandidate (clause, searchfcp->featlist, searchfcp,
-                              match, gene_cluster_opp_strand, bsp,
-                              current_candidate);
-    }
-  }
-}
-
-
-/* This function iterates through the matches in the specified grouping rule.
- * If more than one match is found, the clause with the smallest location is
- * used.
- * If a match is found, the clause is added to the list of clauses for that
- * feature's parent clause.
- */
-static Boolean GroupClauseByRule (
-  FeatureClausePtr clause,
-  ValNodePtr       search_list,
-  MatchRulePtr     grouping_rule,
-  Boolean          gene_cluster_opp_strand,
-  BioseqPtr        bsp
-)
-{
-  Int4               rule_index;
-  MatchCandidateData mcd;  
-  Boolean            rval = FALSE;
-  ValNodePtr         newfeat;
-  
-  mcd.slp = NULL;
-  mcd.matched_clause = NULL;
-
-  for (rule_index = 0;
-       rule_index < grouping_rule->num_match_rules;
-       rule_index ++)
-  {
-  
-    FindBestMatchCandidate (clause, search_list, NULL, 
-                            grouping_rule->match_rules[rule_index],
-                            gene_cluster_opp_strand, bsp, &mcd);
-  }
-  if (mcd.matched_clause != NULL)
-  {
-    newfeat = ValNodeNew (mcd.matched_clause);
-    if (newfeat == NULL) return FALSE;
-    newfeat->choice = DEFLINE_CLAUSEPLUS;
-    newfeat->data.ptrvalue = clause;
-    rval = TRUE;
-  }
-  return rval;
-}
-
-
-/* This function determines whether a subclause contains just a 3' UTR feature
- * and no other details.
- */
-static Boolean Is3UTRClause (FeatureClausePtr clause)
-{  
-  if (clause == NULL
-      || clause->featlist == NULL 
-      || clause->featlist->choice != DEFLINE_FEATLIST
-      || clause->featlist->data.ptrvalue == NULL
-      || clause->featlist->next != NULL)
-  {
-    return FALSE;
-  }
-  return Is3UTR(clause->featlist->data.ptrvalue);
-}
-
-/* This function will move 3' UTRs to the end of any subfeat lists
- * so that they can be listed after the partial/complete CDS.
- */
-static void Move3UTRToEndOfSubFeatList (ValNodePtr clause_list)
-{
-  ValNodePtr vnp, prev, last_vnp;
-  FeatureClausePtr clause;
-  
-  if (clause_list == NULL || clause_list->next == NULL) 
-  {
-    return;
-  }
-  prev = clause_list;
-  for (vnp = clause_list->next; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->data.ptrvalue != NULL && vnp->choice == DEFLINE_CLAUSEPLUS)
-    {
-      clause = vnp->data.ptrvalue;
-      if (Is3UTRClause (clause))
-      {
-        if (vnp->next != NULL)
-        {
-          /* move to end of clause list */
-          last_vnp = vnp->next;
-          while (last_vnp->next != NULL)
-          {
-            last_vnp = last_vnp->next;
-          }
-          prev->next = vnp->next;
-          last_vnp->next = vnp;
-          vnp->next = NULL;
-        }
-      }
-      else
-      {
-        prev = vnp;
-        Move3UTRToEndOfSubFeatList (clause->featlist);
-      }
-    }
-    else
-    {
-      prev = vnp;
-    }
-  }  
-}
-
-/* This function iterates over the list of features, attempting to find and
- * apply grouping rules for each feature.
- */
-static void GroupAllClauses (
-  ValNodePtr PNTR clause_list,
-  Boolean         gene_cluster_opp_strand,
-  BioseqPtr       bsp
-)
-{
-  MatchRulePtr     grouping_rules;
-  ValNodePtr       vnp, prev;
-  FeatureClausePtr clause;
-  SeqFeatPtr       main_feat;
-  Int4             rule_index;
-
-  grouping_rules = InitializeGroupingRules();
-  if (grouping_rules == NULL) return;
-
-  for (vnp = *clause_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
-    {
-      clause = vnp->data.ptrvalue;
-      if (clause->featlist != NULL
-        && clause->featlist->choice == DEFLINE_FEATLIST
-        && clause->featlist->data.ptrvalue != NULL)
-      {
-        main_feat = clause->featlist->data.ptrvalue;
-        for (rule_index = 0;
-             rule_index < NumGroupingRules 
-               && ! grouping_rules[rule_index].is_item (main_feat);
-             rule_index++)
-        {
-        }
-        if (rule_index < NumGroupingRules)
-        {
-          if ( GroupClauseByRule (clause, *clause_list,
-                                  grouping_rules + rule_index, 
-                                  gene_cluster_opp_strand,
-                                  bsp))
-          {
-            vnp->data.ptrvalue = NULL;
-          }
-        }
-      }
-    }
-  }
-  FreeGroupingRules(grouping_rules);
-
-  vnp = *clause_list;
-  prev = NULL;
-  while (vnp != NULL)
-  {
-    if (vnp->data.ptrvalue == NULL)
-    {
-      if (prev == NULL)
-      {
-        *clause_list = vnp->next;
-        vnp->next = NULL;
-        ValNodeFree (vnp);
-        vnp = *clause_list;
-      }
-      else
-      {
-        prev->next = vnp->next;
-        vnp->next = NULL;
-        ValNodeFree (vnp);
-        vnp = prev->next;
-      }
-    }
-    else
-    {
-      prev = vnp;
-      vnp = vnp->next;
-    }
-  }
-  
-  Move3UTRToEndOfSubFeatList (*clause_list);
-}
-
-/* This function exists to handle the special case where two or more exons
- * are alternatively spliced, but there are no CDSs to represent some of the
- * alternatively spliced forms.  In order to make sure that all of the exons
- * that are alternatively spliced together appear with the CDS, they are
- * temporarily consolidated into a single clause with a location that
- * is the intersection of the exons' locations.  The clause will be
- * re-expanded after grouping by the ExpandAltSplicedExons function.
- */
-static void GroupAltSplicedExons (
-  ValNodePtr PNTR clause_list,
-  BioseqPtr       bsp,
-  Boolean         delete_now
-)
-{
-  ValNodePtr       clause, search_clause, vnp;
-  FeatureClausePtr fcp, search_fcp;
-  SeqFeatPtr       sfp, search_sfp;
-  SeqLocPtr        new_slp;
-
-  if (clause_list == NULL) return;
- 
-  for (clause = *clause_list; clause != NULL; clause = clause->next)
-  {
-    if (clause->choice != DEFLINE_CLAUSEPLUS
-      || clause->data.ptrvalue == NULL)
-    {
-      continue;
-    }
-    fcp = clause->data.ptrvalue;
-    if ( ! fcp->is_alt_spliced
-      || fcp->delete_me
-      || fcp->featlist == NULL
-      || fcp->featlist->choice != DEFLINE_FEATLIST)
-    {
-      continue;
-    }
-    sfp = fcp->featlist->data.ptrvalue;
-    if ( ! IsExon (sfp))
-    {
-      continue;
-    }
-
-    for ( search_clause = clause->next; 
-          search_clause != NULL
-            && search_clause->choice == DEFLINE_CLAUSEPLUS
-            && search_clause->data.ptrvalue != NULL
-            && (search_fcp = search_clause->data.ptrvalue) != NULL
-            && ! search_fcp->delete_me
-            && search_fcp->is_alt_spliced
-            && search_fcp->featlist != NULL
-            && search_fcp->featlist->choice == DEFLINE_FEATLIST
-            && (search_sfp = search_fcp->featlist->data.ptrvalue) != NULL
-            && IsExon (search_sfp)
-            && TestFeatOverlap (sfp, search_sfp, SIMPLE_OVERLAP) != -1;
-          search_clause = search_clause->next)
-    {
-      vnp = ValNodeNew (fcp->featlist);
-      if (vnp == NULL) return;
-      vnp->choice = DEFLINE_FEATLIST;
-      vnp->data.ptrvalue = search_sfp;
-      search_fcp->delete_me = TRUE;
-      new_slp = SeqLocIntersection (fcp->slp, search_fcp->slp, bsp);
-      SeqLocFree (fcp->slp);
-      fcp->slp = new_slp;
-    }
-  }
-  if (delete_now)
-  {
-    DeleteFeatureClauses (clause_list);
-  }
-}
-
-/* This function expands a clause filled with alternatively-spliced exons
- * that was created in the GroupAltSplicedExons function.
- */
-static void ExpandAltSplicedExons (
-  ValNodePtr clause_list,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag)
-{
-  ValNodePtr clause, rest_of_list, featlist, new_clause;
-  FeatureClausePtr fcp, new_fcp;
-  SeqFeatPtr sfp;
-
-  for (clause = clause_list;
-       clause != NULL;
-       clause = clause->next)
-  {
-    if (clause->choice != DEFLINE_CLAUSEPLUS
-      || (fcp = clause->data.ptrvalue) == NULL
-      || fcp->featlist == NULL)
-    {
-      continue;
-    }
-    if ( fcp->featlist->choice == DEFLINE_FEATLIST
-      && (sfp = fcp->featlist->data.ptrvalue) != NULL
-      && IsExon (sfp)
-      && fcp->featlist->next != NULL
-      && fcp->featlist->next->choice == DEFLINE_FEATLIST
-      && IsExon (fcp->featlist->next->data.ptrvalue))
-    {
-      rest_of_list = clause->next;
-      clause->next = NULL;
-      for (featlist = fcp->featlist->next;
-           featlist != NULL
-             && featlist->choice == DEFLINE_FEATLIST
-             && IsExon (featlist->data.ptrvalue);
-           featlist = featlist->next)
-      {
-        new_clause = ValNodeNew (clause);
-        if (new_clause == NULL) return;
-        new_fcp = NewFeatureClause (featlist->data.ptrvalue, bsp, suppress_locus_tag);
-        if (new_fcp == NULL) return;
-        new_fcp->grp = fcp->grp;
-        new_fcp->is_alt_spliced = fcp->is_alt_spliced;
-        new_fcp->make_plural = fcp->make_plural;
-        new_clause->choice = DEFLINE_CLAUSEPLUS;
-        new_clause->data.ptrvalue = new_fcp;
-      }
-      ValNodeFree (fcp->featlist->next);
-      fcp->featlist->next = NULL;
-      new_clause->next = rest_of_list;
-
-      /* put back location for first exon - was reduced to union of 
-       * all exon intervals in GroupAltSplicedExons
-       */
-      SeqLocFree (fcp->slp);
-      sfp = fcp->featlist->data.ptrvalue;
-      fcp->slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, TRUE, FALSE);
-    }
-    else
-    {
-      ExpandAltSplicedExons (fcp->featlist, bsp, suppress_locus_tag);
-    }
-  }
-}
-
-static Boolean DoFeaturesShareGene (SeqFeatPtr sfp1, SeqFeatPtr sfp2)
-{
-  Boolean share_gene = FALSE;
-  SeqFeatPtr found_gene1, found_gene2;
-  
-  if (sfp1 != NULL && sfp2 != NULL
-      && !SeqMgrGeneIsSuppressed (SeqMgrGetGeneXref(sfp1))
-      && !SeqMgrGeneIsSuppressed (SeqMgrGetGeneXref(sfp2)))
-  {
-    found_gene1 = SeqMgrGetOverlappingGene (sfp1->location, NULL);
-    found_gene2 = SeqMgrGetOverlappingGene (sfp2->location, NULL);
-    if (found_gene1 == found_gene2 && found_gene1 != NULL)
-    {
-      share_gene = TRUE;
-    }
-  }
-  return share_gene;
-}
-
-/* This function determines whether two features share the same product name */
-static Boolean 
-DoProductNamesMatch 
-(SeqFeatPtr sfp1,
- SeqFeatPtr sfp2, 
- BioseqPtr  bsp,
- Boolean    suppress_locus_tag)
-{
-  CharPtr productname1;
-  CharPtr productname2;
-  Boolean names_match = FALSE;
-   
-  productname1 = GetProductName (sfp1, bsp, suppress_locus_tag);
-  productname2 = GetProductName (sfp2, bsp, suppress_locus_tag);
-  if (StringHasNoText (productname1) && StringHasNoText (productname2))
-  {
-    names_match = TRUE;
-  }
-  else if (StringCmp (productname1, productname2) == 0)
-  {
-    names_match = TRUE;
-  }
-  
-  productname1 = MemFree (productname1);
-  productname2 = MemFree (productname2);
-  
-  return names_match;  
-}
-
-/* This function should combine CDSs that do not have a joined location
- * but are part of the same gene and have the same protein name.
- */
-static void GroupSegmentedCDSs (
-  ValNodePtr PNTR clause_list,
-  BioseqPtr       bsp,
-  Boolean         delete_now,
-  Boolean         suppress_locus_tag
-)
-{
-  ValNodePtr       clause, search_clause, vnp;
-  FeatureClausePtr fcp, search_fcp;
-  SeqFeatPtr       sfp, search_sfp;
-  SeqLocPtr        new_slp;
-
-  if (clause_list == NULL) return;
- 
-  for (clause = *clause_list; clause != NULL; clause = clause->next)
-  {
-    if (clause->choice != DEFLINE_CLAUSEPLUS
-      || clause->data.ptrvalue == NULL)
-    {
-      continue;
-    }
-    fcp = clause->data.ptrvalue;
-    if (fcp->delete_me
-      || fcp->featlist == NULL
-      || fcp->featlist->choice != DEFLINE_FEATLIST)
-    {
-      continue;
-    }
-    sfp = fcp->featlist->data.ptrvalue;
-    if ( ! IsCDS (sfp))
-    {
-      continue;
-    }
-
-    for ( search_clause = clause->next; 
-          search_clause != NULL;
-          search_clause = search_clause->next)
-    {
-      if (search_clause->choice != DEFLINE_CLAUSEPLUS
-          || search_clause->data.ptrvalue == NULL
-          || (search_fcp = search_clause->data.ptrvalue) == NULL
-          || search_fcp->delete_me
-          || search_fcp->featlist == NULL
-          || search_fcp->featlist->choice != DEFLINE_FEATLIST
-          || (search_sfp = search_fcp->featlist->data.ptrvalue) == NULL
-          || ! IsCDS (search_sfp)
-          || ! DoFeaturesShareGene (sfp, search_sfp)
-          || ! DoProductNamesMatch (sfp, search_sfp, bsp, suppress_locus_tag))
-      {
-        continue;
-      }
-      vnp = ValNodeNew (fcp->featlist);
-      if (vnp == NULL) return;
-      vnp->choice = DEFLINE_FEATLIST;
-      vnp->data.ptrvalue = search_sfp;
-      search_fcp->delete_me = TRUE;
-      new_slp = SeqLocMerge (bsp, fcp->slp, search_fcp->slp,
-                             FALSE, TRUE, FALSE);
-
-      SeqLocFree (fcp->slp);
-      fcp->slp = new_slp;
-    }
-  }
-  if (delete_now)
-  {
-    DeleteFeatureClauses (clause_list);
-  }
-}
-
-
-/* This function searches this list for clauses to which this gene should
- * apply.  This is not taken care of by the GroupAllClauses function
- * because genes are added to clauses as a GeneRefPtr instead of as an
- * additional feature in the list, and because a gene can apply to more
- * than one clause, while other features should really only belong to
- * one clause.
- */
-static Boolean AddGeneToClauses 
-( SeqFeatPtr gene,
-  CharPtr    gene_productname,
-  ValNodePtr clause_list,
-  Boolean    suppress_locus_tag)
-{
-  ValNodePtr    clause;
-  FeatureClausePtr fcp;
-  SeqFeatPtr    sfp, found_gene;
-  GeneRefPtr    grp;
-  Boolean    used_gene;
-  
-  if (gene == NULL || gene->data.value.ptrvalue == NULL) return FALSE;
-  if (clause_list == NULL) return FALSE;
-
-  used_gene = FALSE;
-  grp = gene->data.value.ptrvalue;
-  for (clause = clause_list; clause != NULL; clause = clause->next)
-  {
-    fcp = clause->data.ptrvalue;
-    if (fcp == NULL || fcp->featlist == NULL) return FALSE;
-    sfp = fcp->featlist->data.ptrvalue;
-    if (sfp != NULL && !SeqMgrGeneIsSuppressed (SeqMgrGetGeneXref(sfp))
-        && (IsCDS (sfp)
-            || IsrRNA (sfp)
-            || IstRNA (sfp)
-            || IsmRNA (sfp)
-            || IsMiscRNA (sfp)
-            || IssnRNA (sfp)
-            || IsscRNA (sfp)
-            || IssnoRNA (sfp)
-            || IsPrecursorRNA (sfp)
-            || IsNoncodingProductFeat (sfp)))
-    {
-      if (fcp->grp == NULL)
-      {
-        found_gene = SeqMgrGetOverlappingGene (sfp->location, NULL);
-        if (found_gene != NULL)
-        {
-          fcp->grp = (GeneRefPtr) found_gene->data.value.ptrvalue;
-        }
-      }
-
-      if (fcp->grp != NULL && DoGenesMatch (fcp->grp, grp, suppress_locus_tag))
-      {
-        used_gene = TRUE;
-        if (gene_productname != NULL
-          && fcp->feature_label_data.productname == NULL
-          && IsCDS (sfp))
-        {
-          fcp->feature_label_data.productname =
-              StringSave (gene_productname);
-        }
-      }
-      else if (fcp->grp == NULL
-        && IsLocAInBonSameStrand (sfp->location, gene->location))
-      {
-        fcp->grp = grp;
-        used_gene = TRUE;
-        if (gene_productname != NULL
-          && fcp->feature_label_data.productname == NULL
-          && IsCDS (sfp))
-        {
-          fcp->feature_label_data.productname =
-              StringSave (gene_productname);
-        }
-      }
-    }
-  }
-  return used_gene;
-}
-
-/* This function iterates through the list of features and calls
- * AddGeneToClauses for each gene feature it finds.
- */
-static void GroupGenes (ValNodePtr PNTR clause_list, Boolean suppress_locus_tag)
-{
-  ValNodePtr  vnp;
-  ValNodePtr  featlist;
-  FeatureClausePtr fcp;
-
-  for (vnp = *clause_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice != DEFLINE_CLAUSEPLUS) return;
-    fcp = (FeatureClausePtr) vnp->data.ptrvalue;
-    if (fcp == NULL) return;
-
-    featlist = fcp->featlist;
-    if (featlist != NULL
-      && featlist->choice == DEFLINE_FEATLIST
-      && IsGene (featlist->data.ptrvalue))
-    {
-      AddGeneToClauses (featlist->data.ptrvalue,
-                        fcp->feature_label_data.productname,
-                        vnp->next, suppress_locus_tag);
-    }
-  } 
-}
-
-/* This function searches this list for clauses to which this mRNA should
- * apply.  This is not taken care of by the GroupAllClauses function
- * because when an mRNA is added to a CDS, the product for the clause is
- * replaced and the location for the clause is expanded, rather than simply
- * adding the mRNA as an additional feature in the list, and because an 
- * mRNA can apply to more than one clause, while other features should 
- * really only belong to one clause.
- */
-static Boolean AddmRNAToClauses 
-( SeqFeatPtr mRNA,
-  ValNodePtr clause_list,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag)
-{
-  ValNodePtr    clause;
-  FeatureClausePtr fcp;
-  SeqFeatPtr    sfp;
-  Boolean    used_mRNA;
-  CharPtr       productname;
-  SeqLocPtr     new_slp;
-  
-  if (mRNA == NULL || mRNA->data.value.ptrvalue == NULL) return FALSE;
-  if (clause_list == NULL) return FALSE;
-
-  used_mRNA = FALSE;
-  productname = GetProductName (mRNA, bsp, suppress_locus_tag);
-  if (productname == NULL) return TRUE;
-
-  for (clause = clause_list; clause != NULL; clause = clause->next)
-  {
-    fcp = clause->data.ptrvalue;
-    if (fcp == NULL || fcp->featlist == NULL) return FALSE;
-    sfp = fcp->featlist->data.ptrvalue;
-    if (sfp == NULL)
-    {
-    }
-    else if (IsCDS (sfp)
-      && fcp->feature_label_data.productname != NULL
-      && StringCmp (fcp->feature_label_data.productname, productname) == 0)
-    {
-      used_mRNA = TRUE;
-      fcp->has_mrna = TRUE;
-      if (IsLocAInBonSameStrand (sfp->location, mRNA->location))
-      {
-        new_slp = SeqLocMerge (bsp, fcp->slp, mRNA->location,
-                                 FALSE, TRUE, FALSE);
-        if (new_slp == NULL) return FALSE;
-        if (fcp->slp != NULL)
-        {
-          SeqLocFree (fcp->slp);
-        }
-        fcp->slp = new_slp;
-      }
-    }
-    else if (fcp->feature_label_data.productname == NULL
-      && (IsCDS (sfp) || IsGene (sfp))
-      && (IsLocAInBonSameStrand (sfp->location, mRNA->location)
-        || IsLocAInBonSameStrand (mRNA->location, sfp->location)))
-    {
-      fcp->feature_label_data.productname = StringSave (productname);
-      used_mRNA = TRUE;
-      fcp->has_mrna = TRUE;
-      new_slp = SeqLocMerge (bsp, fcp->slp, mRNA->location,
-                                 FALSE, TRUE, FALSE);
-      if (new_slp == NULL) return FALSE;
-      if (fcp->slp != NULL)
-      {
-        SeqLocFree (fcp->slp);
-      }
-      fcp->slp = new_slp;
-    }
-  }
-  return used_mRNA;
-}
-
-/* This function iterates through the list of features and calls
- * AddmRNAToClauses for each mRNA feature it finds.
- */
-static void GroupmRNAs (
-  ValNodePtr PNTR clause_list,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag
-)
-{
-  ValNodePtr  vnp;
-  ValNodePtr  featlist;
-  FeatureClausePtr fcp;
-
-  for (vnp = *clause_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice != DEFLINE_CLAUSEPLUS) return;
-    fcp = (FeatureClausePtr) vnp->data.ptrvalue;
-    if (fcp == NULL) return;
-
-    featlist = fcp->featlist;
-    if (featlist != NULL
-      && featlist->choice == DEFLINE_FEATLIST
-      && IsmRNA (featlist->data.ptrvalue))
-    {
-      if (AddmRNAToClauses (featlist->data.ptrvalue, *clause_list, bsp, suppress_locus_tag))
-      {
-        fcp->delete_me = TRUE;
-      }
-    }
-  } 
-  DeleteFeatureClauses (clause_list);
-}
-
-/* This section of code contains functions for generating labels for
- * clauses for the definition lines.
- */
-
-/* This function examines the specified typeword and determines whether it
- * should appear before or after the description of the feature in the
- * definition line.
- */
-static Boolean IsTypeWordFirst (
-  CharPtr typeword
-)
-{
-  Int4 i;
-  if (typeword == NULL) return FALSE;
-  if (StringCmp (typeword, "exon") == 0
-    || StringCmp (typeword, "intron") == 0
-    || StringCmp (typeword, "endogenous virus") == 0)
-  {
-    return TRUE;
-  }
-  else
-  {
-    i = StartsWithMobileElementKeyword (typeword);
-    if (i >= 0 && i != eMobileElementIntegron) {
-      return TRUE;
-    }
-    return FALSE;
-  }
-}
-
-/* This function determines the word to use to indicate what type of feature
- * is being described in the definition line.  For certain feature types,
- * the word to use in the definition line varies based on the type of
- * molecule in the record.
- */
-static CharPtr GetFeatureTypeWord (
-  Uint1 biomol,
-  SeqFeatPtr sfp
-)
-{
-  if (sfp == NULL) return NULL;
-  if ( IsExon (sfp))
-  {
-    return StringSave ("exon");
-  } 
-  else if(IsIntron (sfp))
-  {
-    return StringSave ("intron");
-  }
-  else if (IsEndogenousVirusSequence (sfp))
-  {
-    return StringSave ("endogenous virus");
-  }
-  else if (IsControlRegion (sfp))
-  {
-    return StringSave ("control region");
-  }
-  else if (IsEndogenousVirusSourceFeature (sfp))
-  {
-    return StringSave ("endogenous virus");
-  }
-  else if (IsDloop (sfp))
-  {
-    return StringSave ("D-loop");
-  }
-  else if (IsLTR (sfp))
-  {
-    return StringSave ("LTR");
-  }
-  else if (Is3UTR (sfp))
-  {
-    return StringSave ("3' UTR");
-  }
-  else if (Is5UTR (sfp))
-  {
-    return StringSave ("5' UTR");
-  }
-  else if (IsOperon (sfp))
-  {
-    return StringSave ("operon");
-  }
-  else if (biomol == MOLECULE_TYPE_GENOMIC || biomol == MOLECULE_TYPE_CRNA)
-  {
-    if (IsPseudo (sfp))
-    {
-      return StringSave ("pseudogene");
-    }
-    else
-    {
-      return StringSave ("gene");
-    }
-  }
-  else if ( IsrRNA (sfp) || IssnoRNA (sfp) || IssnRNA (sfp) || IsscRNA (sfp))
-  {
-    return NULL;
-  }
-  else if (IsPrecursorRNA (sfp))
-  {
-    return StringSave ("precursor RNA");
-  }
-  else if (biomol == MOLECULE_TYPE_MRNA)
-  {
-    if (IsPseudo (sfp))
-    {
-      return StringSave ("pseudogene mRNA");
-    }
-    else
-    {
-      return StringSave ("mRNA");
-    }
-  }
-  else if (biomol == MOLECULE_TYPE_PRE_MRNA)
-  {
-    if (IsPseudo (sfp))
-    {
-      return StringSave ("pseudogene precursor RNA");
-    }
-    else
-    {
-      return StringSave ("precursor RNA");
-    }
-  }
-  else if (biomol == MOLECULE_TYPE_OTHER_GENETIC_MATERIAL)
-  {
-    return StringSave ("gene");
-  }
-  return StringSave ("");
-}
-
-/* Frequently the product associated with a feature is listed as part of the
- * description of the feature in the definition line.  This function determines
- * the name of the product associated with this specific feature.  Some
- * features will be listed with the product of a feature that is associated
- * with the feature being described - this function does not look at other
- * features to determine a product name.
- * If the feature is a misc_feat with particular keywords in the comment,
- * the product will be determined based on the contents of the comment.
- * If the feature is a CDS and is marked as pseudo, the product will be
- * determined based on the contents of the comment.
- * If the feature is a gene and has different strings in the description than
- * in the locus or locus tag, the description will be used as the product for
- * the gene.
- * If none of the above conditions apply, the sequence indexing context label
- * will be used to obtain the product name for the feature.
- */
-static CharPtr GetProductName 
-( SeqFeatPtr cds,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag)
-{
-  CharPtr protein_name;
-  CharPtr semicolon;
-  size_t len_to_copy;
-  SeqMgrFeatContext  context;
-  GeneRefPtr  grp;
-  CharPtr gene_name;
-
-  if (cds == NULL) return NULL;
-  protein_name = NULL;
-  if (IsNoncodingProductFeat (cds))
-  {
-    return GetNoncodingProductFeatProduct (cds);
-  }
-  else if (cds->data.choice == SEQFEAT_CDREGION && cds->pseudo)
-  {
-    if (cds->comment != NULL)
-    {
-      semicolon = StringChr (cds->comment, ';');
-      if (semicolon != NULL)
-      {
-        len_to_copy = semicolon - cds->comment;
-      }
-      else
-      {
-        len_to_copy = StringLen (cds->comment);
-      }
-      protein_name = MemNew (len_to_copy + 1);
-      if (protein_name == NULL) return NULL;
-      StringNCpy (protein_name, cds->comment, len_to_copy);
-      protein_name[len_to_copy] = 0;
-    }
-    return protein_name;
-  }
-  else if (cds->data.choice == SEQFEAT_GENE)
-  {
-    grp = (GeneRefPtr) cds->data.value.ptrvalue;
-    if (grp == NULL) return NULL;
-    gene_name = GetGeneName (grp, suppress_locus_tag);
-    if (grp->desc != NULL
-      && StringCmp (grp->desc, gene_name) != 0)
-    {
-      return StringSave (grp->desc);
-    }
-#if 0
-    /* removed by request from Linda Yankie */    
-    if (grp->locus_tag != NULL && ! suppress_locus_tag
-      && StringCmp (grp->locus_tag, gene_name) != 0)
-    {
-      return StringSave (grp->locus_tag);
-    }
-#endif    
-  }
-  else
-  {
-    if (SeqMgrGetDesiredFeature (0, bsp, 0, 0, cds, &context) == cds
-      && context.label != NULL)
-    {
-      if ( IstRNA (cds) )
-      {
-        if (StringCmp (context.label, "Xxx") == 0) {
-          protein_name = StringSave ("tRNA-OTHER");
-        } else {
-          protein_name = MemNew ( StringLen (context.label) + 6);
-          if ( protein_name == NULL) return NULL;
-          sprintf (protein_name, "tRNA-%s", context.label);
-        }
-        return protein_name;
-      }
-      else if ((IsCDS(cds) && StringCmp (context.label, "CDS") != 0)
-  || (IsmRNA(cds) && StringCmp (context.label, "mRNA") != 0)
-        || (! IsCDS(cds) && ! IsmRNA(cds)))
-      {
-        protein_name = StringSave (context.label);
-        return protein_name;
-      }
-    }
-  }
-  return NULL;
-}
-
-/* This function searches a list of features recursively for a
- * feature that satisfies the itemmatch condition and is associated with
- * the same gene as the fcp clause passed to the function.
- * This is used to obtain a product for a feature that may share a gene with
- * a product-producing feature but may not be contained in the interval of
- * the product-producing feature.
- */
-static FeatureClausePtr FindProductInFeatureList (
-  FeatureClausePtr fcp,
-  ValNodePtr       clause_list,
-  matchFunction    itemmatch,
-  Boolean          suppress_locus_tag)
-{
-  ValNodePtr       vnp;
-  FeatureClausePtr vnp_fcp;
-  
-  for (vnp = clause_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
-    {
-      vnp_fcp = vnp->data.ptrvalue;
-      if (DoGenesMatch (vnp_fcp->grp, fcp->grp, suppress_locus_tag)
-        && vnp_fcp->featlist != NULL
-        && vnp_fcp->featlist->choice == DEFLINE_FEATLIST
-        && itemmatch (vnp_fcp->featlist->data.ptrvalue))
-      {
-        return vnp_fcp;
-      }
-      else
-      {
-        vnp_fcp = FindProductInFeatureList (fcp, vnp_fcp->featlist,
-                                            itemmatch, suppress_locus_tag);
-        if (vnp_fcp != NULL) return vnp_fcp;
-      }
-    }
-  }
-  return NULL;
-}
-
-/* This function uses the available information in the clause to generate
- * a description from the name of the gene (if any) and the name of the
- * product for the feature (if any).
- * If there is only a gene, the description will be the name of the gene.
- * If there is only a product, the description will be the name of the product.
- * If there is a gene and a product, the description will be the name of
- * the product followed by the name of the gene in parentheses.
- */
-static CharPtr GetGeneProtDescription 
-( FeatureClausePtr fcp,
-  BioseqPtr        bsp,
-  Boolean          suppress_locus_tag)
-{
-  SeqFeatPtr    sfp;
-  CharPtr    protein_name;
-  CharPtr    gene_name;
-  size_t    description_length;
-  CharPtr    description;
-
-  if (fcp == NULL
-    || fcp->featlist == NULL
-    || fcp->featlist->data.ptrvalue == NULL)
-  {
-    return NULL;
-  }
-  sfp = fcp->featlist->data.ptrvalue;
-
-  description_length = 0;
-
-  if (fcp->feature_label_data.productname != NULL)
-  {
-    protein_name = StringSave (fcp->feature_label_data.productname);
-  }
-  else
-  {
-    protein_name = GetProductName (sfp, bsp, suppress_locus_tag);
-    if (protein_name == NULL && IsGene (sfp))
-    {
-      
-    }
-  }
-  if (protein_name != NULL)
-  {
-    description_length += StringLen (protein_name);
-  }
-     
-  gene_name = GetGeneName (fcp->grp, suppress_locus_tag);
-  if (gene_name != NULL)
-  {
-    description_length += StringLen (gene_name);
-    if (protein_name != NULL)
-    {
-      description_length += 3;
-    }
-  }
-  description = (CharPtr) MemNew (description_length + 1);
-  if (description == NULL) return NULL;
-  if (protein_name != NULL)
-  {
-    if (gene_name != NULL)
-    {
-      sprintf (description, "%s (%s)", protein_name, gene_name);
-    }
-    else
-    {
-      sprintf (description, "%s", protein_name);
-    }
-  }
-  else
-  {
-    if (gene_name != NULL)
-      sprintf (description, gene_name);
-  }
-  if (protein_name != NULL) MemFree (protein_name);
-  return description;
-}
-
-/* This array of match functions is used to identify, in order of preference,
- * the features that might be used to generate a product for a gene-protein
- * description if the feature has not already been grouped with a product
- * feature.
- */
-static matchFunction productfeatures[] = {
-  IsCDS, IsmRNA, IstRNA
-}; 
-
-/* This function finds gene features without products and looks for 
- * features that might provide products for them.
- */
-static void FindGeneProducts 
-( ValNodePtr clause_list,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag)
-{
-  ValNodePtr       vnp;
-  FeatureClausePtr fcp, productfcp;
-  Int4             i, NumProductFeatureTypes;
-
-  NumProductFeatureTypes = sizeof (productfeatures) / sizeof (matchFunction);
-
-  for (vnp = clause_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_CLAUSEPLUS
-      && (fcp = vnp->data.ptrvalue) != NULL
-      && fcp->featlist != NULL)
-    {
-      if (fcp->featlist->choice == DEFLINE_FEATLIST
-        && IsGene (fcp->featlist->data.ptrvalue)
-        && fcp->feature_label_data.productname == NULL)
-      {
-        productfcp = NULL;
-        for (i=0; i < NumProductFeatureTypes && productfcp == NULL; i++)
-        {
-          productfcp = FindProductInFeatureList (fcp, clause_list,
-                                                 productfeatures[i],
-                                                 suppress_locus_tag);
-        }
-        if (productfcp != NULL)
-        {
-          fcp->is_alt_spliced = productfcp->is_alt_spliced;
-          if (productfcp->feature_label_data.productname != NULL)
-          {
-            fcp->feature_label_data.productname =
-                  StringSave (productfcp->feature_label_data.productname);
-          }
-          else
-          {
-            fcp->feature_label_data.productname
-                  = GetProductName (productfcp->featlist->data.ptrvalue, 
-                                    bsp, suppress_locus_tag);
-          }
-          if (fcp->feature_label_data.description != NULL)
-          {
-            MemFree (fcp->feature_label_data.description);
-            fcp->feature_label_data.description = NULL;
-          }
-          fcp->feature_label_data.description =
-            GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
-        }
-      }
-      else
-      {
-        FindGeneProducts (fcp->featlist, bsp, suppress_locus_tag);
-      }
-    }
-  }
-}
-
-static Boolean ShowInterval (
-  SeqFeatPtr sfp
-)
-{
-  if (IsSatelliteSequence (sfp) || IsExon (sfp) || IsIntron (sfp)
-    || IsPromoter (sfp) || Is3UTR (sfp) || Is5UTR (sfp))
-    return FALSE;
-  return TRUE;
-}
-
-static CharPtr GetExonDescription (
-  BioseqPtr bsp,
-  SeqFeatPtr sfp
-)
-{
-  SeqMgrFeatContext  context;
-  SeqFeatPtr new_sfp;
-  CharPtr    label;
-
-  if ((new_sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, bsp, 0, 0, sfp, &context)) != sfp
-      || context.label == NULL)
-  {
-    if ((new_sfp = SeqMgrGetDesiredFeature (0, bsp, 0, 0, sfp, &context)) != sfp
-      || context.label == NULL)
-    {
-      return NULL;
-    }
-  }
-  if ((IsExon (sfp) && StringCmp (context.label, "exon") == 0)
-    || (IsIntron (sfp) && StringCmp (context.label, "intron") == 0))
-  {
-    return NULL;
-  }
-  
-  label = StringSave (context.label);
-  return label;
-}
-
-static CharPtr GetFeatureDescription 
-( FeatureClausePtr fcp,
-  BioseqPtr        bsp,
-  Boolean          suppress_locus_tag)
-{
-  SeqFeatPtr    sfp;
-
-  if ( fcp == NULL
-    || fcp->featlist == NULL
-    || fcp->featlist->data.ptrvalue == NULL)
-  {
-    return NULL;
-  }
-  sfp = fcp->featlist->data.ptrvalue;
-  if (sfp == NULL) return NULL;
-
-  if (IsExon (sfp) || IsIntron (sfp))
-  {
-    return GetExonDescription (bsp, sfp);
-  }
-  else if (IsEndogenousVirusSequence (sfp))
-  {
-    return GetEndogenousVirusSequenceDescription (sfp);
-  }
-  else if (IsEndogenousVirusSourceFeature (sfp))
-  {
-    return GetEndogenousVirusSourceFeatureDescription (sfp);
-  }
-  else if (IsControlRegion (sfp))
-  {
-    return NULL;
-  }
-  else if (IsDloop (sfp))
-  {
-    return NULL;
-  }
-  else if (Is3UTR (sfp))
-  {
-    return NULL;
-  }
-  else if (Is5UTR (sfp))
-  {
-    return NULL;
-  }
-  else if (IsLTR (sfp))
-  {
-    return GetLTRDescription (sfp);
-  }
-  else
-  {
-    return GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
-  }
-}
-
-static void LIBCALLBACK GetSatelliteFeatureLabel (
-  ValNodePtr      featlist,
-  BioseqPtr       bsp,
-  Uint1           biomol,
-  FeatureLabelPtr flp
-)
-{
-  SeqFeatPtr main_feat;
-  CharPtr    semicolon;
-
-  flp->description = NULL; 
-  flp->typeword = StringSave ("sequence");
-  flp->pluralizable = FALSE;
-  flp->is_typeword_first = FALSE;
- 
-  if (featlist == NULL) return;
-  main_feat = featlist->data.ptrvalue;
-  if (main_feat == NULL) return;
-  if (StringHasNoText (main_feat->comment)) return;
-
-  flp->description = StringSave (main_feat->comment);
-  if ((semicolon = StringStr (flp->description, ";")) != NULL)
-  {
-    *semicolon = 0;
-  }
-}
-
-static void LIBCALLBACK GetPromoterFeatureLabel (
-  ValNodePtr      featlist,
-  BioseqPtr       bsp,
-  Uint1           biomol,
-  FeatureLabelPtr flp
-)
-{
-  SeqFeatPtr main_feat;
-  
-  flp->description = NULL;
-  flp->typeword = StringSave ("promoter region");
-
-  if (featlist == NULL) return;
-  main_feat = featlist->data.ptrvalue;
-  if (main_feat == NULL) return;
-
-  flp->description =  NULL;
-  flp->pluralizable = FALSE;
-  flp->is_typeword_first = FALSE;
-
-}
-
-/* This function temporarily removes a 3' UTR clause from the end of
- * a clause list so that it will not be included in the list of subfeatures
- * before a CDS in the definition line.
- * The 3' UTR clause should be put back if it was not the only clause in the
- * list.
- */
-static ValNodePtr Remove3UTRFromEndOfFeatList (ValNodePtr PNTR featlist)
-{
-  ValNodePtr vnp, prev = NULL;
-  
-  if (featlist == NULL || *featlist == NULL) return NULL;
-  
-  for (vnp = *featlist; vnp != NULL && vnp->next != NULL; vnp = vnp->next)
-  {
-    prev = vnp;
-  }
-  if (vnp->choice == DEFLINE_CLAUSEPLUS && Is3UTRClause (vnp->data.ptrvalue))
-  {
-    if (prev == NULL)
-    {
-      *featlist = NULL;
-    }
-    else
-    {
-      prev->next = NULL;        
-    }
-  }
-  else
-  {
-    vnp = NULL;
-  }
-  return vnp;
-}
-
-static Uint1 GetMoleculeType (BioseqPtr bsp, Uint2     entityID);
-static void ConsolidateClauses (
-  ValNodePtr PNTR list,
-  BioseqPtr  bsp,
-  Uint1      biomol,
-  Boolean    delete_now,
-  Boolean    suppress_locus_tag);
-
-
-/* This function calculates the "interval" for a clause in the definition
- * line.  The interval could be an empty string, it could indicate whether
- * the location of the feature is partial or complete and whether or not
- * the feature is a CDS, the interval could be a description of the
- * subfeatures of the clause, or the interval could be a combination of the
- * last two items if the feature is a CDS.
- */
-static CharPtr GetGenericInterval 
-( FeatureClausePtr fcp,
-  Uint1            biomol,
-  BioseqPtr        bsp,
-  Boolean          suppress_locus_tag)
-{
-  CharPtr    interval;
-  Boolean    partial5, partial3;
-  SeqFeatPtr sfp;
-  ValNodePtr featlist, strings, prev_feat;
-  CharPtr    subfeatlist;
-  Int4       len;
-  Boolean    suppress_final_and;
-  ValNodePtr utr3vnp = NULL;
-  ValNodePtr last_feat;
-  Uint1      molecule_type;
-
-  if ( fcp == NULL || fcp->featlist == NULL) return NULL;
-  if (fcp->is_unknown) return NULL;
-  featlist = fcp->featlist;
-  sfp = featlist->data.ptrvalue;
-  if (sfp == NULL) return NULL;
-  if ( IsExon (sfp) && fcp->is_alt_spliced)
-  {
-    return StringSave ("alternatively spliced");
-  }
-  if ( ! ShowInterval (sfp)) return NULL;
-
-  subfeatlist = NULL;
-  len = 50;
-  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
-
-  strings = NULL;
-  prev_feat = NULL;
-  while (featlist != NULL && featlist->choice != DEFLINE_CLAUSEPLUS)
-  {
-    prev_feat = featlist;
-    featlist = featlist->next;
-  }
-  if (IsCDS (sfp))
-  {
-    utr3vnp = Remove3UTRFromEndOfFeatList (&featlist);
-  }
-  if (featlist != NULL)
-  {
-    suppress_final_and = FALSE;
-    if (( IsCDS (sfp) && ! fcp->clause_info_only)
-        || utr3vnp != NULL)
-    {
-      suppress_final_and = TRUE;
-    }
-    LabelClauses (featlist, biomol, bsp, suppress_locus_tag);
-    
-    molecule_type = GetMoleculeType (bsp, bsp->idx.entityID);
-    /* consolidate genes/proteins with the same names (usually hypothetical proteins) */
-    ConsolidateClauses (&featlist, bsp, molecule_type, TRUE,
-                        suppress_locus_tag);
-
-    /* make sure featlist is still intact - may have consolidated it */
-    if (prev_feat == NULL)
-    {
-      fcp->featlist = featlist;
-    }
-    else
-    {
-      prev_feat->next = featlist;
-    }
-
-    ListClauses (featlist, &strings, FALSE, suppress_final_and);
-    subfeatlist = MergeValNodeStrings (strings, FALSE);
-	  ValNodeFreeData (strings);
-    len += StringLen (subfeatlist) + 7;
-    
-    if (utr3vnp != NULL)
-    {
-      len += 14;
-    }
-  }
-
-  interval = (CharPtr) MemNew (len * sizeof (Char));
-  if (interval == NULL) return NULL;
-  interval[0] = 0;
-
-  if (StringDoesHaveText (subfeatlist))
-  {
-    StringCat (interval, subfeatlist);
-    if ( ! IsCDS (sfp) || fcp->clause_info_only)
-    {
-      if (utr3vnp != NULL)
-      {
-        if (featlist->next != NULL)
-        {
-          StringCat (interval, ",");
-        }
-        StringCat (interval, " and 3' UTR");
-        /* put 3' UTR back at end of featlist */
-        if (featlist != NULL)
-        {
-          last_feat = featlist;
-          while (last_feat != NULL && last_feat->next != NULL)
-          {
-            last_feat = last_feat->next;
-          }
-          last_feat->next = utr3vnp;
-        }
-      }
-      if (subfeatlist != NULL) MemFree (subfeatlist);
-      return interval;
-    }
-    if (utr3vnp == NULL)
-    {
-      StringCat (interval, " and ");
-    }
-    else
-    {
-      StringCat (interval, ", ");
-    }
-  }
-
-  if (FeatureDoesNotGetPartialComplete (sfp)) 
-  {
-    /* don't add partial or complete */
-  } 
-  else if (partial5 || partial3)
-  {
-    StringCat (interval, "partial ");
-  }
-  else
-  {
-    StringCat (interval, "complete ");
-  }
-  if (IsCDS (sfp) && ! IsPseudo (sfp))
-  {
-    StringCat (interval, "cds");
-    if (fcp->is_alt_spliced)
-      StringCat (interval, ", alternatively spliced");
-  }
-  else
-  {
-    StringCat (interval, "sequence");
-    if (IsNoncodingProductFeat (sfp) && fcp->is_alt_spliced)
-    {
-      StringCat (interval, ", alternatively spliced");
-    }
-  }
-  
-  if (utr3vnp != NULL)
-  {
-    /* tack UTR3 on at end of clause */
-    if (StringDoesHaveText (subfeatlist))
-    {
-      StringCat (interval, ",");
-    }
-    StringCat (interval, " and 3' UTR");
-    
-    /* put 3' UTR back at end of featlist */
-    if (featlist != NULL)
-    {
-      last_feat = featlist;
-      while (last_feat != NULL && last_feat->next != NULL)
-      {
-        last_feat = last_feat->next;
-      }
-      last_feat->next = utr3vnp;
-    }
-  }
-  
-  if (subfeatlist != NULL) MemFree (subfeatlist);    
-  
-  return interval;
-} 
-
-/* This function is used to generate feature label information for
- * a feature clause.  It is called by the LabelFeature function if
- * a "GetFeatureLabel" function is not found for the specific feature
- * type.
- * In the future it may be advisable to create "GetFeatureLabel" functions
- * for more of the specific feature types, to reduce the number of times
- * that the feature must be identified as being a certain type.
- */ 
-static void LIBCALLBACK GetGenericFeatureLabel 
-( FeatureClausePtr fcp,
-  BioseqPtr        bsp,
-  Uint1            biomol,
-  FeatureLabelPtr  flp,
-  Boolean          suppress_locus_tag)
-{
-  SeqFeatPtr main_feat;
-  
-  if (fcp == NULL
-    || fcp->featlist == NULL
-    || fcp->featlist->data.ptrvalue == NULL)
-  {
-    return;
-  }
-  main_feat = fcp->featlist->data.ptrvalue;
-  if (main_feat == NULL) return;
-
-  if (flp->typeword == NULL)
-  {
-    flp->typeword = GetFeatureTypeWord (biomol, main_feat);
-    flp->is_typeword_first = IsTypeWordFirst (flp->typeword);
-    flp->pluralizable = TRUE;
-  }
-  if (flp->productname == NULL)
-  {
-    flp->productname = GetProductName (main_feat, bsp, suppress_locus_tag);
-  }
-  if (flp->description == NULL
-    && (! IsMiscRNA (main_feat)
-      || StringStr (flp->productname, "spacer") == NULL ))
-  {
-    flp->description = GetFeatureDescription (fcp, bsp, suppress_locus_tag);
-  }
-
-}
-
-typedef void (LIBCALLBACK *GetFeatureLabelFunction) (
-  ValNodePtr      featlist,
-  BioseqPtr       bsp,
-  Uint1           biomol,
-  FeatureLabelPtr flp
-);
-
-typedef struct matchlabelfunction {
-  matchFunction           itemmatch;
-  GetFeatureLabelFunction labelfunction;
-} MatchLabelFunctionData, PNTR MatchLabelFunctionPtr;
-
-static MatchLabelFunctionData label_functions[] = {
- { IsSatelliteSequence, GetSatelliteFeatureLabel         },
- { IsMobileElement,     GetMobileElementFeatureLabel        },
- { IsPromoter,          GetPromoterFeatureLabel          },
- { IsIntergenicSpacer,  GetIntergenicSpacerFeatureLabel  },
- { IsGeneCluster,       GetGeneClusterFeatureLabel       }
-};
-
-typedef enum {
- DEFLINE_FEATLABEL_Satellite = 0,
- DEFLINE_FEATLABEL_Transposon,
- DEFLINE_FEATLABEL_Promoter,
- DEFLINE_FEATLABEL_IntergenicSpacer,
- DEFLINE_FEATLABEL_GeneCluster,
- NumDefLineFeatLabels
-} DefLineFeatLabel;
-
-static void LabelFeature 
-( BioseqPtr        bsp,
-  Uint1            biomol,
-  FeatureClausePtr new_clauseplus,
-  Boolean          suppress_locus_tag)
-{
-  Int4             i;
-  SeqFeatPtr       main_feat;
-
-  if (new_clauseplus == NULL || new_clauseplus->featlist == NULL) return;
-
-  if (new_clauseplus->featlist->choice == DEFLINE_FEATLIST)
-  {
-    main_feat = (SeqFeatPtr) new_clauseplus->featlist->data.ptrvalue;
-    
-    new_clauseplus->allelename = GetAlleleName (new_clauseplus->grp,
-                                                suppress_locus_tag);
-    if (new_clauseplus->interval == NULL)
-    {
-      new_clauseplus->interval =
-                  GetGenericInterval (new_clauseplus, biomol, bsp, suppress_locus_tag);
-    }
-
-    for (i=0; i < NumDefLineFeatLabels; i++)
-    {
-      if (label_functions [i].itemmatch (main_feat))
-      {
-        label_functions [i].labelfunction ( new_clauseplus->featlist,
-                                          bsp, biomol,
-                                          &new_clauseplus->feature_label_data);
-        return;
-      }
-    }
-
-    GetGenericFeatureLabel ( new_clauseplus, bsp, biomol, 
-                           &new_clauseplus->feature_label_data, suppress_locus_tag);
-    return;
-  }
-}
-
-/* This function is used to calculate the parts of a product name that
- * are "the same" for use as the name of an alternatively spliced product.
- * The common portion of the string must end at a recognized separator,
- * such as a space, comma, or dash instead of in the middle of a word.
- * The matching portions of the string could occur at the beginning or end
- * of the string, or even occasionally at the beginning and end of a
- * string, but not as the center of the string with a different beginning
- * and ending.
- */
-static CharPtr FindStringIntersection (
-  CharPtr str1,
-  CharPtr str2,
-  Boolean str1_previously_stripped
-)
-{
-  Int4 matchleftlen = 0;
-  Int4 matchlefttoken = 0;
-  Int4 matchrightidx1 = 0;
-  Int4 matchrightidx2 = 0;
-  Int4 matchrighttoken = 0;
-  CharPtr match_string;
-  Int4 len1;
-  Int4 len2;
-  Int4 match_len;
-
-  if (str1 == NULL || str2 == NULL) return NULL;
-  if (StringCmp (str1, str2) == 0) return StringSave (str1);
-  len1 = StringLen (str1);
-  len2 = StringLen (str2);
-
-  while (str1[matchleftlen] != 0 && str2[matchleftlen] != 0
-         && str1[matchleftlen] == str2[matchleftlen])
-  {
-    if (str1 [matchleftlen] == ','
-      || str1 [matchleftlen] == '-')
-    {
-      matchlefttoken = matchleftlen;
-    }
-    else if (str1 [matchleftlen] == ' '
-      && matchlefttoken != matchleftlen - 1)
-    {
-      matchlefttoken = matchleftlen;
-    }
-    matchleftlen++;
-  }
-  if (matchleftlen == len1 && str1_previously_stripped) 
-  {
-    matchlefttoken = matchleftlen;
-  }
-  else
-  {
-    matchleftlen = matchlefttoken;
-  }
-
-  matchrightidx1 = len1;
-  matchrightidx2 = len2;
-
-  while (matchrightidx1 > -1 && matchrightidx2 > -1
-         && str1[matchrightidx1] == str2[matchrightidx2])
-  {
-    if (str1 [matchrightidx1] == ' '
-      || str1[matchrightidx1] == ','
-      || str1[matchrightidx1] == '-')
-    {
-      matchrighttoken = matchrightidx1;
-    }
-    matchrightidx1--;
-    matchrightidx2--;
-  }
-  if (matchrightidx1 == -1)
-  {
-    matchrighttoken = matchrightidx1;
-  }
-  else if (matchrighttoken > 0) 
-  {
-    matchrightidx1 = matchrighttoken;
-  } 
-  else if (str1_previously_stripped && matchrightidx1 < len1 - 1)
-  {
-    /* matchrightidx1 = matchrighttoken; */
-    /* do nothing, leave right index where it is */
-  }
-  else
-  {
-    matchrightidx1 = len1;
-  }
-
-  match_len = matchleftlen;
-  if (matchrightidx1 < len1 - 1)
-  {
-    match_len += len1 - matchrightidx1 - 1;
-  }
-
-  if (match_len <= 0) return NULL;
-
-  match_string = MemNew (match_len + 2);
-  if (match_string == NULL) return NULL;
-  if (matchleftlen != 0)
-  {
-    StringNCpy (match_string, str1, matchleftlen);
-    match_string[matchleftlen] = 0;
-  }
-  else
-  {
-    match_string[0] = 0;
-  }
-  if (matchrightidx1 < len1)
-  {
-    if (match_string[0] != 0) StringCat (match_string, " ");
-    StringCat (match_string, str1 + matchrightidx1 + 1);
-  }
-  return match_string;
-}
-
-/* These are the words that are used to introduced the part of the protein
- * name that differs in alt-spliced products - they should not be part of
- * the alt-spliced product name.
- * Note that splice variant is listed before "variant" so that it will be
- * found first and "variant" will not be removed from "splice variant", leaving
- * splice as an orphan.
- */
-
-static CharPtr UnwantedWords [] = {
- "splice variant",
- "splice product",
- "variant",
- "isoform"
-};
-
-static void TrimUnwantedWordsFromAltSpliceProductName (
-  CharPtr productname
-)
-{
-  Int4    num_unwanted_words, i;
-  size_t  unwanted_word_len;
-  CharPtr cp, tmp;
-  
-  num_unwanted_words = sizeof (UnwantedWords) / sizeof (CharPtr);
-  for (i = 0; i < num_unwanted_words; i++)
-  {
-    unwanted_word_len = StringLen (UnwantedWords [i]);
-    cp = StringStr (productname, UnwantedWords [i]);
-    if (cp != NULL)
-    {
-      if (cp == productname)
-      {
-        /* word occurs in beginning of phrase */
-        tmp = StringSave (productname + unwanted_word_len);
-        StringCpy (productname, tmp);
-        MemFree (tmp);
-      }
-      else if (cp - productname < StringLen (productname) - unwanted_word_len)
-      {
-        /* word occurs in middle of phrase */
-        tmp = StringSave (cp + unwanted_word_len);
-        StringCpy (cp - 1, tmp);
-        MemFree (tmp);
-      }
-      else
-      {
-        /* word occurs at end of phrase */
-        *cp = 0;
-      }
-    }
-  }
-}
-
-
-static Boolean PreviouslyStripped (SeqFeatPtr cds, BioseqPtr bsp, CharPtr productname)
-{
-  CharPtr expected_product_name;
-  Boolean rval = FALSE;
-  
-  if (cds == NULL || StringHasNoText (productname)) return FALSE;
-  expected_product_name = GetProductName (cds, bsp, FALSE);
-  if (StringCmp (productname, expected_product_name) != 0) {
-    rval = TRUE;
-  }
-  expected_product_name = MemFree (expected_product_name);
-  return rval;
-}
-
-/* This function determines whether two CDSs meet the conditions for
- * alternative splicing, and if so, it returns the name of the alternatively
- * spliced product.  In order to be alternatively spliced, the two CDSs 
- * must have the same gene, must share a complete interval, and must have
- * similarly named products.
- */
-static CharPtr MeetAltSpliceRules 
-( FeatureClausePtr cdsfcp1,
-  FeatureClausePtr cdsfcp2,
-  BioseqPtr        bsp,
-  Boolean          suppress_locus_tag)
-{
-  SeqFeatPtr cds1, cds2;
-  CharPtr match_string;
-  Int4    res;
-  
-  if (cdsfcp1 == NULL || cdsfcp2 == NULL
-    || cdsfcp1->featlist == NULL || cdsfcp2->featlist == NULL)
-  {
-    return NULL;
-  }
-
-  cds1 = cdsfcp1->featlist->data.ptrvalue;
-  cds2 = cdsfcp2->featlist->data.ptrvalue;
-  if (! DoGenesMatch (cdsfcp1->grp, cdsfcp2->grp, suppress_locus_tag))
-    return NULL;
-
-  if ( (res = TestFeatOverlap (cds1, cds2, COMMON_INTERVAL)) != -1)
-  {
-    match_string = FindStringIntersection (
-                     cdsfcp1->feature_label_data.productname,
-                     cdsfcp2->feature_label_data.productname,
-                     PreviouslyStripped(cds1, bsp, cdsfcp1->feature_label_data.productname));
-    return match_string;
-  }
-  return NULL;
-}
-
-/* This function is used by the FindAltSplices function to locate the
- * next CDS in a list of feature clauses.
- */
-static ValNodePtr FindNextCDSClause (ValNodePtr vnp)
-{
-  FeatureClausePtr fcp;
-
-  while (vnp != NULL)
-  {
-    if (vnp->choice == DEFLINE_CLAUSEPLUS)
-    {
-      fcp = vnp->data.ptrvalue;
-      if (fcp != NULL && !fcp->delete_me && fcp->featlist != NULL
-        && IsCDS (fcp->featlist->data.ptrvalue))
-      {
-        return vnp;
-      }
-    }
-    vnp = vnp->next;
-  }
-  return NULL;
-}
-
-/* This function is used by the FindAltSplices function to move the features
- * and subclauses from the second CDS in an alternatively spliced pair of 
- * CDSs to the feature clause for the first CDS, so that the subfeatures
- * can be properly listed.
- */
-static void MoveSubclauses (
-  FeatureClausePtr dstfcp,
-  FeatureClausePtr srcfcp
-)
-{
-  ValNodePtr dst_last_feat, dst_first_clause, dst_last_clause;
-  ValNodePtr src_last_feat, src_first_clause;
-
-  if (dstfcp == NULL || srcfcp == NULL || srcfcp->featlist == NULL) return;
-
-  dst_first_clause = NULL;
-  dst_last_clause = NULL;
-  src_first_clause = NULL;
-
-  dst_last_feat = dstfcp->featlist;
-  while (dst_last_feat != NULL 
-      && dst_last_feat->next != NULL
-      && dst_last_feat->next->choice == DEFLINE_FEATLIST)
-  {
-    dst_last_feat = dst_last_feat->next;
-  }
-  if (dst_last_feat != NULL)
-  {
-    dst_first_clause = dst_last_feat->next;
-  }
-  dst_last_clause = dst_first_clause;
-  while (dst_last_clause != NULL && dst_last_clause->next != NULL)
-  {
-    dst_last_clause = dst_last_clause->next;
-  }
-
-  src_last_feat = srcfcp->featlist;
-  while (src_last_feat != NULL 
-      && src_last_feat->next != NULL
-      && src_last_feat->next->choice == DEFLINE_FEATLIST)
-  {
-    src_last_feat = src_last_feat->next;
-  }
-  if (src_last_feat != NULL)
-  {
-    src_first_clause = src_last_feat->next;
-  }
-
-  /* insert features before clauses */
-  if (dst_last_feat == NULL)
-  {
-    dstfcp->featlist = srcfcp->featlist;
-    dst_last_feat = src_last_feat;
-  }
-  else
-  {
-    dst_last_feat->next = srcfcp->featlist;
-  }
-  /* insert clauses after feats */
-  if (dst_first_clause != NULL)
-  {
-    src_last_feat->next = dst_first_clause;
-    dst_last_clause->next = src_first_clause;
-  }
-  srcfcp->featlist = NULL;
-}
- 
-/* we want to look through the list for CDS features */
-/* if we find two CDSs that are alternatively spliced, */
-/* we replace the first alternatively spliced CDS feature */
-/* with a new CDS feature that has the new protein name as */
-/* a comment and a data.choice value that indicates alt splicing */
-/* we remove the second alternatively spliced CDS feature from the list */
-
-static void FindAltSplices 
-( ValNodePtr clause_list,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag)
-{
-  FeatureClausePtr  fcp1, fcp2;
-  ValNodePtr cdsclause1, cdsclause2;
-  ValNodePtr searchclause;
-  CharPtr  combined_protein_name;
-  Boolean    partial3_1, partial5_1, partial3_2, partial5_2;
-  Int4       left1, left2, right1, right2;
-
-  if (clause_list == NULL) return;
-  
-  cdsclause1 = FindNextCDSClause (clause_list);
-  while (cdsclause1 != NULL)
-  {
-    fcp1 = (FeatureClausePtr) cdsclause1->data.ptrvalue;
-    if (fcp1->feature_label_data.productname == NULL)
-    {
-      fcp1->feature_label_data.productname = 
-           GetProductName (fcp1->featlist->data.ptrvalue, bsp, suppress_locus_tag);
-    }
-    searchclause = cdsclause1->next;
-    cdsclause2 = FindNextCDSClause (searchclause);
-    while (cdsclause2 != NULL) 
-    {
-      fcp2 = (FeatureClausePtr) cdsclause2->data.ptrvalue;
-      if (fcp2->feature_label_data.productname == NULL)
-      {
-        fcp2->feature_label_data.productname =
-           GetProductName (fcp2->featlist->data.ptrvalue, bsp, suppress_locus_tag);
-      }
-      combined_protein_name = MeetAltSpliceRules (fcp1, fcp2, bsp, suppress_locus_tag);
-      if (combined_protein_name != NULL)
-      {
-        /* get rid of variant, splice variant, splice product, isoform, etc.*/
-        TrimUnwantedWordsFromAltSpliceProductName (combined_protein_name);
-
-        /* get rid of trailing spaces in protein name */
-        TrimSpacesAroundString (combined_protein_name);
-
-        /* copy new protein name into first clause */
-        MemFree (fcp1->feature_label_data.productname);
-        fcp1->feature_label_data.productname = combined_protein_name;
-        CheckSeqLocForPartial (fcp1->slp, &partial5_1, &partial3_1);
-        left1 = GetOffsetInBioseq (fcp1->slp, bsp, SEQLOC_LEFT_END);
-        right1 = GetOffsetInBioseq (fcp1->slp, bsp, SEQLOC_RIGHT_END);
-        CheckSeqLocForPartial (fcp2->slp, &partial5_2, &partial3_2);
-        left2 = GetOffsetInBioseq (fcp2->slp, bsp, SEQLOC_LEFT_END);
-        right2 = GetOffsetInBioseq (fcp2->slp, bsp, SEQLOC_RIGHT_END);
-        fcp1->slp = SeqLocMerge (bsp, fcp1->slp, fcp2->slp,
-                                 FALSE, TRUE, FALSE);
-        if (left1 == left2)
-        {
-          partial5_1 |= partial5_2;
-        }
-        else
-        {
-          partial5_1 = left1 < left2 ? partial5_1 : partial5_2;
-        }
-        if (right1 == right2)
-        {
-          partial3_1 |= partial3_2;
-        }
-        else
-        {
-          partial3_1 = right1 > right2 ? partial3_1 : partial3_2;
-        }
-        SetSeqLocPartial (fcp1->slp, partial5_1, partial3_1);
-        fcp1->is_alt_spliced = TRUE;
-
-        /* copy over fcp2 subclauses */
-        MoveSubclauses (fcp1, fcp2);
-
-        /* remove second clause */
-        fcp2->delete_me = TRUE;
-      }
-      searchclause = cdsclause2->next;
-      cdsclause2 = FindNextCDSClause (searchclause);
-    }
-    cdsclause1 = FindNextCDSClause (cdsclause1->next);
-  } 
-  DeleteFeatureClauses (&clause_list);
-}
-
-static void LabelClauses 
-( ValNodePtr clause_list,
-  Uint1      biomol,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag)
-{
-  ValNodePtr clause;
- 
-  clause = clause_list;
-  while (clause != NULL)
-  { 
-    LabelFeature ( bsp, biomol, clause->data.ptrvalue, suppress_locus_tag);
-    clause = clause->next;
-  }
-}
-
-static CharPtr misc_words [] = {
-  "internal transcribed spacer",
-  "external transcribed spacer",
-  "ribosomal RNA intergenic spacer",
-  "ribosomal RNA",
-  "intergenic spacer"
-};
-
-typedef enum {
-  MISC_RNA_WORD_INTERNAL_SPACER = 0,
-  MISC_RNA_WORD_EXTERNAL_SPACER,
-  MISC_RNA_WORD_RNA_INTERGENIC_SPACER,
-  MISC_RNA_WORD_RNA,
-  MISC_RNA_WORD_INTERGENIC_SPACER,
-  NUM_MISC_RNA_WORDS
-} MiscWord;
-
-static CharPtr separators [] = {
-  ", and ",
-  " and ",
-  ", ",
-  "; "
-};
-
-#define num_separators 3
-
-static ValNodePtr GetMiscRNAelements 
-( SeqFeatPtr misc_rna,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag)
-{
-  CharPtr buffer;
-  Int4    i, best_i;
-  CharPtr cansep [num_separators];
-  CharPtr dataval;
-  Int4    datalen;
-  FeatureClausePtr fcp;
-  FeatureClausePtr lastfcp;
-  Int4    num_clauses;
-  ValNodePtr head, vnp;
-  Boolean partial5, partial3;
-  Int4    word_i;
-  CharPtr to_free;
-  CharPtr word_loc;
-
-  to_free = NULL;
-
-  if (misc_rna == NULL) return NULL;
-  buffer = GetProductName (misc_rna, bsp, suppress_locus_tag);
-  to_free = buffer;
-  if (buffer == NULL) 
-  {
-    buffer = misc_rna->comment;
-  }
-  else if (StringNCmp (buffer, misc_rna->comment, StringLen (buffer) -1) == 0
-    && buffer [ StringLen (buffer) - 1] == '>')
-  {
-    MemFree (buffer);
-    to_free = NULL;
-    buffer = misc_rna->comment;
-  }
-
-  if ( StringStr (buffer, "spacer") == NULL)
-  {
-    if (to_free != NULL)
-    {
-      MemFree (to_free);
-    }
-    return NULL;
-  }
-  
-  if (StringNCmp (buffer, "contains ", 9) == 0)
-  {
-    buffer = buffer + 9;
-  }
-
-  head = NULL;
-  CheckSeqLocForPartial (misc_rna->location, &partial5, &partial3);
-  num_clauses = 0;
-
-  while (buffer != NULL 
-         && buffer[0] != 0)
-  {
-    best_i = -1;
-    for (i=0; i < num_separators; i++)
-    {
-      cansep [i] = StringStr (buffer, separators [i]);
-      if (cansep [i] != NULL 
-        && (best_i == -1 
-          || cansep [i] < cansep [best_i]))
-      {
-        best_i = i;
-      }
-    }
-
-    if (best_i == -1)
-    {
-      datalen = StringLen (buffer);
-    }
-    else
-    {
-      datalen = cansep [best_i] - buffer;
-    }
-
-    dataval = MemNew (datalen + 1);
-    if (dataval == NULL) return NULL;
-    StringNCpy (dataval, buffer, datalen);
-    dataval [datalen] = 0;
-
-    for (word_i=0;
-         word_i < NUM_MISC_RNA_WORDS
-           && (word_loc = StringStr (dataval, misc_words [word_i])) == NULL;
-         word_i++) {}
-    if (word_i < NUM_MISC_RNA_WORDS)
-    {
-      fcp = NewFeatureClause ( misc_rna, bsp, suppress_locus_tag);
-      if (fcp == NULL) return NULL;
-      if (word_i == MISC_RNA_WORD_INTERNAL_SPACER
-        || word_i == MISC_RNA_WORD_EXTERNAL_SPACER
-        || word_i == MISC_RNA_WORD_RNA_INTERGENIC_SPACER
-        || word_i == MISC_RNA_WORD_INTERGENIC_SPACER)
-      {
-        if (word_loc == dataval)
-        {
-          fcp->feature_label_data.is_typeword_first = TRUE;
-          fcp->feature_label_data.typeword = StringSave (misc_words [word_i]);
-          if (StringLen (misc_words [word_i]) + 1 < StringLen (dataval))
-          {
-            fcp->feature_label_data.description =
-                  StringSave ( dataval + StringLen (misc_words [word_i]) + 1);
-          }
-        }
-        else
-        {
-          fcp->feature_label_data.is_typeword_first = FALSE;
-          fcp->feature_label_data.typeword = StringSave (misc_words [word_i]);
-          if (StringLen (misc_words [word_i]) + 1 < StringLen (dataval))
-          {
-            fcp->feature_label_data.description =
-                  StringSave ( dataval);
-            fcp->feature_label_data.description [word_loc - dataval - 1] = 0;
-          }
-        }
-        MemFree (dataval);
-      }
-      else if (word_i == MISC_RNA_WORD_RNA)
-      {
-        fcp->feature_label_data.description = dataval;
-      }
-      if (num_clauses == 0 && partial5)
-      {
-        fcp->interval = StringSave ("partial sequence");
-      }
-      else
-      {
-        fcp->interval = StringSave ("complete sequence");
-      }
-   
-      num_clauses ++;
-      lastfcp = fcp;
-      
-      vnp = ValNodeNew (head);
-      if (head == NULL) head = vnp;
-      if (vnp == NULL) return NULL;
-      vnp->data.ptrvalue = fcp;
-      vnp->choice = DEFLINE_CLAUSEPLUS;
-    }
-    else
-    {
-      MemFree (dataval);
-    }
-    buffer += datalen;
-    if (best_i != -1)
-    {
-      buffer += StringLen ( separators [best_i]);
-    }
-  }
-
-  if ((num_clauses == 1 && partial3 && ! partial5)
-    || (num_clauses > 1 && partial3))
-  {
-    MemFree (lastfcp->interval);
-    lastfcp->interval = StringSave ("partial sequence");
-  }
-  if (to_free != NULL) MemFree (to_free);
-  return head;
-}
-
-/* Some misc_RNA clauses have a comment that actually lists multiple
- * features.  This function creates a clause for each element in the
- * comment and inserts the list of new clauses into the feature list
- * at the point where the single previous clause was.
- */
-static void ReplaceRNAClauses (
-  ValNodePtr PNTR clause_list,
-  BioseqPtr       bsp,
-  Boolean         suppress_locus_tag)
-{
-  FeatureClausePtr fcp;
-  SeqFeatPtr main_feat;
-  ValNodePtr clause, replacement_clauses, nextclause, vnp;
-
-  if (clause_list == NULL || *clause_list == NULL) return;
-  clause = *clause_list;
-  while (clause != NULL)
-  {
-    nextclause = clause->next;
-    fcp = (clause->data.ptrvalue);
-    if (fcp == NULL
-      || fcp->featlist == NULL
-      || fcp->featlist->choice != DEFLINE_FEATLIST)
-    {
-      return;
-    }
-    main_feat = (SeqFeatPtr) fcp->featlist->data.ptrvalue;
-  
-    if (IsrRNA (main_feat) || IsMiscRNA (main_feat))
-    {
-      replacement_clauses = GetMiscRNAelements ( main_feat, bsp, suppress_locus_tag );
-      if (replacement_clauses != NULL)
-      {
-        for (vnp = replacement_clauses; vnp->next != NULL; vnp = vnp->next) {}
-        vnp->next = clause->next;
-        clause->next = replacement_clauses;
-        fcp->delete_me = TRUE;
-      }
-    }
-    clause = nextclause;
-  }
-  DeleteFeatureClauses (clause_list);
-}
-
-/* Some misc_feat clauses have a comment that lists one or more tRNAs and
- * an intergenic spacer.  This function creates a clause for each element 
- * in the comment and inserts the list of new clauses into the feature list
- * at the point where the single previous clause was.
- */
-static void ReplaceIntergenicSpacerClauses (
-  ValNodePtr PNTR clause_list,
-  BioseqPtr       bsp,
-  Boolean         suppress_locus_tag)
-{
-  FeatureClausePtr fcp;
-  SeqFeatPtr main_feat;
-  ValNodePtr clause, replacement_clauses, nextclause, vnp;
-
-  if (clause_list == NULL || *clause_list == NULL) return;
-  clause = *clause_list;
-  while (clause != NULL)
-  {
-    nextclause = clause->next;
-    fcp = (clause->data.ptrvalue);
-    if (fcp == NULL
-      || fcp->featlist == NULL
-      || fcp->featlist->choice != DEFLINE_FEATLIST)
-    {
-      return;
-    }
-    main_feat = (SeqFeatPtr) fcp->featlist->data.ptrvalue;
-  
-    if (IsIntergenicSpacer (main_feat) 
-        && (replacement_clauses = ParsetRNAIntergenicSpacerElements ( main_feat, bsp, suppress_locus_tag)) != NULL)
-    {
-      for (vnp = replacement_clauses; vnp->next != NULL; vnp = vnp->next) {}
-      vnp->next = clause->next;
-      clause->next = replacement_clauses;
-      fcp->delete_me = TRUE;
-    }
-    clause = nextclause;
-  }
-  DeleteFeatureClauses (clause_list);
-}
-
-/* If we are applying a different rule for misc_feats, we need to recalculate
- * their descriptions.
- */
-static void RenameMiscFeats (ValNodePtr clause_list, Uint1 biomol)
-{
-  ValNodePtr       vnp, featlist;
-  FeatureClausePtr fcp, featlistclause;
-  SeqFeatPtr       sfp;
-  Int4             name_len;
-
-  for (vnp = clause_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice != DEFLINE_CLAUSEPLUS || vnp->data.ptrvalue == NULL)
-    {
-      continue;
-    }
-    fcp = vnp->data.ptrvalue;
-    for (featlist = fcp->featlist; featlist != NULL; featlist = featlist->next)
-    {
-      if ( featlist->data.ptrvalue == NULL)
-      {
-        continue;
-      }
-      if (featlist->choice == DEFLINE_CLAUSEPLUS)
-      {
-        featlistclause = featlist->data.ptrvalue;
-        RenameMiscFeats (featlistclause->featlist, biomol);
-        continue;
-      }
-      if (featlist->choice != DEFLINE_FEATLIST)
-      {
-        continue;
-      }
-      sfp = featlist->data.ptrvalue;
-      if (sfp->idx.subtype != FEATDEF_misc_feature
-        || sfp->comment == NULL
-        || IsIntergenicSpacer (sfp)
-        || IsGeneCluster (sfp)
-        || IsControlRegion (sfp)) 
-      {
-        continue;
-      }
-      if (fcp->feature_label_data.description != NULL) 
-      {
-        fcp->feature_label_data.description
-                   = MemFree (fcp->feature_label_data.description);
-      }
-      name_len = StringCSpn (sfp->comment, ";");
-	  /* make sure we have space for terminating NULL */
-      fcp->feature_label_data.description = MemNew ((name_len + 1) * sizeof (Char));
-      if (fcp->feature_label_data.description == NULL) return;
-      StringNCpy (fcp->feature_label_data.description, sfp->comment, name_len);
-      fcp->feature_label_data.description [ name_len ] = 0;
-      fcp->feature_label_data.typeword =
-            MemFree (fcp->feature_label_data.typeword);
-      if (biomol == MOLECULE_TYPE_GENOMIC)
-      {
-        fcp->feature_label_data.typeword = StringSave ("genomic sequence");
-      }
-      else if (biomol == MOLECULE_TYPE_MRNA)
-      {
-        fcp->feature_label_data.typeword = StringSave ("mRNA sequence");
-      }
-      else
-      {
-        fcp->feature_label_data.typeword = StringSave ("sequence");
-      }
-     
-      fcp->interval = MemFree (fcp->interval);
-      fcp->interval = StringSave ("");
-    }
-  }
-}
-
-static void RemoveUnwantedMiscFeats (
-  ValNodePtr PNTR clause_list,
-  Boolean delete_now
-)
-{
-  ValNodePtr       vnp, featlist;
-  FeatureClausePtr fcp, featlistclause;
-  SeqFeatPtr       sfp;
-
-  for (vnp = *clause_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice != DEFLINE_CLAUSEPLUS || vnp->data.ptrvalue == NULL)
-    {
-      continue;
-    }
-    fcp = vnp->data.ptrvalue;
-    for (featlist = fcp->featlist; featlist != NULL; featlist = featlist->next)
-    {
-      if ( featlist->data.ptrvalue == NULL)
-      {
-        continue;
-      }
-      if (featlist->choice == DEFLINE_CLAUSEPLUS)
-      {
-        featlistclause = featlist->data.ptrvalue;
-        RemoveUnwantedMiscFeats (&(featlistclause->featlist), FALSE);
-        continue;
-      }
-      if (featlist->choice != DEFLINE_FEATLIST)
-      {
-        continue;
-      }
-      sfp = featlist->data.ptrvalue;
-      if ( sfp->idx.subtype == FEATDEF_misc_feature
-        && ! IsNoncodingProductFeat (sfp)
-        && ! IsControlRegion (sfp)
-        && ! IsIntergenicSpacer (sfp)
-        && ! IsGeneCluster (sfp))
-      {
-        fcp->delete_me = TRUE;
-      }
-    }
-  }
-  DeleteFeatureClauses (clause_list);
-}
-
-/* When a feature is on the minus strand, the clauses are listed by 
- * sequence indexing in reverse biological order - we reverse the subclauses
- * for the feature in order to have them listed in the definition line
- * in biological order.
- * This is most noticeable when the main feature is a CDS with multiple
- * exons numbered sequentially.  If the exons are on the minus strand and
- * appear as 9, 8, 7, 6, we want to display them in the definition line as
- * 6, 7, 8, 9.
- */
-static void ReverseClauses (
-  ValNodePtr PNTR clause_list,
-  matchFunction   itemmatch
-)
-{
-  ValNodePtr vnp, last_feat, first_feat, next_item, new_list;
-  FeatureClausePtr fcp;
-
-  if (clause_list == NULL || *clause_list == NULL) return;
-
-  last_feat = NULL;
-  first_feat = NULL;
-  new_list = NULL;
-  vnp = *clause_list;
-  while (vnp != NULL)
-  {
-    next_item = vnp->next;
-    fcp = NULL;
-    if (vnp->choice == DEFLINE_CLAUSEPLUS
-      && (fcp = vnp->data.ptrvalue) != NULL
-      && fcp->slp != NULL
-      && SeqLocStrand (fcp->slp) == Seq_strand_minus
-      && fcp->featlist != NULL
-      && fcp->featlist->choice == DEFLINE_FEATLIST
-      && itemmatch (fcp->featlist->data.ptrvalue))
-    {
-      vnp->next = new_list;
-      new_list = vnp;
-    }
-    else
-    {
-      if (first_feat == NULL)
-      {
-        first_feat = vnp;
-        last_feat = vnp;
-      }
-      else
-      {
-        last_feat->next = vnp;
-        last_feat = vnp;
-        last_feat->next = NULL;
-      }
-    }
-    if (fcp != NULL)
-    {
-      ReverseClauses (&(fcp->featlist), itemmatch);
-    }
-    vnp = next_item;
-  }
-  if (first_feat == NULL)
-  {
-    *clause_list = new_list;
-  }
-  else
-  {
-    last_feat->next = new_list;
-    *clause_list = first_feat;
-  }
-}
-
-/* This function is used to determine whether two features are both exons
- * and whether they are numerically sequential - i.e., exon 7 and exon 8
- * are a pair of consecutive exons, exon 7 and exon 9 are not, and exon 7
- * and intron 9 are not.
- */
-static Boolean ClausePairIsTwoConsecutiveExons (
-  ValNodePtr vnp1,
-  ValNodePtr vnp2,
-  BioseqPtr  bsp
-)
-{
-  FeatureClausePtr fcp1, fcp2;
-  SeqFeatPtr       exon1, exon2;
-  Int4 num1, num2;
-  CharPtr          exdesc1, exdesc2;
-
-  if (vnp1 == NULL || vnp2 == NULL 
-    || vnp1->choice != DEFLINE_CLAUSEPLUS
-    || vnp2->choice != DEFLINE_CLAUSEPLUS
-    || vnp1->data.ptrvalue == NULL
-    || vnp2->data.ptrvalue == NULL)
-  {
-    return FALSE;
-  }
-  fcp1 = vnp1->data.ptrvalue;
-  fcp2 = vnp2->data.ptrvalue;
-  if ( fcp1->featlist == NULL
-    || fcp1->featlist->data.ptrvalue == NULL
-    || fcp2->featlist == NULL
-    || fcp2->featlist->data.ptrvalue == NULL
-    || fcp1->featlist->choice != DEFLINE_FEATLIST
-    || fcp2->featlist->choice != DEFLINE_FEATLIST
-    || ! IsExon (fcp1->featlist->data.ptrvalue)
-    || ! IsExon (fcp2->featlist->data.ptrvalue)
-    || (fcp1->is_alt_spliced && ! fcp2->is_alt_spliced)
-    || (! fcp1->is_alt_spliced && fcp2->is_alt_spliced))
-  {
-    return FALSE;
-  }
-
-  exon1 = (SeqFeatPtr)(fcp1->featlist->data.ptrvalue);
-  exon2 = (SeqFeatPtr)(fcp2->featlist->data.ptrvalue);
-
-  exdesc1 = GetExonDescription (bsp, exon1);
-  exdesc2 = GetExonDescription (bsp, exon2);
-  if (exdesc1 == NULL || exdesc2 == NULL)
-  {
-    if (exdesc1 != NULL) MemFree (exdesc1);
-    if (exdesc2 != NULL) MemFree (exdesc2);
-    return FALSE;
-  }
-  
-  num1 = atoi (exdesc1);
-  num2 = atoi (exdesc2);
-  MemFree (exdesc1);
-  MemFree (exdesc2);
-
-  if (abs (num1 - num2) == 1)
-  {
-    return TRUE;
-  }
-
-  return FALSE; 
-}
-
-/* This function counts the number of consecutive exons in a list.
- */
-static Int4 GetNumberOfConsecutiveExons (
-  ValNodePtr list,
-  BioseqPtr  bsp
-)
-{
-  ValNodePtr check;
-  Int4       num_exons;
- 
-  num_exons = 0;
-  check = list->next;
-  if ( ! ClausePairIsTwoConsecutiveExons (list, check, bsp)) return 0;
-  
-  num_exons = 2;
-  while ( check != NULL
-    && ClausePairIsTwoConsecutiveExons (check, check->next, bsp))
-  {
-    num_exons++;
-    check = check->next;
-  }
-  return num_exons;
-}
-
-/* This function replaces a list of three or more consecutive exon clauses
- * with a single "summary" clause that gives the range of exons present -
- * i.e., if you have exons 1, 2, 3, and 4, a clause will be created that
- * contains all four of those features and has a description of "1 through 4".
- */
-static void ReplaceExonClauseList (
-  FeatureClausePtr fcp,
-  ValNodePtr       clause,
-  Int4             num_exons,
-  BioseqPtr        bsp
-)
-{
-  ValNodePtr       lastfeat, tmpclause;
-  FeatureClausePtr tmpfcp;
-  Int4             i;
-  CharPtr          new_description;
-  Int4             new_description_len;
-  CharPtr          exdesc1, exdesc2;
-
-  if (fcp == NULL || clause == NULL) return;
-
-  lastfeat = fcp->featlist;
-  while (lastfeat != NULL && lastfeat->next != NULL)
-  {
-    lastfeat = lastfeat->next;
-  }
-  tmpclause = clause->next;
-  for (i=0; i < num_exons - 1 && tmpclause != NULL; i++)
-  {
-    tmpfcp = tmpclause->data.ptrvalue;
-    tmpfcp->delete_me = TRUE;
-    if (lastfeat == NULL)
-    {
-      fcp->featlist = tmpfcp->featlist;
-    }
-    else
-    {
-      lastfeat->next = tmpfcp->featlist;
-    }
-    tmpfcp->featlist = NULL;
-    while (lastfeat != NULL && lastfeat->next != NULL)
-    {
-      lastfeat = lastfeat->next;
-    }
-          
-    tmpclause = tmpclause->next;
-  }
-
-  exdesc1 = GetExonDescription (bsp, fcp->featlist->data.ptrvalue);
-  exdesc2 = GetExonDescription (bsp, lastfeat->data.ptrvalue);
-  if (exdesc1 == NULL || exdesc2 == NULL)
-  {
-    if (exdesc1 != NULL) MemFree (exdesc1);
-    if (exdesc2 != NULL) MemFree (exdesc2);
-    return;
-  }
-  new_description_len =
-        StringLen (exdesc1)
-      + StringLen (exdesc2)
-      + StringLen (" through ")
-      + 1;
-  new_description = MemNew (new_description_len * sizeof (Char));
-  if (new_description == NULL) return;
-  sprintf (new_description, "%s through %s", exdesc1, exdesc2);
-  MemFree (exdesc1);
-  MemFree (exdesc2);
-  if (fcp->feature_label_data.description != NULL)
-  {
-    MemFree (fcp->feature_label_data.description);
-  }
-  fcp->feature_label_data.description = new_description;
-}
-
-/* This function recursively searches for lists of consecutive exons
- * and calls ReplaceExonClauseList to consolidate the exons into a list
- * clause.
- */
-static void RenameExonSequences (
-  ValNodePtr PNTR list,
-  BioseqPtr       bsp,
-  Boolean         delete_now
-)
-{
-  ValNodePtr       clause;
-  Int4             num_exons;
-  FeatureClausePtr fcp;
- 
-  if (list == NULL) return; 
-  clause = *list;
-  while (clause != NULL)
-  {
-    if (clause->choice == DEFLINE_CLAUSEPLUS
-      && clause->data.ptrvalue != NULL)
-    {
-      fcp = clause->data.ptrvalue;
-      if ( ! fcp->delete_me)
-      {
-        num_exons = GetNumberOfConsecutiveExons (clause, bsp);
-        if (num_exons > 2)
-        {
-          ReplaceExonClauseList (fcp, clause, num_exons, bsp);
-        }
-        else
-        {
-          RenameExonSequences (&fcp->featlist, bsp, FALSE);
-        }
-      }
-    }
-    clause = clause->next;
-  }
-  if (delete_now) DeleteFeatureClauses (list);
-}
-
-static CharPtr organelleByGenome [] = {
-  NULL,
-  NULL,
-  "chloroplast",
-  "chromoplast",
-  "kinetoplast",
-  "mitochondrial",
-  "plastid",
-  "",
-  "",
-  "",
-  "",
-  "",
-  "cyanelle",
-  "",
-  "",
-  "",
-  "apicoplast",
-  "leucoplast",
-  "proplastid",
-  "",
-  "hydrogenosome",
-  NULL,
-};
-
-static CharPtr organelleByPopup [] = {
-  NULL,
-  "mitochondrial",
-  "chloroplast",
-  "kinetoplast",
-  "plastid",
-  "chromoplast",
-  "cyanelle",
-  "apicoplast",
-  "leucoplast",
-  "proplastid",
-  NULL
-};
-#define DEFAULT_ORGANELLE_CLAUSE 10
-
-static void 
-AddProductEnding 
-(CharPtr    str, 
- BioseqPtr  bsp,
- Int2       mitochloroflag,
- ValNodePtr strings)
-{
-  Char orgnelle [80];
-  BioSourcePtr  biop;
-  ValNodePtr last_string;
-  Int4 num_genes;
-  SubSourcePtr  ssp;
-
-  num_genes = 0;
-  biop = GetBiopForBsp (bsp);
-
-  if (biop != NULL) {
-    if (FindStringInStrings (strings, "genes"))
-    {
-      num_genes = 2;
-    }
-    else if ((last_string = FindStringInStrings (strings, "gene")) != NULL
-      && last_string->next != NULL
-      && (last_string = FindStringInStrings (last_string->next, "gene")) != NULL)
-    {
-      num_genes = 2;
-    }
-    else
-    {
-      num_genes = 1;
-    }
-
-    orgnelle [0] = '\0';
-  
-    switch (biop->genome) {
-    case GENOME_macronuclear :
-      StringCat (str, "; macronuclear");
-      break;
-    case GENOME_nucleomorph :
-      StringCat (str, "; nucleomorph");
-      break;
-    case GENOME_apicoplast :
-    case GENOME_chloroplast :
-    case GENOME_chromoplast :
-    case GENOME_kinetoplast :
-    case GENOME_mitochondrion :
-    case GENOME_plastid :
-    case GENOME_cyanelle :
-    case GENOME_leucoplast :
-    case GENOME_proplastid :
-    case GENOME_hydrogenosome :
-      sprintf (orgnelle, "; %s", organelleByGenome [biop->genome]);
-      StringCat (str, orgnelle);
-      break;
-    default :
-      ssp = biop->subtype;
-      while (ssp != NULL && ssp->subtype != 255)
-      {
-        ssp = ssp->next;
-      }
-      if (ssp != NULL
-        && ssp->name != NULL
-        && StringStr (ssp->name, "micronuclear"))
-      {
-        StringCat (str, "; micronuclear");
-      }
-      else if (mitochloroflag > 0) {
-        if (mitochloroflag > 9) {
-          /* beyond list */
-        }
-        else {
-          if (num_genes > 1)
-          {
-            sprintf (orgnelle, "; nuclear genes for %s products",
-                     organelleByPopup [mitochloroflag]);
-          }
-          else 
-          {
-            sprintf (orgnelle, "; nuclear gene for %s product",
-                     organelleByPopup [mitochloroflag]);
-          }
-          StringCat (str, orgnelle);
-        }
-      }
-      break;
-    }
-  }  
-}
-
-/*---------------------------------------------------------------------*/
-/*                                                                     */
-/* AutoDef_AddEnding () -- Add an ending on to the definition line     */
-/*                         after the last feature.                     */
-/*                                                                     */
-/*---------------------------------------------------------------------*/
-
-static void AutoDef_AddEnding (
-  ValNodePtr   clause_list,
-  ValNodePtr PNTR strings,
-  BioseqPtr    bsp,
-  Int2         mitochloroflag,
-  Boolean      alternate_splice_flag
-)
-{
-  Char str [200];
-  ValNodePtr last_string;
-  Int4 new_data_len;
-  CharPtr new_data;
-
-  str[0] = 0;
-  AddProductEnding (str, bsp, mitochloroflag, *strings);
-  if (alternate_splice_flag) {
-    StringCat (str, ", alternatively spliced");
-  }
-
-  StringCat (str, ".");
-
-  last_string = *strings;
-  if (last_string == NULL)
-  {
-    ValNodeAddStr (strings, 0, StringSave ( str));
-  }
-  else
-  {
-    while (last_string->next != NULL) last_string = last_string->next;
-    new_data_len = StringLen (last_string->data.ptrvalue) + StringLen (str) + 1;
-    new_data = (CharPtr) MemNew (new_data_len);
-    if (new_data == NULL) return;
-    StringCpy (new_data, last_string->data.ptrvalue);
-    StringCat (new_data, str);
-    MemFree (last_string->data.ptrvalue);
-    last_string->data.ptrvalue = new_data;
-  }
-}
-
-static Boolean LastIntervalChangeBeforeEnd (
-  FeatureClausePtr onebefore,
-  FeatureClausePtr thisclause,
-  ValNodePtr rest_of_list
-)
-{
-  ValNodePtr       vnp;
-  FeatureClausePtr fcp;
-
-  if (onebefore == NULL || rest_of_list == NULL) return FALSE;
- 
-  if (StringCmp (onebefore->interval, thisclause->interval) == 0) return FALSE;
-  
-  for (vnp = rest_of_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
-    {
-      fcp = vnp->data.ptrvalue;
-      if (StringCmp (thisclause->interval, fcp->interval) != 0) return FALSE;
-    }
-  }
-  return TRUE;
-    
-}
-
-static void PluralizeClauseIntervals (
-  FeatureClausePtr fcp
-)
-{
-  CharPtr new_interval, cp;
-
-  if (fcp->interval != NULL
-    && (cp = StringStr (fcp->interval, "gene, ")) != NULL)
-  {
-    new_interval = MemNew (StringLen (fcp->interval) + 2);
-    if (new_interval == NULL) return;
-    StringCpy (new_interval, fcp->interval);
-    new_interval [ cp - fcp->interval + 4] = 's';
-    StringCpy (new_interval + (cp - fcp->interval) + 5,
-               cp + 4);
-    MemFree (fcp->interval);
-    fcp->interval = new_interval;
-  }
-}  
-
-static Boolean DisplayAlleleName (FeatureClausePtr thisclause)
-{
-  if (thisclause == NULL) return FALSE;
-  if (StringCmp (thisclause->feature_label_data.typeword, "gene") == 0
-    || StringCmp (thisclause->feature_label_data.typeword, "pseudogene") == 0
-    || StringCmp (thisclause->feature_label_data.typeword, "mRNA") == 0
-    || StringCmp (thisclause->feature_label_data.typeword, "pseudogene mRNA") == 0
-    || StringCmp (thisclause->feature_label_data.typeword, "precursor RNA") == 0
-    || StringCmp (thisclause->feature_label_data.typeword, "pseudogene precursor RNA") == 0)
-  {
-    return TRUE;
-  }
-  return FALSE;
-}
-
-static void ListClauses (
-  ValNodePtr clauselist,
-  ValNodePtr PNTR strings,
-  Boolean    allow_semicolons,
-  Boolean    suppress_final_and
-)
-{
-  FeatureClausePtr thisclause, onebefore, twobefore, oneafter, twoafter;
-  Boolean print_typeword;
-  Boolean print_and;
-  Boolean print_comma;
-  Boolean print_semicolon;
-  Boolean print_comma_between_description_and_typeword;
-  Boolean typeword_is_plural;
-  size_t clause_len;
-  CharPtr clause_string;
-  Boolean oneafter_has_detail_change;
-  Boolean oneafter_has_interval_change;
-  Boolean oneafter_has_typeword_change;
-  Boolean onebefore_has_detail_change;
-  Boolean onebefore_has_interval_change;
-  Boolean onebefore_has_typeword_change;
-  SeqFeatPtr main_feat;
-  CharPtr new_interval;
-  ValNodePtr voneafter, vtwoafter;
-
-  while (clauselist != NULL && clauselist->choice != DEFLINE_CLAUSEPLUS)
-  {
-    clauselist = clauselist->next;
-  }
-  if (clauselist == NULL) return;
-
-  thisclause = clauselist->data.ptrvalue;
-  onebefore = NULL;
-  twobefore = NULL;
-  
-  while (thisclause != NULL)
-  {
-    oneafter_has_detail_change = FALSE;
-    oneafter_has_interval_change = FALSE;
-    oneafter_has_typeword_change = FALSE;
-    onebefore_has_detail_change = FALSE;
-    onebefore_has_interval_change = FALSE;
-    onebefore_has_typeword_change = FALSE;
-    if (onebefore != NULL)
-    {
-      if (StringCmp (onebefore->interval, thisclause->interval) != 0)
-        onebefore_has_interval_change = TRUE;
-      if (StringCmp (onebefore->feature_label_data.typeword,
-                     thisclause->feature_label_data.typeword) != 0)
-      {
-        onebefore_has_typeword_change = TRUE;
-      }
-      if (onebefore_has_typeword_change || onebefore_has_interval_change
-          || (DisplayAlleleName (onebefore) && StringLen (onebefore->allelename) != 0)
-          || (DisplayAlleleName (thisclause) && StringLen (thisclause->allelename) != 0))
-     {
-        onebefore_has_detail_change = TRUE;  
-      }
-    }
-    voneafter = clauselist->next;
-    while (voneafter != NULL && voneafter->choice != DEFLINE_CLAUSEPLUS)
-    {
-      voneafter = voneafter->next;
-    }
-    if (voneafter == NULL)
-    {
-      vtwoafter = NULL;
-    }
-    else
-    {
-      vtwoafter = voneafter->next;
-      while (vtwoafter != NULL && vtwoafter->choice != DEFLINE_CLAUSEPLUS)
-      {
-        vtwoafter = vtwoafter->next;
-      }
-    }
-
-    if (voneafter != NULL)
-    {
-      oneafter = voneafter->data.ptrvalue;
-      if (StringCmp (oneafter->interval, thisclause->interval) != 0)
-        oneafter_has_interval_change = TRUE;
-      if (StringCmp (oneafter->feature_label_data.typeword,
-                     thisclause->feature_label_data.typeword) != 0)
-      {
-        oneafter_has_typeword_change = TRUE;
-      }
-      if (oneafter_has_typeword_change  || oneafter_has_interval_change
-          || (DisplayAlleleName (thisclause) && StringLen (thisclause->allelename) != 0)
-          || (DisplayAlleleName (oneafter) && StringLen (oneafter->allelename) != 0))
-      {
-        oneafter_has_detail_change = TRUE;
-      }
-      if (vtwoafter != NULL)
-      {
-        twoafter = vtwoafter->data.ptrvalue;
-      }
-      else
-      {
-        twoafter = NULL;
-      }
-    }
-    else
-    {
-      oneafter = NULL;
-      twoafter = NULL;
-    }
-    print_typeword = FALSE;
-    typeword_is_plural = FALSE;
-    print_and = FALSE;
-    print_comma = FALSE;
-    print_semicolon = FALSE;
-
-    if (thisclause->feature_label_data.is_typeword_first)
-    {
-      if (onebefore == NULL || onebefore_has_detail_change)
-      {
-        print_typeword = TRUE;
-        if (oneafter != NULL && ! oneafter_has_detail_change)
-        {
-          typeword_is_plural = TRUE;
-        }
-        else if (StringStr (thisclause->feature_label_data.description, " through ") != NULL
-          && StringCmp (thisclause->feature_label_data.typeword, "exon") == 0)
-        {
-          typeword_is_plural = TRUE;
-        }
-      }
-    }
-    else
-    {
-      if (oneafter == NULL || oneafter_has_detail_change)
-      {
-        print_typeword = TRUE;
-        if (onebefore != NULL && ! onebefore_has_detail_change)
-        {
-          typeword_is_plural = TRUE;
-        }
-      }
-    }
-
-    /* when to print and before this section */
-    if ( onebefore != NULL
-         && ! onebefore_has_detail_change
-         && (oneafter == NULL || oneafter_has_detail_change))
-    {
-      print_and = TRUE;
-    }
-    else if (oneafter == NULL && onebefore != NULL)
-    {
-      print_and = TRUE;
-    }
-    else if (onebefore != NULL
-         && ! onebefore_has_interval_change
-         && oneafter_has_interval_change)
-    {
-      print_and = TRUE;
-    }
-    else if ( LastIntervalChangeBeforeEnd ( onebefore, 
-                                            thisclause,
-                                            clauselist->next))
-    {
-      print_and = TRUE;
-    }
-
-    if (suppress_final_and && oneafter == NULL)
-    {
-      print_and = FALSE;
-    }
-    if (suppress_final_and && oneafter != NULL && twoafter == NULL)
-    {
-      print_comma = TRUE;
-    }
-    
-    /* when to print semicolon after this section */
-    /* after every interval change except when exons change "interval" */
-    /* exons changing interval are going from alt-spliced to not */
-    /* or vice versa, in either case we don't want a semicolon or comma */
-    if (oneafter != NULL && oneafter_has_interval_change
-      && (StringCmp (thisclause->feature_label_data.typeword, "exon") != 0
-         || StringCmp (oneafter->feature_label_data.typeword, "exon") != 0))
-    {
-      print_semicolon = TRUE;
-    }
-
-    /* when to print comma after this section */
-    if (onebefore != NULL && oneafter != NULL
-      && ! onebefore_has_detail_change
-      && ! oneafter_has_detail_change )
-    {
-      print_comma = TRUE;
-    }
-    else if (oneafter != NULL && onebefore != NULL
-      && ! onebefore_has_interval_change && ! oneafter_has_interval_change
-      &&  onebefore_has_typeword_change &&  oneafter_has_typeword_change)
-    {
-      print_comma = TRUE;
-    }
-    else if (oneafter != NULL && twoafter != NULL
-      && ! oneafter_has_detail_change
-      && StringCmp (twoafter->feature_label_data.typeword,
-                    thisclause->feature_label_data.typeword) == 0
-      && StringCmp (twoafter->interval,
-                    thisclause->interval) == 0)
-    {
-      print_comma = TRUE;
-    }
-    else if (oneafter != NULL  && twoafter != NULL
-      && oneafter_has_typeword_change
-      && StringCmp (twoafter->feature_label_data.typeword,
-                    oneafter->feature_label_data.typeword) == 0
-      && StringCmp (twoafter->interval,
-                    oneafter->interval) == 0
-      && ! print_and)
-    {
-      print_comma = TRUE;
-    }
-    else if (((oneafter_has_interval_change || oneafter == NULL)
-      && StringDoesHaveText (thisclause->interval))
-      || (oneafter_has_interval_change && oneafter != NULL && ! print_semicolon))
-    {
-      print_comma = TRUE;
-    }
-    else if (oneafter != NULL && twoafter != NULL
-      && !oneafter_has_interval_change
-      && StringCmp (thisclause->interval, twoafter->interval) == 0
-      && oneafter_has_typeword_change
-      && StringCmp (thisclause->feature_label_data.typeword,
-                    twoafter->feature_label_data.typeword) != 0)
-    {
-      print_comma = TRUE;
-    }
-    else if (oneafter != NULL && onebefore != NULL && twoafter != NULL
-      && ! oneafter_has_interval_change && ! onebefore_has_interval_change
-      && StringCmp (thisclause->interval, twoafter->interval) == 0
-      && oneafter_has_typeword_change)
-    {
-      print_comma = TRUE;
-    }
-    else if (oneafter != NULL && twoafter != NULL
-      && oneafter_has_typeword_change
-      && StringCmp (oneafter->feature_label_data.typeword,
-                    twoafter->feature_label_data.typeword) != 0
-      && ! oneafter_has_interval_change
-      && StringCmp (oneafter->interval, twoafter->interval) == 0)
-    {
-      /* spacer 1, foo RNA gene, and spacer2, complete sequence */
-      /*         ^ */
-      print_comma = TRUE;
-    }
-    else if (oneafter != NULL && twoafter != NULL 
-      && ! oneafter_has_interval_change && StringCmp (thisclause->interval, twoafter->interval) == 0
-      && ((DisplayAlleleName (oneafter) && StringLen (oneafter->allelename) > 0)
-        || (DisplayAlleleName (thisclause) && StringLen (thisclause->allelename) > 0)))
-    {
-      print_comma = TRUE;  	
-    }
-    else if (oneafter != NULL && onebefore != NULL
-      && ! oneafter_has_interval_change && ! onebefore_has_interval_change
-      && ((DisplayAlleleName (oneafter) && StringLen (oneafter->allelename) > 0)
-        || (DisplayAlleleName (thisclause) && StringLen (thisclause->allelename) > 0)))
-    {
-      print_comma = TRUE;  	
-    }
-
-    if (thisclause->featlist != NULL
-      && thisclause->featlist->data.ptrvalue != NULL
-      && StringDoesHaveText (thisclause->interval)
-      && StringNCmp (thisclause->interval, "partial", 7) != 0
-      && StringNCmp (thisclause->interval, "complete", 8) != 0)
-    {
-      main_feat = thisclause->featlist->data.ptrvalue;
-      if (IsMobileElement (main_feat)
-        || IsEndogenousVirusSourceFeature (main_feat) )
-      {
-        print_comma = FALSE;
-      }
-    }
-
-    if (onebefore != NULL
-      && ! onebefore_has_interval_change
-      && (oneafter_has_interval_change || oneafter == NULL))
-    {
-      PluralizeClauseIntervals (thisclause);
-    }
-
-    if ( thisclause->make_plural )
-    {
-      if ((onebefore != NULL && ! onebefore_has_detail_change)
-        || (oneafter != NULL && !oneafter_has_detail_change))
-      {
-        PluralizeConsolidatedClauseDescription (thisclause);
-      }
-      else
-      {
-        typeword_is_plural = TRUE;
-      }
-    }
-
-    clause_len = StringLen (thisclause->feature_label_data.description) + 1;
-    
-    /* add one in case we need to add the semicolon to this clause (when
-     * the interval has changed because this clause has no interval and
-     * the next one does).
-     */
-    clause_len++;
-
-    /* we need to place a comma between the description and the type word 
-     * when the description ends with "precursor" or when the type word
-     * starts with "precursor"
-     */
-    if ( thisclause->feature_label_data.description != NULL
-      && ! thisclause->feature_label_data.is_typeword_first
-      && print_typeword
-      && ! StringHasNoText (thisclause->feature_label_data.typeword)
-      && ((StringNCmp (thisclause->feature_label_data.typeword, "precursor", 9) == 0
-            && thisclause->feature_label_data.description [StringLen (thisclause->feature_label_data.description) - 1] != ')')
-          || (clause_len > StringLen ("precursor")
-              && StringCmp ( thisclause->feature_label_data.description
-                     + clause_len - StringLen ("precursor") - 2,
-                     "precursor") == 0)))
-    {
-      print_comma_between_description_and_typeword = TRUE;
-      clause_len += 1;
-    }
-    else
-    {
-      print_comma_between_description_and_typeword = FALSE;
-    }
-
-    if (print_typeword)
-      clause_len += StringLen (thisclause->feature_label_data.typeword) + 1;
-    if (typeword_is_plural)
-      clause_len += 1;
-    if (print_and)
-      clause_len += 4;
-    if (print_comma)
-      clause_len += 2;
-    if (DisplayAlleleName (thisclause))
-    {
-      clause_len += StringLen (thisclause->allelename) + 10;
-      if (StringLen (thisclause->allelename) > 0) 
-      {
-        clause_len += StringLen (thisclause->allelename) + StringLen ("allele ");
-      }
-    }
-    
-    clause_string = (CharPtr) MemNew (clause_len);
-    if (clause_string == NULL)
-      return;
-    clause_string[0] = 0;
-    if (print_and)
-      StringCat (clause_string, "and ");
-    if (thisclause->feature_label_data.is_typeword_first && print_typeword
-      && thisclause->feature_label_data.typeword != NULL
-      && ! StringHasNoText (thisclause->feature_label_data.typeword))
-    {
-      StringCat (clause_string, thisclause->feature_label_data.typeword);
-      if (typeword_is_plural)
-        StringCat (clause_string, "s");
-      if (thisclause->feature_label_data.description != NULL)
-        StringCat (clause_string, " ");
-    }
-    if (thisclause->feature_label_data.description != NULL)
-    {
-      StringCat (clause_string, thisclause->feature_label_data.description);
-      if (print_comma_between_description_and_typeword)
-      {
-        StringCat (clause_string, ",");
-      }
-    }
-    if (! thisclause->feature_label_data.is_typeword_first && print_typeword
-      && thisclause->feature_label_data.typeword != NULL
-      && ! StringHasNoText (thisclause->feature_label_data.typeword))
-    {
-      if (thisclause->feature_label_data.description != NULL)
-        StringCat (clause_string, " ");
-      StringCat (clause_string, thisclause->feature_label_data.typeword);
-      if (typeword_is_plural)
-        StringCat (clause_string, "s");
-      if (DisplayAlleleName (thisclause)
-        && thisclause->allelename != NULL)
-      {
-        StringCat (clause_string, ", ");
-        StringCat (clause_string, thisclause->allelename);
-        StringCat (clause_string, " allele");
-      }
-    }
-    if (StringLen (clause_string) > 0 ) 
-    {
-      if (print_comma)
-        StringCat (clause_string, ",");
-      ValNodeAddStr (strings, 0, clause_string);
-    }
-    else 
-    {
-    	MemFree (clause_string);
-    	clause_string = NULL;
-    }
- 
-    if (oneafter == NULL || oneafter_has_interval_change)
-    {
-      if (print_semicolon) {
-        if (thisclause->interval == NULL
-          || StringHasNoText(thisclause->interval)) {
-          if (clause_string != NULL) {
-            StringCat (clause_string, ";");
-          }
-        } else if (thisclause->interval[StringLen (thisclause->interval)] != ';') {
-          new_interval = MemNew (StringLen (thisclause->interval) + 2);
-          if (new_interval == NULL) return;
-          StringCpy (new_interval, thisclause->interval);
-          if (allow_semicolons) 
-          {
-            StringCat (new_interval, ";");
-          }
-          else
-          {
-            StringCat (new_interval, ",");
-          }
-          MemFree (thisclause->interval);
-          thisclause->interval = new_interval;
-        }
-      }
-      if (thisclause->interval != NULL
-        && !StringHasNoText (thisclause->interval))
-      {
-        ValNodeAddStr (strings, 0, StringSave (thisclause->interval));
-      }
-    }
-    twobefore = onebefore;
-    onebefore = thisclause;   
-    thisclause = oneafter;
-    clauselist = voneafter;
-  }
-}
-
-static Uint1 GetMoleculeType 
-(BioseqPtr bsp,
- Uint2     entityID)
-{
-  SeqDescPtr         sdp;
-  MolInfoPtr         mip;
-  SeqMgrDescContext  dcontext;
-
-  if (bsp == NULL) return MOLECULE_TYPE_GENOMIC;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext);
-  if (sdp == NULL) return MOLECULE_TYPE_GENOMIC;
-  mip = (MolInfoPtr) sdp->data.ptrvalue;
-  if (mip == NULL) return MOLECULE_TYPE_GENOMIC;
-  return mip->biomol;
-}
-
-static Boolean SpecialHandlingForSpecialTechniques (
-  BioseqPtr bsp
-)
-{
-  SeqDescPtr sdp;
-  MolInfoPtr mip;
-  ValNodePtr vnp;
-
-  if (bsp == NULL) return MOLECULE_TYPE_GENOMIC;
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, NULL);
-  if (sdp == NULL)
-  {
-    for (sdp = bsp->descr;
-         sdp != NULL && sdp->choice != Seq_descr_molinfo;
-         sdp = sdp->next)
-    {}
-  }
-  if (sdp == NULL) return FALSE;
-  mip = (MolInfoPtr) sdp->data.ptrvalue;
-  if (mip == NULL) return FALSE;
-  if (mip->tech == MI_TECH_htgs_0 ||
-      mip->tech == MI_TECH_htgs_1 ||
-      mip->tech == MI_TECH_htgs_2 ||
-      mip->tech == MI_TECH_est ||
-      mip->tech == MI_TECH_sts ||
-      mip->tech == MI_TECH_survey ||
-      mip->tech == MI_TECH_wgs) {
-    vnp = ValNodeExtract (&(bsp->descr), Seq_descr_title);
-    if (vnp != NULL)
-      vnp = ValNodeFreeData (vnp);
-    return TRUE;
-  }
-
-  return FALSE;
-}
-
-static Boolean LIBCALLBACK ShouldRemoveExon (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp,
-  Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag
-)
-{
-  Boolean partial3, partial5;
-  SeqFeatPtr main_feat;
-
-  if (isSegment || isLonely || isRequested) return FALSE;
-  if (parent_fcp == NULL
-    || parent_fcp->featlist == NULL
-    || parent_fcp->featlist->data.ptrvalue == NULL)
-  {
-    return TRUE;
-  }
-  
-  main_feat = parent_fcp->featlist->data.ptrvalue;
-  if ( IsCDS (main_feat))
-  {
-    CheckSeqLocForPartial (main_feat->location, &partial5, &partial3);
-    if (partial5 || partial3) return FALSE;
-  }
-  else if (IsmRNA (main_feat) || parent_fcp->has_mrna)
-  {
-    return FALSE;
-  }
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK ShouldRemoveCDS (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp,
-  Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag)
-{
-  CharPtr description;
-  Boolean retval = FALSE;
-
-  description = GetGeneProtDescription (this_fcp, bsp, suppress_locus_tag);
-  if (StringHasNoText (description))
-  {
-    retval = TRUE;
-  }
-  if (description != NULL) MemFree (description);
-  return retval;
-}
-
-static Boolean LIBCALLBACK ShouldRemoveNoncodingProductFeat (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp, Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag
-)
-{
-  if (isRequested) return FALSE;
-  return TRUE;
-}
-
-static Boolean LIBCALLBACK ShouldRemovePromoter (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp, Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag
-)
-{
-  /* remove a promoter if it is in an mRNA or gene clause */
-  if (isRequested)
-  {
-    return FALSE;
-  }
-  else if (parent_fcp != NULL 
-      && (parent_fcp->has_mrna 
-        || (parent_fcp->featlist != NULL
-           && parent_fcp->featlist->choice == DEFLINE_FEATLIST
-           && parent_fcp->featlist->data.ptrvalue != NULL
-           && IsmRNA (parent_fcp->featlist->data.ptrvalue))))
-  {
-    return TRUE;
-  }
-  else if (isLonely)
-  {
-    return FALSE;
-  }
-  else
-  {
-    return TRUE;
-  }
-}
-
-static Boolean LIBCALLBACK ShouldRemoveLTR (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp,
-  Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag
-)
-{
-  if (isRequested)
-  {
-    return FALSE;
-  }
-  else if (parent_fcp != NULL)
-  {
-    return TRUE;
-  }
-  else if (isLonely)
-    return FALSE;
-  else
-    return TRUE;
-}
-
-static Boolean LIBCALLBACK ShouldRemove3UTR (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp,
-  Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag
-)
-{ 
-  if (isLonely || isRequested)
-    return FALSE;
-  else
-    return TRUE;
-}
-
-static Boolean LIBCALLBACK ShouldRemove5UTR (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp,
-  Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag
-)
-{
-  if (isLonely || isRequested)
-    return FALSE;
-  else
-    return TRUE;
-}
-
-static Boolean LIBCALLBACK ShouldRemoveIntron (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp, Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag
-)
-{
-  if (isRequested)
-  {
-    return FALSE;
-  }
-  else if (parent_fcp != NULL 
-      && (parent_fcp->has_mrna 
-        || (parent_fcp->featlist != NULL
-           && parent_fcp->featlist->choice == DEFLINE_FEATLIST
-           && parent_fcp->featlist->data.ptrvalue != NULL
-           && IsmRNA (parent_fcp->featlist->data.ptrvalue))))
-  {
-    return TRUE;
-  }
-  else if (isLonely)
-  {
-    return FALSE;
-  }
-  else
-  {
-    return TRUE;
-  }
-}
-
-static Boolean LIBCALLBACK ShouldRemoveMobileElement
-( SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp,
-  Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag)
-{
-  return (!isLonely && !isRequested);
-}
-
-static Boolean LIBCALLBACK ShouldRemoveGeneric 
-( SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp,
-  Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag)
-{
-  CharPtr productname;
-  Boolean rval;
-
-  rval = FALSE;
-  if (IsMiscRNA (sfp) && ( productname = GetProductName (sfp, bsp, suppress_locus_tag)) != NULL)
-  {
-    if (StringStr (productname, "trans-spliced leader") != NULL)
-    {
-      rval = TRUE;
-    }
-    MemFree (productname);
-  }
-    
-  return rval;
-}
-
-
-static Boolean IsBioseqPrecursorRNA (BioseqPtr bsp)
-{
-  SeqDescrPtr       sdp;
-  SeqMgrDescContext context;
-  MolInfoPtr        mol;
-  
-  if (bsp == NULL) return FALSE;
-  
-  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &context);
-  if (sdp != NULL && sdp->data.ptrvalue != NULL)
-  {
-		mol = (MolInfoPtr) sdp->data.ptrvalue;
-    if (mol->biomol == 2)
-    {
-      return TRUE;
-    }
-  }
-  return FALSE;
-}
-
-static Boolean LIBCALLBACK ShouldRemovePrecursorRNA
-( SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp,
-  Boolean isLonely,
-  Boolean isRequested,
-  Boolean isSegment,
-  Boolean suppress_locus_tag)
-{
-  if (!isLonely && IsBioseqPrecursorRNA(bsp))
-  {
-    return TRUE;
-  }
-  else
-  {
-    return ShouldRemoveGeneric (sfp, parent_fcp, this_fcp, bsp, isLonely, 
-                                isRequested, isSegment, suppress_locus_tag);
-  }
-}
-
-
-typedef struct removableitemglobal {
-  matchFunction  itemmatch;
-  ShouldRemoveFunction ShouldRemove;
-  CharPtr  group_name;
-} RemovableItemGlobalData, PNTR RemovableItemGlobalPtr;
-
-typedef struct removableitemlocal {
-  ButtoN  keep_request;
-  Boolean  keep;
-} RemovableItemLocalData, PNTR RemovableItemLocalPtr;
-
-static RemovableItemGlobalData remove_items[] = {
-  { IsExon, ShouldRemoveExon, "Exons" },
-  { IsIntron, ShouldRemoveIntron, "Introns" },
-  { Is5UTR, ShouldRemove5UTR, "5' UTRs" },
-  { Is3UTR, ShouldRemove3UTR, "3' UTRs" },
-  { IsCDS,  ShouldRemoveCDS, "CDSs" },
-  { IsPromoter, ShouldRemovePromoter, "Promoters" },
-  { IsLTR, ShouldRemoveLTR, "LTRs" },
-  { IsPrecursorRNA, ShouldRemovePrecursorRNA, "Precursor RNAs" },
-  { IsNoncodingProductFeat,  ShouldRemoveNoncodingProductFeat, "Misc feats with comments:" },
-  { IsRemovableMobileElement, ShouldRemoveMobileElement, "Optional Mobile Element" }
-};
-
-typedef enum {
-  RemovableExon = 0,
-  RemovableIntron,
-  Removable5UTR,
-  Removable3UTR,
-  RemovableCDS,
-  RemovablePromoter,
-  RemovableLTR,
-  RemovablePrecursorRNA,
-  RemovableNoncodingProductFeat,
-  RemovableMobileElement,
-  NumRemovableItems
-} RemovableList;
-
-typedef enum {
-  DEFLINE_USE_FEATURES = 1,
-  DEFLINE_COMPLETE_SEQUENCE,
-  DEFLINE_COMPLETE_GENOME
-} DefLineType;
-
-typedef struct deflinefeaturerequestlist {
-  RemovableItemLocalData items[NumRemovableItems];
-  Boolean                suppress_alt_splice_phrase;
-  Boolean                remove_subfeatures;
-  DefLineType            feature_list_type;
-  Int4                   misc_feat_parse_rule;
-  Boolean                suppress_locus_tags;
-  ValNodePtr             suppressed_feature_list;
-} DeflineFeatureRequestList, PNTR DeflineFeatureRequestListPtr;
-
-static void InitFeatureRequests (
-  DeflineFeatureRequestListPtr feature_requests
-)
-{
-  Int4 i;
-  for (i=0; i < NumRemovableItems; i++)
-  {
-    feature_requests->items[i].keep_request = NULL;
-    feature_requests->items[i].keep = FALSE;
-  }
-  feature_requests->suppress_alt_splice_phrase = FALSE;
-  feature_requests->remove_subfeatures = FALSE;
-  feature_requests->feature_list_type = DEFLINE_USE_FEATURES;
-  feature_requests->misc_feat_parse_rule = 2;
-  feature_requests->suppress_locus_tags = FALSE;
-  feature_requests->suppressed_feature_list = NULL;
-}
-
-static Boolean RemoveCondition (
-  SeqFeatPtr sfp,
-  FeatureClausePtr parent_fcp,
-  FeatureClausePtr this_fcp,
-  BioseqPtr bsp,
-  Boolean isLonely,
-  Boolean isSegment,
-  DeflineFeatureRequestList *feature_requests
-)
-{
-  Int4 i;
-  if (sfp == NULL) return TRUE;
-  for (i=0; i < NumRemovableItems; i++)
-  {
-    if (remove_items[i].itemmatch (sfp))
-      return remove_items[i].ShouldRemove (sfp, parent_fcp, this_fcp, bsp,
-                                           isLonely, feature_requests->items[i].keep,
-                                           isSegment,
-                                           feature_requests->suppress_locus_tags);
-  }
-  return ShouldRemoveGeneric(sfp, parent_fcp, this_fcp, bsp, isLonely, FALSE,
-                             isSegment, feature_requests->suppress_locus_tags);
-}
-
-static Boolean FindOtherGeneClause 
-( ValNodePtr feature_list,
-  ValNodePtr me,
-  GeneRefPtr grp,
-  Boolean    suppress_locus_tag)
-{
-  ValNodePtr vnp;
-  FeatureClausePtr fcp;
-
-  if (grp == NULL) return FALSE;
-
-  for (vnp = feature_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp == me) continue;
-    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
-    {
-      fcp = vnp->data.ptrvalue;
-      if (fcp->delete_me) continue;
-      if ( fcp->grp == grp
-        || (fcp->grp != NULL && DoGenesMatch (fcp->grp, grp, suppress_locus_tag)))
-      {
-        return TRUE;
-      }
-      if ( FindOtherGeneClause (fcp->featlist, me, grp, suppress_locus_tag))
-      {
-        return TRUE;
-      }
-    }
-  }
-  return FALSE;
-}
- 
-static void RemoveGenesMentionedElsewhere 
-( ValNodePtr PNTR feature_list,
-  ValNodePtr      search_list,
-  Boolean         delete_now,
-  Boolean         suppress_locus_tag)
-{
-  ValNodePtr vnp;
-  FeatureClausePtr fcp;
-
-  for (vnp = *feature_list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
-    {
-      fcp = vnp->data.ptrvalue;
-      if (fcp->featlist == NULL)
-      {
-        continue;
-      }
-      if ( IsGene (fcp->featlist->data.ptrvalue)
-        && fcp->featlist->next == NULL
-        && FindOtherGeneClause ( search_list, vnp, fcp->grp, suppress_locus_tag))
-      {
-        fcp->delete_me = TRUE;
-      }
-      else
-      {
-        RemoveGenesMentionedElsewhere ( &(fcp->featlist), search_list, FALSE, suppress_locus_tag);
-      }
-    }
-  }
-  if (delete_now)
-  {
-    DeleteFeatureClauses (feature_list);
-  }
-}
-
-static void MarkUnwantedFeatureClauseForRemoval (
-  ValNodePtr clause,
-  BioseqPtr  bsp,
-  Boolean    isLonely,
-  FeatureClausePtr parent_fcp,
-  Boolean    isSegment,
-  DeflineFeatureRequestList PNTR feature_requests
-)
-{
-  FeatureClausePtr fcp;
-  ValNodePtr       featlist;
-  ValNodePtr       firstfeat;
-  Int4             clause_count;
-  SeqFeatPtr       sfp;
-
-  if (clause == NULL
-    || clause->choice != DEFLINE_CLAUSEPLUS
-    || clause->data.ptrvalue == NULL)
-  {
-    return;
-  }
-
-  fcp = clause->data.ptrvalue;
-  firstfeat = fcp->featlist;
-  clause_count = 0;
-  for (featlist = firstfeat;
-       featlist != NULL && isLonely;
-       featlist = featlist->next)
-  {
-    if (featlist->choice == DEFLINE_CLAUSEPLUS)
-    {
-      clause_count ++;
-      if (clause_count > 1)
-      {
-        isLonely = FALSE;
-      }
-    }
-  }
-    
-  featlist = firstfeat;
-  while (featlist != NULL)
-  {  
-    if (featlist->choice == DEFLINE_FEATLIST
-      && featlist->data.ptrvalue != NULL)
-    {
-      sfp = (SeqFeatPtr) featlist->data.ptrvalue;
-      if (RemoveCondition (featlist->data.ptrvalue, parent_fcp, fcp, bsp, 
-                          isLonely, isSegment, feature_requests))
-      {
-        fcp->delete_me = TRUE;
-      }
-      else if (! IsGene (sfp) && ! IsmRNA (sfp))
-      {
-        isLonely = FALSE;
-      }
-    }
-    else if (featlist->choice == DEFLINE_CLAUSEPLUS 
-      && featlist->data.ptrvalue != NULL)
-    {
-      MarkUnwantedFeatureClauseForRemoval (featlist, bsp, isLonely, fcp,
-                                           isSegment,
-                                           feature_requests);
-    }
-    featlist = featlist->next;
-  }
-}
-  
-static void RemoveUnwantedFeatures (
-  ValNodePtr PNTR list,
-  BioseqPtr bsp,
-  Boolean   isSegment,
-  DeflineFeatureRequestList PNTR feature_requests
-)
-{
-  ValNodePtr       vnp;
-  Boolean          isLonely;
-
-  if (list == NULL) return;
-
-  isLonely = TRUE;
-
-  for (vnp = *list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->next != NULL) isLonely = FALSE;
-    if (vnp->choice == DEFLINE_CLAUSEPLUS)
-    {
-      MarkUnwantedFeatureClauseForRemoval (vnp, bsp, isLonely, NULL,
-                                           isSegment, feature_requests);
-    }
-  }
-  DeleteFeatureClauses (list);
-}
-
-static Boolean IsFeatureInSelectionList (SeqFeatPtr sfp, ValNodePtr feat_list)
-{
-  ValNodePtr       vnp;
-
-  if (sfp == NULL || feat_list == NULL)
-  {
-    return FALSE;
-  }
-  
-  for (vnp = feat_list; vnp != NULL && sfp->idx.subtype != vnp->choice; vnp = vnp->next)
-  {
-  }
-  if (vnp == NULL)
-  {
-    return FALSE;
-  }
-  else
-  {
-    return TRUE;
-  }
-}
-
-static void MarkSuppressedFeatureClauseForRemoval (
-  ValNodePtr clause,
-  ValNodePtr suppressed_feature_list
-)
-{
-  FeatureClausePtr fcp;
-  ValNodePtr       featlist;
-  ValNodePtr       firstfeat;
-  SeqFeatPtr       sfp;
-
-  if (clause == NULL
-    || clause->choice != DEFLINE_CLAUSEPLUS
-    || clause->data.ptrvalue == NULL)
-  {
-    return;
-  }
-
-  fcp = clause->data.ptrvalue;
-  firstfeat = fcp->featlist;
-    
-  featlist = firstfeat;
-  while (featlist != NULL)
-  {  
-    if (featlist->choice == DEFLINE_FEATLIST
-      && featlist->data.ptrvalue != NULL)
-    {
-      sfp = (SeqFeatPtr) featlist->data.ptrvalue;
-      if (IsFeatureInSelectionList (sfp, suppressed_feature_list))
-      {
-        fcp->delete_me = TRUE;
-      }
-    }
-    else if (featlist->choice == DEFLINE_CLAUSEPLUS 
-      && featlist->data.ptrvalue != NULL)
-    {
-      MarkSuppressedFeatureClauseForRemoval (featlist, suppressed_feature_list);
-    }
-    featlist = featlist->next;
-  }
-}
-  
-static void RemoveSuppressedFeatures (ValNodePtr PNTR list,
-                                      ValNodePtr suppressed_feature_list)
-{
-  ValNodePtr vnp;
-  
-  if (list == NULL || *list == NULL || suppressed_feature_list == NULL)
-  {
-    return;
-  }
-  
-  for (vnp = *list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_CLAUSEPLUS)
-    {
-      MarkSuppressedFeatureClauseForRemoval (vnp, suppressed_feature_list);
-    }
-  }
-  DeleteFeatureClauses (list);  
-}
-
-static Boolean LIBCALLBACK IsMasterClause (
-  SeqFeatPtr sfp
-)
-{
-  if ( IsMobileElement (sfp)) return TRUE;
-  return FALSE;
-}
-
-static void DeleteSubfeatures (
-  ValNodePtr PNTR feature_list,
-  Boolean         delete_now
-)
-{
-  ValNodePtr       clause, featlist;
-  FeatureClausePtr clause_fcp, fcp;
-
-  if (feature_list == NULL) return;
-  for (clause = *feature_list; clause != NULL; clause = clause->next)
-  {
-    if (clause->choice != DEFLINE_CLAUSEPLUS
-      || (clause_fcp = clause->data.ptrvalue) == NULL
-      || clause_fcp->featlist == NULL)
-    {
-      continue;
-    }
-    if (clause_fcp->featlist->choice == DEFLINE_FEATLIST
-      && IsMasterClause (clause_fcp->featlist->data.ptrvalue))
-    {
-      for (featlist = clause_fcp->featlist->next;
-           featlist != NULL;
-           featlist = featlist->next)
-      {
-        if (featlist->choice == DEFLINE_CLAUSEPLUS
-          && (fcp = featlist->data.ptrvalue) != NULL)
-        {
-          fcp->delete_me = TRUE;
-        }
-      }
-    }
-    else
-    {
-      DeleteSubfeatures ( &(clause_fcp->featlist), FALSE);
-    }
-  }
-  if (delete_now) 
-  {
-    DeleteFeatureClauses (feature_list);
-  }
-}
-
-static void DeleteOperonAndGeneClusterSubfeatures (
-  ValNodePtr PNTR feature_list,
-  Boolean         delete_now
-)
-{
-  ValNodePtr       clause, featlist;
-  FeatureClausePtr clause_fcp, fcp;
-
-  if (feature_list == NULL) return;
-  for (clause = *feature_list; clause != NULL; clause = clause->next)
-  {
-    if (clause->choice != DEFLINE_CLAUSEPLUS
-      || (clause_fcp = clause->data.ptrvalue) == NULL
-      || clause_fcp->featlist == NULL)
-    {
-      continue;
-    }
-    if (clause_fcp->featlist->choice == DEFLINE_FEATLIST
-      && (IsOperon (clause_fcp->featlist->data.ptrvalue) 
-          || IsGeneCluster (clause_fcp->featlist->data.ptrvalue)))
-    {
-      for (featlist = clause_fcp->featlist->next;
-           featlist != NULL;
-           featlist = featlist->next)
-      {
-        if (featlist->choice == DEFLINE_CLAUSEPLUS
-          && (fcp = featlist->data.ptrvalue) != NULL)
-        {
-          fcp->delete_me = TRUE;
-        }
-      }
-    }
-    else
-    {
-      DeleteOperonAndGeneClusterSubfeatures ( &(clause_fcp->featlist), FALSE);
-    }
-  }
-  if (delete_now) 
-  {
-    DeleteFeatureClauses (feature_list);
-  }
-}
-
-static void RemoveFeats (
-  ValNodePtr    list,
-  matchFunction itemmatch
-)
-{
-  ValNodePtr vnp;
-  FeatureClausePtr fcp;
-  
-  if (list == NULL) return;
-
-  for (vnp = list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_FEATLIST
-      && itemmatch (vnp->data.ptrvalue))
-    {
-      vnp->choice = DEFLINE_REMOVEFEAT;
-    }
-    else if (vnp->choice == DEFLINE_CLAUSEPLUS
-      && (fcp = vnp->data.ptrvalue) != NULL)
-    {
-      RemoveFeats (fcp->featlist, itemmatch);
-    }
-  }
-}
-
-/* A clause is "tall" if it has only one clause at any level */
-static Boolean IsClauseTall (
-  FeatureClausePtr fcp
-)
-{
-  ValNodePtr featlist;
-  Int4       num_clauses;
-  FeatureClausePtr subclause;
-
-  num_clauses = 0;
-  if (fcp == NULL) return FALSE;
-  subclause = NULL;
-  if (fcp->featlist == NULL) return FALSE;
-  for (featlist = fcp->featlist;
-       featlist != NULL;
-       featlist = featlist->next)
-  {
-    if (featlist->choice == DEFLINE_CLAUSEPLUS)
-    {
-      subclause = featlist->data.ptrvalue;
-      if (subclause == NULL || ! IsClauseTall (subclause))
-      {
-        return FALSE;
-      }
-      num_clauses ++;
-      if (num_clauses > 1) return FALSE;
-    }
-  }
-  if (subclause == NULL || ! subclause->feature_label_data.is_typeword_first)
-  {
-    return TRUE;
-  }
-  return FALSE;
-}
-
-static void SmashOneTallClause (
-  FeatureClausePtr fcp
-)
-{
-  FeatureClausePtr subclause;
-  ValNodePtr       featlist;
-  ValNodePtr       subclause_featlist;
-  ValNodePtr       subclause_firstclause;
-  CharPtr          new_description;
-  Int4             new_description_len;
-  SeqFeatPtr       main_feat;
-
-  if (fcp == NULL || fcp->featlist == NULL) return;
-
-  /* move features up */
-  featlist = fcp->featlist;
-  if (featlist->choice == DEFLINE_FEATLIST)
-  {
-    main_feat = fcp->featlist->data.ptrvalue;
-  }
-  else
-  {
-    main_feat = NULL;
-  }
-  
-  while (featlist != NULL && featlist->choice != DEFLINE_CLAUSEPLUS)
-  {
-    featlist = featlist->next;
-  }
-  if (featlist == NULL) return;
-  subclause = featlist->data.ptrvalue;
-  if (subclause == NULL) return;
- 
-  /* move subclause feats to top of list */
-  if (subclause->featlist != NULL
-    && subclause->featlist->choice == DEFLINE_FEATLIST)
-  {
-    subclause_featlist = subclause->featlist;
-    while (subclause->featlist != NULL
-           && subclause->featlist->next != NULL
-           && subclause->featlist->next->choice == DEFLINE_FEATLIST)
-    {
-      subclause->featlist = subclause->featlist->next;
-    }
-    if (subclause->featlist != NULL)
-    {
-      subclause_firstclause = subclause->featlist->next;
-      subclause->featlist->next = fcp->featlist;
-      fcp->featlist = subclause->featlist;
-      subclause->featlist = subclause_firstclause;
-    }
-  }
-
-  /* create new description */
-  new_description_len = StringLen (subclause->feature_label_data.description)
-                   + StringLen (fcp->feature_label_data.description)
-                   + StringLen (fcp->feature_label_data.typeword)
-                   + 4;
-  new_description = (CharPtr) MemNew (new_description_len);
-  if (new_description == NULL) return;
-  new_description [0] = 0;
-  if ( fcp->feature_label_data.is_typeword_first)
-  {
-    StringCat (new_description, fcp->feature_label_data.typeword);
-    StringCat (new_description, " ");
-  }
-  StringCat (new_description, fcp->feature_label_data.description);
-  if ( ! fcp->feature_label_data.is_typeword_first)
-  {
-    StringCat (new_description, fcp->feature_label_data.typeword);
-  }
-
-  if ( ! IsMobileElement (main_feat)
-    && ! IsEndogenousVirusSourceFeature (main_feat))
-  {
-    StringCat (new_description, ",");
-  }
-  StringCat (new_description, " ");
-  StringCat (new_description, subclause->feature_label_data.description);
-
-  if (fcp->feature_label_data.description != NULL)
-  {
-    MemFree (fcp->feature_label_data.description);
-  }
-  fcp->feature_label_data.description = new_description;
- 
-  /* move interval up */
-  if (fcp->interval != NULL)
-  {
-    MemFree (fcp->interval);
-  }
-  fcp->interval = subclause->interval;
-  subclause->interval = NULL;
-
-  /* move typeword up */
-  fcp->feature_label_data.typeword = subclause->feature_label_data.typeword;
-  fcp->feature_label_data.is_typeword_first = 
-               subclause->feature_label_data.is_typeword_first;
-  subclause->feature_label_data.typeword = NULL;
-  subclause->delete_me = TRUE;
-
-}
-
-static void SmashTallClauses (
-  ValNodePtr PNTR clause_list,
-  Boolean         delete_now
-)
-{
-  ValNodePtr clause;
-  FeatureClausePtr fcp;
-
-  if (clause_list == NULL) return;
-  for (clause = *clause_list; clause != NULL; clause = clause->next)
-  {
-    if (clause->choice != DEFLINE_CLAUSEPLUS || clause->data.ptrvalue == NULL)
-    {
-      continue;
-    }
-    fcp = clause->data.ptrvalue;
-    if ( IsClauseTall (fcp))
-    {
-      SmashOneTallClause (fcp);
-    }
-    else
-    {
-      SmashTallClauses (& (fcp->featlist), FALSE);
-    }
-  }
-  if (delete_now) 
-  {
-    DeleteFeatureClauses (clause_list);
-  }
-}
-
-static ValNodePtr RemoveAllButLastCDS (
-  ValNodePtr list,
-  ValNodePtr last_cds
-)
-{
-  ValNodePtr vnp;
-  FeatureClausePtr fcp;
-
-  /* now remove all CDSs except the last one */
-  for (vnp = list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_FEATLIST
-      && IsCDS (vnp->data.ptrvalue))
-    {
-      if (last_cds != NULL)
-      {
-        last_cds->choice = DEFLINE_REMOVEFEAT;
-      }
-      last_cds = vnp;
-    }
-    else if (vnp->choice == DEFLINE_CLAUSEPLUS
-      && (fcp = vnp->data.ptrvalue) != NULL)
-    {
-      last_cds = RemoveAllButLastCDS (fcp->featlist, last_cds);
-    }
-  }
-  return last_cds;
-}
-
-static Boolean OkToConsolidate (
-  CharPtr last_desc,
-  CharPtr new_desc,
-  Boolean last_partial,
-  Boolean new_partial,
-  FeatureClausePtr last_fcp,
-  FeatureClausePtr fcp
-)
-{
-  if (StringCmp (last_desc, new_desc) != 0) return FALSE;
-  if (new_partial != last_partial) return FALSE;
-  if ( ( fcp->is_alt_spliced && ! last_fcp->is_alt_spliced)
-      || (! fcp->is_alt_spliced && last_fcp->is_alt_spliced))
-  {
-    return FALSE;
-  }
-  if (fcp->featlist == NULL || last_fcp->featlist == NULL) return FALSE;
-  if ( fcp->featlist->choice != DEFLINE_FEATLIST) return FALSE;
-  if ( last_fcp->featlist->choice != DEFLINE_FEATLIST) return FALSE;
-  if ( (IsCDS (fcp->featlist->data.ptrvalue)
-        && ! IsCDS (last_fcp->featlist->data.ptrvalue)
-        && ! IsGene (last_fcp->featlist->data.ptrvalue))
-      || (! IsCDS (fcp->featlist->data.ptrvalue)
-        && ! IsGene (fcp->featlist->data.ptrvalue)
-        && IsCDS (last_fcp->featlist->data.ptrvalue)))
-  {
-    return FALSE;
-  }
-  if ((IsExon (fcp->featlist->data.ptrvalue) && !IsExon(last_fcp->featlist->data.ptrvalue))
-      || (IsExon (last_fcp->featlist->data.ptrvalue) && !IsExon(fcp->featlist->data.ptrvalue))
-      || (IsIntron (fcp->featlist->data.ptrvalue) && !IsIntron(last_fcp->featlist->data.ptrvalue))
-      || (IsIntron (last_fcp->featlist->data.ptrvalue) && !IsIntron(fcp->featlist->data.ptrvalue)))
-  {
-    return FALSE;
-  }
-  return TRUE;
-}
-
-static void RemoveRedundantGeneFeatureFromConsolidatedClause (
-  FeatureClausePtr fcp
-)
-{
-  ValNodePtr featlist, prevfeat, tmpfeat;
-  SeqFeatPtr feat1, feat2;
-
-  prevfeat = NULL;
-  featlist = fcp->featlist;
-  while ( featlist != NULL
-         && featlist->choice == DEFLINE_FEATLIST
-         && featlist->next != NULL
-         && featlist->next->choice == DEFLINE_FEATLIST)
-  {
-    feat1 = featlist->data.ptrvalue;
-    feat2 = featlist->next->data.ptrvalue;
-    if (feat1 == NULL || feat2 == NULL) return;
-    if (IsGene (feat1) && ! IsGene (feat2))
-    {
-      if (prevfeat == NULL)
-      {
-        fcp->featlist = featlist->next;
-        featlist->next = NULL;
-        FreeListElement (featlist);
-        featlist = fcp->featlist->next;
-      }
-      else
-      {
-        prevfeat->next = featlist->next;
-        featlist->next = NULL;
-        FreeListElement (featlist);
-        featlist = prevfeat->next;
-      }
-    }
-    else if ( !IsGene (feat1) && IsGene (feat2))
-    {
-      tmpfeat = featlist->next;
-      featlist->next = tmpfeat->next;
-      tmpfeat->next = NULL;
-      FreeListElement (tmpfeat);
-    }
-    else
-    {
-      featlist = featlist->next;
-    }
-  }
-}
-
-static void PluralizeConsolidatedClauseDescription (
-  FeatureClausePtr fcp
-)
-{
-  CharPtr new_desc;
-
-  /* prevent crash */
-  if (fcp == NULL || fcp->feature_label_data.description == NULL) return;
-
-  /* don't pluralize tRNA names */
-  if (StringNCmp (fcp->feature_label_data.description, "tRNA-", 5) ==0) return;
-
-  new_desc = MemNew (StringLen (fcp->feature_label_data.description) + 2);
-  if (new_desc == NULL) return;
-
-  StringCpy (new_desc, fcp->feature_label_data.description);
-  StringCat (new_desc, "s");
-  MemFree (fcp->feature_label_data.description);
-  fcp->feature_label_data.description = new_desc;
-}
-
-static void ConsolidateClauses (
-  ValNodePtr PNTR list,
-  BioseqPtr  bsp,
-  Uint1      biomol,
-  Boolean    delete_now,
-  Boolean    suppress_locus_tag)
-{
-  ValNodePtr       vnp;
-  FeatureClausePtr fcp;
-  FeatureClausePtr last_cds_fcp;
-  CharPtr          last_desc, new_desc;
-  Boolean          last_partial, new_partial, partial3, partial5;
-
-  if (list == NULL || *list == NULL) return;
-  last_cds_fcp = NULL;
-  last_desc = NULL;
-  for (vnp = *list; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice != DEFLINE_CLAUSEPLUS
-      || (fcp = vnp->data.ptrvalue) == NULL
-      || fcp->featlist == NULL
-      || fcp->featlist->choice != DEFLINE_FEATLIST)
-    {
-      continue;
-    }
-
-    ConsolidateClauses (&(fcp->featlist), bsp, biomol, FALSE, suppress_locus_tag);
-
-    if (last_cds_fcp == NULL)
-    {
-      last_cds_fcp = fcp;
-      if (fcp->feature_label_data.description == NULL)
-      {
-        last_desc = GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
-      }
-      else
-      {
-        last_desc = StringSave (fcp->feature_label_data.description);
-      }
-      CheckSeqLocForPartial (fcp->slp, &partial5, &partial3);
-      if (partial5 || partial3) 
-      {
-        last_partial = TRUE;
-      }
-      else
-      {
-        last_partial = FALSE;
-      }
-    }
-    else 
-    {
-      if (fcp->feature_label_data.description == NULL)
-      {
-        new_desc = GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
-      }
-      else
-      {
-        new_desc = StringSave (fcp->feature_label_data.description);
-      }
-      CheckSeqLocForPartial (fcp->slp, &partial5, &partial3);
-      if (partial5 || partial3) 
-      {
-        new_partial = TRUE;
-      }
-      else
-      {
-        new_partial = FALSE;
-      }
-      if ( OkToConsolidate (last_desc, new_desc,
-                            last_partial, new_partial,
-                            last_cds_fcp, fcp))
-      {
-        /* two clauses have identical descriptions - combine them */
-        MoveSubclauses (last_cds_fcp, fcp);
-        RemoveRedundantGeneFeatureFromConsolidatedClause (last_cds_fcp);
-        fcp->featlist = NULL;
-        fcp->delete_me = TRUE;
-        last_cds_fcp->slp = SeqLocMerge (bsp, last_cds_fcp->slp, fcp->slp,
-                                         FALSE, TRUE, FALSE);
-        /* if we have two clauses that are really identical instead of
-         * just sharing a "prefix", make the description plural
-         */
-        if (StringCmp (last_cds_fcp->interval, fcp->interval) == 0)
-        {
-          last_cds_fcp->make_plural = TRUE;
-/*          PluralizeConsolidatedClauseDescription (last_cds_fcp); */
-        }
-
-        /* Recalculate the interval */
-        if (last_cds_fcp->interval != NULL)
-        {
-          MemFree (last_cds_fcp->interval);
-        }
-        last_cds_fcp->interval =
-                  GetGenericInterval (last_cds_fcp, biomol, bsp, suppress_locus_tag);
-        MemFree (new_desc);
-      }
-      else
-      {
-        MemFree (last_desc);
-        last_desc = new_desc;
-        last_cds_fcp = fcp;
-        last_partial = new_partial;
-      }
-    }  
-  }   
-  if (delete_now) 
-  {
-    DeleteFeatureClauses (list);
-  }
-} 
-
-static void CountUnknownGenes (
-  ValNodePtr PNTR clause_list,
-  BioseqPtr       bsp,
-  Boolean         suppress_locus_tag)
-{
-  FeatureClausePtr fcp, new_fcp;
-  ValNodePtr vnp, new_vnp;
-  CharPtr gene_name;
-  Int4 num_unknown_genes;
-  
-  num_unknown_genes = 0;
-  vnp = *clause_list;
-  new_vnp = NULL;
-  new_fcp = NULL;
-  while (vnp != NULL)
-  {
-    if (vnp->choice == DEFLINE_CLAUSEPLUS
-      && (fcp = vnp->data.ptrvalue) != NULL
-      && ! fcp->is_unknown) 
-    {
-      CountUnknownGenes (&(fcp->featlist), bsp, suppress_locus_tag);
-      gene_name = GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
-      if (StringCmp (gene_name, "unknown") == 0
-        && fcp->featlist != NULL
-        && fcp->featlist->choice == DEFLINE_FEATLIST)
-      {
-        if (new_fcp == NULL)
-        {
-          new_vnp = ValNodeNew (*clause_list);
-          if (new_vnp == NULL) return;
-          new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue, 
-                                      bsp, suppress_locus_tag);
-          new_fcp->is_unknown = TRUE;
-          new_vnp->choice = DEFLINE_CLAUSEPLUS;
-          new_vnp->data.ptrvalue = new_fcp;
-        }
-        else
-        {
-          new_vnp = ValNodeNew (new_fcp->featlist);
-          if (new_vnp == NULL) return;
-          new_vnp->choice = DEFLINE_FEATLIST;
-          new_vnp->data.ptrvalue = fcp->featlist->data.ptrvalue;
-        }  
-        num_unknown_genes ++;
-        fcp->delete_me = TRUE;
-      }
-    }
-    vnp = vnp->next;
-  }
-   
-  if (num_unknown_genes > 0)
-  {
-    DeleteFeatureClauses (clause_list);
-    if (num_unknown_genes > 1)
-    {
-      new_fcp->feature_label_data.typeword = StringSave ("genes");
-    }
-  }
-}
-
-static void ReplaceDefinitionLine (
-  SeqEntryPtr sep,
-  CharPtr defline
-)
-{
-  ValNodePtr ttl;
-  if (sep == NULL || defline == NULL) return;
-
-  ttl = SeqEntryGetSeqDescr (sep, Seq_descr_title, NULL);
-  if (ttl == NULL)
-    ttl = CreateNewDescriptor (sep, Seq_descr_title);
-  if (ttl != NULL) {
-    MemFree (ttl->data.ptrvalue);
-    ttl->data.ptrvalue = defline;
-    defline = NULL;
-  }
-  MemFree (defline);
-}
-
-FeatureClausePtr NewFeatureClause 
-( SeqFeatPtr sfp,
-  BioseqPtr  bsp,
-  Boolean    suppress_locus_tag)
-{
-  FeatureClausePtr fcp;
-  Boolean          partial5, partial3;
-
-  fcp = (FeatureClausePtr) MemNew (sizeof (FeatureClauseData));
-  if (fcp == NULL) return NULL;
-
-  fcp->feature_label_data.typeword = NULL;
-  fcp->feature_label_data.description = NULL;
-  fcp->feature_label_data.productname = NULL;
-  fcp->feature_label_data.pluralizable = FALSE;
-  fcp->feature_label_data.is_typeword_first = FALSE;
-  fcp->allelename = NULL;
-  fcp->interval = NULL;
-  fcp->featlist = NULL;
-  fcp->delete_me = FALSE;
-  fcp->clause_info_only = FALSE;
-  fcp->make_plural = FALSE;
-  fcp->is_unknown = FALSE;
-  fcp->grp = NULL;
-  if (sfp == NULL) return fcp;
-  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
-  fcp->slp = SeqLocMerge (bsp, sfp->location, NULL,
-                                 FALSE, TRUE, FALSE);
-  SetSeqLocPartial (fcp->slp, partial5, partial3);
-  
-  if (sfp->data.choice == SEQFEAT_GENE)
-  {
-    fcp->grp = sfp->data.value.ptrvalue;
-  }
-  else
-  { 
-    fcp->grp = SeqMgrGetGeneXref (sfp);
-  }
-  if (( IsCDS (sfp) || IsExon (sfp) || IsNoncodingProductFeat (sfp))
-    && StringStr (sfp->comment, "alternatively spliced") != NULL) 
-  {
-    fcp->is_alt_spliced = TRUE;
-  }
-  else
-  {
-    fcp->is_alt_spliced = FALSE;
-  }
-  if (IsCDS (sfp))
-  {
-    fcp->feature_label_data.productname = GetProductName (sfp, bsp, suppress_locus_tag);
-  }
-  fcp->featlist = ValNodeNew (NULL);
-  if (fcp->featlist == NULL)
-  {
-    MemFree (fcp);
-    return NULL;
-  }
-
-  fcp->featlist->data.ptrvalue = sfp;
-  fcp->featlist->choice = DEFLINE_FEATLIST;
-  
-  return fcp;
-}
-
-static ValNodePtr GetFeatureList (BioseqPtr bsp, Boolean suppress_locus_tag)
-{
-  ValNodePtr        head, vnp;
-  SeqFeatPtr        sfp;
-  FeatureClausePtr  fcp;
-  SeqMgrFeatContext fcontext;
-
-  if (bsp == NULL) return NULL;
-
-  /* get list of all recognized features */
-  head = NULL;
-  sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
-  while (sfp != NULL)
-  {
-    if (IsRecognizedFeature (sfp))
-    {
-      fcp = NewFeatureClause (sfp, bsp, suppress_locus_tag);
-      if (fcp == NULL) return NULL;
-      fcp->numivals = fcontext.numivals;
-      fcp->ivals = fcontext.ivals;
-      vnp = ValNodeNew (head);
-      if (head == NULL) head = vnp;
-      if (vnp == NULL) return NULL;
-      vnp->data.ptrvalue = fcp;
-      vnp->choice = DEFLINE_CLAUSEPLUS;
-    }
-    sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
-  }
-  return head;
-}
-
-static void ExtractSegmentClauses (
-  ValNodePtr segment_features,
-  ValNodePtr parent_features,
-  ValNodePtr PNTR segment_clauses
-);
-
-static Boolean FeatureIsOnSegment (
-  SeqFeatPtr sfp, 
-  ValNodePtr segment_features
-)
-{
-  ValNodePtr vnp, featclause;
-  FeatureClausePtr fcp;
-
-  for (vnp = segment_features; vnp != NULL; vnp = vnp->next)
-  {
-    fcp = vnp->data.ptrvalue;
-    if (fcp != NULL)
-    {
-      for (featclause = fcp->featlist;
-           featclause != NULL;
-           featclause = featclause->next)
-      {
-        if (featclause->data.ptrvalue == sfp) return TRUE;
-      }
-    }
-  }
-  return FALSE;
-}
-
-static Boolean FeatureClauseIsOnSegment (
-  FeatureClausePtr fcp,
-  ValNodePtr segment_features
-)
-{
-  ValNodePtr vnp;
-
-  if (fcp == NULL || fcp->featlist == NULL) return FALSE;
-  for (vnp = fcp->featlist; vnp != NULL; vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_FEATLIST 
-      && FeatureIsOnSegment (vnp->data.ptrvalue, segment_features))
-    {
-      return TRUE;
-    }
-    else if (vnp->choice == DEFLINE_CLAUSEPLUS)
-    {
-      if (FeatureClauseIsOnSegment (vnp->data.ptrvalue, segment_features))
-      {
-        return TRUE;
-      }     
-    }
-  }
-  return FALSE;
-}
-
-static FeatureClausePtr CopyMatchingClauses (
-  FeatureClausePtr fcp,
-  ValNodePtr segment_features
-)
-{
-  FeatureClausePtr new_fcp, copy_clause;
-  ValNodePtr       featlist, new_feat;
-  Boolean          found_feat_on_segment;
-  Boolean          partial5, partial3;
-
-  new_fcp = (FeatureClausePtr) MemNew (sizeof (FeatureClauseData));
-  if (new_fcp == NULL) return NULL;
-  new_fcp->feature_label_data.pluralizable = 
-    fcp->feature_label_data.pluralizable;
-  new_fcp->feature_label_data.is_typeword_first = 
-    fcp->feature_label_data.is_typeword_first;
-  new_fcp->feature_label_data.typeword =
-    StringSave (fcp->feature_label_data.typeword);
-  new_fcp->feature_label_data.description = 
-    StringSave (fcp->feature_label_data.description);
-  new_fcp->feature_label_data.productname =
-    StringSave (fcp->feature_label_data.productname);
-  new_fcp->allelename = StringSave (fcp->allelename);
-  new_fcp->interval = StringSave (fcp->interval);
-  new_fcp->is_alt_spliced = fcp->is_alt_spliced;
-  CheckSeqLocForPartial (fcp->slp, &partial5, &partial3);
-  new_fcp->slp = (SeqLocPtr) AsnIoMemCopy (fcp->slp, (AsnReadFunc) SeqLocAsnRead,
-                                           (AsnWriteFunc) SeqLocAsnWrite);
-  SetSeqLocPartial (new_fcp->slp, partial5, partial3);
-  new_fcp->grp = fcp->grp;
-  new_fcp->has_mrna = fcp->has_mrna;
-  new_fcp->delete_me = FALSE;
-  new_fcp->clause_info_only = fcp->clause_info_only;
-  new_fcp->featlist = NULL;
-  found_feat_on_segment = FALSE;
-  for (featlist = fcp->featlist; featlist != NULL; featlist = featlist->next)
-  {
-    new_feat = NULL;
-    if (featlist->choice == DEFLINE_FEATLIST)
-    {
-      new_feat = ValNodeNew (new_fcp->featlist);
-      if (new_feat == NULL) return NULL;
-      new_feat->data.ptrvalue = featlist->data.ptrvalue;
-      new_feat->choice = DEFLINE_FEATLIST;
-
-      /* some portions of the clause are present for product and gene info */
-      /* if they aren't actually on the segment */
-      if ( segment_features == NULL
-        || FeatureIsOnSegment (new_feat->data.ptrvalue, segment_features))
-      {
-        found_feat_on_segment = TRUE;
-      }
-    }
-    else if (featlist->choice == DEFLINE_CLAUSEPLUS)
-    {
-      copy_clause = featlist->data.ptrvalue;
-      if ( segment_features == NULL
-        || FeatureClauseIsOnSegment ( copy_clause, segment_features))
-      {
-        new_feat = ValNodeNew (new_fcp->featlist);
-        if (new_feat == NULL) return NULL;
-        new_feat->data.ptrvalue = CopyMatchingClauses ( copy_clause,
-                                                        segment_features);
-        new_feat->choice = DEFLINE_CLAUSEPLUS;
-      }
-    }
-    if (new_feat != NULL && new_fcp->featlist == NULL) 
-    {
-      new_fcp->featlist = new_feat;
-    }
-  }
-  if (found_feat_on_segment)
-  {
-    new_fcp->clause_info_only = FALSE;
-  }
-  else
-  {
-    new_fcp->clause_info_only = TRUE;
-  }
-  return new_fcp; 
-}
-
-static void CopyFeatureList (
-  ValNodePtr match_features,
-  ValNodePtr parent_features,
-  ValNodePtr PNTR new_list
-)
-{
-  ValNodePtr vnp, addvnp;
-
-  for (vnp = parent_features;
-       vnp != NULL;
-       vnp = vnp->next)
-  {
-    if (vnp->choice == DEFLINE_FEATLIST 
-      && (match_features == NULL
-        || FeatureIsOnSegment ( vnp->data.ptrvalue, match_features)))
-    {
-      addvnp = ValNodeNew (*new_list);
-      if (addvnp == NULL) return;
-      addvnp->data.ptrvalue = vnp->data.ptrvalue;
-      addvnp->choice = DEFLINE_FEATLIST;
-      if (*new_list == NULL) *new_list = addvnp;
-    }
-    else if (vnp->choice == DEFLINE_CLAUSEPLUS
-      && (match_features == NULL
-        || FeatureClauseIsOnSegment ( vnp->data.ptrvalue, match_features)))
-    {
-      addvnp = ValNodeNew (*new_list);
-      if (addvnp == NULL) return;
-      addvnp->data.ptrvalue = CopyMatchingClauses ( vnp->data.ptrvalue,
-                                                    match_features);
-      addvnp->choice = DEFLINE_CLAUSEPLUS;
-      if (*new_list == NULL) *new_list = addvnp;
-    }
-  }
-    
-}
-
-static void ExtractSegmentClauses (
-  ValNodePtr segment_features,
-  ValNodePtr parent_features,
-  ValNodePtr PNTR segment_clauses
-)
-{
-  CopyFeatureList (segment_features, parent_features, segment_clauses);
-}
-
-typedef struct segmentdeflinedata {
-  BioseqPtr  parent_bsp;
-  ValNodePtr parent_feature_list;
-  Uint1      molecule_type;
-  DeflineFeatureRequestList PNTR feature_requests;
-  ModifierCombinationPtr m;
-  ModifierItemLocalPtr modList;
-  OrganismDescriptionModifiersPtr odmp;
-  Int2 product_flag;
-} SegmentDefLineData, PNTR SegmentDefLinePtr;
-
-typedef struct segmentdeflinefeatureclausedata {
-  BioseqPtr  parent_bsp;
-  ValNodePtr parent_feature_list;
-  Uint1      molecule_type;
-  DeflineFeatureRequestList PNTR feature_requests;
-  Int2            product_flag;
-  Boolean         alternate_splice_flag;
-  Boolean         gene_cluster_opp_strand;
-  ValNodePtr PNTR list;
-} SegmentDefLineFeatureClauseData, PNTR SegmentDefLineFeatureClausePtr;
-
-typedef struct deflinefeatclause {
-  SeqEntryPtr sep;
-  BioseqPtr   bsp;
-  CharPtr     clauselist;
-} DefLineFeatClauseData, PNTR DefLineFeatClausePtr;
-
-static void DefLineFeatClauseListFree (ValNodePtr vnp)
-{
-  DefLineFeatClausePtr deflist;
-
-  if (vnp == NULL) return;
-  DefLineFeatClauseListFree (vnp->next);
-  vnp->next = NULL;
-  deflist = vnp->data.ptrvalue;
-  if (deflist != NULL)
-  {
-    MemFree (deflist->clauselist);
-    MemFree (deflist);
-  }
-  ValNodeFree (vnp);
-}
-
-
-static Boolean IntervalIntersectsIvals 
-(Int2    numivals,
- Int4Ptr ivals,
- SeqMgrSegmentContextPtr context)
-{
-  Int2 idx;
-  Int4 start, stop;
-
-  if (numivals == 0 || ivals == NULL || context == NULL) return FALSE;
-
-  for (idx = 0; idx < numivals; idx ++) {
-    start = ivals [idx * 2];
-    stop = ivals [idx * 2 + 1];
-    if ( start <= context->cumOffset + context->to - context->from
-         && stop >= context->cumOffset)
-    {
-      return TRUE;
-    }
-  }
-  return FALSE;
-}
-
-
-/* if there are no features at all on this segment, select the genes that 
- * traverse the segment.
- */
-static ValNodePtr GrabTraversingGenes 
-(ValNodePtr              parent_feature_list,
- SeqMgrSegmentContextPtr context,
- BioseqPtr               parent_bsp,
- Boolean                 suppress_locus_tag)
-{
-  FeatureClausePtr  fcp, new_fcp;
-  ValNodePtr        clause;
-  SeqFeatPtr        sfp;
-  ValNodePtr        segment_feature_list;
-  ValNodePtr        vnp;
-
-  segment_feature_list = NULL;
-  for (clause = parent_feature_list;
-       clause != NULL;
-       clause = clause->next)
-  {
-    fcp = clause->data.ptrvalue;
-
-    if (fcp != NULL  &&  fcp->featlist != NULL
-        &&  (sfp = fcp->featlist->data.ptrvalue) != NULL
-        &&  sfp->idx.subtype == FEATDEF_GENE
-        &&  fcp->ivals != NULL && fcp->numivals > 0)
-    {
-      if (IntervalIntersectsIvals (fcp->numivals, fcp->ivals, context)) {
-        new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue, parent_bsp,
-                                    suppress_locus_tag);
-        if (new_fcp == NULL) return FALSE;
-        vnp = ValNodeNew (segment_feature_list);
-        if (vnp == NULL) return FALSE;
-        vnp->data.ptrvalue = new_fcp;
-        vnp->choice = DEFLINE_CLAUSEPLUS;
-        if (segment_feature_list == NULL) segment_feature_list = vnp;
-      }
-    } 
-  }
-  return segment_feature_list;
-}
-
-
-static CharPtr BuildFeatureClauses (
-  BioseqPtr   bsp,
-  Uint1       molecule_type,
-  SeqEntryPtr sep,
-  ValNodePtr  PNTR feature_list,
-  Boolean     isSegment,
-  ValNodePtr  PNTR seg_feature_list,
-  Int2        product_flag,
-  Boolean     alternate_splice_flag,
-  Boolean     gene_cluster_opp_strand,
-  DeflineFeatureRequestList PNTR feature_requests
-);
-
-static Boolean LIBCALLBACK GetFeatureClauseForSeg (
-  SeqLocPtr slp,
-  SeqMgrSegmentContextPtr context)
-{
-  SegmentDefLineFeatureClausePtr sdlp;
-  ValNodePtr        clause, tmp_parent_list;
-  FeatureClausePtr  fcp, new_fcp;
-  Int2              idx;
-  Int4              start, stop;
-  ValNodePtr        segment_feature_list, vnp;
-  SeqIdPtr          sip;
-  BioseqPtr         bsp;
-  Uint2             entityID;
-  SeqLocPtr         loc;
-  DefLineFeatClausePtr deflist;
-
-  if (slp == NULL || context == NULL) return FALSE;
-  sdlp = (SegmentDefLineFeatureClausePtr) context->userdata;
-
-  sip = SeqLocId (slp);
-  
-  if (sip == NULL) {
-    loc = SeqLocFindNext (slp, NULL);
-    if (loc != NULL) {
-      sip = SeqLocId (loc);
-    }
-  }
-  if (sip == NULL) return TRUE;
-
-  bsp = BioseqFind (sip);
-
-  if (bsp == NULL) return TRUE;
-
-
-  segment_feature_list = NULL;
-  for (clause = sdlp->parent_feature_list;
-       clause != NULL;
-       clause = clause->next)
-  {
-    fcp = clause->data.ptrvalue;
-
-    if (fcp != NULL && fcp->ivals != NULL && fcp->numivals > 0)
-    {
-      idx = (fcp->numivals - 1) * 2;
-      start = fcp->ivals [idx];
-      stop = fcp->ivals [idx + 1];
-      if ( stop <= context->cumOffset + context->to - context->from
-           && stop >= context->cumOffset)
-      {
-        new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue,
-                                    sdlp->parent_bsp, 
-                                    sdlp->feature_requests->suppress_locus_tags);
-        if (new_fcp == NULL) return FALSE;
-        vnp = ValNodeNew (segment_feature_list);
-        if (vnp == NULL) return FALSE;
-        vnp->data.ptrvalue = new_fcp;
-        vnp->choice = DEFLINE_CLAUSEPLUS;
-        if (segment_feature_list == NULL) segment_feature_list = vnp;
-      }
-    } 
-  }
-
-  if (segment_feature_list == NULL) {
-    segment_feature_list = GrabTraversingGenes (sdlp->parent_feature_list,
-                                                context, sdlp->parent_bsp,
-                                                sdlp->feature_requests->suppress_locus_tags);
-  }
-
-  entityID = ObjMgrGetEntityIDForPointer (bsp);
-
-  tmp_parent_list = NULL;
-  CopyFeatureList (NULL, sdlp->parent_feature_list, &tmp_parent_list);
-
-  deflist = (DefLineFeatClausePtr) MemNew (sizeof (DefLineFeatClauseData));
-  if (deflist == NULL) return TRUE;
-  deflist->sep = SeqMgrGetSeqEntryForData (bsp);
-  deflist->bsp = bsp;
-  deflist->clauselist = BuildFeatureClauses (sdlp->parent_bsp,
-                            sdlp->molecule_type,
-                            SeqMgrGetSeqEntryForData (bsp),
-                            &tmp_parent_list,
-                            TRUE,
-                            &segment_feature_list,
-                            sdlp->product_flag,
-							              sdlp->alternate_splice_flag,
-							              sdlp->gene_cluster_opp_strand,
-                            sdlp->feature_requests);
-  vnp = ValNodeNew (*(sdlp->list));
-  if (vnp == NULL) return TRUE;
-  if (*(sdlp->list) == NULL) *(sdlp->list) = vnp;
-  vnp->data.ptrvalue = deflist;
-
-  FreeListElement (tmp_parent_list);
-  FreeListElement (segment_feature_list);
-  DeleteMarkedObjects (entityID, 0, NULL);
-  return TRUE;
-}
-
-static void ShowFeatureList (ValNodePtr feature_list, FILE *fp, CharPtr title)
-{
-  Boolean          show_file = FALSE;
-  Char             path[PATH_MAX];
-  SeqFeatPtr       sfp;
-  FeatureClausePtr fcp;
-  SeqMgrFeatContext  context;
-  
-  if (fp == NULL)
-  {
-    TmpNam (path);
-    fp = FileOpen (path, "wb");
-    show_file = TRUE;
-  }
-  while (feature_list != NULL)
-  {
-    if (feature_list->choice == DEFLINE_CLAUSEPLUS)
-    {
-      fcp = (FeatureClausePtr) feature_list->data.ptrvalue;
-      if (fcp == NULL)
-      {
-        fprintf (fp, "Empty clause\n");
-      }
-      else
-      {
-        fprintf (fp, "Clause\n");
-        if (fcp->has_mrna)
-        {
-          fprintf (fp, "Has mRNA\n");
-        }
-        if (fcp->slp == NULL)
-        {
-          fprintf (fp, "Has empty location\n");
-        }
-        ShowFeatureList (fcp->featlist, fp, title);
-        fprintf (fp, "End Clause\n");
-      }
-    }
-    else if (feature_list->choice == DEFLINE_FEATLIST)
-    {
-      sfp = (feature_list->data.ptrvalue);
-      sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, 0, 0, sfp, &context);
-      fprintf (fp, "%d:%s\n", sfp->idx.subtype, context.label);
-    }
-    
-    feature_list = feature_list->next;
-  }
-  if (show_file)
-  {
-    FileClose (fp);
-    LaunchGeneralTextViewer (path, title);
-    FileRemove (path);
-  }
-}
-
-static Boolean HasAnyPromoters (BioseqPtr bsp)
-{
-  SeqFeatPtr sfp;
-  SeqMgrFeatContext fcontext;
-  
-  sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_promoter, &fcontext);
-  if (sfp == NULL) {
-    return FALSE;
-  } else {
-    return TRUE;
-  }
-}
-
-static void AddFakePromoterClause (ValNodePtr PNTR feature_list, BioseqPtr bsp, Boolean suppress_locus_tag)
-{
-  FeatureClausePtr fcp;
-  SeqFeatPtr       sfp = NULL;
-  
-  /* create fake promoter */
-  sfp = CreateNewFeature (SeqMgrGetSeqEntryForData (bsp), NULL,
-                          SEQFEAT_IMP, NULL);
-
-  sfp->location = SeqLocIntNew (0, bsp->length - 1, Seq_strand_plus, SeqIdDup (bsp->id));
-  sfp->data.choice = SEQFEAT_IMP;
-  sfp->idx.subtype = FEATDEF_promoter;
-  /* mark promoter for deletion */
-  sfp->idx.deleteme = TRUE;
-  
-  fcp = NewFeatureClause (sfp, bsp, suppress_locus_tag);
-  if (fcp == NULL) return;
-  fcp->numivals = 1;
-  fcp->ivals = (Int4Ptr) MemNew (sizeof (Int4) * 2);
-  fcp->ivals[0] = 0;
-  fcp->ivals[1] = bsp->length - 1;
-  ValNodeAddPointer (feature_list, DEFLINE_CLAUSEPLUS, fcp);
-  
-}
-
-static Boolean IsInGenProdSet (BioseqPtr bsp)
-{
-  BioseqSetPtr bssp;
-  if (bsp == NULL || bsp->idx.parentptr == NULL || bsp->idx.parenttype != OBJ_BIOSEQSET) {
-    return FALSE;
-  }
-  bssp = (BioseqSetPtr) bsp->idx.parentptr;
-  if (bssp->_class != BioseqseqSet_class_nuc_prot || bssp->idx.parentptr == NULL || bsp->idx.parenttype != OBJ_BIOSEQSET) {
-    return FALSE;
-  }
-  bssp = bssp->idx.parentptr;
-  if (bssp->_class == BioseqseqSet_class_gen_prod_set) {
-    return TRUE;
-  } else {
-    return FALSE;
-  }
-}
-
-/* NOTE: under some circumstances this function will create features that
- * are marked for deletion, so DeleteMarkedObjects should always be called
- * at some later point.
- */
-static CharPtr BuildFeatureClauses (
-  BioseqPtr   bsp,
-  Uint1       molecule_type,
-  SeqEntryPtr sep,
-  ValNodePtr  PNTR feature_list,
-  Boolean     isSegment,
-  ValNodePtr  PNTR seg_feature_list,
-  Int2        product_flag,
-  Boolean     alternate_splice_flag,
-  Boolean     gene_cluster_opp_strand,
-  DeflineFeatureRequestList PNTR feature_requests
-)
-{
-  ValNodePtr   strings = NULL;
-  ValNodePtr   clause;
-  CharPtr      str = NULL;
-  Char         ending_str [200];
-  ValNodePtr   tmp_feat_list;
-  BioSourcePtr biop;
-
-  if ((feature_requests->feature_list_type == DEFLINE_USE_FEATURES
-       || (IsmRNASequence(bsp) && IsInGenProdSet(bsp)))
-      && (! isSegment || (seg_feature_list != NULL && *seg_feature_list != NULL)))
-  {
-    /* remove features that indexer has chosen to suppress before they are grouped
-     * with other features or used to determine loneliness etc.
-     */
-    RemoveSuppressedFeatures (feature_list, feature_requests->suppressed_feature_list);
-  
-    GroupmRNAs (feature_list, bsp, feature_requests->suppress_locus_tags);
-
-    /* genes are added to other clauses */
-    GroupGenes (feature_list, feature_requests->suppress_locus_tags);
-
-    if (! feature_requests->suppress_alt_splice_phrase)
-    {
-      /* find alt-spliced CDSs */
-      FindAltSplices (*feature_list, bsp, feature_requests->suppress_locus_tags);
-    }
-
-    GroupAltSplicedExons (feature_list, bsp, TRUE);
-    
-    if (!isSegment)
-    {
-       /* group CDSs that have the same name and are under the same gene together */
-      GroupSegmentedCDSs (feature_list, bsp, TRUE, feature_requests->suppress_locus_tags);
-    }
-
-    /* per Susan's request, if promoters are requested and no promoters are found, add a promoter */
-    if (feature_requests->items[RemovablePromoter].keep && !HasAnyPromoters (bsp)) {
-      AddFakePromoterClause (feature_list, bsp, feature_requests->suppress_locus_tags);
-    }
-
-    /* now group clauses */
-    GroupAllClauses ( feature_list, gene_cluster_opp_strand, bsp );
-
-    ExpandAltSplicedExons (*feature_list, bsp, feature_requests->suppress_locus_tags);
-
-    FindGeneProducts (*feature_list, bsp, feature_requests->suppress_locus_tags);
-
-    if (seg_feature_list != NULL && *seg_feature_list != NULL)
-    {
-      tmp_feat_list = NULL; 
-      ExtractSegmentClauses ( *seg_feature_list, *feature_list, &tmp_feat_list);
-      FreeListElement (*feature_list);
-      DeleteMarkedObjects (bsp->idx.entityID, 0, NULL);
-      *feature_list = tmp_feat_list;
-    }
-   
-    /* remove exons and other unwanted features */
-    RemoveUnwantedFeatures (feature_list, bsp, isSegment, feature_requests);
-
-    RemoveGenesMentionedElsewhere (feature_list, *feature_list, TRUE,
-                                   feature_requests->suppress_locus_tags);
-
-    if (feature_requests->remove_subfeatures)
-    {
-      DeleteSubfeatures (feature_list, TRUE);
-    }
-
-    DeleteOperonAndGeneClusterSubfeatures (feature_list, TRUE);
-
-    CountUnknownGenes (feature_list, bsp, feature_requests->suppress_locus_tags);
-
-    if (feature_requests->misc_feat_parse_rule == 1)
-    {
-      RenameMiscFeats (*feature_list, molecule_type);
-    }
-    else
-    {
-      RemoveUnwantedMiscFeats (feature_list, TRUE);
-    }
-
-    ReplaceRNAClauses (feature_list, bsp, feature_requests->suppress_locus_tags);
-
-    /* take any exons on the minus strand */
-    /* and reverse their order within the clause */
-    ReverseClauses (feature_list, IsExonOrIntron);
-
-    RenameExonSequences ( feature_list, bsp, TRUE);
-
-    LabelClauses (*feature_list, molecule_type, bsp, 
-                  feature_requests->suppress_locus_tags);
-
-    /* parse lists of tRNA and intergenic spacer clauses in misc_feat notes */
-    /* need to do this after LabelClauses, since LabelClauses labels intergenic
-     * spacers with more relaxed restrictions.  The labels from LabelClauses
-     * for intergenic spacers are the default values.
-     */
-    ReplaceIntergenicSpacerClauses (feature_list, bsp, feature_requests->suppress_locus_tags);
-
-    ConsolidateClauses (feature_list, bsp, molecule_type, TRUE,
-                        feature_requests->suppress_locus_tags);
-
-    /* this allows genes to be listed together even if they are from */
-    /* separate sequences */
-/*    SmashTallClauses (feature_list, TRUE); */
-
-    clause = *feature_list;
-    ListClauses (clause, &strings, TRUE, FALSE);
-
-    AutoDef_AddEnding (clause, &strings, bsp, 
-                       product_flag, alternate_splice_flag);
-    str = MergeValNodeStrings (strings, FALSE);
-	  ValNodeFreeData (strings);
-  }
-  else if (feature_requests->feature_list_type == DEFLINE_COMPLETE_SEQUENCE)
-  {
-    str = StringSave (", complete sequence.");
-  }
-  else if (feature_requests->feature_list_type == DEFLINE_COMPLETE_GENOME)
-  {
-    ending_str [0] = 0;
-    biop = GetBiopForBsp (bsp);
-    if (biop != NULL)
-    {
-      switch (biop->genome) {
-        case GENOME_macronuclear :
-          sprintf (ending_str, "macronuclear");
-          break;
-        case GENOME_nucleomorph :
-          sprintf (ending_str, "nucleomorph");
-          break;
-        case GENOME_mitochondrion :
-          sprintf (ending_str, "mitochondrion");
-          break;
-        case GENOME_apicoplast :
-        case GENOME_chloroplast :
-        case GENOME_chromoplast :
-        case GENOME_kinetoplast :
-        case GENOME_plastid :
-        case GENOME_cyanelle :
-        case GENOME_leucoplast :
-        case GENOME_proplastid :
-        case GENOME_hydrogenosome :
-          sprintf (ending_str, "%s", organelleByGenome [biop->genome]);
-          break;
-      }
-    }
-    StringCat (ending_str, ", complete genome.");
-    str = StringSave (ending_str);
-  }
-  else
-  {
-    str = StringSave ("");
-  }
-  
-  return str;
-}
-
-/* This function looks at the product names for the CDSs on the Bioseq,
- * and sets the flag for the "nuclear genes for X products" ending
- * based on the contents of the CDS products. */
-static Int2 GetProductFlagFromCDSProductNames (BioseqPtr bsp)
-{
-  SeqMgrFeatContext context;
-  SeqFeatPtr        cds = NULL;
-  Int2              product_flag;
-  Int2              i;
-  CharPtr           found;
-  Char              ch_before, ch_after;
-
-  product_flag = 0;
-  for (cds = SeqMgrGetNextFeature (bsp, cds, SEQFEAT_CDREGION, 0, &context);
-       cds != NULL && product_flag == 0;
-       cds = cds->next)
-  {
-    for (i = 1; organelleByPopup[i] != NULL && product_flag == 0; i++)
-    {
-      found = StringStr (context.label, organelleByPopup[i]);
-      if (found != NULL)
-      {
-        if (found == context.label) {
-          ch_before = ' ';
-        } else {
-          ch_before = *(found - 1);
-        }
-        ch_after = *(found + StringLen (organelleByPopup[i]));
-        if (ch_before == ' ' && (ch_after == 0 || ch_after == ' '))
-        {
-          product_flag = i;
-        }
-      }
-    }
-  }
-
-  return product_flag;
-}
-
-static void BuildDefLineFeatClauseList (
-  SeqEntryPtr sep,
-  Uint2 entityID,
-  DeflineFeatureRequestList PNTR feature_requests,
-  Int2 product_flag,
-  Boolean alternate_splice_flag,
-  Boolean gene_cluster_opp_strand,
-  ValNodePtr PNTR list
-)
-{
-  BioseqSetPtr    bssp;
-  BioseqPtr    bsp;
-  ValNodePtr    head;
-  Uint1      molecule_type;
-  SeqEntryPtr   nsep;
-  SegmentDefLineFeatureClauseData sdld;
-  DefLineFeatClausePtr deflist;
-  ValNodePtr    vnp;
-
-  if (sep == NULL || list == NULL) return;
-
-  if ( IS_Bioseq_set (sep))
-  {
-    bssp = (BioseqSetPtr) sep->data.ptrvalue;
-    if (bssp == NULL) return;
-    if ( bssp->_class == 7 || IsPopPhyEtcSet (bssp->_class)
-        || bssp->_class == BioseqseqSet_class_gen_prod_set
-        || bssp->_class == BioseqseqSet_class_not_set)
-    {
-      for (sep = bssp->seq_set; sep != NULL; sep = sep->next)
-      {
-        BuildDefLineFeatClauseList (sep, entityID, feature_requests,
-                                    product_flag, alternate_splice_flag,
-                                    gene_cluster_opp_strand, list);
-      }
-      return;
-    }
-  }
-    
-  nsep = FindNucSeqEntry (sep);
-  if (nsep != NULL)
-  {
-    bsp = (BioseqPtr) nsep->data.ptrvalue;
-    if ( SpecialHandlingForSpecialTechniques (bsp)) 
-    {
-      return;
-    }
-    if (bsp != NULL && bsp->repr == Seq_repr_seg &&
-      bsp->seq_ext != NULL && bsp->seq_ext_type == 1) 
-    {
-      /* get default product flag if necessary */
-	  if (product_flag == -1 || product_flag == DEFAULT_ORGANELLE_CLAUSE) {
-	    product_flag = GetProductFlagFromCDSProductNames (bsp);
-	  }
-
-      sdld.parent_bsp = bsp;
-      sdld.molecule_type = GetMoleculeType (bsp, entityID);
-      sdld.parent_feature_list = GetFeatureList (bsp, 
-                                                 feature_requests->suppress_locus_tags);
-
-      sdld.feature_requests =  feature_requests;
-      sdld.product_flag = product_flag;
-      sdld.alternate_splice_flag = alternate_splice_flag;
-      sdld.gene_cluster_opp_strand = gene_cluster_opp_strand;
-      sdld.list = list;
-      SeqMgrExploreSegments (bsp, (Pointer) &sdld, GetFeatureClauseForSeg);
-      deflist = (DefLineFeatClausePtr) MemNew (sizeof (DefLineFeatClauseData));
-      if (deflist == NULL) return;
-      deflist->sep = SeqMgrGetSeqEntryForData (bsp),
-      deflist->bsp = bsp;
-
-      deflist->clauselist = BuildFeatureClauses (bsp,
-                            sdld.molecule_type,
-                            SeqMgrGetSeqEntryForData (bsp),
-                            &sdld.parent_feature_list,
-                            FALSE,
-                            NULL,
-                            product_flag,
-                            alternate_splice_flag,
-                            gene_cluster_opp_strand,
-                            feature_requests);
-      vnp = ValNodeNew (*list);
-      if (vnp == NULL) return;
-      if (*list == NULL) *list = vnp;
-      vnp->data.ptrvalue = deflist;
-      FreeListElement (sdld.parent_feature_list);
-      DeleteMarkedObjects (entityID, 0, NULL);
-      return;
-    }
-  }
-
-  if (nsep != NULL && nsep != sep)
-    sep = nsep;
-
-  /* get list of all recognized features */
-  bsp = (BioseqPtr) sep->data.ptrvalue;
-  if (bsp == NULL) return;
-  if ( SpecialHandlingForSpecialTechniques (bsp)) 
-  {
-    return;
-  }
-  molecule_type = GetMoleculeType (bsp, entityID);
-  head = GetFeatureList (bsp, feature_requests->suppress_locus_tags);
-
-  /* get default product flag if necessary */
-  if (product_flag == -1 || product_flag == DEFAULT_ORGANELLE_CLAUSE) {
-    product_flag = GetProductFlagFromCDSProductNames (bsp);
-  }
-
-  deflist = (DefLineFeatClausePtr) MemNew (sizeof (DefLineFeatClauseData));
-  if (deflist == NULL) return;
-  deflist->sep = SeqMgrGetSeqEntryForData (bsp),
-  deflist->bsp = bsp;
-  deflist->clauselist = BuildFeatureClauses (bsp,
-                                             molecule_type,
-                                             SeqMgrGetSeqEntryForData (bsp),
-                                             &head,
-                                             FALSE,
-                                             NULL,
-                                             product_flag,
-                                             alternate_splice_flag,
-                                             gene_cluster_opp_strand,
-                                             feature_requests);
-  vnp = ValNodeNew (*list);
-  if (vnp == NULL) return;
-  if (*list == NULL) *list = vnp;
-  vnp->data.ptrvalue = deflist;
-  FreeListElement (head);
-  DeleteMarkedObjects (entityID, 0, NULL);
-}
-
-
-static Boolean IdenticalExceptForPartialComplete (CharPtr str1, CharPtr str2)
-{
-    CharPtr cp, word_in_first, word_in_second;
-    Int4    first_len, second_len, compare_len;
-    
-    if (StringHasNoText (str1) && StringHasNoText (str2)) {
-        return TRUE;
-    } else if (StringHasNoText (str1) || StringHasNoText (str2)) {
-        return FALSE;
-    }
-    
-    word_in_first = StringISearch (str1, "partial");
-    cp = StringISearch (str1, "complete");
-    if (word_in_first == NULL || (cp != NULL && word_in_first > cp)) {
-        word_in_first = cp;
-        first_len = 8;
-    } else {
-        first_len = 7;
-    }
-    
-    word_in_second = StringISearch (str2, "partial");
-    cp = StringISearch (str2, "complete");
-    if (word_in_second == NULL || (cp != NULL && word_in_second > cp)) {
-        word_in_second = cp;
-        second_len = 8;
-    } else {
-        second_len = 7;
-    }
-    
-    if (word_in_first == NULL && word_in_second == NULL) {
-        if (StringCmp (str1, str2) == 0) {
-            return TRUE;
-        } else {
-            return FALSE;
-        }
-    } else if (word_in_first == NULL || word_in_second == NULL) {
-        return FALSE;
-    } else if ((compare_len = word_in_first - str1) != word_in_second - str2) {
-        return FALSE;
-    } else if (StringNCmp (str1, str2, compare_len) != 0) {
-        return FALSE;
-    } else {
-        return IdenticalExceptForPartialComplete (word_in_first + first_len, word_in_second + second_len);
-    }    
-}
-
-
-static Boolean AreFeatureClausesUnique (ValNodePtr list)
-{
-  ValNodePtr vnp1, vnp2;
-  DefLineFeatClausePtr deflist1, deflist2;
-
-  for (vnp1 = list; vnp1 != NULL && vnp1->next != NULL; vnp1 = vnp1->next)
-  {
-    deflist1 = vnp1->data.ptrvalue;
-    if (deflist1 == NULL || deflist1->clauselist == NULL) return FALSE;
-    
-    for (vnp2 = vnp1->next; vnp2 != NULL; vnp2 = vnp2->next)
-    {
-      deflist2 = vnp2->data.ptrvalue;
-      if (deflist2 == NULL || deflist2->clauselist == NULL
-        || IdenticalExceptForPartialComplete (deflist1->clauselist, deflist2->clauselist))
-      {
-        return FALSE;
-      }
-    }
-  }
-  return TRUE;
-}
-
-static void BuildDefinitionLinesFromFeatureClauseLists (
-  ValNodePtr list,
-  ModifierItemLocalPtr modList,
-  ModifierCombinationPtr m,
-  OrganismDescriptionModifiers odmp
-);
 
 typedef struct deflineformdata {
   FEATURE_FORM_BLOCK
 
   ModifierItemLocalPtr modList;
+  ButtoN PNTR modifier_btns;
   DeflineFeatureRequestList feature_requests;
+  ButtoN    feature_btns[NumRemovableItems];
   GrouP     sourceListGrp;
   PopuP     customGrp;
   ButtoN    use_labels;
@@ -10039,6 +72,7 @@ typedef struct deflineformdata {
   ButtoN    exclude_sp;
   ButtoN    exclude_cf;
   ButtoN    exclude_aff;
+  ButtoN    exclude_nr;
   ButtoN    include_country_extra;
   ButtoN    allow_semicolon_in_modifier;
   GrouP     clone_isolate_HIV_rule_num;
@@ -10052,7 +86,9 @@ typedef struct deflineformdata {
   GrouP     featureOptsGrp;
   GrouP     optional_features_grp;
   PopuP     misc_feat_parse_rule;
+  GrouP     promoter_type;
   ButtoN    alternate_splice_flag;
+  ButtoN    use_ncrna_note;
   ButtoN    suppress_locus_tags;
   ButtoN    gene_cluster_opp_strand;
   DialoG    suppressed_feature_list;
@@ -10085,12 +121,13 @@ static void CleanupDefLineForm (
   if (dlfp != NULL) {
     if (dlfp->modList != NULL)
     {
-      for (i=0; i < NumDefLineModifiers; i++)
+      for (i=0; i < NumDefLineModifiers (); i++)
       {
         ValNodeFree (dlfp->modList[i].values_seen);
       }
       MemFree (dlfp->modList);
     }
+    dlfp->modifier_btns = MemFree (dlfp->modifier_btns);
   }
   StdCleanupFormProc (g, data);
 }
@@ -10134,60 +171,11 @@ static void ChangeFeaturePopup (PopuP p)
 }
 
 
-/* This removes redundant titles on nuc-prot sets, which will not be
- * visible in the flat file if all sequences in the nuc-prot set have
- * their own title.
- */
-static void RemoveNucProtSetTitles (SeqEntryPtr sep)
-{
-  BioseqSetPtr bssp;
-  SeqEntryPtr  this_sep;
-  SeqDescrPtr  sdp, prev = NULL, sdp_next;
-  
-  if (sep == NULL || ! IS_Bioseq_set (sep))
-  {
-    return;
-  }
-  bssp = (BioseqSetPtr) sep->data.ptrvalue;
-  if (bssp == NULL) return;
-  for (this_sep = bssp->seq_set; this_sep != NULL; this_sep = this_sep->next)
-  {
-    RemoveNucProtSetTitles (this_sep);
-  }
-  
-  if (bssp->_class != BioseqseqSet_class_nuc_prot) 
-  {
-    return;
-  }
-  for (sdp = bssp->descr; sdp != NULL; sdp = sdp_next)
-  {
-    sdp_next = sdp->next;
-    if (sdp->choice == Seq_descr_title)
-    {
-      if (prev == NULL)
-      {
-        bssp->descr = sdp->next;
-      }
-      else
-      {
-        prev->next = sdp->next;
-      }
-      sdp->next = NULL;
-      SeqDescrFree (sdp);
-    }
-    else
-    {
-      prev = sdp;
-    }
-  }
-}
-
-
 static void DoAutoDefLine (ButtoN b)
 {
   DefLineFormPtr dlfp;
   SeqEntryPtr sep;
-  ModifierCombinationPtr m;
+  ValNodePtr modifier_indices = NULL;
   Int2 feature_index;
   OrganismDescriptionModifiers odmp;
   Int2 product_flag, feature_list_type;
@@ -10207,6 +195,7 @@ static void DoAutoDefLine (ButtoN b)
   odmp.exclude_sp = GetStatus (dlfp->exclude_sp);
   odmp.exclude_cf = GetStatus (dlfp->exclude_cf);
   odmp.exclude_aff = GetStatus (dlfp->exclude_aff);
+  odmp.exclude_nr = GetStatus (dlfp->exclude_nr);
   odmp.include_country_extra = GetStatus (dlfp->include_country_extra);
   odmp.use_modifiers = TRUE;
   odmp.allow_semicolon_in_modifier = GetStatus (dlfp->allow_semicolon_in_modifier);
@@ -10220,28 +209,25 @@ static void DoAutoDefLine (ButtoN b)
     odmp.clone_isolate_HIV_rule_num = GetValue (dlfp->clone_isolate_HIV_rule_num);
   }
 
-  /* create combo with the specified modifiers */
-  m = NewModifierCombo (NULL);
-  if (m == NULL) return;
   if (GetValue (dlfp->customGrp) == 1)
   {
     /* take all features */
-    for (feature_index = 0; feature_index < NumDefLineModifiers; feature_index++)
+    for (feature_index = 0; feature_index < NumDefLineModifiers (); feature_index++)
     {
       if (dlfp->modList[feature_index].any_present)
       {
-        AddQualToModifierCombo (m, dlfp->modList + feature_index, feature_index);
+        ValNodeAddInt (&modifier_indices, 0, feature_index);
       }
     }
   }
   else
   {
     /* take selected features */
-    for (feature_index = 0; feature_index < NumDefLineModifiers; feature_index++)
+    for (feature_index = 0; feature_index < NumDefLineModifiers (); feature_index++)
     {
-      if (GetStatus (dlfp->modList[feature_index].button))
+      if (GetStatus (dlfp->modifier_btns[feature_index]))
       {
-        AddQualToModifierCombo (m, dlfp->modList + feature_index, feature_index);
+        ValNodeAddInt (&modifier_indices, 0, feature_index);
       }
     }
   }
@@ -10265,13 +251,24 @@ static void DoAutoDefLine (ButtoN b)
 
   for (i=0; i< NumRemovableItems; i++)
   {
-    dlfp->feature_requests.items[i].keep 
-              = GetStatus (dlfp->feature_requests.items[i].keep_request);
+    dlfp->feature_requests.keep_items[i] 
+              = GetStatus (dlfp->feature_btns[i]);
+  }
+  if (GetValue (dlfp->promoter_type) == 1) 
+  {
+    dlfp->feature_requests.add_fake_promoters = TRUE;
+  }
+  else
+  {
+    dlfp->feature_requests.add_fake_promoters = FALSE;
   }
 
   dlfp->feature_requests.suppress_alt_splice_phrase = 
                  GetStatus (dlfp->suppress_alt_splice_phrase);
 
+  dlfp->feature_requests.use_ncrna_note = 
+                 GetStatus (dlfp->use_ncrna_note);
+  
   dlfp->feature_requests.remove_subfeatures = 
                  GetStatus (dlfp->remove_subfeatures);
 
@@ -10307,23 +304,12 @@ static void DoAutoDefLine (ButtoN b)
   }
   if (sep == NULL) return;
 
-  RemoveNucProtSetTitles (sep);
-  
-  SeqEntrySetScope (sep);
-
-  BuildDefLineFeatClauseList (sep, dlfp->input_entityID,
-                              &dlfp->feature_requests,
-                              product_flag, alternate_splice_flag,
-                              gene_cluster_opp_strand,
-                              &defline_clauses);
+  AutoDefForSeqEntry (sep, dlfp->input_entityID, &odmp, dlfp->modList, modifier_indices,
+                      &dlfp->feature_requests, product_flag, alternate_splice_flag, gene_cluster_opp_strand);
                               
-  dlfp->feature_requests.suppressed_feature_list = ValNodeFree (dlfp->feature_requests.suppressed_feature_list);                              
+  dlfp->feature_requests.suppressed_feature_list = ValNodeFree (dlfp->feature_requests.suppressed_feature_list);
+  modifier_indices = ValNodeFree (modifier_indices);
 
-  BuildDefinitionLinesFromFeatureClauseLists (defline_clauses, dlfp->modList,
-                                                m, odmp);
-  DefLineFeatClauseListFree (defline_clauses);
-  ClearProteinTitlesInNucProts (dlfp->input_entityID, NULL);
-  InstantiateProteinTitles (dlfp->input_entityID, NULL);
   ArrowCursor ();
   Update ();
   ObjMgrSetDirtyFlag (dlfp->input_entityID, TRUE);
@@ -10388,13 +374,11 @@ static void IsTricky (
 }
 
 static Boolean HasTrickyHIVRecords (
-  BaseFormPtr bfp
+  SeqEntryPtr sep
 )
 {
-  SeqEntryPtr sep;
   Boolean     has_tricky;
 
-  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return FALSE;
   
   has_tricky = FALSE;
@@ -10402,6 +386,48 @@ static Boolean HasTrickyHIVRecords (
   return has_tricky;
 }
 
+
+static void AddSpTaxnameToList (SeqDescrPtr sdp, Pointer userdata)
+{
+  BioSourcePtr biop;
+
+  if (sdp == NULL || sdp->choice != Seq_descr_source || userdata == NULL) return;
+
+  biop = (BioSourcePtr) sdp->data.ptrvalue;
+  if (biop == NULL || biop->org == NULL || !IsSpName (biop->org->taxname)) return;
+
+  ValNodeAddPointer ((ValNodePtr PNTR) userdata, 0, biop->org->taxname);
+}
+
+
+static Boolean ShouldExcludeSp (SeqEntryPtr sep)
+{
+  ValNodePtr name_list = NULL, vnp1, vnp2;
+  Boolean    all_diff = TRUE;
+
+  if (sep == NULL) return TRUE;
+  VisitDescriptorsInSep (sep, &name_list, AddSpTaxnameToList);
+
+  name_list = ValNodeSort (name_list, SortVnpByString);
+
+  if (name_list != NULL && name_list->next != NULL)
+  {
+    for (vnp1 = name_list; vnp1 != NULL && vnp1->next != NULL && all_diff; vnp1 = vnp1->next)
+    {
+      for (vnp2 = vnp1->next; vnp2 != NULL && all_diff; vnp2 = vnp2->next)
+      {
+        if (StringCmp (vnp1->data.ptrvalue, vnp2->data.ptrvalue) == 0)
+        {
+          all_diff = FALSE;
+        }
+      }
+    }
+  }
+  name_list = ValNodeFree (name_list);
+  return all_diff;
+}
+
+
 static GrouP CreateDefLineFormHIVRule (
   GrouP h
 )
@@ -10462,10 +488,10 @@ static void SetHIVRuleEnable (Handle a)
   if (dlfp == NULL) return;
   if (dlfp->clone_isolate_HIV_rule_num == NULL) return;
   if (dlfp->modList == NULL) return;
-  if ((dlfp->modList [DEFLINE_POS_Clone].button != NULL
-       && GetStatus (dlfp->modList [DEFLINE_POS_Clone].button))
-      || (dlfp->modList [DEFLINE_POS_Isolate].button != NULL
-          && GetStatus (dlfp->modList [DEFLINE_POS_Isolate].button)))
+  if ((dlfp->modifier_btns [DEFLINE_POS_Clone] != NULL
+       && GetStatus (dlfp->modifier_btns [DEFLINE_POS_Clone]))
+      || (dlfp->modifier_btns [DEFLINE_POS_Isolate] != NULL
+          && GetStatus (dlfp->modifier_btns [DEFLINE_POS_Isolate])))
   {
     Disable (dlfp->clone_isolate_HIV_rule_num);
   }
@@ -10478,7 +504,7 @@ static void SetHIVRuleEnable (Handle a)
 static GrouP CreateDefLineFormSourceGroup (
   GrouP          h,
   DefLineFormPtr dlfp,
-  BaseFormPtr    bfp
+  SeqEntryPtr    sep
 )
 {
   GrouP p, g, g1, r;
@@ -10491,7 +517,7 @@ static GrouP CreateDefLineFormSourceGroup (
   SetGroupSpacing (p, 10, 10);
 
   count = 0;
-  for (item_index=0; item_index < NumDefLineModifiers; item_index++)
+  for (item_index=0; item_index < NumDefLineModifiers (); item_index++)
   {
     if (dlfp->modList[item_index].any_present)
     {
@@ -10530,17 +556,17 @@ static GrouP CreateDefLineFormSourceGroup (
                                      programFont, NULL);
   SetGroupSpacing (dlfp->sourceListGrp, 10, 10);                                     
 
-  for (item_index=0; item_index < NumDefLineModifiers; item_index++)
+  for (item_index=0; item_index < NumDefLineModifiers (); item_index++)
   {
     if (dlfp->modList[item_index].any_present)
     {
       g1 = HiddenGroup (dlfp->sourceListGrp, num_label_columns, 0, NULL);
       SetGroupSpacing (g1, 10, 10);
-      dlfp->modList[item_index].button = CheckBox (g1,
+      dlfp->modifier_btns[item_index] = CheckBox (g1,
                                              DefLineModifiers[item_index].name,
                                              (BtnActnProc) SetHIVRuleEnable);
-      SetObjectExtra (dlfp->modList[item_index].button, dlfp, NULL);
-      SetStatus (dlfp->modList[item_index].button,
+      SetObjectExtra (dlfp->modifier_btns [item_index], dlfp, NULL);
+      SetStatus (dlfp->modifier_btns [item_index],
                  dlfp->modList[item_index].required);
       
       if (num_label_columns > 1)
@@ -10571,7 +597,7 @@ static GrouP CreateDefLineFormSourceGroup (
     }
     else
     {
-      dlfp->modList[item_index].button = NULL;
+      dlfp->modifier_btns[item_index] = NULL;
       dlfp->modList[item_index].required = FALSE;
     }
   }
@@ -10579,7 +605,7 @@ static GrouP CreateDefLineFormSourceGroup (
   Enable (dlfp->sourceListGrp);
 
 
-  has_tricky = HasTrickyHIVRecords (bfp);
+  has_tricky = HasTrickyHIVRecords (sep);
   if (has_tricky)
   {
     dlfp->clone_isolate_HIV_rule_num = CreateDefLineFormHIVRule (p);
@@ -10590,24 +616,26 @@ static GrouP CreateDefLineFormSourceGroup (
   {
     dlfp->clone_isolate_HIV_rule_num = NULL;
   }
-  r = NormalGroup (p, 0, 2, "Other Options", programFont, NULL);
+  r = NormalGroup (p, 3, 0, "Other Options", programFont, NULL);
   SetGroupSpacing (r, 10, 10);
   dlfp->keep_paren = CheckBox (r, "Leave in parenthetical organism info", NULL);
   SetStatus (dlfp->keep_paren, TRUE);
-  dlfp->exclude_sp = CheckBox (r, "Do not apply modifier to 'sp.' organisms",
-         NULL);
-  SetStatus (dlfp->exclude_sp, TRUE);
   dlfp->include_country_extra = CheckBox (r, "Include text after colon in country", NULL);
   SetStatus (dlfp->include_country_extra, FALSE);
+  dlfp->allow_semicolon_in_modifier = CheckBox (r, "Include text after semicolon in modifiers", NULL);
+  SetStatus (dlfp->allow_semicolon_in_modifier, FALSE);
+  dlfp->exclude_sp = CheckBox (r, "Do not apply modifier to 'sp.' organisms",
+         NULL);
+  SetStatus (dlfp->exclude_sp, ShouldExcludeSp (sep));
   dlfp->exclude_cf = CheckBox (r, "Do not apply modifier to 'cf.' organisms",
          NULL);
   SetStatus (dlfp->exclude_cf, FALSE);
   
-  dlfp->allow_semicolon_in_modifier = CheckBox (r, "Include text after semicolon in modifiers", NULL);
-  SetStatus (dlfp->allow_semicolon_in_modifier, FALSE);
   dlfp->exclude_aff = CheckBox (r, "Do not apply modifier to 'aff.' organisms",
          NULL);
   SetStatus (dlfp->exclude_aff, FALSE);
+  dlfp->exclude_nr = CheckBox (r, "Do not apply modifier to 'nr.' organisms", NULL);
+  SetStatus (dlfp->exclude_nr, FALSE);
   
   AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) dlfp->use_labels,
                               (HANDLE) dlfp->sourceListGrp,
@@ -10666,8 +694,7 @@ static void SetMiscFeatRuleEnable (Handle a)
   {
     return;
   }
-  if (dlfp->feature_requests.items != NULL
-    && GetStatus (dlfp->feature_requests.items[RemovableNoncodingProductFeat].keep_request))
+  if (GetStatus (dlfp->feature_btns[RemovableNoncodingProductFeat]))
   {
     Enable (dlfp->misc_feat_parse_rule);
   }
@@ -10675,6 +702,14 @@ static void SetMiscFeatRuleEnable (Handle a)
   {
     Disable (dlfp->misc_feat_parse_rule);
   }
+  if (GetStatus (dlfp->feature_btns[RemovablePromoter]))
+  {
+    Enable (dlfp->promoter_type);
+  }
+  else
+  {
+    Disable (dlfp->promoter_type);
+  }
 }
   
 static GrouP CreateDefLineFormFeatureOptionsGroup (
@@ -10682,7 +717,7 @@ static GrouP CreateDefLineFormFeatureOptionsGroup (
   DefLineFormPtr dlfp
 )
 {
-  GrouP p, g1, s1, s2;
+  GrouP p, g1, s1, s2, k, k2;
   Int4  i;
   SeqEntryPtr sep;
 
@@ -10697,34 +732,49 @@ static GrouP CreateDefLineFormFeatureOptionsGroup (
   dlfp->organelle_popup = CreateDefLineFormOrganellePopup (s1);
   dlfp->alternate_splice_flag = CheckBox (s1,
 	                "Append 'alternatively spliced'", NULL);
+  dlfp->use_ncrna_note = CheckBox (s1, "Use ncRNA note if no class or product", NULL);
   AlignObjects (ALIGN_CENTER, (HANDLE) dlfp->featurePopup, 
                               (HANDLE) dlfp->organelle_popup, 
+                              (HANDLE) dlfp->use_ncrna_note, 
                               (HANDLE) dlfp->alternate_splice_flag, NULL);
   
-  dlfp->optional_features_grp = NormalGroup (g1, 0, 4,
+  dlfp->optional_features_grp = NormalGroup (g1, 3, 0,
                    "Optional Features", programFont, NULL);
                    SetGroupSpacing (dlfp->optional_features_grp, 10, 10);
   for (i=0; i < NumRemovableItems; i++)
   {
+    if (i == 0 || i == 4 || i == 7)
+    {
+      k = HiddenGroup (dlfp->optional_features_grp, 0, 4, NULL);
+      SetGroupSpacing (k, 10, 10);
+    }
     if (i != RemovableCDS)
     {
-      dlfp->feature_requests.items[i].keep_request = 
-                     CheckBox (dlfp->optional_features_grp, remove_items[i].group_name, 
+      dlfp->feature_btns[i] = 
+                     CheckBox (k, GetRemovableItemName (i), 
                                (BtnActnProc) SetMiscFeatRuleEnable);
-      SetObjectExtra (dlfp->feature_requests.items[i].keep_request, dlfp, NULL);
-      SetStatus (dlfp->feature_requests.items[i].keep_request, FALSE);
+      SetObjectExtra (dlfp->feature_btns[i], dlfp, NULL);
+      SetStatus (dlfp->feature_btns[i], FALSE);
       if (i == RemovableNoncodingProductFeat) {
-        s2 = HiddenGroup (dlfp->optional_features_grp, 2, 0, NULL);
+        s2 = HiddenGroup (k, 2, 0, NULL);
         StaticPrompt (s2, "        ", 8, popupMenuHeight, programFont, 'l');
         dlfp->misc_feat_parse_rule = PopupList (s2, TRUE, NULL);
         PopupItem (dlfp->misc_feat_parse_rule, "Use comment before first semicolon");
         PopupItem (dlfp->misc_feat_parse_rule, "Look for Noncoding Products");
         SetValue (dlfp->misc_feat_parse_rule, 2);
         Disable (dlfp->misc_feat_parse_rule);
-      }
-      else if (i == RemovablePrecursorRNA) {
-        /* put in blank space */
-        StaticPrompt (dlfp->optional_features_grp, "", 0, popupMenuHeight, programFont, 'l');
+      } else if (i == RemovablePromoter) {
+        k2 = HiddenGroup (k, 2, 0, NULL);
+        SetGroupSpacing (k2, 10, 10);
+        StaticPrompt (k2, "        ", 8, popupMenuHeight, programFont, 'l');
+        dlfp->promoter_type = HiddenGroup (k2, 0, 2, NULL);
+        RadioButton (dlfp->promoter_type, "All");
+        RadioButton (dlfp->promoter_type, "If present");
+        SetValue (dlfp->promoter_type, 1);
+        Disable (dlfp->promoter_type);
+        AlignObjects (ALIGN_CENTER, (HANDLE) dlfp->feature_btns[i],
+                                    (HANDLE) dlfp->promoter_type,
+                                    NULL);
       }
     }
   }
@@ -10762,6 +812,7 @@ static void CreateDefLineForm (
   WindoW         w;
   GrouP          h, k, g1, c, feat_opts;
   ButtoN         b;
+  SeqEntryPtr    sep;
 
   dlfp = MemNew (sizeof (DefLineFormData));
   if (dlfp == NULL) return;
@@ -10769,6 +820,10 @@ static void CreateDefLineForm (
   dlfp->input_itemID = bfp->input_itemID;
   dlfp->input_itemtype = bfp->input_itemtype;
 
+  dlfp->modifier_btns = (ButtoN PNTR) MemNew (sizeof (ButtoN) * NumDefLineModifiers());
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+
   w = FixedWindow (-50, -33, -10, -10, "Automatic Definition Line",
   StdCloseWindowProc);
   SetObjectExtra (w, dlfp, CleanupDefLineForm);
@@ -10783,7 +838,7 @@ static void CreateDefLineForm (
 
   k = HiddenGroup (h, -1, 0, NULL);
   SetGroupSpacing (k, 10, 10);
-  g1 = CreateDefLineFormSourceGroup (k, dlfp, bfp);
+  g1 = CreateDefLineFormSourceGroup (k, dlfp, sep);
 
   feat_opts = CreateDefLineFormFeatureOptionsGroup (k, dlfp);
   AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) feat_opts, NULL);
@@ -10810,75 +865,20 @@ static void CreateDefLineForm (
   Update ();
 }
 
-static CharPtr GetKeywordPrefix (SeqEntryPtr sep)
-{
-  ValNodePtr vnp;
-  GBBlockPtr gbp;
-  
-  vnp = SeqEntryGetSeqDescr (sep, Seq_descr_genbank, NULL);
-	if (vnp != NULL) {
-	  gbp = (GBBlockPtr) vnp->data.ptrvalue;
-	  if (gbp != NULL)
-	  {
-	    for (vnp = gbp->keywords; vnp != NULL; vnp = vnp->next)
-	    {
-	      if (StringICmp((CharPtr)vnp->data.ptrvalue, "TPA:inferential") == 0)
-	      {
-	        return "TPA_inf: ";
-	      }
-	      else if (StringICmp((CharPtr)vnp->data.ptrvalue, "TPA:experimental") == 0)
-	      {
-	        return "TPA_exp: ";
-	      }
-	    }
-	  }
-	}
-	return "";
-}
 
-static void BuildDefinitionLinesFromFeatureClauseLists (
-  ValNodePtr list,
-  ModifierItemLocalPtr modList,
-  ModifierCombinationPtr m,
-  OrganismDescriptionModifiers odmp
+/* The AddBestComboModifiersToModList function sets the modifiers
+ * selected by the FindBestCombo process as selected.
+ */
+static void AddBestModifiersToModList (
+  ValNodePtr modifier_indices,
+  ModifierItemLocalPtr modList
 )
 {
   ValNodePtr vnp;
-  DefLineFeatClausePtr defline_featclause;
-  CharPtr    org_desc, tmp_str, keyword_prefix;
 
-  for (vnp = list; vnp != NULL; vnp = vnp->next)
+  for (vnp = modifier_indices; vnp != NULL; vnp = vnp->next)
   {
-    if (vnp->data.ptrvalue != NULL)
-    {
-      defline_featclause = vnp->data.ptrvalue;
-      
-      keyword_prefix = GetKeywordPrefix (defline_featclause->sep);
-      
-      org_desc = GetOrganismDescription (defline_featclause->bsp,
-                                         modList, m, &odmp);
-      tmp_str = (CharPtr) MemNew (StringLen (keyword_prefix) 
-                                  + StringLen (org_desc) 
-                                  + StringLen (defline_featclause->clauselist) + 2);
-      if (tmp_str == NULL) return;
-      tmp_str [0] = 0;
-      if (keyword_prefix != NULL)
-      {
-        StringCat (tmp_str, keyword_prefix);
-      }
-      StringCat (tmp_str, org_desc);
-      if (defline_featclause->clauselist != NULL
-        && defline_featclause->clauselist [0] != ','
-        && defline_featclause->clauselist [0] != '.'
-        && defline_featclause->clauselist [0] != 0)
-      {
-        StringCat (tmp_str, " ");
-      }
-      StringCat (tmp_str, defline_featclause->clauselist);
-      tmp_str [0] = toupper (tmp_str [0]);
-      ReplaceDefinitionLine (defline_featclause->sep, tmp_str);
-      MemFree (org_desc);
-    }
+    modList[vnp->data.intvalue].required = TRUE;
   }
 }
 
@@ -10892,7 +892,7 @@ extern void AutoDefBaseFormCommon (
   SeqEntryPtr sep;
   DeflineFeatureRequestList feature_requests;
   ModifierItemLocalPtr modList;
-  ModifierCombinationPtr m;
+  ValNodePtr modifier_indices = NULL;
   OrganismDescriptionModifiers odmp;
   Int4 index;
   ValNodePtr defline_clauses = NULL;
@@ -10903,63 +903,71 @@ extern void AutoDefBaseFormCommon (
 
   InitFeatureRequests (&feature_requests);
 
-  modList = MemNew (NumDefLineModifiers * sizeof (ModifierItemLocalData));
+  modList = MemNew (NumDefLineModifiers () * sizeof (ModifierItemLocalData));
   if (modList == NULL) return;
   SetRequiredModifiers (modList);
   CountModifiers (modList, sep);
   if (use_form)
   {
-    m = FindBestCombo (sep, modList);
-    AddBestComboModifiersToModList ( m, modList);
+    modifier_indices = FindBestModifiers (sep, modList);
+    AddBestModifiersToModList ( modifier_indices, modList);
+    modifier_indices = ValNodeFree (modifier_indices);
     CreateDefLineForm (bfp, modList, &feature_requests);
   }
   else
   {
-    RemoveNucProtSetTitles (sep);
-    SeqEntrySetScope (sep);
     WatchCursor ();
     Update ();
     odmp.use_labels = TRUE;
     odmp.max_mods = -99;
     odmp.keep_paren = TRUE;
-    odmp.exclude_sp = TRUE;
+    odmp.exclude_sp = ShouldExcludeSp (sep);
     odmp.exclude_cf = FALSE;
     odmp.exclude_aff = FALSE;
+    odmp.exclude_nr = FALSE;
     odmp.include_country_extra = FALSE;
     odmp.clone_isolate_HIV_rule_num = clone_isolate_HIV_rule_want_both;
     odmp.use_modifiers = use_modifiers;
     odmp.allow_semicolon_in_modifier = FALSE;
-    ClearProteinTitlesInNucProts (bfp->input_entityID, NULL);
+
+    RemoveNucProtSetTitles (sep);  
+    SeqEntrySetScope (sep);
+
     BuildDefLineFeatClauseList (sep, bfp->input_entityID, &feature_requests,
                                 DEFAULT_ORGANELLE_CLAUSE, FALSE, FALSE,
                                 &defline_clauses);
     if ( AreFeatureClausesUnique (defline_clauses))
     {
-      m = CreateComboFromModList (modList);
+      modifier_indices = GetModifierIndicesFromModList (modList);
     }
     else
     {
-      m = FindBestCombo (sep, modList);
+      modifier_indices = FindBestModifiers (sep, modList);
     }
 
     BuildDefinitionLinesFromFeatureClauseLists (defline_clauses, modList,
-                                                m, odmp);
+                                                modifier_indices, &odmp);
+
     DefLineFeatClauseListFree (defline_clauses);
     if (modList != NULL)
     {
-      for (index=0; index < NumDefLineModifiers; index++)
+      for (index=0; index < NumDefLineModifiers (); index++)
       {
         ValNodeFree (modList[index].values_seen);
       }
       MemFree (modList);
     }
+    modifier_indices = ValNodeFree (modifier_indices);
+
+    ClearProteinTitlesInNucProts (bfp->input_entityID, NULL);
+    InstantiateProteinTitles (bfp->input_entityID, NULL);
+
     ArrowCursor ();
     Update ();
     ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);  
     ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
     SeqEntrySetScope (NULL);
   }
-  FreeModifierCombo (m);
 }
 
 static void AutoDefCommon (IteM i, Boolean use_form, Boolean use_modifiers)
@@ -11008,17 +1016,40 @@ extern void AutoDefOptionsToolBtn (ButtoN b)
   AutoDefBaseFormCommon (bfp, TRUE, TRUE);
 }
 
+
+static void TrimQuotesAroundString (CharPtr str)
+{
+  Int4 len;
+  CharPtr src, dst;
+
+  if (StringHasNoText (str) || *str != '"') return;
+  len = StringLen (str);
+  if (str[len - 1] != '"') return;
+  src = str + 1;
+  dst = str;
+  while (*src != '"')
+  {
+    *dst = *src;
+    dst++;
+    src++;
+  }
+  *dst = 0;
+}
+
+
 typedef struct tablelinedata {
   Int4 num_parts;
   ValNodePtr parts;
 } TableLineData, PNTR TableLinePtr;
 
-static TableLinePtr MakeTableData (CharPtr line)
+static TableLinePtr MakeTableData (CharPtr line, ValNodePtr PNTR special_list)
 {
   TableLinePtr tlp;
   CharPtr p_start, p_end;
   Int4    plen;
   Boolean found_end;
+  CharPtr val;
+  ValNodePtr vnp;
 
   if (line == NULL) return NULL;
   tlp = MemNew (sizeof (TableLineData));
@@ -11030,11 +1061,8 @@ static TableLinePtr MakeTableData (CharPtr line)
     plen = StringCSpn (p_start, "\t\n");
     if (plen == 0)
     {
-      if (tlp->num_parts > 0)
-      {
-        ValNodeAddStr (&tlp->parts, 0, StringSave (""));
-        tlp->num_parts ++;
-      }
+      ValNodeAddStr (&tlp->parts, 0, StringSave (""));
+      tlp->num_parts ++;
       p_start++;
       if (*p_start == 0) {
         if (tlp->num_parts > 0)
@@ -11055,7 +1083,11 @@ static TableLinePtr MakeTableData (CharPtr line)
       *p_end = 0;
     }
     TrimSpacesAroundString (p_start);
-    ValNodeAddStr (&tlp->parts, 0, StringSave (p_start));
+    TrimQuotesAroundString (p_start);
+    val = StringSave (p_start);
+
+    vnp = ValNodeAddStr (&tlp->parts, 0, val);
+    SpecialCharFindWithContext ((CharPtr PNTR)&(vnp->data.ptrvalue), special_list, NULL, NULL);
     tlp->num_parts ++;
     if (!found_end)
     {
@@ -11066,23 +1098,27 @@ static TableLinePtr MakeTableData (CharPtr line)
   {
     MemFree (tlp);
     return NULL;
-  }
+  } 
   return tlp;  
 }
 
 static void CleanUpTableData (ValNodePtr vnp)
 {
   TableLinePtr tlp;
+  ValNodePtr   vnp_next;
 
-  if (vnp == NULL) return;
-  CleanUpTableData (vnp->next);
-  vnp->next = NULL;
-  tlp = vnp->data.ptrvalue;
-  if (tlp != NULL)
+  while (vnp != NULL)
   {
-    ValNodeFreeData (tlp->parts);
+    vnp_next = vnp->next;
+    vnp->next = NULL;
+    tlp = vnp->data.ptrvalue;
+    if (tlp != NULL)
+    {
+      ValNodeFreeData (tlp->parts);
+    }
+    vnp = ValNodeFree (vnp);
+    vnp = vnp_next;
   }
-  ValNodeFree (vnp);
 }
 
 static void FormatPopupWithTableDataColumns (PopuP p, ValNodePtr header_line)
@@ -11112,26 +1148,240 @@ static void FormatPopupWithTableDataColumns (PopuP p, ValNodePtr header_line)
 }
 
 
-typedef struct orgmodlineformdata {
-  Int4    column_number;
-  CharPtr value_string;
-  GrouP   action_choice;
-  PopuP   match_choice;
-  DialoG  apply_choice_dlg;
-  GrouP   container;
-} OrgModLineFormData, PNTR OrgModLineFormPtr;
+enum orgmodmatchtype 
+{
+  eMatchAccession = 1,
+  eMatchLocalID,
+  eMatchTaxName,
+  eMatchTMSMART,
+  eMatchBankIt,
+  eMatchGeneral,
+  eMatchNone
+};
+
+
+typedef struct orgmodtablecolumn {
+  Int4       match_choice;
+  ValNodePtr apply_choice;
+} OrgModTableColumnData, PNTR OrgModTableColumnPtr;
+
+
+static OrgModTableColumnPtr OrgModTableColumnFree (OrgModTableColumnPtr t)
+{
+  if (t != NULL) {
+    t->apply_choice = ValNodeFreeData (t->apply_choice);
+    t = MemFree (t);
+  }
+  return t;
+}
+
+
+static ValNodePtr OrgModTableColumnListFree (ValNodePtr vnp)
+{
+  ValNodePtr vnp_next;
+
+  while (vnp != NULL) 
+  {
+    vnp_next = vnp->next;
+    vnp->next = NULL;
+    vnp->data.ptrvalue = OrgModTableColumnFree (vnp->data.ptrvalue);
+    vnp = ValNodeFree (vnp);
+    vnp = vnp_next;
+  }
+  return vnp;
+}
+
+
+typedef struct orgmodtablecolumndlg {
+  DIALOG_MESSAGE_BLOCK
+
+  GrouP  action_choice;
+  PopuP  match_choice;
+  DialoG apply_choice;
+ 
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer              change_userdata;
+} OrgModTableColumnDlgData, PNTR OrgModTableColumnDlgPtr;
+
+static Pointer OrgModTableColumnDialogToData (DialoG d)
+{
+  OrgModTableColumnPtr o;
+  OrgModTableColumnDlgPtr dlg;
+  
+  dlg = (OrgModTableColumnDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  o = (OrgModTableColumnPtr) MemNew (sizeof (OrgModTableColumnData));
+
+  if (GetValue (dlg->action_choice) == 1) 
+  {
+    o->match_choice = GetValue (dlg->match_choice);
+    o->apply_choice = NULL;
+  }
+  else
+  {
+    o->match_choice = 0;
+    o->apply_choice = DialogToPointer (dlg->apply_choice);
+  }
+  return o;
+}
+
+
+static void ChangeOrgModTableColumnMatchChoice (PopuP p)
+{
+  OrgModTableColumnDlgPtr dlg;
+
+  dlg = (OrgModTableColumnDlgPtr) GetObjectExtra (p);
+  if (dlg == NULL) return;
+  if (dlg->change_notify != NULL) 
+  {
+    (dlg->change_notify) (dlg->change_userdata);
+  }  
+}
+  
+
+static void ChangeOrgModTableColumnActionChoice (GrouP g)
+{
+  OrgModTableColumnDlgPtr dlg;
+
+  dlg = (OrgModTableColumnDlgPtr) GetObjectExtra (g);
+  if (dlg == NULL) return;
+
+  if (GetValue (dlg->action_choice) == 1)
+  {
+    Enable (dlg->match_choice);
+    Disable (dlg->apply_choice);
+  }
+  else
+  {
+    Enable (dlg->apply_choice);
+    Disable (dlg->match_choice);
+  }  
+  if (dlg->change_notify != NULL) 
+  {
+    (dlg->change_notify) (dlg->change_userdata);
+  }  
+}
+
+
+static void OrgModTableColumnDataToDialog (DialoG d, Pointer data)
+{
+  OrgModTableColumnPtr o;
+  OrgModTableColumnDlgPtr dlg;
+  
+  dlg = (OrgModTableColumnDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  o = (OrgModTableColumnPtr) data;
+
+  if (o == NULL)
+  {
+    SetValue (dlg->action_choice, 1);
+    SetValue (dlg->match_choice, eMatchNone);
+    PointerToDialog (dlg->apply_choice, NULL);
+  }
+  else
+  {
+    if (o->match_choice == 0)
+    {
+      SetValue (dlg->action_choice, 2);
+      PointerToDialog (dlg->apply_choice, o->apply_choice);
+    } 
+    else
+    {
+      SetValue (dlg->action_choice, 1);
+      SetValue (dlg->match_choice, o->match_choice);
+    }
+  }
+  ChangeOrgModTableColumnActionChoice (dlg->action_choice);
+}
+
+
+static DialoG 
+OrgModTableColumnDialog 
+(GrouP                h,
+ CharPtr              value_string,
+ Int4                 num_blank,
+ Nlm_ChangeNotifyProc change_notify,
+ Pointer              change_userdata)
+{
+  OrgModTableColumnDlgPtr dlg;
+  GrouP            p, g;
+  ValNodePtr       qual_selection_list;
+  CharPtr real_title;
+  CharPtr title_fmt = "%s (%d are blank)";
+
+  dlg = (OrgModTableColumnDlgPtr) MemNew (sizeof (OrgModTableColumnDlgData));
+
+  if (num_blank > 0) {
+    real_title = (CharPtr) MemNew (sizeof (Char) * (StringLen (title_fmt) + StringLen (value_string) + 15));
+    sprintf (real_title, title_fmt, value_string, num_blank);
+  } else {
+    real_title = value_string;
+  }
+
+  p = NormalGroup (h, 3, 0, real_title, programFont, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+
+  if (real_title != value_string) {
+    real_title = MemFree (real_title);
+  }
+
+  dlg->dialog = (DialoG) p;
+  dlg->fromdialog = OrgModTableColumnDialogToData;
+  dlg->todialog = OrgModTableColumnDataToDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->action_choice = HiddenGroup (p, 0, 2, ChangeOrgModTableColumnActionChoice);
+  SetObjectExtra (dlg->action_choice, dlg, NULL);
+  SetGroupSpacing (dlg->action_choice, 10, 10);
+  RadioButton (dlg->action_choice, "Match to");
+  RadioButton (dlg->action_choice, "Apply to");
+  SetValue (dlg->action_choice, 1);
+
+  g = HiddenGroup (p, 0, 3, NULL);
+  /* list of matchable items */
+  dlg->match_choice = PopupList (g, TRUE, ChangeOrgModTableColumnMatchChoice);
+  SetObjectExtra (dlg->match_choice, dlg, NULL);
+  PopupItem (dlg->match_choice, "Accession");
+  PopupItem (dlg->match_choice, "Local ID");
+  PopupItem (dlg->match_choice, "Organism Taxonomy Name");
+  PopupItem (dlg->match_choice, "TMSMART ID");
+  PopupItem (dlg->match_choice, "BankIt ID");
+  PopupItem (dlg->match_choice, "General ID");
+  PopupItem (dlg->match_choice, "None");
+  SetValue (dlg->match_choice, eMatchNone);
+
+
+  /* list of organism modifiers */
+  qual_selection_list = GetSourceQualDescList (TRUE, TRUE, FALSE, FALSE);
+  
+  ValNodeAddPointer (&qual_selection_list, 1, StringSave ("Tax Name"));
+  
+    /* note - the ValNodeSelectionDialog will free the qual_selection_list when done */
+  dlg->apply_choice = ValNodeSelectionDialog (g, qual_selection_list, 8, SourceQualValNodeName,
+                                ValNodeSimpleDataFree, SourceQualValNodeDataCopy,
+                                SourceQualValNodeMatch, "qual choice", 
+                                change_notify, change_userdata, FALSE);
+
+  ChangeOrgModTableColumnActionChoice(dlg->action_choice);
+  return (DialoG) p;  
+}
+
 
 typedef struct orgmodloadformdata {
   FEATURE_FORM_BLOCK
 
   ValNodePtr        line_list;
   BioSourcePtr PNTR biop_list;
-  OrgModLineFormPtr line_forms;
-  Int4              num_line_forms;
+  DialoG PNTR       columns;
+  Int4              num_columns;
   Uint2             entityID;
   ButtoN            replace_with_blank_btn;
   ButtoN            accept_button;
   ButtoN            leave_dlg_up_btn;
+  DialoG            taxname_options;
 
   /* These members are for importing modifiers in the
    * submission dialogs.
@@ -11142,49 +1392,46 @@ typedef struct orgmodloadformdata {
   
 } OrgModLoadFormData, PNTR OrgModLoadFormPtr;
 
-enum orgmodmatchtype 
-{
-  eMatchAccession = 1,
-  eMatchLocalID,
-  eMatchTaxName,
-  eMatchTMSMART,
-  eMatchBankIt,
-  eMatchGeneral,
-  eMatchNone
-};
-
-static void SetFormModsAccept (Pointer userdata)
+static void SetFormModsEnable (Pointer userdata)
 {
   OrgModLoadFormPtr form_data;
+  OrgModTableColumnPtr o;
   Boolean           have_apply = FALSE;
-  Boolean           have_action;
+  Boolean           have_action = FALSE;
+  Boolean           have_apply_taxname = FALSE;
   Int4              column_index;
-  ValNodePtr        vnp;
 
   form_data = (OrgModLoadFormPtr) userdata;
   if (form_data == NULL) return;
  
-  have_apply = FALSE;
-  have_action = FALSE;
   for (column_index = 0;
-       column_index < form_data->num_line_forms;
+       column_index < form_data->num_columns;
        column_index ++)
   {
-    if ( GetValue (form_data->line_forms [ column_index].action_choice) == 2)
+    o = (OrgModTableColumnPtr) DialogToPointer (form_data->columns[column_index]);
+    if (o == NULL) continue;
+    if (o->match_choice > 0 && o->match_choice != eMatchNone)
     {
-      vnp = DialogToPointer (form_data->line_forms[column_index].apply_choice_dlg);
-      if (vnp != NULL)
-      {
-        have_apply = TRUE;
-      }
-      vnp = ValNodeFreeData (vnp);
+      have_action = TRUE;
     }
-    else if (GetValue (form_data->line_forms [column_index].action_choice) == 1
-      && GetValue (form_data->line_forms [column_index].match_choice) > 0
-      && GetValue (form_data->line_forms [column_index].match_choice) < eMatchNone)
+    else if (o->apply_choice != NULL) 
     {
-      have_action = TRUE;
+      have_apply = TRUE;
+      if (o->apply_choice->choice > 0 && StringCmp (o->apply_choice->data.ptrvalue, "Tax Name") == 0)
+      {
+        have_apply_taxname = TRUE;
+      }
     }
+    o = OrgModTableColumnFree (o);
+  }
+
+  if (have_apply_taxname)
+  {
+    Enable (form_data->taxname_options);
+  }
+  else
+  {
+    Disable (form_data->taxname_options);
   }
 
   /* must have an action selected if there is more than one line */
@@ -11206,77 +1453,6 @@ static void SetFormModsAccept (Pointer userdata)
   }
 }
 
-static void SetFormModsAcceptButton (Handle a)
-{
-  SetFormModsAccept (GetObjectExtra (a));
-}
-
-extern CharPtr GetModifierPopupPositionName (Int2 val)
-{
-  if (val <= 1)
-  {
-    return NULL;
-  }
-  else if (val > NumDefLineModifiers + 1)
-  {
-    return "Organism";
-  }
-  else
-  {
-    return DefLineModifiers[val - 2].name;
-  }  
-}
-
-static void BuildOrgModLineForm (
-  CharPtr           value_string,
-  Int4              column_number,
-  GrouP             parent_group,
-  OrgModLineFormPtr omlfp,
-  OrgModLoadFormPtr parent_form
-)
-{
-  GrouP g;
-  ValNodePtr qual_selection_list = NULL;
-
-  omlfp->column_number = column_number;
-  omlfp->value_string = value_string;
-  omlfp->container = NormalGroup (parent_group, 3, 0, value_string,
-                                  programFont, NULL);
-  omlfp->action_choice = HiddenGroup (omlfp->container, 0, 3,
-                                      (GrpActnProc) SetFormModsAcceptButton);
-  SetObjectExtra (omlfp->action_choice, parent_form, NULL);
-  SetGroupSpacing (omlfp->action_choice, 10 , 10);
-  RadioButton (omlfp->action_choice, "Match to");
-  RadioButton (omlfp->action_choice, "Apply to");
-
-  /* list of matchable items */
-  g = HiddenGroup (omlfp->container, 0, 2, NULL);
-  omlfp->match_choice = PopupList (g, TRUE,
-                                   (PupActnProc) SetFormModsAcceptButton);
-  SetObjectExtra (omlfp->match_choice, parent_form, NULL);
-  PopupItem (omlfp->match_choice, "Accession");
-  PopupItem (omlfp->match_choice, "Local ID");
-  PopupItem (omlfp->match_choice, "Organism Taxonomy Name");
-  PopupItem (omlfp->match_choice, "TMSMART ID");
-  PopupItem (omlfp->match_choice, "BankIt ID");
-  PopupItem (omlfp->match_choice, "General ID");
-  PopupItem (omlfp->match_choice, "None");
-  SetValue (omlfp->match_choice, eMatchNone);
-
-  /* list of organism modifiers */
-  qual_selection_list = GetSourceQualDescList (TRUE, TRUE, FALSE, FALSE);
-  
-  ValNodeAddPointer (&qual_selection_list, 1, StringSave ("Tax Name"));
-  
-    /* note - the ValNodeSelectionDialog will free the qual_selection_list when done */
-  omlfp->apply_choice_dlg = ValNodeSelectionDialog (g, qual_selection_list, 8, SourceQualValNodeName,
-                                ValNodeSimpleDataFree, SourceQualValNodeDataCopy,
-                                SourceQualValNodeMatch, "qual choice", 
-                                SetFormModsAccept, parent_form, FALSE);
-
-  SetValue (omlfp->action_choice, 1);
-}
-
 static void CleanupOrgModLoadForm (
   GraphiC g,
   VoidPtr data
@@ -11286,7 +1462,7 @@ static void CleanupOrgModLoadForm (
 
   form_data = (OrgModLoadFormPtr)data;
   if (form_data == NULL) return;
-  MemFree (form_data->line_forms);
+  form_data->columns = MemFree (form_data->columns);
   CleanUpTableData (form_data->line_list);
   StdCleanupFormProc (g, data);
 } 
@@ -11669,36 +1845,31 @@ static ValNodePtr TableToBioSourceListFree (ValNodePtr vnp)
 }
 
 
-static TableToBioSourcePtr TableToBioSourceFromTableLine (OrgModLoadFormPtr f, TableLinePtr tlp)
+static TableToBioSourcePtr TableToBioSourceFromTableLine (OrgModTableColumnPtr PNTR o_list, Int4 num_columns, TableLinePtr tlp)
 {
   Int4       column_index;
   ValNodePtr part;
   TableToBioSourcePtr t;
-  Int4                action_choice, match_choice;
   ApplyColumnPtr      a;
   
-  if (f == NULL || tlp == NULL || tlp->parts == NULL) return NULL;
+  if (o_list == NULL || tlp == NULL || tlp->parts == NULL) return NULL;
 
   t = (TableToBioSourcePtr) MemNew (sizeof (TableToBioSourceData));
   for (column_index = 0, part = tlp->parts;
-       column_index < f->num_line_forms;
+       column_index < num_columns;
        column_index ++)
   {
-    action_choice = GetValue (f->line_forms[column_index].action_choice);
-    if (action_choice == 1) 
+    if (o_list[column_index] == NULL) continue;
+    if (o_list[column_index]->match_choice > 0 
+        && o_list[column_index]->match_choice != eMatchNone
+        && part != NULL)
     {
-      if (part != NULL) 
-      {
-        match_choice = GetValue (f->line_forms[column_index].match_choice);
-        if (match_choice != eMatchNone) {
-          ValNodeAddPointer (&(t->identifiers), match_choice, StringSave (part->data.ptrvalue));
-        }
-      }
+      ValNodeAddPointer (&(t->identifiers), o_list[column_index]->match_choice, StringSave (part->data.ptrvalue));
     }
-    else if (action_choice == 2)
+    else if (o_list[column_index]->apply_choice != NULL)
     {
       a = (ApplyColumnPtr) MemNew (sizeof (ApplyColumnData));
-      a->apply_choice = DialogToPointer (f->line_forms[column_index].apply_choice_dlg);
+      a->apply_choice = SourceQualValNodeDataCopy (o_list[column_index]->apply_choice);
       if (part == NULL)
       {
         a->apply_value = StringSave ("");
@@ -11707,6 +1878,7 @@ static TableToBioSourcePtr TableToBioSourceFromTableLine (OrgModLoadFormPtr f, T
       {   
         a->apply_value = StringSave (part->data.ptrvalue);
       }
+
       ValNodeAddPointer (&(t->columns_to_apply), 0, a);
     }
 
@@ -11723,13 +1895,28 @@ static ValNodePtr OrgModLoadFormToApplyList (OrgModLoadFormPtr f)
 {
   ValNodePtr line;
   ValNodePtr apply_list = NULL;
+  ValNodePtr column_options = NULL;
+  Int4       column_index;
+  OrgModTableColumnPtr PNTR o_list;
 
   if (f == NULL) return NULL;
 
+  o_list = (OrgModTableColumnPtr PNTR) MemNew (f->num_columns * sizeof (OrgModTableColumnPtr));
+  for (column_index = 0; column_index < f->num_columns; column_index++)
+  {
+    o_list[column_index] = (OrgModTableColumnPtr) DialogToPointer (f->columns[column_index]);
+  }
+
   for (line = f->line_list; line != NULL; line = line->next)
   {
-    ValNodeAddPointer (&apply_list, 0, TableToBioSourceFromTableLine (f, line->data.ptrvalue));
+    ValNodeAddPointer (&apply_list, 0, TableToBioSourceFromTableLine (o_list, f->num_columns, line->data.ptrvalue));
   }
+  
+  for (column_index = 0; column_index < f->num_columns; column_index++)
+  {
+    o_list[column_index] = OrgModTableColumnFree (o_list[column_index]);
+  }
+  o_list = MemFree (o_list);
   return apply_list;
 }
 
@@ -11903,7 +2090,32 @@ static Boolean ListOrganismsWithMultipleRows (ValNodePtr apply_list)
         {
           if (vnp_biop2->data.ptrvalue == biop)
           {
-            fprintf (lip->fp, "Two rows (%d and %d) match the same organism.\n", row1_num, row2_num);
+            fprintf (lip->fp, "Two rows (%d and %d) match the same organism", row1_num, row2_num);
+            if (t->identifiers != NULL && t->identifiers->data.ptrvalue != NULL
+                && t2->identifiers != NULL && t2->identifiers->data.ptrvalue != NULL)
+            {
+              if (StringCmp (t->identifiers->data.ptrvalue, t2->identifiers->data.ptrvalue) == 0)
+              {
+                fprintf (lip->fp, " (both are %s).\n", t->identifiers->data.ptrvalue);
+              }
+              else
+              {
+                fprintf (lip->fp, " (%s and %s).\n", t->identifiers->data.ptrvalue, t2->identifiers->data.ptrvalue);
+              }
+            }
+            else if (t->identifiers != NULL && t->identifiers->data.ptrvalue != NULL)
+            {
+              fprintf (lip->fp, " (%s).\n", t->identifiers->data.ptrvalue);
+            }
+            else if (t2->identifiers != NULL && t2->identifiers->data.ptrvalue != NULL)
+            {
+              fprintf (lip->fp, " (%s).\n", t2->identifiers->data.ptrvalue);
+            }
+            else
+            {
+              fprintf (lip->fp, ".\n");
+            }
+                
             lip->data_in_log = TRUE;
           }
         }
@@ -12094,7 +2306,12 @@ static GetSamplePtr DetectExistingModifiersForTableToBioSourceList (ValNodePtr a
 }
 
 
-static void ApplyOneTableToBioSource (TableToBioSourcePtr t, Boolean replace_with_blank, ExistingTextPtr etp)
+static void 
+ApplyOneTableToBioSource 
+(TableToBioSourcePtr t,
+ Boolean             replace_with_blank,
+ ExistingTextPtr     etp,
+ TaxnameOptionsPtr   taxname_options)
 {
   ValNodePtr vnp_col, vnp_biop;
   BioSourcePtr biop;
@@ -12122,7 +2339,8 @@ static void ApplyOneTableToBioSource (TableToBioSourcePtr t, Boolean replace_wit
                 && (StringICmp (a->apply_choice->data.ptrvalue, "Tax Name") == 0
                     || StringICmp (a->apply_choice->data.ptrvalue, "Organism") == 0))
       {  
-        ApplyTaxNameToOrg (biop, a->apply_value, etp);   
+        ApplyTaxNameToOrg (biop, a->apply_value, etp);
+        ApplyTaxnameOptionsToBioSource (biop, taxname_options);
       }
       else if (a->apply_choice->choice > 0 && StringICmp (a->apply_choice->data.ptrvalue, "Location") == 0)
       {
@@ -12133,13 +2351,18 @@ static void ApplyOneTableToBioSource (TableToBioSourcePtr t, Boolean replace_wit
 }
 
 
-static void ApplyTableToBioSourceList (ValNodePtr apply_list, Boolean replace_with_blank, ExistingTextPtr etp)
+static void 
+ApplyTableToBioSourceList 
+(ValNodePtr        apply_list,
+ Boolean           replace_with_blank,
+ ExistingTextPtr   etp,
+ TaxnameOptionsPtr taxname_options)
 {
   ValNodePtr vnp;
 
   for (vnp = apply_list; vnp != NULL; vnp = vnp->next)
   {
-    ApplyOneTableToBioSource (vnp->data.ptrvalue, replace_with_blank, etp);
+    ApplyOneTableToBioSource (vnp->data.ptrvalue, replace_with_blank, etp, taxname_options);
   }
 }
 
@@ -12152,6 +2375,7 @@ static void DoAcceptFormMods (ButtoN b)
   ValNodePtr apply_list;
   Boolean    replace_with_blank;
   ExistingTextPtr etp;
+  TaxnameOptionsPtr taxname_options;
 
   form_data = GetObjectExtra (b);
   if (form_data == NULL) return;
@@ -12164,7 +2388,7 @@ static void DoAcceptFormMods (ButtoN b)
   FindOrganismsForTableToBioSourceList (apply_list, sep);
   if (ListOrganismsWithMultipleRows (apply_list)) 
   {
-    Message (MSG_ERROR, "Multiple rows in the table apply to the same organism!");
+    Message (MSG_ERROR, "Multiple rows in the table apply to the same organism!  Table cannot be imported.");
     apply_list = TableToBioSourceListFree (apply_list);
     return;
   }
@@ -12185,7 +2409,9 @@ static void DoAcceptFormMods (ButtoN b)
     apply_list = TableToBioSourceListFree (apply_list);
     return;
   }
-  ApplyTableToBioSourceList (apply_list, replace_with_blank, etp);
+  taxname_options = DialogToPointer (form_data->taxname_options);
+  ApplyTableToBioSourceList (apply_list, replace_with_blank, etp, taxname_options);
+  taxname_options = MemFree (taxname_options);
   etp = MemFree (etp);
   apply_list = TableToBioSourceListFree (apply_list);
 
@@ -12198,6 +2424,7 @@ static void DoAcceptFormMods (ButtoN b)
   }
 }
 
+
 static ValNodePtr ReadTableData (void)
 {
   Char          path [PATH_MAX];
@@ -12208,6 +2435,7 @@ static ValNodePtr ReadTableData (void)
   ValNodePtr    vnp;
   ReadBufferData rbd;
   CharPtr        line;
+  ValNodePtr     special_list = NULL;
 
   path [0] = '\0';
   if (! GetInputFileName (path, sizeof (path), NULL, "TEXT")) return NULL;
@@ -12222,7 +2450,7 @@ static ValNodePtr ReadTableData (void)
   line = AbstractReadFunction (&rbd);
   while (line != NULL) 
   {
-    tlp = MakeTableData (line);
+    tlp = MakeTableData (line, &special_list);
     if (tlp != NULL)
     {
       vnp = ValNodeNew (line_list);
@@ -12239,8 +2467,13 @@ static ValNodePtr ReadTableData (void)
     line = AbstractReadFunction (&rbd);
   }
   FileClose (rbd.fp);
+  if (special_list != NULL && !FixSpecialCharactersForStringsInList (special_list, "The table contains special characters\nand cannot be used until they are replaced.", FALSE))
+  {
+    line_list = ValNodeFreeData (line_list);
+    header_line = NULL;
+  }
   /* throw out all lines before header line */
-  if (header_line != line_list)
+  else if (header_line != line_list)
   {
     vnp = line_list;
     while (vnp != NULL && vnp->next != header_line)
@@ -12251,10 +2484,44 @@ static ValNodePtr ReadTableData (void)
     ValNodeFreeData (line_list);
     line_list = NULL;
   }
+  special_list = FreeContextList (special_list);
   return header_line;
 }
 
-extern void LoadOrganismModifierTable (IteM i)
+
+static Int4Ptr GetColumnBlankCounts (ValNodePtr header_line, Int4 num_columns)
+{
+  ValNodePtr   line_vnp, part_vnp;
+  TableLinePtr tlp;
+  Int4         i;
+  Int4Ptr      blank_list;
+  
+  if (header_line == NULL || num_columns < 1) return NULL;
+
+  blank_list = (Int4Ptr) MemNew (sizeof (Int4) * num_columns);
+
+  for (line_vnp = header_line; line_vnp != NULL; line_vnp = line_vnp->next)
+  {
+    if (line_vnp->data.ptrvalue == NULL) continue;
+    tlp = (TableLinePtr) line_vnp->data.ptrvalue;
+    part_vnp = tlp->parts;
+    for (i = 0; i < num_columns; i++) 
+    {
+      if (part_vnp == NULL || StringHasNoText (part_vnp->data.ptrvalue)) 
+      {
+        blank_list[i]++;
+      }
+      if (part_vnp != NULL) 
+      {
+        part_vnp = part_vnp->next;
+      }
+    }
+  }
+  return blank_list;
+}
+
+
+static void LoadOrganismModifierTableEx (IteM i, Boolean IsTaxConsult)
 {
   BaseFormPtr   bfp;
   ValNodePtr    header_line;
@@ -12265,6 +2532,8 @@ extern void LoadOrganismModifierTable (IteM i)
   OrgModLoadFormPtr form_data;
   Int4          index;
   Int4          max_columns;
+  Int4Ptr       blank_list = NULL;
+  OrgModTableColumnData o;
 
 #ifdef WIN_MAC
   bfp = currentFormDataPtr;
@@ -12286,9 +2555,9 @@ extern void LoadOrganismModifierTable (IteM i)
   if (form_data == NULL) return;
   form_data->entityID = bfp->input_entityID;
   form_data->line_list = header_line;
-  form_data->num_line_forms = max_columns;
-  form_data->line_forms = MemNew (max_columns * sizeof (OrgModLineFormData));
-  if (form_data->line_forms == NULL) return;
+
+  form_data->num_columns = max_columns;
+  form_data->columns = (DialoG PNTR) MemNew (max_columns * sizeof (DialoG));
 
   /* now create a dialog to display values */
   w = FixedWindow (-50, -33, -10, -10, "Table Conversion", StdCloseWindowProc);
@@ -12298,36 +2567,61 @@ extern void LoadOrganismModifierTable (IteM i)
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
   g = HiddenGroup (h, 3, 0, NULL);
+
+  /* pre-analyze table for blanks, so we can display the information in the column dialogs */
+  blank_list = GetColumnBlankCounts (header_line, form_data->num_columns);
+
   tlp = header_line->data.ptrvalue;
-  vnp = tlp->parts;
-  for (index = 0; index < max_columns; index++)
+  for (index = 0, vnp = tlp->parts; index < max_columns; index++)
   {
-    BuildOrgModLineForm (vnp->data.ptrvalue, index, g,
-                         form_data->line_forms + index, form_data);
-    vnp = vnp->next;
+    form_data->columns[index] = OrgModTableColumnDialog (g, vnp == NULL ? NULL : vnp->data.ptrvalue,
+                                                         blank_list == NULL ? 0 : blank_list[index],
+                                                         SetFormModsEnable, form_data);
+    if (vnp != NULL) vnp = vnp->next;
   }
+  blank_list = MemFree (blank_list);
+  if (max_columns > 1 && IsTaxConsult)
+  {
+    o.match_choice = eMatchAccession;
+    o.apply_choice = NULL;
+    PointerToDialog (form_data->columns[0], &o);
+    o.match_choice = 0;
+    ValNodeAddPointer (&o.apply_choice, 1, "Tax Name");
+    PointerToDialog (form_data->columns[1], &o);
+    o.apply_choice = ValNodeFree (o.apply_choice);
+  }
+
   k = HiddenGroup (h, 1, 0, NULL);
   form_data->replace_with_blank_btn = CheckBox (k, "Erase current value when blank found in table", NULL);
 
+  form_data->taxname_options = TaxnameOptionsDialog (h, NULL, NULL);
+  Disable (form_data->taxname_options);
+
   c = HiddenGroup (h, 4, 0, NULL);
   form_data->accept_button = DefaultButton (c, "Accept", DoAcceptFormMods);
   SetObjectExtra (form_data->accept_button, form_data, NULL);
-  Disable (form_data->accept_button);
   PushButton (c, "Cancel", StdCancelButtonProc);
   form_data->leave_dlg_up_btn = CheckBox (c, "Leave Dialog Up", NULL);
 
-  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) k, (HANDLE) c, NULL);
+  SetFormModsEnable(form_data);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) k, (HANDLE) form_data->taxname_options, (HANDLE) c, NULL);
 
   RealizeWindow (w);
   Show (w);
   Update ();
 }
 
-typedef struct orgmodlinedata 
+extern void LoadOrganismModifierTable (IteM i)
+{
+  LoadOrganismModifierTableEx (i, FALSE);
+}
+
+extern void LoadTaxConsult (IteM i)
 {
-  Int4    column_number;
-  Int4    apply_choice;  
-} OrgModLineData, PNTR OrgModLinePtr;
+  LoadOrganismModifierTableEx (i, TRUE);
+}
+
 
 extern Boolean ReplaceImportModifierName (CharPtr PNTR orig_name, Int4 col_num)
 {
@@ -12568,7 +2862,7 @@ static void ExportOneOrganism (BioSourcePtr biop, Pointer userdata)
   }
   
   /* print modifiers for each available column */
-  for (i= 0; i < NumDefLineModifiers; i++)
+  for (i= 0; i < NumDefLineModifiers (); i++)
   {
     if (eotp->modList[i].any_present)
     {
@@ -12630,13 +2924,17 @@ static void ExportOrganisms (SeqEntryPtr sep, ExportOrgTablePtr eotp)
 {
   BioseqSetPtr bssp;
   SeqEntryPtr  nsep;
+  BioseqPtr    bsp;
   
   if (sep == NULL || eotp == NULL || sep->data.ptrvalue == NULL) return;
   
   if (IS_Bioseq (sep))
   {
-    eotp->bsp = (BioseqPtr) sep->data.ptrvalue;
-    VisitBioSourcesOnBsp (eotp->bsp, eotp, ExportOneOrganism);  
+    bsp = (BioseqPtr) sep->data.ptrvalue;
+    if (bsp != NULL && !ISA_aa (bsp->mol)) {
+      eotp->bsp = bsp;
+      VisitBioSourcesOnBsp (eotp->bsp, eotp, ExportOneOrganism);
+    }
   }
   else if (IS_Bioseq_set (sep))
   {
@@ -12876,7 +3174,7 @@ static Boolean SelectModifiersForExport (ExportOrgTablePtr eotp)
     return FALSE;
   }
 
-  for (idx = 0; idx < NumDefLineModifiers; idx++)
+  for (idx = 0; idx < NumDefLineModifiers (); idx++)
   {
     if (eotp->modList[idx].any_present)
     {
@@ -12989,7 +3287,7 @@ static Boolean SelectModifiersForExport (ExportOrgTablePtr eotp)
       selected_mods = NULL;
     }
 
-    for (idx = 0; idx < NumDefLineModifiers; idx++)
+    for (idx = 0; idx < NumDefLineModifiers (); idx++)
     {
       if (eotp->modList[idx].any_present)
       {
@@ -13037,7 +3335,7 @@ extern void ExportOrganismTable (IteM i)
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
 
-  eotd.modList = MemNew (NumDefLineModifiers * sizeof (ModifierItemLocalData));
+  eotd.modList = MemNew (NumDefLineModifiers () * sizeof (ModifierItemLocalData));
   if (eotd.modList == NULL) return;
 
   CountModifiers (eotd.modList, sep);
@@ -13080,7 +3378,7 @@ extern void ExportOrganismTable (IteM i)
 		  lead_str [0] = '\t';
 		}
 
-        for (idx = 0; idx < NumDefLineModifiers; idx++)
+        for (idx = 0; idx < NumDefLineModifiers (); idx++)
         {
           if (eotd.modList[idx].any_present)
           {
@@ -13095,7 +3393,7 @@ extern void ExportOrganismTable (IteM i)
 	  }
 	}
   }
-  for (idx=0; idx < NumDefLineModifiers; idx++)
+  for (idx=0; idx < NumDefLineModifiers (); idx++)
   {
     ValNodeFree (eotd.modList[idx].values_seen);
   }
@@ -14190,6 +4488,266 @@ extern void LoadFeatureQualifierTable (IteM i)
   Update ();
 }
 
+
+typedef struct qualloadformdata {
+  FEATURE_FORM_BLOCK
+  ValNodePtr             table;
+  DialoG                 list_dlg;
+  DialoG PNTR            column_list;
+  Int4                   num_columns;
+  ButtoN                 accept_button;
+} QualLoadFormData, PNTR QualLoadFormPtr;
+
+static void CleanupQualLoadForm (
+  GraphiC g,
+  VoidPtr data
+)
+{
+  QualLoadFormPtr form_data;
+
+  form_data = (QualLoadFormPtr)data;
+  if (form_data == NULL) return;
+  form_data->table = FreeTabTable (form_data->table);
+  StdCleanupFormProc (g, data);
+} 
+
+
+static void ChangeTabColumnChoice (Pointer data)
+{
+  QualLoadFormPtr form_data;
+  Int4            i;
+  Boolean         have_match = FALSE, have_apply = FALSE;
+  TabColumnConfigPtr t;
+  ValNodePtr         err_list = NULL;
+
+  if (data == NULL) return;
+
+  form_data = (QualLoadFormPtr) data;
+  /* must have one and only one match choice, must have at least one apply choice */
+
+  if (form_data->list_dlg == NULL) {
+    for (i = 0; i < form_data->num_columns; i++) {
+      t = (TabColumnConfigPtr) DialogToPointer (form_data->column_list[i]);
+      if (t != NULL) {
+        if (t->match_type > 0) {
+          if (have_match) {
+            Disable (form_data->accept_button);
+            return;
+          } else {
+            have_match = TRUE;
+          }
+        } else if (!IsFieldTypeEmpty(t->field)) {
+          have_apply = TRUE;
+        }
+      }
+      t = TabColumnConfigFree (t);
+    }
+    if (have_match && have_apply) {
+      Enable (form_data->accept_button);
+    } else {
+      Disable (form_data->accept_button);
+    }
+  } else {
+    err_list = TestDialog (form_data->list_dlg);
+    if (err_list == NULL) {
+      Enable (form_data->accept_button);
+    } else {
+      Disable (form_data->accept_button);
+      err_list = ValNodeFree (err_list);
+    }
+  }
+}
+
+
+static void DoAcceptQuals (ButtoN b)
+{
+  QualLoadFormPtr form_data;
+  ValNodePtr      columns = NULL;
+  Int4            i;
+  TabColumnConfigPtr t;
+  ValNodePtr      err_list = NULL, vnp;
+  SeqEntryPtr     sep;
+  LogInfoPtr      lip;
+  ValNodePtr      obj_table = NULL, dup_dest_errs;
+
+  form_data = (QualLoadFormPtr) GetObjectExtra (b);
+  if (form_data == NULL) return;
+
+  if (form_data->list_dlg == NULL) {
+    for (i = 0; i < form_data->num_columns; i++) {
+      t = DialogToPointer (form_data->column_list[i]);
+      ValNodeAddPointer (&columns, 0, t);
+    }
+  } else {
+    columns = DialogToPointer (form_data->list_dlg);
+  }
+
+  lip = OpenLog ("Table Problems");
+
+  err_list = ValidateTabTableValues (form_data->table, columns);
+  for (vnp = err_list; vnp != NULL; vnp = vnp->next) {
+    fprintf (lip->fp, "%s\n", vnp->data.ptrvalue);
+    lip->data_in_log = TRUE;
+  }
+  err_list = ValNodeFreeData (err_list);
+
+  sep = GetTopSeqEntryForEntityID (form_data->input_entityID);
+
+  obj_table = GetObjectTableForTabTable (sep, form_data->table, columns, &err_list);
+
+  dup_dest_errs = CheckObjTableForRowsThatApplyToTheSameDestination (obj_table);
+  if (dup_dest_errs != NULL) {
+    for (vnp = dup_dest_errs; vnp != NULL; vnp = vnp->next) {
+      fprintf (lip->fp, "%s\n", vnp->data.ptrvalue);
+      lip->data_in_log = TRUE;
+    }
+    CloseLog (lip);
+    Message (MSG_ERROR, "For one or more columns, two or more rows in the table apply to the same object.  Cannot continue.");
+    dup_dest_errs = ValNodeFreeData (dup_dest_errs);
+    err_list = ValNodeFreeData (err_list);
+    FreeLog (lip);
+    columns = TabColumnConfigListFree (columns);
+    obj_table = FreeObjectTableForTabTable (obj_table);
+    return;
+  }
+
+  ValNodeLink (&err_list, CheckObjTableForExistingText (sep, form_data->table, columns, obj_table));
+
+  for (vnp = err_list; vnp != NULL; vnp = vnp->next) {
+    fprintf (lip->fp, "%s\n", vnp->data.ptrvalue);
+    lip->data_in_log = TRUE;
+  }
+  err_list = ValNodeFreeData (err_list);
+
+  CloseLog (lip);
+  if (lip->data_in_log) {
+    if (ANS_CANCEL == Message (MSG_OKC, "Continue with errors?")) {
+      columns = TabColumnConfigListFree (columns);
+      FreeLog (lip);
+      return;
+    }
+  }
+  FreeLog (lip);
+
+  err_list =  ApplyTableValuesToObjectTable (sep, form_data->table, columns, obj_table);
+
+  lip = OpenLog ("Table Problems");
+  for (vnp = err_list; vnp != NULL; vnp = vnp->next) {
+    fprintf (lip->fp, "%s\n", vnp->data.ptrvalue);
+    lip->data_in_log = TRUE;
+  }
+  err_list = ValNodeFreeData (err_list);
+  CloseLog (lip);
+  FreeLog (lip);
+  columns = TabColumnConfigListFree (columns);
+  obj_table = FreeObjectTableForTabTable (obj_table);
+  ObjMgrSetDirtyFlag (form_data->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, form_data->input_entityID, 0, 0);
+  Remove (form_data->form);
+  Update();
+
+}
+
+extern void NewLoadFeatureQualifierTable (IteM i)
+{
+  BaseFormPtr  bfp;
+  Char         path [PATH_MAX];
+  FILE *fp;
+
+  ValNodePtr   table, blank_list;
+  ValNodePtr   col_vnp, blank_vnp;
+  Int4         index;
+  WindoW        w;
+  GrouP         h, g, c;
+  QualLoadFormPtr form_data;
+  CharPtr         title;
+  Int4            col_for_list = 3;
+  Char            buf[15];
+  ValNodePtr      special_list;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+
+  path [0] = '\0';
+  if (! GetInputFileName (path, sizeof (path), NULL, "TEXT")) return;
+  
+  fp = FileOpen (path, "r");
+
+  table = ReadTabTableFromFile (fp);
+  FileClose (fp);
+  if (table == NULL) return;
+  special_list = ScanTabTableForSpecialCharacters (table);
+  if (special_list != NULL 
+      && !FixSpecialCharactersForStringsInList (special_list, 
+                                                "The table contains special characters\nand cannot be used until they are replaced.",
+                                                FALSE)) {
+    special_list = FreeContextList (special_list);
+    return;
+  }
+  special_list = FreeContextList (special_list);
+  
+  form_data = MemNew (sizeof (QualLoadFormData));
+  if (form_data == NULL) return;
+  form_data->input_entityID = bfp->input_entityID;
+  form_data->table = table;
+  blank_list = CountTabTableBlanks (form_data->table);
+  form_data->num_columns = ValNodeLen (blank_list);
+  form_data->column_list = (DialoG PNTR) MemNew (sizeof (DialoG) * form_data->num_columns);
+
+  /* now create a dialog to display values */
+  w = FixedWindow (-50, -33, -10, -10, "Apply Qualifiers", StdCloseWindowProc);
+  SetObjectExtra (w, form_data, CleanupQualLoadForm);
+  form_data->form = (ForM) w;
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  if (GetSequinAppParam ("SETTINGS", "tablecolumns", NULL, buf, sizeof (buf))) {
+    col_for_list = atoi (buf);
+  }
+
+
+  if (form_data->num_columns >= col_for_list) {
+    form_data->list_dlg = TabColumnConfigListDialog (h, form_data->table->data.ptrvalue, blank_list, ChangeTabColumnChoice, form_data);
+    g = (GrouP) form_data->list_dlg;
+  } else {
+    g = HiddenGroup (h, 3, 0, NULL);
+    col_vnp = form_data->table->data.ptrvalue;
+    blank_vnp = blank_list;
+    for (index = 0; index < form_data->num_columns; index++) {
+      if (col_vnp == NULL || StringHasNoText (col_vnp->data.ptrvalue)) {
+        title = "First row value is blank";
+      } else {
+        title = col_vnp->data.ptrvalue;
+      }
+      form_data->column_list[index] = TabColumnConfigDialog (g, title, blank_vnp->data.intvalue, ChangeTabColumnChoice, form_data);
+      if (col_vnp != NULL) {
+        col_vnp = col_vnp->next;
+      }
+      blank_vnp = blank_vnp->next;
+    }
+  }
+  c = HiddenGroup (h, 4, 0, NULL);
+  form_data->accept_button = DefaultButton (c, "Accept", DoAcceptQuals);
+  SetObjectExtra (form_data->accept_button, form_data, NULL);
+  Disable (form_data->accept_button);
+  PushButton (c, "Cancel", StdCancelButtonProc);
+
+  AlignObjects (ALIGN_CENTER,
+                (HANDLE) g, 
+                (HANDLE) c, NULL);
+
+  RealizeWindow (w);
+  Show (w);
+  Update ();
+  blank_list = ValNodeFree (blank_list);
+}
+
+
 typedef struct prefixformdata {
   FEATURE_FORM_BLOCK
 
@@ -14212,7 +4770,7 @@ static void CleanupPrefixForm (
   if (pfp != NULL) {
     if (pfp->modList != NULL)
     {
-      for (i=0; i < NumDefLineModifiers; i++)
+      for (i=0; i < NumDefLineModifiers (); i++)
       {
         ValNodeFree (pfp->modList[i].values_seen);
       }
@@ -14236,7 +4794,7 @@ static Int4 GetDefLineModifierPopupIndex (
   
   want_index = 0;
   for (index = 0;
-       index < NumDefLineModifiers && want_index < popup_index;
+       index < NumDefLineModifiers () && want_index < popup_index;
        index++)
   {
     if (modList [index].any_present)
@@ -14244,7 +4802,7 @@ static Int4 GetDefLineModifierPopupIndex (
       want_index ++;
     }
   }
-  if (index >= NumDefLineModifiers || index == 0
+  if (index >= NumDefLineModifiers () || index == 0
     || want_index < popup_index)
   {
     return -1;
@@ -14304,13 +4862,13 @@ static void AddPrefixesToOneDefLine (
   if (orp == NULL) return;
   onp = orp->orgname;
   if (onp == NULL) return;
-  for (index = 0; index < NumDefLineModifiers; index ++)
+  for (index = 0; index < NumDefLineModifiers (); index ++)
   {
     if (pfp->popup_list [ index] != NULL
       && (popup_choice = GetValue (pfp->popup_list [ index])) > 0)
     {
       qual_index = GetDefLineModifierPopupIndex (popup_choice, pfp->modList);
-      if (qual_index < 0 || qual_index >= NumDefLineModifiers) continue;
+      if (qual_index < 0 || qual_index >= NumDefLineModifiers ()) continue;
       if (DefLineModifiers[qual_index].isOrgMod)
       {
         mod = onp->mod;
@@ -14326,11 +4884,11 @@ static void AddPrefixesToOneDefLine (
           {
             sprintf (modifier_text, "from ");
             if (no_semicolon_len > sizeof (modifier_text) - 6) {
-			  prefix_len = sizeof (modifier_text) - 1;
+              prefix_len = sizeof (modifier_text) - 1;
               no_semicolon_len = sizeof (modifier_text) - 6;
-			} else {
-			  prefix_len = no_semicolon_len + 5;
-			}
+            } else {
+	            prefix_len = no_semicolon_len + 5;
+            }
             StringNCpy (modifier_text + 5, mod->subname, no_semicolon_len);
             modifier_text[prefix_len] = 0;
           }
@@ -14341,10 +4899,10 @@ static void AddPrefixesToOneDefLine (
               StringCat (modifier_text, " ");
             if (no_semicolon_len > sizeof (modifier_text) - StringLen (modifier_text) - 1) {
               no_semicolon_len = sizeof (modifier_text) - StringLen (modifier_text) - 1;
-			  prefix_len = sizeof (modifier_text) - 1;
-			} else {
-			  prefix_len = no_semicolon_len + StringLen (modifier_text);
-			}
+	            prefix_len = sizeof (modifier_text) - 1;
+            } else {
+	            prefix_len = no_semicolon_len + StringLen (modifier_text);
+            }
 
             StringNCat (modifier_text, mod->subname, no_semicolon_len);
             modifier_text[prefix_len] = 0;
@@ -14486,7 +5044,7 @@ extern void PrefixDefLines (IteM i)
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
 
-  modList = MemNew (NumDefLineModifiers * sizeof (ModifierItemLocalData));
+  modList = MemNew (NumDefLineModifiers () * sizeof (ModifierItemLocalData));
   if (modList == NULL) return;
   CountModifiers (modList, sep);
 
@@ -14494,7 +5052,7 @@ extern void PrefixDefLines (IteM i)
   if (pfp == NULL) return;
   pfp->input_entityID = bfp->input_entityID;
   pfp->modList = modList;
-  pfp->popup_list = MemNew (sizeof (PopuP) * NumDefLineModifiers);
+  pfp->popup_list = MemNew (sizeof (PopuP) * NumDefLineModifiers ());
   if (pfp->popup_list == NULL) return;
 
   w = FixedWindow (-50, -33, -10, -10, "Definition Line Prefixes",
@@ -14505,12 +5063,12 @@ extern void PrefixDefLines (IteM i)
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
   g = HiddenGroup (h, 4, 0, NULL);
-  for (index = 0; index < NumDefLineModifiers; index++)
+  for (index = 0; index < NumDefLineModifiers (); index++)
   {
     pfp->popup_list [index] = NULL;
   }
   popup_index = 0;
-  for (index = 0; index < NumDefLineModifiers; index++)
+  for (index = 0; index < NumDefLineModifiers (); index++)
   {
     if (modList [ index].any_present)
     {
@@ -14519,7 +5077,7 @@ extern void PrefixDefLines (IteM i)
       StaticPrompt (k, label, 0, popupMenuHeight, programFont, 'l');
       pfp->popup_list[popup_index] = PopupList (k, TRUE, NULL);
       listed_index = 0;
-      for (item_index = 0; item_index < NumDefLineModifiers; item_index ++)
+      for (item_index = 0; item_index < NumDefLineModifiers (); item_index ++)
       {
         if (modList [item_index].any_present)
         {
@@ -15840,53 +6398,6 @@ static SeqFeatPtr GetFeatureForFieldByMatchList (ValNodePtr field, ValNodePtr ma
 }
 
 
-static SeqFeatPtr GetmRNAForFeature (SeqFeatPtr sfp)
-{
-  SeqMgrFeatContext fcontext;
-  BioseqPtr         pbsp;
-
-  if (sfp == NULL) return NULL;
-  if (sfp->data.choice == SEQFEAT_PROT) 
-  { 
-    pbsp = BioseqFindFromSeqLoc (sfp->location);
-    sfp = SeqMgrGetCDSgivenProduct (pbsp, NULL);
-    if (sfp == NULL) return NULL;
-  }
-  return SeqMgrGetOverlappingmRNA (sfp->location, &fcontext);
-}
-
-
-static Int4Ptr GetColumnBlankCounts (ValNodePtr header_line, Int4 num_columns)
-{
-  ValNodePtr   line_vnp, part_vnp;
-  TableLinePtr tlp;
-  Int4         i;
-  Int4Ptr      blank_list;
-  
-  if (header_line == NULL || num_columns < 1) return NULL;
-
-  blank_list = (Int4Ptr) MemNew (sizeof (Int4) * num_columns);
-
-  for (line_vnp = header_line; line_vnp != NULL; line_vnp = line_vnp->next)
-  {
-    if (line_vnp->data.ptrvalue == NULL) continue;
-    tlp = (TableLinePtr) line_vnp->data.ptrvalue;
-    part_vnp = tlp->parts;
-    for (i = 0; i < num_columns; i++) 
-    {
-      if (part_vnp == NULL || StringHasNoText (part_vnp->data.ptrvalue)) 
-      {
-        blank_list[i]++;
-      }
-      if (part_vnp != NULL) 
-      {
-        part_vnp = part_vnp->next;
-      }
-    }
-  }
-  return blank_list;
-}
-
 static void 
 GetExistingValueCounts 
 (TableLinePtr                     tlp,
@@ -15941,40 +6452,6 @@ GetExistingValueCounts
 }
 
 
-static Boolean AdjustmRNAProductToMatchProteinProduct (SeqFeatPtr sfp)
-{
-  SeqFeatPtr mrna;
-  ProtRefPtr prp;
-  RnaRefPtr  rrp;
-
-  if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT) return FALSE;
-
-  prp = (ProtRefPtr) sfp->data.value.ptrvalue;
-  mrna = GetmRNAForFeature (sfp);
-
-  if (mrna == NULL) return FALSE;
-
-  rrp = (RnaRefPtr) mrna->data.value.ptrvalue;
-  if (rrp == NULL) 
-  {
-    rrp = RnaRefNew();
-    mrna->data.value.ptrvalue = rrp;
-  }
-
-  rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
-  if (prp == NULL || prp->name == NULL || StringHasNoText (prp->name->data.ptrvalue))
-  {
-    rrp->ext.choice = 0;
-  }
-  else
-  {
-    rrp->ext.choice = 1;
-    rrp->ext.value.ptrvalue = StringSave (prp->name->data.ptrvalue);
-  }
-  return TRUE;
-}
-
-
 static Int4 
 ApplyProteinIDTableLine 
 (TableLinePtr                     tlp,
@@ -15991,14 +6468,16 @@ ApplyProteinIDTableLine
 
   if (tlp == NULL || f_list == NULL || match_list == NULL) return 0;
 
-  for (index = 0, vnp = tlp->parts; index < num_columns && vnp != NULL; index++, vnp = vnp->next) 
+  index = 0;
+  vnp = tlp->parts;
+  while (index < num_columns)
   {
     if (f_list[index]->field_choice != NULL) 
     {
       sfp = GetFeatureForFieldByMatchList (f_list[index]->field_choice, match_list, &errors);
       if (sfp != NULL)
       {
-        if (StringHasNoText (vnp->data.ptrvalue)) 
+        if (vnp == NULL || StringHasNoText (vnp->data.ptrvalue)) 
         {
           if (f_list[index]->erase_when_blank)
           {
@@ -16026,6 +6505,11 @@ ApplyProteinIDTableLine
         }
       }
     }
+    index++;
+    if (vnp != NULL) 
+    {
+      vnp = vnp->next;
+    }
   }
   errors = ValNodeFreeData (errors);
   return fields_affected;
@@ -16181,13 +6665,13 @@ static DialoG FeatureFieldColumnChoiceDialog
   ButtoN b1, b2;
   PrompT ppt;
   CharPtr real_title;
-  CharPtr title_fmt = "%s (%d are blank)";
+  CharPtr title_fmt = "(%d are blank)%s";
 
   dlg = (FeatureFieldColumnChoiceDlgPtr) MemNew (sizeof (FeatureFieldColumnChoiceDlgData));
 
   if (num_blank > 0) {
     real_title = (CharPtr) MemNew (sizeof (Char) * (StringLen (title_fmt) + StringLen (title) + 15));
-    sprintf (real_title, title_fmt, title, num_blank);
+    sprintf (real_title, title_fmt, num_blank, title);
   } else {
     real_title = title;
   }
@@ -16605,3 +7089,594 @@ extern void LoadFeatureFieldTable (IteM i)
   Update ();
 }
 
+static Pointer GetRevSectionSequence (Uint1 data_choice, Pointer data, Pointer metadata)
+{
+  BioseqPtr bsp;
+  Char        id_str[45];
+
+  if (data == NULL)
+  {
+    return NULL;
+  } 
+  else
+  {
+    bsp = (BioseqPtr) data;
+    SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_str, PRINTID_REPORT, 39);
+    return StringSave (id_str);
+  }
+}
+
+
+static Pointer GetRevSectionInterval (Uint1 data_choice, Pointer data, Pointer metadata)
+{
+  BioseqPtr bsp;
+  DeltaSeqPtr dsp;
+  Uint1       seg_num = 0;
+  Int4        pos = 0;
+  SeqLocPtr   loc;
+  SeqLitPtr   slip;
+  Char        buf[50];
+
+  if ((bsp = (BioseqPtr)data) == NULL || bsp->repr != Seq_repr_delta || bsp->seq_ext == NULL)
+  {
+    return NULL;
+  } 
+
+  for (dsp = (DeltaSeqPtr)(bsp->seq_ext); dsp != NULL; dsp = dsp->next) {
+    switch (dsp->choice)
+    {
+      case 1:      /* SeqLocPtr */
+        if ((loc = (SeqLocPtr)dsp->data.ptrvalue) != NULL) {
+          if (loc->choice != SEQLOC_NULL) {
+            seg_num++;
+            pos += SeqLocLen (loc);
+          }
+        }
+        break;
+      case 2:   /* SeqLitPtr */
+        slip = (SeqLitPtr)(dsp->data.ptrvalue);
+        if (slip != NULL) {
+          if (slip->seq_data != NULL) {
+            if (seg_num == data_choice) {
+              sprintf (buf, "%d-%d", pos + 1, pos + 1 + slip->length);
+              return StringSave (buf);
+            } else {
+              seg_num++;
+            }
+            pos += slip->length;
+          }
+        }
+        break;
+    }
+  }
+  return NULL;
+}
+
+
+static BulkEdFieldData revsection_fields[] = {
+  { "Sequence", NULL, NULL, GetRevSectionSequence, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
+  { "Interval", NULL, NULL, GetRevSectionInterval, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
+  { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
+
+
+typedef struct deltaseqint {
+  BioseqPtr bsp;
+  Int4      start;
+  Int4      stop;
+  SeqLitPtr slip;
+} DeltaSeqIntData, PNTR DeltaSeqIntPtr;
+
+
+static DeltaSeqIntPtr DeltaSeqIntNew (BioseqPtr bsp, Int4 start, Int4 stop, SeqLitPtr slip)
+{
+  DeltaSeqIntPtr dsip;
+
+  dsip = (DeltaSeqIntPtr) MemNew (sizeof (DeltaSeqIntData));
+  dsip->bsp = bsp;
+  dsip->start = start;
+  dsip->stop = stop;
+  dsip->slip = slip;
+  return dsip;
+}
+
+
+static void ListDeltaSeqIntervalsCallback (BioseqPtr bsp, Pointer userdata)
+{
+  ValNodePtr PNTR interval_list;
+  DeltaSeqPtr dsp;
+  Uint1       seg_num = 0;
+  Int4        pos = 0;
+  SeqLocPtr   loc;
+  SeqLitPtr   slip;
+  Char        id_str[45];
+  ClickableItemPtr cip;
+  
+  if (bsp == NULL || bsp->repr != Seq_repr_delta || bsp->seq_ext == NULL || (interval_list = (ValNodePtr PNTR)userdata) == NULL) {
+    return;
+  }
+
+  SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_str, PRINTID_REPORT, sizeof (id_str) - 1);
+
+  for (dsp = (DeltaSeqPtr)(bsp->seq_ext); dsp != NULL; dsp = dsp->next) {
+    switch (dsp->choice)
+    {
+      case 1:      /* SeqLocPtr */
+        if ((loc = (SeqLocPtr)dsp->data.ptrvalue) != NULL) {
+          if (loc->choice != SEQLOC_NULL) {
+            seg_num++;
+            pos += SeqLocLen (loc);
+          }
+        }
+        break;
+      case 2:   /* SeqLitPtr */
+        slip = (SeqLitPtr)(dsp->data.ptrvalue);
+        if (slip != NULL) {
+          if (slip->seq_data != NULL) {
+            cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
+            cip->description = (CharPtr) MemNew (sizeof (Char) * (StringLen (id_str) + 65));
+            sprintf (cip->description, "%s:%d-%d", id_str, pos + 1, pos + slip->length);
+            cip->clickable_item_type = seg_num;
+            ValNodeAddPointer (&cip->item_list, 0, DeltaSeqIntNew (bsp, pos, pos + slip->length - 1, slip));
+            ValNodeAddPointer (interval_list, 0, cip);
+            seg_num++;
+          }
+          pos += slip->length;
+        }
+        break;
+    }
+  }
+}
+
+
+static Int4 GetHighestInterval (ValNodePtr int_list)
+{
+  Int4 max = 0;
+  ClickableItemPtr cip;
+
+  while (int_list != NULL) {
+    cip = (ClickableItemPtr) int_list->data.ptrvalue;
+    if (cip != NULL && cip->clickable_item_type > max) {
+      max = cip->clickable_item_type;
+    }
+    int_list = int_list->next;
+  }
+  return max;
+}
+
+
+typedef struct revseqintform {
+  FORM_MESSAGE_BLOCK
+  DialoG          clickable_list; 
+  PopuP           interval_choice;
+  ButtoN          also_reverse_feats;
+  ValNodePtr      delta_list;
+} RevSeqIntFormData, PNTR RevSeqIntFormPtr;
+
+static void CleanupRevSeqIntForm (GraphiC g, VoidPtr data)
+{
+  RevSeqIntFormPtr f;
+  ValNodePtr       vnp;
+  ClickableItemPtr cip;
+
+  f = (RevSeqIntFormPtr) data;
+  if (f != NULL) {
+    for (vnp = f->delta_list; vnp != NULL; vnp = vnp->next) {
+      /* note - the rest of the ClickableItem will be freed by the clickableItemlist */
+      cip = (ClickableItemPtr) vnp->data.ptrvalue;
+      if (cip != NULL && cip->item_list != NULL) {
+        cip->item_list->data.ptrvalue = MemFree (cip->item_list->data.ptrvalue);
+      }
+    }
+  }
+  StdCleanupFormProc (g, data);
+}
+
+
+static void CheckIntervals (ButtoN b)
+{
+  RevSeqIntFormPtr f;
+  ValNodePtr       vnp;
+  ClickableItemPtr cip;
+  Int4             val;
+
+  f = (RevSeqIntFormPtr) GetObjectExtra (b);
+  if (f == NULL) return;
+
+  val = GetValue (f->interval_choice);
+  for (vnp = f->delta_list; vnp != NULL; vnp = vnp->next) {
+    cip = (ClickableItemPtr) vnp->data.ptrvalue;
+    if (cip != NULL && cip->clickable_item_type == val - 1) {
+      cip->chosen = TRUE;
+    }
+  }
+  PointerToDialog (f->clickable_list, f->delta_list);
+}
+
+
+static Int4 RevCompCoordInInterval (Int4 coord, Int4 start, Int4 stop)
+{
+  Int4 offset;
+
+  if (coord < start || coord > stop) return coord;
+
+  offset = coord - start;
+  coord = stop - offset;
+  return coord;
+}
+
+
+static void RevCompIntFuzz (IntFuzzPtr ifp, Int4 start, Int4 stop)
+{
+  Int4 tmp, offset;
+
+  if (ifp == NULL) return;
+
+	switch (ifp->choice)
+	{
+		case 1:      /* plus/minus - no changes */
+		case 3:      /* percent - no changes */
+			break;
+		case 2:      /* range */
+      tmp = RevCompCoordInInterval (ifp->a, start, stop);
+      ifp->a = RevCompCoordInInterval (ifp->b, start, stop);
+      ifp->b = tmp;
+			break;
+		case 4:     /* lim */
+			switch (ifp->a)
+			{
+				case 1:    /* greater than */
+					ifp->a = 2;
+					break;
+				case 2:    /* less than */
+					ifp->a = 1;
+					break;
+				case 3:    /* to right of residue */
+					ifp->a = 4;
+					break;
+				case 4:    /* to left of residue */
+					ifp->a = 3;
+					break;
+				default:
+					break;
+			}
+			break;
+	}
+}
+
+static Uint1 RevStrand (Uint1 strand)
+{
+  if (strand == Seq_strand_minus) {
+    strand = Seq_strand_plus;
+  } else {
+    strand = Seq_strand_minus;
+  }
+  return strand;
+}
+
+
+static void RevCompSeqPntForFlippedInterval (SeqPntPtr spp, BioseqPtr bsp, Int4 start, Int4 stop)
+{
+
+  if (spp == NULL || bsp == NULL) return;
+  if (!SeqIdIn (spp->id, bsp->id)) return;
+  if (spp->point < start || spp->point > stop) return;
+
+  /* flip */
+  spp->point = RevCompCoordInInterval (spp->point, start, stop);
+  spp->strand = RevStrand (spp->strand);
+  RevCompIntFuzz (spp->fuzz, start, stop);
+}
+
+
+static void RevCompLocationForFlippedInterval (SeqLocPtr head, BioseqPtr bsp, Int4 start, Int4 stop)
+{
+	SeqLocPtr newhead = NULL, slp;
+	SeqIntPtr sip;
+	SeqPntPtr spp;
+	PackSeqPntPtr pspp, pspp2;
+	SeqBondPtr sbp;
+	SeqIdPtr oldids;
+	Int4 numpnt, i, tpos, tmp;
+	Boolean do_rev;
+	IntFuzzPtr ifp;
+	
+	if ((head == NULL) || (bsp == NULL)) return;
+
+	oldids = bsp->id;
+	switch (head->choice)
+	{    
+    case SEQLOC_BOND:   /* bond -- 2 seqs */
+			sbp = (SeqBondPtr)(head->data.ptrvalue);
+      RevCompSeqPntForFlippedInterval (sbp->a, bsp, start, stop);
+      RevCompSeqPntForFlippedInterval (sbp->b, bsp, start, stop);
+			break;
+    case SEQLOC_FEAT:   /* feat -- can't track yet */
+    case SEQLOC_NULL:    /* NULL */
+    case SEQLOC_EMPTY:    /* empty */
+			break;
+    case SEQLOC_WHOLE:    /* whole */
+      /* nothing to reverse */
+			break;
+    case SEQLOC_EQUIV:    /* does it stay equiv? */
+    case SEQLOC_MIX:    /* mix -- more than one seq */
+    case SEQLOC_PACKED_INT:    /* packed int */
+			for (slp = (SeqLocPtr)(head->data.ptrvalue); slp != NULL; slp = slp->next)
+			{
+        RevCompLocationForFlippedInterval (slp, bsp, start, stop);
+      }
+      break;
+    case SEQLOC_INT:    /* int */
+			sip = (SeqIntPtr)(head->data.ptrvalue);
+			if (SeqIdIn(sip->id, oldids))
+			{
+        if (sip->from < start || sip->to > stop) {
+          /* not contained in interval */
+          break;
+        }
+        tmp = RevCompCoordInInterval (sip->from, start, stop);
+        sip->from = RevCompCoordInInterval (sip->to, start, stop);
+        sip->to = tmp;
+        sip->strand = RevStrand (sip->strand);
+        RevCompIntFuzz (sip->if_to, start, stop);
+        RevCompIntFuzz (sip->if_from, start, stop);
+        ifp = sip->if_to;
+        sip->if_to = sip->if_from;
+        sip->if_from = ifp;
+      }
+      break;
+    case SEQLOC_PNT:    /* pnt */
+			spp = (SeqPntPtr)(head->data.ptrvalue);
+      RevCompSeqPntForFlippedInterval (spp, bsp, start, stop);
+      break;
+    case SEQLOC_PACKED_PNT:    /* packed pnt */
+			pspp = (PackSeqPntPtr)(head->data.ptrvalue);
+      do_rev = FALSE;
+			if (SeqIdIn(pspp->id, oldids))
+			{
+        do_rev = TRUE;
+				numpnt = PackSeqPntNum(pspp);
+        /* can only reverse set if all are in interval */
+				for (i = 0; i < numpnt && do_rev; i++)
+				{
+					tpos = PackSeqPntGet(pspp, i);
+          if (tpos < start || tpos > stop) {
+            do_rev = FALSE;
+          }
+        }
+        if (do_rev) {
+				  pspp2 = PackSeqPntNew();
+  				pspp2->id = pspp->id;
+          pspp2->fuzz = pspp->fuzz;
+          pspp->fuzz = NULL;
+          RevCompIntFuzz (pspp2->fuzz, start, stop);
+				  for (i = 0; i < numpnt && do_rev; i++)
+				  {
+					  tpos = PackSeqPntGet(pspp, i);
+            tpos = RevCompCoordInInterval (tpos, start, stop);
+            PackSeqPntPut (pspp2, tpos);
+          }
+          pspp2->strand = RevStrand (pspp->strand);
+          pspp = PackSeqPntFree (pspp);
+          head->data.ptrvalue = pspp2;
+			  }
+      }
+      break;
+    default:
+      break;
+	}
+}
+
+
+static void RevCompOneFeatForBioseqInterval (SeqFeatPtr sfp, BioseqPtr bsp, Int4 start, Int4 stop)
+{
+  CodeBreakPtr cbp;
+  CdRegionPtr  crp;
+  RnaRefPtr    rrp;
+  tRNAPtr      trp;
+
+  if (sfp == NULL || bsp == NULL) return;
+
+  RevCompLocationForFlippedInterval (sfp->location, bsp, start, stop);
+  switch (sfp->data.choice) {
+    case SEQFEAT_CDREGION :
+      crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+      if (crp != NULL) {
+        for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
+          RevCompLocationForFlippedInterval (cbp->loc, bsp, start, stop);
+        }
+      }
+      break;
+    case SEQFEAT_RNA :
+      rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+      if (rrp != NULL && rrp->ext.choice == 2) {
+        trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+        if (trp != NULL && trp->anticodon != NULL) {
+          RevCompLocationForFlippedInterval (trp->anticodon, bsp, start, stop);
+        }
+      }
+      break;
+    default :
+      break;
+  }
+}
+
+
+static void FlipSelectedSequenceIntervals (ButtoN b)
+{
+  RevSeqIntFormPtr f;
+  ValNodePtr       vnp;
+  ClickableItemPtr cip;
+  Int4             num_disc;
+  DeltaSeqIntPtr   dsip;
+  Boolean          rev_feats;
+  SeqFeatPtr        sfp;
+  SeqMgrFeatContext fcontext;
+
+  f = (RevSeqIntFormPtr) GetObjectExtra (b);
+  if (f == NULL) return;
+  num_disc = CountChosenDiscrepancies (f->delta_list, FALSE);
+  if (num_disc == 0) {
+    Message (MSG_ERROR, "No intervals selected");
+    return;
+  }
+
+  rev_feats = GetStatus (f->also_reverse_feats);
+
+  for (vnp = f->delta_list; vnp != NULL; vnp = vnp->next) {
+    cip = (ClickableItemPtr) vnp->data.ptrvalue;
+    if (cip != NULL && cip->chosen && cip->item_list != NULL) {
+      dsip = (DeltaSeqIntPtr) cip->item_list->data.ptrvalue;
+      if (dsip != NULL && dsip->slip != NULL) {
+        ReverseSeqData (dsip->slip->seq_data_type, dsip->slip->length, dsip->slip->seq_data);
+        ComplementSeqData (dsip->slip->seq_data_type, dsip->slip->length, dsip->slip->seq_data);
+        if (rev_feats) {
+          for (sfp = SeqMgrGetNextFeature (dsip->bsp, NULL, 0, 0, &fcontext);
+               sfp != NULL && fcontext.left <= dsip->stop;
+               sfp = SeqMgrGetNextFeature (dsip->bsp, sfp, 0, 0, &fcontext)) {
+            if (fcontext.left >= dsip->start && fcontext.right <= dsip->stop) {
+              RevCompOneFeatForBioseqInterval (sfp, dsip->bsp, dsip->start, dsip->stop);
+            }
+          }
+        }
+      }
+    }
+  }
+  Update ();
+  ObjMgrSetDirtyFlag (f->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, f->input_entityID, 0, 0);
+  Remove (f->form);
+}
+
+NLM_EXTERN void FlipSequenceIntervals (IteM i)
+{
+  BaseFormPtr         bfp;
+  RevSeqIntFormPtr    f;
+  SeqEntryPtr         sep;
+  WindoW              w;
+  GrouP               h, g, c;
+  ButtoN              b;
+  ValNodePtr          delta_list = NULL;
+  Int4                max, n;
+  Char                buf[15];
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL || bfp->input_entityID == 0) return;
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+
+  VisitBioseqsInSep (sep, &delta_list, ListDeltaSeqIntervalsCallback);
+
+  if (delta_list == NULL)
+  {
+    Message (MSG_OK, "No sequence intervals");
+    return;
+  }
+
+
+  f = (RevSeqIntFormPtr) MemNew (sizeof (RevSeqIntFormData));
+  if (f == NULL)
+  {
+    return;
+  }
+  f->delta_list = delta_list;
+  
+  f->input_entityID = bfp->input_entityID;
+  w = FixedWindow (-50, -33, -10, -10, "Reverse Sequence Intervals", StdCloseWindowProc);
+  SetObjectExtra (w, f, CleanupRevSeqIntForm);
+  f->form = (ForM) w;
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+  
+  f->clickable_list = CreateClickableListDialog (h, "Intervals", "",
+                                                 NULL, NULL, NULL, NULL);
+  PointerToDialog (f->clickable_list, f->delta_list);
+
+  max = GetHighestInterval (f->delta_list);
+  
+  g = HiddenGroup (h, 4, 0, NULL);
+  StaticPrompt (g, "Check Interval ", 0, popupMenuHeight, programFont, 'l');
+  f->interval_choice = PopupList (g, TRUE, NULL);
+  for (n = 0; n <= max; n++) {
+    sprintf (buf, "%d", n + 1);
+    PopupItem (f->interval_choice, buf);
+  }
+  SetValue (f->interval_choice, 1);
+  StaticPrompt (g, " for every sequence", 0, popupMenuHeight, programFont, 'l');
+  b = PushButton (g, "Check", CheckIntervals);
+  SetObjectExtra (b, f, NULL);
+
+  f->also_reverse_feats = CheckBox (h, "Also reverse features", NULL);
+
+  c = HiddenGroup (h, 4, 0, NULL);
+  SetGroupSpacing (c, 10, 10);
+
+  b = PushButton (c, "Flip Checked Intervals", FlipSelectedSequenceIntervals);
+  SetObjectExtra (b, f, NULL);
+    
+  PushButton (c, "Dismiss", StdCancelButtonProc);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) f->clickable_list, (HANDLE) g, (HANDLE) f->also_reverse_feats, (HANDLE) c, NULL);
+
+  RealizeWindow (w);
+  
+  Show (w);
+}
+
+
+#ifdef OS_MSWIN
+#include <undefwin.h>
+#include <windows.h>
+
+NLM_EXTERN Int4 RunSilent(const char *cmdline) {
+    int status = -1;
+
+    STARTUPINFO         StartupInfo;
+    PROCESS_INFORMATION ProcessInfo;
+
+    DWORD dwCreateFlags;
+
+#ifndef COMP_METRO
+    /* code warrior headers do not have this, so comment out to allow compilation */
+    _flushall();
+#endif
+
+    /* Set startup info */
+    memset(&StartupInfo, 0, sizeof(StartupInfo));
+    StartupInfo.cb          = sizeof(STARTUPINFO);
+    StartupInfo.dwFlags     = STARTF_USESHOWWINDOW;
+    StartupInfo.wShowWindow = SW_HIDE;
+    dwCreateFlags           = CREATE_NEW_CONSOLE;
+
+    /* Run program */
+    if (CreateProcess(NULL, (LPSTR)cmdline, NULL, NULL, FALSE,
+                      dwCreateFlags, NULL, NULL, &StartupInfo, &ProcessInfo))
+    {
+        /* wait running process */
+        DWORD exitcode = -1;
+        WaitForSingleObject(ProcessInfo.hProcess, INFINITE);
+        GetExitCodeProcess(ProcessInfo.hProcess, &exitcode);
+        status = exitcode;
+        CloseHandle(ProcessInfo.hProcess);
+        CloseHandle(ProcessInfo.hThread);
+    }
+    else
+    {
+	DWORD dw = GetLastError();
+	/* check for common errors first */
+	if(dw == ERROR_FILE_NOT_FOUND)
+	    Message(MSG_ERROR, "CreateProcess() failed: file not found.");
+	else
+	    /* generic error message */
+	    Message(MSG_ERROR, "CreateProcess() failed, error code %d.",
+		    (int)dw);
+    }
+
+    return status;
+}
+#endif
+
diff --git a/sequin/sequin2.c b/sequin/sequin2.c
index ebec40d1..b2372c1d 100644
--- a/sequin/sequin2.c
+++ b/sequin/sequin2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.636 $
+* $Revision: 6.647 $
 *
 * File Description: 
 *
@@ -70,6 +70,7 @@
 #endif
 #include <actutils.h>
 #include <salpanel.h>
+#include <findrepl.h>
 
 extern EnumFieldAssoc  biosource_genome_simple_alist [];
 extern EnumFieldAssoc  biosource_origin_alist [];
@@ -86,7 +87,8 @@ static ENUM_ALIST(biomol_nucX_alist)
   {"Other-Genetic",            9},
   {"cRNA",                    11},
   {"Small nucleolar RNA",     12},
-  {"Transcribed RNA",         13},  
+  {"Transcribed RNA",         13}, 
+  {"Transfer-messenger RNA", MOLECULE_TYPE_TMRNA },
 END_ENUM_ALIST
 
 static ENUM_ALIST(biomol_nucGen_alist)
@@ -4231,6 +4233,45 @@ static Int4 FindLineForBadReadChar (FILE *fp, Char badchar)
 }
 
 
+static void CleanTitles (SeqEntryPtr sep, ValNodePtr PNTR special_list)
+{
+  BioseqPtr    bsp;
+  BioseqSetPtr bssp;
+  SeqDescrPtr  sdp = NULL;
+
+  while (sep != NULL)
+  {
+    sdp = NULL;
+    if (sep->choice == 1)
+    {
+      bsp = sep->data.ptrvalue;
+      if (bsp != NULL) 
+      {
+        sdp = bsp->descr;
+      }
+    }
+    else if (sep->choice == 2)
+    {
+      bssp = sep->data.ptrvalue;
+      if (bssp != NULL)
+      {
+        CleanTitles (bssp->seq_set, special_list);
+        sdp = bssp->descr;
+      }
+    }
+    while (sdp != NULL)
+    {
+      if (sdp->choice == Seq_descr_title)
+      {
+        SpecialCharFindWithContext ((CharPtr PNTR) &(sdp->data.ptrvalue), special_list, NULL, NULL);
+      }
+      sdp = sdp->next;
+    }
+    sep = sep->next;
+  }
+}
+
+
 static SeqEntryPtr ImportOnlyProteinSequences 
 (FILE            *fp,
  SeqEntryPtr     sep_list,
@@ -4245,6 +4286,7 @@ static SeqEntryPtr ImportOnlyProteinSequences
   Boolean       error_reading = FALSE;
   Int4          pos, bad_start;
   BioseqPtr     bsp;
+  ValNodePtr    special_list = NULL;
 
   oldscope = SeqEntrySetScope (NULL);
 
@@ -4306,6 +4348,15 @@ static SeqEntryPtr ImportOnlyProteinSequences
     Message (MSG_ERROR, "Unable to read file, starting at line %d!", bad_start);
     new_list = SeqEntryFree (new_list);
   }
+  else
+  {
+    CleanTitles (new_list, &special_list);
+    if (!FixSpecialCharactersForStringsInList (special_list, "Definition lines contain special characters.\nThe sequences cannot be imported unless the characters are replaced.", FALSE))
+    {
+      new_list = SeqEntryFree (new_list);
+    }
+    special_list = FreeContextList (special_list);
+  }
   
   lastsep = sep_list;
   while (lastsep != NULL && lastsep->next != NULL) 
@@ -4351,6 +4402,7 @@ ImportSequencesFromFile
   Boolean       this_chars_stripped = FALSE;
   Boolean       isASN = FALSE, isOnlyFASTA = FALSE;
   Int4          bad_start = 0, bad_line = 0;
+  ValNodePtr    special_list = NULL;
   
   if (chars_stripped != NULL)
   {
@@ -4570,6 +4622,15 @@ ImportSequencesFromFile
     }
     new_sep_list = SeqEntryFree (new_sep_list);
   }
+  else
+  {
+    CleanTitles (new_sep_list, &special_list);
+    if (!FixSpecialCharactersForStringsInList (special_list, "Definition lines contain special characters.\nThe sequences cannot be imported unless the characters are replaced.", FALSE))
+    {
+      new_sep_list = SeqEntryFree (new_sep_list);
+    }
+    special_list = FreeContextList (special_list);
+  }
   
   last = sep_list;
   while (last != NULL && last->next != NULL) 
@@ -7113,8 +7174,6 @@ extern BioSourcePtr ExtractFromDeflineToBioSource (CharPtr defline, BioSourcePtr
   
 }
 
-static void RemoveTaxRef (OrgRefPtr orp);
-
 extern Boolean ProcessOneNucleotideTitle (Int2 seqPackage,
                                           SeqEntryPtr nsep, SeqEntryPtr top);
                                           
@@ -8784,6 +8843,44 @@ PickCodingRegionLocationsForProteinNucleotidePairs
   return !errors_found;
 }
 
+
+static Int2 FindGeneticCodeForBioseq (BioseqPtr bsp, Int2 default_code)
+{
+  Int2         code = default_code;
+  BioSourcePtr biop;
+  SeqEntryPtr  nsep;
+  BioseqSetPtr bssp;
+  SeqDescrPtr  sdp = NULL;
+
+  if (bsp == NULL) return default_code;
+  nsep = GetBestTopParentForData (ObjMgrGetEntityIDForPointer (bsp), bsp);
+  if (nsep == NULL || nsep->data.ptrvalue == NULL) return default_code;
+  if (nsep->choice == 1)
+  {
+    bsp = nsep->data.ptrvalue;
+    sdp = bsp->descr;
+  }
+  else if (nsep->choice == 2)
+  {
+    bssp = nsep->data.ptrvalue;
+    sdp = bssp->descr;
+  }
+  while (sdp != NULL)
+  {
+    if (sdp->choice == Seq_descr_source && sdp->data.ptrvalue != NULL)
+    {
+      biop = (BioSourcePtr) sdp->data.ptrvalue;
+      if (biop->org != NULL && biop->org->orgname != NULL)
+      {
+        code = BioSourceToGeneticCode (biop);
+      }
+    }
+    sdp = sdp->next;
+  }
+  return code;
+}
+
+
 /* This function takes a ValNode list of coding region SeqLocs,
  * the list of nucleotide sequences, and the list of protein sequences
  * and creates the nuc-prot sets.
@@ -8803,6 +8900,7 @@ AssignProteinsToSelectedNucleotides
   BioseqPtr PNTR bsp_array;
   Int4           prot_num;
   ValNodePtr     descr = NULL;
+  Int2           genCode;
 
   if (assoc_list == NULL || nuc_list == NULL || prot_list == NULL)
   {
@@ -8856,10 +8954,12 @@ AssignProteinsToSelectedNucleotides
       {
         nsep = GetBestTopParentForData (ObjMgrGetEntityIDForPointer (nbsp), nbsp); 
       }
+      genCode = FindGeneticCodeForBioseq (nbsp, code);
       if (nsep != NULL && nsep->data.ptrvalue == nbsp) {
         descr = ExtractBioSourceAndPubs (nsep);
       }
-      AssignOneProtein (prot_sep, sqfp, nsep, vnp_assoc->loc, nbsp, code, makeMRNA);
+      AssignOneProtein (prot_sep, sqfp, nsep, vnp_assoc->loc, nbsp, 
+                        genCode, makeMRNA);
       if (descr != NULL) {
         ReplaceBioSourceAndPubs (nsep, descr);
       }
@@ -9051,14 +9151,13 @@ static void ReplaceDuplicateProteinIDs (SeqEntryPtr nuc_list, SeqEntryPtr prot_l
             if (cp != NULL) {
               *cp = 0;
             }
+            tmp_str = StringSave (tmp_str);
           
             iatep_prot->id_list [prot_seq_num_check] = MemFree (iatep_prot->id_list [prot_seq_num_check]);
             iatep_prot->id_list [prot_seq_num_check] = BuildProteinIDUniqueInIDAndTitleEdit (tmp_str,
                                                                                              iatep_nuc,
                                                                                              iatep_prot);
-            if (cp != NULL) {
-              *cp = '|';
-            }
+            tmp_str = MemFree (tmp_str);
           }
         }
       }
@@ -11645,12 +11744,16 @@ static CharPtr SuggestCorrectBracketing (CharPtr str)
               if (*next_next_next_token == '=')
               {
                 step_back = GetModNameStartFromEqLoc (next_next_next_token, next_next_token);
-                while (step_back > next_next_token + 1
-                       && isspace (*(step_back - 1)))
-                {
-                  step_back --;
+                if (step_back == next_next_token) {
+                  /* no name before second equals sign, put bracket after value */
+                } else {
+                  while (step_back > next_next_token + 1
+                        && isspace (*(step_back - 1)))
+                  {
+                    step_back --;
+                  }
+                  offset = step_back - new_str;
                 }
-                offset = step_back - new_str;
               }
             }
             tmp_new = InsertStringAtOffset (new_str, "]", offset);
@@ -26174,6 +26277,25 @@ extern void DownloadAndDisplay (Int4 uid)
   }
 }
 
+
+static Boolean IsAllDigits (CharPtr str)
+{
+  CharPtr cp;
+
+  if (StringHasNoText (str)) return FALSE;
+
+  cp = str;
+  while (*cp != 0 && isdigit (*cp)) {
+    cp++;
+  }
+  if (*cp == 0) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+
 static void DownloadProc (ButtoN b)
 
 {
@@ -26189,6 +26311,7 @@ static void DownloadProc (ButtoN b)
   Int2          handled;
   Boolean       idTypes [NUM_SEQID];
   Boolean       isReplaced = FALSE;
+  Boolean       isTrace = FALSE;
   SeqEntryPtr   sep;
   Char          str [32];
   Int4          uid;
@@ -26244,15 +26367,23 @@ static void DownloadProc (ButtoN b)
     }
     SeqIdFree (sip);
     */
-    uid = AccessionToGi (str);
-    accn = str;
+    if (StringNICmp (str, "ti|", 3) == 0 && IsAllDigits (str + 3)) {
+      if (! StrToLong (str + 3, &uid)) {
+        uid = 0;
+      } else {
+        isTrace = TRUE;
+      }
+    } else {      
+      uid = AccessionToGi (str);
+      accn = str;
+    }
   } else {
     if (! StrToLong (str, &uid)) {
      uid = 0;
     }
   }
   if (uid > 0) {
-    sep = PubSeqSynchronousQuery (uid, 0, -1);
+    sep = PubSeqSynchronousQueryEx (uid, 0, -1, isTrace);
     /* EntrezFini (); */
     if (sep == NULL) {
       ArrowCursor ();
@@ -26525,13 +26656,12 @@ static void CancelFetchProc (ButtoN b)
   Select (startupForm);
 }
 
+
 static void FetchTextProc (TexT t)
 
 {
   Boolean       alldigits;
-  Char          ch;
   FetchFormPtr  ffp;
-  CharPtr       ptr;
   Char          str [32];
 
   ffp = (FetchFormPtr) GetObjectExtra (t);
@@ -26542,16 +26672,7 @@ static void FetchTextProc (TexT t)
   } else {
     SafeEnable (ffp->accept);
     TrimSpacesAroundString (str);
-    alldigits = TRUE;
-    ptr = str;
-    ch = *ptr;
-    while (ch != '\0') {
-      if (! IS_DIGIT (ch)) {
-        alldigits = FALSE;
-      }
-      ptr++;
-      ch = *ptr;
-    }
+    alldigits = IsAllDigits (str);
     if (alldigits) {
       SafeSetValue (ffp->accntype, 2);
     } else {
@@ -27834,36 +27955,6 @@ extern ValNodePtr BuildFeatureValNodeList (
   return head;
 }
 
-static void RemoveTaxRef (OrgRefPtr orp)
-{
-  ValNodePtr      vnp, next;
-  ValNodePtr PNTR prev;
-  DbtagPtr        dbt;
-
-  if (orp == NULL)
-  {
-    return;
-  }
- 
-  vnp = orp->db;
-  if (vnp == NULL) return;
-  prev = (ValNodePtr PNTR) &(orp->db);
-  while (vnp != NULL) {
-    next = vnp->next;
-    dbt = (DbtagPtr) vnp->data.ptrvalue;
-    if (dbt != NULL && StringICmp ((CharPtr) dbt->db, "taxon") == 0) {
-      *prev = vnp->next;
-      vnp->next = NULL;
-      DbtagFree (dbt);
-      ValNodeFree (vnp);
-    } else {
-      prev = (ValNodePtr PNTR) &(vnp->next);
-    }
-    vnp = next;
-  }
-  
-}
-
 extern void RemoveOldName (OrgRefPtr orp)
 {
   OrgModPtr prev = NULL, curr, next_mod;
@@ -28739,6 +28830,9 @@ static LisT MakeAlignmentSequenceListControl (GrouP g, SeqEntryPtr sep, Nlm_LstA
 
 typedef struct removeseqfromaligndata {
   FORM_MESSAGE_BLOCK
+  DialoG      clickable_list_dlg;
+  DialoG      constraint_dlg;
+  ValNodePtr  seq_list;
   LisT        sequence_list_ctrl;
   SeqEntryPtr sep;
   Boolean     remove_all_from_alignments;
@@ -28929,21 +29023,14 @@ static void RemoveBioseqProducts (ValNodePtr product_feature_list, RemoveSeqFrom
   }
 }
 
-static void RemoveEmptyNucProtSet (SeqEntryPtr sep)
+static void RemoveNucProtSet (SeqEntryPtr sep)
 {
   BioseqSetPtr bssp;
-  BioseqPtr    bsp;
 
   if (sep == NULL || !IS_Bioseq_set (sep)) return;
   bssp = (BioseqSetPtr) sep->data.ptrvalue;
   if (bssp->_class != BioseqseqSet_class_nuc_prot) return;
 
-  for (sep = bssp->seq_set; sep != NULL; sep = sep->next)
-  {
-  	if (!IS_Bioseq (sep)) return;
-  	bsp = sep->data.ptrvalue;
-  	if (bsp != NULL && !bsp->idx.deleteme) return;
-  }
   bssp->idx.deleteme = TRUE;
 }
 
@@ -29003,66 +29090,6 @@ static void RemoveAlnOrProductNoAll (ButtoN b)
   rp->done = TRUE;
 }
 
-static Boolean GetRemoveAlignments (RemoveSeqFromAlignPtr rp, CharPtr idstr)
-{
-  RemoveAlnOrProductAnsData rd;
-
-  GrouP                    g, h, c;
-  ButtoN                   b;
-  CharPtr                  prompt_fmt = "%s is part of an alignment - would you like to remove it from the alignment before deleting it?";
-  CharPtr                  prompt_str = NULL;
-  
-  if (rp == NULL || idstr == NULL) return FALSE;
-  if (rp->remove_all_from_alignments) return TRUE;
-  if (rp->no_remove_all_from_alignments) return FALSE;
-
-  prompt_str = (CharPtr) MemNew (sizeof (Char) * (StringLen (prompt_fmt) + StringLen (idstr)));
-  if (prompt_str == NULL) return FALSE;
-  sprintf (prompt_str, prompt_fmt, idstr);
-  rd.w = ModalWindow(-20, -13, -10, -10, NULL);
-  h = HiddenGroup(rd.w, -1, 0, NULL);
-  SetGroupSpacing (h, 10, 10);
-  rd.done = FALSE;
-  g = HiddenGroup (h, 1, 0, NULL);
-  StaticPrompt (g, prompt_str, 0, popupMenuHeight, programFont, 'l');
-  c = HiddenGroup (h, 4, 0, NULL);
-  b = PushButton(c, "Yes", RemoveAlnOrProductYes);
-  SetObjectExtra (b, &rd, NULL);
-  b = PushButton(c, "Remove All", RemoveAlnOrProductYesAll);
-  SetObjectExtra (b, &rd, NULL);
-  b = DefaultButton(c, "No", RemoveAlnOrProductNo);
-  SetObjectExtra (b, &rd, NULL);
-  b = DefaultButton(c, "Remove None", RemoveAlnOrProductNoAll);
-  SetObjectExtra (b, &rd, NULL);
-  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
-  prompt_str = MemFree (prompt_str);
-  
-  Show(rd.w); 
-  Select (rd.w);
-  rd.done = FALSE;
-  while (!rd.done)
-  {
-    ProcessExternalEvent ();
-    Update ();
-  }
-  ProcessAnEvent ();
-  if (rd.do_all)
-  {
-    if (rd.ans)
-    {
-  	  rp->remove_all_from_alignments = TRUE;
-  	  rp->no_remove_all_from_alignments = FALSE;
-    }
-    else
-    {
-  	  rp->remove_all_from_alignments = FALSE;
-  	  rp->no_remove_all_from_alignments = TRUE;
-    }
-  }
-  return rd.ans;
-}
-
-
 static Boolean GetRemoveProducts (RemoveSeqFromAlignPtr rp, CharPtr idstr)
 {
   RemoveAlnOrProductAnsData rd;
@@ -29135,10 +29162,22 @@ static void RemoveBioseq (BioseqPtr bsp, RemoveSeqFromAlignPtr rp)
 
   if (IsBioseqInAnyAlignment (bsp, rp->input_entityID))
   {
-    if (GetRemoveAlignments (rp, str))
+    if (!rp->remove_all_from_alignments && !rp->no_remove_all_from_alignments) 
     {
+	    if (ANS_YES == Message (MSG_YN, "This sequence is part of an alignment.  Would you like to remove it from the alignment?")) 
+      {
+        rp->remove_all_from_alignments = TRUE;
+      }
+      else
+      {
+        rp->no_remove_all_from_alignments = TRUE;
+      }
+    }
+
+    if (rp->remove_all_from_alignments) {
       RemoveSequenceFromAlignments (rp->sep, bsp->id);
     }
+
   }
   VisitFeaturesOnBsp (bsp, &product_feature_list, DoesBioseqHaveFeaturesWithProductsCallback);
   if (product_feature_list != NULL)
@@ -29150,10 +29189,11 @@ static void RemoveBioseq (BioseqPtr bsp, RemoveSeqFromAlignPtr rp)
   }
         
   bsp->idx.deleteme = TRUE;
-  /* remove nuc-prot set if we are deleting the nucleotide and its proteins */
-  sep = GetBestTopParentForData (rp->input_entityID, bsp);
-  RemoveEmptyNucProtSet (sep);
-
+  if (ISA_na (bsp->mol)) {
+    /* remove nuc-prot set if we are deleting the nucleotide */
+    sep = GetBestTopParentForData (rp->input_entityID, bsp);
+    RemoveNucProtSet (sep);
+  }
   ValNodeFree (product_feature_list);
   
 }
@@ -29163,9 +29203,10 @@ static void DoRemoveSequencesFromRecord (ButtoN b)
 {
   RemoveSeqFromAlignPtr    rp;
   WindoW                   w;
-  ValNodePtr               sip_list, vnp;
-  SeqIdPtr                 sip;
+  ValNodePtr               vnp, item_vnp;
   BioseqPtr                bsp;
+  ClickableItemPtr         cip;
+  Boolean                  any_removed = FALSE;
   
   if (b == NULL) return;
   rp = (RemoveSeqFromAlignPtr) GetObjectExtra (b);
@@ -29174,17 +29215,26 @@ static void DoRemoveSequencesFromRecord (ButtoN b)
   w = (WindoW) rp->form;
   Hide (w);
 
-  sip_list = GetSelectedSequenceList (rp->sequence_list_ctrl);
-  for (vnp = sip_list; vnp != NULL; vnp = vnp->next)
-  {
-    sip = (SeqIdPtr) vnp->data.ptrvalue;
-    bsp = BioseqFind (sip);
-	  if (bsp != NULL)
-	  {
-	    RemoveBioseq (bsp, rp);
-	  }
+  for (vnp = rp->seq_list; vnp != NULL; vnp = vnp->next) {
+    cip = (ClickableItemPtr) vnp->data.ptrvalue;
+    if (!cip->chosen) continue;
+    if (cip != NULL && cip->item_list != NULL) {
+      for (item_vnp = cip->item_list; item_vnp != NULL; item_vnp = item_vnp->next) {
+        if (item_vnp->choice == OBJ_BIOSEQ) {
+          bsp = item_vnp->data.ptrvalue;
+	        if (bsp != NULL) {
+	          RemoveBioseq (bsp, rp);
+            any_removed = TRUE;
+	        }
+        }
+      }
+    }
+  }
+  if (!any_removed) {
+    Show (w);
+    Message (MSG_ERROR, "You have not selected any sequences for removal!\n(Mark the sequences you want to remove by checking the box next to the sequence or by using the Mark button next to the constraint.)");
+    return;
   }
-  ValNodeFree (sip_list);
   
   DeleteMarkedObjects (rp->input_entityID, 0, NULL);
   ObjMgrSetDirtyFlag (rp->input_entityID, TRUE);
@@ -29192,6 +29242,34 @@ static void DoRemoveSequencesFromRecord (ButtoN b)
   Remove (rp->form);  
 }
 
+
+static void SelectSequenceIDsForRemoval (ButtoN b)
+{
+  RemoveSeqFromAlignPtr rp;
+  StringConstraintXPtr  scp;
+
+  rp = (RemoveSeqFromAlignPtr) GetObjectExtra (b);
+  if (rp == NULL) return;
+
+  scp = DialogToPointer (rp->constraint_dlg);
+  ChooseCategoriesByStringConstraint (rp->seq_list, scp, TRUE);
+  PointerToDialog (rp->clickable_list_dlg, rp->seq_list);
+  scp = StringConstraintXFree (scp);
+}
+
+
+static void UnselectAllSequences (ButtoN b)
+{
+  RemoveSeqFromAlignPtr rp;
+
+  rp = (RemoveSeqFromAlignPtr) GetObjectExtra (b);
+  if (rp != NULL) {
+    ChooseCategories (rp->seq_list, FALSE);
+    PointerToDialog (rp->clickable_list_dlg, rp->seq_list);
+  }
+}
+
+
 extern void RemoveSequencesFromRecord (IteM i)
 {
   BaseFormPtr              bfp;
@@ -29199,6 +29277,9 @@ extern void RemoveSequencesFromRecord (IteM i)
   RemoveSeqFromAlignPtr    rp;
   GrouP                    h, k, c;
   ButtoN                   b;
+  SeqEntryPtr              sep;
+  StringConstraintData     scd;
+  PrompT                   ppt;
 
 #ifdef WIN_MAC
   bfp = currentFormDataPtr;
@@ -29233,16 +29314,43 @@ extern void RemoveSequencesFromRecord (IteM i)
   SetObjectExtra (w, rp, StdCleanupFormProc);
   
   h = HiddenGroup (w, -1, 0, NULL);
+
+  rp->clickable_list_dlg = CreateClickableListDialogEx (h, "Sequences to Remove", "",
+                                                      "Use checkbox to mark sequences to remove",
+                                                      "Single click to navigate to sequence in record",
+                                                      ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
+                                                      GetDiscrepancyItemText,
+                                                      stdCharWidth * 30,
+                                                      stdCharWidth * 30 + 5,
+                                                      TRUE, FALSE);
+
   k = HiddenGroup (h, 2, 0, NULL);
+  rp->constraint_dlg =  StringConstraintDialogX (k, "Mark sequences where sequence ID", TRUE);
+  scd.insensitive = TRUE;
+  scd.match_location = eStringConstraintInList;
+  scd.match_text = NULL;
+  scd.not_present = FALSE;
+  scd.whole_word = FALSE;
+  PointerToDialog (rp->constraint_dlg, &scd);
+  b = PushButton (k, "Mark", SelectSequenceIDsForRemoval);
+  SetObjectExtra (b, rp, NULL);
 
-  rp->sequence_list_ctrl = MakeSequenceListControl (k, rp->sep, NULL, NULL, TRUE, TRUE);
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  VisitBioseqsInSep (sep, &(rp->seq_list), ListAllSequences);
+
+  PointerToDialog (rp->clickable_list_dlg, rp->seq_list);
+
+  ppt = StaticPrompt (h, "Warning - this will remove sequence from Sequin and SMART", 0, dialogTextHeight, programFont, 'c');
 
   c = HiddenGroup (h, 4, 0, NULL);
   b = DefaultButton (c, "Accept", DoRemoveSequencesFromRecord);
   SetObjectExtra (b, rp, NULL);
+  b = PushButton (c, "Unmark All Sequences", UnselectAllSequences);
+  SetObjectExtra (b, rp, NULL);
   b = PushButton (c, "Cancel", StdCancelButtonProc); 
   SetObjectExtra (b, rp, NULL);
-  AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) c, NULL);
+  AlignObjects (ALIGN_CENTER, (HANDLE) rp->clickable_list_dlg, (HANDLE) k, (HANDLE) ppt, (HANDLE) c, NULL);
   RealizeWindow (w);
   Show (w);
   Update ();  
diff --git a/sequin/sequin3.c b/sequin/sequin3.c
index 29a08245..e7157a87 100644
--- a/sequin/sequin3.c
+++ b/sequin/sequin3.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/22/95
 *
-* $Revision: 6.825 $
+* $Revision: 6.861 $
 *
 * File Description: 
 *
@@ -74,7 +74,8 @@
 #include <asn2gnbi.h>
 #include <alignval.h>
 #include <cdrgn.h>
-
+#include <macrodlg.h>
+#include <macroapi.h>
 
 /* For converting primer names to primer seqs and vice versa */
 static void PrimerSeqToPrimerNameCallback (BioSourcePtr biop, Pointer userdata)
@@ -153,6 +154,7 @@ typedef struct fndeldata {
   Int4        gap_count;
   Int4        bsp_length;
   Boolean     in_gap;
+  Boolean     unk_gap;
   ValNodePtr  head;
   ValNodePtr  last;
 } DelData, PNTR DelDataPtr;
@@ -163,6 +165,7 @@ static void AddNextBlock (
 
 {
   ByteStorePtr  bs;
+  IntFuzzPtr    ifp;
   SeqLitPtr     slitp;
   CharPtr       str;
   ValNodePtr    vnp;
@@ -173,6 +176,13 @@ static void AddNextBlock (
     if (slitp != NULL) {
       slitp->length = ddp->gap_count;
       ddp->bsp_length += slitp->length;
+      if (ddp->unk_gap) {
+        ifp = IntFuzzNew ();
+        if (ifp != NULL) {
+          ifp->choice = 4;
+          slitp->fuzz = ifp;
+        }
+      }
       vnp = ValNodeAddPointer (&(ddp->last), 2, (Pointer) slitp);
       if (ddp->head == NULL) {
         ddp->head = vnp;
@@ -222,10 +232,11 @@ static void LIBCALLBACK FarToNearCallback (
   str = ddp->curr;
 
   while (ch != '\0') {
-    if (ch != '-') {
+    if (ch != '-' && ch != '+') {
       if (ddp->in_gap) {
         AddNextBlock (ddp);
         ddp->in_gap = FALSE;
+        ddp->unk_gap = FALSE;
         ddp->gap_count = 0;
         ddp->curr = ddp->buffer;
         ddp->seqlen = 0;
@@ -246,6 +257,7 @@ static void LIBCALLBACK FarToNearCallback (
       if (! ddp->in_gap) {
         AddNextBlock (ddp);
         ddp->in_gap = TRUE;
+        ddp->unk_gap = (Boolean) (ch == '-');
         ddp->gap_count = 0;
         ddp->curr = ddp->buffer;
         ddp->seqlen = 0;
@@ -272,7 +284,7 @@ static void FarToNearProc (BioseqPtr bsp, Pointer userdata)
   if (dd.buffer == NULL) return;
   dd.curr = dd.buffer;
   dd.seqlen = 0;
-  SeqPortStream (bsp, EXPAND_GAPS_TO_DASHES, (Pointer) &dd, FarToNearCallback);
+  SeqPortStream (bsp, EXPAND_GAPS_TO_DASHES | KNOWN_GAP_AS_PLUS, (Pointer) &dd, FarToNearCallback);
   AddNextBlock (&dd);
   MemFree (dd.buffer);
   olddelta = bsp->seq_ext;
@@ -1107,7 +1119,8 @@ static void AddEnvironmentalSampleQual (BioSourcePtr biop, Pointer userdata)
   
   if (biop == NULL || biop->org == NULL || biop->org->orgname == NULL) return;
 
-  if (StringISearch (biop->org->orgname->lineage, "environmental sample") == NULL)
+  if (StringISearch (biop->org->orgname->lineage, "environmental sample") == NULL
+      && StringCmp (biop->org->orgname->div, "ENV") != 0)
   {
   	return;
   }
@@ -1340,6 +1353,45 @@ static void ReassignFeatIDs (IteM i)
   Update ();
 }
 
+static void UniqifyFeatIDs (IteM i)
+
+{
+  MsgAnswer     ans;
+  BaseFormPtr   bfp;
+  BioseqSetPtr  bssp;
+  Int4          count;
+  Int4          offset = 0;
+  SeqEntryPtr   sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+
+  if (! IS_Bioseq_set (sep)) return;
+  bssp = (BioseqSetPtr) sep->data.ptrvalue;
+  if (bssp == NULL || bssp->_class != BioseqseqSet_class_genbank) return;
+
+  ans = Message (MSG_OKC, "Are you sure you want to make merged feature identifiers unique?");
+  if (ans == ANS_CANCEL) return;
+
+  for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
+    count = FindHighestFeatureID (sep);
+    OffsetFeatureIDs (sep, offset);
+    OffsetFeatureIDXrefs (sep, offset);
+    offset += count;
+  }
+
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+  ObjMgrDeSelect (0, 0, 0, 0, NULL);
+  Update ();
+}
+
 static void ClearFeatIDsAndLinks (IteM i)
 
 {
@@ -1687,6 +1739,25 @@ static void ForceTaxonFixup (IteM i)
   ForceTaxonFixupBtn (i, NULL);
 }
 
+static void JustTaxonFixup (IteM i)
+
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  Taxon3ReplaceOrgInSeqEntry (sep, FALSE);
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
 static void DupFeatRemovalWarning (SeqFeatPtr sfp)
 
 {
@@ -4665,7 +4736,7 @@ ConvertRawBioseqToDelta
 
   sep = GetTopSeqEntryForEntityID (bsp->idx.entityID);
 
-  VisitFeaturesInSep (sep, bsp, AdjustCDSLocationsForUnknownGapsCallback);
+  VisitFeaturesInSep (sep, (Pointer) Sequin_GlobalAlign2Seq, AdjustCDSLocationsForUnknownGapsCallback);
   
 }
 
@@ -4909,7 +4980,7 @@ static void DoConvertRawToDeltaWithGapLocations (ButtoN b)
   
   if (GetStatus (dcp->adjust_CDS_locations))
   {
-    VisitFeaturesInSep (sep, NULL, AdjustCDSLocationsForUnknownGapsCallback);
+    VisitFeaturesInSep (sep, (Pointer)Sequin_GlobalAlign2Seq, AdjustCDSLocationsForUnknownGapsCallback);
     DeleteMarkedObjects (dcp->input_entityID, 0, NULL);
   }  
   
@@ -7617,7 +7688,7 @@ static void DoConvertPubDescStringConstraint (ButtoN b)
   Remove (cpdp->form);
 }
 
-static void CreateConvertPubDescStringConstraintDialog (IteM i)
+static void CreateConvertPubDescStringConstraintDialogX (IteM i)
 {
   BaseFormPtr       bfp;
   ConvertPubDescPtr cpdp;
@@ -8032,6 +8103,27 @@ static void UpdateECnumbers (IteM i)
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
+
+static void ParseGoTermsFromUserFieldsItem (IteM i)
+
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL) return;
+  ParseGoTermsFromFields (sep);
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+
 /*---------------------------------------------------------------------*/
 /*                                                                     */
 /* HasInternalStops () -- Checks to see if a given protein has         */
@@ -10010,24 +10102,11 @@ static void FreeMolInfoBlockData (MolInfoBlockPtr mibp)
 }
 
 
-typedef struct sequenceconstraint 
-{
-  Boolean nucs_ok;
-  Boolean prots_ok;
-  
-  Int4                other_constraint_type;
-  StringConstraintPtr string_constraint;
-  ChoiceConstraintPtr source_constraint;
-  ValNodePtr          feature_list;
-  
-} SequenceConstraintData, PNTR SequenceConstraintPtr;
-
-
-static SequenceConstraintPtr SequenceConstraintFree (SequenceConstraintPtr scp)
+extern SequenceConstraintXPtr SequenceConstraintXFree (SequenceConstraintXPtr scp)
 {
   if (scp != NULL)
   {
-    scp->string_constraint = StringConstraintFree (scp->string_constraint);
+    scp->string_constraint = StringConstraintXFree (scp->string_constraint);
     scp->source_constraint = ChoiceConstraintFree (scp->source_constraint);
     scp->feature_list = ValNodeFree (scp->feature_list);
     scp = MemFree (scp);
@@ -10046,7 +10125,7 @@ typedef struct sequenceconstraintdlg
   DialoG feature_string_constraint;
   DialoG id_string_constraint;
   
-} SequenceConstraintDlgData, PNTR SequenceConstraintDlgPtr;
+} SequenceConstraintXDlgData, PNTR SequenceConstraintXDlgPtr;
 
 
 enum sequenceconstraintothertype 
@@ -10058,12 +10137,12 @@ enum sequenceconstraintothertype
 };
 
 
-static void ChangeSequenceConstraintType (GrouP g)
+static void ChangeSequenceConstraintXType (GrouP g)
 {
-  SequenceConstraintDlgPtr scdp;
+  SequenceConstraintXDlgPtr scdp;
   Int4                     other_constraint_type;
   
-  scdp = (SequenceConstraintDlgPtr) GetObjectExtra (g);
+  scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (g);
   if (scdp == NULL)
   {
     return;
@@ -10086,11 +10165,11 @@ static void ChangeSequenceConstraintType (GrouP g)
   }
 }
 
-static void ResetSequenceConstraintDialog (DialoG d)
+static void ResetSequenceConstraintXDialog (DialoG d)
 {
-  SequenceConstraintDlgPtr scdp;
+  SequenceConstraintXDlgPtr scdp;
   
-  scdp = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+  scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (d);
   if (scdp == NULL)
   {
     return;
@@ -10098,25 +10177,25 @@ static void ResetSequenceConstraintDialog (DialoG d)
   
   SetValue (scdp->seq_type_constraint, 1);
   SetValue (scdp->other_constraint_type, SEQ_CONSTRAINT_ANY + 1);
-  ChangeSequenceConstraintType (scdp->other_constraint_type);
+  ChangeSequenceConstraintXType (scdp->other_constraint_type);
 }
 
-static void SequenceConstraintToDialog (DialoG d, Pointer data)
+static void SequenceConstraintXToDialog (DialoG d, Pointer data)
 {
-  SequenceConstraintPtr    scp;
-  SequenceConstraintDlgPtr scdp;
+  SequenceConstraintXPtr    scp;
+  SequenceConstraintXDlgPtr scdp;
   
-  scdp = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+  scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (d);
   if (scdp == NULL)
   {
     return;
   }
   
-  scp = (SequenceConstraintPtr) data;
+  scp = (SequenceConstraintXPtr) data;
   
   if (scp == NULL)
   {
-    ResetSequenceConstraintDialog (d);
+    ResetSequenceConstraintXDialog (d);
   }
   else
   {
@@ -10146,23 +10225,23 @@ static void SequenceConstraintToDialog (DialoG d, Pointer data)
           PointerToDialog (scdp->id_string_constraint, scp->string_constraint);
           break;
     }
-    ChangeSequenceConstraintType (scdp->other_constraint_type);
+    ChangeSequenceConstraintXType (scdp->other_constraint_type);
   }
 }
 
 
-static Pointer DialogToSequenceConstraint (DialoG d)
+static Pointer DialogToSequenceConstraintX (DialoG d)
 {
-  SequenceConstraintPtr    scp;
-  SequenceConstraintDlgPtr scdp;
+  SequenceConstraintXPtr    scp;
+  SequenceConstraintXDlgPtr scdp;
   
-  scdp = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+  scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (d);
   if (scdp == NULL)
   {
     return NULL;
   }
   
-  scp = (SequenceConstraintPtr) MemNew (sizeof (SequenceConstraintData));
+  scp = (SequenceConstraintXPtr) MemNew (sizeof (SequenceConstraintXData));
   if (scp != NULL)
   {
     switch (GetValue (scdp->seq_type_constraint))
@@ -10198,16 +10277,16 @@ static Pointer DialogToSequenceConstraint (DialoG d)
 }
 
 
-static void SequenceConstraintMessage (DialoG d, Int2 mssg)
+static void SequenceConstraintXMessage (DialoG d, Int2 mssg)
 
 {
-  SequenceConstraintDlgPtr scdp;
+  SequenceConstraintXDlgPtr scdp;
 
-  scdp = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+  scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (d);
   if (scdp != NULL) {
     switch (mssg) {
       case VIB_MSG_INIT :
-        ResetSequenceConstraintDialog (d);        
+        ResetSequenceConstraintXDialog (d);        
         break;
       case VIB_MSG_ENTER :
         Select (scdp->other_constraint_type);
@@ -10218,19 +10297,19 @@ static void SequenceConstraintMessage (DialoG d, Int2 mssg)
   }
 }
 
-static ValNodePtr TestSequenceConstraintDialog (DialoG d)
+static ValNodePtr TestSequenceConstraintXDialog (DialoG d)
 
 {
   return NULL;
 }
 
 
-static DialoG SequenceConstraintDialog (GrouP g)
+extern DialoG SequenceConstraintXDialog (GrouP g)
 {
-  SequenceConstraintDlgPtr dlg;
+  SequenceConstraintXDlgPtr dlg;
   GrouP p, k;
   
-  dlg = (SequenceConstraintDlgPtr) MemNew (sizeof (SequenceConstraintDlgData));
+  dlg = (SequenceConstraintXDlgPtr) MemNew (sizeof (SequenceConstraintXDlgData));
   if (dlg == NULL) return NULL;
 
   p = HiddenGroup (g, -1, 0, NULL);
@@ -10238,10 +10317,10 @@ static DialoG SequenceConstraintDialog (GrouP g)
   SetGroupSpacing (p, 10, 10);
 
   dlg->dialog = (DialoG) p;
-  dlg->todialog = SequenceConstraintToDialog;
-  dlg->fromdialog = DialogToSequenceConstraint;
-  dlg->dialogmessage = SequenceConstraintMessage;
-  dlg->testdialog = TestSequenceConstraintDialog;
+  dlg->todialog = SequenceConstraintXToDialog;
+  dlg->fromdialog = DialogToSequenceConstraintX;
+  dlg->dialogmessage = SequenceConstraintXMessage;
+  dlg->testdialog = TestSequenceConstraintXDialog;
 
   dlg->seq_type_constraint = HiddenGroup (p, 4, 0, NULL);
   RadioButton (dlg->seq_type_constraint, "All Sequences");
@@ -10249,21 +10328,21 @@ static DialoG SequenceConstraintDialog (GrouP g)
   RadioButton (dlg->seq_type_constraint, "Proteins");
   SetValue (dlg->seq_type_constraint, 2);
 
-  dlg->other_constraint_type = HiddenGroup (p, 2, 0, ChangeSequenceConstraintType);
+  dlg->other_constraint_type = HiddenGroup (p, 2, 0, ChangeSequenceConstraintXType);
   RadioButton (dlg->other_constraint_type, "Any sequence");
   StaticPrompt (dlg->other_constraint_type, "", 0, dialogTextHeight, systemFont, 'l');  
   
   RadioButton (dlg->other_constraint_type, "Where sequence source");
-  dlg->source_constraint = SourceConstraintDialog (dlg->other_constraint_type, FALSE);
+  dlg->source_constraint = SourceConstraintDialogX (dlg->other_constraint_type, FALSE);
     
   RadioButton (dlg->other_constraint_type, "Where feature text");
   k = HiddenGroup (dlg->other_constraint_type, 2, 0, NULL);
   SetGroupSpacing (k, 10, 10);
   dlg->feature_list = FeatureSelectionDialog (k, TRUE, NULL, NULL);
-  dlg->feature_string_constraint = StringConstraintDialog (k, NULL, FALSE);
+  dlg->feature_string_constraint = StringConstraintDialogX (k, NULL, FALSE);
     
   RadioButton (dlg->other_constraint_type, "Where sequence ID");
-  dlg->id_string_constraint = StringConstraintDialog (dlg->other_constraint_type, NULL, FALSE);
+  dlg->id_string_constraint = StringConstraintDialogX (dlg->other_constraint_type, NULL, FALSE);
   
   SetValue (dlg->other_constraint_type, CHOICE_CONSTRAINT_ANY);
   SetObjectExtra (dlg->other_constraint_type, dlg, NULL);
@@ -10280,7 +10359,7 @@ static DialoG SequenceConstraintDialog (GrouP g)
 }
 
 
-extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr string_constraint)
+extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintXPtr string_constraint)
 {
   Char       id [41];
   CharPtr    cp, cp_dst;
@@ -10303,7 +10382,7 @@ extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr
     sip->next = NULL;
     id [0] = '\0';
     SeqIdWrite (sip, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
-    match = DoesStringMatchConstraint (id, string_constraint);
+    match = DoesStringMatchConstraintX (id, string_constraint);
     if (!match) 
     {
       changed = FALSE;
@@ -10330,7 +10409,7 @@ extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr
       }  
       if (changed) 
       {
-        match = DoesStringMatchConstraint (id, string_constraint);
+        match = DoesStringMatchConstraintX (id, string_constraint);
       }
 
       /* if search text doesn't have ., try ID without version */
@@ -10340,7 +10419,7 @@ extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr
         if (cp != NULL) 
         {
           *cp = 0;
-          match = DoesStringMatchConstraint (id, string_constraint);
+          match = DoesStringMatchConstraintX (id, string_constraint);
         }
       }       
     }
@@ -10370,7 +10449,7 @@ extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr
 }
 
 
-static Boolean DoesSequenceMatchSequenceConstraint (BioseqPtr bsp, SequenceConstraintPtr scp)
+extern Boolean DoesSequenceMatchSequenceConstraintX (BioseqPtr bsp, SequenceConstraintXPtr scp)
 {
   SeqDescrPtr       sdp;
   SeqMgrDescContext dcontext;
@@ -10392,7 +10471,7 @@ static Boolean DoesSequenceMatchSequenceConstraint (BioseqPtr bsp, SequenceConst
       }
       break;
     case SEQ_CONSTRAINT_FEATURE_TEXT:
-      return DoBioseqFeaturesMatchSequenceConstraint (bsp, scp->feature_list, scp->string_constraint);
+      return DoBioseqFeaturesMatchSequenceConstraintX (bsp, scp->feature_list, scp->string_constraint);
       break;
     case SEQ_CONSTRAINT_ID:
       return DoesIDListMeetStringConstraint(bsp->id, scp->string_constraint);
@@ -10407,7 +10486,7 @@ typedef struct molinfoedit {
   MolInfoBlock    from;
   MolInfoBlock    to;
   DialoG          sequence_constraint;
-  SequenceConstraintPtr scp;
+  SequenceConstraintXPtr scp;
   Boolean               allow_existing;
 } MolInfoEdit, PNTR MolInfoEditPtr;
 
@@ -10487,7 +10566,7 @@ static void EditMolInfoCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, In
   if (IS_Bioseq (sep)) {
 
     bsp = (BioseqPtr) sep->data.ptrvalue;
-    if (DoesSequenceMatchSequenceConstraint (bsp, miep->scp)) {
+    if (DoesSequenceMatchSequenceConstraintX (bsp, miep->scp)) {
       if ((Uint1)GetValNodePopup (miep->from.molPopup,
                                   miep->from.mol_values) == bsp->mol
         || GetValue (miep->from.molPopup) == 1)
@@ -10593,7 +10672,7 @@ static void DoProcessEditMolInfo (ButtoN b)
   SeqEntryExplore (miep->sep, (Pointer) miep, EditMolInfoCallback);
   FreeMolInfoBlockData (&(miep->from));
   FreeMolInfoBlockData (&(miep->to));
-  miep->scp = SequenceConstraintFree (miep->scp);
+  miep->scp = SequenceConstraintXFree (miep->scp);
   ArrowCursor ();
   Update ();
   ObjMgrSetDirtyFlag (miep->input_entityID, TRUE);
@@ -10639,7 +10718,7 @@ static void EditMolInfoFields (IteM i)
   StaticPrompt (h, "To", 0, 0, programFont, 'c');
   CreateMolInfoBlock (&miep->to, h, TRUE);
 
-  miep->sequence_constraint = SequenceConstraintDialog (w);
+  miep->sequence_constraint = SequenceConstraintXDialog (w);
 
   c = HiddenGroup (w, 2, 0, NULL);
   b = DefaultButton (c, "Accept", DoProcessEditMolInfo);
@@ -10717,14 +10796,14 @@ static void RibosomalRNAToGenomicDNAToolBtn (ButtoN b)
   RibosomalRNAToGenomicDNA (bfp);
 }
 
-static Boolean MolInfoOkForSeqEntry (SeqEntryPtr sep, SequenceConstraintPtr scp)
+static Boolean MolInfoOkForSeqEntry (SeqEntryPtr sep, SequenceConstraintXPtr scp)
 {
   BioseqSetPtr bssp;
   SeqEntryPtr  seq_set;
 
   if (IS_Bioseq (sep)) 
   {
-    return DoesSequenceMatchSequenceConstraint(sep->data.ptrvalue, scp);
+    return DoesSequenceMatchSequenceConstraintX(sep->data.ptrvalue, scp);
   } 
   else if (IS_Bioseq_set (sep)) 
   {
@@ -10843,7 +10922,7 @@ static void DoApplyMolInfo (SeqEntryPtr sep, MolInfoEditPtr miep)
 
   if (IS_Bioseq (sep)) {
     bsp = (BioseqPtr) sep->data.ptrvalue;
-    if (DoesSequenceMatchSequenceConstraint(bsp, miep->scp)) {
+    if (DoesSequenceMatchSequenceConstraintX(bsp, miep->scp)) {
       DoApplyMolInfoToBioseq (bsp, miep);
     } else return;
   } else if (IS_Bioseq_set (sep)) {
@@ -10902,7 +10981,7 @@ static Boolean WillEditMolInfo (MolInfoEditPtr miep)
 }
 
 typedef struct molinfocheck {
-  SequenceConstraintPtr scp;
+  SequenceConstraintXPtr scp;
   Int4                  num_with;
   Int4                  num_without;
 } MolInfoCheckData, PNTR MolInfoCheckPtr;
@@ -11077,7 +11156,7 @@ static void DoProcessApplyMolInfo (ButtoN b)
 
   DoApplyMolInfo (miep->sep, miep);
   FreeMolInfoBlockData (&miep->to);
-  miep->scp = SequenceConstraintFree (miep->scp);
+  miep->scp = SequenceConstraintXFree (miep->scp);
   ArrowCursor ();
   Update ();
   ObjMgrSetDirtyFlag (miep->input_entityID, TRUE);
@@ -11119,7 +11198,7 @@ static void ApplyMolInfo (IteM i)
   h = HiddenGroup (g, 0, 2, NULL);
   CreateMolInfoBlock (&miep->to, h, TRUE);
 
-  miep->sequence_constraint = SequenceConstraintDialog (w);
+  miep->sequence_constraint = SequenceConstraintXDialog (w);
 
   c = HiddenGroup (w, 2, 0, NULL);
   b = DefaultButton (c, "Accept", DoProcessApplyMolInfo);
@@ -12055,7 +12134,9 @@ static void CaptureFFLineEx (
         MemSet (subcip, 0, sizeof (ClickableItemData));
         subcip->clickable_item_type = blocktype;
         subcip->description = StringSave (ptr);
-        ValNodeAddPointer (&(subcip->item_list), item_list->choice, item_list->data.ptrvalue);
+        if (item_list != NULL) {
+          ValNodeAddPointer (&(subcip->item_list), item_list->choice, item_list->data.ptrvalue);
+        }
         ValNodeAddPointer (&(cip->subcategories), 0, subcip);
         /* iterate to add the rest of the lines of the qual */
         while (ch != 0 && tmp != NULL && (qual_name = StartsWithQualOrFeat (tmp + 1)) == NULL) {
@@ -12070,7 +12151,9 @@ static void CaptureFFLineEx (
             MemSet (subcip, 0, sizeof (ClickableItemData));
             subcip->clickable_item_type = blocktype;
             subcip->description = StringSave (ptr);
-            ValNodeAddPointer (&(subcip->item_list), item_list->choice, item_list->data.ptrvalue);
+            if (item_list != NULL) {
+              ValNodeAddPointer (&(subcip->item_list), item_list->choice, item_list->data.ptrvalue);
+            }
             ValNodeAddPointer (&(cip->subcategories), 0, subcip);
           }
         }
@@ -12160,6 +12243,7 @@ extern ValNodePtr GetSUCCommonList (SeqEntryPtr sep, Boolean reverse, Boolean by
   ErrSev          level;
   Boolean         okay;
   SeqEntryPtr     oldscope;
+  Uint2           entityID;
 
   if (sep == NULL) return NULL;
   
@@ -12191,6 +12275,8 @@ extern ValNodePtr GetSUCCommonList (SeqEntryPtr sep, Boolean reverse, Boolean by
   oldscope = SeqEntrySetScope (sep);
   okay = SeqEntryToGnbk (sep, NULL, GENBANK_FMT, SEQUIN_MODE, NORMAL_STYLE,
                          SHOW_CONTIG_FEATURES, 0, 0, &xtra, NULL);
+  entityID = SeqMgrGetEntityIDForSeqEntry (sep);
+  SeqMgrIndexFeatures (entityID, NULL);
   SeqEntrySetScope (oldscope);
   ErrSetMessageLevel (level);
   if (okay) {
@@ -15723,6 +15809,7 @@ static void UnsetPartialForTruncatedProteins (SeqFeatPtr sfp, Pointer userdata)
   change_name = (BoolPtr) userdata;
   CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
   SetSeqLocPartial (sfp->location, partial5, FALSE);
+  sfp->partial = partial5;
   if (*change_name) {
     prp = sfp->data.value.ptrvalue;
     if (prp != NULL && prp->name != NULL 
@@ -15754,6 +15841,7 @@ static void UnsetCDSPartialForTruncatedProteins (SeqFeatPtr sfp, Pointer userdat
   if (product_bsp == prot_bsp) {
     CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
     SetSeqLocPartial (sfp->location, partial5, FALSE);
+    sfp->partial = partial5;
 
     cds_len = (prot_bsp->length + 1) * 3 ;
     crp = (CdRegionPtr) sfp->data.value.ptrvalue;
@@ -15903,6 +15991,7 @@ static void TruncProtsCallback (BioseqPtr bsp, Pointer userdata)
       SetSeqLocPartial (slp, partial5, partial3);
       SeqLocFree (gene->location);
       gene->location = slp;
+      gene->partial = partial5 || partial3;
     }
     else
     {
@@ -18801,271 +18890,6 @@ static void ReverseNameOrderInAuthor (AuthorPtr pAuthor)
 
 }
 
-typedef struct replaceitempair {
-  CharPtr FindString;
-  CharPtr ReplaceString;
-} ReplaceItemPair, PNTR ReplaceItemPairPtr;
-
-
-ReplaceItemPair AbbreviationList[] = {
- { "arabidopsis thaliana", "Arabidopsis thaliana" },
- { "adp", "ADP" },
- { "adp-", "ADP-" },
- { "atp", "ATP" },
- { "atp-", "ATP-" },
- { "bac", "BAC" },
- { "caenorhabditis elegans", "Caenorhabditis elegans" },
- { "cdna", "cDNA" },
- { "cdnas", "cDNAs" },
- { "coa", "CoA" },
- { "coi", "COI" },
- { "coii", "COII" },
- { "danio rerio", "Danio rerio" },
- { "dna", "DNA" },
- { "dna-", "DNA-" },
- { "drosophila melanogaster", "Drosophila melanogaster" },
- { "dsrna", "dsRNA" },
- { "escherichia coli", "Escherichia coli" },
- { "hiv", "HIV" },
- { "hiv-1", "HIV-1" },
- { "hiv-2", "HIV-2" },
- { "hnrna", "hnRNA" },
- { "homo sapiens", "Homo sapiens" },
- { "mhc", "MHC" },
- { "mrna", "mRNA" },
- { "mtdna", "mtDNA" },
- { "mus musculus", "Mus musculus" },
- { "nadh", "NADH" },
- { "nov.", "nov." },
- { "nov..", "nov.." },
- { "pcr", "PCR" },
- { "pcr-", "PCR-" },
- { "rattus norvegicus", "Rattus norvegicus" },
- { "rapd", "RAPD" },
- { "rdna", "rDNA" },
- { "rna", "RNA" },
- { "rna-", "RNA-" },
- { "rrna", "rRNA" },
- { "rt-pcr", "RT-PCR" },
- { "saccharomyces cerevisiae", "Saccharomyces cerevisiae" },
- { "scrna", "scRNA" },
- { "siv-1", "SIV-1" },
- { "snp", "SNP"     },
- { "snps", "SNPs"   },
- { "snrna", "snRNA" },
- { "sp.", "sp." },
- { "sp..", "sp.." },
- { "ssp.", "ssp." },
- { "ssp..", "ssp.." },
- { "ssrna", "ssRNA" },
- { "subsp.", "subsp." },
- { "subsp..", "subsp.." },
- { "trna", "tRNA" },
- { "trna-", "tRNA-" },
- { "var.", "var." },
- { "var..", "var.." },
- { "usa", "USA" },
- { "U.S.A.", "USA" },
- { "U.S.A", "USA" },
- { "United States of America", "USA" },
- {"(hiv)", "(HIV)" },
- {"(hiv1)", "(HIV1)" },
- {"(hiv-1)", "(HIV-1)" }
-};
-
-ReplaceItemPair SpecialAbbreviationList[] = {
- { "sp.", "sp." },
- { "nov.", "nov." },
- { "ssp.", "ssp." },
- { "var.", "var." },
- { "subsp.", "subsp." }
-};
-
-static void FixAbbreviationsInElement (CharPtr PNTR pEl)
-{
-  int i;
-  CharPtr NewPtr;
-  Boolean whole_word;
-
-  if (pEl == NULL) return;
-  if (*pEl == NULL) return;
-
-  for (i = 0; i < sizeof (AbbreviationList) / sizeof (ReplaceItemPair); i++)
-  {
-    if (AbbreviationList[i].FindString[StringLen (AbbreviationList[i].FindString) - 1] == '-')
-    {
-      whole_word = FALSE;
-    }
-    else
-    {
-      whole_word = TRUE;
-    }
-    FindReplaceString (pEl, AbbreviationList[i].FindString,
-			AbbreviationList[i].ReplaceString, FALSE, whole_word);
-  }
-  for (i = 0; i < sizeof (SpecialAbbreviationList) / sizeof (ReplaceItemPair); i++)
-  {
-    FindReplaceString (pEl, SpecialAbbreviationList[i].FindString,
-			SpecialAbbreviationList[i].ReplaceString, FALSE, TRUE);
-    if (StringLen (*pEl) >= StringLen (SpecialAbbreviationList[i].ReplaceString)
-      && StringCmp ((*pEl) + StringLen (*pEl) - StringLen (SpecialAbbreviationList[i].ReplaceString), SpecialAbbreviationList[i].ReplaceString) == 0)
-    {
-      NewPtr = MemNew (StringLen (*pEl) + 2);
-      if (NewPtr == NULL) return;
-      StringCpy (NewPtr, *pEl);
-      StringCat (NewPtr, ".");
-      MemFree (*pEl);
-      *pEl = NewPtr;
-    }
-  }
-}
-
-ReplaceItemPair ShortWordList[] = {
- { "A", "a" },
- { "About", "about" },
- { "And", "and" },
- { "At", "at" },
- { "But", "but" },
- { "By", "by" },
- { "For", "for" },
- { "In", "in" },
- { "Is", "is" },
- { "Of", "of" },
- { "On", "on" },
- { "Or", "or" },
- { "The", "the" },
- { "To", "to" },
- { "With", "with" }
-};
-
-static void FixShortWordsInElement (CharPtr PNTR pEl)
-{
-  Int2 i;
-
-  if (pEl == NULL) return;
-  if (*pEl == NULL) return;
-
-  for (i = 0; i < sizeof (ShortWordList) / sizeof (ReplaceItemPair); i++)
-  {
-    FindReplaceString (pEl, ShortWordList[i].FindString,
-			ShortWordList[i].ReplaceString, FALSE, TRUE);
-  }
-  if (isalpha ((Int4)((*pEl)[0])))
-  {
-    (*pEl)[0] = toupper ((*pEl)[0]);
-  }
-}
-
-static void 
-FixCapitalizationInElement 
-(CharPtr PNTR pEl,
- Boolean      bAbbrev, 
- Boolean      bShortWords,
- Boolean      bApostrophes)
-{
-  CharPtr pCh;
-  Boolean bSendToLower;
- 
-  if(pEl == NULL) return; 
-  if(*pEl == NULL) return; 
-
-  bSendToLower = FALSE;
-  for(pCh = *pEl; *pCh != 0; pCh++)
-  {
-    if(isalpha((Int4)(*pCh)))
-    {
-      if(bSendToLower)
-      {
-        *pCh = tolower(*pCh);
-      }
-      else
-      {
-        *pCh = toupper(*pCh);
-        bSendToLower = TRUE;
-      }
-    }
-    else if (bApostrophes || *pCh != '\'')
-    {
-      bSendToLower = FALSE;
-    }
-  }
-  if (bShortWords)
-    FixShortWordsInElement (pEl);
-  if (bAbbrev)
-    FixAbbreviationsInElement (pEl);
-}
-
-
-static void FixOrgNamesInString (CharPtr str, ValNodePtr org_names)
-{
-  ValNodePtr vnp;
-  CharPtr    cp, taxname;
-  Int4       taxname_len;
-  
-  if (StringHasNoText (str) || org_names == NULL) return;
-  for (vnp = org_names; vnp != NULL; vnp = vnp->next)
-  {
-    taxname = (CharPtr) org_names->data.ptrvalue;
-    taxname_len = StringLen (taxname);
-    cp = StringISearch (str, taxname);
-    while (cp != NULL)
-    {
-      StringNCpy (cp, taxname, taxname_len);
-      cp = StringISearch (cp + taxname_len, taxname);
-    }
-  }
-}
-
-
-extern void ResetCapitalization (Boolean first_is_upper, CharPtr pString)
-{
-  CharPtr pCh;
-  Boolean was_digit = FALSE;
-
-  pCh = pString;
-  if (pCh == NULL) return;
-  if (*pCh == '\0') return;
-  
-  if (first_is_upper)
-  {
-    /* Set first character to upper */
-    *pCh = toupper (*pCh);	
-  }
-  else
-  {
-    /* set first character to lower */
-    *pCh = tolower (*pCh);	
-  }
-  
-  if (isdigit ((Int4)(*pCh)))
-  {
-  	was_digit = TRUE;
-  }
-  pCh++;
-  /* Set rest of characters to lower */
-  while (*pCh != '\0')
-  {
-    if (was_digit 
-        && (*pCh == 'S' || *pCh == 's') 
-        && (isspace ((Int4)(*(pCh + 1))) || *(pCh + 1) == 0))
-    {
-      *pCh = toupper (*pCh);
-      was_digit = FALSE;
-    }
-    else if (isdigit ((Int4)(*pCh)))
-    {
-      was_digit = TRUE;
-    }
-    else
-    {
-      was_digit = FALSE;
-      *pCh = tolower (*pCh);
-    }
-    pCh++;
-  }  
-}
-
-
 extern void 
 FixCapitalizationInTitle 
 (CharPtr PNTR pTitle,
@@ -19142,7 +18966,7 @@ static void TruncateAuthorMiddleInitials (AuthorPtr pAuthor)
   }
 }
 
-static void ChangeAuthorLastNameToConsortium (AuthorPtr pAuthor, StringConstraintPtr author_scp)
+static void ChangeAuthorLastNameToConsortium (AuthorPtr pAuthor, StringConstraintXPtr author_scp)
 {
   NameStdPtr pNameStandard;
   CharPtr    consortium;
@@ -19160,7 +18984,7 @@ static void ChangeAuthorLastNameToConsortium (AuthorPtr pAuthor, StringConstrain
       len = StringLen (pNameStandard->names[0]);
       if (len > 0)
       {
-        if (DoesStringMatchConstraint (pNameStandard->names[0], author_scp))
+        if (DoesStringMatchConstraintX (pNameStandard->names[0], author_scp))
         {
     	    consortium = (CharPtr) MemNew ((len + 1) * sizeof (Char));
     	    if (consortium != NULL)
@@ -19190,7 +19014,7 @@ static void ChangeAuthorLastNameToConsortium (AuthorPtr pAuthor, StringConstrain
 typedef struct fixpubdesc 
 {
   Int4                iType;
-  StringConstraintPtr author_scp;
+  StringConstraintXPtr author_scp;
   ValNodePtr          org_names;
 } FixPubdescData, PNTR FixPubdescPtr;
 
@@ -19336,7 +19160,7 @@ extern void GetOrgNamesInRecordCallback (BioSourcePtr biop, Pointer userdata)
 
 
 /* This function is used to apply fixes to citations */
-static void FixPubs (Uint2 entityID, Int4 iType, StringConstraintPtr author_scp)
+static void FixPubs (Uint2 entityID, Int4 iType, StringConstraintXPtr author_scp)
 {
   SeqEntryPtr  sep;
   SelStructPtr	sel;
@@ -19477,7 +19301,7 @@ static void ChangeAllAuthorNameToConsortium (IteM i)
 static void ChangeAuthorNameWithConsortiumToConsortium (IteM i)
 {
   BaseFormPtr bfp;
-  StringConstraintPtr scp;
+  StringConstraintXPtr scp;
 
 #ifdef WIN_MAC
   bfp = currentFormDataPtr;
@@ -19487,7 +19311,7 @@ static void ChangeAuthorNameWithConsortiumToConsortium (IteM i)
 
   if (bfp == NULL) return;
   
-  scp = (StringConstraintPtr) MemNew (sizeof (StringConstraintData));
+  scp = (StringConstraintXPtr) MemNew (sizeof (StringConstraintData));
   if (scp == NULL)
   {
     return;
@@ -19500,7 +19324,7 @@ static void ChangeAuthorNameWithConsortiumToConsortium (IteM i)
   scp->not_present = FALSE;   
   
   FixPubs (bfp->input_entityID, FIX_PUB_SWAP_NAME_CONSORTIUM, scp);
-  scp = StringConstraintFree (scp);
+  scp = StringConstraintXFree (scp);
 }
 
 typedef struct authornamestringconstraintform 
@@ -19512,7 +19336,7 @@ typedef struct authornamestringconstraintform
 static void DoChangeAuthorNameToConsortiumWithConstraint (ButtoN b)
 {
   AuthorNameStringConstraintFormPtr frm;
-  StringConstraintPtr               scp;
+  StringConstraintXPtr               scp;
   
   frm = (AuthorNameStringConstraintFormPtr) GetObjectExtra (b);
   if (frm == NULL)
@@ -19520,14 +19344,14 @@ static void DoChangeAuthorNameToConsortiumWithConstraint (ButtoN b)
     return;
   }
   
-  scp = (StringConstraintPtr) DialogToPointer (frm->author_name_constraint_dlg);
+  scp = (StringConstraintXPtr) DialogToPointer (frm->author_name_constraint_dlg);
   
   Hide (frm->form);
   WatchCursor ();
   Update ();
   
   FixPubs (frm->input_entityID, FIX_PUB_SWAP_NAME_CONSORTIUM, scp);
-  scp = StringConstraintFree (scp);
+  scp = StringConstraintXFree (scp);
   Remove ((WindoW)frm->form);  
   ArrowCursor ();
   Update ();
@@ -19563,7 +19387,7 @@ static void ChangeAuthorNameToConsortiumWithConstraint (IteM i)
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
 
-  frm->author_name_constraint_dlg =  StringConstraintDialog (h, "Where author last name", TRUE);
+  frm->author_name_constraint_dlg =  StringConstraintDialogX (h, "Where author last name", TRUE);
   
   c = HiddenGroup (h, 2, 0, NULL);
   SetGroupSpacing (h, 10, 10);
@@ -19873,6 +19697,35 @@ static void RenormalizeNucProtSetsMenuItem (IteM i)
 }
 
 
+static void AddAllDbxrefsBioseqCallback (BioseqPtr bsp, Pointer data)
+{
+  AddAllDbxrefsToBioseq (bsp);
+}
+
+
+static void AddAllDbxrefsMenuItem (IteM i)
+{
+  BaseFormPtr  bfp;
+  SeqEntryPtr  sep;
+ 
+  /* Get the current data */
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+
+  if (bfp == NULL)
+    return;
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+
+  VisitBioseqsInSep (sep, NULL, AddAllDbxrefsBioseqCallback);
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
 extern void LookupAllPubs (IteM i);
 extern void ResolveExistingLocalIDs (IteM i);
 extern void PromoteAlignsToBestIDProc (IteM i);
@@ -19945,7 +19798,7 @@ static void ShowDiscrepancyReport (IteM i)
 
   if (bfp == NULL) return;
   
-  CreateDiscrepancyReportWindow (bfp);
+  CreateDiscrepancyReportWindow (/* bfp */);
 }
 
 static void TestTax3 (IteM i, Int4 taxid, CharPtr name)
@@ -20224,7 +20077,7 @@ static void MakeSpecialOrganismMenu (MenU m, BaseFormPtr bfp)
   MenU  x;
   
   s = SubMenu (m, "Organism/ G");
-  i = CommandItem (s, "Parse Text", ParseTaxnameToSourceQual);
+  i = CommandItem (s, "Parse Text After Bionomial", ParseTaxnameToSourceQual);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
   i = CommandItem (s, "Parse ATCC Strain to Xref", AtccStrainToXref);
@@ -20249,6 +20102,8 @@ static void MakeSpecialOrganismMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Lat-lon Tool", LatLonTool);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Lat-Lon Country Conflict Tool", LatLonCountryTool);
+  SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Fix Specific-Host Values", FixSpecificHostValues);
   SetObjectExtra (i, bfp, NULL);
 
@@ -20288,6 +20143,8 @@ static void MakeSpecialOrganismMenu (MenU m, BaseFormPtr bfp)
   x = SubMenu(s, "Parse Organism Modifiers");
   i = CommandItem (x, "Load From File", LoadOrganismModifierTable);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "Load Tax Consult File", LoadTaxConsult);
+  SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Export To File", ExportOrganismTable);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Export Last Lineage Table", ExportLastLineage);
@@ -20371,6 +20228,9 @@ static void MakeSpecialProjectsMenu (MenU m, BaseFormPtr bfp)
     SetObjectExtra (i, bfp, NULL);
     i = CommandItem (s, "Apply BARCODE Dbxrefs", ApplyBarcodeDbxrefs);
     SetObjectExtra (i, bfp, NULL);
+    SeparatorItem (s);
+    i = CommandItem (s, "Add Note to Coding Regions in Source Features", ApplyTagToCodingRegionsInSourceFeatures);
+    SetObjectExtra (i, bfp, NULL);
   }
 }
 
@@ -20680,7 +20540,7 @@ static void MakeSpecialConvertMenu (MenU m, BaseFormPtr bfp)
   z = SubMenu (y, "Publication");
   i = CommandItem (z, "All", ConvertPubDescToFeat);
   SetObjectExtra (i, bfp, NULL);
-  i = CommandItem (z, "By Constraint", CreateConvertPubDescStringConstraintDialog);
+  i = CommandItem (z, "By Constraint", CreateConvertPubDescStringConstraintDialogX);
   SetObjectExtra (i, bfp, NULL);
 
   y = SubMenu (x, "Convert Full Length Feature to Descriptor");
@@ -20718,6 +20578,8 @@ static void MakeSpecialConvertMenu (MenU m, BaseFormPtr bfp)
     x = SubMenu (s, "Convert IDs, Accessions, or GenBank.names");
     i = CommandItem (x, "LocalIDs to GeneralIDs", ConvertLocalToGeneral);
     SetObjectExtra (i, bfp, NULL);
+    i = CommandItem (x, "Convert GeneralIDs to LocalIDs", ConvertGeneralIdToLocalID);
+    SetObjectExtra (i, bfp, NULL);
     y = SubMenu (x, "Accession to LocalIDs");
     i = CommandItem (y, "For All Sequences", ConvertToLocalProcAll);
     SetObjectExtra (i, bfp, NULL);
@@ -20756,7 +20618,7 @@ static void MakeSpecialEditMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Exception", FeatureExceptionEditor);
   SetObjectExtra (i, bfp, NULL);
-  i = CommandItem (x, "Partial", FeaturePartialEditor);
+  i = CommandItem (x, "Location", FeaturePartialEditor);
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Strand", FeatureStrandEditor);
   SetObjectExtra (i, bfp, NULL);
@@ -20770,6 +20632,10 @@ static void MakeSpecialEditMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Reverse Location Interval Order", ReverseFeatureIntervals);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "Resolve Intersecting Feature Locations", ResolveFeatureOverlaps);
+  SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "Update Features", UpdateFeatures);
+  SetObjectExtra (i, bfp, NULL);
 
   SeparatorItem (s);
   x = SubMenu (s, "Bulk Edit");
@@ -20786,8 +20652,12 @@ static void MakeSpecialEditMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
 
   SeparatorItem (s);
-  i = CommandItem (s, "Extend Partial Features", ExtendPartialFeatures);
+  x = SubMenu (s, "Extend Partial Features");
+  i = CommandItem (x, "All", ExtendPartialFeatures);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "With Constraint", ExtendPartialFeaturesWithConstraint);
+  SetObjectExtra (i, bfp, NULL);
+
   i = CommandItem (s, "Extend Gene", ExtendGeneReg);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
@@ -20912,6 +20782,9 @@ static void MakeSpecialGapSequencesMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Remove Unnecessary Gap Features", RemoveUnnecessaryGapFeatures);
   SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+  i = CommandItem (s, "Flip Intervals Between Gaps", FlipSequenceIntervals);
+  SetObjectExtra (i, bfp, NULL);
 }
 
 static void MakeSpecialSelectMenu (MenU m, BaseFormPtr bfp)
@@ -20947,6 +20820,8 @@ static void MakeSpecialLinkMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Reassign", ReassignFeatIDs);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (x, "Unique in Merged Set", UniqifyFeatIDs);
+  SetObjectExtra (i, bfp, NULL);
   i = CommandItem (x, "Clear IDs and Links", ClearFeatIDsAndLinks);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
@@ -20967,7 +20842,6 @@ static void MakeSpecialLinkMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
 }
 
-
 extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
 
 {
@@ -21095,6 +20969,11 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
 
   i = CommandItem (s, "Load Feature Fields from File", LoadFeatureFieldTable);
   SetObjectExtra (i, bfp, NULL);
+#if 1
+  i = CommandItem (s, "New Load Feature Fields from File", NewLoadFeatureQualifierTable);
+  SetObjectExtra (i, bfp, NULL);
+#endif
+
     
   MakeSpecialRemoveMenu (m, bfp);
 
@@ -21216,6 +21095,8 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   SetObjectExtra (i, bfp, NULL);
   i = CommandItem (s, "Add Cit-sub for update", AddCitSubForUpdate);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Fix USA and States", AbbreviateCitSubAffilStates);
+  SetObjectExtra (i, bfp, NULL);
   
   MakeSpecialGapSequencesMenu (m, bfp);
 
@@ -21376,11 +21257,18 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
   i = CommandItem (s, "Force Locus Fixup", ForceLocusFixup);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
+  /*
+  i = CommandItem (s, "Just Taxonomy Fixup", JustTaxonFixup);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (s);
+  */
   i = CommandItem (s, "Correct CDS Genetic Codes", CorrectCDSGenCodes);
   SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
   i = CommandItem (s, "Update Replace EC_numbers", UpdateECnumbers);
   SetObjectExtra (i, bfp, NULL);
+  i = CommandItem (s, "Parse GO Terms from User Fields", ParseGoTermsFromUserFieldsItem);
+  SetObjectExtra (i, bfp, NULL);
   SeparatorItem (s);
   i = CommandItem (s, "NC_Cleanup", DoNCCleanup);
   SetObjectExtra (i, bfp, NULL);
@@ -21461,11 +21349,20 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
     SetObjectExtra (i, bfp, NULL);
 #endif
     
+#if 0
     SeparatorItem (m);
-    i = CommandItem (m, "Discrepancy Report", ShowDiscrepancyReport);
+    i = CommandItem (m, "Add All Dbxrefs", AddAllDbxrefsMenuItem);
     SetObjectExtra (i, bfp, NULL);
+#endif
     
   }
+  SeparatorItem (m);
+  i = CommandItem (m, "Discrepancy Report", ShowDiscrepancyReport);
+  SetObjectExtra (i, bfp, NULL);
+  SeparatorItem (m);
+  i = CommandItem (m, "Macro Editor", LaunchMacroEditor);
+  SetObjectExtra (i, bfp, NULL);
+
 /*#ifdef INTERNAL_NCBI_SEQUIN*/
 /*#ifdef NEW_TAXON_SERVICE*/
 /*
diff --git a/sequin/sequin4.c b/sequin/sequin4.c
index 087c2b7a..5cbdd2ba 100644
--- a/sequin/sequin4.c
+++ b/sequin/sequin4.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   6/28/96
 *
-* $Revision: 6.399 $
+* $Revision: 6.411 $
 *
 * File Description: 
 *
@@ -79,25 +79,18 @@
 #include <seqpanel.h>
 #include <salpanel.h>
 #include <findrepl.h>
+#include <macrodlg.h>
+#include <macroapi.h>
 
 static Int2 LIBCALLBACK CreateSegSet (Pointer data);
 static Int2 LIBCALLBACK ConvertToDeltaSequence (Pointer data);
 static Int2 LIBCALLBACK FeatToDeltaSeq (Pointer data);
 static Int2 LIBCALLBACK CopyMasterSourceToSegments (Pointer data);
 
-#define REGISTER_CREATESEGSET ObjMgrProcLoadEx (OMPROC_FILTER,"Create Segmented Set", "CreateSegSet", 0,0,0,0,NULL,CreateSegSet, PROC_PRIORITY_DEFAULT, "Indexer")
-#define REGISTER_UPDATESEGSET ObjMgrProcLoadEx (OMPROC_FILTER,"Update Segmented Set","UpdateSegSet",0,0,0,0,NULL,UpdateSegSet,PROC_PRIORITY_DEFAULT, "Indexer")
-
-#define REGISTER_NEWUPDATESEGSET ObjMgrProcLoadEx (OMPROC_FILTER,"New Update Segmented Set","NewUpdateSegSet",0,0,0,0,NULL,NewUpdateSegSet,PROC_PRIORITY_DEFAULT, "Indexer")
-
-#define REGISTER_ADJUSTMULTISEGSEQ ObjMgrProcLoadEx (OMPROC_FILTER,"Adjust SegSeq Length","AdjustSegLength",0,0,0,0,NULL,AdjustSegSeqLength,PROC_PRIORITY_DEFAULT, "Indexer")
-
 #define REGISTER_REMOVESET ObjMgrProcLoadEx (OMPROC_FILTER,"Remove Set","RemoveSet",0,0,0,0,NULL,RemoveSet,PROC_PRIORITY_DEFAULT, "Indexer")
 
 #define REGISTER_REMOVESETSINSET ObjMgrProcLoadEx (OMPROC_FILTER,"Remove Sets in Selected Set","RemoveSetsInSelectedSet",0,0,0,0,NULL,RemoveSetsInSelectedSet,PROC_PRIORITY_DEFAULT, "Indexer")
 
-#define REGISTER_UNDOSEGSET ObjMgrProcLoadEx (OMPROC_FILTER,"Undo Segmented Set","UndoSegSet",0,0,0,0,NULL,UndoSegSet,PROC_PRIORITY_DEFAULT, "Indexer")
-
 #define REGISTER_REPACKAGE_PARTS ObjMgrProcLoadEx (OMPROC_FILTER,"Repackage Segmented Parts","RepackageParts",0,0,0,0,NULL,PackagePartsInPartsSet,PROC_PRIORITY_DEFAULT, "Indexer")
 
 #define REGISTER_NORMALIZE_NUCPROT ObjMgrProcLoadEx (OMPROC_FILTER,"Normalize Nuc-Prot","NormalizeNucProts",0,0,0,0,NULL,NormalizeNucProts,PROC_PRIORITY_DEFAULT, "Indexer")
@@ -118,18 +111,6 @@ static Int2 LIBCALLBACK CopyMasterSourceToSegments (Pointer data);
 
 #define REGISTER_DELETE_BY_TEXT ObjMgrProcLoadEx (OMPROC_FILTER, "Delete By Text","DeleteByText",0,0,0,0,NULL,CreateDeleteByTextWindow,PROC_PRIORITY_DEFAULT, "Indexer")
 
-#define REGISTER_SEGREGATE_BY_TEXT ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Text","SegregateByText",0,0,0,0,NULL,CreateSegregateByTextWindow,PROC_PRIORITY_DEFAULT, "Indexer")
-
-#define REGISTER_SEGREGATE_BY_FIELD ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Options","NewSegregateByOptions",0,0,0,0,NULL,SegregateSetsByField,PROC_PRIORITY_DEFAULT, "Indexer")
-
-#define REGISTER_SEGREGATE_BY_FEATURE ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Feature","SegregateByFeature",0,0,0,0,NULL,CreateSegregateByFeatureWindow,PROC_PRIORITY_DEFAULT, "Indexer")
-
-#define REGISTER_SEGREGATE_BY_DESCRIPTOR ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Descriptor","SegregateByDescriptor",0,0,0,0,NULL,CreateSegregateByDescriptorWindow,PROC_PRIORITY_DEFAULT, "Indexer")
-
-#define REGISTER_SEGREGATE_BY_MOLECULE_TYPE ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Molecule Type","SegregateByMoleculeType",0,0,0,0,NULL,CreateSegregateByMoleculeTypeWindow,PROC_PRIORITY_DEFAULT, "Indexer")
-
-#define REGISTER_SEGREGATE_BY_ID ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By ID","SegregateByID",0,0,0,0,NULL,CreateSegregateByIdWindow,PROC_PRIORITY_DEFAULT, "Indexer")
-
 #define REGISTER_REORDER_BY_ID ObjMgrProcLoadEx (OMPROC_FILTER, "Reorder by ID","ReorderByID",0,0,0,0,NULL,ReorderSetByAccession,PROC_PRIORITY_DEFAULT, "Indexer")
 
 #define REGISTER_CONVERTSEQALIGN ObjMgrProcLoadEx (OMPROC_FILTER,"Convert SeqAlign","ConvertSeqAlign",0,0,0,0,NULL,ConvertToTrueMultipleAlignment,PROC_PRIORITY_DEFAULT, "Alignment")
@@ -176,6 +157,7 @@ static Int2 LIBCALLBACK CopyMasterSourceToSegments (Pointer data);
 #define REGISTER_BIOSEQ_REVCOMP_NOTFEAT ObjMgrProcLoadEx (OMPROC_FILTER, "Bioseq only RevComp", "BioseqOnlyRevComp", OBJ_BIOSEQ, 0, OBJ_BIOSEQ, 0, NULL, RevCompFunc, PROC_PRIORITY_DEFAULT, "Utilities")
 #define REGISTER_BIOSEQ_REVERSE ObjMgrProcLoadEx (OMPROC_FILTER, "Bioseq Reverse", "BioseqReverse", OBJ_BIOSEQ, 0, OBJ_BIOSEQ, 0, NULL, RevFunc, PROC_PRIORITY_DEFAULT, "Utilities")
 #define REGISTER_BIOSEQ_COMPLEMENT ObjMgrProcLoadEx (OMPROC_FILTER, "Bioseq Complement", "BioseqComplement", OBJ_BIOSEQ, 0, OBJ_BIOSEQ, 0, NULL, CompFunc, PROC_PRIORITY_DEFAULT, "Utilities")
+#define REGISTER_BIOSEQ_REVCOMP_BYID ObjMgrProcLoadEx (OMPROC_FILTER, "Bioseq and Features RevComp By ID", "RevCompByID", OBJ_BIOSEQ, 0, OBJ_BIOSEQ, 0, NULL, BioseqRevCompByID, PROC_PRIORITY_DEFAULT, "Utilities")
 
 #define REGISTER_BIOSEQ_SEG_REPORT ObjMgrProcLoadEx (OMPROC_FILTER, "Bioseq Seg Report", "BioseqSegReport", OBJ_BIOSEQ, 0, OBJ_BIOSEQ, 0, NULL, ReportDeltaSegments, PROC_PRIORITY_DEFAULT, "Misc")
 
@@ -250,6 +232,28 @@ extern Int2 LIBCALLBACK StruCommUserGenFunc (Pointer data);
 #define REGISTER_CORRECTRNASTRAND ObjMgrProcLoadEx (OMPROC_FILTER, "Correct RNA Strand","CorrectRNAStrand",0,0,0,0,NULL,CorrectRNAStrandedness,PROC_PRIORITY_DEFAULT, "Analysis")
 #endif
 
+/* commands for Desktop Segregate menu */
+#define REGISTER_SEGREGATE_BY_TEXT ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Text","SegregateByText",0,0,0,0,NULL,CreateSegregateByTextWindow,PROC_PRIORITY_DEFAULT, "Segregate")
+
+#define REGISTER_SEGREGATE_BY_FIELD ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Options","NewSegregate",0,0,0,0,NULL,SegregateSetsByField,PROC_PRIORITY_DEFAULT, "Segregate")
+
+#define REGISTER_SEGREGATE_BY_FEATURE ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Feature","SegregateByFeature",0,0,0,0,NULL,CreateSegregateByFeatureWindow,PROC_PRIORITY_DEFAULT, "Segregate")
+
+#define REGISTER_SEGREGATE_BY_DESCRIPTOR ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Descriptor","SegregateByDescriptor",0,0,0,0,NULL,CreateSegregateByDescriptorWindow,PROC_PRIORITY_DEFAULT, "Segregate")
+
+#define REGISTER_SEGREGATE_BY_MOLECULE_TYPE ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Molecule Type","SegregateByMoleculeType",0,0,0,0,NULL,CreateSegregateByMoleculeTypeWindow,PROC_PRIORITY_DEFAULT, "Segregate")
+
+#define REGISTER_SEGREGATE_BY_ID ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By ID","SegregateByID",0,0,0,0,NULL,CreateSegregateByIdWindow,PROC_PRIORITY_DEFAULT, "Segregate")
+
+/* commands for Desktop SegmentedSets menu */
+#define REGISTER_CREATESEGSET ObjMgrProcLoadEx (OMPROC_FILTER,"Create Segmented Set", "CreateSegSet", 0,0,0,0,NULL,CreateSegSet, PROC_PRIORITY_DEFAULT, "SegmentedSets")
+#define REGISTER_UPDATESEGSET ObjMgrProcLoadEx (OMPROC_FILTER,"Update Segmented Set","UpdateSegSet",0,0,0,0,NULL,UpdateSegSet,PROC_PRIORITY_DEFAULT, "SegmentedSets")
+#define REGISTER_NEWUPDATESEGSET ObjMgrProcLoadEx (OMPROC_FILTER,"New Update Segmented Set","NewUpdateSegSet",0,0,0,0,NULL,NewUpdateSegSet,PROC_PRIORITY_DEFAULT, "SegmentedSets")
+#define REGISTER_ADJUSTMULTISEGSEQ ObjMgrProcLoadEx (OMPROC_FILTER,"Adjust SegSeq Length","AdjustSegLength",0,0,0,0,NULL,AdjustSegSeqLength,PROC_PRIORITY_DEFAULT, "SegmentedSets")
+#define REGISTER_UNDOSEGSET ObjMgrProcLoadEx (OMPROC_FILTER,"Undo Segmented Set","UndoSegSet",0,0,0,0,NULL,UndoSegSet,PROC_PRIORITY_DEFAULT, "SegmentedSets")
+#define REGISTER_SEGSETREMOVESETSINSET ObjMgrProcLoadEx (OMPROC_FILTER,"Remove Sets in Selected Set (Like Undo SegSet)","RemoveSetsInSelectedSet",0,0,0,0,NULL,RemoveSetsInSelectedSet,PROC_PRIORITY_DEFAULT, "SegmentedSets")
+
+
 typedef struct {
   CharPtr  oldStr;
   SeqIdPtr newSip;
@@ -1736,7 +1740,7 @@ static void SplitSegmentedFeatsOnOneSet (BioseqSetPtr set)
             crp->frame = new_frame;
  
             new_sfp->product = SeqLocFree (new_sfp->product);
-            SeqEdTranslateOneCDS (new_sfp, last_bsp, sfp->idx.entityID);
+            SeqEdTranslateOneCDS (new_sfp, last_bsp, sfp->idx.entityID, Sequin_GlobalAlign2Seq);
            
             SplitSegmentedProduct (BioseqFindFromSeqLoc (sfp->product),
                                    BioseqFindFromSeqLoc (new_sfp->product),
@@ -1766,7 +1770,7 @@ static void SplitSegmentedFeatsOnOneSet (BioseqSetPtr set)
         sfp->partial = TRUE;
         if (sfp->data.choice == SEQFEAT_CDREGION && sfp->product != NULL)
         {
-          SeqEdTranslateOneCDS (sfp, last_bsp, sfp->idx.entityID);
+          SeqEdTranslateOneCDS (sfp, last_bsp, sfp->idx.entityID, Sequin_GlobalAlign2Seq);
           
           ResynchCDSPartials (sfp, NULL);
         }
@@ -5814,7 +5818,7 @@ SetExplodedProtein
   }
   
   /* retranslate coding region */
-  SeqEdTranslateOneCDS (sfp, nucbsp, nucbsp->idx.entityID);
+  SeqEdTranslateOneCDS (sfp, nucbsp, nucbsp->idx.entityID, Sequin_GlobalAlign2Seq);
 }
 
 static Boolean ExplodeGroup (SeqEntryPtr sep, SeqFeatPtr sfp)
@@ -7588,61 +7592,6 @@ static void LIBCALLBACK LookForOrfs (
   }
 }
 
-static Boolean get_src (GatherContextPtr gcp)
-{
-	ValNodePtr	vnp, new;
-	ValNodePtr	PNTR vnpp;
-	
-	vnpp = gcp->userdata;
-	switch (gcp->thistype)
-	{
-		case OBJ_SEQDESC:
-			vnp = (ValNodePtr) (gcp->thisitem);
-			if (vnp->choice == Seq_descr_source) {
-				if (vnp->data.ptrvalue != NULL) {
-					new = SeqDescrNew(NULL);
-					new = MemCopy(new, vnp, sizeof(ValNode));
-					new->next = NULL;
-					*vnpp = new;
-					return FALSE;  /*only top level BioSource will be returned*/
-				}
-			} 
-			break;
-		default:
-			break;
-	}
-	return TRUE;
-}
-
-static Int2 GetGcodeFromBioseq(BioseqPtr bsp)
-{
-	GatherScope gs;
-	BioSourcePtr biop;
-	Int2 code = -1;
-	Uint2	entityID;
-	ValNodePtr vnp = NULL;	
-	   
-	entityID = ObjMgrGetEntityIDForPointer(bsp);
-  	MemSet ((Pointer) (&gs), 0, sizeof (GatherScope));
-  	gs.get_feats_location = TRUE;
-	MemSet ((Pointer) (gs.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof(Boolean)));
-	gs.ignore[OBJ_SEQDESC] = FALSE;
-	
-	GatherEntity(entityID, &vnp, get_src, &gs);
-	if (vnp == NULL) {
-		ErrPostStr(SEV_WARNING, 0, 0, "BioSource not found");
-		return code;
-	}
-	if (vnp) {
-		biop = vnp->data.ptrvalue;
-		code = BioSourceToGeneticCode(biop);
-		if (code == 0) {
-			code = 1;  /* try standard genetic code if it's not found */
-		}
-	}
-	return code;
-}
-
 static ValNodePtr ListOrfs (
   BioseqPtr bsp,
   Boolean altstart,
@@ -8870,20 +8819,67 @@ static Int2 LIBCALLBACK MapToNucFunc (Pointer data)
   }
 }
 
+
+NLM_EXTERN void RevCompOneFeatForBioseq (SeqFeatPtr sfp, BioseqPtr bsp)
+{
+  SeqIdPtr     sip;
+  SeqLocPtr    slp;
+  CodeBreakPtr cbp;
+  CdRegionPtr  crp;
+  RnaRefPtr    rrp;
+  tRNAPtr      trp;
+  Boolean      split;
+
+  if (sfp == NULL || bsp == NULL) return;
+
+  sip = SeqLocId (sfp->location);
+  if (sip != NULL) {
+    if (SeqIdIn (sip, bsp->id)) {
+      slp = SeqLocCopyRegion (sip, sfp->location, bsp, 0,
+                              bsp->length - 1, Seq_strand_minus, &split);
+      sfp->location = SeqLocFree (sfp->location);
+      sfp->location = slp;
+      switch (sfp->data.choice) {
+        case SEQFEAT_CDREGION :
+          crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+          if (crp != NULL) {
+            for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
+              sip = SeqLocId (cbp->loc);
+              slp = SeqLocCopyRegion (sip, cbp->loc, bsp, 0,
+                                      bsp->length - 1, Seq_strand_minus, &split);
+              cbp->loc = SeqLocFree (cbp->loc);
+              cbp->loc = slp;
+            }
+          }
+          break;
+        case SEQFEAT_RNA :
+          rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+          if (rrp != NULL && rrp->ext.choice == 2) {
+            trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+            if (trp != NULL && trp->anticodon != NULL) {
+              sip = SeqLocId (trp->anticodon);
+              slp = SeqLocCopyRegion (sip, trp->anticodon, bsp, 0,
+                                      bsp->length - 1, Seq_strand_minus, &split);
+              trp->anticodon = SeqLocFree (trp->anticodon);
+              trp->anticodon = slp;
+            }
+          }
+          break;
+        default :
+          break;
+      }
+    }
+  }
+}
+
+
 static void RevCompFeats (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent)
 
 {
   BioseqPtr     bsp;
   BioseqSetPtr  bssp;
-  CodeBreakPtr  cbp;
-  CdRegionPtr   crp;
-  RnaRefPtr     rrp;
   SeqAnnotPtr   sap;
   SeqFeatPtr    sfp;
-  SeqIdPtr      sip;
-  SeqLocPtr     slp;
-  Boolean       split;
-  tRNAPtr       trp;
 
   if (mydata == NULL) return;
   if (sep == NULL || sep->data.ptrvalue == NULL) return;
@@ -8901,44 +8897,7 @@ static void RevCompFeats (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 inde
     if (sap->type == 1) {
       sfp = (SeqFeatPtr) sap->data;
       while (sfp != NULL) {
-        sip = SeqLocId (sfp->location);
-        if (sip != NULL) {
-          if (SeqIdIn (sip, bsp->id)) {
-            slp = SeqLocCopyRegion (sip, sfp->location, bsp, 0,
-                                    bsp->length - 1, Seq_strand_minus, &split);
-            sfp->location = SeqLocFree (sfp->location);
-            sfp->location = slp;
-            switch (sfp->data.choice) {
-              case SEQFEAT_CDREGION :
-                crp = (CdRegionPtr) sfp->data.value.ptrvalue;
-                if (crp != NULL) {
-                  for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
-                    sip = SeqLocId (cbp->loc);
-                    slp = SeqLocCopyRegion (sip, cbp->loc, bsp, 0,
-                                            bsp->length - 1, Seq_strand_minus, &split);
-                    cbp->loc = SeqLocFree (cbp->loc);
-                    cbp->loc = slp;
-                  }
-                }
-                break;
-              case SEQFEAT_RNA :
-                rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
-                if (rrp != NULL && rrp->ext.choice == 2) {
-                  trp = (tRNAPtr) rrp->ext.value.ptrvalue;
-                  if (trp != NULL && trp->anticodon != NULL) {
-                    sip = SeqLocId (trp->anticodon);
-                    slp = SeqLocCopyRegion (sip, trp->anticodon, bsp, 0,
-                                            bsp->length - 1, Seq_strand_minus, &split);
-                    trp->anticodon = SeqLocFree (trp->anticodon);
-                    trp->anticodon = slp;
-                  }
-                }
-                break;
-              default :
-                break;
-            }
-          }
-        }
+        RevCompOneFeatForBioseq (sfp, bsp);
         sfp = sfp->next;
       }
     }
@@ -9018,30 +8977,22 @@ extern void ReverseBioseqInAlignment (SeqAlignPtr salp, Pointer userdata)
 }
 
 
-static void ProcessMultipleBioseqFunctions (OMProcControlPtr ompcp, BioseqFunc func,
-                                            Boolean revCompFeats, Boolean check_for_aln)
+static void RevCompBioseqList (ValNodePtr bsp_list, Uint2 entityID, BioseqFunc func,
+                               Boolean revCompFeats, Boolean check_for_aln)
 
 {
-  BioseqPtr     bsp;
-  ValNodePtr    head;
-  SelStructPtr  sel;
   SeqEntryPtr   sep;
+  BioseqPtr     bsp;
   ValNodePtr    vnp, seq_in_aln = NULL, aln_bsp = NULL;
   Char          id_str[255];
   CharPtr       msg;
   MsgAnswer     ans;
 
-  if (ompcp == NULL || ompcp->input_entityID == 0 || func == NULL) return;
-  head = NULL;
-  for (sel = ObjMgrGetSelected (); sel != NULL; sel = sel->next) {
-    GatherItem (sel->entityID, sel->itemID, sel->itemtype,
-                (Pointer) &head, AddBspToVnp);
-  }
-  if (head == NULL) return;
+  if (bsp_list == NULL) return;
   
-  if (check_for_aln) {
+  if (func != NULL && check_for_aln) {
     /* check for alignments, warn about reversals, allow cancel */
-    for (vnp = head; vnp != NULL; vnp = vnp->next) {
+    for (vnp = bsp_list; vnp != NULL; vnp = vnp->next) {
       bsp = (BioseqPtr) vnp->data.ptrvalue;
       if (bsp != NULL && IsBioseqInAnyAlignment (bsp, bsp->idx.entityID)) {
         SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_str, PRINTID_REPORT, sizeof (id_str) - 1);
@@ -9072,13 +9023,15 @@ static void ProcessMultipleBioseqFunctions (OMProcControlPtr ompcp, BioseqFunc f
     }
   }
   
-  sep = GetTopSeqEntryForEntityID (ompcp->input_entityID);
+  sep = GetTopSeqEntryForEntityID (entityID);
   
-  for (vnp = head; vnp != NULL; vnp = vnp->next) {
+  for (vnp = bsp_list; vnp != NULL; vnp = vnp->next) {
     bsp = (BioseqPtr) vnp->data.ptrvalue;
-    func (bsp);
-    if (check_for_aln) {
-      VisitAlignmentsInSep (sep, (Pointer) bsp, ReverseBioseqInAlignment);
+    if (func != NULL) {
+      func (bsp);
+      if (check_for_aln) {
+        VisitAlignmentsInSep (sep, (Pointer) bsp, ReverseBioseqInAlignment);
+      }
     }
     if (revCompFeats) {
       if (bsp->repr == Seq_repr_raw || bsp->repr == Seq_repr_const) {
@@ -9089,18 +9042,168 @@ static void ProcessMultipleBioseqFunctions (OMProcControlPtr ompcp, BioseqFunc f
       }
     }
   }
-  ValNodeFree (head);
   
   /* flip alignments if all sequences in alignment were flipped */
   if (aln_bsp != NULL) {
-    VisitAnnotsInSep (GetTopSeqEntryForEntityID (ompcp->input_entityID), aln_bsp, FlipEntireAlignmentIfAllSequencesFlipped);
+    VisitAnnotsInSep (GetTopSeqEntryForEntityID (entityID), aln_bsp, FlipEntireAlignmentIfAllSequencesFlipped);
     aln_bsp = ValNodeFree (aln_bsp);    
   }
   
-  ObjMgrSetDirtyFlag (ompcp->input_entityID, TRUE);
-  ObjMgrSendMsg (OM_MSG_UPDATE, ompcp->input_entityID, 0, 0);
+  ObjMgrSetDirtyFlag (entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0);
+}
+
+static void ProcessMultipleBioseqFunctions (OMProcControlPtr ompcp, BioseqFunc func,
+                                            Boolean revCompFeats, Boolean check_for_aln)
+
+{
+  ValNodePtr    head;
+  SelStructPtr  sel;
+
+  if (ompcp == NULL || ompcp->input_entityID == 0 || func == NULL) return;
+  head = NULL;
+  for (sel = ObjMgrGetSelected (); sel != NULL; sel = sel->next) {
+    GatherItem (sel->entityID, sel->itemID, sel->itemtype,
+                (Pointer) &head, AddBspToVnp);
+  }
+  if (head == NULL) return;
+
+  RevCompBioseqList (head, ompcp->input_entityID, func, revCompFeats, check_for_aln);
+  head = ValNodeFree (head);
+}
+
+
+typedef struct collectbioseqwithconstraint 
+{
+  SequenceConstraintXPtr scp;
+  ValNodePtr            bsp_list;
+} CollectBioseqWithConstraintData, PNTR CollectBioseqWithConstraintPtr;
+
+static void CollectBioseqsWithConstraintCallback (BioseqPtr bsp, Pointer userdata)
+{
+  CollectBioseqWithConstraintPtr p;
+
+  if (bsp == NULL || userdata == NULL) return;
+
+  p = (CollectBioseqWithConstraintPtr) userdata;
+  if (DoesSequenceMatchSequenceConstraintX (bsp, p->scp))
+  {
+    ValNodeAddPointer (&p->bsp_list, OBJ_BIOSEQ, bsp);
+  }
+}
+
+static ValNodePtr CollectBioseqsWithConstraint (SeqEntryPtr sep, SequenceConstraintXPtr scp)
+{
+  CollectBioseqWithConstraintData p;
+
+  p.scp = scp;
+  p.bsp_list = NULL;
+
+  VisitBioseqsInSep (sep, &p, CollectBioseqsWithConstraintCallback);
+  return p.bsp_list;
+}
+
+
+typedef struct revcompbyidfrm {
+  FORM_MESSAGE_BLOCK
+  DialoG sequence_constraint;
+  ButtoN revcomp_seq;
+  ButtoN reverse_feats; 
+  ButtoN accept;
+} RevCompByIdFrmData, PNTR RevCompByIdFrmPtr;
+
+
+static void ChangeRevComp (ButtoN b)
+{
+  RevCompByIdFrmPtr f;
+
+  f = (RevCompByIdFrmPtr) GetObjectExtra (b);
+  if (f == NULL) return;
+
+  if (!GetStatus (f->revcomp_seq) && !GetStatus (f->reverse_feats))
+  {
+    Disable (f->accept);
+  }
+  else
+  {
+    Enable (f->accept);
+  }
+}
+
+
+static void DoRevComp (ButtoN b)
+{
+  RevCompByIdFrmPtr f;
+  SequenceConstraintXPtr scp;
+  ValNodePtr            bsp_list;
+  SeqEntryPtr           sep;
+
+  f = (RevCompByIdFrmPtr) GetObjectExtra (b);
+  if (f == NULL) return;
+
+  sep = GetTopSeqEntryForEntityID (f->input_entityID);
+  scp = DialogToPointer (f->sequence_constraint);
+  bsp_list = CollectBioseqsWithConstraint (sep, scp);
+  scp = SequenceConstraintXFree (scp);
+
+  if (bsp_list == NULL) 
+  {
+    Message (MSG_ERROR, "No sequences match constraint!");
+  }
+  else
+  {
+    RevCompBioseqList (bsp_list, f->input_entityID, 
+                       GetStatus (f->revcomp_seq) ? BioseqRevComp : NULL, 
+                       GetStatus (f->reverse_feats), GetStatus (f->revcomp_seq));
+    Remove (f->form);
+  }
+  bsp_list = ValNodeFree (bsp_list);
+}
+
+static Int2 LIBCALLBACK BioseqRevCompByID (Pointer data)
+
+{
+  OMProcControlPtr ompcp;
+  GrouP            c;
+  GrouP            h;
+  RevCompByIdFrmPtr f;
+  WindoW           w;
+
+  ompcp = (OMProcControlPtr) data;
+  if (ompcp == NULL) return OM_MSG_RET_ERROR;
+
+  f = (RevCompByIdFrmPtr) MemNew (sizeof (RevCompByIdFrmData));
+  if (f == NULL) return OM_MSG_RET_ERROR;
+  w = FixedWindow (-50, -33, -10, -10, "Reverse Complement", StdCloseWindowProc);
+  SetObjectExtra (w, f, StdCleanupFormProc);
+  f->form = (ForM) w;
+  f->formmessage = NULL;
+
+  f->input_entityID = ompcp->input_entityID;
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  f->revcomp_seq = CheckBox (h, "Reverse complement sequence", ChangeRevComp);
+  SetStatus (f->revcomp_seq, TRUE);
+  f->reverse_feats = CheckBox (h, "Reverse features", ChangeRevComp);
+  SetStatus (f->reverse_feats, TRUE);
+
+  f->sequence_constraint = SequenceConstraintXDialog (h);
+
+  c = HiddenGroup (h, 2, 0, NULL);
+  f->accept = DefaultButton (c, "Accept", DoRevComp);
+  SetObjectExtra (f->accept, f, NULL);
+  PushButton (c, "Cancel", StdCancelButtonProc);
+  AlignObjects (ALIGN_CENTER, (HANDLE) f->sequence_constraint,
+                              (HANDLE) f->revcomp_seq,
+                              (HANDLE) f->reverse_feats,
+                              (HANDLE) c, NULL);
+  RealizeWindow (w);
+  Show (w);
+  Update ();
+  return OM_MSG_RET_DONE;
 }
 
+
 extern void ReverseComplementBioseqAndFeats (BioseqPtr bsp, Uint2 entityID)
 {
   SeqEntryPtr sep;
@@ -10738,6 +10841,7 @@ extern void SetupSequinFilters (void)
   REGISTER_BIOSEQ_REVERSE;
   REGISTER_BIOSEQ_REVCOMP_WITHFEAT;
   REGISTER_BIOSEQ_REVCOMP_NOTFEAT;
+  REGISTER_BIOSEQ_REVCOMP_BYID;
 
 #if defined(OS_UNIX) || defined(OS_MSWIN) 
   if (indexerVersion) {
@@ -10776,9 +10880,10 @@ extern void SetupSequinFilters (void)
     REGISTER_INTERVAL_COMBINE_AND_FUSE;
     REGISTER_INTERVAL_COMBINE;
     REGISTER_REPACKAGE_PARTS;
-    REGISTER_UNDOSEGSET;
     REGISTER_REMOVESET;
     REGISTER_REMOVESETSINSET;
+    REGISTER_UNDOSEGSET;
+    REGISTER_SEGSETREMOVESETSINSET;
     REGISTER_ADJUSTMULTISEGSEQ;
     REGISTER_UPDATESEGSET;
     REGISTER_NEWUPDATESEGSET;
@@ -10796,8 +10901,8 @@ extern void SetupSequinFilters (void)
     REGISTER_SEGREGATE_BY_MOLECULE_TYPE;
     REGISTER_SEGREGATE_BY_FEATURE;
     REGISTER_SEGREGATE_BY_DESCRIPTOR;
-    REGISTER_SEGREGATE_BY_FIELD;
     REGISTER_SEGREGATE_BY_TEXT;
+    REGISTER_SEGREGATE_BY_FIELD;
     REGISTER_FIND_NON_ACGT;
     REGISTER_BSP_INDEX;
     REGISTER_POPSET_WITHIN_GENBANK;
@@ -10821,57 +10926,6 @@ extern void SetupSequinFilters (void)
   
 }
 
-extern CharPtr MergeValNodeStrings (ValNodePtr list, Boolean useReturn)
-
-{
-  size_t      len;
-  CharPtr     ptr;
-  CharPtr     str;
-  CharPtr     tmp;
-  ValNodePtr  vnp;
-
-
-  ptr = NULL;
-  if (list != NULL) {
-    vnp = list;
-    len = 0;
-    while (vnp != NULL) {
-      if (vnp->data.ptrvalue != NULL) {
-        len += StringLen ((CharPtr) vnp->data.ptrvalue) + 1;
-      }
-      vnp = vnp->next;
-    }
-    if (len > 0) {
-      ptr = MemNew (sizeof (Char) * (len + 2));
-      if (ptr != NULL) {
-        vnp = list;
-        tmp = NULL;
-        while (vnp != NULL) {
-          str = (CharPtr) vnp->data.ptrvalue;
-          if (str != NULL) {
-            if (tmp == NULL) {
-              tmp = ptr;
-            } else if (useReturn) {
-              tmp = StringMove (tmp, "\n");
-            } else if (IsJapanese () && (tmp - ptr > 2) &&
-            		IsMBLetter (tmp - 2) && IsMBLetter (str)) {
-              /* no space required between two Japanese letters. */
-              tmp = tmp;
-            } else if (str [0] != ',' && str [0] != ';' && str [0] != ':') {
-              tmp = StringMove (tmp, " ");
-            } else {
-              tmp = StringMove (tmp, " ");
-            }
-            tmp = StringMove (tmp, str);
-          }
-          vnp = vnp->next;
-        }
-      }
-    }
-  }
-  return ptr;
-}
-
 
 /* resolve existing colliding ids section */
 
@@ -11869,33 +11923,14 @@ extern void ConsolidateOrganismNotes (IteM i)
 }
 
 
-static void CountryLookupProc (BioSourcePtr biop, Pointer userdata)
-{
-  CharPtr PNTR  list;
-  SubSourcePtr  ssp;
-  CharPtr       new_country;
+typedef struct countryfixup {
+  CharPtr PNTR country_list;
+  ValNodePtr warning_list;
+  Boolean capitalize_after_colon;
+} CountryFixupData, PNTR CountryFixupPtr;
 
-  if (biop == NULL || (list = (CharPtr PNTR)userdata) == NULL)
-  {
-  	return;
-  }
 
-  for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) 
-  {
-  	if (ssp->subtype == SUBSRC_country && !StringHasNoText (ssp->name))
-    {
-      new_country = GetCountryFix (ssp->name, list);
-      if (new_country != NULL)
-      {
-        ssp->name = MemFree (ssp->name);
-        ssp->name = new_country;
-      }
-    }
-  }
-}
-
-
-static void CapitalizeFirstLetterOfEveryWord (CharPtr pString)
+extern void CapitalizeFirstLetterOfEveryWord (CharPtr pString)
 {
   CharPtr pCh;
 
@@ -11929,39 +11964,110 @@ static void CapitalizeFirstLetterOfEveryWord (CharPtr pString)
 }
 
 
-static void CountryCapitalizationFixup (BioSourcePtr biop, Pointer userdata)
+static void CountryFixupItem (Uint1 choice, Pointer data, CountryFixupPtr c)
 {
-  SubSourcePtr  ssp;
-  CharPtr       cp;
+  BioSourcePtr biop;
+  SubSourcePtr ssp;
+  CharPtr      new_country;
+  CharPtr      cp;
 
-  if (biop == NULL)
-  {
-  	return;
-  }
+  if (data == NULL || c == NULL) return;
+
+  biop = GetBioSourceFromObject (choice, data);
+  if (biop == NULL) return;
 
   for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) 
   {
-  	if (ssp->subtype != SUBSRC_country || ssp->name == NULL) continue;
-    cp = StringChr (ssp->name, ':');
-  	if (cp != NULL)
-  	{
-  	  /* skip colon */
-  	  cp++;
-  	  /* skip over space after colon */
-  	  cp += StringSpn (cp, " \t");
- 	  
-  	  /* reset capitalization */
-  	  CapitalizeFirstLetterOfEveryWord (cp);
-  	}
-  }  
+  	if (ssp->subtype == SUBSRC_country && !StringHasNoText (ssp->name))
+    {
+      new_country = GetCountryFix (ssp->name, c->country_list);
+      if (new_country == NULL) {
+        ValNodeAddPointer (&c->warning_list, choice, data);
+      } else {
+        if (c->capitalize_after_colon) {
+          cp = StringChr (new_country, ':');
+  	      if (cp != NULL)
+  	      {
+  	        /* skip colon */
+  	        cp++;
+  	        /* skip over space after colon */
+  	        cp += StringSpn (cp, " \t");
+       	  
+  	        /* reset capitalization */
+  	        CapitalizeFirstLetterOfEveryWord (cp);
+          }
+        }
+        ssp->name = MemFree (ssp->name);
+        ssp->name = new_country;
+      }
+    }
+  }
+}
 
+
+static void CountryFixupDesc (SeqDescrPtr sdp, Pointer userdata)
+{
+  if (sdp != NULL && userdata != NULL && sdp->choice == Seq_descr_source) {
+    CountryFixupItem (OBJ_SEQDESC, sdp, (CountryFixupPtr) userdata);
+  }
 }
 
+
+static void CountryFixupFeat (SeqFeatPtr sfp, Pointer userdata)
+{
+  if (sfp != NULL && userdata != NULL && sfp->data.choice == SEQFEAT_BIOSRC) {
+    CountryFixupItem (OBJ_SEQFEAT, sfp, (CountryFixupPtr) userdata);
+  }
+}
+
+
+static Pointer GetCountry (Uint1 data_choice, Pointer data, Pointer metadata)
+{
+  ValNode vn;
+
+  vn.choice = SourceQualChoice_textqual;
+  vn.data.intvalue = Source_qual_country;
+  vn.next = NULL;
+  return GetSourceQualFromBioSource (GetBioSourceFromObject (data_choice, data), &vn, NULL);
+}
+
+
+static Pointer GetAccession (Uint1 data_choice, Pointer data, Pointer metadata)
+{
+  ValNode vn;
+
+  vn.choice = data_choice;
+  vn.data.ptrvalue = data;
+  vn.next = NULL;
+  return GetParentLabelForDiscrepancyItem (&vn);
+}
+
+static void BulkSetCountry (Pointer target, Pointer data)
+{
+  ValNode    vn;
+  SeqDescrPtr sdp = (SeqDescrPtr) target;
+
+  if (sdp == NULL || sdp->choice != Seq_descr_source) return;
+
+  vn.choice = SourceQualChoice_textqual;
+  vn.data.intvalue = Source_qual_country;
+  vn.next = NULL;
+
+  SetSourceQualInBioSource (sdp->data.ptrvalue, &vn, NULL, (CharPtr) data, ExistingTextOption_replace_old);
+}
+
+
+static BulkEdFieldData country_fields[] = {
+  { "Country", BulkSetCountry, BulkSetSimpleTextString, GetCountry, BulkDisplaySimpleText, BulkFreeSimpleText, BulkSimpleTextDialog, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
+  { "Accession", NULL, NULL, GetAccession, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
+  { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
+
+
 static void CountryLookup (IteM i, Boolean with_cap_fix)
 {
   BaseFormPtr  bfp;
   SeqEntryPtr  sep;
-  CharPtr PNTR list;
+  CountryFixupData c;
 
 
 #ifdef WIN_MAC
@@ -11973,13 +12079,16 @@ static void CountryLookup (IteM i, Boolean with_cap_fix)
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
   if (sep == NULL) return;
   
-  list = GetValidCountryList ();
-  if (list == NULL) return;
-  VisitBioSourcesInSep (sep, list, CountryLookupProc);
-  if (with_cap_fix)
-  {
-    VisitBioSourcesInSep (sep, NULL, CountryCapitalizationFixup);
+  c.country_list = GetValidCountryList ();
+  if (c.country_list == NULL) return;
+  c.capitalize_after_colon = with_cap_fix;
+  c.warning_list = NULL;
+  VisitDescriptorsInSep (sep, &c, CountryFixupDesc);
+  VisitFeaturesInSep (sep, &c, CountryFixupFeat);
+  if (c.warning_list != NULL) {
+    BulkEditorObjectList (bfp->input_entityID, "Country Modifiers That Could Not Be Autocorrected", c.warning_list, country_fields);
   }
+
   ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
diff --git a/sequin/sequin5.c b/sequin/sequin5.c
index 334466c7..9d98eb65 100644
--- a/sequin/sequin5.c
+++ b/sequin/sequin5.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   8/26/97
 *
-* $Revision: 6.581 $
+* $Revision: 6.637 $
 *
 * File Description:
 *
@@ -72,10 +72,12 @@
 #include <salutil.h>
 
 #include <asn2gnbp.h> /* added for  parse to flatfile */
-#include <seqpanel.h> /* added to include SeqEdTranslateOneCDS */
+#include <sqnutils.h> /* added to include SeqEdTranslateOneCDS */
+#include <seqpanel.h>
 #include <salpanel.h>
 #include <tax3api.h> /* added for specific-host corrections */
 #include <findrepl.h>
+#include <valid.h> /* added for latloncountry conflict checking */
 
 static void CommonLaunchBioseqViewer (SeqEntryPtr sep, CharPtr path, Boolean directToEditor)
 
@@ -2270,6 +2272,11 @@ static Boolean ConvertImpToRNA
   case FEATDEF_snoRNA :
     rrp->type = 7;
     break;
+  case FEATDEF_ncRNA :
+    rrp->type = 255;
+    rrp->ext.choice = 1;
+    rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+    break;
   case FEATDEF_otherRNA :
     rrp->type = 255;
     break;
@@ -2382,10 +2389,11 @@ static Boolean ConvertRNAToMiscFeat
  Uint2      featdef_to,
  Pointer    extradata)
 {
-  GBQualPtr  gbqual;
+  GBQualPtr  gbqual, q_p, q_n;
   ImpFeatPtr ifp;
-  CharPtr    rnaname;
+  CharPtr    rnaname, newnote;
   RnaRefPtr  rrp;
+  Int4       note_len = 0;
 
   if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA)
   {
@@ -2400,10 +2408,11 @@ static Boolean ConvertRNAToMiscFeat
 
   rnaname = NULL;
   rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
-  if (rrp != NULL) {
+  if (rrp != NULL && rrp->type != 255 && rrp->ext.choice == 1) {
     if (rrp->ext.choice == 1) {
       rnaname = (CharPtr) rrp->ext.value.ptrvalue;
       rrp->ext.value.ptrvalue = NULL;
+      note_len = StringLen (rnaname) + 2;
     }
   }
 
@@ -2413,15 +2422,50 @@ static Boolean ConvertRNAToMiscFeat
   sfp->data.value.ptrvalue = (Pointer) ifp;
   ifp->key = StringSave ("misc_feature");
 
-  if (! StringHasNoText (rnaname)) {
-    gbqual = GBQualNew ();
-    if (gbqual != NULL) {
-      gbqual->qual = StringSave ("product");
-      gbqual->val = rnaname;
-      gbqual->next = sfp->qual;
-      sfp->qual = gbqual;
+  for (gbqual = sfp->qual; gbqual != NULL; gbqual = gbqual->next) {
+    if (StringCmp (gbqual->qual, "product") == 0) {
+      note_len += StringLen (gbqual->val) + 2;
+    }
+  }
+  
+  if (note_len > 0) {
+    if (!StringHasNoText (sfp->comment)) {
+      note_len += StringLen (sfp->comment) + 2;
+    }
+    newnote = (CharPtr) MemNew (sizeof (Char) * (note_len + 1));
+    if (!StringHasNoText (sfp->comment)) {
+      StringCpy (newnote, sfp->comment);
+      StringCat (newnote, "; ");
     }
+    if (rnaname != NULL) {
+      StringCat (newnote, rnaname);
+      StringCat (newnote, "; ");
+      rnaname = MemFree (rnaname);
+    }
+    gbqual = sfp->qual;
+    q_p = NULL;
+    while (gbqual != NULL) {
+      q_n = gbqual->next;
+      if (StringCmp (gbqual->qual, "product") == 0) {
+        StringCat (newnote, gbqual->val);
+        if (q_p == NULL) {
+          sfp->qual = q_n;
+        } else {
+          q_p->next = q_n;
+        }
+        gbqual->next = NULL;
+        gbqual = GBQualFree (gbqual);
+      } else {
+        q_p = gbqual;
+      }
+      gbqual = q_n;
+    }
+    /* trim trailing semicolon */
+    newnote[note_len - 2] = 0;
+    sfp->comment = MemFree (sfp->comment);
+    sfp->comment = newnote;
   }
+
   return TRUE;
 }
 
@@ -2493,6 +2537,151 @@ static Boolean ConvertProtToRegion
   return TRUE;
 }
 
+static Boolean ConvertRNAToNcRNA
+(SeqFeatPtr sfp)
+{
+  RnaRefPtr  rrp;
+  GBQualPtr  gbq;
+  tRNAPtr    trp; 
+  
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return FALSE;
+  
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (NULL == rrp) {
+    rrp = RnaRefNew ();
+    sfp->data.value.ptrvalue = rrp;
+  }
+
+  if (rrp->ext.choice == 2) {
+    trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+    if (trp != NULL) {
+      trp->anticodon = SeqLocFree (trp->anticodon);
+      trp = MemFree (trp);
+      rrp->ext.value.ptrvalue = trp;
+    }
+    rrp->ext.choice = 0;
+  } 
+
+  /* might be converting from other ncRNA, tmRNA, or misc_RNA */
+  if (rrp->ext.choice == 1) {
+    if (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0) {
+      /* already ncRNA */
+    } else if (StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0) {
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+    } else if (StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0) {
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+    } else {
+      /* not one of the specified types, copy to product gbqual */
+      gbq = GBQualNew ();
+      gbq->qual = StringSave ("product");
+      gbq->val = rrp->ext.value.ptrvalue;
+      gbq->next = sfp->qual;
+      sfp->qual = gbq;
+      rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+    }
+  } else {
+    rrp->ext.choice = 1;
+    rrp->ext.value.ptrvalue = StringSave ("ncRNA");
+  }
+  
+  if (rrp->type == 5) {
+    gbq = GBQualNew ();
+    gbq->qual = StringSave ("ncRNA_class");
+    gbq->val = StringSave ("snRNA");
+    gbq->next = sfp->qual;
+    sfp->qual = gbq;
+  } else if (rrp->type == 6) {
+    gbq = GBQualNew ();
+    gbq->qual = StringSave ("ncRNA_class");
+    gbq->val = StringSave ("scRNA");
+    gbq->next = sfp->qual;
+    sfp->qual = gbq;
+  } else if (rrp->type == 7) {
+    gbq = GBQualNew ();
+    gbq->qual = StringSave ("ncRNA_class");
+    gbq->val = StringSave ("snoRNA");
+    gbq->next = sfp->qual;
+    sfp->qual = gbq;
+  }
+
+  rrp->type = 255;
+  return TRUE;
+}
+
+
+static void ConvertFromncRNAtoMiscRNA (SeqFeatPtr sfp)
+{
+  RnaRefPtr rrp;
+  GBQualPtr gbq, gbq_prev = NULL;
+  CharPtr tmp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return;
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+  if (rrp == NULL || rrp->ext.choice != 1 || StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0) {
+    return;
+  }
+  rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+  rrp->ext.choice = 0;
+  /* find new value for product */
+  gbq = sfp->qual;
+  while (gbq != NULL && StringCmp (gbq->qual, "product") != 0) {
+    gbq_prev = gbq;
+    gbq = gbq->next;
+  }
+
+  if (gbq != NULL) {
+    rrp->ext.choice = 1;
+    rrp->ext.value.ptrvalue = StringSave (gbq->val);
+    if (gbq_prev == NULL) {
+      sfp->qual = gbq->next;
+    } else {
+      gbq_prev->next = gbq->next;
+    }
+    gbq->next = NULL;
+    gbq = GBQualFree (gbq);
+  } else if (!StringHasNoText (sfp->comment)) {
+    rrp->ext.choice = 1;
+    rrp->ext.value.ptrvalue = StringSave (sfp->comment);
+    sfp->comment = MemFree (sfp->comment);
+  }
+
+  /* move ncRNA_class elsewhere */
+  gbq = sfp->qual;
+  gbq_prev = NULL;
+  while (gbq != NULL && StringCmp (gbq->qual, "ncRNA_class") != 0) {
+    gbq_prev = gbq;
+    gbq = gbq->next;
+  }
+
+  if (gbq != NULL) {
+    if (StringCmp (gbq->val, "other") != 0) {
+      if (rrp->ext.choice == 0) {
+        rrp->ext.choice = 1;
+        rrp->ext.value.ptrvalue = StringSave (gbq->val);
+      } else {
+        if (StringHasNoText (sfp->comment)) {
+          sfp->comment = MemFree (sfp->comment);
+          sfp->comment = StringSave (gbq->val);
+        } else {
+          tmp = (CharPtr) MemNew (sizeof (Char) * (StringLen (sfp->comment) + StringLen (gbq->val) + 3));
+          sprintf (tmp, "%s; %s", sfp->comment, gbq->val);
+          sfp->comment = MemFree (sfp->comment);
+          sfp->comment = tmp;
+        }
+      }
+    }
+    if (gbq_prev == NULL) {
+      sfp->qual = gbq->next;
+    } else {
+      gbq_prev->next = gbq->next;
+    }
+    gbq->next = NULL;
+    gbq = GBQualFree (gbq);
+  }    
+}
+
 
 static Boolean ConvertRNAToRNA 
 (SeqFeatPtr sfp,
@@ -2500,11 +2689,17 @@ static Boolean ConvertRNAToRNA
  Pointer    extradata)
 {
   RnaRefPtr  rrp;
+  Boolean    from_misc = FALSE, to_misc = FALSE;
+  GBQualPtr  gbq, gbq_p = NULL;
 
   rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
   if (NULL == rrp)
     return FALSE;
 
+  if (rrp->type == 255) {
+    from_misc = TRUE;
+  }
+
   switch (featdef_to) {
     case FEATDEF_preRNA :
       rrp->type = 1;
@@ -2520,19 +2715,49 @@ static Boolean ConvertRNAToRNA
       break;
     case FEATDEF_snRNA :
       rrp->type = 5;
+      to_misc = TRUE;
       break;
     case FEATDEF_scRNA :
       rrp->type = 6;
+      to_misc = TRUE;
       break;
     case FEATDEF_snoRNA :
       rrp->type = 7;
+      to_misc = TRUE;
+      break;
+    case FEATDEF_ncRNA :
+      return ConvertRNAToNcRNA (sfp);
       break;
     case FEATDEF_otherRNA :
       rrp->type = 255;
+      ConvertFromncRNAtoMiscRNA (sfp);
       break;
     default:
       break;
   }
+  if (from_misc && !to_misc && rrp->ext.choice == 1 && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0) {
+    /* move product qual to string */
+    gbq = sfp->qual;
+    while (gbq != NULL && StringCmp (gbq->qual, "product") != 0) {
+      gbq_p = gbq;
+      gbq = gbq->next;
+    }
+    if (gbq == NULL) {
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.choice = 0;
+    } else {
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.value.ptrvalue = gbq->val;
+      gbq->val = NULL;
+      if (gbq_p == NULL) {
+        sfp->qual = gbq->next;
+      } else {
+        gbq_p->next = gbq->next;
+      }
+      gbq->next = NULL;
+      gbq = GBQualFree (gbq);
+    }
+  }
   return TRUE;
 }
 
@@ -3754,7 +3979,7 @@ static Boolean IntValNodeMatch (ValNodePtr vnp1, ValNodePtr vnp2)
   }
 }
 
-static void LocationConstraintClearText (LocationConstraintPtr lcp)
+static void LocationConstraintXClearText (LocationConstraintXPtr lcp)
 {
   if (lcp != NULL)
   {
@@ -3763,20 +3988,20 @@ static void LocationConstraintClearText (LocationConstraintPtr lcp)
   }
 }
 
-static LocationConstraintPtr LocationConstraintFree (LocationConstraintPtr lcp)
+static LocationConstraintXPtr LocationConstraintXFree (LocationConstraintXPtr lcp)
 {
   lcp = MemFree (lcp);
   return lcp;
 }
 
-static LocationConstraintPtr LocationConstraintCopy (LocationConstraintPtr lcp)
+static LocationConstraintXPtr LocationConstraintXCopy (LocationConstraintXPtr lcp)
 {
-  LocationConstraintPtr lcp_new;
+  LocationConstraintXPtr lcp_new;
   if (lcp == NULL)
   {
     return NULL;
   }
-  lcp_new = (LocationConstraintPtr) MemNew (sizeof (LocationConstraintData));
+  lcp_new = (LocationConstraintXPtr) MemNew (sizeof (LocationConstraintXData));
   if (lcp_new != NULL)
   {
     lcp_new->left = lcp->left;
@@ -3789,7 +4014,7 @@ static LocationConstraintPtr LocationConstraintCopy (LocationConstraintPtr lcp)
   return lcp_new;
 }
 
-extern StringConstraintPtr StringConstraintFree (StringConstraintPtr scp)
+extern StringConstraintXPtr StringConstraintXFree (StringConstraintXPtr scp)
 {
   if (scp == NULL) return NULL;
   scp->match_text = MemFree (scp->match_text);
@@ -3797,7 +4022,7 @@ extern StringConstraintPtr StringConstraintFree (StringConstraintPtr scp)
   return scp;  
 }
 
-static void StringConstraintClearText (StringConstraintPtr scp)
+static void StringConstraintClearText (StringConstraintXPtr scp)
 {
   if (scp != NULL)
   {
@@ -3805,15 +4030,15 @@ static void StringConstraintClearText (StringConstraintPtr scp)
   }
 }
 
-static StringConstraintPtr StringConstraintCopy (StringConstraintPtr scp)
+static StringConstraintXPtr StringConstraintCopy (StringConstraintXPtr scp)
 {
-  StringConstraintPtr scp_new;
+  StringConstraintXPtr scp_new;
   if (scp == NULL)
   {
     return NULL;
   }
   
-  scp_new = (StringConstraintPtr) MemNew (sizeof (StringConstraintData));
+  scp_new = (StringConstraintXPtr) MemNew (sizeof (StringConstraintData));
   if (scp_new != NULL)
   {
     scp_new->match_text = StringSave (scp->match_text);
@@ -3845,7 +4070,7 @@ extern ChoiceConstraintPtr ChoiceConstraintFree (ChoiceConstraintPtr scp)
   if (scp == NULL) return NULL;
   scp->qual_choice = ValNodeFuncFree (scp->qual_choice, scp->free_vn_proc);
   scp->qual_choice_match = ValNodeFuncFree (scp->qual_choice, scp->free_vn_proc);
-  scp->string_constraint = StringConstraintFree (scp->string_constraint);
+  scp->string_constraint = StringConstraintXFree (scp->string_constraint);
   scp->pseudo_constraint = MemFree (scp->pseudo_constraint);
   scp = MemFree (scp);
   return scp;
@@ -3900,7 +4125,7 @@ extern void FilterSetClearText (FilterSetPtr fsp)
   {
     StringConstraintClearText (fsp->scp);
     ChoiceConstraintClearText (fsp->ccp);
-    LocationConstraintClearText (fsp->lcp);
+    LocationConstraintXClearText (fsp->lcp);
     StringConstraintClearText (fsp->id_list);
   }
 }
@@ -3924,11 +4149,11 @@ extern FilterSetPtr FilterSetFree (FilterSetPtr fsp)
 {
   if (fsp != NULL)
   {
-    fsp->scp = StringConstraintFree (fsp->scp);
+    fsp->scp = StringConstraintXFree (fsp->scp);
     fsp->ccp = ChoiceConstraintFree (fsp->ccp);
-    fsp->lcp = LocationConstraintFree (fsp->lcp);
+    fsp->lcp = LocationConstraintXFree (fsp->lcp);
     fsp->cgp = ChoiceConstraintFree (fsp->cgp);
-    fsp->id_list = StringConstraintFree (fsp->id_list);
+    fsp->id_list = StringConstraintXFree (fsp->id_list);
     fsp = MemFree (fsp);
   }
   return fsp;
@@ -3947,7 +4172,7 @@ static FilterSetPtr FilterSetCopy (FilterSetPtr fsp)
   {
     fsp_new->scp = StringConstraintCopy (fsp->scp);
     fsp_new->ccp = ChoiceConstraintCopy (fsp->ccp);
-    fsp_new->lcp = LocationConstraintCopy (fsp->lcp);
+    fsp_new->lcp = LocationConstraintXCopy (fsp->lcp);
     fsp_new->cgp = ChoiceConstraintCopy (fsp->cgp);
     fsp_new->id_list = StringConstraintCopy (fsp->id_list);
   }
@@ -4019,20 +4244,21 @@ static SetSamplePtr SetSampleCopy (SetSamplePtr ssp)
 #define PARSE_FIELD_BIOSRC_STRING 2
 #define PARSE_FIELD_SOURCE_QUAL   3
 #define PARSE_FIELD_GENE_FIELD    4
-#define PARSE_FIELD_MRNA_FIELD    5
+#define PARSE_FIELD_RNA_FIELD    5
 #define PARSE_FIELD_CDS_COMMENT   6
 #define PARSE_FIELD_PROTEIN_FIELD 7
 #define PARSE_FIELD_IMPORT_QUAL   8
 #define PARSE_FIELD_FEATURE_NOTE  9
 #define PARSE_FIELD_COMMENT_DESC  10
+#define PARSE_FIELD_DBXREF        11
 
-#define MAX_PARSE_FIELD_TYPE   10
-#define SEARCH_FIELD_PUBLICATION  11
+#define MAX_PARSE_FIELD_TYPE   11
+#define SEARCH_FIELD_PUBLICATION  12
 
 #define PARSE_FIELD_FIRST_FEATURE 4
 #define PARSE_FIELD_LAST_FEATURE  9
 
-extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp);
+extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintXPtr lcp);
 
 typedef struct acceptpolicy 
 {
@@ -4822,7 +5048,7 @@ static Boolean OrgModSpecialMatch (OrgModPtr mod, FilterSetPtr fsp)
     return TRUE;
   }
   
-  if (DoesStringMatchConstraint (mod->subname, fsp->ccp->string_constraint))
+  if (DoesStringMatchConstraintX (mod->subname, fsp->ccp->string_constraint))
   {
     if (fsp->ccp->string_constraint->not_present)
     {
@@ -4869,7 +5095,7 @@ static Boolean SubSrcSpecialMatch (SubSourcePtr ssp, FilterSetPtr fsp)
   {
     return TRUE;
   }
-  if (DoesStringMatchConstraint (ssp->name, fsp->ccp->string_constraint))
+  if (DoesStringMatchConstraintX (ssp->name, fsp->ccp->string_constraint))
   {
     if (fsp->ccp->string_constraint->not_present)
     {
@@ -4893,13 +5119,63 @@ static Boolean SubSrcSpecialMatch (SubSourcePtr ssp, FilterSetPtr fsp)
   }
 }
 
+
+static CharPtr GetSubfield (CharPtr str, Uint1 subfield)
+{
+  CharPtr cp, cp2;
+  Int4    num_colons = 0;
+  CharPtr new_val = NULL;
+
+  if (StringHasNoText (str)) {
+    return NULL;
+  }
+
+  cp = StringChr (str, ':');
+  while (cp != NULL) {
+    num_colons ++;
+    cp = StringChr (cp + 1, ':');
+  }
+
+  if (subfield == 0) {
+    new_val = StringSave (str);
+  } else if (subfield == 1) {
+    if (num_colons == 0) {
+      return NULL;
+    } else {
+      cp = StringChr (str, ':');
+      new_val = (CharPtr) MemNew (sizeof (Char) * (cp - str + 1));
+      StringNCpy (new_val, str, cp - str);
+      new_val[cp - str] = 0;
+    }
+  } else if (subfield == 2) {
+    if (num_colons == 0 || num_colons == 1) {
+      return NULL;
+    } else {
+      cp = StringChr (str, ':');
+      cp2 = StringChr (cp + 1, ':');
+      new_val = (CharPtr) MemNew (sizeof (Char) * (cp2 - cp));
+      StringNCpy (new_val, cp + 1, cp2 - cp - 1);
+      new_val[cp2 - cp - 1] = 0;
+    }
+  } else {
+    if (num_colons == 0) {
+      new_val = StringSave (str);
+    } else {
+      cp = StringRChr (str, ':');
+      new_val = StringSave (cp + 1);
+    }
+  }
+  return new_val;
+}
+
+
 static CharPtr 
 GetSourceQualQualValueFromBiop 
 (BioSourcePtr      biop,
  SourceQualDescPtr sqdp,
  FilterSetPtr      fsp)
 {
-  CharPtr            str = NULL, tmp_str;
+  CharPtr            str = NULL, field, tmp_str;
   OrgModPtr          mod;
   SubSourcePtr       ssp;
   
@@ -4919,15 +5195,21 @@ GetSourceQualQualValueFromBiop
             && !StringHasNoText (mod->subname)
             && OrgModSpecialMatch (mod, fsp))
         {
-          if (str == NULL) {
-            str = StringSave (mod->subname);
+          field = GetSubfield (mod->subname, sqdp->subfield);
+          if (!StringHasNoText (field)) {
+            if (str == NULL) {
+              str = field;
+            } else {
+              tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (field) + 3) * sizeof (Char));
+              StringCpy (tmp_str, str);
+              StringCat (tmp_str, "; ");
+              StringCat (tmp_str, field);
+              field = MemFree (field);
+              str = MemFree (str);
+              str = tmp_str;
+            }
           } else {
-            tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (mod->subname) + 3) * sizeof (Char));
-            StringCpy (tmp_str, str);
-            StringCat (tmp_str, "; ");
-            StringCat (tmp_str, mod->subname);
-            str = MemFree (str);
-            str = tmp_str;
+            field = MemFree (field);
           }
         }
         mod = mod->next;
@@ -4943,16 +5225,22 @@ GetSourceQualQualValueFromBiop
           && !StringHasNoText (ssp->name)
           && SubSrcSpecialMatch (ssp, fsp))
       {
+        field = GetSubfield (ssp->name, sqdp->subfield);
+        if (!StringHasNoText (field)) {
           if (str == NULL) {
-            str = StringSave (ssp->name);
+            str = field;
           } else {
-            tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (ssp->name) + 3) * sizeof (Char));
+            tmp_str = (CharPtr) MemNew ((StringLen (str) + StringLen (field) + 3) * sizeof (Char));
             StringCpy (tmp_str, str);
             StringCat (tmp_str, "; ");
-            StringCat (tmp_str, ssp->name);
+            StringCat (tmp_str, field);
+            field = MemFree (field);
             str = MemFree (str);
             str = tmp_str;
           }
+        } else {
+          field = MemFree (field);
+        }
       }
       ssp = ssp->next;
     }
@@ -5391,8 +5679,9 @@ static void ApplyStringToSource (BioSourcePtr biop, Pointer userdata)
     {
       biop->org = OrgRefNew();
     }
-    if (avp->field_list->choice == 3
-        || avp->field_list->choice == 4)
+    if (biop->org->orgname == NULL 
+        && (avp->field_list->choice == 3
+            || avp->field_list->choice == 4))
     {
       biop->org->orgname = OrgNameNew ();
     }
@@ -5487,6 +5776,164 @@ static void RemoveStringFromSourceDescriptor (SeqDescrPtr sdp, Pointer userdata,
 
 static void RemoveSourceQualFromBioSource (BioSourcePtr biop, Pointer userdata, FilterSetPtr fsp);
 
+static CharPtr RemoveSubfield (CharPtr orig, Uint1 subfield)
+{
+  CharPtr cp, cp2;
+  Int4    num_colons = 0;
+  CharPtr new_val;
+
+  cp = StringChr (orig, ':');
+  while (cp != NULL) {
+    num_colons ++;
+    cp = StringChr (cp + 1, ':');
+  }
+  new_val = orig;
+
+  if (subfield == 0) {
+    new_val = MemFree (new_val);
+  } else if (subfield == 1) {
+    if (num_colons == 0) {
+      /* no INST, just specID, nothing to remove */
+    } else if (num_colons == 1) {
+      cp = StringChr (orig, ':');
+      new_val = StringSave (cp + 1);
+      orig = MemFree (orig);
+    } else {
+      cp = StringChr (orig, ':');
+      new_val = StringSave (cp);
+      orig = MemFree (orig);
+    }
+  } else if (subfield == 2) {
+    if (num_colons == 0 || num_colons == 1) {
+      /* no COLL, nothing to remove */
+    } else {
+      cp = StringChr (orig, ':');
+      cp2 = StringChr (cp + 1, ':');
+      new_val = (CharPtr) MemNew (sizeof (Char) * (cp - orig + StringLen (cp2) + 1));
+      StringNCpy (new_val, orig, cp - orig);
+      StringCat (new_val, cp2);
+      orig = MemFree (orig);
+      if (StringCmp (new_val, ":") == 0) {
+        new_val = MemFree (new_val);
+      }
+    }
+  } else {
+    /* specid */
+    if (num_colons == 0) {
+      new_val = MemFree (new_val);
+    } else {
+      cp = StringRChr (new_val, ':');
+      *(cp + 1) = 0;
+    }
+  }
+  return new_val;
+}
+
+
+static CharPtr ApplyToSubfield (CharPtr orig, ApplyValuePtr avp, Uint1 subfield)
+{
+  CharPtr cp, cp2;
+  Int4    num_colons = 0, len;
+  CharPtr new_field, new_val;
+
+  cp = StringChr (orig, ':');
+  while (cp != NULL) {
+    num_colons ++;
+    cp = StringChr (cp + 1, ':');
+  }
+
+  new_val = orig;
+  if (subfield == 0) {
+    /* whole field */
+    new_val = HandleApplyValue (orig, avp);
+  } else if (subfield == 1) {
+    /* INST */
+    if (num_colons == 0) {
+      /* all we have is the specID, we are adding INST */
+      new_field = HandleApplyValue (NULL, avp);
+      if (!StringHasNoText (new_field)) {
+        new_val = (CharPtr) MemNew (sizeof (Char) * (StringLen (new_field) + StringLen (orig) + 2));
+        sprintf (new_val, "%s:%s", new_field, orig == NULL ? "" : orig);
+        orig = MemFree (orig);
+      } else {
+        new_val = orig;
+      }
+      new_field = MemFree (new_field);
+    } else {
+      cp = StringChr (orig, ':');
+      len = cp - orig + 1;
+      new_field = (CharPtr) MemNew (sizeof (Char) * len);
+      StringNCpy (new_field, orig, len - 1);
+      new_field[len - 1] = 0;
+      new_field = HandleApplyValue (new_field, avp);
+      new_val = (CharPtr) MemNew (sizeof (Char) * (StringLen (new_field) + StringLen (cp) + 1));
+      sprintf (new_val, "%s%s", new_field == NULL ? "" : new_field, cp);
+      orig = MemFree (orig);
+      new_field = MemFree (new_field);
+    }
+  } else if (subfield == 2) {
+    /* COLL */
+    if (num_colons == 0) {
+      /* add blank INST, then COLL, then existing specID */
+      new_field = HandleApplyValue (NULL, avp);
+      if (!StringHasNoText (new_field)) {
+        new_val = (CharPtr) MemNew (sizeof (Char) * (3 + StringLen (new_field) +  StringLen (orig)));
+        sprintf (new_val, ":%s:%s", new_field, orig == NULL ? "" : orig);
+        orig = MemFree (orig);
+      } else {
+        new_val = orig;
+      }
+      new_field = MemFree (new_field);
+    } else if (num_colons == 1) {
+      /* have INST and specID */
+      new_field = HandleApplyValue (NULL, avp);
+      if (!StringHasNoText (new_field)) {
+        new_val = (CharPtr) MemNew (sizeof (Char) * (3 + StringLen (new_field) +  StringLen (orig)));
+        cp = StringChr (orig, ':');
+        len = cp - orig;
+        StringNCpy (new_val, orig, len);
+        StringCat (new_val, ":");
+        StringCat (new_val, new_field);
+        StringCat (new_val, cp);
+        orig = MemFree (orig);
+      } else {
+        new_val = orig;
+      }
+      new_field = MemFree (new_field);
+    } else {
+      cp = StringChr (orig, ':');
+      cp2 = StringChr (cp + 1, ':');
+      len = cp2 - cp;
+      new_field = (CharPtr) MemNew (sizeof (Char) * len);
+      StringNCpy (new_field, cp + 1, len - 1);
+      new_field[len - 1] = 0;
+      new_field = HandleApplyValue (new_field, avp);
+      new_val = (CharPtr) MemNew (sizeof (Char) * (cp - orig + 1 + StringLen (new_field) + StringLen (cp2) + 1));
+      StringNCpy (new_val, orig, cp - orig + 1);
+      StringCat (new_val, new_field);
+      StringCat (new_val, cp2);
+      orig = MemFree (orig);
+      new_field = MemFree (new_field);
+    }
+  } else {
+    /* specid */
+    if (num_colons == 0) {
+      new_val = HandleApplyValue (orig, avp);
+    } else {
+      cp = StringRChr (orig, ':');
+      new_field = StringSave (cp + 1);
+      new_field = HandleApplyValue (new_field, avp);
+      new_val = (CharPtr) MemNew (sizeof (Char) + (cp - orig + 1 + StringLen (new_field) + 1));
+      StringNCpy (new_val, orig, cp - orig + 1);
+      StringCat (new_val, new_field);
+      orig = MemFree (orig);
+      new_field = MemFree (new_field);
+    }
+  }
+  return new_val;
+}
+
+
 static void ApplySourceQualBioSourceCallback (BioSourcePtr biop, Pointer userdata, FilterSetPtr fsp)
 {
   ApplyValuePtr         avp;
@@ -5546,7 +5993,7 @@ static void ApplySourceQualBioSourceCallback (BioSourcePtr biop, Pointer userdat
         {
           if (!is_nontext)
           {
-            mod->subname = HandleApplyValue (mod->subname, avp); 
+            mod->subname = ApplyToSubfield (mod->subname, avp, sqdp->subfield);
           }
           found = TRUE;
         }
@@ -5563,7 +6010,7 @@ static void ApplySourceQualBioSourceCallback (BioSourcePtr biop, Pointer userdat
         }
         else
         {
-          mod->subname = StringSave (avp->new_text);
+          mod->subname = ApplyToSubfield (mod->subname, avp, sqdp->subfield);
         }
         if (last_mod == NULL)
         {
@@ -5585,7 +6032,7 @@ static void ApplySourceQualBioSourceCallback (BioSourcePtr biop, Pointer userdat
       {
         if (! is_nontext)
         {
-          ssp->name = HandleApplyValue (ssp->name, avp);
+          ssp->name = ApplyToSubfield (ssp->name, avp, sqdp->subfield);
         }
         found = TRUE;
       }
@@ -5602,7 +6049,7 @@ static void ApplySourceQualBioSourceCallback (BioSourcePtr biop, Pointer userdat
       }
       else
       {
-        ssp->name = StringSave (avp->new_text);
+        ssp->name = ApplyToSubfield (ssp->name, avp, sqdp->subfield);
       }
       if (last_ssp == NULL)
       {
@@ -5634,7 +6081,7 @@ static void ApplySourceQualDescriptorCallback (SeqDescrPtr sdp, Pointer userdata
   ApplySourceQualBioSourceCallback (sdp->data.ptrvalue, userdata, fsp);
 }
 
-static void RemoveOrgModFromBioSource (BioSourcePtr biop, Uint1 subtype, FilterSetPtr fsp)
+static void RemoveOrgModFromBioSource (BioSourcePtr biop, Uint1 subtype, Uint1 subfield, FilterSetPtr fsp)
 {
   OrgModPtr mod = NULL, prev_mod = NULL, next_mod;
   
@@ -5647,16 +6094,21 @@ static void RemoveOrgModFromBioSource (BioSourcePtr biop, Uint1 subtype, FilterS
       if (mod->subtype == subtype
           && OrgModSpecialMatch (mod, fsp))
       {
-        if (prev_mod == NULL)
-        {
-          biop->org->orgname->mod = mod->next;
-        }
-        else
-        {
-          prev_mod->next = mod->next;
+        mod->subname = RemoveSubfield (mod->subname, subfield);
+        if (StringHasNoText (mod->subname)) {
+          if (prev_mod == NULL)
+          {
+            biop->org->orgname->mod = mod->next;
+          }
+          else
+          {
+            prev_mod->next = mod->next;
+          }
+          mod->next = NULL;
+          OrgModFree (mod);
+        } else {
+          prev_mod = mod;
         }
-        mod->next = NULL;
-        OrgModFree (mod);
       }
       else
       {
@@ -5667,7 +6119,7 @@ static void RemoveOrgModFromBioSource (BioSourcePtr biop, Uint1 subtype, FilterS
   }
 }
 
-static void RemoveSubSourceFromBioSource (BioSourcePtr biop, Uint2 subtype, FilterSetPtr fsp)
+static void RemoveSubSourceFromBioSource (BioSourcePtr biop, Uint2 subtype, Uint1 subfield, FilterSetPtr fsp)
 {
   SubSourcePtr ssp = NULL, prev_ssp = NULL, next_ssp;
 
@@ -5680,16 +6132,21 @@ static void RemoveSubSourceFromBioSource (BioSourcePtr biop, Uint2 subtype, Filt
       if (ssp->subtype == subtype
           && SubSrcSpecialMatch (ssp, fsp))
       {
-        if (prev_ssp == NULL)
-        {
-          biop->subtype = ssp->next;
-        }
-        else
-        {
-          prev_ssp->next = ssp->next;
+        ssp->name = RemoveSubfield (ssp->name, subfield);
+        if (StringHasNoText (ssp->name)) {
+          if (prev_ssp == NULL)
+          {
+            biop->subtype = ssp->next;
+          }
+          else
+          {
+            prev_ssp->next = ssp->next;
+          }
+          ssp->next = NULL;
+          SubSourceFree (ssp);
+        } else {
+          prev_ssp = ssp;
         }
-        ssp->next = NULL;
-        SubSourceFree (ssp);
       }
       else
       {
@@ -5720,18 +6177,18 @@ static void RemoveSourceQualFromBioSource (BioSourcePtr biop, Pointer userdata,
     sqdp = (SourceQualDescPtr) avp->field_list->data.ptrvalue;
     if (sqdp->isOrgMod)
     {
-      RemoveOrgModFromBioSource (biop, sqdp->subtype, fsp);
+      RemoveOrgModFromBioSource (biop, sqdp->subtype, sqdp->subfield, fsp);
     }
     else
     {
-      RemoveSubSourceFromBioSource (biop, sqdp->subtype, fsp);
+      RemoveSubSourceFromBioSource (biop, sqdp->subtype, sqdp->subfield, fsp);
     }
   }
   else if (avp->field_list->choice == 1 
            && StringCmp (avp->field_list->data.ptrvalue, "All Notes") == 0)
   {
-    RemoveOrgModFromBioSource (biop, 255, fsp);
-    RemoveSubSourceFromBioSource (biop, 255, fsp);
+    RemoveOrgModFromBioSource (biop, 255, 0, fsp);
+    RemoveSubSourceFromBioSource (biop, 255, 0, fsp);
   }
 }
 
@@ -6273,12 +6730,13 @@ static void SetDbxrefFromString (SeqFeatPtr sfp, ApplyValuePtr avp, FilterSetPtr
   
 }
 
+static void SetRNAProduct (SeqFeatPtr sfp, ApplyValuePtr avp);
+
 static void SetGBQualString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
 {
   GBQualPtr     gbqual, gbqual_last = NULL;
   ApplyValuePtr avp;
   Boolean       found = FALSE;
-  RnaRefPtr     rrp;
   GeneRefPtr    grp;
   
   if (sfp == NULL || userdata == NULL)
@@ -6306,19 +6764,7 @@ static void SetGBQualString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
   else if (StringICmp (EditQualifierList[avp->field_list->data.intvalue - 1].name, "product") == 0
            && sfp->data.choice == SEQFEAT_RNA)
   {
-    rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
-    if (rrp != NULL)
-    {
-      if (rrp->ext.choice == 0)
-      {
-        rrp->ext.choice = 1;
-        rrp->ext.value.ptrvalue = NULL;
-      }
-      if (rrp->ext.choice == 1)
-      {
-        rrp->ext.value.ptrvalue = HandleApplyValue (rrp->ext.value.ptrvalue, avp);        
-      }
-    }
+    SetRNAProduct (sfp, avp);
     return;
   }
   else if (StringICmp (EditQualifierList [avp->field_list->data.intvalue - 1].name, "map") == 0
@@ -6541,29 +6987,29 @@ static void RemoveGBQualByNameConstraint (SeqFeatPtr sfp, Pointer userdata, Filt
   GBQualPtr           gbqual, gbqual_last = NULL, gbqual_next;
   RnaRefPtr           rrp;
   GeneRefPtr          grp;
-  StringConstraintPtr scp;
+  StringConstraintXPtr scp;
   
   if (sfp == NULL || userdata == NULL)
   {
     return;
   }
-  scp = (StringConstraintPtr) userdata;
+  scp = (StringConstraintXPtr) userdata;
   if (scp == NULL)
   {
     return;
   }
   
-  if (DoesStringMatchConstraint ("note", scp))
+  if (DoesStringMatchConstraintX ("note", scp))
   {
     sfp->comment = MemFree (sfp->comment);
   }
   
-  if (DoesStringMatchConstraint ("exception", scp))
+  if (DoesStringMatchConstraintX ("exception", scp))
   {
     sfp->except_text = MemFree (sfp->except_text);
   }
 
-  if (DoesStringMatchConstraint ("product", scp) && sfp->data.choice == SEQFEAT_RNA)
+  if (DoesStringMatchConstraintX ("product", scp) && sfp->data.choice == SEQFEAT_RNA)
   {
     rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
     if (rrp != NULL && rrp->ext.choice == 1)
@@ -6573,7 +7019,7 @@ static void RemoveGBQualByNameConstraint (SeqFeatPtr sfp, Pointer userdata, Filt
     }
   }
   
-  if (DoesStringMatchConstraint ("map", scp) && sfp->data.choice == SEQFEAT_GENE)
+  if (DoesStringMatchConstraintX ("map", scp) && sfp->data.choice == SEQFEAT_GENE)
   {
     grp = (GeneRefPtr) sfp->data.value.ptrvalue;
     if (grp != NULL)
@@ -6582,22 +7028,22 @@ static void RemoveGBQualByNameConstraint (SeqFeatPtr sfp, Pointer userdata, Filt
     }
   }
   
-  if (DoesStringMatchConstraint ("db_xref", scp))
+  if (DoesStringMatchConstraintX ("db_xref", scp))
   {
     sfp->dbxref = RemoveDbxrefList (sfp->dbxref);
   }
   
-  if (DoesStringMatchConstraint ("go_process", scp))
+  if (DoesStringMatchConstraintX ("go_process", scp))
   {
     RemoveGoTerm (sfp, "process");
   }
   
-  if (DoesStringMatchConstraint ("go_function", scp))
+  if (DoesStringMatchConstraintX ("go_function", scp))
   {
     RemoveGoTerm (sfp, "function");
   }
 
-  if (DoesStringMatchConstraint ("go_component", scp))
+  if (DoesStringMatchConstraintX ("go_component", scp))
   {
     RemoveGoTerm (sfp, "component");
   }
@@ -6606,7 +7052,7 @@ static void RemoveGBQualByNameConstraint (SeqFeatPtr sfp, Pointer userdata, Filt
   while (gbqual != NULL)
   {
     gbqual_next = gbqual->next;
-    if (DoesStringMatchConstraint (gbqual->qual, scp))
+    if (DoesStringMatchConstraintX (gbqual->qual, scp))
     {
       if (gbqual_last == NULL)
       {
@@ -6699,7 +7145,7 @@ static void StripFieldNameFromText(CharPtr text,
 }
 
 
-static CharPtr ReplaceStringForParse(CharPtr src_text, TextPortionPtr text_portion)
+static CharPtr ReplaceStringForParse(CharPtr src_text, TextPortionXPtr text_portion)
 {
   CharPtr         found_loc;
   Int4            found_len;
@@ -6711,7 +7157,7 @@ static CharPtr ReplaceStringForParse(CharPtr src_text, TextPortionPtr text_porti
   /* for parse, replace the source text with the portion we want */
   found_loc = NULL;
   found_len = 0;
-  FindTextPortionInString (src_text, text_portion, &found_loc, &found_len);
+  FindTextPortionXInString (src_text, text_portion, &found_loc, &found_len);
   if (found_loc != NULL) 
   {
     dst_txt = (CharPtr)MemNew (found_len + 1);
@@ -8072,6 +8518,8 @@ static void RemoveProteinFieldString (SeqFeatPtr sfp, ValNodePtr protein_field)
   }      
 }
 
+extern ValNodePtr ApplyValueToValNodeStringListAsText (ValNodePtr list, Int2 choice, ApplyValuePtr avp);
+
 static void SetProteinFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
 {
   ProtRefPtr    prp;
@@ -8144,14 +8592,7 @@ static void SetProteinFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPt
       prp->desc = HandleApplyValue (prp->desc, avp);
       break;
     case PROTEINFIELD_EC_NUM:
-      if (prp->ec == NULL || !StringHasNoText(avp->text_to_replace))
-      {
-        prp->ec = ApplyValueToValNodeStringList (prp->ec, 0, avp);
-      }
-      else
-      {
-        prp->ec->data.ptrvalue = HandleApplyValue (prp->ec->data.ptrvalue, avp);
-      }
+      prp->ec = ApplyValueToValNodeStringListAsText (prp->ec, 0, avp);
       break;
     case PROTEINFIELD_ACTIVITY:
       if (prp->activity == NULL || !StringHasNoText(avp->text_to_replace))
@@ -8419,7 +8860,7 @@ static Boolean DoesConstraintDisqualifyFeature (SeqFeatPtr sfp, ChoiceConstraint
   else if (ccp->constraint_type == CHOICE_CONSTRAINT_STRING)
   {
     str = GetCDSGeneProtField (sfp, ccp->qual_choice, NULL);
-    does_match = DoesStringMatchConstraint (str, ccp->string_constraint);
+    does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
     MemFree (str);
     if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
     {
@@ -8576,16 +9017,16 @@ SetCDSGeneProtField
   return TRUE;
 }
 
-#define RNAFIELD_NAME              1
+#define RNAFIELD_PRODUCT           1
 #define RNAFIELD_COMMENT           2
-#define RNAFIELD_PRODUCT           3
-#define RNAFIELD_CODONS_RECOGNIZED 4
+#define RNAFIELD_CODONS_RECOGNIZED 3
+#define RNAFIELD_NCRNA_CLASS       4
 #define RNAFIELD_ANTICODON         5
 #define RNAFIELD_TRANSCRIPT_ID     6
 
 static CharPtr rna_field_list [] = 
 {
-  "Name", "Comment", "Product GBQual", "Codons Recognized", "Anticodon", "Transcript ID"
+  "Product", "Comment", "Codons Recognized", "ncRNA class", "Anticodon", "Transcript ID"
 };
 
 static Int4 num_rna_fields = sizeof (rna_field_list) / sizeof (CharPtr);
@@ -8681,7 +9122,7 @@ RNAFieldSelectionDialog
   DialoG     dlg;
   Int4       i;
   
-  for (i = 0; i < 3; i++)
+  for (i = 0; i < 4; i++)
   {
     ValNodeAddInt (&choice_list, 0, i + 1);
   }
@@ -8700,7 +9141,7 @@ RNAFieldSelectionDialog
 }
 
 static CharPtr rna_subtype_list [] = { "misc_RNA", "preRna", "mRNA", "tRNA",
-                                        "rRNA", "snRNA", "scRNA", "snoRNA"};
+                                        "rRNA", "ncRNA", "tmRNA"};
 static Int2    num_rna_subtypes = sizeof (rna_subtype_list) / sizeof (CharPtr); 
 
 static CharPtr GetRNASubtypeName (ValNodePtr vnp)
@@ -8729,9 +9170,8 @@ static DialoG RNASubtypeSelectionDialog
   ValNodeAddInt (&choice_list, 2, FEATDEF_mRNA);
   ValNodeAddInt (&choice_list, 3, FEATDEF_tRNA);
   ValNodeAddInt (&choice_list, 4, FEATDEF_rRNA);
-  ValNodeAddInt (&choice_list, 5, FEATDEF_snRNA);
-  ValNodeAddInt (&choice_list, 6, FEATDEF_scRNA);
-  ValNodeAddInt (&choice_list, 7, FEATDEF_snoRNA);
+  ValNodeAddInt (&choice_list, 5, FEATDEF_ncRNA);
+  ValNodeAddInt (&choice_list, 6, FEATDEF_tmRNA);
 
   dlg = ValNodeSelectionDialog (h, choice_list, TALL_SELECTION_LIST,
                                 GetRNASubtypeName, NULL, 
@@ -8742,28 +9182,55 @@ static DialoG RNASubtypeSelectionDialog
 }
 
 
-static CharPtr GetRNANameString (SeqFeatPtr sfp)
+static CharPtr GetRNAProductString (SeqFeatPtr sfp)
 {
   RnaRefPtr  rrp;
   SeqMgrFeatContext context;
   CharPtr    str = NULL;
+  GBQualPtr  gbqual;
 
   if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL)
   {
     return NULL;
   }
+
   rrp = sfp->data.value.ptrvalue;
-  if (rrp->ext.choice == 1 && !StringHasNoText (rrp->ext.value.ptrvalue))
+  if (rrp->ext.choice == 0 
+      || (rrp->ext.choice == 1 && StringHasNoText (rrp->ext.value.ptrvalue))
+      || (rrp->ext.choice == 1 
+          && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0 
+              || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
+              || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0)))
   {
-    str = StringSave (rrp->ext.value.ptrvalue);        
+    gbqual = sfp->qual;
+    while (gbqual != NULL && str == NULL) {
+    if (StringICmp (gbqual->qual, "product") == 0
+        && !StringHasNoText (gbqual->val)) 
+    {
+      str = StringSave (gbqual->val);
+      }
+      gbqual = gbqual->next;
+    }
   }
-  else if (rrp->ext.choice == 2 && rrp->ext.value.ptrvalue != NULL)
+
+  if (str == NULL)
   {
-    if (SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, 0, 0, sfp, &context) != NULL
-        && !StringHasNoText (context.label))
+    if (rrp->ext.choice == 1 && !StringHasNoText (rrp->ext.value.ptrvalue)
+        && StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0
+        && StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0
+        && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") != 0)
     {
-      str = (CharPtr) MemNew (sizeof (Char) + (StringLen (context.label) + 6));
-      sprintf (str, "tRNA-%s", context.label);
+      str = StringSave (rrp->ext.value.ptrvalue);        
+    }
+    else if (rrp->ext.choice == 2 && rrp->ext.value.ptrvalue != NULL)
+    {
+      if (SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, 0, 0, sfp, &context) != NULL
+          && !StringHasNoText (context.label)
+          && StringCmp (context.label, "tRNA") != 0)
+      {
+        str = (CharPtr) MemNew (sizeof (Char) + (StringLen (context.label) + 6));
+        sprintf (str, "tRNA-%s", context.label);
+      }
     }
   }
   return str;
@@ -8773,12 +9240,12 @@ extern CharPtr GetRNAFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr f
 {
   RnaRefPtr  rrp;
   CharPtr    str = NULL;
-  GBQualPtr  gbqual;
   ValNode    vn;
   GeneRefPtr grp;
   SeqFeatPtr gene;
   SeqMgrFeatContext context;
   Int4              field_choice;
+  GBQualPtr         qual;
   
   if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || vnp == NULL)
   {
@@ -8792,8 +9259,8 @@ extern CharPtr GetRNAFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr f
     field_choice = vnp->data.intvalue;
     switch (vnp->data.intvalue)
     {
-      case RNAFIELD_NAME :
-        str = GetRNANameString (sfp);
+      case RNAFIELD_PRODUCT :        
+        str = GetRNAProductString (sfp);
         break;
       case RNAFIELD_COMMENT :
         if (!StringHasNoText (sfp->comment))
@@ -8801,15 +9268,14 @@ extern CharPtr GetRNAFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr f
           str = StringSave (sfp->comment);
         }
         break;
-      case RNAFIELD_PRODUCT :
-        gbqual = sfp->qual;
-        while (gbqual != NULL && str == NULL) {
-          if (StringICmp (gbqual->qual, "product") == 0
-              && !StringHasNoText (gbqual->val)) 
+      case RNAFIELD_NCRNA_CLASS :
+        for (qual = sfp->qual; qual != NULL && str == NULL; qual = qual->next)
+        {
+          if (StringCmp (qual->qual, "ncRNA_class") == 0
+              && !StringHasNoText (qual->val))
           {
-            str = StringSave (gbqual->val);
+            str = StringSave (qual->val);
           }
-          gbqual = gbqual->next;
         }
         break;
       default:
@@ -8874,20 +9340,29 @@ static void SettRNAName (SeqFeatPtr sfp, ApplyValuePtr avp)
   GBQualPtr         gbqual, gbqual_last = NULL;
 
   if (sfp == NULL || sfp->data.value.ptrvalue == NULL 
-      || sfp->data.choice != SEQFEAT_RNA
+      || sfp->idx.subtype != FEATDEF_tRNA
       || avp == NULL)
   {
     return;
   }
   
   rrp = sfp->data.value.ptrvalue;
+  if (rrp->ext.choice == 0)
+  {
+    trp = MemNew (sizeof (tRNA));
+    trp->aatype = 0;
+    MemSet (trp->codon, 255, sizeof (trp->codon));
+    trp->anticodon = NULL;
+    rrp->ext.value.ptrvalue = trp;
+    rrp->ext.choice = 2;
+  }
   if (rrp->ext.choice != 2)
   {
     return;
   }
   trp = (tRNAPtr) rrp->ext.value.ptrvalue;
   
-  name_string = GetRNANameString (sfp);
+  name_string = GetRNAProductString (sfp);
   name_string = HandleApplyValue (name_string, avp);
   if (!IsParseabletRNAName(name_string))
   {
@@ -8930,19 +9405,87 @@ static void SettRNAName (SeqFeatPtr sfp, ApplyValuePtr avp)
   {
     new_aa = ParseTRnaString (name_string, &justTrnaText, codon, TRUE);
     trp->aa = new_aa;
+    trp->aatype = 2;
     name_string = MemFree (name_string);
   }
 }
 
 
+static void SetRNAProduct (SeqFeatPtr sfp, ApplyValuePtr avp)
+{
+  RnaRefPtr rrp;
+  GBQualPtr gbq, prev_gbq = NULL;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL || avp == NULL)
+  {
+    return;
+  }
+
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+
+  gbq = sfp->qual;
+  while (gbq != NULL && StringCmp (gbq->qual, "product") != 0)
+  {
+    prev_gbq = gbq;
+    gbq = gbq->next;
+  }
+  if (gbq != NULL)
+  {
+    gbq->val = HandleApplyValue (gbq->val, avp);
+    if (StringHasNoText (gbq->val))
+    {
+      if (prev_gbq == NULL)
+      {
+        sfp->qual = gbq->next;
+      }
+      else
+      {
+        prev_gbq->next = gbq->next;
+      }
+      gbq->next = NULL;
+      gbq = GBQualFree (gbq);
+    }
+  }
+  else if (sfp->idx.subtype == FEATDEF_tRNA || rrp->ext.choice == 2)
+  {
+    SettRNAName (sfp, avp);
+  }
+  else if (rrp->ext.choice == 1
+           && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
+               || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
+               || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))
+  {
+    gbq = GBQualNew();
+    gbq->qual = StringSave ("product");
+    gbq->val = HandleApplyValue (gbq->val, avp);
+    gbq->next = sfp->qual;
+    sfp->qual = gbq;
+  }
+  else if (rrp->ext.choice == 1 || rrp->ext.choice == 0)
+  {
+    rrp->ext.value.ptrvalue = HandleApplyValue (rrp->ext.value.ptrvalue, avp);
+    if (StringHasNoText (rrp->ext.value.ptrvalue))
+    {
+      rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+      rrp->ext.choice = 0;
+    }
+    else
+    {
+      rrp->ext.choice = 1;
+    }
+  }
+}
+
+
 static void SetRNAFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
 {
   RnaRefPtr     rrp;
   ApplyValuePtr avp;
-  GBQualPtr     gbqual, gbqual_last = NULL;
   SeqFeatPtr    gene;
   GeneRefPtr    grp;
   SeqMgrFeatContext context;
+  GBQualPtr         qual;
+  Boolean           found = FALSE;
   
   if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || userdata == NULL)
   {
@@ -8959,63 +9502,28 @@ static void SetRNAFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fs
     
   switch (avp->field_list->data.intvalue)
   {
-    case RNAFIELD_NAME :
-      if (rrp != NULL)
-      {
-        if (rrp->ext.choice == 0)
-        {
-          rrp->ext.choice = 1;
-          rrp->ext.value.ptrvalue = NULL;
-        }
-        if (rrp->ext.choice == 1)
-        {
-          rrp->ext.value.ptrvalue = HandleApplyValue (rrp->ext.value.ptrvalue, avp);        
-        }
-        else if (rrp->ext.choice == 2)
-        {
-          SettRNAName (sfp, avp);
-        }
-      }
+    case RNAFIELD_PRODUCT :
+      SetRNAProduct (sfp, avp);
       break;
     case RNAFIELD_COMMENT :
       sfp->comment = HandleApplyValue (sfp->comment, avp);
       break;
-    case RNAFIELD_PRODUCT :
-      gbqual = sfp->qual;
-      while (gbqual != NULL && StringICmp (gbqual->qual, "product") != 0)
+    case RNAFIELD_NCRNA_CLASS :
+      for (qual = sfp->qual; qual != NULL; qual = qual->next)
       {
-        gbqual_last = gbqual;
-        gbqual = gbqual->next;
-      }
-      if (gbqual == NULL)
-      {
-        if (StringHasNoText (avp->text_to_replace))
+        if (StringCmp (qual->qual, "ncRNA_class") == 0)
         {
-          gbqual = GBQualNew ();
-          if (gbqual == NULL)
-          {
-            return;
-          }
-          gbqual->qual = StringSave ("product");
-          gbqual->val = StringSave (avp->new_text);
-          if (gbqual_last == NULL)
-          {
-            sfp->qual = gbqual;
-          }
-          else
-          {
-            gbqual->next = gbqual_last->next;
-            gbqual_last->next = gbqual;
-          }
-        }
-        else
-        {
-          /* don't create new product for edit/replace */
+          qual->val = HandleApplyValue (qual->val, avp);
+          found = TRUE;
         }
       }
-      else
-      {        
-        gbqual->val = HandleApplyValue (gbqual->val, avp);
+      if (!found)
+      {
+        qual = GBQualNew ();
+        qual->qual = StringSave ("ncRNA_class");
+        qual->val = StringSave (avp->new_text);
+        qual->next = sfp->qual;
+        sfp->qual = qual;
       }
       break;
     default:
@@ -9038,16 +9546,76 @@ static void SetRNAFieldString (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fs
   }
 }
 
+
+static void RemoveRNAProduct (SeqFeatPtr sfp)
+{
+  RnaRefPtr rrp;
+  GBQualPtr gbq, prev_gbq = NULL;
+  tRNAPtr     trp;
+
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL)
+  {
+    return;
+  }
+
+  rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+
+  gbq = sfp->qual;
+  while (gbq != NULL && StringCmp (gbq->qual, "product") != 0)
+  {
+    prev_gbq = gbq;
+    gbq = gbq->next;
+  }
+  if (gbq != NULL)
+  {
+    if (prev_gbq == NULL)
+    {
+      sfp->qual = gbq->next;
+    }
+    else
+    {
+      prev_gbq->next = gbq->next;
+    }
+    gbq->next = NULL;
+    gbq = GBQualFree (gbq);
+  }
+  else if (rrp->ext.choice == 1
+           && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
+               || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0
+               || StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0))
+  {
+    /* do nothing - already have no product */
+  }
+  else if (rrp->ext.choice == 0)
+  {
+    /* do nothing - already have no product */
+  }
+  else if (rrp->ext.choice == 1)
+  {
+    rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
+    rrp->ext.choice = 0;
+  }
+  else if (rrp->ext.choice == 2)
+  {
+    trp = (tRNAPtr) rrp->ext.value.ptrvalue;
+    if (trp != NULL)
+    {
+      trp->aatype = 0;
+    }
+  }
+}
+
+
 static void RemoveRNAField (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
 {
   RnaRefPtr     rrp;
-  GBQualPtr     gbqual, prev_qual = NULL, next_qual;
   tRNAPtr       trp;
   ApplyValuePtr avp;
   SeqFeatPtr    gene;
   GeneRefPtr    grp;
   ValNode       vn;
   SeqMgrFeatContext context;
+  GBQualPtr         qual, qual_prev = NULL, qual_next;
   
   if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || userdata == NULL)
   {
@@ -9064,51 +9632,37 @@ static void RemoveRNAField (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
 
   switch (avp->field_list->data.intvalue)
   {
-    case RNAFIELD_NAME :
-      if (rrp != NULL && rrp->ext.value.ptrvalue != NULL)
-      {
-        if (rrp->ext.choice == 1)
-        {
-          rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue);
-        }
-        else if (rrp->ext.choice == 2)
-        {
-          trp = (tRNAPtr) rrp->ext.value.ptrvalue;
-          if (trp != NULL)
-          {
-            trp->aatype = 0;
-          }
-        }
-      }
+    case RNAFIELD_PRODUCT :
+      RemoveRNAProduct (sfp);
       break;
     case RNAFIELD_COMMENT :
       sfp->comment = MemFree (sfp->comment);
       break;
-    case RNAFIELD_PRODUCT :
-      gbqual = sfp->qual;
-      while (gbqual != NULL) 
+    case RNAFIELD_NCRNA_CLASS :
+      qual = sfp->qual;
+      while (qual != NULL)
       {
-        next_qual = gbqual->next;
-        if (StringICmp (gbqual->qual, "product") == 0)
+        qual_next = qual->next;
+        if (StringCmp (qual->qual, "ncRNA_class") == 0)
         {
-          if (prev_qual == NULL)
+          if (qual_prev == NULL)
           {
-            sfp->qual = sfp->qual->next;
+            sfp->qual = qual_next;
           }
           else
           {
-            prev_qual->next = gbqual->next;
+            qual_prev->next = qual_next;
           }
-          gbqual->next = NULL;
-          GBQualFree (gbqual);
+          qual->next = NULL;
+          qual = GBQualFree (qual);
         }
         else
         {
-          prev_qual = gbqual;
+          qual_prev = qual;
         }
-        gbqual = next_qual;
+        qual = qual_next;
       }
-      break;    
+      break;
     case RNAFIELD_ANTICODON :
       if (rrp->ext.choice == 2) {
         trp = (tRNAPtr) rrp->ext.value.ptrvalue;
@@ -9487,6 +10041,143 @@ static void ApplySourceStringDescriptorCallback (SeqDescrPtr sdp, Pointer userda
 }
 
 
+static CharPtr GetDbxrefFromBioSource (BioSourcePtr biop, ValNodePtr vnp)
+{
+  ValNodePtr dbx;
+  DbtagPtr   dbtag;
+  Char       buf[20];
+
+  if (biop == NULL || vnp == NULL || vnp->data.ptrvalue == NULL || biop->org == NULL)
+  {
+    return NULL;
+  }
+  
+  dbx = biop->org->db;
+  while (dbx != NULL)
+  {
+    dbtag = (DbtagPtr) dbx->data.ptrvalue;
+    if (dbtag != NULL && dbtag->tag != NULL
+        && StringCmp (dbtag->db, vnp->data.ptrvalue) == 0)
+    {
+      if (dbtag->tag->str == NULL)
+      {
+        sprintf (buf, "%d", dbtag->tag->id);
+        return StringSave (buf);
+      }
+      else
+      {
+        return StringSave (dbtag->tag->str);
+      }
+    }
+    dbx = dbx->next;
+  }
+  return NULL;
+}
+
+static CharPtr 
+GetBioSourceFeatureDbxrefString 
+(SeqFeatPtr   sfp,
+ ValNodePtr   vnp,
+ FilterSetPtr fsp)
+{
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || vnp == NULL)
+  {
+    return NULL;
+  }
+  
+  return GetDbxrefFromBioSource (sfp->data.value.ptrvalue, vnp);
+}
+
+static CharPtr 
+GetBioSourceDescriptorDbxrefString 
+(SeqDescrPtr  sdp,
+ ValNodePtr   vnp,
+ FilterSetPtr fsp)
+{
+  if (sdp == NULL || sdp->choice != Seq_descr_source || vnp == NULL)
+  {
+    return NULL;
+  }
+  return GetDbxrefFromBioSource (sdp->data.ptrvalue, vnp);
+}
+
+
+static void ApplyBioSourceDbxrefBioSourceCallback (BioSourcePtr biop, Pointer userdata)
+{
+  ApplyValuePtr avp;
+  ValNodePtr    dbx;
+  DbtagPtr      dbtag;
+  Boolean       found = FALSE;
+  Char          buf[20];
+  
+  if (biop == NULL || userdata == NULL)
+  {
+    return;
+  }
+  
+  avp = (ApplyValuePtr) userdata;
+  if (avp->field_list != NULL && !StringHasNoText (avp->new_text))
+  {
+    if (biop->org == NULL)
+    {
+      biop->org = OrgRefNew();
+    }
+    dbx = biop->org->db;
+    while (dbx != NULL && !found)
+    {
+      dbtag = (DbtagPtr) dbx->data.ptrvalue;
+      if (dbtag != NULL && dbtag->tag != NULL
+          && StringCmp (dbtag->db, avp->field_list->data.ptrvalue) == 0)
+      {
+        found = TRUE;
+      }
+      if (!found)
+      {
+        dbx = dbx->next;
+      }
+    }
+    if (!found)
+    {
+      dbtag = DbtagNew();
+      dbtag->db = StringSave (avp->field_list->data.ptrvalue);      
+      ValNodeAddPointer (&(biop->org->db), 0, dbtag);
+    }
+    if (dbtag->tag == NULL)
+    {
+      dbtag->tag = ObjectIdNew();
+    }
+    /* if it was a number before, make it a string now */
+    if (dbtag->tag->id > 0 && dbtag->tag->str == NULL)
+    {
+      sprintf (buf, "%s", dbtag->tag->id);
+      dbtag->tag->id = 0;
+      dbtag->tag->str = StringSave (buf);
+    }
+    dbtag->tag->str = HandleApplyValue (dbtag->tag->str, avp);
+  }
+  
+}
+
+static void ApplyBioSourceDbxrefFeatureCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
+{
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || userdata == NULL)
+  {
+    return;
+  }
+  ApplyBioSourceDbxrefBioSourceCallback (sfp->data.value.ptrvalue, userdata);
+}
+
+static void ApplyBioSourceDbxrefDescriptorCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
+{
+  if (sdp == NULL || sdp->choice != Seq_descr_source || userdata == NULL)
+  {
+    return;
+  }
+  ApplyBioSourceDbxrefBioSourceCallback (sdp->data.ptrvalue, userdata);
+}
+
+
+
 #define TEXT_PORTION_START_AFTER 1
 #define TEXT_PORTION_START_WITH  2
 #define TEXT_PORTION_END_AFTER   1
@@ -9500,40 +10191,86 @@ typedef struct textportiondialog
   TexT   start_text;
   GrouP  end_choice;
   TexT   end_text;
+  ButtoN rem_before;
+  ButtoN also_rem_before;
+  ButtoN rem_after;
+  ButtoN also_rem_after;
   ButtoN insensitive;
   ButtoN whole_word;
 
+  Boolean inside;
+
   Nlm_ChangeNotifyProc     change_notify;
   Pointer                  change_userdata;
-} TextPortionDialogData, PNTR TextPortionDialogPtr;
+} TextPortionXDialogData, PNTR TextPortionXDialogPtr;
 
-static void ResetTextPortionDialog (TextPortionDialogPtr tp)
+
+static void OutsideEnableDisable (TextPortionXDialogPtr tp)
+{
+  if (tp == NULL || tp->inside)
+  {
+    return;
+  }
+  if (GetStatus (tp->rem_before)) 
+  {
+    Enable (tp->start_text);
+    Enable (tp->also_rem_before);
+  }
+  else
+  {
+    Disable (tp->start_text);
+    Disable (tp->also_rem_before);
+  }
+  if (GetStatus (tp->rem_after)) 
+  {
+    Enable (tp->end_text);
+    Enable (tp->also_rem_after);
+  }
+  else
+  {
+    Disable (tp->end_text);
+    Disable (tp->also_rem_after);
+  }
+}
+
+static void ResetTextPortionXDialog (TextPortionXDialogPtr tp)
 {
   if (tp == NULL)
   {
     return;
   }
-  SetValue (tp->start_choice, TEXT_PORTION_START_AFTER);
+  if (tp->inside)
+  {
+    SetValue (tp->start_choice, TEXT_PORTION_START_AFTER);
+    SetValue (tp->end_choice, TEXT_PORTION_END_AFTER);
+  }
+  else
+  {
+    SetStatus (tp->rem_before, FALSE);
+    SetStatus (tp->also_rem_before, FALSE);
+    SetStatus (tp->rem_after, FALSE);
+    SetStatus (tp->also_rem_after, FALSE);
+  }
   SetTitle (tp->start_text, "");
-  SetValue (tp->end_choice, TEXT_PORTION_END_AFTER);
   SetTitle (tp->end_text, "");
   SetStatus (tp->insensitive, FALSE);
   SetStatus (tp->whole_word, FALSE);
+  OutsideEnableDisable (tp);
 }
 
-static void TextPortionToDialog (DialoG d, Pointer data)
+static void TextPortionXToDialog (DialoG d, Pointer data)
 {
-  TextPortionDialogPtr tdlg;
-  TextPortionPtr       tdata;
+  TextPortionXDialogPtr tdlg;
+  TextPortionXPtr       tdata;
   Int4                 start_choice, end_choice;
   
-  tdlg = (TextPortionDialogPtr) GetObjectExtra (d);
+  tdlg = (TextPortionXDialogPtr) GetObjectExtra (d);
   if (tdlg == NULL)
   {
     return;
   }
-  tdata = (TextPortionPtr) data;
-  ResetTextPortionDialog (tdlg);  
+  tdata = (TextPortionXPtr) data;
+  ResetTextPortionXDialog (tdlg);  
   if (tdata != NULL)
   {
     start_choice = tdata->end_choice;
@@ -9546,8 +10283,32 @@ static void TextPortionToDialog (DialoG d, Pointer data)
     {
       end_choice = TEXT_PORTION_END_AFTER;
     }
-    SetValue (tdlg->start_choice, start_choice);
-    SetValue (tdlg->end_choice, end_choice);
+    if (tdlg->inside)
+    {
+      SetValue (tdlg->start_choice, start_choice);
+      SetValue (tdlg->end_choice, end_choice);
+    }
+    else
+    {
+      SetStatus (tdlg->rem_before, StringHasNoText (tdata->start_text));
+      SetStatus (tdlg->rem_after, StringHasNoText (tdata->end_text));
+      if (start_choice == TEXT_PORTION_START_AFTER)
+      {
+        SetStatus (tdlg->also_rem_before, TRUE);
+      }
+      else
+      {
+        SetStatus (tdlg->also_rem_before, FALSE);
+      }
+      if (end_choice == TEXT_PORTION_END_AFTER)
+      {
+        SetStatus (tdlg->also_rem_after, TRUE);
+      }
+      else
+      {
+        SetStatus (tdlg->also_rem_after, FALSE);
+      }
+    }
     if (tdata->start_text != NULL)
     {
       SetTitle (tdlg->start_text, tdata->start_text);
@@ -9559,42 +10320,84 @@ static void TextPortionToDialog (DialoG d, Pointer data)
     SetStatus (tdlg->insensitive, tdata->insensitive);
     SetStatus (tdlg->whole_word, tdata->whole_word);
   }
+  OutsideEnableDisable (tdlg);
 }
 
-static Pointer DialogToTextPortion (DialoG d)
+static Pointer DialogToTextPortionX (DialoG d)
 {
-  TextPortionDialogPtr tdlg;
-  TextPortionPtr       tdata;
+  TextPortionXDialogPtr tdlg;
+  TextPortionXPtr       tdata;
 
-  tdlg = (TextPortionDialogPtr) GetObjectExtra (d);
+  tdlg = (TextPortionXDialogPtr) GetObjectExtra (d);
   if (tdlg == NULL)
   {
     return NULL;
   }
 
-  tdata = (TextPortionPtr) MemNew (sizeof (TextPortionData));
+  tdata = (TextPortionXPtr) MemNew (sizeof (TextPortionXData));
   if (tdata != NULL)
   {
-    tdata->start_choice = GetValue (tdlg->start_choice);
-    tdata->end_choice = GetValue (tdlg->end_choice);
-    tdata->start_text = JustSaveStringFromText (tdlg->start_text);
-    tdata->end_text = JustSaveStringFromText (tdlg->end_text);
+    if (tdlg->inside)
+    {
+      tdata->start_choice = GetValue (tdlg->start_choice);
+      tdata->end_choice = GetValue (tdlg->end_choice);
+      tdata->start_text = JustSaveStringFromText (tdlg->start_text);
+      tdata->end_text = JustSaveStringFromText (tdlg->end_text);
+    }
+    else
+    {
+      if (GetStatus (tdlg->rem_before))
+      {
+        tdata->start_text = JustSaveStringFromText (tdlg->start_text);
+      }
+      else
+      {
+        tdata->start_text = NULL;
+      }
+      if (GetStatus (tdlg->rem_after))
+      {
+        tdata->end_text = JustSaveStringFromText (tdlg->end_text);
+      }
+      else
+      {
+        tdata->end_text = NULL;
+      }
+
+      if (GetStatus (tdlg->also_rem_before))
+      {
+        tdata->start_choice = TEXT_PORTION_START_AFTER;
+      }
+      else
+      {
+        tdata->start_choice = TEXT_PORTION_START_WITH;
+      }
+      if (GetStatus (tdlg->also_rem_after))
+      {
+        tdata->end_choice = TEXT_PORTION_END_AFTER;
+      }
+      else
+      {
+        tdata->end_choice = TEXT_PORTION_END_WITH;
+      }
+
+    }
+        
     tdata->insensitive = GetStatus (tdlg->insensitive);
     tdata->whole_word = GetStatus (tdlg->whole_word);
   }
   return tdata;
 }
 
-static void TextPortionMessage (DialoG d, Int2 mssg)
+static void TextPortionXMessage (DialoG d, Int2 mssg)
 
 {
-  TextPortionDialogPtr tp;
+  TextPortionXDialogPtr tp;
 
-  tp = (TextPortionDialogPtr) GetObjectExtra (d);
+  tp = (TextPortionXDialogPtr) GetObjectExtra (d);
   if (tp != NULL) {
     switch (mssg) {
       case VIB_MSG_INIT :
-        ResetTextPortionDialog (tp);        
+        ResetTextPortionXDialog (tp);        
         break;
       case VIB_MSG_ENTER :
         Select (tp->start_text);
@@ -9605,17 +10408,17 @@ static void TextPortionMessage (DialoG d, Int2 mssg)
   }
 }
 
-static ValNodePtr TestTextPortionDialog (DialoG d)
+static ValNodePtr TestTextPortionXDialog (DialoG d)
 
 {
   return NULL;
 }
 
-static void ChangeTextPortionGroup (GrouP g)
+static void ChangeTextPortionXGroup (GrouP g)
 {
-  TextPortionDialogPtr tp;
+  TextPortionXDialogPtr tp;
 
-  tp = (TextPortionDialogPtr) GetObjectExtra (g);
+  tp = (TextPortionXDialogPtr) GetObjectExtra (g);
   if (tp == NULL) return;
 
   if (tp->change_notify != NULL)
@@ -9624,11 +10427,11 @@ static void ChangeTextPortionGroup (GrouP g)
   }
 }
 
-static void ChangeTextPortionText (TexT t)
+static void ChangeTextPortionXText (TexT t)
 {
-  TextPortionDialogPtr tp;
+  TextPortionXDialogPtr tp;
 
-  tp = (TextPortionDialogPtr) GetObjectExtra (t);
+  tp = (TextPortionXDialogPtr) GetObjectExtra (t);
   if (tp == NULL) return;
 
   if (tp->change_notify != NULL)
@@ -9638,12 +10441,13 @@ static void ChangeTextPortionText (TexT t)
 }
 
 
-static void ChangeTextPortionBtn (ButtoN b)
+static void ChangeTextPortionXBtn (ButtoN b)
 {
-  TextPortionDialogPtr tp;
+  TextPortionXDialogPtr tp;
 
-  tp = (TextPortionDialogPtr) GetObjectExtra (b);
+  tp = (TextPortionXDialogPtr) GetObjectExtra (b);
   if (tp == NULL) return;
+  OutsideEnableDisable (tp);
 
   if (tp->change_notify != NULL)
   {
@@ -9653,12 +10457,12 @@ static void ChangeTextPortionBtn (ButtoN b)
 
 
 
-extern DialoG TextPortionDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+extern DialoG TextPortionXDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
 {
-  TextPortionDialogPtr tp;
+  TextPortionXDialogPtr tp;
   GrouP                p, g1, g2;
   
-  tp = (TextPortionDialogPtr) MemNew (sizeof (TextPortionDialogData));
+  tp = (TextPortionXDialogPtr) MemNew (sizeof (TextPortionXDialogData));
   if (tp == NULL)
   {
     return NULL;
@@ -9668,13 +10472,14 @@ extern DialoG TextPortionDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc
   SetObjectExtra (p, tp, StdCleanupExtraProc);
 
   tp->dialog = (DialoG) p;
-  tp->todialog = TextPortionToDialog;
-  tp->fromdialog = DialogToTextPortion;
-  tp->dialogmessage = TextPortionMessage;
-  tp->testdialog = TestTextPortionDialog;
+  tp->todialog = TextPortionXToDialog;
+  tp->fromdialog = DialogToTextPortionX;
+  tp->dialogmessage = TextPortionXMessage;
+  tp->testdialog = TestTextPortionXDialog;
 
   tp->change_notify = change_notify;
   tp->change_userdata = change_userdata;
+  tp->inside = inside;
 
   g1 = HiddenGroup (p, 3, 0, NULL);
   SetGroupSpacing (g1, 10, 10);
@@ -9682,67 +10487,58 @@ extern DialoG TextPortionDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc
   if (inside) 
   {
     StaticPrompt (g1, "Between", 0, popupMenuHeight, programFont, 'r');
-    tp->start_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionGroup);
+    tp->start_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionXGroup);
     RadioButton (tp->start_choice, "just after");
     RadioButton (tp->start_choice, "starting at");
     SetValue (tp->start_choice, TEXT_PORTION_START_AFTER);
     SetObjectExtra (tp->start_choice, tp, NULL);
 
-    tp->start_text = DialogText (g1, "", 10, ChangeTextPortionText);
+    tp->start_text = DialogText (g1, "", 10, ChangeTextPortionXText);
     SetObjectExtra (tp->start_text, tp, NULL);
     
     StaticPrompt (g1, "And", 0, popupMenuHeight, programFont, 'r');
-    tp->end_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionGroup);
+    tp->end_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionXGroup);
     RadioButton (tp->end_choice, "up to");
     RadioButton (tp->end_choice, "including");
     SetValue (tp->end_choice, TEXT_PORTION_END_AFTER);
     SetObjectExtra (tp->start_choice, tp, NULL);
       
-    tp->end_text = DialogText (g1, "", 10, ChangeTextPortionText);
+    tp->end_text = DialogText (g1, "", 10, ChangeTextPortionXText);
     SetObjectExtra (tp->start_text, tp, NULL);
   }
   else
   {
-
-    StaticPrompt (g1, "On left:", 0, popupMenuHeight, programFont, 'r');
-    tp->start_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionGroup);
-    RadioButton (tp->start_choice, "including");
-    RadioButton (tp->start_choice, "up to");
-    SetValue (tp->start_choice, TEXT_PORTION_END_AFTER);
-    SetObjectExtra (tp->start_choice, tp, NULL);
-      
-    tp->start_text = DialogText (g1, "", 10, ChangeTextPortionText);
+    tp->rem_before = CheckBox (g1, "Before", ChangeTextPortionXBtn);
+    SetObjectExtra (tp->rem_before, tp, NULL);
+    tp->start_text = DialogText (g1, "", 10, ChangeTextPortionXText);
     SetObjectExtra (tp->start_text, tp, NULL);
+    tp->also_rem_before = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionXBtn);
 
-    StaticPrompt (g1, "On right:", 0, popupMenuHeight, programFont, 'r');
-    tp->end_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionGroup);
-    RadioButton (tp->end_choice, "starting at");
-    RadioButton (tp->end_choice, "just after");
-    SetValue (tp->end_choice, TEXT_PORTION_START_AFTER);
-    SetObjectExtra (tp->end_choice, tp, NULL);
-
-    tp->end_text = DialogText (g1, "", 10, ChangeTextPortionText);
+    tp->rem_after = CheckBox (g1, "After", ChangeTextPortionXBtn);
+    SetObjectExtra (tp->rem_after, tp, NULL);
+    tp->end_text = DialogText (g1, "", 10, ChangeTextPortionXText);
     SetObjectExtra (tp->end_text, tp, NULL);
+    tp->also_rem_after = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionXBtn);    
   }
   
   g2 = HiddenGroup (p, 2, 0, NULL);
-  tp->insensitive = CheckBox (g2, "Case insensitive", ChangeTextPortionBtn);
+  tp->insensitive = CheckBox (g2, "Case insensitive", ChangeTextPortionXBtn);
   SetObjectExtra (tp->insensitive, tp, NULL);
-  tp->whole_word = CheckBox (g2, "Whole word", ChangeTextPortionBtn);
+  tp->whole_word = CheckBox (g2, "Whole word", ChangeTextPortionXBtn);
   SetObjectExtra (tp->whole_word, tp, NULL);
   
   AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL);
   
-  ResetTextPortionDialog (tp);
+  ResetTextPortionXDialog (tp);
   return (DialoG) p;
 }
 
-extern DialoG TextPortionDialog (GrouP h)
+extern DialoG TextPortionXDialog (GrouP h)
 {
-  return TextPortionDialogEx (h, TRUE, NULL, NULL);
+  return TextPortionXDialogEx (h, TRUE, NULL, NULL);
 }
 
-extern TextPortionPtr TextPortionFree (TextPortionPtr tp)
+extern TextPortionXPtr TextPortionXFree (TextPortionXPtr tp)
 {
   if (tp == NULL) return NULL;
   tp->start_text = MemFree (tp->start_text);
@@ -9785,9 +10581,9 @@ static Boolean IsWholeWordMatch (CharPtr start, CharPtr found, Int4 match_len)
 }
 
 extern void 
-FindTextPortionInString 
+FindTextPortionXInString 
 (CharPtr        str, 
- TextPortionPtr tp, 
+ TextPortionXPtr tp, 
  CharPtr PNTR   ploc, 
  Int4Ptr        plen)
 {
@@ -9985,9 +10781,9 @@ typedef struct stringconstraintdialog
   TexT   match_text;
   ButtoN insensitive;
   ButtoN whole_word;   
-} StringConstraintDialogData, PNTR StringConstraintDialogPtr;
+} StringConstraintDialogXData, PNTR StringConstraintDialogXPtr;
 
-static void ResetStringConstraintDialog (StringConstraintDialogPtr scdp)
+static void ResetStringConstraintDialogX (StringConstraintDialogXPtr scdp)
 {
   if (scdp == NULL) return;
   
@@ -9998,7 +10794,7 @@ static void ResetStringConstraintDialog (StringConstraintDialogPtr scdp)
 }
 
 
-static Int4 GetPopupPosForStringConstraint (StringConstraintPtr scp)
+static Int4 GetPopupPosForStringConstraint (StringConstraintXPtr scp)
 {
   Int4 rval = 1;
 
@@ -10050,11 +10846,11 @@ static Int4 GetPopupPosForStringConstraint (StringConstraintPtr scp)
 static void StringConstraintToDialog (DialoG d, Pointer data)
 
 {
-  StringConstraintDialogPtr scdp;
-  StringConstraintPtr       scp;
+  StringConstraintDialogXPtr scdp;
+  StringConstraintXPtr       scp;
 
-  scdp = (StringConstraintDialogPtr) GetObjectExtra (d);
-  scp = (StringConstraintPtr) data;
+  scdp = (StringConstraintDialogXPtr) GetObjectExtra (d);
+  scp = (StringConstraintXPtr) data;
   if (scdp == NULL)
   {
     return;
@@ -10062,7 +10858,7 @@ static void StringConstraintToDialog (DialoG d, Pointer data)
 
   if (scp == NULL)
   {
-    ResetStringConstraintDialog (scdp);
+    ResetStringConstraintDialogX (scdp);
   }
   else
   {
@@ -10085,16 +10881,16 @@ static void StringConstraintToDialog (DialoG d, Pointer data)
 static Pointer DialogToStringConstraint (DialoG d)
 
 {
-  StringConstraintDialogPtr scdp;
-  StringConstraintPtr       scp;
+  StringConstraintDialogXPtr scdp;
+  StringConstraintXPtr       scp;
   Int4                      match_choice;
 
-  scdp = (StringConstraintDialogPtr) GetObjectExtra (d);
+  scdp = (StringConstraintDialogXPtr) GetObjectExtra (d);
   if (scdp == NULL)
   {
     return NULL;
   }
-  scp = (StringConstraintPtr) MemNew (sizeof (StringConstraintData));
+  scp = (StringConstraintXPtr) MemNew (sizeof (StringConstraintData));
   if (scp != NULL)
   {
     scp->match_text = SaveStringFromText (scdp->match_text);
@@ -10155,13 +10951,13 @@ static Pointer DialogToStringConstraint (DialoG d)
 static void StringConstraintMessage (DialoG d, Int2 mssg)
 
 {
-  StringConstraintDialogPtr scdp;
+  StringConstraintDialogXPtr scdp;
 
-  scdp = (StringConstraintDialogPtr) GetObjectExtra (d);
+  scdp = (StringConstraintDialogXPtr) GetObjectExtra (d);
   if (scdp != NULL) {
     switch (mssg) {
       case VIB_MSG_INIT :
-        ResetStringConstraintDialog (scdp);        
+        ResetStringConstraintDialogX (scdp);        
         break;
       case VIB_MSG_ENTER :
         Select (scdp->match_text);
@@ -10172,20 +10968,20 @@ static void StringConstraintMessage (DialoG d, Int2 mssg)
   }
 }
 
-static ValNodePtr TestStringConstraintDialog (DialoG d)
+static ValNodePtr TestStringConstraintDialogX (DialoG d)
 
 {
   return NULL;
 }
 
-extern DialoG StringConstraintDialog (GrouP h, CharPtr label, Boolean clear_btn)
+extern DialoG StringConstraintDialogX (GrouP h, CharPtr label, Boolean clear_btn)
 
 {
-  StringConstraintDialogPtr scdp;
+  StringConstraintDialogXPtr scdp;
   GrouP                     p, g, k;
   ButtoN                    b = NULL;
   
-  scdp = (StringConstraintDialogPtr) MemNew (sizeof (StringConstraintDialogData));
+  scdp = (StringConstraintDialogXPtr) MemNew (sizeof (StringConstraintDialogXData));
   if (scdp == NULL)
   {
     return NULL;
@@ -10198,7 +10994,7 @@ extern DialoG StringConstraintDialog (GrouP h, CharPtr label, Boolean clear_btn)
   scdp->todialog = StringConstraintToDialog;
   scdp->fromdialog = DialogToStringConstraint;
   scdp->dialogmessage = StringConstraintMessage;
-  scdp->testdialog = TestStringConstraintDialog;
+  scdp->testdialog = TestStringConstraintDialogX;
 
   g = HiddenGroup (p, 3, 0, NULL);
   SetGroupSpacing (g, 10, 10);
@@ -10622,7 +11418,7 @@ ConstraintChoiceDialog
   RadioButton (scdp->constraint_type, "When");
   q = HiddenGroup (scdp->constraint_type, 2, 0, NULL);
   scdp->string_qual_choice = func_string (q, TRUE, NULL, NULL);
-  scdp->string_constraint = StringConstraintDialog (q, NULL, FALSE);
+  scdp->string_constraint = StringConstraintDialogX (q, NULL, FALSE);
   
   RadioButton (scdp->constraint_type, "When");
   q = HiddenGroup (scdp->constraint_type, 3, 0, NULL);
@@ -10663,7 +11459,7 @@ ConstraintChoiceDialog
   return (DialoG) p;
 }
 
-extern DialoG SourceConstraintDialog (GrouP h, Boolean clear_btn)
+extern DialoG SourceConstraintDialogX (GrouP h, Boolean clear_btn)
 {
   return ConstraintChoiceDialog (h, SourceQualTypeConstraintSelectionDialog, 
                                  SourceStringConstraintSelectionDialog,
@@ -10695,7 +11491,7 @@ extern DialoG CDSGeneProtConstraintDialog (GrouP h, Boolean clear_btn)
                                  clear_btn, TRUE);
 }
 
-typedef struct locationconstraintdialog 
+typedef struct LocationConstraintXdialog 
 {
   DIALOG_MESSAGE_BLOCK
   PopuP  interval_end_choice;
@@ -10708,15 +11504,15 @@ typedef struct locationconstraintdialog
   PopuP  strand;
   PopuP  sequence_type;
   Boolean show_interval_controls;
-} LocationConstraintDialogData, PNTR LocationConstraintDialogPtr;
+} LocationConstraintXDialogData, PNTR LocationConstraintXDialogPtr;
 
 static void ShowLocationChoiceControls (PopuP p)
 
 {
-  LocationConstraintDialogPtr lcdp;
+  LocationConstraintXDialogPtr lcdp;
   Int4                        match_choice;
 
-  lcdp = (LocationConstraintDialogPtr) GetObjectExtra (p);
+  lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (p);
   if (lcdp == NULL || lcdp->interval_end_choice == NULL) return;
   
   if (GetValue (lcdp->interval_end_choice) == LOCATION_CONSTRAINT_WHOLE_INTERVAL)
@@ -10767,7 +11563,7 @@ static void ShowLocationChoiceControls (PopuP p)
   }
 }
 
-static void ResetLocationConstraintDialog (LocationConstraintDialogPtr lcdp)
+static void ResetLocationConstraintXDialog (LocationConstraintXDialogPtr lcdp)
 {
   if (lcdp == NULL) return;
   
@@ -10781,25 +11577,25 @@ static void ResetLocationConstraintDialog (LocationConstraintDialogPtr lcdp)
   ShowLocationChoiceControls (lcdp->interval_end_choice);
 }
 
-static void LocationConstraintToDialog (DialoG d, Pointer data)
+static void LocationConstraintXToDialog (DialoG d, Pointer data)
 
 {
-  LocationConstraintDialogPtr lcdp;
-  LocationConstraintPtr       lcp;
+  LocationConstraintXDialogPtr lcdp;
+  LocationConstraintXPtr       lcp;
   Int4                        interval_end_choice;
   Int4                        match_choice;
   Char                        tmp [15];
   Int4                        strand;
   Int4                        sequence_type;
 
-  lcdp = (LocationConstraintDialogPtr) GetObjectExtra (d);
+  lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (d);
   if (lcdp == NULL)
   {
     return;
   }
-  lcp = (LocationConstraintPtr) data;
+  lcp = (LocationConstraintXPtr) data;
   
-  ResetLocationConstraintDialog (lcdp);
+  ResetLocationConstraintXDialog (lcdp);
   if (lcp != NULL)
   {
     interval_end_choice = lcp->interval_end_choice;
@@ -10875,19 +11671,19 @@ static void LocationConstraintToDialog (DialoG d, Pointer data)
   ShowLocationChoiceControls (lcdp->interval_match_choice);
 }
 
-static Pointer DialogToLocationConstraint (DialoG d)
+static Pointer DialogToLocationConstraintX (DialoG d)
 
 {
-  LocationConstraintDialogPtr lcdp;
-  LocationConstraintPtr       lcp;
+  LocationConstraintXDialogPtr lcdp;
+  LocationConstraintXPtr       lcp;
   CharPtr                     tmp;
 
-  lcdp = (LocationConstraintDialogPtr) GetObjectExtra (d);
+  lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (d);
   if (lcdp == NULL)
   {
     return NULL;
   }
-  lcp = (LocationConstraintPtr) MemNew (sizeof (LocationConstraintData));
+  lcp = (LocationConstraintXPtr) MemNew (sizeof (LocationConstraintXData));
   if (lcp != NULL)
   {
     if (lcdp->show_interval_controls)
@@ -10957,16 +11753,16 @@ static Pointer DialogToLocationConstraint (DialoG d)
   return lcp;
 }
 
-static void LocationConstraintMessage (DialoG d, Int2 mssg)
+static void LocationConstraintXMessage (DialoG d, Int2 mssg)
 
 {
-  LocationConstraintDialogPtr lcdp;
+  LocationConstraintXDialogPtr lcdp;
 
-  lcdp = (LocationConstraintDialogPtr) GetObjectExtra (d);
+  lcdp = (LocationConstraintXDialogPtr) GetObjectExtra (d);
   if (lcdp != NULL) {
     switch (mssg) {
       case VIB_MSG_INIT :
-        ResetLocationConstraintDialog (lcdp);        
+        ResetLocationConstraintXDialog (lcdp);        
         break;
       case VIB_MSG_ENTER :
         if (lcdp->show_interval_controls)
@@ -10984,7 +11780,7 @@ static void LocationConstraintMessage (DialoG d, Int2 mssg)
   }
 }
 
-static ValNodePtr TestLocationConstraintDialog (DialoG d)
+static ValNodePtr TestLocationConstraintXDialog (DialoG d)
 
 {
   return NULL;
@@ -10992,17 +11788,17 @@ static ValNodePtr TestLocationConstraintDialog (DialoG d)
 
 
 extern DialoG 
-LocationConstraintDialog 
+LocationConstraintXDialog 
 (GrouP   h,
  Boolean show_interval_controls, 
  Boolean clear_btn)
 
 {
-  LocationConstraintDialogPtr lcdp;
+  LocationConstraintXDialogPtr lcdp;
   GrouP                       p, g, k, val_grp, strand_grp, g2, g3, g4;
   ButtoN                      b = NULL;
   
-  lcdp = (LocationConstraintDialogPtr) MemNew (sizeof (LocationConstraintDialogData));
+  lcdp = (LocationConstraintXDialogPtr) MemNew (sizeof (LocationConstraintXDialogData));
   if (lcdp == NULL)
   {
     return NULL;
@@ -11012,10 +11808,10 @@ LocationConstraintDialog
   SetObjectExtra (p, lcdp, StdCleanupExtraProc);
 
   lcdp->dialog = (DialoG) p;
-  lcdp->todialog = LocationConstraintToDialog;
-  lcdp->fromdialog = DialogToLocationConstraint;
-  lcdp->dialogmessage = LocationConstraintMessage;
-  lcdp->testdialog = TestLocationConstraintDialog;
+  lcdp->todialog = LocationConstraintXToDialog;
+  lcdp->fromdialog = DialogToLocationConstraintX;
+  lcdp->dialogmessage = LocationConstraintXMessage;
+  lcdp->testdialog = TestLocationConstraintXDialog;
   
   lcdp->show_interval_controls = show_interval_controls;
 
@@ -11097,7 +11893,7 @@ LocationConstraintDialog
   return (DialoG) p;
 }
 
-static Boolean DoesStrandMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
+static Boolean DoesStrandMatchConstraint (SeqLocPtr slp, LocationConstraintXPtr lcp)
 {
   Uint2 strand;
   Boolean rval = FALSE;
@@ -11139,7 +11935,7 @@ static Boolean DoesStrandMatchConstraint (SeqLocPtr slp, LocationConstraintPtr l
   return rval;
 }
 
-static Boolean DoesSequenceTypeMatchContraint (SeqLocPtr slp, LocationConstraintPtr lcp)
+static Boolean DoesSequenceTypeMatchContraint (SeqLocPtr slp, LocationConstraintXPtr lcp)
 {
   Boolean   rval = FALSE;
   BioseqPtr bsp;
@@ -11170,7 +11966,7 @@ static Boolean DoesSequenceTypeMatchContraint (SeqLocPtr slp, LocationConstraint
   return rval;
 }
 
-extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintPtr lcp)
+extern Boolean DoesLocationMatchConstraint (SeqLocPtr slp, LocationConstraintXPtr lcp)
 
 {
   Boolean rval = FALSE;
@@ -11543,17 +12339,17 @@ FilterGroup
     num_pages = 0;
     if (has_source_constraint)
     {
-      ffp->source_constraint = SourceConstraintDialog (k, FALSE);
+      ffp->source_constraint = SourceConstraintDialogX (k, FALSE);
       ffp->pages [num_pages++] = ffp->source_constraint;
     }
     if (has_string_constraint)
     {
-      ffp->string_constraint = StringConstraintDialog (k, string_constraint_label, FALSE);
+      ffp->string_constraint = StringConstraintDialogX (k, string_constraint_label, FALSE);
       ffp->pages [num_pages++] = ffp->string_constraint;
     }
     if (has_location_constraint)
     {
-      ffp->location_constraint = LocationConstraintDialog (k, FALSE, FALSE);
+      ffp->location_constraint = LocationConstraintXDialog (k, FALSE, FALSE);
       ffp->pages [num_pages++] = ffp->location_constraint;
     }
     if (has_cds_gene_prot_constraint)
@@ -11563,7 +12359,7 @@ FilterGroup
     }
     if (has_id_list_constraint)
     {
-      ffp->id_list_constraint = StringConstraintDialog (k, "Where sequence ID", FALSE);
+      ffp->id_list_constraint = StringConstraintDialogX (k, "Where sequence ID", FALSE);
       ffp->pages[num_pages++] = ffp->id_list_constraint;
     }
     for (i = 1; i < num_pages; i++)
@@ -11583,15 +12379,15 @@ FilterGroup
   {
     if (has_source_constraint)
     {
-      ffp->source_constraint = SourceConstraintDialog (g, TRUE);
+      ffp->source_constraint = SourceConstraintDialogX (g, TRUE);
     }
     else if (has_string_constraint)
     {
-      ffp->string_constraint = StringConstraintDialog (g, string_constraint_label, TRUE);
+      ffp->string_constraint = StringConstraintDialogX (g, string_constraint_label, TRUE);
     }
     else if (has_location_constraint)
     {
-      ffp->location_constraint = LocationConstraintDialog (g, FALSE, TRUE);
+      ffp->location_constraint = LocationConstraintXDialog (g, FALSE, TRUE);
     }
     else if (has_cds_gene_prot_constraint)
     {
@@ -11599,7 +12395,7 @@ FilterGroup
     }
     else if (has_id_list_constraint)
     {
-      ffp->id_list_constraint = StringConstraintDialog (g, "Where sequence ID", TRUE);
+      ffp->id_list_constraint = StringConstraintDialogX (g, "Where sequence ID", TRUE);
     }
   }
   return (DialoG) g;
@@ -11608,7 +12404,7 @@ FilterGroup
 /* Operations on constrained features and descriptors */
 typedef struct objecthasstring
 {
-  StringConstraintPtr scp;
+  StringConstraintXPtr scp;
   Boolean             found;
 } ObjectHasStringData, PNTR ObjectHasStringPtr;
 
@@ -11628,7 +12424,7 @@ typedef struct constraintop
   Uint1                  descriptorChoice;
 } ConstraintOpData, PNTR ConstraintOpPtr;
 
-extern Boolean DoesStringMatchConstraint (CharPtr pchSource, StringConstraintPtr scp)
+extern Boolean DoesStringMatchConstraintX (CharPtr pchSource, StringConstraintXPtr scp)
 {
   CharPtr pFound;
   Boolean rval = FALSE;
@@ -11783,6 +12579,10 @@ extern Boolean DoesStringMatchConstraint (CharPtr pchSource, StringConstraintPtr
           }
         }
       }
+      if (!rval) {
+        /* look for spans */
+        rval = IsStringInSpanInList (pchSource, scp->match_text);
+      }
       break;
 	}
 	return rval;
@@ -11798,7 +12598,7 @@ static void LIBCALLBACK AsnWriteConstraintCallBack (AsnExpOptStructPtr pAEOS)
   if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp))) 
   {
 	  pchSource = (CharPtr) pAEOS->dvp->ptrvalue;
-	  ohsp->found |= DoesStringMatchConstraint (pchSource, ohsp->scp);
+	  ohsp->found |= DoesStringMatchConstraintX (pchSource, ohsp->scp);
   }
 }
 
@@ -11829,14 +12629,14 @@ DoesObjectMatchStringConstraint
     }
 
     sfp = SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, sfp->idx.itemID, 0, sfp, &fcontext);
-    ohsp->found = DoesStringMatchConstraint (fcontext.label, ohsp->scp);
+    ohsp->found = DoesStringMatchConstraintX (fcontext.label, ohsp->scp);
     if (!ohsp->found && sfp != NULL && sfp->idx.subtype == FEATDEF_tRNA)
     {
       search_txt = (CharPtr) MemNew ((StringLen (fcontext.label) + 6) * sizeof (Char));
       if (search_txt != NULL)
       {
         sprintf (search_txt, "tRNA-%s", fcontext.label);
-        ohsp->found = DoesStringMatchConstraint (search_txt, ohsp->scp);
+        ohsp->found = DoesStringMatchConstraintX (search_txt, ohsp->scp);
         search_txt = MemFree (search_txt);
       }
     }
@@ -11844,7 +12644,7 @@ DoesObjectMatchStringConstraint
   return ohsp->found;
 }
 
-static Boolean DoesDbtagMatchStringConstraint (DbtagPtr db_tag, StringConstraintPtr scp)
+static Boolean DoesDbtagMatchStringConstraint (DbtagPtr db_tag, StringConstraintXPtr scp)
 {
   Boolean rval = FALSE;
   Char    tmp_str [15];
@@ -11857,20 +12657,20 @@ static Boolean DoesDbtagMatchStringConstraint (DbtagPtr db_tag, StringConstraint
   {
     rval = TRUE;
   }
-  else if (DoesStringMatchConstraint (db_tag->db, scp))
+  else if (DoesStringMatchConstraintX (db_tag->db, scp))
   {
     rval = TRUE;
   }
   else if (db_tag->tag != NULL)
   {
-    if (DoesStringMatchConstraint (db_tag->tag->str, scp))
+    if (DoesStringMatchConstraintX (db_tag->tag->str, scp))
     {
       rval = TRUE;
     }
     else if (db_tag->tag->str == NULL)
     {
       sprintf (tmp_str, "%d", db_tag->tag->id);
-      if (DoesStringMatchConstraint (tmp_str, scp))
+      if (DoesStringMatchConstraintX (tmp_str, scp))
       {
         rval = TRUE;
       }
@@ -12118,21 +12918,21 @@ DoesOneSourceMatchConstraint
     {
       if (biop->org != NULL)
       {
-        does_match = DoesStringMatchConstraint (biop->org->taxname, scp->string_constraint);
+        does_match = DoesStringMatchConstraintX (biop->org->taxname, scp->string_constraint);
         if (biop->org->orgname != NULL)
         {
           mod = biop->org->orgname->mod;
         }
         while (! does_match && mod != NULL)
         {
-          does_match = DoesStringMatchConstraint (mod->subname, scp->string_constraint);
+          does_match = DoesStringMatchConstraintX (mod->subname, scp->string_constraint);
           mod = mod->next;
         }
       }
       ssp = biop->subtype;
       while (!does_match && ssp != NULL)
       {
-        does_match = DoesStringMatchConstraint (ssp->name, scp->string_constraint);
+        does_match = DoesStringMatchConstraintX (ssp->name, scp->string_constraint);
         ssp = ssp->next;
       }
     }
@@ -12140,21 +12940,21 @@ DoesOneSourceMatchConstraint
     {
       if (biop->org != NULL)
       {
-        does_match = DoesStringMatchConstraint (biop->org->taxname, scp->string_constraint);
+        does_match = DoesStringMatchConstraintX (biop->org->taxname, scp->string_constraint);
       }
     }
     else if (scp->qual_choice->choice > 0 && StringICmp (scp->qual_choice->data.ptrvalue, "Lineage") == 0)
     {
       if (biop->org != NULL && biop->org->orgname != NULL)
       {
-        does_match = DoesStringMatchConstraint (biop->org->orgname->lineage,
+        does_match = DoesStringMatchConstraintX (biop->org->orgname->lineage,
                                                 scp->string_constraint);
       }
     }
     else if (scp->qual_choice->choice > 0 && StringICmp (scp->qual_choice->data.ptrvalue, "Location") == 0)
     {
       location = GetLocationFromSource (biop, NULL);
-      does_match = DoesStringMatchConstraint (location, scp->string_constraint);
+      does_match = DoesStringMatchConstraintX (location, scp->string_constraint);
       location = MemFree (location);
     }
     else
@@ -12170,7 +12970,7 @@ DoesOneSourceMatchConstraint
         {
           if (mod->subtype == sqdp->subtype)
           {
-            does_match = DoesStringMatchConstraint (mod->subname, scp->string_constraint);
+            does_match = DoesStringMatchConstraintX (mod->subname, scp->string_constraint);
           }
           mod = mod->next;
         }
@@ -12182,7 +12982,7 @@ DoesOneSourceMatchConstraint
         {
           if (ssp->subtype == sqdp->subtype)
           {
-            does_match = DoesStringMatchConstraint (ssp->name, scp->string_constraint);
+            does_match = DoesStringMatchConstraintX (ssp->name, scp->string_constraint);
           }
           ssp = ssp->next;
         }
@@ -12223,7 +13023,7 @@ static void SeqEntryConstrainedFeaturesCallback (SeqFeatPtr sfp, Pointer userdat
     if (cop->fsp->scp->not_present)
     {
       if (DoesObjectMatchStringConstraint (cop->omtp, cop->aip, (Pointer) sfp, &(cop->ohsd))
-          || DoesStringMatchConstraint (fcontext.label, cop->fsp->scp))
+          || DoesStringMatchConstraintX (fcontext.label, cop->fsp->scp))
       {
         feature_matches = FALSE; 
       }
@@ -12231,7 +13031,7 @@ static void SeqEntryConstrainedFeaturesCallback (SeqFeatPtr sfp, Pointer userdat
     else
     {
       if (! DoesObjectMatchStringConstraint (cop->omtp, cop->aip, (Pointer) sfp, &(cop->ohsd))
-          && ! DoesStringMatchConstraint (fcontext.label, cop->fsp->scp))
+          && ! DoesStringMatchConstraintX (fcontext.label, cop->fsp->scp))
       {
         feature_matches = FALSE;
       }
@@ -12267,6 +13067,13 @@ static void BioseqConstrainedFeaturesCallback (BioseqPtr bsp, Pointer userdata)
   if (omdp == NULL || omdp->datatype != OBJ_BIOSEQ) return;
 
   bspextra = (BioseqExtraPtr) omdp->extradata;
+  if (bspextra == NULL) {
+    SeqMgrIndexFeatures (bsp->idx.entityID, NULL);
+    omdp = SeqMgrGetOmdpForBioseq (bsp);
+    if (omdp == NULL || omdp->datatype != OBJ_BIOSEQ) return;
+
+    bspextra = (BioseqExtraPtr) omdp->extradata;
+  }
   if (bspextra == NULL) return;
 
   for (index = 0; index < bspextra->numfeats; index++)
@@ -12997,70 +13804,186 @@ extern ValNodePtr ApplyValueToValNodeStringList (ValNodePtr list, Int2 choice, A
   return list;
 }
 
+
+
+static void MakeSemicolonStringsIntoSeparateItems (ValNodePtr PNTR list)
+{
+  ValNodePtr prev = NULL, vnp_next, vnp, vnp_new;
+  CharPtr    cp;
+
+  if (list == NULL || *list == NULL) return;
+
+  vnp = *list;
+  while (vnp != NULL)
+  {
+    vnp_next = vnp->next;
+    if (StringHasNoText (vnp->data.ptrvalue))
+    {
+      if (prev == NULL)
+      {
+        *list = vnp_next;
+      }
+      else
+      {
+        prev->next = vnp_next;
+      }
+      vnp->next = NULL;
+      vnp = ValNodeFreeData (vnp);
+    }
+    else if ((cp = StringChr (vnp->data.ptrvalue, ';')) != NULL)
+    {
+      vnp_new = ValNodeNew (NULL);
+      vnp_new->choice = vnp->choice;
+      vnp_new->data.ptrvalue = StringSave (cp + 1);
+      vnp_new->next = vnp_next;
+      *cp = 0;
+      vnp->next = vnp_new;
+      vnp_next = vnp_new;
+      prev = vnp;
+    }
+    else
+    {
+      prev = vnp;
+    }
+    vnp = vnp_next;
+  }
+}
+
+
+extern ValNodePtr ApplyValueToValNodeStringListAsText (ValNodePtr list, Int2 choice, ApplyValuePtr avp)
+{
+  ValNodePtr vnp;
+  
+  if (avp == NULL)
+  {
+    return NULL;
+  }
+  
+  if (!StringHasNoText (avp->text_to_replace))
+  {
+    for (vnp = list; vnp != NULL; vnp = vnp->next)
+    {
+      vnp->data.ptrvalue = HandleApplyValue (vnp->data.ptrvalue, avp);
+    }
+  }
+  else
+  {
+    if (avp->etp == NULL
+        || avp->etp->existing_text_choice == eExistingTextChoiceReplaceOld)
+    {
+      list = ValNodeFree (list);
+      ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
+    }
+    else if (avp->etp->existing_text_choice == eExistingTextChoiceAppendSemi)
+    {
+      ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
+    }
+    else if (avp->etp->existing_text_choice == eExistingTextChoicePrefixSemi)
+    {
+      vnp = ValNodeNew(NULL);
+      vnp->choice = (Uint1) choice;
+      vnp->data.ptrvalue = StringSave (avp->new_text);
+      vnp->next = list;
+      list = vnp;
+    }
+    else if (avp->etp->existing_text_choice == eExistingTextChoiceLeaveOld)
+    {
+      if (list == NULL)
+      {
+        ValNodeAddPointer (&list, choice, StringSave (avp->new_text));
+      }
+    } else {
+      for (vnp = list; vnp != NULL; vnp = vnp->next)
+      {
+        vnp->data.ptrvalue = HandleApplyValue (vnp->data.ptrvalue, avp);
+      }
+    }
+  }
+
+  if (avp->etp == NULL || avp->etp->existing_text_choice != eExistingTextChoiceLeaveOld) 
+  {
+    MakeSemicolonStringsIntoSeparateItems (&list);
+  }
+  return list;
+}
+
+
 typedef struct parsefielddialog
 {
   DIALOG_MESSAGE_BLOCK
-  PopuP                    parse_field_type;
+  DialoG                   parse_field_type;
   DialoG                   biosrc_string_choice;
   DialoG                   source_qual_choice;
   DialoG                   gene_field;
-  DialoG                   mrna_field;
+  DialoG                   rna_subtype;
+  DialoG                   rna_field;
   DialoG                   protein_field;
   DialoG                   import_feature;
   DialoG                   import_qual;
   DialoG                   feature;
+  GrouP                    dbxref_grp;
+  TexT                     dbxref_db;
   GrouP                    feat_or_desc;
   Nlm_ChangeNotifyProc     change_notify;
   Pointer                  change_userdata;
   Boolean                  is_search_field;
 } ParseFieldDialogData, PNTR ParseFieldDialogPtr;
 
-static void ChangeParseFieldType (PopuP p)
+static void ChangeParseFieldType (Pointer data)
 {
   ParseFieldDialogPtr dlg;
-  Int4                parse_field_type;
+  ValNodePtr          vnp;
 
-  dlg = (ParseFieldDialogPtr) GetObjectExtra (p);
+  dlg = (ParseFieldDialogPtr) data;
   if (dlg == NULL)
   {
     return;
   }
-  parse_field_type = GetValue (dlg->parse_field_type);
+  vnp = DialogToPointer (dlg->parse_field_type);
   Hide (dlg->biosrc_string_choice);
   Hide (dlg->feat_or_desc);
   Hide (dlg->source_qual_choice);
   Hide (dlg->gene_field);
-  Hide (dlg->mrna_field);
+  Hide (dlg->rna_subtype);
+  Hide (dlg->rna_field);
   Hide (dlg->protein_field);
   Hide (dlg->import_feature);
   Hide (dlg->import_qual);
   Hide (dlg->feature);
-  switch (parse_field_type)
+  Hide (dlg->dbxref_grp);
+  if (vnp != NULL)
   {
-    case PARSE_FIELD_BIOSRC_STRING:
-      Show (dlg->biosrc_string_choice);
-      Show (dlg->feat_or_desc);
-      break;
-    case PARSE_FIELD_SOURCE_QUAL:
-      Show (dlg->source_qual_choice);
-      Show (dlg->feat_or_desc);
-      break;
-    case PARSE_FIELD_GENE_FIELD:
-      Show (dlg->gene_field);
-      break;
-    case PARSE_FIELD_MRNA_FIELD:
-      Show (dlg->mrna_field);
-      break;
-    case PARSE_FIELD_PROTEIN_FIELD:
-      Show (dlg->protein_field);
-      break;
-    case PARSE_FIELD_IMPORT_QUAL:
-      Show (dlg->import_feature);
-      Show (dlg->import_qual);
-      break;
-    case PARSE_FIELD_FEATURE_NOTE:
-      Show (dlg->feature);
-      break;
+    switch (vnp->choice)
+    {
+      case PARSE_FIELD_BIOSRC_STRING:
+        Show (dlg->biosrc_string_choice);
+        Show (dlg->feat_or_desc);
+        break;
+      case PARSE_FIELD_SOURCE_QUAL:
+        Show (dlg->source_qual_choice);
+        Show (dlg->feat_or_desc);
+        break;
+      case PARSE_FIELD_GENE_FIELD:
+        Show (dlg->gene_field);
+        break;
+      case PARSE_FIELD_RNA_FIELD:
+        Show (dlg->rna_subtype);
+        Show (dlg->rna_field);
+        break;
+      case PARSE_FIELD_PROTEIN_FIELD:
+        Show (dlg->protein_field);
+        break;
+      case PARSE_FIELD_IMPORT_QUAL:
+        Show (dlg->import_feature);
+        Show (dlg->import_qual);
+        break;
+      case PARSE_FIELD_FEATURE_NOTE:
+        Show (dlg->feature);
+        break;
+      case PARSE_FIELD_DBXREF:
+        Show (dlg->dbxref_grp);
+        break;
+    }
   }
   if (dlg->change_notify != NULL)
   {
@@ -13070,12 +13993,17 @@ static void ChangeParseFieldType (PopuP p)
 
 static void ResetParseFieldDialog (ParseFieldDialogPtr dlg)
 {
+  ValNode vn;
+
   if (dlg == NULL)
   {
     return;
   }
-  SetValue (dlg->parse_field_type, PARSE_FIELD_DEFLINE);
-  ChangeParseFieldType (dlg->parse_field_type);
+  vn.choice = PARSE_FIELD_DEFLINE;
+  vn.data.ptrvalue = NULL;
+  vn.next = NULL;
+  PointerToDialog (dlg->parse_field_type, &vn);
+  ChangeParseFieldType (dlg);
 }
 
 static void ParseFieldToDialog (DialoG d, Pointer data)
@@ -13083,6 +14011,7 @@ static void ParseFieldToDialog (DialoG d, Pointer data)
   ParseFieldDialogPtr dlg;
   ParseFieldPtr       parse_field;
   Int4                parse_field_type;
+  ValNode             vn;
 
   dlg = (ParseFieldDialogPtr) GetObjectExtra (d);
   if (dlg == NULL)
@@ -13100,7 +14029,10 @@ static void ParseFieldToDialog (DialoG d, Pointer data)
     {
       parse_field_type = PARSE_FIELD_DEFLINE;
     }
-    SetValue (dlg->parse_field_type, parse_field_type);
+    vn.choice = parse_field_type;
+    vn.data.ptrvalue = NULL;
+    vn.next = NULL;
+    PointerToDialog (dlg->parse_field_type, &vn);
     switch (parse_field_type)
     {
       case PARSE_FIELD_BIOSRC_STRING:
@@ -13124,12 +14056,55 @@ static void ParseFieldToDialog (DialoG d, Pointer data)
         break;
       case PARSE_FIELD_SOURCE_QUAL:
         PointerToDialog (dlg->source_qual_choice, parse_field->feature_field);
+        if (parse_field->do_desc && parse_field->do_feat)
+        {
+          SetValue (dlg->feat_or_desc, 1);
+        }
+        else if (parse_field->do_desc)
+        {
+          SetValue (dlg->feat_or_desc, 2);
+        }
+        else if (parse_field->do_feat)
+        {
+          SetValue (dlg->feat_or_desc, 3);
+        }
+        else
+        {
+          SetValue (dlg->feat_or_desc, 1);
+        }
+        break;
+      case PARSE_FIELD_DBXREF:
+        if (parse_field->feature_field == NULL || parse_field->feature_field->data.ptrvalue == NULL)
+        {
+          SetTitle (dlg->dbxref_db, "");
+        }
+        else
+        {
+          SetTitle (dlg->dbxref_db, parse_field->feature_field->data.ptrvalue);
+        }
+        if (parse_field->do_desc && parse_field->do_feat)
+        {
+          SetValue (dlg->feat_or_desc, 1);
+        }
+        else if (parse_field->do_desc)
+        {
+          SetValue (dlg->feat_or_desc, 2);
+        }
+        else if (parse_field->do_feat)
+        {
+          SetValue (dlg->feat_or_desc, 3);
+        }
+        else
+        {
+          SetValue (dlg->feat_or_desc, 1);
+        }
         break;
       case PARSE_FIELD_GENE_FIELD:
         PointerToDialog (dlg->gene_field, parse_field->feature_field);
         break;
-      case PARSE_FIELD_MRNA_FIELD:
-        PointerToDialog (dlg->mrna_field, parse_field->feature_field);
+      case PARSE_FIELD_RNA_FIELD:
+        PointerToDialog (dlg->rna_subtype, parse_field->feature_subtype);
+        PointerToDialog (dlg->rna_field, parse_field->feature_field);
         break;
       case PARSE_FIELD_PROTEIN_FIELD:
         PointerToDialog (dlg->protein_field, parse_field->feature_field);
@@ -13146,7 +14121,7 @@ static void ParseFieldToDialog (DialoG d, Pointer data)
         break;
     }
   }
-  ChangeParseFieldType (dlg->parse_field_type);
+  ChangeParseFieldType (dlg);
 }
 
 static Pointer DialogToParseField (DialoG d)
@@ -13154,16 +14129,23 @@ static Pointer DialogToParseField (DialoG d)
   ParseFieldDialogPtr dlg;
   ParseFieldPtr       parse_field;
   Int4                val;
+  ValNodePtr          vnp;
 
   dlg = (ParseFieldDialogPtr) GetObjectExtra (d);
   if (dlg == NULL)
   {
     return NULL;
   }
+  vnp = DialogToPointer (dlg->parse_field_type);
+  if (vnp == NULL)
+  {
+    return NULL;
+  }
+
   parse_field = (ParseFieldPtr) MemNew (sizeof (ParseFieldData));
   if (parse_field != NULL)
   {
-    parse_field->parse_field_type = GetValue (dlg->parse_field_type);
+    parse_field->parse_field_type = vnp->choice;
     parse_field->feature_field = NULL;
     switch (parse_field->parse_field_type)
     {
@@ -13207,11 +14189,35 @@ static Pointer DialogToParseField (DialoG d)
             break;
         }
         break;
+      case PARSE_FIELD_DBXREF:        
+        if (!TextHasNoText (dlg->dbxref_db))
+        {
+          ValNodeAddPointer (&(parse_field->feature_field), 0, SaveStringFromText (dlg->dbxref_db));
+        }
+        val = GetValue (dlg->feat_or_desc);
+        switch (val)
+        {
+          case 2:
+            parse_field->do_desc = TRUE;
+            parse_field->do_feat = FALSE;
+            break;
+          case 3:
+            parse_field->do_desc = FALSE;
+            parse_field->do_feat = TRUE;
+            break;
+          case 1:
+          default:
+            parse_field->do_desc = TRUE;
+            parse_field->do_feat = TRUE;
+            break;
+        }
+        break;
       case PARSE_FIELD_GENE_FIELD:
         parse_field->feature_field = DialogToPointer (dlg->gene_field);
         break;
-      case PARSE_FIELD_MRNA_FIELD:
-        parse_field->feature_field = DialogToPointer (dlg->mrna_field);
+      case PARSE_FIELD_RNA_FIELD:
+        parse_field->feature_subtype = DialogToPointer (dlg->rna_subtype);
+        parse_field->feature_field = DialogToPointer (dlg->rna_field);
         break;
       case PARSE_FIELD_PROTEIN_FIELD:
         parse_field->feature_field = DialogToPointer (dlg->protein_field);
@@ -13228,6 +14234,7 @@ static Pointer DialogToParseField (DialoG d)
         break;
     }
   }
+  vnp = ValNodeFreeData (vnp);
   return parse_field;
 }
 
@@ -13263,100 +14270,163 @@ static ValNodePtr TestParseFieldDialog (DialoG d)
   
   if (dlg != NULL)
   {
-    parse_field_type = GetValue (dlg->parse_field_type);
-    switch (parse_field_type)
+    vnp = DialogToPointer (dlg->parse_field_type);
+    if (vnp == NULL) 
     {
-      case PARSE_FIELD_DEFLINE:
-      case PARSE_FIELD_CDS_COMMENT:
-      case PARSE_FIELD_COMMENT_DESC:
-        /* don't need any extra information */
-        break;
-      case PARSE_FIELD_BIOSRC_STRING:
-        vnp = DialogToPointer (dlg->biosrc_string_choice);
-        if (vnp == NULL)
-        {
-          head = AddStringToValNodeChain (head, "biosrc string type", 1);
-        }
-        ValNodeFree (vnp);
-        break;
-      case PARSE_FIELD_SOURCE_QUAL:
-        vnp = DialogToPointer (dlg->source_qual_choice);
-        if (vnp == NULL)
-        {
-          head = AddStringToValNodeChain (head, "source qual type", 1);
-        }
-        ValNodeFree (vnp);
-        break;
-      case PARSE_FIELD_GENE_FIELD:
-        vnp = DialogToPointer (dlg->gene_field);
-        if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
-        {
-          head = AddStringToValNodeChain (head, "gene field", 1);
-        }
-        ValNodeFree (vnp);
-        break;
-      case PARSE_FIELD_MRNA_FIELD:
-        vnp = DialogToPointer (dlg->mrna_field);
-        if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
-        {
-          head = AddStringToValNodeChain (head, "mRNA field", 1);
-        }
-        ValNodeFree (vnp);
-        break;
-      case PARSE_FIELD_PROTEIN_FIELD:
-        vnp = DialogToPointer (dlg->protein_field);
-        if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
-        {
-          head = AddStringToValNodeChain (head, "protein field", 1);
-        }
-        ValNodeFree (vnp);
-        break;
-      case PARSE_FIELD_IMPORT_QUAL:
-        vnp = DialogToPointer (dlg->import_qual);
-        if (vnp == NULL)
-        {
-          ValNodeAddPointer (&head, 1, "import qualifier");
-        }
-        ValNodeFree (vnp);
-        vnp = DialogToPointer (dlg->import_feature);
-        if (vnp == NULL)
-        {
-          ValNodeAddPointer (&head, 1, "import feature");
-        }
-        ValNodeFree (vnp);
-        break;
-      case PARSE_FIELD_FEATURE_NOTE:
-        vnp = DialogToPointer (dlg->feature);
-        if (vnp == NULL)
-        {
-          ValNodeAddPointer (&head, 1, "feature");
+      head = AddStringToValNodeChain (head, "destination type", 1);
+    }
+    else
+    {
+      parse_field_type = vnp->choice;
+      vnp = ValNodeFreeData (vnp);
+      switch (parse_field_type)
+      {
+        case PARSE_FIELD_DEFLINE:
+        case PARSE_FIELD_CDS_COMMENT:
+        case PARSE_FIELD_COMMENT_DESC:
+          /* don't need any extra information */
+          break;
+        case PARSE_FIELD_BIOSRC_STRING:
+          vnp = DialogToPointer (dlg->biosrc_string_choice);
+          if (vnp == NULL)
+          {
+            head = AddStringToValNodeChain (head, "biosrc string type", 1);
+          }
           ValNodeFree (vnp);
-        }
-        break;
-      case SEARCH_FIELD_PUBLICATION:
-        if (!dlg->is_search_field) 
-        {
+          break;
+        case PARSE_FIELD_SOURCE_QUAL:
+          vnp = DialogToPointer (dlg->source_qual_choice);
+          if (vnp == NULL)
+          {
+            head = AddStringToValNodeChain (head, "source qual type", 1);
+          }
+          ValNodeFree (vnp);
+          break;
+        case PARSE_FIELD_GENE_FIELD:
+          vnp = DialogToPointer (dlg->gene_field);
+          if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
+          {
+            head = AddStringToValNodeChain (head, "gene field", 1);
+          }
+          ValNodeFree (vnp);
+          break;
+        case PARSE_FIELD_RNA_FIELD:
+          vnp = DialogToPointer (dlg->rna_subtype);
+          if (vnp == NULL)
+          {
+            head = AddStringToValNodeChain (head, "RNA subtype", 1);
+          }
+          ValNodeFree (vnp);
+          vnp = DialogToPointer (dlg->rna_field);
+          if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
+          {
+            head = AddStringToValNodeChain (head, "RNA field", 1);
+          }
+          ValNodeFree (vnp);          
+          break;
+        case PARSE_FIELD_PROTEIN_FIELD:
+          vnp = DialogToPointer (dlg->protein_field);
+          if (vnp == NULL || vnp->data.intvalue == FEATUREFIELD_NONE)
+          {
+            head = AddStringToValNodeChain (head, "protein field", 1);
+          }
+          ValNodeFree (vnp);
+          break;
+        case PARSE_FIELD_IMPORT_QUAL:
+          vnp = DialogToPointer (dlg->import_qual);
+          if (vnp == NULL)
+          {
+            ValNodeAddPointer (&head, 1, "import qualifier");
+          }
+          ValNodeFree (vnp);
+          vnp = DialogToPointer (dlg->import_feature);
+          if (vnp == NULL)
+          {
+            ValNodeAddPointer (&head, 1, "import feature");
+          }
+          ValNodeFree (vnp);
+          break;
+        case PARSE_FIELD_FEATURE_NOTE:
+          vnp = DialogToPointer (dlg->feature);
+          if (vnp == NULL)
+          {
+            ValNodeAddPointer (&head, 1, "feature");
+            ValNodeFree (vnp);
+          }
+          break;
+        case PARSE_FIELD_DBXREF:
+          if (TextHasNoText (dlg->dbxref_db))
+          {
+            ValNodeAddPointer (&head, 1, "specify database");
+          }
+          break;
+        case SEARCH_FIELD_PUBLICATION:
+          if (!dlg->is_search_field) 
+          {
+            head = AddStringToValNodeChain (head, "field type", 1);
+          }
+          break;
+        default:
           head = AddStringToValNodeChain (head, "field type", 1);
-        }
-        break;
-      default:
-        head = AddStringToValNodeChain (head, "field type", 1);
-        break;
+          break;
+      }
     }
   }      
 
   return head;
 }
 
+
+static ValNodePtr GetParseFieldDestList (Boolean include_pub, Boolean include_dbxref)
+{
+  ValNodePtr list = NULL;
+
+  ValNodeAddPointer (&list, PARSE_FIELD_DEFLINE, StringSave ("Definition Line"));
+  ValNodeAddPointer (&list, PARSE_FIELD_BIOSRC_STRING, StringSave ("Biosource"));
+  ValNodeAddPointer (&list, PARSE_FIELD_SOURCE_QUAL, StringSave ("Source Qualifier"));
+  ValNodeAddPointer (&list, PARSE_FIELD_GENE_FIELD, StringSave ("Gene Field"));
+  ValNodeAddPointer (&list, PARSE_FIELD_RNA_FIELD, StringSave ("RNA Field"));
+  ValNodeAddPointer (&list, PARSE_FIELD_CDS_COMMENT, StringSave ("CDS Comment"));
+  ValNodeAddPointer (&list, PARSE_FIELD_PROTEIN_FIELD, StringSave ("Protein Field"));
+  ValNodeAddPointer (&list, PARSE_FIELD_IMPORT_QUAL, StringSave ("Import Feature"));
+  ValNodeAddPointer (&list, PARSE_FIELD_FEATURE_NOTE, StringSave ("Feature Note"));
+  ValNodeAddPointer (&list, PARSE_FIELD_COMMENT_DESC, StringSave ("Comment Descriptor"));
+  if (include_dbxref)
+  {
+    ValNodeAddPointer (&list, PARSE_FIELD_DBXREF, StringSave ("Dbxref"));
+  }
+  if (include_pub)
+  {
+    ValNodeAddPointer (&list, SEARCH_FIELD_PUBLICATION, StringSave ("Publication"));
+  }
+  return list;  
+}
+
+
+static void ChangeParseFieldDestText (TexT t)
+{
+  ParseFieldDialogPtr dlg;
+
+  dlg = (ParseFieldDialogPtr) GetObjectExtra (t);
+  if (dlg != NULL && dlg->change_notify != NULL)
+  {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
 extern DialoG ParseFieldDestDialogEx 
 (GrouP                    h,
  Nlm_ChangeNotifyProc     change_notify,
  Pointer                  change_userdata,
- Boolean                  is_search_field)
+ Boolean                  is_search_field,
+ Boolean                  include_dbxref)
 {
   ParseFieldDialogPtr dlg;
   GrouP               p, m, g;
   GrouP               subgrp;
+  ValNodePtr          choice_list;
+  ValNode             vn;
   
   dlg = (ParseFieldDialogPtr) MemNew (sizeof (ParseFieldDialogData));
   if (dlg == NULL)
@@ -13377,22 +14447,12 @@ extern DialoG ParseFieldDestDialogEx
   dlg->is_search_field = is_search_field;
   
   m = HiddenGroup (p, 2, 0, NULL);
-  dlg->parse_field_type = PopupList (m, TRUE, ChangeParseFieldType);  
-  PopupItem (dlg->parse_field_type, "Definition Line");
-  PopupItem (dlg->parse_field_type, "Biosource");
-  PopupItem (dlg->parse_field_type, "Source Qualifier");
-  PopupItem (dlg->parse_field_type, "Gene Field");
-  PopupItem (dlg->parse_field_type, "mRNA Field");
-  PopupItem (dlg->parse_field_type, "CDS Comment");
-  PopupItem (dlg->parse_field_type, "Protein Field");
-  PopupItem (dlg->parse_field_type, "Import Feature");
-  PopupItem (dlg->parse_field_type, "Feature Note");
-  PopupItem (dlg->parse_field_type, "Comment Descriptor");
-  if (dlg->is_search_field) {
-    PopupItem (dlg->parse_field_type, "Publication");
-  }
-  SetValue (dlg->parse_field_type, PARSE_FIELD_DEFLINE);
-  SetObjectExtra (dlg->parse_field_type, dlg, NULL);
+
+  choice_list = GetParseFieldDestList (is_search_field, include_dbxref);
+  dlg->parse_field_type = ValNodeSelectionDialog (m, choice_list, TALL_SELECTION_LIST, ValNodeStringName,
+                                ValNodeSimpleDataFree, ValNodeStringCopy,
+                                ValNodeChoiceMatch, "parse destination", 
+                                ChangeParseFieldType, dlg, FALSE);
 
   subgrp = HiddenGroup (m, 0, 0, NULL);
   dlg->biosrc_string_choice = BioSourceStringDialog (subgrp, FALSE, change_notify, change_userdata);
@@ -13401,8 +14461,13 @@ extern DialoG ParseFieldDestDialogEx
   Hide (dlg->source_qual_choice);
   dlg->gene_field = GeneFieldSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
   Hide (dlg->gene_field);
-  dlg->mrna_field = MRNAFieldSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
-  Hide (dlg->mrna_field);
+  g = HiddenGroup (subgrp, 2, 0, NULL);
+  dlg->rna_subtype = RNASubtypeSelectionDialog (g, FALSE, NULL, change_notify, change_userdata);
+  Hide (dlg->rna_subtype);
+  dlg->rna_field = RNAFieldSelectionDialog (g, FALSE, 
+                                            change_notify, 
+                                            change_userdata);
+  Hide (dlg->rna_field);
   dlg->protein_field = ProteinFieldSelectionDialog (subgrp, FALSE, change_notify, change_userdata);
   Hide (dlg->protein_field);
   g = HiddenGroup (subgrp, 2, 0, NULL);
@@ -13412,6 +14477,23 @@ extern DialoG ParseFieldDestDialogEx
   Hide (dlg->import_qual);
   dlg->feature = FeatureSelectionDialog (subgrp, TRUE, change_notify, change_userdata);
   Hide (dlg->feature);
+  if (include_dbxref)
+  {
+    dlg->dbxref_grp = HiddenGroup (subgrp, 2, 0, NULL);
+    StaticPrompt (dlg->dbxref_grp, "Database:", 0, 0, programFont, 'r');
+    dlg->dbxref_db = DialogText (dlg->dbxref_grp, "", 5, ChangeParseFieldDestText);
+    SetObjectExtra (dlg->dbxref_db, dlg, NULL);
+    Hide (dlg->dbxref_grp);
+  }
+  else
+  {
+    dlg->dbxref_db = NULL;
+  }
+
+  vn.choice = PARSE_FIELD_DEFLINE;
+  vn.data.ptrvalue = NULL;
+  vn.next = NULL;
+  PointerToDialog (dlg->parse_field_type, &vn);
 
   dlg->feat_or_desc = HiddenGroup (p, 3, 0, NULL);
   RadioButton (dlg->feat_or_desc, "Descriptors and Features");
@@ -13430,7 +14512,7 @@ extern DialoG ParseFieldDestDialog
  Nlm_ChangeNotifyProc     change_notify,
  Pointer                  change_userdata)
 {
-  return ParseFieldDestDialogEx (h, change_notify, change_userdata, FALSE);
+  return ParseFieldDestDialogEx (h, change_notify, change_userdata, FALSE, FALSE);
 }
 /* Search Field dialog is identical to ParseFieldDestDialog except that it allows
  * an additional option, Publication.
@@ -13440,38 +14522,46 @@ extern DialoG SearchFieldDialog
  Nlm_ChangeNotifyProc     change_notify,
  Pointer                  change_userdata)
 {
-  return ParseFieldDestDialogEx (h, change_notify, change_userdata, TRUE);
+  return ParseFieldDestDialogEx (h, change_notify, change_userdata, TRUE, FALSE);
 }
 
 
-#define PARSE_FIELD_SRC_DEFLINE          1
-#define PARSE_FIELD_SRC_GENBANK_FLATFILE 2
-#define PARSE_FIELD_SRC_LOCAL_ID         3
-#define PARSE_FIELD_SRC_TAXNAME          4
-#define PARSE_FIELD_SRC_COMMENT          5
-#define PARSE_FIELD_BANKIT_COMMENT       6
-#define PARSE_FIELD_STRUCTURED_COMMENT   7
-#define PARSE_FIELD_SRC_TAXNAME_AFTER_NOMIAL 8
-#define MAX_PARSE_FIELD                  8
+typedef enum
+{
+ eParseFieldSrcDefLine = 1,
+ eParseFieldSrcGenBankFlatFile,
+ eParseFieldSrcLocalID,
+ eParseFieldSrcTaxName,
+ eParseFieldSrcSourceQual,
+ eParseFieldSrcComment,
+ eParseFieldSrcBankitComment,
+ eParseFieldSrcStructuredComment,
+ eParseFieldSrcTaxNameAfterNomial,
+ eParseFieldSrcFileID
+} EParseFieldSrc;
+
+const Int4 MAX_PARSE_FIELD = eParseFieldSrcFileID;
 
 static CharPtr parse_src_field_list [] = 
 {
-  "Definition Line", "GenBank Flatfile", "Local ID", "Organism Name", "Comment", "Bankit Comment", 
-  "Structured Comment", "Taxname after Binomial/Trinomial"
+  "Definition Line", "GenBank Flatfile", "Local ID", "Organism Name", "Source Qualifier", "Comment", "Bankit Comment", 
+  "Structured Comment", "Taxname after Binomial/Trinomial", "File ID"
 };
 
 static int num_parse_src_fields = sizeof (parse_src_field_list) / sizeof (CharPtr);
 
 typedef struct parsefieldsrc 
 {
-  Int4    parse_field;
-  CharPtr comment_field;
+  Int4              parse_field;
+  SourceQualDescPtr sqdp;
+  CharPtr           comment_field;
 } ParseFieldSrcData, PNTR ParseFieldSrcPtr;
 
 static ParseFieldSrcPtr ParseFieldSrcFree (ParseFieldSrcPtr pfsp)
 {
   if (pfsp != NULL) {
     pfsp->comment_field = MemFree (pfsp->comment_field);
+    pfsp->sqdp = MemFree (pfsp->sqdp);
     pfsp = MemFree (pfsp);
   }
   return pfsp;
@@ -13483,6 +14573,7 @@ typedef struct parsefieldsrcdlg
   DialoG     parse_field;
   PopuP      comment_field;
   ValNodePtr comment_field_list;
+  DialoG     src_qual;
   Nlm_ChangeNotifyProc     change_notify;
   Pointer                  change_userdata;      
 } ParseFieldSrcDlgData, PNTR ParseFieldSrcDlgPtr;
@@ -13535,11 +14626,16 @@ static void ParseFieldChange (Pointer userdata)
   if (dlg == NULL) return;
    
   vnp = DialogToPointer (dlg->parse_field);
-  if (vnp == NULL || vnp->data.intvalue != PARSE_FIELD_STRUCTURED_COMMENT) {
+  if (vnp == NULL || vnp->data.intvalue != eParseFieldSrcStructuredComment) {
     Hide (dlg->comment_field);
   } else {
     Show (dlg->comment_field);
   }
+  if (vnp == NULL || vnp->data.intvalue != eParseFieldSrcSourceQual) {
+    Hide (dlg->src_qual);
+  } else {
+    Show (dlg->src_qual);
+  }
   
   if (dlg->change_notify != NULL) {
     (dlg->change_notify)(dlg->change_userdata);
@@ -13583,6 +14679,8 @@ static void DataToParseFieldSrcDialog(DialoG d, Pointer data)
       vn.choice = 0;
       PointerToDialog (dlg->parse_field, &vn);
       SetValue (dlg->comment_field, FindCommentFieldPosition (pfsp->comment_field, dlg->comment_field_list));
+      vn.data.ptrvalue = pfsp->sqdp;
+      PointerToDialog (dlg->src_qual, &vn);
     }
   }
   ParseFieldChange (dlg);     
@@ -13607,7 +14705,8 @@ static Pointer ParseFieldSrcDialogToData(DialoG d)
     vnp = ValNodeFree (vnp);
   }
   pfsp->comment_field = NULL;
-  if (pfsp->parse_field == PARSE_FIELD_STRUCTURED_COMMENT) {
+  pfsp->sqdp = NULL;
+  if (pfsp->parse_field == eParseFieldSrcStructuredComment) {
     field_pos = GetValue (dlg->comment_field);
     if (field_pos > 0) {
       vnp = dlg->comment_field_list;
@@ -13620,7 +14719,15 @@ static Pointer ParseFieldSrcDialogToData(DialoG d)
         pfsp->comment_field = StringSave (vnp->data.ptrvalue);
       }
     }
+  } else if (pfsp->parse_field == eParseFieldSrcSourceQual) {
+    vnp = DialogToPointer (dlg->src_qual);
+    if (vnp != NULL) {
+      pfsp->sqdp = vnp->data.ptrvalue;
+      vnp->data.ptrvalue = NULL;
+      vnp = ValNodeFreeData (vnp);
+    }
   }
+  
   return pfsp;
 }
 
@@ -13665,6 +14772,36 @@ static void AddCommentFieldName (SeqDescrPtr sdp, Pointer userdata)
   }
 }
 
+
+static ValNodePtr TestParseFieldSource (DialoG d)
+
+{
+  ParseFieldSrcDlgPtr dlg;
+  ValNodePtr          head = NULL, vnp, vnp2;
+
+  dlg = (ParseFieldSrcDlgPtr) GetObjectExtra (d);
+  
+  vnp = DialogToPointer (dlg->parse_field);
+  if (vnp == NULL)
+  {
+    head = AddStringToValNodeChain (head, "field choice", 1);
+  }
+  else if (vnp->data.intvalue == eParseFieldSrcSourceQual)
+  {
+    vnp2 = DialogToPointer (dlg->src_qual);
+    if (vnp2 == NULL)
+    {
+      head = AddStringToValNodeChain (head, "source qual", 1);
+    }
+    vnp2 = ValNodeFree (vnp2);
+  }
+
+  vnp = ValNodeFree (vnp);
+  
+  return head;  
+}
+
+
 extern DialoG ParseFieldSourceDialog
 (GrouP                    h,
  SeqEntryPtr              sep,
@@ -13672,7 +14809,7 @@ extern DialoG ParseFieldSourceDialog
  Pointer                  change_userdata)
 {
   ParseFieldSrcDlgPtr dlg;
-  GrouP               p;
+  GrouP               p, k;
   ValNodePtr          vnp;
   
   dlg = (ParseFieldSrcDlgPtr) MemNew (sizeof (ParseFieldSrcDlgData));
@@ -13689,7 +14826,7 @@ extern DialoG ParseFieldSourceDialog
   dlg->todialog = DataToParseFieldSrcDialog;
   dlg->fromdialog = ParseFieldSrcDialogToData;
   dlg->dialogmessage = ParseFieldSourceDialogMessage;
-  dlg->testdialog = NULL;
+  dlg->testdialog = TestParseFieldSource;
   dlg->change_notify = change_notify;
   dlg->change_userdata = change_userdata;
 
@@ -13697,7 +14834,11 @@ extern DialoG ParseFieldSourceDialog
                                                   num_parse_src_fields, parse_src_field_list, 
                                                   ParseFieldChange, dlg);
 
-  dlg->comment_field = PopupList (p, TRUE, NULL);
+  k = HiddenGroup (p, 0, 0, NULL);
+  dlg->comment_field = PopupList (k, TRUE, NULL);
+  dlg->src_qual = SourceQualTypeSelectionDialogEx (k, FALSE, change_notify,
+                                                   change_userdata, 6, FALSE, FALSE);
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->comment_field, (HANDLE) dlg->src_qual, NULL);
   
   /* Add to comment_field list all user fields found in SeqEntry sep */
   VisitDescriptorsInSep (sep, &(dlg->comment_field_list), AddCommentFieldName);
@@ -14782,7 +15923,7 @@ extern DialoG FeatureFieldChoiceDialog
 
 typedef struct parseaction
 {
-  TextPortionPtr tp;
+  TextPortionXPtr tp;
   FilterSetPtr   fsp;
   Int4           src_field;
   CharPtr        comment_field;
@@ -14822,238 +15963,6 @@ static void ResetParseActionVisitData (ParseActionPtr pap)
   }
 }
 
-static void DoParseAction (CharPtr src_str, ParseActionOpPtr paop)
-{
-  CharPtr          found_loc = NULL;
-  Int4             found_len = 0;
-
-  if (StringHasNoText (src_str) || paop == NULL 
-      || paop->parse_action_data == NULL
-      || paop->parse_action == NULL)
-  {
-    return;
-  }
-  
-  FindTextPortionInString (src_str, paop->parse_action_data->tp, &found_loc, &found_len);
-  
-  if (found_loc != NULL)
-  {
-    (paop->parse_action) (paop->parse_action_data, paop->parse_userdata, found_loc, found_len);
-    paop->parse_complete = TRUE;
-  }
-  
-}
-
-static void ParseActionDeflineText (SeqDescrPtr sdp, Pointer userdata)
-{
-  ParseActionOpPtr paop;
-  CharPtr          tmp_string;
-  Int4             last_pos;
-  
-  paop = (ParseActionOpPtr) userdata;
-  if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL
-      || sdp == NULL || sdp->choice != Seq_descr_title)
-  {
-    return;
-  }
-  
-  tmp_string = StringSave (sdp->data.ptrvalue);
-  if (tmp_string != NULL)
-  {
-    last_pos = StringLen (tmp_string) - 1;
-    if (tmp_string [last_pos] == '.')
-    {
-      tmp_string [last_pos] = 0;
-    }
-  }
-  DoParseAction (tmp_string, paop);
-  tmp_string = MemFree (tmp_string);
-}
-
-static void ParseActionTaxnameText (BioSourcePtr biop, Pointer userdata)
-{
-  ParseActionOpPtr paop;
-  
-  paop = (ParseActionOpPtr) userdata;
-  if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL
-      || biop == NULL || biop->org == NULL)
-  {
-    return;
-  }
-  
-  if (paop->parse_action_data->fsp != NULL
-      && ! DoesOneSourceMatchConstraint (biop, paop->parse_action_data->fsp->ccp))
-  {
-    return;
-  }
-  
-  DoParseAction (biop->org->taxname, paop);
-}
-
-static void ParseActionLocalIDText (BioseqPtr bsp, Pointer userdata)
-{
-  ParseActionOpPtr paop;
-  SeqIdPtr         sip;
-  ObjectIdPtr      oip;
-  Char             tmp_str [128];
-  
-  paop = (ParseActionOpPtr) userdata;
-  if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL
-      || bsp == NULL || ISA_aa (bsp->mol))
-  {
-    return;
-  }
-  
-  for (sip = bsp->id; sip != NULL; sip = sip->next)
-  {
-    if (sip->choice == SEQID_LOCAL && sip->data.ptrvalue != NULL)
-    {
-      oip = (ObjectIdPtr) sip->data.ptrvalue;
-      if (oip->str == NULL)
-      {
-        sprintf (tmp_str, "%d", oip->id);
-        DoParseAction (tmp_str, paop);
-      }
-      else
-      {
-        DoParseAction (oip->str, paop);
-      }
-    }
-  }
-}
-
-static void ParseActionBankitComment (SeqDescrPtr sdp, Pointer userdata)
-{
-  ParseActionOpPtr paop;
-  UserObjectPtr    uop;
-  ObjectIdPtr      oip;
-  UserFieldPtr     ufp;
-  
-  if (sdp == NULL || userdata == NULL || sdp->data.ptrvalue == NULL)
-  {
-    return;
-  }
-  
-  paop = (ParseActionOpPtr) userdata;
-  if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL)
-  {
-    return;
-  }
-
-  if (sdp->choice == Seq_descr_user && sdp->extended != 0)
-  {
-    /* Bankit Comments */
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    oip = uop->type;
-    if (oip != NULL && StringCmp (oip->str, "Submission") == 0)
-    {
-      for (ufp = uop->data; ufp != NULL; ufp = ufp->next)
-      {
-        oip = ufp->label;
-        if (oip != NULL && StringCmp (oip->str, "AdditionalComment") == 0)
-        {
-          DoParseAction (ufp->data.ptrvalue, paop);
-        }
-      }
-    }
-  }
-}
-
-static void ParseActionCommentDescriptor (SeqDescrPtr sdp, Pointer userdata)
-{
-  ParseActionOpPtr paop;
-  UserObjectPtr    uop;
-  ObjectIdPtr      oip;
-  UserFieldPtr     ufp;
-  
-  if (sdp == NULL || userdata == NULL || sdp->data.ptrvalue == NULL)
-  {
-    return;
-  }
-  
-  paop = (ParseActionOpPtr) userdata;
-  if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL)
-  {
-    return;
-  }
-
-  if (sdp->choice == Seq_descr_comment)
-  {
-    DoParseAction (sdp->data.ptrvalue, paop);
-  }
-  else if (sdp->choice == Seq_descr_user && sdp->extended != 0)
-  {
-    /* Bankit Comments */
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    oip = uop->type;
-    if (oip != NULL && StringCmp (oip->str, "Submission") == 0)
-    {
-      for (ufp = uop->data; ufp != NULL; ufp = ufp->next)
-      {
-        oip = ufp->label;
-        if (oip != NULL && StringCmp (oip->str, "AdditionalComment") == 0)
-        {
-          DoParseAction (ufp->data.ptrvalue, paop);
-        }
-      }
-    }
-  }
-}
-
-static void ParseActionCommentFeature (SeqFeatPtr sfp, Pointer userdata)
-{
-  ParseActionOpPtr paop;
-
-  if (sfp == NULL || sfp->data.choice != SEQFEAT_COMMENT || userdata == NULL)
-  {
-    return;
-  }
-  paop = (ParseActionOpPtr) userdata;
-  DoParseAction (sfp->comment, paop);
-}
-
-
-static void ParseActionStructuredComment(SeqDescrPtr sdp, Pointer userdata)
-{
-  ParseActionOpPtr paop;
-  UserObjectPtr    uop;
-  ObjectIdPtr      oip;
-  UserFieldPtr     ufp;
-  
-  if (sdp == NULL || userdata == NULL || sdp->data.ptrvalue == NULL)
-  {
-    return;
-  }
-  
-  paop = (ParseActionOpPtr) userdata;
-  if (paop == NULL || paop->parse_action_data == NULL || paop->parse_action == NULL)
-  {
-    return;
-  }
-
-  if (sdp->choice == Seq_descr_comment)
-  {
-    DoParseAction (sdp->data.ptrvalue, paop);
-  }
-  else if (sdp->choice == Seq_descr_user && sdp->extended != 0)
-  {
-    /* Bankit Comments */
-    uop = (UserObjectPtr) sdp->data.ptrvalue;
-    oip = uop->type;
-    if (oip != NULL && StringCmp (oip->str, "Submission") == 0)
-    {
-      for (ufp = uop->data; ufp != NULL; ufp = ufp->next)
-      {
-        oip = ufp->label;
-        if (oip != NULL && StringCmp (oip->str, "AdditionalComment") == 0)
-        {
-          DoParseAction (ufp->data.ptrvalue, paop);
-        }
-      }
-    }
-  }
-}
-
 static void SetSourceAndTitle (ParseActionPtr pap, SeqDescrPtr sdp, SeqAnnotPtr sap)
 {
   SeqFeatPtr sfp;
@@ -15104,19 +16013,6 @@ static void SetSourceAndTitle (ParseActionPtr pap, SeqDescrPtr sdp, SeqAnnotPtr
   }
 }
 
-static void ParseFromSource (BioSourcePtr biop, ParseActionPtr pap, ParseActionOpPtr paop)
-{
-  if (biop == NULL || pap == NULL || paop == NULL)
-  {
-    return;
-  }
-
-  if (pap->src_field == PARSE_FIELD_SRC_TAXNAME)
-  {
-    ParseActionTaxnameText (biop, paop);
-  }
-}
-
 typedef struct parsesourceinfo 
 {
   BioseqPtr   bsp;
@@ -15189,11 +16085,12 @@ static ValNodePtr ParseSourceListFree (ValNodePtr vnp)
 typedef struct parsesource
 {
   Int4           src_field;
+  SourceQualDescPtr sqdp;
   CharPtr        comment_field;
   FilterSetPtr   fsp;
   ParseFieldPtr  dst_field_data;
   ValNodePtr     source_list; /* ptrvalue points to ParseSourceInfo struct */
-  TextPortionPtr tp;
+  TextPortionXPtr tp;
 } ParseSourceData, PNTR ParseSourcePtr;
 
 
@@ -15201,7 +16098,7 @@ static void
 GetDeflineSourcesForBioseq 
 (BioseqPtr       bsp,
  FilterSetPtr    fsp, 
- TextPortionPtr  tp,
+ TextPortionXPtr  tp,
  ValNodePtr PNTR source_list)
 {
   SeqDescrPtr        sdp;
@@ -15220,9 +16117,9 @@ GetDeflineSourcesForBioseq
   {
     if (fsp == NULL
         || fsp->ccp == NULL
-        || DoesStringMatchConstraint (sdp->data.ptrvalue, fsp->ccp->string_constraint))
+        || DoesStringMatchConstraintX (sdp->data.ptrvalue, fsp->ccp->string_constraint))
     {
-      FindTextPortionInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
+      FindTextPortionXInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
       if (found_loc != NULL)
       {
         parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
@@ -15250,19 +16147,74 @@ GetDeflineSourcesForBioseq
   }
 }
 
+
+static CharPtr GetIDSrc (SeqIdPtr sip, Uint1 id_type, CharPtr tag, FilterSetPtr fsp)
+{
+  DbtagPtr    dbt = NULL;
+  ObjectIdPtr oip = NULL;
+  Char        id_str[128];
+  CharPtr     str_src = NULL;
+
+  if (sip == NULL || sip->choice != id_type) return NULL;
+
+  if (id_type == SEQID_GENERAL)
+  {
+    dbt = (DbtagPtr) sip->data.ptrvalue;
+    if (dbt == NULL || (tag != NULL && StringCmp (dbt->db, tag) != 0)) return NULL;
+    oip = dbt->tag;
+  }
+  else if (id_type == SEQID_LOCAL)
+  {
+    oip = sip->data.ptrvalue;
+  }
+
+  id_str[0] = 0;
+  if (fsp != NULL && fsp->ccp != NULL)
+  {
+    SeqIdWrite (sip, id_str, PRINTID_REPORT, sizeof (id_str));
+    if (!DoesStringMatchConstraintX (id_str, fsp->ccp->string_constraint))
+    {
+      return NULL;
+    }
+  }
+
+  if (oip == NULL)
+  {
+    if (id_str[0] == 0)
+    {
+      SeqIdWrite (sip, id_str, PRINTID_REPORT, sizeof (id_str));
+    }
+    str_src = StringSave (id_str);
+  }
+  else
+  {
+    if (oip->str == NULL)
+    {
+      sprintf (id_str, "%d", oip->id);
+      str_src = StringSave (id_str);
+    }
+    else
+    {
+      str_src = StringSave (oip->str);
+    }
+  }
+  return str_src;
+}
+
+
 static void
-GetLocalIDSourcesForBioseq
+GetIDSourcesForBioseq
 (BioseqPtr       bsp,
  FilterSetPtr    fsp, 
- TextPortionPtr  tp,
+ TextPortionXPtr  tp,
+ Uint1           id_type,
+ CharPtr         tag,
  ValNodePtr PNTR source_list)
 {
   SeqIdPtr           sip;
   ParseSourceInfoPtr psip;
-  Char               id_str [128];
   CharPtr            src_str, found_loc = NULL, parse_src_txt;
   Int4               found_len;
-  ObjectIdPtr        oip;
   
   if (bsp == NULL || source_list == NULL)
   {
@@ -15272,53 +16224,59 @@ GetLocalIDSourcesForBioseq
   sip = bsp->id;
   while (sip != NULL)
   {
-    if (sip->choice == SEQID_LOCAL)
-    {
-      SeqIdWrite (sip, id_str, PRINTID_REPORT, sizeof (id_str));
-      if (fsp == NULL
-          || fsp->ccp == NULL
-          || DoesStringMatchConstraint (id_str, fsp->ccp->string_constraint))
+    if ((src_str = GetIDSrc (sip, id_type, tag, fsp)) != NULL)
+    {          
+      FindTextPortionXInString (src_str, tp, &found_loc, &found_len);
+      if (found_loc != NULL)
       {
-        oip = (ObjectIdPtr) sip->data.ptrvalue;
-        if (oip->str == NULL)
+        parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
+        StringNCpy (parse_src_txt, found_loc, found_len);
+        parse_src_txt [found_len] = 0;
+        psip = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
+        if (psip != NULL)
         {
-          sprintf (id_str, "%d", oip->id);
-          src_str = id_str;
+          psip->bsp = bsp;
+          psip->sdp = NULL;
+          psip->sfp = NULL;
+          psip->sip = sip;
+          psip->dest_list = NULL;
+          psip->parse_src_txt = parse_src_txt;
+          ValNodeAddPointer (source_list, 0, psip);
         }
         else
         {
-          src_str = oip->str;
-        }
-        FindTextPortionInString (src_str, tp, &found_loc, &found_len);
-        if (found_loc != NULL)
-        {
-          parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
-          StringNCpy (parse_src_txt, found_loc, found_len);
-          parse_src_txt [found_len] = 0;
-          psip = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
-          if (psip != NULL)
-          {
-            psip->bsp = bsp;
-            psip->sdp = NULL;
-            psip->sfp = NULL;
-            psip->sip = sip;
-            psip->dest_list = NULL;
-            psip->parse_src_txt = parse_src_txt;
-            ValNodeAddPointer (source_list, 0, psip);
-          }
-          else
-          {
-            parse_src_txt = MemFree (parse_src_txt);
-          }
+          parse_src_txt = MemFree (parse_src_txt);
         }
       }
+      src_str = MemFree (src_str);
     }
     sip = sip->next;
   }
 }
 
 
-const CharPtr nomial_keywords[] = {
+static void
+GetLocalIDSourcesForBioseq
+(BioseqPtr       bsp,
+ FilterSetPtr    fsp, 
+ TextPortionXPtr  tp,
+ ValNodePtr PNTR source_list)
+{
+  GetIDSourcesForBioseq (bsp, fsp, tp, SEQID_LOCAL, NULL, source_list);
+}
+
+
+static void GetNcbiFileSourceForBioseq
+(BioseqPtr       bsp,
+ FilterSetPtr    fsp, 
+ TextPortionXPtr  tp,
+ ValNodePtr PNTR source_list)
+{
+  GetIDSourcesForBioseq (bsp, fsp, tp, SEQID_GENERAL, "NCBIFILE", source_list);
+}
+
+
+const CharPtr nomial_keywordsx[] = {
 "f. sp. ",
 "var.",
 "pv.",
@@ -15326,7 +16284,7 @@ const CharPtr nomial_keywords[] = {
 "serovar",
 "subsp." };
 
-const Int4 num_nomial_keywords = sizeof(nomial_keywords) / sizeof (CharPtr);
+const Int4 num_nomial_keywordsx = sizeof(nomial_keywordsx) / sizeof (CharPtr);
 
 static CharPtr GetTextAfterNomial (CharPtr taxname)
 
@@ -15357,20 +16315,27 @@ static CharPtr GetTextAfterNomial (CharPtr taxname)
   while (found_keyword) {
     found_keyword = FALSE;
     /* if the next word is a nomial keyword, skip that plus the first word that follows it. */
-    for (i = 0; i < num_nomial_keywords; i++) {
-      if (StringNCmp (ptr, nomial_keywords[i], StringLen(nomial_keywords[i])) == 0)
+    for (i = 0; i < num_nomial_keywordsx && *nomial_end != 0; i++) {
+      if (StringNCmp (ptr, nomial_keywordsx[i], StringLen(nomial_keywordsx[i])) == 0)
       {
-        ptr += StringLen(nomial_keywords[i]);
+        ptr += StringLen(nomial_keywordsx[i]);
         while (*ptr == ' ' )
         {
           ptr++;
         }
         nomial_end = StringChr (ptr, ' ');
-        ptr = nomial_end;
-        while (*ptr == ' ') {
-          ptr++;
+        if (nomial_end == NULL)
+        {
+          nomial_end = ptr + StringLen (ptr);
+        }
+        else 
+        {          
+          ptr = nomial_end;
+          while (*ptr == ' ') {
+            ptr++;
+          }
+          found_keyword = TRUE;
         }
-        found_keyword = TRUE;
       }
     }
   }
@@ -15381,7 +16346,7 @@ static void
 GetTaxNameSourcesForBioseqEx
 (BioseqPtr       bsp,
  FilterSetPtr    fsp, 
- TextPortionPtr  tp,
+ TextPortionXPtr  tp,
  ValNodePtr PNTR source_list,
  Boolean         skip_nomial)
 {
@@ -15411,9 +16376,9 @@ GetTaxNameSourcesForBioseqEx
     {
       if (skip_nomial) {
         nomial = GetTextAfterNomial(biop->org->taxname);
-        FindTextPortionInString (nomial, tp, &found_loc, &found_len);
+        FindTextPortionXInString (nomial, tp, &found_loc, &found_len);
       } else {
-        FindTextPortionInString (biop->org->taxname, tp, &found_loc, &found_len);
+        FindTextPortionXInString (biop->org->taxname, tp, &found_loc, &found_len);
       }
       if (found_loc != NULL)
       {
@@ -15450,7 +16415,7 @@ GetTaxNameSourcesForBioseqEx
         || fsp->ccp == NULL
         || DoesOneSourceMatchConstraint (sfp->data.value.ptrvalue, fsp->ccp)))
     {
-      FindTextPortionInString (biop->org->taxname, tp, &found_loc, &found_len);
+      FindTextPortionXInString (biop->org->taxname, tp, &found_loc, &found_len);
       if (found_loc != NULL)
       {
         parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
@@ -15483,7 +16448,7 @@ static void
 GetTaxNameSourcesForBioseq 
 (BioseqPtr       bsp,
  FilterSetPtr    fsp, 
- TextPortionPtr  tp,
+ TextPortionXPtr  tp,
  ValNodePtr PNTR source_list)
 {
   GetTaxNameSourcesForBioseqEx (bsp, fsp, tp, source_list, FALSE);
@@ -15494,18 +16459,126 @@ static void
 GetTaxNameAfterNomialSourcesForBioseq
 (BioseqPtr       bsp,
  FilterSetPtr    fsp, 
- TextPortionPtr  tp,
+ TextPortionXPtr  tp,
  ValNodePtr PNTR source_list)
 {
   GetTaxNameSourcesForBioseqEx (bsp, fsp, tp, source_list, TRUE);
 }
 
 
+static CharPtr 
+GetSourceQualSourceTextForBioSource
+(BioSourcePtr      biop,
+ SourceQualDescPtr sqdp,
+ FilterSetPtr      fsp, 
+ TextPortionXPtr    tp)
+{
+  CharPtr str;
+  CharPtr found_loc = NULL, parse_src_txt = NULL;
+  Int4    found_len;
+
+  if (biop == NULL || biop->org == NULL || sqdp == NULL
+      || (fsp != NULL
+          && fsp->ccp != NULL
+          && !DoesOneSourceMatchConstraint (biop, fsp->ccp)))
+  {
+    return NULL;
+  }
+
+  str = GetSourceQualQualValueFromBiop (biop, sqdp, fsp);
+  if (!StringHasNoText (str))
+  {
+    FindTextPortionXInString (str, tp, &found_loc, &found_len);
+    if (found_loc != NULL)
+    {
+      parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
+      StringNCpy (parse_src_txt, found_loc, found_len);
+      parse_src_txt [found_len] = 0;
+    }
+  }
+  str = MemFree (str);
+  return parse_src_txt;
+}
+
+
+static void 
+GetSourceQualSourcesForBioseq
+(BioseqPtr       bsp,
+ SourceQualDescPtr sqdp,
+ FilterSetPtr    fsp, 
+ TextPortionXPtr  tp,
+ ValNodePtr PNTR source_list)
+{
+  SeqDescrPtr        sdp;
+  SeqFeatPtr         sfp;
+  SeqMgrFeatContext  fcontext;
+  SeqMgrDescContext  dcontext;
+  ParseSourceInfoPtr psip;
+  CharPtr            parse_src_txt;
+  BioSourcePtr       biop;
+  
+  if (bsp == NULL || source_list == NULL)
+  {
+    return;
+  }
+  
+  sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext);
+  while (sdp != NULL)
+  {
+    if ((biop = sdp->data.ptrvalue) != NULL
+        && (parse_src_txt = GetSourceQualSourceTextForBioSource (biop, sqdp, fsp, tp)) != NULL) 
+    {      
+      psip = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
+      if (psip != NULL)
+      {
+        psip->bsp = bsp;
+        psip->sdp = sdp;
+        psip->sfp = NULL;
+        psip->sip = NULL;
+        psip->dest_list = NULL;
+        psip->parse_src_txt = parse_src_txt;
+        ValNodeAddPointer (source_list, 0, psip);
+      }
+      else
+      {
+        parse_src_txt = MemFree (parse_src_txt);
+      }
+    }
+    sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext);
+  }
+  
+  sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext);
+  while (sfp != NULL)
+  {
+    if ((biop = sfp->data.value.ptrvalue) != NULL
+        && (parse_src_txt = GetSourceQualSourceTextForBioSource (biop, sqdp, fsp, tp)) != NULL) 
+    {      
+      psip = (ParseSourceInfoPtr) MemNew (sizeof (ParseSourceInfoData));
+      if (psip != NULL)
+      {
+        psip->bsp = bsp;
+        psip->sdp = NULL;
+        psip->sfp = sfp;
+        psip->sip = NULL;
+        psip->dest_list = NULL;
+        psip->parse_src_txt = parse_src_txt;
+        ValNodeAddPointer (source_list, 0, psip);
+      }
+      else
+      {
+        parse_src_txt = MemFree (parse_src_txt);
+      }
+    }
+    sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext);
+  }    
+}
+
+
 static void
 GetBankitCommentSourcesForBioseq 
 (BioseqPtr       bsp,
  FilterSetPtr    fsp, 
- TextPortionPtr  tp,
+ TextPortionXPtr  tp,
  ValNodePtr PNTR source_list)
 {
   SeqDescrPtr        sdp;
@@ -15541,9 +16614,9 @@ GetBankitCommentSourcesForBioseq
             {
               if (fsp == NULL
                   || fsp->ccp == NULL
-                  || DoesStringMatchConstraint (ufp->data.ptrvalue, fsp->ccp->string_constraint))
+                  || DoesStringMatchConstraintX (ufp->data.ptrvalue, fsp->ccp->string_constraint))
               {
-                FindTextPortionInString (ufp->data.ptrvalue, tp, &found_loc, &found_len);
+                FindTextPortionXInString (ufp->data.ptrvalue, tp, &found_loc, &found_len);
                 if (found_loc != NULL)
                 {
                   parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
@@ -15580,7 +16653,7 @@ static void
 GetCommentSourcesForBioseq 
 (BioseqPtr       bsp,
  FilterSetPtr    fsp, 
- TextPortionPtr  tp,
+ TextPortionXPtr  tp,
  ValNodePtr PNTR source_list)
 {
   SeqDescrPtr        sdp;
@@ -15601,9 +16674,9 @@ GetCommentSourcesForBioseq
   {
     if (fsp == NULL
         || fsp->ccp == NULL
-        || DoesStringMatchConstraint (sdp->data.ptrvalue, fsp->ccp->string_constraint))
+        || DoesStringMatchConstraintX (sdp->data.ptrvalue, fsp->ccp->string_constraint))
     {
-      FindTextPortionInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
+      FindTextPortionXInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
       if (found_loc != NULL)
       {
         parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
@@ -15635,9 +16708,9 @@ GetCommentSourcesForBioseq
   {
     if (fsp == NULL
         || fsp->ccp == NULL
-        || DoesStringMatchConstraint (sfp->data.value.ptrvalue, fsp->ccp->string_constraint))
+        || DoesStringMatchConstraintX (sfp->data.value.ptrvalue, fsp->ccp->string_constraint))
     {
-      FindTextPortionInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
+      FindTextPortionXInString (sdp->data.ptrvalue, tp, &found_loc, &found_len);
       if (found_loc != NULL)
       {
         parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
@@ -15670,7 +16743,7 @@ static void
 GetStructuredCommentSourcesForBioseq 
 (BioseqPtr       bsp,
  FilterSetPtr    fsp, 
- TextPortionPtr  tp,
+ TextPortionXPtr  tp,
  CharPtr         comment_field,
  ValNodePtr PNTR source_list)
 {
@@ -15703,9 +16776,9 @@ GetStructuredCommentSourcesForBioseq
           if (oip != NULL && StringCmp (oip->str, comment_field) == 0
               && (fsp == NULL
                   || fsp->ccp == NULL
-                  || DoesStringMatchConstraint (sdp->data.ptrvalue, fsp->ccp->string_constraint)))
+                  || DoesStringMatchConstraintX (sdp->data.ptrvalue, fsp->ccp->string_constraint)))
           {
-            FindTextPortionInString (ufp->data.ptrvalue, tp, &found_loc, &found_len);
+            FindTextPortionXInString (ufp->data.ptrvalue, tp, &found_loc, &found_len);
             if (found_loc != NULL)
             {
               parse_src_txt = (CharPtr) MemNew (sizeof (Char) + (found_len + 1));
@@ -15748,60 +16821,77 @@ static void FindParseSourceBioseqCallback (BioseqPtr bsp, Pointer userdata)
   psp = (ParseSourcePtr) userdata;
   switch (psp->src_field)
   {
-    case PARSE_FIELD_SRC_DEFLINE:
+    case eParseFieldSrcDefLine:
       if (!ISA_aa (bsp->mol))
       {
         GetDeflineSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
       }
       break;
-    case PARSE_FIELD_SRC_LOCAL_ID:
+    case eParseFieldSrcLocalID:
       if (! ISA_aa (bsp->mol) && bsp->repr != Seq_repr_seg)
       {
         GetLocalIDSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
       }
       break;
-    case PARSE_FIELD_SRC_TAXNAME:
-      GetTaxNameSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
+    case eParseFieldSrcFileID:
+      GetNcbiFileSourceForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
       break;
-    case PARSE_FIELD_SRC_COMMENT:
+    case eParseFieldSrcTaxName:
+      if (! ISA_aa (bsp->mol))
+      {
+        GetTaxNameSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
+      }
+      break;
+    case eParseFieldSrcSourceQual:
+      if (! ISA_aa (bsp->mol))
+      {
+        GetSourceQualSourcesForBioseq (bsp, psp->sqdp, psp->fsp, psp->tp, &(psp->source_list));
+      }
+      break;
+    case eParseFieldSrcComment:
       GetCommentSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
       break;
-    case PARSE_FIELD_STRUCTURED_COMMENT:
+    case eParseFieldSrcStructuredComment:
       GetStructuredCommentSourcesForBioseq(bsp, psp->fsp, psp->tp, psp->comment_field, &(psp->source_list));
       break;
-    case PARSE_FIELD_BANKIT_COMMENT:
+    case eParseFieldSrcBankitComment:
       if (!ISA_aa (bsp->mol))
       {
         GetBankitCommentSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
       }
       break;
-    case PARSE_FIELD_SRC_TAXNAME_AFTER_NOMIAL:
-      GetTaxNameAfterNomialSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
+    case eParseFieldSrcTaxNameAfterNomial:
+      if (! ISA_aa (bsp->mol))
+      {
+        GetTaxNameAfterNomialSourcesForBioseq (bsp, psp->fsp, psp->tp, &(psp->source_list));
+      }
       break;
   }
 }
 
 
-static void StripFromParsedField (ParseSourceInfoPtr psip, TextPortionPtr tp, Int4 parse_field_type, CharPtr comment_field)
+static void StripFromParsedField (ParseSourceInfoPtr psip, TextPortionXPtr tp, Int4 parse_field_type, SourceQualDescPtr sqdp, CharPtr comment_field)
 {
-  CharPtr       str_found;
+  CharPtr       str_found, tmp;
   BioSourcePtr  biop = NULL;
   UserObjectPtr uop;
   ObjectIdPtr   oip;
   UserFieldPtr  ufp;
+  ApplyValueData avd;
+  ValNode        vn;
   
   if (psip == NULL || tp == NULL) {
     return;
   }
   switch (parse_field_type) {
-    case PARSE_FIELD_SRC_DEFLINE:
-    case PARSE_FIELD_SRC_COMMENT:
+    case eParseFieldSrcDefLine:
+    case eParseFieldSrcComment:
       if (psip->sdp != NULL) {
         str_found = ReplaceStringForParse(psip->sdp->data.ptrvalue, tp);
         str_found = MemFree (str_found);
       }
       break;
-    case PARSE_FIELD_SRC_TAXNAME:
+    case eParseFieldSrcTaxName:
       if (psip->sdp != NULL) {
         biop = psip->sdp->data.ptrvalue;
       } else if (psip->sfp != NULL) {
@@ -15812,7 +16902,30 @@ static void StripFromParsedField (ParseSourceInfoPtr psip, TextPortionPtr tp, In
         str_found = MemFree (str_found);
       }
       break;
-    case PARSE_FIELD_SRC_TAXNAME_AFTER_NOMIAL:
+    case eParseFieldSrcSourceQual:
+      if (psip->sdp != NULL) {
+        biop = psip->sdp->data.ptrvalue;
+      } else if (psip->sfp != NULL) {
+        biop = psip->sfp->data.value.ptrvalue;
+      }
+      if (biop != NULL) {
+        tmp = GetSourceQualQualValueFromBiop (biop, sqdp, NULL);
+        str_found = ReplaceStringForParse (tmp, tp);
+        str_found = MemFree (str_found);
+        avd.etp = NULL;
+        vn.choice = 0;
+        vn.data.ptrvalue = sqdp;
+        vn.next = NULL;
+        avd.field_list = &vn;
+        avd.new_text = tmp;
+        avd.text_to_replace = NULL;
+        avd.where_to_replace = EditApplyFindLocation_anywhere;
+
+        ApplySourceQualBioSourceCallback (biop, &avd, NULL);
+        tmp = MemFree (tmp);
+      }
+      break;
+    case eParseFieldSrcTaxNameAfterNomial:
       if (psip->sdp != NULL) {
         biop = psip->sdp->data.ptrvalue;
       } else if (psip->sfp != NULL) {
@@ -15824,7 +16937,7 @@ static void StripFromParsedField (ParseSourceInfoPtr psip, TextPortionPtr tp, In
         str_found = MemFree (str_found);
       }
       break;
-    case PARSE_FIELD_STRUCTURED_COMMENT:
+    case eParseFieldSrcStructuredComment:
       if (psip->sdp != NULL
           && psip->sdp->extended != 0
           && psip->sdp->data.ptrvalue != NULL) {
@@ -15844,7 +16957,7 @@ static void StripFromParsedField (ParseSourceInfoPtr psip, TextPortionPtr tp, In
         }
       }
       break;
-    case PARSE_FIELD_BANKIT_COMMENT:
+    case eParseFieldSrcBankitComment:
       if (psip->sdp != NULL
           && psip->sdp->extended != 0
           && psip->sdp->data.ptrvalue != NULL) {
@@ -15943,6 +17056,7 @@ GetFeatureDestinationsForBioseq
   SeqFeatPtr         sfp;
   SeqMgrFeatContext  fcontext;
   SeqAnnotPtr        sap;
+  ProtRefPtr         prp;
 
   if (bsp == NULL || dest_list == NULL)
   {
@@ -15950,11 +17064,21 @@ GetFeatureDestinationsForBioseq
   }
   
   sfp = SeqMgrGetNextFeature (bsp, NULL, seqFeatChoice, featDefChoice, &fcontext);
-  while (sfp != NULL)
-  {
+  if (sfp == NULL 
+      && (featDefChoice == FEATDEF_PROT 
+          || (seqFeatChoice == SEQFEAT_PROT && featDefChoice == 0))) {
+    sfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_PROT, NULL);
+    prp = ProtRefNew ();
+    sfp->data.value.ptrvalue = prp;
+  	SeqMgrIndexFeatures (bsp->idx.entityID, NULL);    
     ValNodeAddPointer (dest_list, 1, sfp);
-    sfp = SeqMgrGetNextFeature (bsp, sfp, seqFeatChoice, featDefChoice, &fcontext);
-  }  
+  } else {
+    while (sfp != NULL)
+    {
+      ValNodeAddPointer (dest_list, 1, sfp);
+      sfp = SeqMgrGetNextFeature (bsp, sfp, seqFeatChoice, featDefChoice, &fcontext);
+    }  
+  }
   
   sap = bsp->annot;
   while (sap != NULL)
@@ -16047,19 +17171,35 @@ FindDestinationsForParseSourceInfo
   switch (dst_field_data->parse_field_type)
   {
     case PARSE_FIELD_SOURCE_QUAL:
-      GetBioSourceDestinationsForBioseq (psip->bsp, dst_field_data->do_feat, dst_field_data->do_desc, &(psip->dest_list));
+    case PARSE_FIELD_BIOSRC_STRING :
+    case PARSE_FIELD_DBXREF :
+      if ((dst_field_data->do_desc && psip->sdp != NULL && psip->sdp->choice == Seq_descr_source) 
+          || (dst_field_data->do_feat && psip->sfp != NULL && psip->sfp->data.choice == SEQFEAT_BIOSRC))
+      {
+        if (dst_field_data->do_desc && psip->sdp != NULL)
+        {
+          ValNodeAddPointer (&(psip->dest_list), 2, psip->sdp);
+        }
+        if (dst_field_data->do_feat && psip->sfp != NULL)
+        {
+          ValNodeAddPointer (&(psip->dest_list), 1, psip->sfp);
+        }
+      }
+      else
+      {
+        GetBioSourceDestinationsForBioseq (psip->bsp, dst_field_data->do_feat, dst_field_data->do_desc, &(psip->dest_list));
+      }
       break;
     case PARSE_FIELD_DEFLINE :
       GetDeflineDestinationsForBioseq (psip->bsp, &(psip->dest_list));
       break;
-    case PARSE_FIELD_BIOSRC_STRING :
-      GetBioSourceDestinationsForBioseq (psip->bsp, dst_field_data->do_feat, dst_field_data->do_desc, &(psip->dest_list));
-      break;
     case PARSE_FIELD_GENE_FIELD :
       GetFeatureDestinationsForBioseq (psip->bsp, SEQFEAT_GENE, 0, &(psip->dest_list));
       break;
-    case PARSE_FIELD_MRNA_FIELD :
-      GetFeatureDestinationsForBioseq (psip->bsp, SEQFEAT_RNA, FEATDEF_mRNA, &(psip->dest_list));
+    case PARSE_FIELD_RNA_FIELD :
+      GetFeatureDestinationsForBioseq (psip->bsp, SEQFEAT_RNA,
+                                       dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue,
+                                       &(psip->dest_list));
       break;
     case PARSE_FIELD_CDS_COMMENT:
       GetFeatureDestinationsForBioseq (psip->bsp, SEQFEAT_CDREGION, FEATDEF_CDS, &(psip->dest_list));
@@ -16348,8 +17488,8 @@ CheckParseActionPairListForExistingText
       gsp->copy_vn_proc = IntValNodeCopy;
       gsp->requested_field = IntValNodeCopy (psp->dst_field_data->feature_field);
       break;
-    case PARSE_FIELD_MRNA_FIELD:
-      gsp->fieldstring_func = GetmRNAFieldString;
+    case PARSE_FIELD_RNA_FIELD:
+      gsp->fieldstring_func = GetRNAFieldString;
       gsp->copy_vn_proc = IntValNodeCopy;
       gsp->requested_field = IntValNodeCopy (psp->dst_field_data->feature_field);
       break;
@@ -16379,6 +17519,13 @@ CheckParseActionPairListForExistingText
       gsp->copy_vn_proc = ValNodeStringCopy;
       gsp->requested_field = ValNodeStringCopy (psp->dst_field_data->feature_field);
       break;
+    case PARSE_FIELD_DBXREF:
+      gsp->fieldstring_func = GetBioSourceFeatureDbxrefString;
+      gsp->descrstring_func = GetBioSourceDescriptorDbxrefString;
+      gsp->free_vn_proc = ValNodeSimpleDataFree;
+      gsp->copy_vn_proc = ValNodeStringCopy;
+      gsp->requested_field = ValNodeStringCopy (psp->dst_field_data->feature_field);
+      break;
   }
   
   for (vnp = psp->source_list; vnp != NULL; vnp = vnp->next)
@@ -16427,8 +17574,8 @@ ParseToOneFeature
     case PARSE_FIELD_GENE_FIELD :
       set_string_func = SetGeneFieldString;
       break;
-    case PARSE_FIELD_MRNA_FIELD :
-      set_string_func = SetmRNAFieldString;
+    case PARSE_FIELD_RNA_FIELD :
+      set_string_func = SetRNAFieldString;
       break;
     case PARSE_FIELD_CDS_COMMENT:
       set_string_func = SetCDSComment;
@@ -16464,7 +17611,7 @@ ParseToOneFeature
       if (prot_bsp == NULL)
       {
         bsp = BioseqFindFromSeqLoc (sfp->location);
-  	    SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID);
+  	    SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID, Sequin_GlobalAlign2Seq);
   	    SeqMgrIndexFeatures (sfp->idx.entityID, NULL);
         prot_bsp = BioseqFindFromSeqLoc (sfp->product);
       }
@@ -16634,7 +17781,7 @@ ParsePairListItem
 (ParseSourceInfoPtr psip, 
  Int4               src_field,
  ParseFieldPtr      dst_field_data,
- TextPortionPtr     tp,
+ TextPortionXPtr     tp,
  ExistingTextPtr    etp)
 {
   ApplyValueData  avd;
@@ -16680,13 +17827,18 @@ ParsePairListItem
 #endif      
       break;
     case PARSE_FIELD_GENE_FIELD :
-    case PARSE_FIELD_MRNA_FIELD :
+    case PARSE_FIELD_RNA_FIELD :
     case PARSE_FIELD_CDS_COMMENT:
     case PARSE_FIELD_PROTEIN_FIELD:
     case PARSE_FIELD_IMPORT_QUAL :
     case PARSE_FIELD_FEATURE_NOTE :
       avd.field_list = dst_field_data->feature_field;
       break;
+    case PARSE_FIELD_DBXREF :
+      avd.field_list = dst_field_data->feature_field;
+      feature_action = ApplyBioSourceDbxrefFeatureCallback;
+      descriptor_action = ApplyBioSourceDbxrefDescriptorCallback;
+      break;
   }
   
   for (dest_vnp = psip->dest_list; dest_vnp != NULL; dest_vnp = dest_vnp->next)
@@ -16701,7 +17853,7 @@ ParsePairListItem
     }
     else if (dest_vnp->choice == 1 
              && (dst_field_data->parse_field_type == PARSE_FIELD_GENE_FIELD
-                 || dst_field_data->parse_field_type == PARSE_FIELD_MRNA_FIELD
+                 || dst_field_data->parse_field_type == PARSE_FIELD_RNA_FIELD
                  || dst_field_data->parse_field_type == PARSE_FIELD_CDS_COMMENT
                  || dst_field_data->parse_field_type == PARSE_FIELD_PROTEIN_FIELD
                  || dst_field_data->parse_field_type == PARSE_FIELD_IMPORT_QUAL
@@ -16718,10 +17870,11 @@ static Boolean
 FindParseActionPairList 
 (SeqEntryPtr   sep, 
  Int4          src_field,
+ SourceQualDescPtr sqdp,
  CharPtr       comment_field,
  ParseFieldPtr dst_field_data,
  FilterSetPtr  fsp,
- TextPortionPtr tp,
+ TextPortionXPtr tp,
  Boolean        remove_from_parsed,
  ChangeCasePtr  ccp)
 {
@@ -16738,6 +17891,7 @@ FindParseActionPairList
   psd.source_list = NULL;
   psd.src_field = src_field;
   psd.comment_field = comment_field;
+  psd.sqdp = sqdp;
   psd.dst_field_data = dst_field_data;
   psd.fsp = fsp;
   psd.tp = tp;
@@ -16803,7 +17957,7 @@ FindParseActionPairList
     {
       if (vnp->data.ptrvalue == NULL) continue;
       psip = (ParseSourceInfoPtr) vnp->data.ptrvalue;
-      StripFromParsedField (psip, tp, src_field, comment_field);      
+      StripFromParsedField (psip, tp, src_field, sqdp, comment_field);      
     }      
     
     rval = TRUE;
@@ -16814,233 +17968,14 @@ FindParseActionPairList
   /* free orgname list if we created it */
   orgnames = ValNodeFree (orgnames);
 
+  comment_field = MemFree (comment_field);
+  sqdp = MemFree (sqdp);
+
   psd.source_list = ParseSourceListFree (psd.source_list);
   source_list_for_removal = ParseSourceListFree (source_list_for_removal);
   return rval;
 }
 
-static void 
-VisitSeqEntriesForParseAction 
-(SeqEntryPtr sep,
- ParseActionPtr pap,
- ParseActnProc   parse_action,
- Pointer        parse_data,
- Boolean        ok_to_parse)
-{
-  SeqDescrPtr       sdp, sdp_tmp;
-  SeqAnnotPtr       sap, sap_tmp;
-  SeqFeatPtr        sfp;
-  ParseActionOpData paod;
-  BioseqSetPtr      bssp = NULL;
-  
-  SeqEntryPtr       old_title_sep;
-  SeqEntryPtr       old_biop_sep;
-  
-  if (sep == NULL || pap == NULL || parse_action == NULL) 
-  {
-    return;
-  }
-  
-  paod.parse_action_data = pap;
-  paod.parse_action = parse_action;
-  paod.parse_userdata = parse_data;
-  paod.parse_complete = FALSE;
-  
-  pap->sep = sep;
-  if (IS_Bioseq (pap->sep))
-  {
-    pap->bsp = (BioseqPtr) pap->sep->data.ptrvalue;
-    sdp = pap->bsp->descr;
-    sap = pap->bsp->annot;
-  }
-  else if (IS_Bioseq_set (sep))
-  {
-    bssp = (BioseqSetPtr) sep->data.ptrvalue;
-    pap->bssp = bssp;
-    sdp = pap->bssp->descr;
-    sap = pap->bssp->annot;
-  }
-  
-  old_title_sep = pap->title_sep;
-  old_biop_sep = pap->biop_sep;
-  
-  if (pap->fsp != NULL
-      && pap->fsp->ccp != NULL 
-      && pap->fsp->ccp->constraint_type != CHOICE_CONSTRAINT_ANY)
-  {
-    ok_to_parse = FALSE;
-    /* try to find BioSource descriptor to match source constraint */
-    sdp_tmp = sdp;
-    while (sdp_tmp != NULL && ! ok_to_parse)
-    {
-      if (sdp_tmp->choice == Seq_descr_source)
-      {
-        if (DoesOneSourceMatchConstraint (sdp_tmp->data.ptrvalue, pap->fsp->ccp))
-        {
-          ok_to_parse = TRUE;
-        }
-      }
-      sdp_tmp = sdp_tmp->next;
-    }
-    /* try to find BioSource feature to match source constraint */
-    sap_tmp = sap;
-    while (sap_tmp != NULL && ! ok_to_parse)
-    {
-      if (sap_tmp->type == 1)
-      {
-        sfp = (SeqFeatPtr) sap_tmp->data;
-        while (sfp != NULL && !ok_to_parse)
-        {
-          if (sfp->data.choice == SEQFEAT_BIOSRC)
-          {
-            if (DoesOneSourceMatchConstraint (sfp->data.value.ptrvalue, pap->fsp->ccp))
-            {
-              ok_to_parse = TRUE;
-            }
-          }
-          sfp = sfp->next;
-        }
-      }
-      sap_tmp = sap_tmp->next;
-    }
-  }
-  else
-  {
-    ok_to_parse = TRUE;
-  }
-  if (ok_to_parse)
-  {
-    SetSourceAndTitle (pap, sdp, sap);
-    if (pap->biop_sep != old_biop_sep)
-    {
-      sdp_tmp = sdp;
-      while (sdp_tmp != NULL)
-      {
-        if (sdp_tmp->choice == Seq_descr_source)
-        {
-          ParseFromSource (sdp_tmp->data.ptrvalue, pap, &paod);
-        }
-        sdp_tmp = sdp_tmp->next;
-      }
-      sap_tmp = sap;
-      while (sap_tmp != NULL)
-      {
-        if (sap_tmp->type == 1)
-        {
-          sfp = sap_tmp->data;
-          while (sfp != NULL)
-          {
-            if (sfp->data.choice == SEQFEAT_BIOSRC)
-            {
-              ParseFromSource (sfp->data.value.ptrvalue, pap, &paod);
-            }
-            sfp = sfp->next;
-          }
-        }
-        sap_tmp = sap_tmp->next;
-      }
-    }
-    if (pap->title_sep != old_title_sep 
-        && pap->src_field == PARSE_FIELD_SRC_DEFLINE)
-    {
-      sdp_tmp = sdp;
-      while (sdp_tmp != NULL)
-      {
-        if (sdp_tmp->choice == Seq_descr_title)
-        {
-          ParseActionDeflineText (sdp_tmp, &paod);
-        }
-        sdp_tmp = sdp_tmp->next;
-      }
-    }
-      
-    if (pap->src_field == PARSE_FIELD_SRC_LOCAL_ID && IS_Bioseq (sep))
-    {
-      if (pap->biop_sep == NULL)
-      {
-        pap->biop_sep = sep;
-      }
-      if (pap->title_sep == NULL)
-      {
-        pap->title_sep = sep;
-      }
-      ParseActionLocalIDText (sep->data.ptrvalue, &paod);
-    }
-    if (pap->src_field == PARSE_FIELD_SRC_COMMENT)
-    {
-      sdp_tmp = sdp;
-      while (sdp_tmp != NULL)
-      {
-        ParseActionCommentDescriptor (sdp_tmp, &paod);
-        sdp_tmp = sdp_tmp->next;
-      }
-      
-      sap_tmp = sap;
-      while (sap_tmp != NULL)
-      {
-        if (sap_tmp->type == 1)
-        {
-          sfp = sap_tmp->data;
-          while (sfp != NULL)
-          {
-            ParseActionCommentFeature (sfp, &paod);
-            sfp = sfp->next;
-          }
-        }
-        sap_tmp = sap_tmp->next;
-      }
-    }
-    if (pap->src_field == PARSE_FIELD_BANKIT_COMMENT)
-    {
-      sdp_tmp = sdp;
-      while (sdp_tmp != NULL)
-      {
-        ParseActionBankitComment (sdp_tmp, &paod);
-        sdp_tmp = sdp_tmp->next;
-      }      
-    }
-  }
-  
-  if (bssp != NULL && !paod.parse_complete)
-  {
-    VisitSeqEntriesForParseAction (bssp->seq_set, pap, parse_action, parse_data, ok_to_parse);
-  }
-
-  pap->title_sep = old_title_sep;
-  pap->biop_sep = old_biop_sep;
-  
-  VisitSeqEntriesForParseAction (sep->next, pap, parse_action, parse_data, ok_to_parse);
-}
-
-typedef struct parseactionlog 
-{
-  FILE    *fp;
-  Boolean data_in_log;
-} ParseActionLogData, PNTR ParseActionLogPtr;
-
-static void  ParseActionSample (ParseActionPtr pap, Pointer userdata, CharPtr found_text, Int4 found_len)
-{
-  CharPtr           log_text;
-  ParseActionLogPtr palp;
-  
-  palp = (ParseActionLogPtr) userdata;
-  if (palp == NULL || found_len == 0 || found_text == NULL || palp->fp == NULL)
-  {
-    return;
-  }
-  
-  log_text = (CharPtr) MemNew ((found_len + 1) * sizeof (Char));
-  if (log_text != NULL)
-  {
-    StringNCpy (log_text, found_text, found_len);
-    log_text[found_len] = 0;
-    fprintf (palp->fp, "%s\n", log_text);
-    palp->data_in_log = TRUE;
-    MemFree (log_text);
-  }
-}
-
-
 typedef ValNodePtr (*AdjustConvertFeatureListFunc) PROTO ((ValNodePtr, Pointer, BaseFormPtr, BoolPtr cancel));
 typedef Pointer (*CollectConvertFeatureOptionsFunc) PROTO ((ValNodePtr, BaseFormPtr, BoolPtr cancel));
 typedef Pointer (*FreeConvertFeatureOptionsFunc) PROTO ((Pointer));
@@ -17152,7 +18087,7 @@ static ConvertFeatureProcsData ConvertFeaturesTable[] = {
        "Creates a misc_feature with the gene description and locus prepended to the original comment, separated by semicolons." },
   { SEQFEAT_RNA,      FEATDEF_ANY,                SEQFEAT_IMP,    FEATDEF_misc_feature,
        NULL, NULL, NULL, ConvertRNAToMiscFeat, NULL,
-       "Creates a misc_feature with the RNA product name as a /product qualifier." } ,
+       "Creates a misc_feature and adds the RNA product name to the comment." } ,
   { SEQFEAT_SITE,     FEATDEF_ANY,                SEQFEAT_IMP,    FEATDEF_misc_feature,
        NULL, NULL, NULL, ConvertSiteToMiscFeat, NULL,
        "Creates a misc_feature with the site type name as a /note qualifier." } ,
@@ -17294,6 +18229,7 @@ static void FeatureRemoveChangeNotify (Pointer userdata)
   ValNodePtr          err_list, vnp_from, vnp_to;
   Int4                table_line;
   RecT                r;
+  Boolean             need_original = FALSE;
 
   mrfp = (FeatureSelRemConvFormPtr) userdata;
   if (mrfp == NULL) return;
@@ -17333,6 +18269,7 @@ static void FeatureRemoveChangeNotify (Pointer userdata)
     }
     else
     {
+      /* set help text */
       table_line = GetConvertFeatureTableLine (FindFeatFromFeatDefType (vnp_from->choice),
                                                vnp_from->choice,
                                                FindFeatFromFeatDefType (vnp_to->choice),
@@ -17349,11 +18286,23 @@ static void FeatureRemoveChangeNotify (Pointer userdata)
       {
         AppendText (mrfp->help_text, ConvertFeaturesTable[table_line].help_text, NULL, NULL, systemFont);
       }
+
+      /* if converting from CDS to site, bond, or region, "leave original" must be checked */
+      if ((vnp_from->choice == FEATDEF_CDS
+           || vnp_from->choice == FEATDEF_ANY)
+          && (vnp_to->choice == FEATDEF_SITE 
+              || vnp_to->choice == FEATDEF_BOND
+              || vnp_to->choice == FEATDEF_REGION))
+      {
+        need_original = TRUE;
+        AppendText (mrfp->help_text, "If converting from CDS to site or bond, or region, you must check Leave Original Feature.", NULL, NULL, systemFont);
+      }
     }
     vnp_from = ValNodeFreeData (vnp_from);
     vnp_to = ValNodeFreeData (vnp_to);
     ObjectRect (mrfp->help_text, &r);
     InvalRect (&r);  
+
   }
   else
   {
@@ -17364,7 +18313,7 @@ static void FeatureRemoveChangeNotify (Pointer userdata)
     }
   }
   
-  if (err_list == NULL)
+  if (err_list == NULL && (!need_original || GetStatus (mrfp->leave_original_feature_btn)))
   {
     EnableAcceptCancelDialogAccept (mrfp->accept_cancel);
   }
@@ -17375,6 +18324,17 @@ static void FeatureRemoveChangeNotify (Pointer userdata)
   ValNodeFree (err_list);
 }
 
+
+static void FeatureRemoveChangeButton (ButtoN b)
+{
+  FeatureSelRemConvFormPtr mrfp;
+  
+  mrfp = (FeatureSelRemConvFormPtr) GetObjectExtra (b);
+  if (mrfp == NULL) return;
+  FeatureRemoveChangeNotify (mrfp);
+}
+
+
 static void FeatureRemoveOrConvertCenterAction (PopuP p)
 {
   FeatureSelRemConvFormPtr mrfp;
@@ -18847,6 +19807,7 @@ static Boolean FeatureRemoveOrConvertAction (Pointer userdata)
   RemoveFeatureData     rfd;
   OrigFeatPtr           ofp;
   SeqFeatPtr            sfp;
+  Boolean               rval = TRUE;
   
   if (userdata == NULL) return FALSE;
   
@@ -18895,7 +19856,7 @@ static Boolean FeatureRemoveOrConvertAction (Pointer userdata)
     switch (window_action)
     {
       case FEATURE_CONVERT:
-        NewConvertFeaturesByList (sep, fsp, feat_def_choice, mrfp);
+        rval = NewConvertFeaturesByList (sep, fsp, feat_def_choice, mrfp);
         break;
       case FEATURE_REMOVE:
         rfd.bsplist = NULL;
@@ -18950,7 +19911,7 @@ static Boolean FeatureRemoveOrConvertAction (Pointer userdata)
   ObjMgrSetDirtyFlag (mrfp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, mrfp->input_entityID, 0, 0);  
   Update ();
-  return TRUE;
+  return rval;
 }
 
 static void FeatureRemoveOrConvert (IteM i, Int4 first_action)
@@ -19022,7 +19983,8 @@ static void FeatureRemoveOrConvert (IteM i, Int4 first_action)
   SelectFont (systemFont);
   mrfp->help_text = DocumentPanel (g, stdCharWidth * 12, LineHeight () * (TALL_SELECTION_LIST + 1));
 
-  mrfp->leave_original_feature_btn = CheckBox (mrfp->convert_grp, "Leave Original Feature", NULL);
+  mrfp->leave_original_feature_btn = CheckBox (mrfp->convert_grp, "Leave Original Feature", FeatureRemoveChangeButton);
+  SetObjectExtra (mrfp->leave_original_feature_btn, mrfp, NULL);
   SetStatus (mrfp->leave_original_feature_btn, FALSE);
   AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) mrfp->leave_original_feature_btn, NULL);
   
@@ -19334,12 +20296,13 @@ extern ParseFieldPtr ParseFieldFree (ParseFieldPtr pfp)
     switch (pfp->parse_field_type) {
       case PARSE_FIELD_SOURCE_QUAL :
       case PARSE_FIELD_FEATURE_NOTE:
-       pfp->feature_field = ValNodeFreeData (pfp->feature_field);
+      case PARSE_FIELD_DBXREF:
+        pfp->feature_field = ValNodeFreeData (pfp->feature_field);
         break;
       case PARSE_FIELD_DEFLINE:
       case PARSE_FIELD_BIOSRC_STRING:
       case PARSE_FIELD_GENE_FIELD:
-      case PARSE_FIELD_MRNA_FIELD:
+      case PARSE_FIELD_RNA_FIELD:
       case PARSE_FIELD_CDS_COMMENT:
       case PARSE_FIELD_COMMENT_DESC:
       case PARSE_FIELD_IMPORT_QUAL:
@@ -19350,7 +20313,14 @@ extern ParseFieldPtr ParseFieldFree (ParseFieldPtr pfp)
         pfp->feature_field = ValNodeFree (pfp->feature_field);
     }
 
-    pfp->feature_subtype = ValNodeFreeData (pfp->feature_subtype);
+    if (pfp->parse_field_type == PARSE_FIELD_RNA_FIELD)
+    {
+      pfp->feature_subtype = ValNodeFree (pfp->feature_subtype);
+    }
+    else
+    {
+      pfp->feature_subtype = ValNodeFreeData (pfp->feature_subtype);
+    }
     pfp = MemFree (pfp);
   }
   return pfp;
@@ -19435,6 +20405,16 @@ GetSampleForSeqEntry
                                             SEQFEAT_BIOSRC, 0,
                                             Seq_descr_source);
       break;
+    case PARSE_FIELD_DBXREF:
+      gsp = CheckForExistingTextInSeqEntry (sep, 
+                                            dst_field_data->feature_field, 
+                                            GetBioSourceFeatureDbxrefString,
+                                            GetBioSourceDescriptorDbxrefString,
+                                            ValNodeSimpleDataFree, ValNodeStringCopy,
+                                            fsp,
+                                            SEQFEAT_BIOSRC, 0,
+                                            Seq_descr_source);
+      break;
     case PARSE_FIELD_GENE_FIELD:
       gsp = CheckForExistingTextInSeqEntry (sep, 
                                             dst_field_data->feature_field, 
@@ -19444,14 +20424,15 @@ GetSampleForSeqEntry
                                             fsp,
                                             SEQFEAT_GENE, 0, 0);
       break;
-    case PARSE_FIELD_MRNA_FIELD:
+    case PARSE_FIELD_RNA_FIELD:
       gsp = CheckForExistingTextInSeqEntry (sep, 
                                             dst_field_data->feature_field, 
-                                            GetmRNAFieldString,
+                                            GetRNAFieldString,
                                             NULL,
                                             NULL, IntValNodeCopy,
                                             fsp,
-                                            SEQFEAT_RNA, FEATDEF_mRNA, 0);
+                                            SEQFEAT_RNA, 
+                                            dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue, 0);
       break;
     case PARSE_FIELD_CDS_COMMENT:
       gsp = CheckForExistingTextInSeqEntry (sep, 
@@ -19553,63 +20534,6 @@ GetSampleForSeqEntry
   return gsp;  
 }
 
-static void GetParseToExistingTextCallback (ParseActionPtr pap, Pointer userdata, CharPtr found_text, Int4 found_len)
-{
-  ParseFormPtr mp;
-  GetSamplePtr gsp = NULL;
-  SeqEntryPtr  sep;
-  ValNodePtr   sum_vnp;
-
-  mp = (ParseFormPtr) userdata;
-  if (mp == NULL || mp->dst_field_data == NULL)
-  {
-    return;
-  }
-  
-  if (mp->dst_field_data->parse_field_type == PARSE_FIELD_SOURCE_QUAL
-      || mp->dst_field_data->parse_field_type == PARSE_FIELD_BIOSRC_STRING)
-  {
-    sep = pap->biop_sep;
-  }
-  else if (mp->dst_field_data->parse_field_type == PARSE_FIELD_DEFLINE)
-  {
-    sep = pap->title_sep;
-  }
-  else
-  {
-    sep = pap->sep;
-  }
-  
-  gsp = GetSampleForSeqEntry (sep, mp->input_entityID, mp->dst_field_data, NULL);
-  
-  if (gsp == NULL)
-  {
-    return;
-  }
-  if (mp->gsp == NULL)
-  {
-    mp->gsp = gsp;
-  }
-  else
-  {
-    mp->gsp->num_found += gsp->num_found;
-    if (StringCmp (mp->gsp->sample_text, gsp->sample_text) != 0)
-    {
-      mp->gsp->all_same = FALSE;
-    }
-    
-    sum_vnp = AddValNodeLists (mp->gsp->feat_dest_list, gsp->feat_dest_list);
-    mp->gsp->feat_dest_list = ValNodeFree (mp->gsp->feat_dest_list);
-    mp->gsp->feat_dest_list = sum_vnp;
-    
-    sum_vnp = AddValNodeLists (mp->gsp->descr_dest_list, gsp->descr_dest_list);
-    mp->gsp->descr_dest_list = ValNodeFree (mp->gsp->descr_dest_list);
-    mp->gsp->descr_dest_list = sum_vnp;
-    
-    gsp = GetSampleFree (gsp);
-  } 
-}
-
 static void 
 ParseToFeaturesOnBioseq 
 (BioseqPtr             bsp, 
@@ -19640,7 +20564,7 @@ ParseToFeaturesOnBioseq
       prot_bsp = BioseqFindFromSeqLoc (sfp->product);
       if (prot_bsp == NULL)
       {
-  	    SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID);
+  	    SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID, Sequin_GlobalAlign2Seq);
   	    SeqMgrIndexFeatures (sfp->idx.entityID, NULL);
         prot_bsp = BioseqFindFromSeqLoc (sfp->product);
       }
@@ -19720,8 +20644,8 @@ ParseToFeatures
     case PARSE_FIELD_GENE_FIELD :
       set_string_func = SetGeneFieldString;
       break;
-    case PARSE_FIELD_MRNA_FIELD :
-      set_string_func = SetmRNAFieldString;
+    case PARSE_FIELD_RNA_FIELD :
+      set_string_func = SetRNAFieldString;
       break;
     case PARSE_FIELD_CDS_COMMENT:
       set_string_func = SetCDSComment;
@@ -19843,15 +20767,22 @@ static void ParseToDest (ParseActionPtr pap, Pointer userdata, CharPtr found_tex
                                            ApplySourceStringFeatureCallback,
                                            ApplySourceStringDescriptorCallback,
                                            0, 0, 0, &avd);
+    case PARSE_FIELD_DBXREF :
+      avd.field_list = mp->dst_field_data->feature_field;
+      OperateOnSeqEntryConstrainedObjects (pap->biop_sep, NULL, 
+                                           ApplyBioSourceDbxrefFeatureCallback,
+                                           ApplyBioSourceDbxrefDescriptorCallback,
+                                           0, 0, 0, &avd);
+      break;
     case PARSE_FIELD_GENE_FIELD :
       avd.field_list = mp->dst_field_data->feature_field;
       ParseToFeatures (pap->sep, &avd, mp->dst_field_data->parse_field_type,
                        FEATDEF_GENE);
       break;
-    case PARSE_FIELD_MRNA_FIELD :
+    case PARSE_FIELD_RNA_FIELD :
       avd.field_list = mp->dst_field_data->feature_field;
       ParseToFeatures (pap->sep, &avd, mp->dst_field_data->parse_field_type,
-                       FEATDEF_mRNA);
+                       mp->dst_field_data->feature_subtype == NULL ? 0 : mp->dst_field_data->feature_subtype->data.intvalue);
       break;
     case PARSE_FIELD_CDS_COMMENT:
       avd.field_list = NULL;
@@ -19936,6 +20867,15 @@ GetDestSample
                                             NULL,
                                             SEQFEAT_BIOSRC, 0, Seq_descr_source);
       break;
+    case PARSE_FIELD_DBXREF:
+      gsp = CheckForExistingTextInSeqEntry (sep, dst_field_data->feature_field,
+                                            GetBioSourceFeatureDbxrefString,
+                                            GetBioSourceDescriptorDbxrefString,
+                                            ValNodeSimpleDataFree,
+                                            ValNodeStringCopy,
+                                            NULL,
+                                            SEQFEAT_BIOSRC, 0, Seq_descr_source);
+      break;
     case PARSE_FIELD_GENE_FIELD:
       gsp = CheckForExistingTextInSeqEntry (sep, dst_field_data->feature_field, 
                                             GetGeneFieldString,
@@ -19943,12 +20883,12 @@ GetDestSample
                                             NULL, IntValNodeCopy,
                                             NULL, SEQFEAT_GENE, 0, 0);
       break;
-    case PARSE_FIELD_MRNA_FIELD:
+    case PARSE_FIELD_RNA_FIELD:
       gsp = CheckForExistingTextInSeqEntry (sep, dst_field_data->feature_field, 
-                                            GetmRNAFieldString,
+                                            GetRNAFieldString,
                                             NULL,
                                             NULL, IntValNodeCopy,
-                                            NULL, SEQFEAT_RNA, FEATDEF_mRNA, 0);
+                                            NULL, SEQFEAT_RNA, dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue, 0);
       break;
     case PARSE_FIELD_CDS_COMMENT:
       gsp = CheckForExistingTextInSeqEntry (sep, NULL, 
@@ -20012,79 +20952,6 @@ GetDestSample
   return gsp;
 }
 
-static Boolean ParseFileToDest (ParseFormPtr mp, FilterSetPtr fsp, TextPortionPtr tp, SeqEntryPtr sep)
-{
-  ParseActionData     pad;
-  FILE                *fp;
-  Char                path [PATH_MAX];
-  ReadBufferData      rbd;
-  CharPtr             line;
-  CharPtr             found_loc = NULL;
-  Int4                found_len = 0;
-  GetSamplePtr        gsp;
-
-  if (mp == NULL || tp == NULL || sep == NULL)
-  {
-    return FALSE;
-  }
-  ResetParseActionVisitData (&pad);
-  pad.fsp = fsp;
-  pad.tp = tp;
-
-  gsp = GetDestSample (sep, mp->dst_field_data);
-  mp->etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);        
-  gsp = GetSampleFree (gsp);
-  if (mp->etp != NULL && mp->etp->existing_text_choice == eExistingTextChoiceCancel)
-  {
-    mp->etp = MemFree (mp->etp);
-    return FALSE;
-  }
-  
-
-  if (! GetInputFileName (path, sizeof (path), "", "TEXT")) 
-  {
-    mp->etp = MemFree (mp->etp);
-    return FALSE;
-  }
-  
-  fp = FileOpen (path, "r");
-  if (fp == NULL)
-  {
-    Message (MSG_ERROR, "Unable to open %s", path);
-    mp->etp = MemFree (mp->etp);
-    return FALSE;
-  }
-
-  ResetParseActionVisitData (&pad);
-  pad.sep = sep;
-  pad.title_sep = sep;
-  pad.biop_sep = sep;
-
-  rbd.fp = fp;
-  rbd.current_data = NULL;
-  line = AbstractReadFunction (&rbd);
-  while (line != NULL)
-  {
-    found_loc = NULL;
-    found_len = 0;
-    FindTextPortionInString (line, tp, &found_loc, &found_len);
-  
-    if (found_loc != NULL)
-    {
-      ParseToDest (&pad, mp, found_loc, found_len);
-    }
-    line = AbstractReadFunction (&rbd);
-  }
-
-  FileClose (fp);
-  mp->etp = MemFree (mp->etp);
-  
-  ObjMgrSetDirtyFlag (mp->input_entityID, TRUE);
-  ObjMgrSendMsg (OM_MSG_UPDATE, mp->input_entityID, 0, 0);
-  ArrowCursor ();
-  Update ();    
-  return TRUE;
-}
 
 static GetSamplePtr GetFlatFileParseProteinFieldSamples (Uint2 entityID, SeqEntryPtr sep, GetSamplePtr gsp, ParseFieldPtr dst_field_data)
 {
@@ -20167,7 +21034,7 @@ ParseFlatfileForSample
         string = asn2gnbk_format (ajp, (Int4) index);
         if (string != NULL && *string != '\0') {
           CompressSpaces (string);
-          FindTextPortionInString (string, pap->tp, &found_loc, &found_len);
+          FindTextPortionXInString (string, pap->tp, &found_loc, &found_len);
   
           if (found_loc != NULL)
           {
@@ -20260,7 +21127,7 @@ ParseFlatfileToDest
         string = asn2gnbk_format (ajp, (Int4) index);
         if (string != NULL && *string != '\0') {
           CompressSpaces (string);
-          FindTextPortionInString (string, pap->tp, &found_loc, &found_len);
+          FindTextPortionXInString (string, pap->tp, &found_loc, &found_len);
   
           if (found_loc != NULL)
           {
@@ -20299,11 +21166,10 @@ static Boolean ParseTextAction (Pointer data)
 {
   ParseFormPtr      mp;
   SeqEntryPtr         sep;
-  Char                path [PATH_MAX];
-  ParseActionLogData  pald;
   ParseActionData     pad;
   Boolean             rval = FALSE;
-  ParseFieldSrcPtr pfsp;
+  ParseFieldSrcPtr    pfsp;
+  SourceQualDescPtr   sqdp;
   Boolean             remove_from_parsed = FALSE;
 
   mp = (ParseFormPtr) data;
@@ -20320,9 +21186,10 @@ static Boolean ParseTextAction (Pointer data)
 
   pfsp = DialogToPointer (mp->source_field);
   if (pfsp == NULL 
-      || pfsp->parse_field < PARSE_FIELD_SRC_DEFLINE 
+      || pfsp->parse_field < eParseFieldSrcDefLine 
       || pfsp->parse_field > MAX_PARSE_FIELD
-      || (pfsp->parse_field == PARSE_FIELD_STRUCTURED_COMMENT && StringHasNoText (pfsp->comment_field)))
+      || (pfsp->parse_field == eParseFieldSrcStructuredComment && StringHasNoText (pfsp->comment_field))
+      || (pfsp->parse_field == eParseFieldSrcSourceQual && pfsp->sqdp == NULL))
   {
     pfsp = ParseFieldSrcFree (pfsp);
     return FALSE;
@@ -20330,6 +21197,8 @@ static Boolean ParseTextAction (Pointer data)
   pad.src_field = pfsp->parse_field;
   pad.comment_field = pfsp->comment_field;
   pfsp->comment_field = NULL;
+  sqdp = pfsp->sqdp;
+  pfsp->sqdp = NULL;
   pfsp = ParseFieldSrcFree (pfsp);
   
   pad.tp = DialogToPointer (mp->text_portion);
@@ -20340,7 +21209,7 @@ static Boolean ParseTextAction (Pointer data)
 
   mp->change_case = DialogToPointer (mp->change_case_dlg);
   
-  if (pad.src_field == PARSE_FIELD_SRC_GENBANK_FLATFILE)
+  if (pad.src_field == eParseFieldSrcGenBankFlatFile)
   {
     WatchCursor ();
     ResetParseActionVisitData (&pad);
@@ -20369,12 +21238,13 @@ static Boolean ParseTextAction (Pointer data)
       case PARSE_FIELD_DEFLINE:
       case PARSE_FIELD_BIOSRC_STRING:
       case PARSE_FIELD_GENE_FIELD:
-      case PARSE_FIELD_MRNA_FIELD:
+      case PARSE_FIELD_RNA_FIELD:
       case PARSE_FIELD_CDS_COMMENT:
       case PARSE_FIELD_PROTEIN_FIELD:
       case PARSE_FIELD_IMPORT_QUAL:
       case PARSE_FIELD_FEATURE_NOTE:
       case PARSE_FIELD_COMMENT_DESC:
+      case PARSE_FIELD_DBXREF:
         WatchCursor ();
         Update ();
         
@@ -20382,29 +21252,19 @@ static Boolean ParseTextAction (Pointer data)
             remove_from_parsed = GetStatus(mp->remove_from_parsed);
         }
         
-        rval = FindParseActionPairList (sep, pad.src_field, pad.comment_field, mp->dst_field_data, pad.fsp, pad.tp, remove_from_parsed, mp->change_case);
+        rval = FindParseActionPairList (sep, pad.src_field, sqdp, pad.comment_field, mp->dst_field_data, pad.fsp, pad.tp, remove_from_parsed, mp->change_case);
         ObjMgrSetDirtyFlag (mp->input_entityID, TRUE);
         ObjMgrSendMsg (OM_MSG_UPDATE, mp->input_entityID, 0, 0);
         ArrowCursor ();
         Update ();    
         break;
       default:
-        pald.data_in_log = FALSE;
-        TmpNam (path);
-        pald.fp = FileOpen (path, "wb");
-        if (pald.fp != NULL)
-        {
-          VisitSeqEntriesForParseAction (sep, &pad, ParseActionSample, &pald, FALSE);
-          FileClose (pald.fp);
-          LaunchGeneralTextViewer (path, "Found Text");
-          FileRemove (path);
-          rval = TRUE;
-        }
+        Message (MSG_ERROR, "Unknown destination");
         break;
     }
   }
   
-  pad.tp = TextPortionFree (pad.tp);
+  pad.tp = TextPortionXFree (pad.tp);
   pad.comment_field = MemFree (pad.comment_field);
   FilterSetFree (pad.fsp);
   return rval;
@@ -20428,7 +21288,7 @@ static void ParseFormClear (Pointer data)
 static void ParseFormClearText (Pointer data)
 {
   ParseFormPtr      mp;
-  TextPortionPtr      tp;
+  TextPortionXPtr      tp;
 
   mp = (ParseFormPtr) data;
   if (mp == NULL)
@@ -20476,8 +21336,9 @@ static void ParseChangeNotify (Pointer userdata)
   /* only allow remove_from_parsed if not parsing from flatfile or local ID */
   pfsp = DialogToPointer (mp->source_field);
   if (pfsp != NULL 
-      && (pfsp->parse_field == PARSE_FIELD_SRC_GENBANK_FLATFILE
-          || pfsp->parse_field == PARSE_FIELD_SRC_LOCAL_ID)) {
+      && (pfsp->parse_field == eParseFieldSrcGenBankFlatFile
+          || pfsp->parse_field == eParseFieldSrcLocalID
+          || pfsp->parse_field == eParseFieldSrcFileID)) {
       Disable (mp->remove_from_parsed);
   } else {
       Enable (mp->remove_from_parsed);
@@ -20512,7 +21373,7 @@ static void ParseText (Uint2 input_entityID, Int4 from_field, Int4 to_field)
   
   g1 = HiddenGroup (h, 2, 0, NULL);
   StaticPrompt (g1, "Select text", 0, dialogTextHeight, systemFont, 'l');
-  mp->text_portion = TextPortionDialog (g1);
+  mp->text_portion = TextPortionXDialog (g1);
   
   g2 = HiddenGroup (h, 2, 0, NULL);
   StaticPrompt (g2, "From", 0, dialogTextHeight, systemFont, 'l');
@@ -20520,7 +21381,7 @@ static void ParseText (Uint2 input_entityID, Int4 from_field, Int4 to_field)
   
   g3 = HiddenGroup (h, 2, 0, NULL);
   StaticPrompt (g3, "And place in", 0, dialogTextHeight, systemFont, 'l');
-  mp->destination_field = ParseFieldDestDialog (g3, ParseChangeNotify, mp);
+  mp->destination_field =   ParseFieldDestDialogEx (g3, ParseChangeNotify, mp, FALSE, TRUE);
   
   mp->change_case_dlg = ChangeCaseDialog (h);
 
@@ -20540,6 +21401,7 @@ static void ParseText (Uint2 input_entityID, Int4 from_field, Int4 to_field)
   {
     pfsd.parse_field = from_field;
     pfsd.comment_field = NULL;
+    pfsd.sqdp = NULL;
     PointerToDialog (mp->source_field, &pfsd);
   }
   if (to_field > 0)
@@ -20567,17 +21429,17 @@ static void ParseTextItem (IteM i, Int4 from_field, Int4 to_field)
 
 extern void ParseDefLineToSourceQual (IteM i)
 {
-  ParseTextItem (i, PARSE_FIELD_SRC_DEFLINE, PARSE_FIELD_SOURCE_QUAL);
+  ParseTextItem (i, eParseFieldSrcDefLine, PARSE_FIELD_SOURCE_QUAL);
 }
 
 extern void ParseTaxnameToSourceQual (IteM i)
 {
-  ParseTextItem (i, PARSE_FIELD_SRC_TAXNAME_AFTER_NOMIAL, PARSE_FIELD_SOURCE_QUAL);
+  ParseTextItem (i, eParseFieldSrcTaxNameAfterNomial, PARSE_FIELD_SOURCE_QUAL);
 }
 
 extern void ParseFlatfileToSourceQual (IteM i)
 {
-  ParseTextItem (i, PARSE_FIELD_SRC_GENBANK_FLATFILE, PARSE_FIELD_SOURCE_QUAL);
+  ParseTextItem (i, eParseFieldSrcGenBankFlatFile, PARSE_FIELD_SOURCE_QUAL);
 }
 
 static void ParseTextToolBtn (ButtoN b, Int4 from_field, Int4 to_field)
@@ -20592,7 +21454,7 @@ static void ParseTextToolBtn (ButtoN b, Int4 from_field, Int4 to_field)
 
 extern void ParseLocalIDToSourceQual (ButtoN b)
 {
-  ParseTextToolBtn (b, PARSE_FIELD_SRC_LOCAL_ID, PARSE_FIELD_SOURCE_QUAL);
+  ParseTextToolBtn (b, eParseFieldSrcLocalID, PARSE_FIELD_SOURCE_QUAL);
 }
 
 
@@ -21010,24 +21872,23 @@ static GrouP FeatureEditorCitationGroup (GrouP h, FeatEdPtr mp)
 
 static GrouP FeatureEditorPartialGroup (GrouP h, FeatEdPtr mp)
 {
-  GrouP g, k1, k2;
+  GrouP g, g1, g2,k1, k2;
+  PrompT p1, p2;
   
   if (mp == NULL)
   {
     return NULL;
   }
   
-  g = HiddenGroup (h, -1, 0, NULL);
+  g = HiddenGroup (h, 2, 0, NULL);
   SetGroupSpacing (g, 10, 10);
+  StaticPrompt (g, "", 0, dialogTextHeight, systemFont, 'l');
+  StaticPrompt (g, "", 0, dialogTextHeight, systemFont, 'l');
   
-  mp->convert_choice = PopupList (g, TRUE, NULL);
-  PopupItem (mp->convert_choice, "Do not convert location");
-  PopupItem (mp->convert_choice, "Convert location to join");
-  PopupItem (mp->convert_choice, "Convert location to order");
-  PopupItem (mp->convert_choice, "Convert location to single interval");
-  SetValue (mp->convert_choice, 1);
-  
-  k1 = HiddenGroup (g, 2, 0, NULL);
+  p1 = StaticPrompt (g, "Partials:", 0, dialogTextHeight, systemFont, 'l');
+  g1 = NormalGroup (g, 1, 0, "", programFont, NULL);
+  k1 = HiddenGroup (g1, 2, 0, NULL);
+
   SetGroupSpacing (k1, 10, 10);
   StaticPrompt (k1, "5' partial:", 0, dialogTextHeight, systemFont, 'l');
   mp->partial5_choice = PopupList (k1, TRUE, NULL);
@@ -21041,9 +21902,11 @@ static GrouP FeatureEditorPartialGroup (GrouP h, FeatEdPtr mp)
   PopupItem (mp->partial5_choice, "Do not change");
   SetValue (mp->partial5_choice, 8);
   
-  mp->extend5_btn = CheckBox (g, "Extend to 5' end of sequence if setting 5' partial", NULL);
-  
-  k2 = HiddenGroup (g, 2, 0, NULL);
+  mp->extend5_btn = CheckBox (g1, "Extend to 5' end of sequence if setting 5' partial", NULL);
+
+  StaticPrompt (g1, "", 0, dialogTextHeight, systemFont, 'l');
+
+  k2 = HiddenGroup (g1, 2, 0, NULL);
   SetGroupSpacing (k2, 10, 10);
   StaticPrompt (k2, "3' partial:", 0, dialogTextHeight, systemFont, 'l');
   mp->partial3_choice = PopupList (k2, TRUE, NULL);
@@ -21056,14 +21919,16 @@ static GrouP FeatureEditorPartialGroup (GrouP h, FeatEdPtr mp)
   PopupItem (mp->partial3_choice, "Do not change");
   SetValue (mp->partial3_choice, 7);
   
-  mp->extend3_btn = CheckBox (g, "Extend to 3' end of sequence if setting 3' partial", NULL);
-  
-  AlignObjects (ALIGN_CENTER, (HANDLE) mp->convert_choice,
-                              (HANDLE) k1,
-                              (HANDLE) mp->extend5_btn,
-                              (HANDLE) k2,
-                              (HANDLE) mp->extend3_btn,
-                              NULL);
+  mp->extend3_btn = CheckBox (g1, "Extend to 3' end of sequence if setting 3' partial", NULL);
+
+  p2 = StaticPrompt (g, "Join/Order/Merge:", 0, dialogTextHeight, systemFont, 'l');
+  g2 = NormalGroup (g, 1, 0, "", programFont, NULL);
+  mp->convert_choice = PopupList (g2, TRUE, NULL);
+  PopupItem (mp->convert_choice, "Do not convert location");
+  PopupItem (mp->convert_choice, "Convert location to join");
+  PopupItem (mp->convert_choice, "Convert location to order");
+  PopupItem (mp->convert_choice, "Convert location to single interval");
+  SetValue (mp->convert_choice, 1);
   
   return g;
 }
@@ -21196,7 +22061,7 @@ static GrouP FeatureEditorActionGroup (GrouP h, FeatEdPtr mp, Int4 first_action)
   SetObjectExtra (mp->action_choice_grp, mp, NULL);
   RadioButton (mp->action_choice_grp, "Evidence");
   RadioButton (mp->action_choice_grp, "Exceptions");
-  RadioButton (mp->action_choice_grp, "Partials");
+  RadioButton (mp->action_choice_grp, "Location");
   RadioButton (mp->action_choice_grp, "Strands");
   RadioButton (mp->action_choice_grp, "Citations");
   RadioButton (mp->action_choice_grp, "Experiment");
@@ -22418,10 +23283,264 @@ static ValNodePtr AlreadyInCDSList (ValNodePtr cds_list, SeqFeatPtr sfp)
   return NULL;
 }
 
+typedef struct buildcdset2
+{
+  ValNodePtr cds_list;
+  ValNodePtr mrna_list;
+  ValNodePtr gene_list;
+} BuildCDSet2Data, PNTR BuildCDSet2Ptr;
+
+static void BuildCDSet2Callback (SeqFeatPtr sfp, Pointer userdata)
+{
+  BuildCDSet2Ptr b;
+
+  if (sfp == NULL || sfp->idx.deleteme || userdata == NULL) return;
+  b = (BuildCDSet2Ptr) userdata;
+  if (sfp->data.choice == SEQFEAT_CDREGION)
+  {
+    ValNodeAddPointer (&(b->cds_list), OBJ_SEQFEAT, sfp);
+  }
+  else if (sfp->data.choice == SEQFEAT_GENE)
+  {
+    ValNodeAddPointer (&(b->gene_list), OBJ_SEQFEAT, sfp);
+  }
+  else if (sfp->idx.subtype == FEATDEF_mRNA)
+  {
+    ValNodeAddPointer (&(b->mrna_list), OBJ_SEQFEAT, sfp);
+  }
+  else if (SeqMgrGetGeneXref (sfp) != NULL)
+  {
+    ValNodeAddPointer (&(b->gene_list), OBJ_SEQFEAT, sfp);
+  }
+}
+
+
+static void UnmarkFeatureList (ValNodePtr list)
+{
+  SeqFeatPtr sfp;
+
+  while (list != NULL)
+  {
+    sfp = list->data.ptrvalue;
+    if (sfp != NULL)
+    {
+      sfp->idx.deleteme = FALSE;
+    }
+    list = list->next;
+  }
+}
+
+
+static SeqFeatPtr GetGeneForCDSetFeature (SeqFeatPtr sfp)
+{
+  GeneRefPtr        grp;
+  SeqFeatPtr        gene = NULL;
+  SeqMgrFeatContext fcontext;
+
+  grp = SeqMgrGetGeneXref (sfp);
+  if (grp == NULL)
+  {
+    gene = SeqMgrGetOverlappingGene (sfp->location, &fcontext);
+  }
+  else if (!SeqMgrGeneIsSuppressed (grp))
+  {
+    if (!StringHasNoText (grp->locus_tag))
+    {
+      gene = SeqMgrGetGeneByLocusTag (BioseqFindFromSeqLoc (sfp->location), grp->locus_tag, &fcontext);
+    }
+  }
+  return gene;
+}
+
+
+static CDSetPtr BuildCDSetFromCodingRegion (SeqFeatPtr cds, BoolPtr indexing_needed)
+{
+  SeqMgrFeatContext fcontext;
+  SeqFeatPtr        gene = NULL, mrna, prot;
+  BioseqPtr         protbsp;
+  CDSetPtr          cdsp;
+  ProtRefPtr        prp;
+
+  if (cds == NULL || cds->data.choice != SEQFEAT_CDREGION) return NULL;
+
+  cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
+  ValNodeAddPointer (&(cdsp->cds_list), 0, cds);
+
+  gene = GetGeneForCDSetFeature (cds);
+  if (gene != NULL)
+  {
+    ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
+    /* mark gene, so that we'll know it isn't lonely */
+    gene->idx.deleteme = TRUE;
+  }
+
+  mrna = SeqMgrGetOverlappingmRNA (cds->location, &fcontext);
+  if (mrna != NULL)
+  {
+    ValNodeAddPointer (&(cdsp->mrna_list), 0, mrna);
+    /* mark mrna, so that we'll know it's already in a set */
+    mrna->idx.deleteme = TRUE;
+  }
+
+  if (cds->product != NULL)
+  {
+    protbsp = BioseqFindFromSeqLoc (cds->product);
+    if (protbsp != NULL)
+    {
+      prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext);
+      /* if there is no full-length protein feature, make one */
+      if (prot == NULL)
+      {
+        prp = ProtRefNew ();
+        prot = CreateNewFeatureOnBioseq (protbsp, SEQFEAT_PROT, NULL);
+        if (prot != NULL)
+        {
+          prot->data.value.ptrvalue = prp;
+          if (indexing_needed != NULL)
+          {
+            *indexing_needed = TRUE;
+          }
+        }
+      }
+      if (prot != NULL)
+      {
+        ValNodeAddPointer (&(cdsp->prot_list), 0, prot);
+      }
+      
+      /* also add in mat_peptides from protein feature */
+      prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext);
+      while (prot != NULL)
+      {
+        ValNodeAddPointer (&(cdsp->prot_list), 0, prot);
+        prot = SeqMgrGetNextFeature (protbsp, prot, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext);
+      }
+    }
+  }  
+  return cdsp;
+}
+
+
+static CDSetPtr BuildCDSetFrommRNA (SeqFeatPtr mrna)
+{
+  SeqFeatPtr        gene;
+  CDSetPtr          cdsp;
+
+  if (mrna == NULL || mrna->idx.deleteme || mrna->idx.subtype != FEATDEF_mRNA) return NULL;
+
+  cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
+  ValNodeAddPointer (&(cdsp->mrna_list), 0, mrna);
+
+  gene = GetGeneForCDSetFeature (mrna);
+  if (gene != NULL)
+  {
+    ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
+    /* mark gene, so that we'll know it isn't lonely */
+    gene->idx.deleteme = TRUE;
+  }
+
+  return cdsp;
+}
+
+
+static Boolean DoesCDSetMatchConstraint (CDSetPtr cdsp, ChoiceConstraintPtr ccp);
+
+static ValNodePtr BuildCDSet2List (Uint2 entityID, ChoiceConstraintPtr  ccp)
+{
+  SeqEntryPtr    sep;
+  BuildCDSet2Data b;
+  CDSetPtr       cdsp;
+  ValNodePtr     vnp, vnp_next, vnp_prev;
+  ValNodePtr     cdset_list = NULL;
+  SeqFeatPtr     cds, gene, mrna;
+  Boolean        need_indexing = FALSE;
+  
+  sep = GetTopSeqEntryForEntityID (entityID);
+
+  b.cds_list = NULL;
+  b.gene_list = NULL;
+  b.mrna_list = NULL;
+  
+  VisitFeaturesInSep (sep, &b, BuildCDSet2Callback);
+
+  /* build cdsets that have coding regions */
+  for (vnp = b.cds_list; vnp != NULL; vnp = vnp->next)
+  {
+    cds = (SeqFeatPtr) vnp->data.ptrvalue;
+    if (cds == NULL) continue;
+    cdsp = BuildCDSetFromCodingRegion (cds, &need_indexing);
+    if (cdsp != NULL)
+    {
+      ValNodeAddPointer (&cdset_list, 0, cdsp);
+    }
+  }
+  if (need_indexing)
+  {
+    /* indexing because we have created full-length protein features */
+    SeqMgrIndexFeatures (entityID, NULL);
+  }
+
+  /* build cdsets for mrna features that don't have coding regions */
+  for (vnp = b.mrna_list; vnp != NULL; vnp = vnp->next)
+  {
+    mrna = (SeqFeatPtr) vnp->data.ptrvalue;
+    if (mrna == NULL || mrna->idx.deleteme) continue;
+    cdsp = BuildCDSetFrommRNA (mrna);
+    if (cdsp != NULL)
+    {
+      ValNodeAddPointer (&cdset_list, 0, cdsp);
+    }
+  }
+
+  /* build cdsets for lonely genes / features with gene xrefs that are not coding regions or mrnas */
+  for (vnp = b.gene_list; vnp != NULL; vnp = vnp->next)
+  {
+    gene = (SeqFeatPtr) vnp->data.ptrvalue;
+    if (gene == NULL || gene->idx.deleteme) continue;
+    cdsp = (CDSetPtr) MemNew (sizeof (CDSetData));
+    ValNodeAddPointer (&(cdsp->gene_list), 0, gene);
+    ValNodeAddPointer (&cdset_list, 0, cdsp);
+  }
+
+  /* now unmark features */
+  UnmarkFeatureList (b.cds_list);
+  UnmarkFeatureList (b.mrna_list);
+  UnmarkFeatureList (b.gene_list);
+
+  b.cds_list = ValNodeFree (b.cds_list);
+  b.mrna_list = ValNodeFree (b.mrna_list);
+  b.gene_list = ValNodeFree (b.gene_list);
+
+  /* now remove sets that don't match our choice constraint */
+  vnp_prev = NULL;
+  for (vnp = cdset_list; vnp != NULL; vnp = vnp_next)
+  {
+    vnp_next = vnp->next;
+    if (!DoesCDSetMatchConstraint (vnp->data.ptrvalue, ccp))
+    {
+      if (vnp_prev == NULL)
+      {
+        cdset_list = vnp->next;
+      }
+      else
+      {
+        vnp_prev->next = vnp->next;
+      }
+      vnp->next = NULL;
+      FreeCDSetList (vnp);     
+    }
+    else
+    {
+      vnp_prev = vnp;
+    }
+  }
+  
+  return cdset_list;
+}
+
 typedef struct buildcdset
 {
   ValNodePtr cdset_list;
-  ValNodePtr lonely_gene_list;  
+  ValNodePtr lonely_gene_list;
 } BuildCDSetData, PNTR BuildCDSetPtr;
 
 static void BuildCDSSetCallback (SeqFeatPtr sfp, Pointer userdata)
@@ -22484,11 +23603,11 @@ static void BuildCDSSetCallback (SeqFeatPtr sfp, Pointer userdata)
     {
       cds = sfp;
       mrna = SeqMgrGetOverlappingmRNA (sfp->location, &fcontext);
-	  if (mrna != NULL)
-	  {
+      if (mrna != NULL)
+      {
         mrna_gene = SeqMgrGetOverlappingGene (mrna->location, &fcontext);
-		if (mrna_gene == gene)
-		{
+        if (mrna_gene == gene)
+        {
           vnp = AlreadyInCDSList (bp->cdset_list, mrna);
           if (vnp != NULL && vnp->data.ptrvalue != NULL)
           {
@@ -22497,8 +23616,8 @@ static void BuildCDSSetCallback (SeqFeatPtr sfp, Pointer userdata)
             if (AlreadyInList (cdsp->gene_list, gene))
             {
               gene = NULL;
-			}
-		  }
+            }
+          }
         }
       }
     }
@@ -22543,7 +23662,9 @@ static void BuildCDSSetCallback (SeqFeatPtr sfp, Pointer userdata)
         if (prot != NULL)
         {
           prot->data.value.ptrvalue = prp;
-  	      SeqMgrIndexFeatures (protbsp->idx.entityID, NULL);
+          if (SeqMgrFeaturesAreIndexed (protbsp->idx.entityID) == 0) {
+  	        SeqMgrIndexFeatures (protbsp->idx.entityID, NULL);
+          }
         }
       }
       if (prot != NULL && ! AlreadyInList (cdsp->prot_list, prot))
@@ -22850,7 +23971,7 @@ static Boolean DoesCDSetMatchConstraint (CDSetPtr cdsp, ChoiceConstraintPtr ccp)
       {
         field_vn.data.intvalue = field_choice;
         str = GetCDSetField (cdsp, &field_vn);
-        does_match = DoesStringMatchConstraint (str, ccp->string_constraint);
+        does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
         MemFree (str);
       }
       if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
@@ -22864,7 +23985,7 @@ static Boolean DoesCDSetMatchConstraint (CDSetPtr cdsp, ChoiceConstraintPtr ccp)
       for (sfp_vnp = cdsp->prot_list; sfp_vnp != NULL && !does_match; sfp_vnp = sfp_vnp->next)
       {
         str = GetCDSGeneProtField (sfp_vnp->data.ptrvalue, ccp->qual_choice, NULL);
-        does_match = DoesStringMatchConstraint (str, ccp->string_constraint);
+        does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
         if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
         {
           does_match = ! does_match;
@@ -22875,7 +23996,7 @@ static Boolean DoesCDSetMatchConstraint (CDSetPtr cdsp, ChoiceConstraintPtr ccp)
     else
     {
       str = GetCDSetField (cdsp, ccp->qual_choice);
-      does_match = DoesStringMatchConstraint (str, ccp->string_constraint);
+      does_match = DoesStringMatchConstraintX (str, ccp->string_constraint);
       MemFree (str);
       if (ccp->string_constraint != NULL && ccp->string_constraint->not_present)
       {
@@ -22915,7 +24036,7 @@ static ValNodePtr BuildCDSetList (Uint2 entityID, ChoiceConstraintPtr  ccp)
   bd.lonely_gene_list = NULL;
   
   VisitFeaturesInSep (sep, &bd, BuildCDSSetCallback);
-  
+
   for (vnp = bd.lonely_gene_list; vnp != NULL; vnp = vnp->next)
   {
     /* only create sets for lonely genes if they have not been added to other sets */
@@ -23701,6 +24822,10 @@ ApplyEditConvertRemoveCombo
   SetObjectExtra (w, mp, NULL);
   mp->form = (ForM) w;
   mp->input_entityID = bfp->input_entityID;
+
+#ifndef WIN_MAC
+  CreateStandardEditMenu (w);
+#endif
   
   n = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (n, 10, 10);
@@ -23835,264 +24960,6 @@ static Boolean CheckFeaturesForPresample (Uint2 entityID)
 }
 
 
-#if 0
-typedef struct EditApplydlg
-{
-  DIALOG_MESSAGE_BLOCK
-  TexT           find_txt;
-  TexT           repl_txt;
-  TexT           apply_txt;
-  Int4           action_choice;
-  GrouP          location_choice;
-  Nlm_ChangeNotifyProc     change_notify;
-  Pointer                  change_userdata;
-} EditApplyDlgData, PNTR EditApplyDlgPtr;
-
-static void ResetEditApplyDlg (EditApplyDlgPtr dlg)
-{
-  if (dlg != NULL)
-  {
-    if (dlg->find_txt != NULL)
-    {
-      SetTitle (dlg->find_txt, "");
-    }
-    if (dlg->repl_txt != NULL)
-    {
-      SetTitle (dlg->repl_txt, "");
-    }
-    if (dlg->apply_txt != NULL)
-    {
-      SetTitle (dlg->apply_txt, "");
-    }
-    if (dlg->location_choice != NULL) {
-      SetValue (dlg->location_choice, EditApplyFindLocation_anywhere);
-    }
-  }
-}
-
-static void EditApplyDialogChangeText (TexT t)
-{
-  EditApplyDlgPtr dlg;
-
-  dlg = (EditApplyDlgPtr) GetObjectExtra (t);
-  if (dlg != NULL && dlg->change_notify != NULL)
-  {
-    (dlg->change_notify)(dlg->change_userdata);
-  }
-}
-
-static void EditApplyToDialog (DialoG d, Pointer userdata)
-{
-  EditApplyDlgPtr dlg;
-  EditApplyPtr    data;
-  
-  dlg = (EditApplyDlgPtr) GetObjectExtra (d);
-  if (dlg == NULL)
-  {
-    return;
-  }
-  
-  ResetEditApplyDlg (dlg);
-  data = (EditApplyPtr) userdata;
-  if (data != NULL)
-  {
-    if (dlg->find_txt != NULL && !StringHasNoText (data->find_txt))
-    {
-      SetTitle (dlg->find_txt, data->find_txt);
-    }
-    if (dlg->repl_txt != NULL && !StringHasNoText (data->repl_txt))
-    {
-      SetTitle (dlg->repl_txt, data->repl_txt);
-    }
-    if (dlg->apply_txt != NULL && !StringHasNoText (data->apply_txt))
-    {
-      SetTitle (dlg->apply_txt, data->apply_txt);
-    }
-    if (dlg->location_choice != NULL) {
-      SetValue (dlg->location_choice, data->find_location);
-    }
-  }
-}
-
-static Pointer DialogToEditApply (DialoG d)
-{
-  EditApplyDlgPtr dlg;
-  EditApplyPtr    data;
-  
-  dlg = (EditApplyDlgPtr) GetObjectExtra (d);
-  if (dlg == NULL)
-  {
-    return NULL;
-  }
-  
-  data = (EditApplyPtr) MemNew (sizeof (EditApplyData));
-  if (data != NULL)
-  {
-    if (dlg->find_txt != NULL)
-    {
-      data->find_txt = JustSaveStringFromText (dlg->find_txt);
-    }
-    if (dlg->repl_txt != NULL)
-    {
-      data->repl_txt = JustSaveStringFromText (dlg->repl_txt);
-    }
-    if (dlg->apply_txt != NULL)
-    {
-      data->apply_txt = JustSaveStringFromText (dlg->apply_txt);
-    }
-    if (dlg->location_choice != NULL) {
-      data->find_location = GetValue (dlg->location_choice);
-    } else {
-      data->find_location = EditApplyFindLocation_anywhere;
-    }
-  }
-  return data;
-}
-
-static void EditApplyMessage (DialoG d, Int2 mssg)
-
-{
-  EditApplyDlgPtr  dlg;
-
-  dlg = (EditApplyDlgPtr) GetObjectExtra (d);
-  if (dlg != NULL) {
-    switch (mssg) 
-    {
-      case VIB_MSG_INIT :
-        /* reset list */
-        ResetEditApplyDlg (dlg);
-        break;
-      case VIB_MSG_ENTER :
-        if (dlg->find_txt != NULL)
-        {
-          Select (dlg->find_txt);
-        }
-        else if (dlg->apply_txt != NULL)
-        {
-          Select (dlg->apply_txt);
-        }
-        break;
-      case AECR_VIB_MSG_SET_DEFAULT :
-        ResetEditApplyDlg (dlg);
-        break;
-      case AECR_VIB_MSG_CLEAR_TEXT :
-        ResetEditApplyDlg (dlg);
-        break;
-      default :
-        break;
-    }
-  }
-}
-
-static ValNodePtr TestEditApply (DialoG d)
-{
-  EditApplyDlgPtr dlg;
-  ValNodePtr      total_err_list = NULL;
-  
-  dlg = (EditApplyDlgPtr) GetObjectExtra (d);
-  if (dlg == NULL)
-  {
-    return FALSE;
-  }
-
-  if (dlg->action_choice == AECR_APPLY)
-  {
-    if (TextHasNoText (dlg->apply_txt))
-    {
-      ValNodeAddPointer (&total_err_list, 0, "apply text");
-    }
-  }
-  else if (dlg->action_choice == AECR_EDIT)
-  {
-    if (TextHasNoText (dlg->find_txt))
-    {
-      ValNodeAddPointer (&total_err_list, 0, "find text");
-    }
-  }
-  return total_err_list;
-}
-
-static void EditApplyDialogCopy (ButtoN b)
-{
-  EditApplyDlgPtr dlg;
-  CharPtr         str = NULL;
-
-  dlg = (EditApplyDlgPtr) GetObjectExtra (b);
-  if (dlg == NULL)
-  {
-    return;
-  }
-  str = JustSaveStringFromText (dlg->find_txt);
-  SetTitle (dlg->repl_txt, str);
-  str = MemFree (str);
-}
-
-static DialoG EditApplyDialog 
-(GrouP                    h,
- Int4                     action_choice, 
- CharPtr                  apply_label,
- Nlm_ChangeNotifyProc     change_notify,
- Pointer                  change_userdata)
-{
-  EditApplyDlgPtr dlg;
-  GrouP           p, p1;
-  ButtoN          b;
-  
-  dlg = (EditApplyDlgPtr) MemNew (sizeof (EditApplyDlgData));
-  if (dlg == NULL)
-  {
-    return NULL;
-  }
-
-  p = HiddenGroup (h, -1, 0, NULL);
-  SetObjectExtra (p, dlg, StdCleanupExtraProc);
-  SetGroupSpacing (p, 10, 10);
-
-  dlg->dialog = (DialoG) p;
-  dlg->todialog = EditApplyToDialog;
-  dlg->fromdialog = DialogToEditApply;
-  dlg->dialogmessage = EditApplyMessage;
-  dlg->testdialog = TestEditApply;
-  dlg->action_choice = action_choice;
-  dlg->change_notify = change_notify;
-  dlg->change_userdata = change_userdata;
-
-  p1 = HiddenGroup (p, 3, 0, NULL);
-  SetGroupSpacing (p1, 10, 10);
-  
-  if (action_choice == AECR_APPLY)
-  {
-    StaticPrompt (p1, apply_label, 0, dialogTextHeight, systemFont, 'r');
-    dlg->apply_txt = DialogText (p1, "", 20, EditApplyDialogChangeText);
-    SetObjectExtra (dlg->apply_txt, dlg, NULL);
-    dlg->location_choice = NULL;
-  }
-  else if (action_choice == AECR_EDIT)
-  {
-    StaticPrompt (p1, "Find", 0, dialogTextHeight, systemFont, 'r');
-    dlg->find_txt = DialogText (p1, "", 18, EditApplyDialogChangeText);
-    SetObjectExtra (dlg->find_txt, dlg, NULL);
-    b = PushButton (p1, "Copy", EditApplyDialogCopy);
-    SetObjectExtra (b, dlg, NULL);
-    Hide (b);
-    StaticPrompt (p1, "Replace", 0, dialogTextHeight, systemFont, 'r');
-    dlg->repl_txt = DialogText (p1, "", 18, EditApplyDialogChangeText);
-    SetObjectExtra (dlg->repl_txt, dlg, NULL);
-    b = PushButton (p1, "Copy", EditApplyDialogCopy);
-    SetObjectExtra (b, dlg, NULL);
-
-    dlg->location_choice = HiddenGroup (p, 3, 0, NULL);
-    RadioButton (dlg->location_choice, "Anywhere in field");
-    RadioButton (dlg->location_choice, "At the beginning of the field");
-    RadioButton (dlg->location_choice, "At the end of the field");
-    SetValue (dlg->location_choice, EditApplyFindLocation_anywhere);
-  }
-  AlignObjects (ALIGN_CENTER, (HANDLE) p1, (HANDLE) dlg->location_choice, NULL);
-
-  return (DialoG) p;
-}
-#endif
-
 typedef struct conversionconflict 
 {
   ConvertFieldPtr cfp;
@@ -24289,7 +25156,7 @@ AddEditApplyDataToApplyValue
   Boolean         leave_on_original;    \
   Boolean         strip_name_from_text; \
   EditApplyPtr    edit_apply;           \
-  TextPortionPtr  text_portion;         \
+  TextPortionXPtr  text_portion;         \
   Boolean         remove_parsed;        \
   FreeValNodeProc free_field_vn_proc;   \
   FreeValNodeProc free_subtype_vn_proc;
@@ -24307,7 +25174,7 @@ static void AECRDataBlockFreeContents (SimpleAECRPtr sp)
     sp->field_list_to = ValNodeFuncFree (sp->field_list_to, sp->free_field_vn_proc);
     sp->subtype_list = ValNodeFuncFree (sp->subtype_list, sp->free_subtype_vn_proc);
     sp->edit_apply = EditApplyFree (sp->edit_apply);
-    sp->text_portion = TextPortionFree(sp->text_portion);
+    sp->text_portion = TextPortionXFree(sp->text_portion);
   }
 }
 
@@ -24577,6 +25444,19 @@ static ValNodePtr TestSimpleAECR (DialoG d)
   return total_err_list;
 }
 
+static void SimpleAECRButtonChange (ButtoN b)
+{
+  SimpleAECRDlgPtr dlg;
+
+  dlg = (SimpleAECRDlgPtr) GetObjectExtra (b);
+  if (dlg == NULL) return;
+
+  if (dlg->change_notify != NULL) 
+  {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
 static DialoG SimpleAECRDialogEx
 (GrouP                    h,
  Int4                     action_choice, 
@@ -24651,11 +25531,13 @@ static DialoG SimpleAECRDialogEx
                                              change_userdata);
     if (action_choice == AECR_CONVERT && is_text)
     {
-      dlg->leave_on_original = CheckBox (p, "Leave on original", NULL);
+      dlg->leave_on_original = CheckBox (p, "Leave on original", SimpleAECRButtonChange);
+      SetObjectExtra (dlg->leave_on_original, dlg, NULL);
     }
     if (strip_name)
     {
-      dlg->strip_name_from_text = CheckBox (p, "Strip name from text", NULL);
+      dlg->strip_name_from_text = CheckBox (p, "Strip name from text", SimpleAECRButtonChange);
+      SetObjectExtra (dlg->strip_name_from_text, dlg, NULL);
     }
   }
   else
@@ -24708,9 +25590,10 @@ static DialoG SimpleAECRDialogEx
   {
     dlg->edit_apply = NULL;
     if (is_text) {
-        dlg->text_portion = TextPortionDialog(p);
+        dlg->text_portion = TextPortionXDialog(p);
     }
-    dlg->remove_parsed = CheckBox (p, "Remove from parsed field", NULL);
+    dlg->remove_parsed = CheckBox (p, "Remove from parsed field", SimpleAECRButtonChange);
+    SetObjectExtra (dlg->remove_parsed, dlg, NULL);
   }
   else
   {
@@ -24989,7 +25872,7 @@ static DialoG CDSGeneProtAECRDialog
   else if (action_choice == AECR_PARSE)
   {
     dlg->edit_apply = NULL;
-    dlg->text_portion = TextPortionDialog(p);
+    dlg->text_portion = TextPortionXDialog(p);
     dlg->remove_parsed = CheckBox (p, "Remove from parsed field", NULL);
   }
   else
@@ -25608,6 +26491,10 @@ static ValNodePtr CollectCDSetList (Uint2 entityID, FilterSetPtr fsp)
   ValNodePtr cdset_list;
 
   /* need to create a list of sets */
+#if 1
+  cdset_list = BuildCDSet2List (entityID, fsp == NULL || fsp->cgp == NULL ? NULL : fsp->cgp);
+
+#else
   if (fsp == NULL || fsp->cgp == NULL)
   {
     /* if we are applying to mat_peptides AND the constraint involved mat_peptides,
@@ -25619,6 +26506,7 @@ static ValNodePtr CollectCDSetList (Uint2 entityID, FilterSetPtr fsp)
   {
     cdset_list = BuildCDSetList (entityID, fsp->cgp);
   }
+#endif
   return cdset_list;
 }
 
@@ -25863,6 +26751,7 @@ typedef struct sourcequalaecrdata
   SimpleAECRPtr origin;
   SimpleAECRPtr strings;
   
+  TaxnameOptionsPtr taxname_options;
 } SourceQualAECRData, PNTR SourceQualAECRPtr;
 
 static SourceQualAECRPtr SourceQualAECRFree (SourceQualAECRPtr sp)
@@ -25870,6 +26759,7 @@ static SourceQualAECRPtr SourceQualAECRFree (SourceQualAECRPtr sp)
   if (sp != NULL)
   {
     sp->source_qual = SimpleAECRFree (sp->source_qual);
+    sp->taxname_options = MemFree (sp->taxname_options);
     sp = MemFree (sp);
   }
   return sp;
@@ -25884,6 +26774,8 @@ typedef struct sourcequalaecrdlg
   DialoG location;
   DialoG origin;
   DialoG strings;
+
+  DialoG taxname_options;
   
   Int4   action_choice;
   Nlm_ChangeNotifyProc     change_notify;
@@ -25891,10 +26783,55 @@ typedef struct sourcequalaecrdlg
   
 } SourceQualAECRDlgData, PNTR SourceQualAECRDlgPtr;
 
+
+static Boolean AreTaxNameOptionsRelevant (Int4 action_choice, SimpleAECRPtr sp)
+{
+  Boolean relevant = FALSE;
+  if (sp == NULL) return FALSE;
+
+  switch (action_choice)
+  {
+    case AECR_APPLY:
+    case AECR_EDIT:
+    case AECR_REMOVE:
+      if (sp->field_list != NULL && sp->field_list->choice == 1)
+      {
+        relevant = TRUE;
+      }
+      break;
+    case AECR_SWAP:
+      if ((sp->field_list != NULL && sp->field_list->choice == 1) 
+          || (sp->field_list_to != NULL && sp->field_list_to->choice == 1))
+      {
+        relevant = TRUE;
+      }
+      break;
+    case AECR_CONVERT:
+      if ((sp->field_list != NULL && sp->field_list->choice == 1 && !sp->leave_on_original) 
+          || (sp->field_list_to != NULL && sp->field_list_to->choice == 1))
+      {
+        relevant = TRUE;
+      }
+      break;
+    case AECR_PARSE:
+      if ((sp->field_list != NULL && sp->field_list->choice == 1 && sp->remove_parsed)
+          || (sp->field_list_to != NULL && sp->field_list_to->choice == 1))
+      {
+        relevant = TRUE;
+      }
+      break;
+    default:
+      relevant = FALSE;
+      break;
+  }
+  return relevant;
+}
+
 static void ChangeQualKind (GrouP g)
 {
   SourceQualAECRDlgPtr dlg;
   Int4                 qual_kind;
+  SimpleAECRPtr        sp;
 
   dlg = (SourceQualAECRDlgPtr) GetObjectExtra (g);
   if (dlg == NULL)
@@ -25906,6 +26843,7 @@ static void ChangeQualKind (GrouP g)
   Hide (dlg->location);
   Hide (dlg->origin);
   Hide (dlg->strings);
+  Hide (dlg->taxname_options);
   qual_kind = GetValue (dlg->qual_kind);
   switch (qual_kind)
   {
@@ -25920,6 +26858,17 @@ static void ChangeQualKind (GrouP g)
       break;
     case QUALKIND_STRINGS :
       Show (dlg->strings);
+      Show (dlg->taxname_options);
+      sp = DialogToPointer (dlg->strings);
+      if (AreTaxNameOptionsRelevant (dlg->action_choice, sp))
+      {
+        Enable (dlg->taxname_options);
+      }
+      else
+      {
+        Disable (dlg->taxname_options);
+      }
+      sp = SimpleAECRFree (sp);
       break;
   }
   if (dlg->change_notify != NULL)
@@ -25940,6 +26889,7 @@ static void ResetSourceQualAECRDlg (SourceQualAECRDlgPtr dlg)
   PointerToDialog (dlg->origin, NULL);
   PointerToDialog (dlg->strings, NULL);
   ChangeQualKind (dlg->qual_kind);
+  PointerToDialog (dlg->taxname_options, NULL);
 }
 
 static void ClearTextSourceQualAECRDlg (SourceQualAECRDlgPtr dlg)
@@ -25985,6 +26935,7 @@ static void SourceQualAECRToDialog (DialoG d, Pointer userdata)
            && (dlg->action_choice == AECR_EDIT || dlg->action_choice == AECR_SWAP))
   {
     SetValue (dlg->qual_kind, QUALKIND_STRINGS);
+    PointerToDialog (dlg->taxname_options, data->taxname_options);
   }
   else if (data->qual_kind > QUALKIND_ORIGIN)
   {
@@ -26011,6 +26962,7 @@ static Pointer DialogToSourceQualAECR (DialoG d)
   data = (SourceQualAECRPtr) MemNew (sizeof (SourceQualAECRData));
   if (data != NULL)
   {
+    data->taxname_options = NULL;
     data->qual_kind = GetValue (dlg->qual_kind);
     switch (data->qual_kind)
     {
@@ -26025,6 +26977,10 @@ static Pointer DialogToSourceQualAECR (DialoG d)
         break;
       case QUALKIND_STRINGS :
         data->strings = DialogToPointer (dlg->strings);
+        if (AreTaxNameOptionsRelevant (dlg->action_choice, data->strings))
+        {
+          data->taxname_options = DialogToPointer (dlg->taxname_options);
+        }
         break;
     }
     
@@ -26054,6 +27010,7 @@ static void SourceQualAECRMessage (DialoG d, Int2 mssg)
         SendMessageToDialog (dlg->location, AECR_VIB_MSG_SET_DEFAULT);
         SendMessageToDialog (dlg->origin, AECR_VIB_MSG_SET_DEFAULT);
         SendMessageToDialog (dlg->strings, AECR_VIB_MSG_SET_DEFAULT);
+        PointerToDialog (dlg->taxname_options, NULL);
         ChangeQualKind (dlg->qual_kind);
         break;
       case AECR_VIB_MSG_CLEAR_TEXT :
@@ -26480,6 +27437,35 @@ static DialoG ConvertSourceLocationDialog
   return (DialoG) p;
 }
 
+
+static void ChangeTaxonomyStrings (Pointer data)
+{
+  SourceQualAECRDlgPtr dlg;
+  SimpleAECRPtr        sp;
+
+  dlg = (SourceQualAECRDlgPtr) data;
+  if (dlg == NULL) return;
+
+  if (GetValue (dlg->qual_kind) == QUALKIND_STRINGS)
+  {
+    sp = DialogToPointer (dlg->strings);
+    if (AreTaxNameOptionsRelevant (dlg->action_choice, sp))
+    {
+      Enable (dlg->taxname_options);
+    }
+    else
+    {
+      Disable (dlg->taxname_options);
+    }
+    sp = SimpleAECRFree (sp);
+  }
+  if (dlg->change_notify != NULL)
+  {
+    (dlg->change_notify)(dlg->change_userdata);
+  }
+
+}
+
 static DialoG SourceQualAECRDialog 
 (GrouP                    h,
  Int4                     action_choice, 
@@ -26563,7 +27549,7 @@ static DialoG SourceQualAECRDialog
   }
   
   /* Taxonomy Strings dialog */
-  dlg->strings = SimpleAECRDialog (g1, action_choice, change_notify, change_userdata,
+  dlg->strings = SimpleAECRDialog (g1, action_choice, ChangeTaxonomyStrings, dlg,
                            ValNodeSimpleDataFree, NULL,
                            SourceStringSelectionDialog, NULL, NULL,
                            "Taxonomy", NULL, TRUE, entityID);
@@ -26602,6 +27588,10 @@ static DialoG SourceQualAECRDialog
                            SourceOriginSelectionDialog, NULL, NULL,
                            "Origin", NULL, FALSE, entityID);
   }
+
+  dlg->taxname_options = TaxnameOptionsDialog (p, change_notify, change_userdata);
+
+  Disable (dlg->taxname_options);
   
   AlignObjects (ALIGN_CENTER, (HANDLE) dlg->source_qual,
                               (HANDLE) dlg->location,
@@ -26611,47 +27601,35 @@ static DialoG SourceQualAECRDialog
                               
   AlignObjects (ALIGN_CENTER, (HANDLE) dlg->qual_kind,
                               (HANDLE) g1,
+                              (HANDLE) dlg->taxname_options,
                               NULL);
                            
   ChangeQualKind (dlg->qual_kind);                         
   return (DialoG) p;
 }
 
-typedef struct multiqual
-{
-  Boolean           multi_found;
-  SourceQualDescPtr sqdp;
-  FilterSetPtr      fsp;
-} MultiQualData, PNTR MultiQualPtr;
 
-static void CheckForMultipleQuals (BioSourcePtr biop, Pointer userdata)
+static Boolean BioSourceHasMultipleQuals (BioSourcePtr biop, SourceQualDescPtr sqdp, FilterSetPtr fsp)
 {
-  MultiQualPtr mqp;
-  Boolean      found_one = FALSE;
   OrgModPtr    mod;
-  SubSourcePtr       ssp;
-  
-  if (biop == NULL || userdata == NULL)
-  {
-    return;
-  }
-  
-  mqp = (MultiQualPtr) userdata;
-  if (mqp->sqdp == NULL || mqp->multi_found) return;
+  SubSourcePtr ssp;
+  Boolean      found_one = FALSE;
+
+  if (biop == NULL || sqdp == NULL) return FALSE;
 
-  if (mqp->sqdp->isOrgMod)
+  if (sqdp->isOrgMod)
   {
     if (biop->org != NULL && biop->org->orgname != NULL)
     {
       mod = biop->org->orgname->mod;
-      while (mod != NULL && !mqp->multi_found)
+      while (mod != NULL)
       {
-        if (mod->subtype == mqp->sqdp->subtype
+        if (mod->subtype == sqdp->subtype
             && !StringHasNoText (mod->subname)
-            && OrgModSpecialMatch (mod, mqp->fsp))
+            && OrgModSpecialMatch (mod, fsp))
         {
           if (found_one) {
-            mqp->multi_found = TRUE;
+            return TRUE;
           } else {
             found_one = TRUE;
           }
@@ -26663,14 +27641,14 @@ static void CheckForMultipleQuals (BioSourcePtr biop, Pointer userdata)
   else
   {
     ssp = biop->subtype;
-    while (ssp != NULL && !mqp->multi_found)
+    while (ssp != NULL)
     {
-      if (ssp->subtype == mqp->sqdp->subtype
+      if (ssp->subtype == sqdp->subtype
           && !StringHasNoText (ssp->name)
-          && SubSrcSpecialMatch (ssp, mqp->fsp))
+          && SubSrcSpecialMatch (ssp, fsp))
       {
         if (found_one) {
-          mqp->multi_found = TRUE;
+          return TRUE;
         } else {
           found_one = TRUE;
         }
@@ -26678,6 +27656,279 @@ static void CheckForMultipleQuals (BioSourcePtr biop, Pointer userdata)
       ssp = ssp->next;
     }
   }
+  return FALSE;
+}
+
+static Boolean CheckBioSrcListForMultipleQuals (ValNodePtr biosrc_list, SourceQualDescPtr sqdp, FilterSetPtr fsp)
+{
+  ValNodePtr   vnp;
+  SeqFeatPtr   sfp;
+  SeqDescrPtr  sdp;
+  Boolean      has_multiple = FALSE;
+
+  if (sqdp == NULL) return FALSE;
+
+  for (vnp = biosrc_list; vnp != NULL && !has_multiple; vnp = vnp->next)
+  {
+    if (vnp->data.ptrvalue == NULL) continue;
+    if (vnp->choice == OBJ_SEQFEAT)
+    {
+      sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+      if (sfp->data.choice == SEQFEAT_BIOSRC)
+      {
+        has_multiple = BioSourceHasMultipleQuals ((BioSourcePtr)sfp->data.value.ptrvalue, sqdp, fsp);
+      }
+    }
+    else if (vnp->choice == OBJ_SEQDESC)
+    {
+      sdp = (SeqDescrPtr) vnp->data.ptrvalue;
+      if (sdp->choice == Seq_descr_source)
+      {
+        has_multiple = BioSourceHasMultipleQuals ((BioSourcePtr)sdp->data.ptrvalue, sqdp, fsp);
+      }
+    }
+  }
+  return has_multiple;
+}
+
+
+typedef struct taxnameoptionsdlg
+{
+  DIALOG_MESSAGE_BLOCK
+  ButtoN               remove_taxref;
+  ButtoN               remove_common;
+  ButtoN               remove_old_name;
+  Nlm_ChangeNotifyProc change_notify;
+  Pointer              change_userdata;
+} TaxnameOptionsDlgData, PNTR TaxnameOptionsDlgPtr;
+
+static void TaxnameOptionsToDialog (DialoG d, Pointer data)
+{
+  TaxnameOptionsDlgPtr dlg;
+  TaxnameOptionsPtr    top;
+
+  dlg = (TaxnameOptionsDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return;
+
+  top = (TaxnameOptionsPtr) data;
+  if (top == NULL)
+  {
+    SetStatus (dlg->remove_taxref, TRUE);
+    SetStatus (dlg->remove_common, TRUE);
+    SetStatus (dlg->remove_old_name, TRUE);
+  }
+  else
+  {
+    SetStatus (dlg->remove_taxref, top->remove_taxref);
+    SetStatus (dlg->remove_common, top->remove_common);
+    SetStatus (dlg->remove_old_name, top->remove_old_name);
+  }
+  if (dlg->change_notify != NULL)
+  {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+static Pointer TaxnameOptionsFromDialog (DialoG d)
+{
+  TaxnameOptionsDlgPtr dlg;
+  TaxnameOptionsPtr    top;
+
+  dlg = (TaxnameOptionsDlgPtr) GetObjectExtra (d);
+  if (dlg == NULL) return NULL;
+
+  top = (TaxnameOptionsPtr) MemNew (sizeof (TaxnameOptionsData));
+  top->remove_taxref = GetStatus (dlg->remove_taxref);
+  top->remove_common = GetStatus (dlg->remove_common);
+  top->remove_old_name = GetStatus (dlg->remove_old_name);
+  return top;
+}
+
+
+static void ChangeTaxnameOptions (ButtoN b)
+{
+  TaxnameOptionsDlgPtr dlg;
+
+  dlg = (TaxnameOptionsDlgPtr) GetObjectExtra (b);
+  if (dlg != NULL && dlg->change_notify != NULL)
+  {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+extern DialoG TaxnameOptionsDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  TaxnameOptionsDlgPtr dlg;
+  GrouP                p;
+  
+  dlg = (TaxnameOptionsDlgPtr) MemNew (sizeof (TaxnameOptionsDlgData));
+  if (dlg == NULL)
+  {
+    return NULL;
+  }
+
+  p = HiddenGroup (h, 3, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+  SetGroupSpacing (p, 10, 10);
+  
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = TaxnameOptionsToDialog;
+  dlg->fromdialog = TaxnameOptionsFromDialog;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+
+  dlg->remove_taxref = CheckBox (p, "Remove taxonomy xref", ChangeTaxnameOptions);
+  SetObjectExtra (dlg->remove_taxref, dlg, NULL);
+  SetStatus (dlg->remove_taxref, TRUE);
+  dlg->remove_common = CheckBox (p, "Remove GenBank common name", ChangeTaxnameOptions);
+  SetObjectExtra (dlg->remove_common, dlg, NULL);
+  SetStatus (dlg->remove_common, TRUE);
+  dlg->remove_old_name = CheckBox (p, "Remove old_name qualifier", ChangeTaxnameOptions);
+  SetObjectExtra (dlg->remove_old_name, dlg, NULL);
+  SetStatus (dlg->remove_old_name, TRUE);
+  return (DialoG) p;
+}
+
+extern void ApplyTaxnameOptionsToBioSource (BioSourcePtr biop, TaxnameOptionsPtr top)
+{
+  if (biop == NULL || top == NULL) return;
+
+  if (top->remove_taxref)
+  {
+    RemoveTaxRef (biop->org);
+  }
+  if (top->remove_old_name)
+  {
+    RemoveOldName (biop->org);
+  }
+  if (top->remove_common) 
+  {
+    if (biop->org != NULL)
+    {
+      biop->org->common = MemFree (biop->org->common);
+    }
+  }
+}
+
+static void HandleTaxnameOptionsFeature (SeqFeatPtr sfp, TaxnameOptionsPtr top)
+{
+  if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC || top == NULL)
+  {
+    return;
+  }
+  ApplyTaxnameOptionsToBioSource (sfp->data.value.ptrvalue, top);
+}
+
+static void HandleTaxnameOptionsDescriptorCallback (SeqDescrPtr sdp, TaxnameOptionsPtr top)
+{
+  if (sdp == NULL || sdp->choice != Seq_descr_source || top == NULL)
+  {
+    return;
+  }
+  ApplyTaxnameOptionsToBioSource (sdp->data.ptrvalue, top);
+}
+
+
+static void HandleTaxnameOptionsForBioSourceList (ValNodePtr biosrc_list, TaxnameOptionsPtr top)
+{
+  ValNodePtr vnp;
+
+  if (top == NULL) return;
+  for (vnp = biosrc_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == OBJ_SEQFEAT) 
+    {
+      HandleTaxnameOptionsFeature (vnp->data.ptrvalue, top);
+    }
+    else if (vnp->choice == OBJ_SEQDESC)
+    {
+      HandleTaxnameOptionsDescriptorCallback (vnp->data.ptrvalue, top);
+    }
+  }  
+}
+
+static void CollectBioSourceFeatureFieldCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
+{
+  if (sfp == NULL || userdata == NULL)
+  {
+    return;
+  }
+  ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_SEQFEAT, sfp);  
+}
+
+static void CollectBioSourceDescriptorFieldCallback (SeqDescrPtr sdp, Pointer userdata, FilterSetPtr fsp)
+{  
+  if (sdp == NULL || userdata == NULL)
+  {
+    return;
+  }
+  
+  ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_SEQDESC, sdp);  
+}
+
+
+static void RemoveSourceQualEditNonMatches (ValNodePtr PNTR biosrc_list, ApplyValuePtr avp)
+{
+  ValNodePtr vnp_prev = NULL, vnp_next, vnp_this;
+  CharPtr    val1, val2;
+  Boolean    do_remove;
+
+  if (biosrc_list == NULL || avp == NULL || StringHasNoText (avp->text_to_replace))
+  {
+    return;
+  }
+
+  vnp_this = *biosrc_list;
+  while (vnp_this != NULL)
+  {
+    vnp_next = vnp_this->next;
+    do_remove = FALSE;
+    if (vnp_this->choice == OBJ_SEQFEAT)
+    {
+      val1 = GetSourceQualFeatureString (vnp_this->data.ptrvalue, avp->field_list, NULL);
+    }
+    else if (vnp_this->choice == OBJ_SEQDESC)
+    {
+      val1 = GetSourceQualDescrString (vnp_this->data.ptrvalue, avp->field_list, NULL);
+    } 
+    else
+    {
+      val1 = NULL;
+    }
+    if (val1 == NULL)
+    {
+      do_remove = TRUE;
+    }
+    else
+    {
+      val2 = HandleApplyValue (StringSave (val1), avp);
+      if (StringCmp (val1, val2) == 0)
+      {
+        do_remove = TRUE;
+      }
+      val1 = MemFree (val1);
+      val2 = MemFree (val2);
+    }
+    if (do_remove)
+    {
+      if (vnp_prev == NULL)
+      {
+        *biosrc_list = vnp_this->next;
+      }
+      else
+      {
+        vnp_prev->next = vnp_this->next;
+      }
+      vnp_this->next = NULL;
+      vnp_this = ValNodeFree (vnp_this);
+    }
+    else
+    {
+      vnp_prev = vnp_this;
+    }
+    vnp_this = vnp_next;
+  }
 }
 
 
@@ -26694,7 +27945,8 @@ SourceQualQualApplyEditConvertRemoveAction
  GetFeatureFieldString       fieldstring_func,
  GetDescriptorFieldString    descrstring_func,
  Boolean                     non_text,
- NameFromValNodeProc         name_field_func)
+ NameFromValNodeProc         name_field_func,
+ TaxnameOptionsPtr           top)
 
 {
   SeqEntryPtr               sep;
@@ -26704,9 +27956,10 @@ SourceQualQualApplyEditConvertRemoveAction
   GetSamplePtr              gsp;
   Boolean                   rval = TRUE;
   ValNodePtr                vnp;
-  MultiQualData             mqd;
   CharPtr                   field_name = NULL;
   MsgAnswer                 ans;
+  ValNodePtr                biosrc_list = NULL;
+  SourceQualDescPtr         multi_sqdp = NULL;
   
   sep = GetTopSeqEntryForEntityID (ap->input_entityID);
   if (sp == NULL
@@ -26727,21 +27980,25 @@ SourceQualQualApplyEditConvertRemoveAction
   avd.where_to_replace = EditApplyFindLocation_anywhere;
 
   fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
+
+  /* collect list of BioSources that will be acted upon */
+  OperateOnSeqEntryConstrainedObjects (sep, fsp, 
+                                       CollectBioSourceFeatureFieldCallback,
+                                       CollectBioSourceDescriptorFieldCallback,
+                                       SEQFEAT_BIOSRC, 0, Seq_descr_source,
+                                       &biosrc_list);    
   
   if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
   {
     /* check for multiple sources */
-    mqd.fsp = fsp;
-    mqd.multi_found = FALSE;
-    mqd.sqdp = sp->field_list->data.ptrvalue;
-    VisitBioSourcesInSep (sep, &mqd, CheckForMultipleQuals);
-    if (!mqd.multi_found && action_choice == AECR_SWAP) {
-      mqd.sqdp = sp->field_list_to->data.ptrvalue;
-      VisitBioSourcesInSep (sep, &mqd, CheckForMultipleQuals);
-    }
-    if (mqd.multi_found) {
+    if ((sp->field_list->choice == 0
+         && (multi_sqdp = sp->field_list->data.ptrvalue) != NULL
+         && CheckBioSrcListForMultipleQuals(biosrc_list, multi_sqdp, fsp))
+        || (action_choice == AECR_SWAP && sp->field_list_to->choice == 0
+            && (multi_sqdp = sp->field_list_to->data.ptrvalue) != NULL
+            && CheckBioSrcListForMultipleQuals(biosrc_list, multi_sqdp, fsp))) {
       if (name_field_func != NULL) {  
-        if (action_choice == AECR_SWAP && mqd.sqdp == sp->field_list_to->data.ptrvalue) {
+        if (action_choice == AECR_SWAP && multi_sqdp == sp->field_list_to->data.ptrvalue) {
           field_name = name_field_func(sp->field_list_to);
         } else {
           field_name = name_field_func(sp->field_list);
@@ -26864,6 +28121,13 @@ SourceQualQualApplyEditConvertRemoveAction
     if (rval)
     {
       AddEditApplyDataToApplyValue (action_choice, sp->edit_apply, &avd);
+
+      if (action_choice == AECR_EDIT)
+      {
+        /* remove items that don't contain text that will be replaced */
+        RemoveSourceQualEditNonMatches (&biosrc_list, &avd);
+      }
+
    
       if (action_choice == AECR_EDIT || action_choice == AECR_APPLY)
       {
@@ -26889,13 +28153,18 @@ SourceQualQualApplyEditConvertRemoveAction
     }
     avd.etp = MemFree (avd.etp);
   }
+
   FilterSetFree (fsp);
   
   if (rval)
   {
+    /* Handle taxname options */
+    HandleTaxnameOptionsForBioSourceList (biosrc_list, top);
+
     ObjMgrSetDirtyFlag (ap->input_entityID, TRUE);
     ObjMgrSendMsg (OM_MSG_UPDATE, ap->input_entityID, 0, 0);
   }
+  biosrc_list = ValNodeFree (biosrc_list);
   ArrowCursor ();
   Update (); 
   
@@ -26942,7 +28211,8 @@ static Boolean SourceQualApplyEditConvertRemoveAction (Pointer userdata)
                                        GetSourceQualFeatureString,
                                        GetSourceQualDescrString,
                                        FALSE,
-                                       SourceQualValNodeName);
+                                       SourceQualValNodeName,
+                                       NULL);
       break;
     case QUALKIND_STRINGS :
       rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->strings, 
@@ -26955,7 +28225,8 @@ static Boolean SourceQualApplyEditConvertRemoveAction (Pointer userdata)
                                        GetStringFromSourceFeature,
                                        GetStringFromSourceDescriptor,
                                        FALSE,
-                                       NULL);
+                                       NULL,
+                                       sp->taxname_options);
       break;
     case QUALKIND_LOCATION :
       rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->location, 
@@ -26968,7 +28239,8 @@ static Boolean SourceQualApplyEditConvertRemoveAction (Pointer userdata)
                                        GetLocationFromSourceFeature,
                                        GetLocationFromSourceDescriptor,
                                        TRUE,
-                                       ValNodeStringName);
+                                       ValNodeStringName,
+                                       NULL);
       break;      
     case QUALKIND_ORIGIN :
       rval = SourceQualQualApplyEditConvertRemoveAction (ap, sp->origin, 
@@ -26981,7 +28253,8 @@ static Boolean SourceQualApplyEditConvertRemoveAction (Pointer userdata)
                                        GetOriginFromSourceFeature,
                                        GetOriginFromSourceDescriptor,
                                        TRUE,
-                                       ValNodeStringName);
+                                       ValNodeStringName,
+                                       NULL);
       break;      
   }
   sp = SourceQualAECRFree (sp);
@@ -27080,18 +28353,15 @@ extern void RemoveSourceQual (IteM i)
   SourceQualApplyEditConvertRemove (i, AECR_REMOVE, FALSE);
 }
 
-static CharPtr rna_sample_field_list [] = { "Name", 
-                                            "Comment", 
-                                            "Product GBQual" };
+static CharPtr rna_sample_field_list [] = { "Product", 
+                                            "Comment" };
 static Int2    num_rna_sample_fields = sizeof (rna_sample_field_list) / sizeof (CharPtr);
 
 
-
 static CharPtr GetRNASampleFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSetPtr fsp)
 {
   RnaRefPtr  rrp;
   CharPtr    str = NULL;
-  GBQualPtr  gbqual;
   Int2       rna_subtype, rna_field_type;
   GeneRefPtr grp;
   SeqFeatPtr gene;
@@ -27109,19 +28379,52 @@ static CharPtr GetRNASampleFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSe
   {
     rna_subtype = (vnp->data.intvalue - 1) / (num_rna_sample_fields + num_gene_fields);
     rna_field_type = (vnp->data.intvalue - 1) % (num_rna_sample_fields + num_gene_fields);
-    if (rna_subtype == 0)
-    {
-      rna_subtype = 255;
-    }
-    if (rna_subtype != rrp->type)
+    switch (rna_subtype)
     {
-      vnp = vnp->next;
-      continue;
+      case 0:
+        if (rrp->type != 255 
+            || (rrp->ext.choice == 1
+                && (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") == 0
+                    || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") == 0)))
+        {
+          vnp = vnp->next;
+          continue;
+        }
+        break;
+      case 1:
+      case 2:
+      case 3:
+      case 4:
+        if (rna_subtype != rrp->type)
+        {
+          vnp = vnp->next;
+          continue;
+        }
+        break;
+      case 5:
+        if (rrp->type != 255 
+            || rrp->ext.choice != 1
+            || StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0)
+        {
+          vnp = vnp->next;
+          continue;
+        }
+        break;
+      case 6:
+        if (rrp->type != 255 
+            || rrp->ext.choice != 1
+            || StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0)
+        {
+          vnp = vnp->next;
+          continue;
+        }
+        break;
     }
+
     switch (rna_field_type)
     {
       case 0 :
-        str = GetRNANameString (sfp);
+        str = GetRNAProductString (sfp);
         break;
       case 1 :
         if (!StringHasNoText (sfp->comment))
@@ -27129,17 +28432,6 @@ static CharPtr GetRNASampleFieldString (SeqFeatPtr sfp, ValNodePtr vnp, FilterSe
           str = StringSave (sfp->comment);
         }
         break;
-      case 2 :
-        gbqual = sfp->qual;
-        while (gbqual != NULL && str == NULL) {
-          if (StringICmp (gbqual->qual, "product") == 0
-              && !StringHasNoText (gbqual->val)) 
-          {
-            str = StringSave (gbqual->val);
-          }
-          gbqual = gbqual->next;
-        }
-        break;
       default :
         vn.next = NULL;
         vn.choice = 0;
@@ -27240,21 +28532,26 @@ static DialoG GetRNAQualSample (GrouP h, Uint2 entityID)
   return d;
 }
 
-typedef struct applyrnaqual
+typedef struct aecrrnaqual
 {
   ValNodePtr   field_list;
-  ValNodePtr   subtype_list;
+  ValNodePtr   field_list_to;
+  RnaTypePtr   rna_type;
   EditApplyPtr edit_apply;
   ValNodePtr   codons;
   SeqLocPtr    anticodon;
-} ApplyRNAQualData, PNTR ApplyRNAQualPtr;
+  TextPortionXPtr text_portion;
+  Boolean        leave_on_original;
+  Boolean        remove_parsed;
+} AECRRNAQualData, PNTR AECRRNAQualPtr;
 
-static ApplyRNAQualPtr ApplyRNAQualFree (ApplyRNAQualPtr ap)
+static AECRRNAQualPtr AECRRNAQualFree (AECRRNAQualPtr ap)
 {
   if (ap != NULL)
   {
     ap->field_list = ValNodeFree (ap->field_list);
-    ap->subtype_list = ValNodeFree (ap->subtype_list);
+    ap->field_list_to = ValNodeFree (ap->field_list_to);
+    ap->rna_type = RnaTypeFree (ap->rna_type);
     ap->edit_apply = EditApplyFree (ap->edit_apply);
     ap->codons = ValNodeFreeData (ap->codons);
     ap = MemFree (ap);
@@ -27262,13 +28559,19 @@ static ApplyRNAQualPtr ApplyRNAQualFree (ApplyRNAQualPtr ap)
   return ap;
 }
 
-typedef struct applyrnaqualdlg
+typedef struct aecrrnaqualdlg
 {
   DIALOG_MESSAGE_BLOCK
   DialoG               field_list;
-  DialoG               subtype_list;
+  DialoG               field_list_to;
+  DialoG               rna_type;
   DialoG               edit_apply;
   DialoG               codons;
+  DialoG               ncrna_class;
+  DialoG               text_portion;
+  ButtoN               leave_on_original;
+  ButtoN               remove_parsed;
+
   Nlm_ChangeNotifyProc change_notify;
   Pointer              change_userdata;
   Uint2                entityID;
@@ -27276,108 +28579,136 @@ typedef struct applyrnaqualdlg
   /* The following is used to create the anticodon location dialog */
   FeatureForm          ff;
   DialoG               anticodon;
-} ApplyRNAQualDlgData, PNTR ApplyRNAQualDlgPtr;
+} AECRRNAQualDlgData, PNTR AECRRNAQualDlgPtr;
 
-static void ClearTextApplyRNAQualDlg (ApplyRNAQualDlgPtr dlg)
+static void ClearTextAECRRNAQualDlg (AECRRNAQualDlgPtr dlg)
 {
   if (dlg != NULL)
   {
     PointerToDialog (dlg->edit_apply, NULL);
     PointerToDialog (dlg->codons, NULL);
+    PointerToDialog (dlg->ncrna_class, NULL);
   }
 }
 
-static void ResetApplyRNAQualDlg (ApplyRNAQualDlgPtr dlg)
+static void ResetAECRRNAQualDlg (AECRRNAQualDlgPtr dlg)
 {
   if (dlg != NULL)
   {
     PointerToDialog (dlg->field_list, NULL);
+    PointerToDialog (dlg->field_list_to, NULL);
     SendMessageToDialog (dlg->field_list, NUM_VIB_MSG + 1);
-    PointerToDialog (dlg->subtype_list, NULL);
-    ClearTextApplyRNAQualDlg (dlg);
+    PointerToDialog (dlg->rna_type, NULL);
+    PointerToDialog (dlg->text_portion, NULL);
+    SafeSetStatus (dlg->leave_on_original, FALSE);
+    SafeSetStatus (dlg->remove_parsed, FALSE);
+    ClearTextAECRRNAQualDlg (dlg);
   }
 }
 
-static void ApplyRNAQualToDialog (DialoG d, Pointer userdata)
+static void AECRRNAQualToDialog (DialoG d, Pointer userdata)
 {
-  ApplyRNAQualDlgPtr dlg;
-  ApplyRNAQualPtr    data;
+  AECRRNAQualDlgPtr dlg;
+  AECRRNAQualPtr    data;
   
-  dlg = (ApplyRNAQualDlgPtr) GetObjectExtra (d);
+  dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
   if (dlg == NULL)
   {
     return;
   }
   
-  ResetApplyRNAQualDlg (dlg);
-  data = (ApplyRNAQualPtr) userdata;
+  ResetAECRRNAQualDlg (dlg);
+  data = (AECRRNAQualPtr) userdata;
   if (data != NULL)
   {
     PointerToDialog (dlg->field_list, data->field_list);
-    PointerToDialog (dlg->subtype_list, data->subtype_list);
+    PointerToDialog (dlg->field_list_to, data->field_list_to);
+    PointerToDialog (dlg->rna_type, data->rna_type);
     PointerToDialog (dlg->edit_apply, data->edit_apply);
     PointerToDialog (dlg->codons, data->codons);
+    if (data->field_list != NULL && data->field_list->data.intvalue == RNAFIELD_NCRNA_CLASS) {
+      if (data->edit_apply == NULL) {
+        PointerToDialog (dlg->ncrna_class, NULL);
+      } else {
+        PointerToDialog (dlg->ncrna_class, data->edit_apply->apply_txt);
+      }
+    }
     PointerToDialog (dlg->anticodon, data->anticodon);
+    PointerToDialog (dlg->text_portion, data->text_portion);
+    SafeSetStatus (dlg->leave_on_original, data->leave_on_original);
+    SafeSetStatus (dlg->remove_parsed, data->remove_parsed);
   }
 }
 
-static Pointer DialogToApplyRNAQual (DialoG d)
+static Pointer DialogToAECRRNAQual (DialoG d)
 {
-  ApplyRNAQualDlgPtr dlg;
-  ApplyRNAQualPtr    data;
+  AECRRNAQualDlgPtr dlg;
+  AECRRNAQualPtr    data;
   
-  dlg = (ApplyRNAQualDlgPtr) GetObjectExtra (d);
+  dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
   if (dlg == NULL)
   {
     return NULL;
   }
   
-  data = (ApplyRNAQualPtr) MemNew (sizeof (ApplyRNAQualData));
+  data = (AECRRNAQualPtr) MemNew (sizeof (AECRRNAQualData));
   if (data != NULL)
   {
     data->field_list = DialogToPointer (dlg->field_list);
-    data->subtype_list = DialogToPointer (dlg->subtype_list);
-    data->edit_apply = DialogToPointer (dlg->edit_apply);
+    data->field_list_to = DialogToPointer (dlg->field_list_to);
+    data->rna_type = DialogToPointer (dlg->rna_type);
+    if (data->field_list != NULL && data->field_list->data.intvalue == RNAFIELD_NCRNA_CLASS
+        && dlg->ncrna_class != NULL) {
+      data->edit_apply = EditApplyNew ();
+      data->edit_apply->apply_txt = DialogToPointer (dlg->ncrna_class);
+    } else {
+      data->edit_apply = DialogToPointer (dlg->edit_apply);
+    }
     data->codons = DialogToPointer (dlg->codons);
     data->anticodon = DialogToPointer (dlg->anticodon);
+    data->text_portion = DialogToPointer (dlg->text_portion);
+    data->leave_on_original = (dlg->leave_on_original == NULL) ? FALSE : GetStatus (dlg->leave_on_original);
+    data->remove_parsed = (dlg->remove_parsed == NULL) ? FALSE : GetStatus (dlg->remove_parsed);
   }
   return data;
 }
 
+static ValNodePtr GetRNAFeatureList (SeqEntryPtr sep, FilterSetPtr fsp, RnaTypePtr rtp);
+static GetSamplePtr GetRnaExistingTextForList (ValNodePtr rna_list, ValNodePtr requested_field);
+
 static CharPtr 
 RNAQualAutopopulate 
-(ValNodePtr subtype_list,
+(RnaTypePtr rna_type,
  ValNodePtr field_list,
  Uint2      entityID)
 {
+  SeqEntryPtr  sep;
   GetSamplePtr gsp;
+  ValNodePtr   rna_list;
   CharPtr      rval = NULL;
-  ValNodePtr   vnp;
 
-  for (vnp = subtype_list; vnp != NULL && rval == NULL; vnp = vnp->next)
+  sep = GetTopSeqEntryForEntityID (entityID);
+  rna_list = GetRNAFeatureList (sep, NULL, rna_type);
+  gsp = GetRnaExistingTextForList (rna_list, field_list);
+  if (gsp != NULL && !StringHasNoText (gsp->sample_text))
   {
-    gsp = CheckForExistingText (entityID,
-                                field_list,
-                                GetRNAFieldString,
-                                NULL, NULL, IntValNodeCopy,
-                                NULL, SEQFEAT_RNA, vnp->data.intvalue, 0);
-    if (gsp != NULL && !StringHasNoText (gsp->sample_text))
-    {
-      rval = gsp->sample_text;
-      gsp->sample_text = NULL;
-    }
-    GetSampleFree (gsp);
+    rval = gsp->sample_text;
+    gsp->sample_text = NULL;
   }
+  GetSampleFree (gsp);
+  rna_list = ValNodeFree (rna_list);
   return rval;
 }
 
 static void RNAQualChangeNotify (Pointer userdata)
 {
-  ApplyRNAQualDlgPtr dlg;
-  ValNodePtr         field_list = NULL, subtype_list = NULL;
+  AECRRNAQualDlgPtr  dlg;
+  ValNodePtr         field_list = NULL;
+  RnaTypePtr         rna_type;
   EditApplyPtr       eap;
+  CharPtr            ncrna_class;
 
-  dlg = (ApplyRNAQualDlgPtr) userdata;
+  dlg = (AECRRNAQualDlgPtr) userdata;
   if (dlg == NULL)
   {
     return;
@@ -27389,33 +28720,52 @@ static void RNAQualChangeNotify (Pointer userdata)
     Hide (dlg->edit_apply);
     Hide (dlg->anticodon);
     Hide (dlg->codons);
+    Hide (dlg->ncrna_class);
   }  
   else if (field_list->data.intvalue == RNAFIELD_CODONS_RECOGNIZED)
   {
     Show (dlg->codons);
     Hide (dlg->edit_apply);
     Hide (dlg->anticodon);
+    Hide (dlg->ncrna_class);
   }
   else if (field_list->data.intvalue == RNAFIELD_ANTICODON)
   {
     Show (dlg->anticodon);
     Hide (dlg->edit_apply);
     Hide (dlg->codons);
+    Hide (dlg->ncrna_class);
+  }
+  else if (field_list->data.intvalue == RNAFIELD_NCRNA_CLASS && dlg->ncrna_class != NULL)
+  {
+    Show (dlg->ncrna_class);
+    Hide (dlg->codons);
+    Hide (dlg->edit_apply);
+    Hide (dlg->anticodon);
+    /* autopopulate */
+    rna_type = DialogToPointer (dlg->rna_type);
+    ncrna_class = RNAQualAutopopulate (rna_type, field_list, dlg->entityID);
+    PointerToDialog (dlg->ncrna_class, ncrna_class);
+    ncrna_class = MemFree (ncrna_class);
   }
   else
   {
     Show (dlg->edit_apply);
     Hide (dlg->codons);
     Hide (dlg->anticodon);
+    Hide (dlg->ncrna_class);
 
     /* autopopulate text fields */
-    subtype_list = DialogToPointer (dlg->subtype_list);
-    eap = DialogToPointer (dlg->edit_apply);
-    eap->apply_txt = MemFree (eap->apply_txt);
-    eap->apply_txt = RNAQualAutopopulate (subtype_list, field_list, dlg->entityID);
-    PointerToDialog (dlg->edit_apply, eap);
-    EditApplyFree (eap);    
-    subtype_list = ValNodeFree (subtype_list);
+    if (dlg->edit_apply != NULL)
+    {    
+      rna_type = DialogToPointer (dlg->rna_type);
+      eap = DialogToPointer (dlg->edit_apply);
+      eap->apply_txt = MemFree (eap->apply_txt);
+      eap->apply_txt = RNAQualAutopopulate (rna_type, field_list, dlg->entityID);
+      PointerToDialog (dlg->edit_apply, eap);
+      EditApplyFree (eap);    
+      rna_type = RnaTypeFree (rna_type);
+    }
   }
   
   field_list = ValNodeFree (field_list);
@@ -27426,36 +28776,29 @@ static void RNAQualChangeNotify (Pointer userdata)
   }  
 }
 
-static void ApplyRNAQualMessage (DialoG d, Int2 mssg)
+static void AECRRNAQualMessage (DialoG d, Int2 mssg)
 
 {
-  ApplyRNAQualDlgPtr  dlg;
+  AECRRNAQualDlgPtr  dlg;
 
-  dlg = (ApplyRNAQualDlgPtr) GetObjectExtra (d);
+  dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
   if (dlg != NULL) {
     switch (mssg) 
     {
       case VIB_MSG_INIT :
         /* reset list */
-        ResetApplyRNAQualDlg (dlg);
+        ResetAECRRNAQualDlg (dlg);
         break;
       case VIB_MSG_ENTER :
-        if (dlg->subtype_list != NULL)
-        {
-          Select (dlg->subtype_list);
-        }
-        else
-        {
-          Select (dlg->field_list);
-        }
+        Select (dlg->rna_type);
         break;
       case AECR_VIB_MSG_SET_DEFAULT :
         SendMessageToDialog (dlg->field_list, AECR_VIB_MSG_SET_DEFAULT);
-        SendMessageToDialog (dlg->subtype_list, AECR_VIB_MSG_SET_DEFAULT);
-        ClearTextApplyRNAQualDlg (dlg);
+        SendMessageToDialog (dlg->rna_type, AECR_VIB_MSG_SET_DEFAULT);
+        ClearTextAECRRNAQualDlg (dlg);
         break;
       case AECR_VIB_MSG_CLEAR_TEXT :
-        ClearTextApplyRNAQualDlg (dlg);
+        ClearTextAECRRNAQualDlg (dlg);
         break;
       case AECR_VIB_MSG_AUTOPOPULATE:
         RNAQualChangeNotify (dlg);
@@ -27466,45 +28809,61 @@ static void ApplyRNAQualMessage (DialoG d, Int2 mssg)
   }
 }
 
-static ValNodePtr TestApplyRNAQual (DialoG d)
+static ValNodePtr TestAECRRNAQual (DialoG d)
 {
-  ApplyRNAQualDlgPtr dlg;
-  ValNodePtr         err_list = NULL;
+  AECRRNAQualDlgPtr dlg;
   ValNodePtr         total_err_list = NULL;
   ValNodePtr         field_list;
   
-  dlg = (ApplyRNAQualDlgPtr) GetObjectExtra (d);
+  dlg = (AECRRNAQualDlgPtr) GetObjectExtra (d);
   if (dlg == NULL)
   {
     return NULL;
   }
 
-  total_err_list = TestDialog (dlg->subtype_list);
+  total_err_list = TestDialog (dlg->rna_type);
   
-  err_list = TestDialog (dlg->field_list);
-  total_err_list = ValNodeAppend (total_err_list, err_list);
+  ValNodeLink (&total_err_list, TestDialog (dlg->field_list));
       
   field_list = DialogToPointer (dlg->field_list);
-  if (field_list != NULL && field_list->data.intvalue != RNAFIELD_CODONS_RECOGNIZED)
-  {
-    err_list = TestDialog (dlg->edit_apply);
-    total_err_list = ValNodeAppend (total_err_list, err_list);
+  if (field_list != NULL) {
+    if (field_list->data.intvalue == RNAFIELD_NCRNA_CLASS && dlg->ncrna_class != NULL) {
+      ValNodeLink (&total_err_list, TestDialog (dlg->ncrna_class));
+    } else if (field_list->data.intvalue != RNAFIELD_CODONS_RECOGNIZED) {
+      ValNodeLink (&total_err_list, TestDialog (dlg->edit_apply));
+    }
   }
       
   return total_err_list;
 }
 
-static DialoG ApplyRNAQualDialog
+
+static void AECRRNAQualButtonChange (ButtoN b)
+{
+  AECRRNAQualDlgPtr dlg;
+
+  dlg = (AECRRNAQualDlgPtr) GetObjectExtra (b);
+  if (dlg == NULL) return;
+
+  if (dlg->change_notify != NULL) 
+  {
+    (dlg->change_notify) (dlg->change_userdata);
+  }
+}
+
+
+static DialoG RNAQualListDialog
 (GrouP                    h,
+ Int4                     action_choice, 
  Nlm_ChangeNotifyProc     change_notify,
  Pointer                  change_userdata,
  Uint2                    entityID)
 {
-  ApplyRNAQualDlgPtr dlg;
-  GrouP              p, g1, g2;
+  AECRRNAQualDlgPtr dlg;
+  GrouP              p, g1, g2 = NULL;
   SeqEntryPtr        sep;
   
-  dlg = (ApplyRNAQualDlgPtr) MemNew (sizeof (ApplyRNAQualDlgData));
+  dlg = (AECRRNAQualDlgPtr) MemNew (sizeof (AECRRNAQualDlgData));
   if (dlg == NULL)
   {
     return NULL;
@@ -27515,43 +28874,104 @@ static DialoG ApplyRNAQualDialog
   SetGroupSpacing (p, 10, 10);
   
   dlg->dialog = (DialoG) p;
-  dlg->todialog = ApplyRNAQualToDialog;
-  dlg->fromdialog = DialogToApplyRNAQual;
-  dlg->dialogmessage = ApplyRNAQualMessage;
-  dlg->testdialog = TestApplyRNAQual;
+  dlg->todialog = AECRRNAQualToDialog;
+  dlg->fromdialog = DialogToAECRRNAQual;
+  dlg->dialogmessage = AECRRNAQualMessage;
+  dlg->testdialog = TestAECRRNAQual;
   dlg->change_notify = change_notify;
   dlg->change_userdata = change_userdata;
   dlg->entityID = entityID;
+
+
+  if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
+  {
+    g1 = HiddenGroup (p, 3, 0, NULL);
+    StaticPrompt (g1, "", 0, dialogTextHeight, systemFont, 'l');
+    StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'l');
+    StaticPrompt (g1, "To", 0, dialogTextHeight, systemFont, 'l');
+    dlg->rna_type = RnaTypeDialog (g1, TRUE, RNAQualChangeNotify, dlg);
+
+    dlg->field_list = RNAFieldSelectionDialog (g1, FALSE, 
+                                          change_notify, 
+                                          change_userdata);
+    dlg->field_list_to = RNAFieldSelectionDialog (g1, FALSE, 
+                                             change_notify, 
+                                             change_userdata);
+    if (action_choice == AECR_CONVERT)
+    {
+      dlg->leave_on_original = CheckBox (p, "Leave on original", AECRRNAQualButtonChange);
+      SetObjectExtra (dlg->leave_on_original, dlg, NULL);
+    }
+  }
+  else
+  {
+    g1 = HiddenGroup (p, 2, 0, NULL);
+    StaticPrompt (g1, "", 0, dialogTextHeight, systemFont, 'l');
+    StaticPrompt (g1, "RNA Field", 0, dialogTextHeight, systemFont, 'l');
+    dlg->rna_type = RnaTypeDialog (g1, TRUE, RNAQualChangeNotify, dlg);
+    if (action_choice == AECR_REMOVE)
+    {
+      dlg->field_list = RNARemoveFieldSelectionDialog (g1, TRUE, 
+                                            RNAQualChangeNotify, dlg);
+    }
+    else
+    {
+      dlg->field_list = RNAFieldSelectionDialog (g1, FALSE, 
+                                            RNAQualChangeNotify, 
+                                            dlg);
+    }
+  }
+
+  if (action_choice == AECR_APPLY)
+  {
+    g2 = HiddenGroup (p, 0, 0, NULL);
+    dlg->edit_apply = EditApplyDialog (g2, eEditApplyChoice_Apply, "New Text", NULL,
+                                       change_notify, change_userdata);
   
-  g1 = HiddenGroup (p, 2, 0, NULL);
-  StaticPrompt (g1, "RNA Type", 0, dialogTextHeight, systemFont, 'l');
-  StaticPrompt (g1, "RNA Field", 0, dialogTextHeight, systemFont, 'l');
-  dlg->subtype_list = RNASubtypeSelectionDialog (g1, TRUE, NULL,
-                                                 RNAQualChangeNotify,
-                                                 dlg);
-  dlg->field_list = RNAAddFieldSelectionDialog (g1, FALSE, 
-                                                RNAQualChangeNotify,
-                                                dlg);
-  
-  g2 = HiddenGroup (p, 0, 0, NULL);
-  dlg->edit_apply = EditApplyDialog (g2, eEditApplyChoice_Apply, "New Text", NULL,
-                                     change_notify, change_userdata);
-  
-  dlg->codons = CreateVisibleStringDialog (g2, 3, -1, 4);
+    dlg->codons = CreateVisibleStringDialog (g2, 3, -1, 4);
+
+    dlg->ncrna_class = CreatencRNAClassDialog (g2, FALSE, change_notify, change_userdata);
   
-  sep = GetTopSeqEntryForEntityID (entityID);
+    sep = GetTopSeqEntryForEntityID (entityID);
   
-  dlg->anticodon = NULL;
-/*
-  dlg->anticodon = CreateIntervalEditorDialogEx (g2, NULL, 2, 2, sep, TRUE, FALSE,
-                                                  TRUE, TRUE, FALSE,
-                                                  &(dlg->ff),
-                                                  NULL); */
+    dlg->anticodon = NULL;
+  /*
+    dlg->anticodon = CreateIntervalEditorDialogEx (g2, NULL, 2, 2, sep, TRUE, FALSE,
+                                                    TRUE, TRUE, FALSE,
+                                                    &(dlg->ff),
+                                                    NULL); */
 
-  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->edit_apply,
-                              (HANDLE) dlg->codons,
-                              (HANDLE) dlg->anticodon,
-                              NULL);
+    AlignObjects (ALIGN_CENTER, (HANDLE) dlg->edit_apply,
+                                (HANDLE) dlg->codons,
+                                (HANDLE) dlg->ncrna_class,
+                                (HANDLE) dlg->anticodon,
+                                NULL);
+  }
+  else if (action_choice == AECR_EDIT)
+  {
+    g2 = HiddenGroup (p, 1, 0, NULL);
+    dlg->edit_apply = EditApplyDialog (g2, eEditApplyChoice_Edit,
+                                       "New Text", NULL,
+                                       change_notify, change_userdata);
+    dlg->text_portion = NULL;
+    dlg->remove_parsed = NULL;
+  }
+  else if (action_choice == AECR_PARSE)
+  {
+    g2 = HiddenGroup (p, -1, 0, NULL);
+    dlg->edit_apply = NULL;
+    dlg->text_portion = TextPortionXDialog(p);
+    dlg->remove_parsed = CheckBox (p, "Remove from parsed field", SimpleAECRButtonChange);
+    SetObjectExtra (dlg->remove_parsed, dlg, NULL);
+    AlignObjects (ALIGN_CENTER, (HANDLE) dlg->edit_apply, (HANDLE) dlg->remove_parsed, NULL);
+  }
+  else
+  {
+    dlg->edit_apply = NULL;
+    dlg->text_portion = NULL;
+    dlg->remove_parsed = NULL;
+  }
+  
 
   AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL);
   
@@ -27560,50 +28980,6 @@ static DialoG ApplyRNAQualDialog
   return (DialoG) p;
 }
 
-static DialoG RNAQualListDialog 
-(GrouP                    h,
- Int4                     action_choice,
- Nlm_ChangeNotifyProc     change_notify,
- Pointer                  change_userdata,
- Uint2                    entityID)
-{
-  DialoG d = NULL;
-  
-  switch (action_choice)
-  {
-    case AECR_REMOVE:
-      d = SimpleAECRDialog (h, action_choice, change_notify, change_userdata,
-                            NULL, NULL,
-                            RNARemoveFieldSelectionDialog,
-                            RNASubtypeSelectionDialog,
-                            NULL,
-                            "RNA Field", "RNA type", FALSE, entityID);
-      break;
-    case AECR_CONVERT:
-    case AECR_SWAP:
-    case AECR_PARSE:
-      d = SimpleAECRDialog (h, action_choice, change_notify, change_userdata,
-                            NULL, NULL,
-                            RNAFieldSelectionDialog,
-                            RNASubtypeSelectionDialog,
-                            NULL,
-                            "RNA Field", "RNA type", TRUE, entityID);
-      break;
-      break;
-    case AECR_EDIT:
-      d = SimpleAECRDialog (h, action_choice, change_notify, change_userdata,
-                            NULL, NULL,
-                            RNAFieldSelectionDialog,
-                            RNASubtypeSelectionDialog,
-                            RNAQualAutopopulate,
-                            "RNA Field", "RNA type", TRUE, entityID);
-      break;
-    case AECR_APPLY:
-      d = ApplyRNAQualDialog (h, change_notify, change_userdata, entityID);
-      break;
-  }
-  return d;
-}
 
 static void ApplyRNACodonsCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
 {
@@ -27658,46 +29034,108 @@ static void ApplyRNAAnticodonCallback (SeqFeatPtr sfp, Pointer userdata, FilterS
   }
 }
 
-static Boolean AcceptRNAApply (ApplyEditConvertRemovePtr ap)
-{
-  ApplyRNAQualPtr rp;
-  FilterSetPtr    fsp;
-  ApplyValueData  avd;
-  Boolean         rval = TRUE;
-  SeqEntryPtr     sep;
-  ValNodePtr      vnp;
-  GetSamplePtr    gsp, gsp_new, gsp_sum;
-  
-  if (ap == NULL)
+
+static void CollectRNAFeaturesCallback (SeqFeatPtr sfp, Pointer userdata, FilterSetPtr fsp)
+{  
+  if (sfp != NULL && sfp->data.choice == SEQFEAT_RNA && userdata != NULL)
   {
-    return FALSE;
+    ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_SEQFEAT, sfp);
   }
   
-  rp = DialogToPointer (ap->aecr_pages[AECR_APPLY - 1]);
-  
-  sep = GetTopSeqEntryForEntityID (ap->input_entityID);
-  if (rp->subtype_list == NULL || rp->field_list == NULL)
+}
+
+
+static ValNodePtr GetRNAFeatureList (SeqEntryPtr sep, FilterSetPtr fsp, RnaTypePtr rtp)
+{
+  ValNodePtr rna_list = NULL, vnp_rna;
+  ValNodePtr not_match;
+  SeqFeatPtr sfp;
+  Boolean    matches;
+
+  if (sep == NULL) return NULL;
+
+  OperateOnSeqEntryConstrainedObjects (sep, fsp, CollectRNAFeaturesCallback,
+                                       NULL, SEQFEAT_RNA, 0, 0, &rna_list);  
+
+  if (rtp != NULL)
+  {
+    for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
+    {  
+      matches = FALSE;
+      sfp = vnp_rna->data.ptrvalue;
+      if (!MatchesRnaType (sfp, rtp))
+      {
+        vnp_rna->choice = 0;
+      }
+    }
+
+    not_match = ValNodeExtractList (&rna_list, 0);
+    not_match = ValNodeFree (not_match);
+  }
+  return rna_list;
+}
+
+
+static GetSamplePtr GetRnaExistingTextForList (ValNodePtr rna_list, ValNodePtr requested_field)
+{
+  GetSamplePtr gsp;
+  ValNodePtr   vnp;
+  SeqFeatPtr   sfp;
+
+  if (rna_list == NULL || requested_field == NULL) return NULL;
+
+  gsp = GetSampleNew ();
+  gsp->sample_text = NULL;
+  gsp->fieldstring_func = GetRNAFieldString;
+  gsp->descrstring_func = NULL;
+  gsp->free_vn_proc = NULL;
+  gsp->copy_vn_proc = IntValNodeCopy;
+  gsp->requested_field = (gsp->copy_vn_proc) (requested_field);
+  gsp->num_found = 0;
+  gsp->all_same = TRUE;
+
+  for (vnp = rna_list; vnp != NULL; vnp = vnp->next)
+  {  
+    sfp = vnp->data.ptrvalue;
+    GetSampleFeatureCallback (sfp, gsp, NULL);
+  }
+  return gsp;
+}
+
+
+static Boolean ApplyToRNAList (ValNodePtr rna_list, AECRRNAQualPtr rp, FilterSetPtr fsp)
+{
+  ValNodePtr      vnp_rna;
+  SeqFeatPtr      sfp;
+  ApplyValueData  avd;
+  Boolean         rval = TRUE;
+  GetSamplePtr    gsp;
+
+  if (rna_list == NULL || rp == NULL || rp->field_list == NULL)
   {
-    rp = ApplyRNAQualFree (rp);
     return FALSE;
   }
-  
-  fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
-  
+
   if (rp->field_list->data.intvalue == RNAFIELD_CODONS_RECOGNIZED)
   {
-    for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
+    for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
     {
-      OperateOnSeqEntryConstrainedObjects (sep, fsp, ApplyRNACodonsCallback,
-                                           NULL, SEQFEAT_RNA, FEATDEF_tRNA, 0, rp->codons);  
+      sfp = vnp_rna->data.ptrvalue;
+      if (sfp->idx.subtype == FEATDEF_tRNA)
+      {
+        ApplyRNACodonsCallback (sfp, rp->codons, fsp);
+      }
     }
   }
   else if (rp->field_list->data.intvalue == RNAFIELD_ANTICODON)
   {
-    for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
+    for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
     {
-      OperateOnSeqEntryConstrainedObjects (sep, fsp, ApplyRNAAnticodonCallback,
-                                           NULL, SEQFEAT_RNA, FEATDEF_tRNA, 0, rp->anticodon);  
+      sfp = vnp_rna->data.ptrvalue;
+      if (sfp->idx.subtype == FEATDEF_tRNA)
+      {
+        ApplyRNAAnticodonCallback (sfp, rp->anticodon, fsp);
+      }
     }
   }
   else
@@ -27706,21 +29144,9 @@ static Boolean AcceptRNAApply (ApplyEditConvertRemovePtr ap)
     avd.where_to_replace = EditApplyFindLocation_anywhere;
     
     /* get handling for existing text */
-    gsp_sum = NULL;
-    for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
-    {
-      gsp = CheckForExistingText (ap->input_entityID,
-                                  avd.field_list,
-                                  GetRNAFieldString,
-                                  NULL, NULL, IntValNodeCopy,
-                                  fsp, SEQFEAT_RNA, vnp->data.intvalue, 0);
-      gsp_new = GetSampleAdd (gsp_sum, gsp);
-      gsp = GetSampleFree (gsp);
-      gsp_sum = GetSampleFree (gsp_sum);
-      gsp_sum = gsp_new;
-    }
-    avd.etp = GetExistingTextHandlerInfo (gsp_sum == NULL ? 0 : gsp_sum->num_found, FALSE);
-    gsp_sum = GetSampleFree (gsp_sum);
+    gsp = GetRnaExistingTextForList (rna_list, rp->field_list);
+    avd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
+    gsp = GetSampleFree (gsp);
   
     if (avd.etp != NULL 
         && avd.etp->existing_text_choice == eExistingTextChoiceCancel)
@@ -27732,162 +29158,171 @@ static Boolean AcceptRNAApply (ApplyEditConvertRemovePtr ap)
     {
       AddEditApplyDataToApplyValue (AECR_APPLY, rp->edit_apply, &avd);
      
-      for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
+      for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
       {
-        OperateOnSeqEntryConstrainedObjects (sep, fsp, SetRNAFieldString,
-                                             NULL, SEQFEAT_RNA, vnp->data.intvalue, 0, &avd);  
+        sfp = vnp_rna->data.ptrvalue;
+        SetRNAFieldString (sfp, &avd, fsp);
       }
       avd.text_to_replace = MemFree (avd.text_to_replace);
       avd.new_text = MemFree (avd.new_text);
     }
     avd.etp = MemFree (avd.etp);
   }
-  
-  FilterSetFree (fsp);
-  
   return rval;
 }
 
+
 static Boolean 
-AcceptRNAQualEditRemoveConvert 
-(ApplyEditConvertRemovePtr ap,
- Int4                      action_choice,
- SimpleAECRPtr             rp)
+RNAQualConvertSwapParseList
+(ValNodePtr      rna_list,
+ AECRRNAQualPtr  rp,
+ Int4            action_choice,
+ FilterSetPtr    fsp)
 {
-  SeqEntryPtr      sep;
-  FilterSetPtr     fsp;
-  ConvertFieldData cfd;
-  GetSamplePtr     gsp, gsp_new, gsp_sum;
-  ValNodePtr       vnp;
-  ApplyValueData   avd;
-  Boolean          rval = TRUE;
+  ConvertFieldData       cfd;
+  ConversionConflictData ccd;
+  ValNodePtr             vnp_rna;
+  ApplyValueData         avd;
+  Boolean                rval = TRUE;
+  SeqFeatPtr             sfp;
   
-  if (ap == NULL
+  if (rna_list == NULL
+      || rp == NULL
       || action_choice < AECR_EDIT 
       || action_choice > NUM_AECR
-      || rp == NULL
-      || rp->subtype_list == NULL || rp->field_list == NULL
-      || ((action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE) 
-           && rp->field_list_to == NULL))
+      || rp->field_list == NULL
+      || rp->field_list_to == NULL)
   {
     return FALSE;
   }
 
-  sep = GetTopSeqEntryForEntityID (ap->input_entityID);
-
-  fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
-
   avd.where_to_replace = EditApplyFindLocation_anywhere;
   
-  if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP || action_choice == AECR_PARSE)
-  {
-    cfd.src_field_list = rp->field_list;
-    cfd.dst_field_list = rp->field_list_to;
-    cfd.etp = NULL;
-    cfd.get_str_func = GetRNAFieldString;
-    cfd.set_str_func = SetRNAFieldString;
-    cfd.remove_str_func = RemoveRNAField;
-    cfd.get_d_str_func = NULL;
-    cfd.set_d_str_func = NULL;
-    cfd.remove_d_str_func = NULL;
-    cfd.fsp = fsp;
-    cfd.strip_name_from_text = rp->strip_name_from_text;
-    cfd.name_field_func = NULL;
-    cfd.text_portion = rp->text_portion;
-    cfd.remove_parsed = rp->remove_parsed;
+  cfd.src_field_list = rp->field_list;
+  cfd.dst_field_list = rp->field_list_to;
+  cfd.etp = NULL;
+  cfd.get_str_func = GetRNAFieldString;
+  cfd.set_str_func = SetRNAFieldString;
+  cfd.remove_str_func = RemoveRNAField;
+  cfd.get_d_str_func = NULL;
+  cfd.set_d_str_func = NULL;
+  cfd.remove_d_str_func = NULL;
+  cfd.fsp = fsp;
+  cfd.strip_name_from_text = FALSE;
+  cfd.name_field_func = NULL;
+  cfd.text_portion = rp->text_portion;
+  cfd.remove_parsed = rp->remove_parsed;
 
-    if (action_choice == AECR_CONVERT)
-    {
-      if (rp->leave_on_original)
-      {
-        cfd.convert_type = CONVERT_TYPE_COPY;
-      }
-      else
-      {
-        cfd.convert_type = CONVERT_TYPE_MOVE;
-      }
-    }
-    else if (action_choice == AECR_SWAP)
+  if (action_choice == AECR_CONVERT)
+  {
+    if (rp->leave_on_original)
     {
-      cfd.convert_type = CONVERT_TYPE_SWAP;
+      cfd.convert_type = CONVERT_TYPE_COPY;
     }
-    else if (action_choice == AECR_PARSE)
+    else
     {
-      cfd.convert_type = CONVERT_TYPE_PARSE;
+      cfd.convert_type = CONVERT_TYPE_MOVE;
     }
-    
-    if (cfd.convert_type == CONVERT_TYPE_MOVE || cfd.convert_type == CONVERT_TYPE_COPY || cfd.convert_type == CONVERT_TYPE_PARSE)
+  }
+  else if (action_choice == AECR_SWAP)
+  {
+    cfd.convert_type = CONVERT_TYPE_SWAP;
+  }
+  else if (action_choice == AECR_PARSE)
+  {
+    cfd.convert_type = CONVERT_TYPE_PARSE;
+  }
+  
+  if (cfd.convert_type == CONVERT_TYPE_MOVE || cfd.convert_type == CONVERT_TYPE_COPY || cfd.convert_type == CONVERT_TYPE_PARSE)
+  {
+    /* get existing text sample */
+    ccd.cfp = &cfd;
+    ccd.gsp = GetSampleNew();
+
+    for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
     {
-      /* get existing text sample */
-      gsp_sum = NULL;
-      for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
-      {
-        gsp = CheckForConversionExistingTextInSeqEntry (sep, &cfd, fsp,
-                                                        SEQFEAT_RNA,
-                                                        vnp->data.intvalue,
-                                                        0);
-        gsp_new = GetSampleAdd (gsp_sum, gsp);
-        gsp = GetSampleFree (gsp);
-        gsp_sum = GetSampleFree (gsp_sum);
-        gsp_sum = gsp_new;
-      }
-      cfd.etp = GetExistingTextHandlerInfo (gsp_sum == NULL ? 0 : gsp_sum->num_found, FALSE);
-      gsp_sum = GetSampleFree (gsp_sum);
-      if (cfd.etp != NULL && cfd.etp->existing_text_choice == eExistingTextChoiceCancel)
-      {
-        rval = FALSE;
-      }
+      sfp = vnp_rna->data.ptrvalue;
+      GetConversionConflictsFeatureCallback (sfp, &ccd, fsp);
     }
-    else
-    {
-      cfd.etp = NULL;
-    }  
-
-    if (rval)
+    cfd.etp = GetExistingTextHandlerInfo (ccd.gsp == NULL ? 0 : ccd.gsp->num_found, FALSE);
+    ccd.gsp = GetSampleFree (ccd.gsp);
+    if (cfd.etp != NULL && cfd.etp->existing_text_choice == eExistingTextChoiceCancel)
     {
-      for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
-      {
-        OperateOnSeqEntryConstrainedObjects (sep, fsp, 
-                                             ConvertFeatureFieldCallback, NULL,
-                                             SEQFEAT_RNA, vnp->data.intvalue, 
-                                             0, &cfd);
-      }
+      rval = FALSE;
     }
   }
   else
   {
-    avd.field_list = rp->field_list;
-    avd.etp = NULL;
-    AddEditApplyDataToApplyValue (action_choice, rp->edit_apply, &avd);
-     
-    for (vnp = rp->subtype_list; vnp != NULL; vnp = vnp->next)
+    cfd.etp = NULL;
+  }  
+
+  if (rval)
+  {
+    for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
     {
-      if (action_choice == AECR_EDIT)
-      {
-        OperateOnSeqEntryConstrainedObjects (sep, fsp, SetRNAFieldString,
-                                             NULL, SEQFEAT_RNA, vnp->data.intvalue, 0, &avd);  
-      }
-      else if (action_choice == AECR_REMOVE)
-      {
-        OperateOnSeqEntryConstrainedObjects (sep, fsp, RemoveRNAField,
-                                             NULL, SEQFEAT_RNA, vnp->data.intvalue, 0, &avd);  
-      }
+      sfp = vnp_rna->data.ptrvalue;
+      ConvertFeatureFieldCallback (sfp, &cfd, fsp);
     }
-    avd.text_to_replace = MemFree (avd.text_to_replace);
-    avd.new_text = MemFree (avd.new_text);
   }
 
-  FilterSetFree (fsp);
   return rval;
+}
 
+
+static Boolean RNAQualEditRemoveList 
+(ValNodePtr    rna_list,
+ AECRRNAQualPtr  rp,
+ Int4          action_choice,
+ FilterSetPtr  fsp)
+{
+  SeqFeatPtr       sfp;
+  ValNodePtr       vnp_rna;
+  ApplyValueData   avd;
+  Boolean          rval = TRUE;
+  
+  if (rna_list == NULL
+      || rp == NULL
+      || (action_choice != AECR_EDIT && action_choice != AECR_REMOVE)
+      || rp->field_list == NULL)
+  {
+    return FALSE;
+  }
+
+  avd.where_to_replace = EditApplyFindLocation_anywhere;
+  avd.field_list = rp->field_list;
+  avd.etp = NULL;
+  AddEditApplyDataToApplyValue (action_choice, rp->edit_apply, &avd);
+
+  for (vnp_rna = rna_list; vnp_rna != NULL; vnp_rna = vnp_rna->next)
+  {
+    sfp = vnp_rna->data.ptrvalue;
+    if (action_choice == AECR_EDIT)
+    {
+      SetRNAFieldString (sfp, &avd, fsp);
+    }
+    else if (action_choice == AECR_REMOVE)
+    {
+      RemoveRNAField (sfp, &avd, fsp);
+    }
+  }
+    
+  avd.text_to_replace = MemFree (avd.text_to_replace);
+  avd.new_text = MemFree (avd.new_text);
+  return TRUE;
 }
 
+
+
+
 static Boolean AcceptRNAQualApplyEditRemoveConvert (Pointer userdata)
 {
   ApplyEditConvertRemovePtr ap;
-  SimpleAECRPtr             rp = NULL;
+  AECRRNAQualPtr            rp;
   Int4                      action_choice;
   Boolean                   rval = TRUE;
+  FilterSetPtr              fsp;
+  ValNodePtr                rna_list;
+  SeqEntryPtr               sep;
 
   ap = (ApplyEditConvertRemovePtr) userdata;
   if (ap == NULL)
@@ -27906,16 +29341,26 @@ static Boolean AcceptRNAQualApplyEditRemoveConvert (Pointer userdata)
   {
     action_choice = GetValue (ap->action_popup);
   }
+
+  rp = (AECRRNAQualPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
+  if (rp == NULL) return FALSE;
+
+  fsp = (FilterSetPtr) DialogToPointer (ap->constraints);
+  sep = GetTopSeqEntryForEntityID (ap->input_entityID);
+  rna_list = GetRNAFeatureList (sep, fsp, rp->rna_type);
   
   if (action_choice == AECR_APPLY)
   {
-    rval = AcceptRNAApply (ap);
+    rval = ApplyToRNAList (rna_list, rp, fsp);
+  }
+  else if (action_choice == AECR_CONVERT || action_choice == AECR_SWAP
+           || action_choice == AECR_PARSE)
+  {
+    rval = RNAQualConvertSwapParseList (rna_list, rp, action_choice, fsp);
   }
   else if (action_choice > AECR_APPLY && action_choice <= NUM_AECR)
   {
-    rp = (SimpleAECRPtr) DialogToPointer (ap->aecr_pages[action_choice - 1]);
-    rval = AcceptRNAQualEditRemoveConvert (ap, action_choice, rp);
-    rp = SimpleAECRFree (rp);
+    rval = RNAQualEditRemoveList (rna_list, rp, action_choice, fsp);
   }
     
   if (rval)
@@ -28002,7 +29447,7 @@ typedef struct removegbqual
 {
   ValNodePtr          field_list;
   ValNodePtr          subtype_list;
-  StringConstraintPtr scp;
+  StringConstraintXPtr scp;
   Boolean             use_field_list;
 } RemoveGBQualData, PNTR RemoveGBQualPtr;
 
@@ -28012,7 +29457,7 @@ static RemoveGBQualPtr RemoveGBQualFree (RemoveGBQualPtr ap)
   {
     ap->field_list = ValNodeFree (ap->field_list);
     ap->subtype_list = ValNodeFree (ap->subtype_list);
-    ap->scp = StringConstraintFree (ap->scp);
+    ap->scp = StringConstraintXFree (ap->scp);
     ap = MemFree (ap);
   }
   return ap;
@@ -28248,7 +29693,7 @@ static DialoG GBQualRemoveDialog
   dlg->field_list = GBQualSelectionDialog (dlg->list_or_txt_grp, FALSE, 
                                                 change_notify,
                                                 change_userdata);
-  dlg->qual_name_constraint = StringConstraintDialog (dlg->list_or_txt_grp, "Where qualifier name contains", FALSE);
+  dlg->qual_name_constraint = StringConstraintDialogX (dlg->list_or_txt_grp, "Where qualifier name contains", FALSE);
   SetValue (dlg->list_or_txt_grp, 1);
   Disable (dlg->qual_name_constraint);
     
@@ -28713,6 +30158,162 @@ extern void RemoveGBQual (IteM i)
 }
 
 
+static CharPtr  alltargetsTabs [] = {
+  "BioSource", "GenBank Qualifiers", "RNA Qualifiers", "CDS-Gene-Prot-mRNA", NULL
+};
+
+typedef enum 
+{
+  eAllTargetsAllActions_BioSource = 0,
+  eAllTargetsAllActions_GBQual,
+  eAllTargetsAllActions_RNAQual,
+  eAllTargetsAllActions_CDSGeneProtmRNA,
+  eNumAllTargetsAllActions
+} EAllTargetsAllActions;
+
+typedef struct allactionsalltargetsdlg
+{
+  DIALOG_MESSAGE_BLOCK
+  DialoG                   tbs; /* folder tab for switching between target types */
+  Int2                     currentPage;
+  GrouP                    target_pages [eNumAllTargetsAllActions];
+  DialoG                   aecr_pages [NUM_AECR * eNumAllTargetsAllActions];
+  PopuP                    action_popup;
+
+  DialoG                   accept_cancel;
+  DialoG                   constraints;
+  ButtoN                   clear_constraints_on_action_change;
+  Nlm_ChangeAECRActionProc change_action;
+  Int4                     prev_page;
+  Boolean                  crippled;
+  Int4                     crippled_action;
+  Uint2                    entityID;
+  Nlm_ChangeNotifyProc     change_notify;
+  Pointer                  change_userdata;
+} AllActionsAllTargetsDlgData, PNTR AllActionsAllTargetsDlgPtr;
+
+
+static void ChangeAllActionsAllTargetsTarget (VoidPtr data, Int2 newval, Int2 oldval)
+{
+  AllActionsAllTargetsDlgPtr  dlg;
+
+  dlg = (AllActionsAllTargetsDlgPtr) data;
+  if (dlg != NULL) {
+    dlg->currentPage = newval;
+    SafeHide (dlg->target_pages [oldval]);
+    SafeShow (dlg->target_pages [newval]);
+    Update ();
+    if (dlg->change_notify != NULL) {
+      (dlg->change_notify) (dlg->change_userdata);
+    }
+  }
+}
+
+static void ChangeAllActionsAllTargetsAction (PopuP p)
+{
+  AllActionsAllTargetsDlgPtr  dlg;
+  Int4                        i;
+  
+  dlg = (AllActionsAllTargetsDlgPtr) GetObjectExtra (p);
+  if (dlg == NULL) return;
+
+  for (i = 0; i < NUM_AECR; i++)
+  {
+    Hide (dlg->aecr_pages[(dlg->currentPage * NUM_AECR) + i]);
+  }
+  i = GetValue (dlg->action_popup);
+  if (i > 0 && i <= NUM_AECR)
+  {
+    Show (dlg->aecr_pages[(dlg->currentPage * NUM_AECR) + i - 1]);
+    SendMessageToDialog (dlg->aecr_pages[(dlg->currentPage * NUM_AECR) + i - 1], VIB_MSG_ENTER);
+  }
+  
+}
+
+static DialoG AllActionsAllTargetsDialog (GrouP h, Uint2 entityID, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata)
+{
+  AllActionsAllTargetsDlgPtr dlg;
+  GrouP                      p, g;
+  Int4                       i;
+
+  dlg = (AllActionsAllTargetsDlgPtr) MemNew (sizeof (AllActionsAllTargetsDlgData));
+
+  p = HiddenGroup (h, -1, 0, NULL);
+  SetObjectExtra (p, dlg, StdCleanupExtraProc);
+  SetGroupSpacing (p, 10, 10);
+  
+  dlg->dialog = (DialoG) p;
+  dlg->todialog = NULL;
+  dlg->fromdialog = NULL;
+  dlg->dialogmessage = NULL;
+  dlg->testdialog = NULL;
+  dlg->change_notify = change_notify;
+  dlg->change_userdata = change_userdata;
+  dlg->entityID = entityID;
+
+  dlg->action_popup = PopupList (p, TRUE, ChangeAllActionsAllTargetsAction);
+  SetObjectExtra (dlg->action_popup, dlg, NULL);
+  PopupItem (dlg->action_popup, "Apply");
+  PopupItem (dlg->action_popup, "Edit");
+  PopupItem (dlg->action_popup, "Convert");
+  PopupItem (dlg->action_popup, "Swap");
+  PopupItem (dlg->action_popup, "Parse");
+  PopupItem (dlg->action_popup, "Remove");
+  SetValue (dlg->action_popup, 1);
+
+
+  dlg->tbs = CreateFolderTabs (p, alltargetsTabs, eAllTargetsAllActions_BioSource,
+                               0, 0, SYSTEM_FOLDER_TAB,
+                               ChangeAllActionsAllTargetsTarget, (Pointer) dlg);
+
+  g = HiddenGroup (p, 0, 0, NULL);
+  dlg->target_pages[eAllTargetsAllActions_BioSource] = HiddenGroup (g, 0, 0, NULL);
+  for (i = 0; i < NUM_AECR; i++)
+  {
+    dlg->aecr_pages[(eAllTargetsAllActions_BioSource * NUM_AECR) + i] 
+               = SourceQualAECRDialog (dlg->target_pages[eAllTargetsAllActions_BioSource],
+                                       i + 1, change_notify, change_userdata, entityID);
+    Hide (dlg->aecr_pages[(eAllTargetsAllActions_BioSource * NUM_AECR) + i]);
+  }
+  
+  dlg->target_pages[eAllTargetsAllActions_GBQual] = HiddenGroup (g, 0, 0, NULL);
+  for (i = 0; i < NUM_AECR; i++)
+  {
+    dlg->aecr_pages[(eAllTargetsAllActions_GBQual * NUM_AECR) + i] 
+               = GBQualListDialog (dlg->target_pages[eAllTargetsAllActions_GBQual],
+                                       i + 1, change_notify, change_userdata, entityID);
+    Hide (dlg->aecr_pages[(eAllTargetsAllActions_GBQual * NUM_AECR) + i]);
+  }
+
+  dlg->target_pages[eAllTargetsAllActions_RNAQual] = HiddenGroup (g, 0, 0, NULL);
+  for (i = 0; i < NUM_AECR; i++)
+  {
+    dlg->aecr_pages[(eAllTargetsAllActions_RNAQual * NUM_AECR) + i] 
+               = RNAQualListDialog (dlg->target_pages[eAllTargetsAllActions_RNAQual],
+                                       i + 1, change_notify, change_userdata, entityID);
+    Hide (dlg->aecr_pages[(eAllTargetsAllActions_RNAQual * NUM_AECR) + i]);
+  }
+
+  dlg->target_pages[eAllTargetsAllActions_CDSGeneProtmRNA] = HiddenGroup (g, 0, 0, NULL);
+  for (i = 0; i < NUM_AECR; i++)
+  {
+    dlg->aecr_pages[(eAllTargetsAllActions_CDSGeneProtmRNA * NUM_AECR) + i] 
+               = CDSGeneProtAECRDialog (dlg->target_pages[eAllTargetsAllActions_CDSGeneProtmRNA],
+                                       i + 1, change_notify, change_userdata, entityID);
+    Hide (dlg->aecr_pages[(eAllTargetsAllActions_CDSGeneProtmRNA * NUM_AECR) + i]);
+  }
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) dlg->tbs, (HANDLE) g, NULL);
+
+  return (DialoG) p;
+}
+
+
+extern void AllActionsAllTargets (IteM i)
+{
+
+}
+
 typedef struct locustagtooldlocustag 
 {
   FORM_MESSAGE_BLOCK
@@ -29053,7 +30654,7 @@ typedef struct combinecds
   
   Int2                action_choice;
   Boolean             cover_sequence;
-  StringConstraintPtr string_constraint;
+  StringConstraintXPtr string_constraint;
   LogInfoPtr          lip;
   
   /* for string constraint */
@@ -29097,7 +30698,7 @@ static void GetCombinedCDSLocationCallback (SeqFeatPtr sfp, Pointer userdata)
       && !DoesObjectMatchStringConstraint (ccp->omtp, ccp->aip, sfp, &(ccp->ohsd)))
   {
     sfp = SeqMgrGetDesiredFeature (ccp->input_entityID, NULL, 0, 0, sfp, &fcontext);
-    if (sfp == NULL || !DoesStringMatchConstraint (fcontext.label, ccp->ohsd.scp))
+    if (sfp == NULL || !DoesStringMatchConstraintX (fcontext.label, ccp->ohsd.scp))
     {
       return;
     }
@@ -29340,7 +30941,7 @@ static void DoCombineCDS (ButtoN b)
   
   CloseLog (ccp->lip);
   FreeLog (ccp->lip);  
-  ccp->string_constraint = StringConstraintFree (ccp->string_constraint);
+  ccp->string_constraint = StringConstraintXFree (ccp->string_constraint);
   Remove (ccp->form);
   DeleteMarkedObjects (ccp->input_entityID, 0, NULL);
   ObjMgrSetDirtyFlag (ccp->input_entityID, TRUE);
@@ -29428,7 +31029,7 @@ extern void CombineMultipleCDS (IteM i)
   SetValue (ccp->prod_name_choice_grp, 1);
   Disable (ccp->prod_name_txt);
   
-  ccp->string_constraint_dlg = StringConstraintDialog (ccp->new_cds_grp, "Where CDS field", TRUE);
+  ccp->string_constraint_dlg = StringConstraintDialogX (ccp->new_cds_grp, "Where CDS field", TRUE);
   Disable (ccp->new_cds_grp);
   
   AlignObjects (ALIGN_CENTER, (HANDLE) ccp->cover_sequence_btn,
@@ -29715,7 +31316,7 @@ static void CombineClickableLists (ValNodePtr PNTR list1, ValNodePtr list2)
     if (cip2 != NULL) {
       cip1 = FindExistingCategory (cip2->description, *list1);
       if (cip1 == NULL) {
-        ValNodeAddPointer (list1, 0, cip1);
+        ValNodeAddPointer (list1, 0, cip2);
         vnp->data.ptrvalue = NULL;
       } else {
         CombineClickableItemLists (&(cip1->item_list), cip2->item_list);
@@ -29883,6 +31484,15 @@ GetUniqueValueListForSeqEntry
                                             SEQFEAT_BIOSRC, 0,
                                             Seq_descr_source);
       break;
+    case PARSE_FIELD_DBXREF:
+      unique_values = CheckForUniqueValuesInSeqEntry (sep, dst_field_data->feature_field,
+                                            GetBioSourceFeatureDbxrefString,
+                                            GetBioSourceDescriptorDbxrefString,
+                                            ValNodeSimpleDataFree,
+                                            ValNodeStringCopy,
+                                            fsp,
+                                            SEQFEAT_BIOSRC, 0, Seq_descr_source);
+      break;
     case PARSE_FIELD_GENE_FIELD:
       unique_values = CheckForUniqueValuesInSeqEntry (sep, 
                                             dst_field_data->feature_field, 
@@ -29892,14 +31502,16 @@ GetUniqueValueListForSeqEntry
                                             fsp,
                                             SEQFEAT_GENE, 0, 0);
       break;
-    case PARSE_FIELD_MRNA_FIELD:
+    case PARSE_FIELD_RNA_FIELD:
       unique_values = CheckForUniqueValuesInSeqEntry (sep, 
                                             dst_field_data->feature_field, 
-                                            GetmRNAFieldString,
+                                            GetRNAFieldString,
                                             NULL,
                                             NULL, IntValNodeCopy,
                                             fsp,
-                                            SEQFEAT_RNA, FEATDEF_mRNA, 0);
+                                            SEQFEAT_RNA, 
+                                            dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue,
+                                            0);
       break;
     case PARSE_FIELD_CDS_COMMENT:
       unique_values = CheckForUniqueValuesInSeqEntry (sep, 
@@ -30497,7 +32109,7 @@ static void AddNewUniqueDescriptors (SeqDescrPtr PNTR new_set, SeqDescrPtr paren
       sdp_next = sdp->next;
       sdp->next = NULL;
       for (sdp_tmp = *new_set, found_match = FALSE;
-           sdp != NULL && !found_match; 
+           sdp_tmp != NULL && !found_match; 
            sdp_tmp = sdp_tmp->next) {
         sdp_tmp_next = sdp_tmp->next;
         sdp_tmp->next = NULL;
@@ -30536,6 +32148,62 @@ static void AddNewUniqueDescriptorsToSeqEntry (SeqEntryPtr sep, SeqDescrPtr pare
   }
 }
 
+static void AddNewUniqueAnnotations (SeqAnnotPtr PNTR new_set, SeqAnnotPtr parent_set)
+{
+  SeqAnnotPtr sap, sap_next, sap_tmp, sap_tmp_next, sap_copy, last_sap;
+  Boolean     found_match;
+
+  if (new_set == NULL || parent_set == NULL) return;
+
+  sap = parent_set;
+  while (sap != NULL) {
+    sap_next = sap->next;
+    sap->next = NULL;
+    last_sap = NULL;
+    for (sap_tmp = *new_set, found_match = FALSE;
+         sap_tmp != NULL && !found_match;
+         sap_tmp = sap_tmp->next) {
+      sap_tmp_next = sap_tmp->next;
+      sap_tmp->next = NULL;
+      if (AsnIoMemComp (sap, sap_tmp, (AsnWriteFunc) SeqAnnotAsnWrite)) {
+        found_match = TRUE;
+      }
+      sap_tmp->next = sap_tmp->next;
+      last_sap = sap_tmp;
+    }
+    if (!found_match) {        
+      sap_copy = (SeqAnnotPtr) AsnIoMemCopy ((Pointer) sap, (AsnReadFunc) SeqAnnotAsnRead, (AsnWriteFunc) SeqAnnotAsnWrite); 
+      if (last_sap == NULL) {
+        *new_set = sap_copy;
+      } else {
+        last_sap->next = sap_copy;
+      }
+    }
+    sap->next = sap_next;
+    sap = sap->next;
+  }
+}
+
+
+static void AddNewUniqueAnnotationsToSeqEntry (SeqEntryPtr sep, SeqAnnotPtr parent_set)
+{
+  BioseqPtr    bsp;
+  BioseqSetPtr bssp;
+
+  if (IS_Bioseq(sep)) {
+    bsp = (BioseqPtr) sep->data.ptrvalue;
+    if (bsp != NULL) {
+      AddNewUniqueAnnotations (&(bsp->annot), parent_set);
+    }
+  } else if (IS_Bioseq_set (sep)) {
+    bssp = (BioseqSetPtr) sep->data.ptrvalue;
+    if (bssp != NULL) {
+      AddNewUniqueAnnotations (&(bssp->annot), parent_set);
+    }
+  }
+}
+
+
 static void AddCategorySeqEntriesToSet (BioseqSetPtr newset, ClickableItemPtr category)
 {
   ValNodePtr vnp_item;
@@ -30597,6 +32265,9 @@ static void AddCategorySeqEntriesToSet (BioseqSetPtr newset, ClickableItemPtr ca
       /* add descriptors from the orig_parent to the new parent */
       AddNewUniqueDescriptors (&(newset->descr), orig_parent->descr);
 
+      /* add annotations from the orig_parent to the new parent */
+      AddNewUniqueAnnotations (&(newset->annot), orig_parent->annot);
+
       /* add to new parent */
       sep->next = NULL;
       if (last_sep == NULL) {
@@ -30772,13 +32443,21 @@ static BioseqSetPtr MakeGroupsForUniqueValues
   return parent_set;
 }
 
-#define NUM_SEG_PAGES 6
+typedef enum {
+  eSegPageId = 1,
+  eSegPageText,
+  eSegPageField,
+  eSegPageMolInfo,
+  eSegPageFeatureType,
+  eSegPageDescriptorType,
+  eNumSegPages
+} ESegPage;
 
 typedef struct segbyfield {
   FORM_MESSAGE_BLOCK
   GrouP        seg_choice_grp;
 
-  GrouP        pages[NUM_SEG_PAGES];
+  GrouP        pages[eNumSegPages];
   /* for segregating by field */
   DialoG       field_dlg;
   DialoG       group_list_dlg;
@@ -30799,7 +32478,6 @@ typedef struct segbyfield {
 
   /* for segregating by ID */
   DialoG       id_constraint;
-  TexT         id_txt;
 
   ButtoN       accept;
   ButtoN       leave_dlg_up;
@@ -30891,7 +32569,7 @@ static void SegregateByField_Callback (ButtoN b)
     }
   }
 
-  if (GetValue (sfp->seg_choice_grp) == 6) {
+  if (GetValue (sfp->seg_choice_grp) == eSegPageId) {
     /* put all selected sequences into one group */
     cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
     cip->chosen = TRUE;
@@ -30998,7 +32676,7 @@ static void SegTextChange (TexT t)
 }
 
 
-static void ListAllSequences (BioseqPtr bsp, Pointer userdata)
+extern void ListAllSequences (BioseqPtr bsp, Pointer userdata)
 {
   ClickableItemPtr cip;
   Char             id_str[100];
@@ -31006,7 +32684,7 @@ static void ListAllSequences (BioseqPtr bsp, Pointer userdata)
   if (bsp != NULL && userdata != NULL && ! ISA_aa (bsp->mol))
   {
     cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData));
-    SeqIdWrite (SeqIdFindBest (bsp->id, 0), id_str, PRINTID_REPORT, sizeof (id_str) - 1);
+    SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_str, PRINTID_REPORT, sizeof (id_str) - 1);
     cip->description = StringSave (id_str);
 
     ValNodeAddPointer (&(cip->item_list), OBJ_BIOSEQ, bsp);
@@ -31196,7 +32874,7 @@ static void ChangeSegChoice (GrouP g)
 
   seg_choice = GetValue (sfp->seg_choice_grp);
 
-	for (i = 0; i < NUM_SEG_PAGES; i++) {
+	for (i = 0; i < eNumSegPages; i++) {
     if (i == seg_choice - 1) {
         Show (sfp->pages[i]);
 	  } else {
@@ -31204,29 +32882,38 @@ static void ChangeSegChoice (GrouP g)
 	  }
 	}
 	switch (seg_choice) {
-	  case 1:
+	  case eSegPageField:
         ChangeSegField (sfp);
 	      break;
-	  case 2:
+	  case eSegPageMolInfo:
         ChangeMol(sfp->mol_class_btn);
         break;
-	  case 3:
+	  case eSegPageFeatureType:
         SegFeatureChangeNotify (sfp);
         break;
-    case 4:
+    case eSegPageDescriptorType:
         SegDescriptorChangeNotify (sfp);
         break;
-    case 5:
+    case eSegPageText:
         SegTextChangeNotify (sfp);
         break;
-    case 6:
+    case eSegPageId:
         ChooseSegId (sfp);
         break;
   }
+  if (seg_choice == eSegPageId) {
+    SetClickableListDialogTitles (sfp->group_list_dlg, "Sequences for New Set", "",
+                                                       "Use checkbox to mark sequences for new set",
+                                                       "Single click to navigate to sequence in record");
+  } else {
+    SetClickableListDialogTitles (sfp->group_list_dlg, "New Sets", "Sequences in Highlighted Set",
+                                                       "Use checkbox to mark sets to create",
+                                                       "");
+  }
 }
 
 
-static void ChooseCategories (ValNodePtr value_list, Boolean do_choose)
+extern void ChooseCategories (ValNodePtr value_list, Boolean do_choose)
 {
   ClickableItemPtr cip;
 
@@ -31241,7 +32928,7 @@ static void ChooseCategories (ValNodePtr value_list, Boolean do_choose)
 }
 
 
-static void ChooseCategoriesByStringConstraint (ValNodePtr value_list, StringConstraintPtr scp, Boolean do_choose)
+extern void ChooseCategoriesByStringConstraint (ValNodePtr value_list, StringConstraintXPtr scp, Boolean do_choose)
 {
   ClickableItemPtr cip;
 
@@ -31289,7 +32976,7 @@ static void UnselectSegCategories (ButtoN b)
 static void SelectSequenceIDsForSegregate (ButtoN b)
 {
   SegByFieldPtr       sfp;
-  StringConstraintPtr scp;
+  StringConstraintXPtr scp;
 
   sfp = (SegByFieldPtr) GetObjectExtra (b);
   if (sfp == NULL) return;
@@ -31297,65 +32984,10 @@ static void SelectSequenceIDsForSegregate (ButtoN b)
   scp = DialogToPointer (sfp->id_constraint);
   ChooseCategoriesByStringConstraint (sfp->value_lists, scp, TRUE);
   PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
-  scp = StringConstraintFree (scp);
+  scp = StringConstraintXFree (scp);
 }
 
 
-static void ChooseCategoriesBySeqIdList (ValNodePtr list, ValNodePtr sip_list, Boolean do_choose)
-{
-  ValNodePtr       vnp, vnp_id;
-  ClickableItemPtr cip;
-  BioseqPtr        bsp;
-  Boolean          match;
-
-  for (vnp = list; vnp != NULL; vnp = vnp->next)
-  {
-    cip = (ClickableItemPtr) vnp->data.ptrvalue;
-    if (cip != NULL) 
-    {
-      match = FALSE;
-      if (cip->item_list != NULL && cip->item_list->choice == OBJ_BIOSEQ 
-          && cip->item_list->data.ptrvalue != NULL)
-      {
-        bsp = (BioseqPtr) cip->item_list->data.ptrvalue;
-        for (vnp_id = sip_list; vnp_id != NULL && !match; vnp_id = vnp_id->next)
-        {
-          if (SeqIdIn (vnp_id->data.ptrvalue, bsp->id)) 
-          {
-            match = TRUE;
-          }
-        }
-      }
-      if (match) 
-      {
-        cip->chosen = do_choose;
-      }
-      else
-      {
-        ChooseCategoriesBySeqIdList (cip->subcategories, sip_list, do_choose);
-      }
-    }
-  }
-}
-
-
-static void SelectSequenceIDRangeForSegregate (ButtoN b)
-{
-  SegByFieldPtr sfp;
-  ValNodePtr    sip_list;
-  CharPtr       id_str;
-
-  sfp = (SegByFieldPtr) GetObjectExtra (b);
-  if (sfp == NULL) return;
-
-  id_str = SaveStringFromText (sfp->id_txt);
-  sip_list = ParseAccessionNumberListFromString (id_str, SeqMgrGetSeqEntryForData (sfp->target_set));
-
-  ChooseCategoriesBySeqIdList (sfp->value_lists, sip_list, TRUE);
-  PointerToDialog (sfp->group_list_dlg, sfp->value_lists);
-  sip_list = FreeSeqIdList (sip_list);
-}
-
 static void CleanupSegregateByFieldForm (GraphiC g, VoidPtr data)
 
 {
@@ -31374,12 +33006,13 @@ extern Int2 LIBCALLBACK SegregateSetsByField (Pointer data)
 {
   GrouP              c;
   SegByFieldPtr      cfp;
-  GrouP              h, k, page_grp, g1, g2;
+  GrouP              h, k, page_grp, g1, g2, g3;
   OMProcControlPtr   ompcp;
   PrompT             p, p2;
   StdEditorProcsPtr  sepp;
   WindoW             w;
   ButtoN             b;
+  StringConstraintData scd;
 
   /* Check parameters and get a pointer to the current data */
 
@@ -31423,77 +33056,87 @@ extern Int2 LIBCALLBACK SegregateSetsByField (Pointer data)
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
 
-  cfp->group_list_dlg = CreateClickableListDialog (h, "Groups", "Sequences",
-                                                   ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
-                                                   GetDiscrepancyItemText);
-
-  cfp->seg_choice_grp = HiddenGroup (h, NUM_SEG_PAGES, 0, ChangeSegChoice);
+  cfp->group_list_dlg = CreateClickableListDialogEx (h, "New Sets", "Sequences for New Set",
+                                                      "Use checkbox to mark sets to create",
+                                                      "",
+                                                      ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
+                                                      GetDiscrepancyItemText,
+                                                      stdCharWidth * 30,
+                                                      stdCharWidth * 30 + 5,
+                                                      TRUE, FALSE);
+
+  g3 = NormalGroup (h, 2, 0, "", programFont, NULL);
+  SetGroupSpacing (g3, 10, 10);
+  StaticPrompt (g3, "Segregate Based on", 0, dialogTextHeight, programFont, 'c');
+  cfp->seg_choice_grp = HiddenGroup (g3, eNumSegPages, 0, ChangeSegChoice);
   SetObjectExtra (cfp->seg_choice_grp, cfp, NULL);
   SetGroupSpacing (cfp->seg_choice_grp, 10, 10);
 
+  RadioButton (cfp->seg_choice_grp, "ID");
+  RadioButton (cfp->seg_choice_grp, "Text");
   RadioButton (cfp->seg_choice_grp, "Field");
   RadioButton (cfp->seg_choice_grp, "MolInfo");
   RadioButton (cfp->seg_choice_grp, "Feature Type");
   RadioButton (cfp->seg_choice_grp, "Descriptor Type");
-  RadioButton (cfp->seg_choice_grp, "Text");
-  RadioButton (cfp->seg_choice_grp, "ID");
 
   page_grp = HiddenGroup (h, 0, 0, NULL);
   /* identical fields */
-  cfp->pages[0] = HiddenGroup (page_grp, 2, 0, NULL);
-  SetGroupSpacing (cfp->pages[0], 10, 10);
-  p = StaticPrompt (cfp->pages[0], "Segregate sequences with identical", 0, dialogTextHeight,
+  cfp->pages[eSegPageField - 1] = HiddenGroup (page_grp, 2, 0, NULL);
+  SetGroupSpacing (cfp->pages[eSegPageField - 1], 10, 10);
+  p = StaticPrompt (cfp->pages[eSegPageField - 1], "Segregate sequences with identical", 0, dialogTextHeight,
 		            programFont, 'c');  
-  cfp->field_dlg = ParseFieldDestDialog (cfp->pages[0], ChangeSegField, cfp);
+  cfp->field_dlg = ParseFieldDestDialog (cfp->pages[eSegPageField - 1], ChangeSegField, cfp);
 
   /* molinfo */
-  cfp->pages[1] = HiddenGroup (page_grp, 0, 2, NULL);
-  SetGroupSpacing (cfp->pages[1], 10, 10);
-  cfp->mol_class_btn = CheckBox (cfp->pages[1], "Molecule Class", ChangeMol);
+  cfp->pages[eSegPageMolInfo - 1] = HiddenGroup (page_grp, 0, 2, NULL);
+  SetGroupSpacing (cfp->pages[eSegPageMolInfo - 1], 10, 10);
+  cfp->mol_class_btn = CheckBox (cfp->pages[eSegPageMolInfo - 1], "Molecule Class", ChangeMol);
   SetObjectExtra (cfp->mol_class_btn, cfp, NULL);
   SetStatus (cfp->mol_class_btn, TRUE);
-  cfp->mol_type_btn = CheckBox (cfp->pages[1], "Molecule Type", ChangeMol);
+  cfp->mol_type_btn = CheckBox (cfp->pages[eSegPageMolInfo - 1], "Molecule Type", ChangeMol);
   SetObjectExtra (cfp->mol_type_btn, cfp, NULL);
   SetStatus (cfp->mol_type_btn, TRUE);
 
   /* features */
-  cfp->pages[2] = HiddenGroup (page_grp, 2, 0, NULL);
-  SetGroupSpacing (cfp->pages[2], 10, 10);
-  StaticPrompt (cfp->pages[2], "Segregate by Feature", 0, dialogTextHeight,
+  cfp->pages[eSegPageFeatureType - 1] = HiddenGroup (page_grp, 2, 0, NULL);
+  SetGroupSpacing (cfp->pages[eSegPageFeatureType - 1], 10, 10);
+  StaticPrompt (cfp->pages[eSegPageFeatureType - 1], "Segregate by Feature", 0, dialogTextHeight,
 	            programFont, 'c');
-  cfp->feature_select =  FeatureSelectionDialogEx (cfp->pages[2], FALSE, NULL,
+  cfp->feature_select =  FeatureSelectionDialogEx (cfp->pages[eSegPageFeatureType - 1], FALSE, NULL,
                                                    SegFeatureChangeNotify, 
                                                    cfp);
 
   /* descriptors */
-  cfp->pages[3] = HiddenGroup (page_grp, 2, 0, NULL);
-  SetGroupSpacing (cfp->pages[3], 10, 10);
-  StaticPrompt (cfp->pages[3], "Segregate by Descriptor", 0, dialogTextHeight,
+  cfp->pages[eSegPageDescriptorType - 1] = HiddenGroup (page_grp, 2, 0, NULL);
+  SetGroupSpacing (cfp->pages[eSegPageDescriptorType - 1], 10, 10);
+  StaticPrompt (cfp->pages[eSegPageDescriptorType - 1], "Segregate by Descriptor", 0, dialogTextHeight,
                 programFont, 'c');
-  cfp->descriptor_select = DescriptorSelectionDialog (cfp->pages[3], FALSE, 
+  cfp->descriptor_select = DescriptorSelectionDialog (cfp->pages[eSegPageDescriptorType - 1], FALSE, 
                                                       SegDescriptorChangeNotify, cfp);
 
   /* text */
-  cfp->pages[4] = HiddenGroup (page_grp, 4, 0, NULL);
-  SetGroupSpacing (cfp->pages[4], 10, 10);
-  StaticPrompt (cfp->pages[4], "Create group with sequences where", 0, dialogTextHeight, programFont, 'l');
-  cfp->search_text = DialogText (cfp->pages[4], "", 10, SegTextChange);
+  cfp->pages[eSegPageText - 1] = HiddenGroup (page_grp, 4, 0, NULL);
+  SetGroupSpacing (cfp->pages[eSegPageText - 1], 10, 10);
+  StaticPrompt (cfp->pages[eSegPageText - 1], "Create set with sequences where", 0, dialogTextHeight, programFont, 'l');
+  cfp->search_text = DialogText (cfp->pages[eSegPageText - 1], "", 10, SegTextChange);
   SetObjectExtra (cfp->search_text, cfp, NULL);
-  StaticPrompt (cfp->pages[4], "appears in", 0, dialogTextHeight, programFont, 'l');
-  cfp->search_field = SearchFieldDialog (cfp->pages[4], SegTextChangeNotify, cfp);
+  StaticPrompt (cfp->pages[eSegPageText - 1], "appears in", 0, dialogTextHeight, programFont, 'l');
+  cfp->search_field = SearchFieldDialog (cfp->pages[eSegPageText - 1], SegTextChangeNotify, cfp);
 
   /* id */
-  cfp->pages[5] = HiddenGroup (page_grp, -1, 0, NULL);
-  SetGroupSpacing (cfp->pages[5], 10, 10);
-  p2 = StaticPrompt (cfp->pages[5], "Create group with selected sequences", 0, dialogTextHeight, programFont, 'l');
-  g1 = HiddenGroup (cfp->pages[5], 3, 0, NULL);
-  StaticPrompt (g1, "Select IDs in list", 0, dialogTextHeight, programFont, 'l');
-  cfp->id_txt = DialogText (g1, "", 10, NULL);
-  b = PushButton (g1, "Select", SelectSequenceIDRangeForSegregate);
-  SetObjectExtra (b, cfp, NULL);
-  g2 = HiddenGroup (cfp->pages[5], 2, 0, NULL);
-  cfp->id_constraint = StringConstraintDialog (g2, "Select sequences where sequence ID", TRUE);
-  b = PushButton (g2, "Select", SelectSequenceIDsForSegregate);
+  cfp->pages[eSegPageId - 1] = HiddenGroup (page_grp, -1, 0, NULL);
+  SetGroupSpacing (cfp->pages[eSegPageId - 1], 10, 10);
+  p2 = StaticPrompt (cfp->pages[eSegPageId - 1], "Create set with marked sequences", 0, dialogTextHeight, programFont, 'l');
+  g1 = HiddenGroup (cfp->pages[eSegPageId - 1], 3, 0, NULL);
+  g2 = HiddenGroup (cfp->pages[eSegPageId - 1], 2, 0, NULL);
+  cfp->id_constraint = StringConstraintDialogX (g2, "Mark sequences where sequence ID", TRUE);
+  scd.insensitive = TRUE;
+  scd.match_location = eStringConstraintInList;
+  scd.match_text = NULL;
+  scd.not_present = FALSE;
+  scd.whole_word = FALSE;
+  PointerToDialog (cfp->id_constraint, &scd);
+  b = PushButton (g2, "Mark", SelectSequenceIDsForSegregate);
   SetObjectExtra (b, cfp, NULL);
   AlignObjects (ALIGN_CENTER, (HANDLE) p2, (HANDLE) g1, (HANDLE) g2, NULL);
 
@@ -31506,13 +33149,12 @@ extern Int2 LIBCALLBACK SegregateSetsByField (Pointer data)
                               NULL);
 
   SetValue (cfp->seg_choice_grp, 1);
-  Hide (cfp->pages[1]);
 
   /* add select all/unselect all buttons */
   k = HiddenGroup (h, 2, 0, NULL);
-  b = PushButton (k, "Select All", SelectSegCategories);
+  b = PushButton (k, "Mark All", SelectSegCategories);
   SetObjectExtra (b, cfp, NULL);
-  b = PushButton (k, "Unselect All", UnselectSegCategories);
+  b = PushButton (k, "Unmark All", UnselectSegCategories);
   SetObjectExtra (b, cfp, NULL);  
 
 
@@ -31527,7 +33169,7 @@ extern Int2 LIBCALLBACK SegregateSetsByField (Pointer data)
 
   /* Line things up nicely */
 
-  AlignObjects (ALIGN_CENTER, (HANDLE) cfp->seg_choice_grp,
+  AlignObjects (ALIGN_CENTER, (HANDLE) g3,
                               (HANDLE) cfp->group_list_dlg,
                               (HANDLE) page_grp,
 							  (HANDLE) k,
@@ -31652,7 +33294,11 @@ static void FixCaseByFieldCallback (ButtoN b)
   Update();
 
   /* if we will be fixing capitalization, get org names to use in fixes */
-  VisitBioSourcesInSep (sep, &(fcp->orgnames), GetOrgNamesInRecordCallback);
+  if (dst_field_data->parse_field_type != PARSE_FIELD_BIOSRC_STRING
+      || dst_field_data->feature_field == NULL
+      || dst_field_data->feature_field->data.intvalue != PARSE_FIELD_BIOSRC_TAXNAME) {
+    VisitBioSourcesInSep (sep, &(fcp->orgnames), GetOrgNamesInRecordCallback);
+  }
 
   switch (dst_field_data->parse_field_type)
   {
@@ -31699,6 +33345,19 @@ static void FixCaseByFieldCallback (ButtoN b)
                                            SEQFEAT_BIOSRC, 0,
                                            Seq_descr_source, fcp);
       break;
+    case PARSE_FIELD_DBXREF:
+      fcp->fieldstring_func = GetBioSourceFeatureDbxrefString;
+      fcp->descrstring_func = GetBioSourceDescriptorDbxrefString;
+      fcp->feature_apply_action = ApplyBioSourceDbxrefFeatureCallback;
+      fcp->descriptor_apply_action = ApplyBioSourceDbxrefDescriptorCallback;
+      fcp->free_vn_proc = ValNodeSimpleDataFree;
+      fcp->copy_vn_proc = ValNodeStringCopy;
+      fcp->requested_field = dst_field_data->feature_field;
+      OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback, 
+                                           FixCaseDescriptorCallback,
+                                           SEQFEAT_BIOSRC, 0,
+                                           Seq_descr_source, fcp);
+      break;
     case PARSE_FIELD_GENE_FIELD:
       fcp->fieldstring_func = GetGeneFieldString;
       fcp->descrstring_func = NULL;
@@ -31712,17 +33371,18 @@ static void FixCaseByFieldCallback (ButtoN b)
                                            SEQFEAT_GENE, 0,
                                            0, fcp);
       break;
-    case PARSE_FIELD_MRNA_FIELD:
-      fcp->fieldstring_func = GetmRNAFieldString;
+    case PARSE_FIELD_RNA_FIELD:
+      fcp->fieldstring_func = GetRNAFieldString;
       fcp->descrstring_func = NULL;
-      fcp->feature_apply_action = SetmRNAFieldString;
+      fcp->feature_apply_action = SetRNAFieldString;
       fcp->descriptor_apply_action = NULL;
       fcp->free_vn_proc = NULL;
       fcp->copy_vn_proc = IntValNodeCopy;
       fcp->requested_field = dst_field_data->feature_field;
       OperateOnSeqEntryConstrainedObjects (sep, fsp, FixCaseFeatureCallback, 
                                            NULL,
-                                           SEQFEAT_RNA, FEATDEF_mRNA,
+                                           SEQFEAT_RNA,
+                                           dst_field_data->feature_subtype == NULL ? 0 : dst_field_data->feature_subtype->data.intvalue,
                                            0, fcp);
       break;
     case PARSE_FIELD_CDS_COMMENT:
@@ -31847,7 +33507,7 @@ extern void FixCaseByField (IteM i)
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
 
-  cfp->field_dlg = ParseFieldDestDialog (h, NULL, NULL);
+  cfp->field_dlg = ParseFieldDestDialogEx (h, NULL, NULL, FALSE, TRUE);
 
   cfp->case_dlg = ChangeCaseDialog (h);
   ccd.change = eChangeCaseAllLower;
@@ -31877,31 +33537,6 @@ extern void FixCaseByField (IteM i)
   Update ();
 }
 
-typedef void (*BulkSetFieldFunc) PROTO ((Pointer, Pointer));
-typedef Pointer (*BulkSetFieldStringFunc) PROTO ((Pointer, ApplyValuePtr));
-typedef Pointer (*BulkGetFieldFunc) PROTO ((Pointer));
-typedef CharPtr (*BulkDisplayFieldFunc) PROTO ((Pointer));
-typedef void (*BulkFreeFieldFunc) PROTO ((Pointer));
-typedef DialoG (*BulkCreateDlgFunc) PROTO ((GrouP, CharPtr, SeqEntryPtr));
-typedef Int4 (*BulkFormatColumnFunc) PROTO ((ColPtr, CharPtr));
-typedef void (*BulkDrawColumnFunc) PROTO ((Pointer, RectPtr));
-typedef Pointer (*BulkReleaseCellFunc) PROTO ((Pointer));
-typedef Pointer (*BulkCopyFieldFunc) PROTO ((Pointer));
-
-typedef struct bulkedfield {
-  CharPtr name;
-  BulkSetFieldFunc set_func;
-  BulkSetFieldStringFunc set_str_func;
-  BulkGetFieldFunc get_func;
-  BulkDisplayFieldFunc display_func;
-  BulkFreeFieldFunc free_func;
-  BulkCreateDlgFunc create_dlg_func;
-  BulkFormatColumnFunc format_col_func;
-  BulkDrawColumnFunc  draw_col_func;
-  BulkReleaseCellFunc release_cell_func;
-  BulkCopyFieldFunc   copy_func;
-} BulkEdFieldData, PNTR BulkEdFieldPtr;
-
 static void FormatBoxColumn (ColPtr col)
 {
   if (col == NULL) return;
@@ -32271,7 +33906,7 @@ static Boolean AllBulkEditorRowsSelected (BulkEditorRowPtr berp)
 }
 
 
-static void SelectBulkEditorRowsByStringConstraint (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, Int4 col, StringConstraintPtr scp, Boolean val)
+static void SelectBulkEditorRowsByStringConstraint (BulkEditorRowPtr berp, BulkEdFieldPtr field_list, Int4 col, StringConstraintXPtr scp, Boolean val)
 {
   ValNodePtr vnp;
   CharPtr    str = NULL;
@@ -32285,7 +33920,7 @@ static void SelectBulkEditorRowsByStringConstraint (BulkEditorRowPtr berp, BulkE
       if (vnp != NULL) {
         str = field_list[col].display_func(vnp->data.ptrvalue);
       }
-      match = DoesStringMatchConstraint (str, scp);
+      match = DoesStringMatchConstraintX (str, scp);
       str = MemFree (str);
       if (scp != NULL && scp->not_present) {
         match = !match;
@@ -32579,19 +34214,19 @@ static void ApplyValueToOneBulkEditorRow (BulkEditorRowPtr berp, Int2 col, BulkE
 }
 
 
-static void PopulateSingleBulkEditRowFromData (BulkEditorRowPtr berp, Uint1 data_choice, Pointer data, BulkEdFieldPtr field_list)
+static void PopulateSingleBulkEditRowFromData (BulkEditorRowPtr berp, Uint1 data_choice, Pointer data, BulkEdFieldPtr field_list, Pointer metadata)
 {
   Int4 col;
 
   /* add values for all columns */
   for (col = 0; field_list[col].name != NULL; col++) {
-    ValNodeAddPointer (&(berp->values_list), 0, (field_list[col].get_func (data)));
+    ValNodeAddPointer (&(berp->values_list), 0, (field_list[col].get_func (data_choice, data, metadata)));
   }
   /* add feature */
   ValNodeAddPointer (&(berp->object_list), data_choice, data);
 }
 
-static BulkEditorRowPtr MakeBulkEditorRowsFromObjectList (ValNodePtr object_list, BulkEdFieldPtr field_list, Int4 sort_column)
+static BulkEditorRowPtr MakeBulkEditorRowsFromObjectList (ValNodePtr object_list, BulkEdFieldPtr field_list, Int4 sort_column, Pointer metadata)
 {
   ValNodePtr       vnp;
   BulkEditorRowPtr bulk_ed_rows = NULL, sorted_rows = NULL;
@@ -32607,7 +34242,7 @@ static BulkEditorRowPtr MakeBulkEditorRowsFromObjectList (ValNodePtr object_list
 
   for (vnp = object_list, row_num = 0; vnp != NULL; vnp = vnp->next, row_num++)
   {
-    PopulateSingleBulkEditRowFromData (bulk_ed_rows + row_num, vnp->choice, vnp->data.ptrvalue, field_list); 
+    PopulateSingleBulkEditRowFromData (bulk_ed_rows + row_num, vnp->choice, vnp->data.ptrvalue, field_list, metadata); 
   }
 
   if (sort_column >= 0)
@@ -32863,14 +34498,14 @@ typedef struct twofieldbulkedit
   Boolean strip_name;
   Boolean leave_on_original;
   Boolean remove_parsed;
-  TextPortionPtr text_portion;
+  TextPortionXPtr text_portion;
 } TwoFieldBulkEditData, PNTR TwoFieldBulkEditPtr;
 
 
 static TwoFieldBulkEditPtr TwoFieldBulkEditFree (TwoFieldBulkEditPtr tfp)
 {
   if (tfp != NULL) {
-    tfp->text_portion = TextPortionFree (tfp->text_portion);
+    tfp->text_portion = TextPortionXFree (tfp->text_portion);
     tfp = MemFree (tfp);
   }
   return tfp;
@@ -32995,7 +34630,7 @@ static DialoG TwoFieldBulkEditDialog
 
   if (action_choice == eBulkParseField) 
   {
-    dlg->text_portion = TextPortionDialog(p);
+    dlg->text_portion = TextPortionXDialog(p);
   }
 
   g2 = HiddenGroup (p, 3, 0, NULL);
@@ -33102,6 +34737,7 @@ typedef struct bulkeditordlg {
   Boolean           collapse_by_default;
   ClickableCallback single_click_func;
   ClickableCallback double_click_func;
+  Pointer           metadata;
 } BulkEditorDlgData, PNTR BulkEditorDlgPtr;
 
 
@@ -33881,7 +35517,7 @@ AddSampleDataForBulkEditorSelectedFeatures
  Int4             col,
  Int4             col_src,
  GetSamplePtr     gsp,
- TextPortionPtr   text_portion)
+ TextPortionXPtr   text_portion)
 {
   CharPtr    str, str_src, str_parse;
   ValNodePtr vnp, vnp_src;
@@ -33941,7 +35577,7 @@ GetSampleDataForBulkEditorSelectedFeatures
  BulkEdFieldPtr   field_list,
  Int4             col,
  Int4             col_src,
- TextPortionPtr   text_portion)
+ TextPortionXPtr   text_portion)
 {
   GetSamplePtr gsp;
 
@@ -34079,7 +35715,7 @@ static void BulkEditorStringConstraintCheck (ButtoN b)
   BulkEditorDlgPtr    dlg;
   RecT                r;
   Int4                field_num;
-  StringConstraintPtr scp;
+  StringConstraintXPtr scp;
   Boolean             val;
 
   dlg = (BulkEditorDlgPtr) GetObjectExtra (b);
@@ -34096,7 +35732,7 @@ static void BulkEditorStringConstraintCheck (ButtoN b)
 
   SelectBulkEditorRowsByStringConstraint (dlg->row_list, dlg->field_list, field_num, scp, val);
   
-  scp = StringConstraintFree (scp);
+  scp = StringConstraintXFree (scp);
   UpdateCheckStatus (dlg);
 
   ObjectRect (dlg->doc, &r);
@@ -34115,7 +35751,7 @@ static void ObjectListToBulkEditorDialog (DialoG d, Pointer data)
   object_list = (ValNodePtr) data;
     
   dlg->row_list = FreeBulkEditorRows(dlg->row_list, dlg->field_list);
-  dlg->row_list = MakeBulkEditorRowsFromObjectList (object_list, dlg->field_list, dlg->last_sorted_col);
+  dlg->row_list = MakeBulkEditorRowsFromObjectList (object_list, dlg->field_list, dlg->last_sorted_col, dlg->metadata);
   if (dlg->collapse_by_default) {
     CollapseAllBulkEditRows (dlg->row_list);
   } else {
@@ -34141,14 +35777,15 @@ static Pointer GetSelectedObjectsFromBulkEditorDialog (DialoG d)
 
 
 static DialoG 
-CreateBulkEditorDialog 
+CreateBulkEditorDialogEx 
 (GrouP               h,
  BulkEdFieldPtr      field_list,
  ValNodePtr          feat_list,
  SeqEntryPtr         sep, 
  Boolean             collapse_by_default,
  ClickableCallback   single_click_func,
- ClickableCallback   double_click_func)
+ ClickableCallback   double_click_func,
+ Pointer             metadata)
 {
   GrouP            p;
   BulkEditorDlgPtr dlg;
@@ -34171,11 +35808,12 @@ CreateBulkEditorDialog
   dlg->single_click_func = single_click_func;
   dlg->double_click_func = double_click_func;
   dlg->field_list = field_list;
+  dlg->metadata = metadata;
 
   dlg->last_viewed_row = 0;
   dlg->last_viewed_col = 0;
   dlg->last_sorted_col = 0;
-  dlg->row_list = MakeBulkEditorRowsFromObjectList(feat_list, dlg->field_list, dlg->last_sorted_col);
+  dlg->row_list = MakeBulkEditorRowsFromObjectList(feat_list, dlg->field_list, dlg->last_sorted_col, dlg->metadata);
   if (dlg->collapse_by_default) {
     CollapseAllBulkEditRows (dlg->row_list);
   } else {
@@ -34238,7 +35876,7 @@ CreateBulkEditorDialog
   RadioButton (dlg->sel_unsel_grp, "Uncheck features where");
   SetValue (dlg->sel_unsel_grp, 1);
   dlg->check_constraint_field = MakeBulkEditorFieldListPopup (g2, dlg->field_list, FALSE);
-  dlg->check_constraint = StringConstraintDialog (g2, NULL, FALSE);
+  dlg->check_constraint = StringConstraintDialogX (g2, NULL, FALSE);
   b = PushButton (g2, "Apply", BulkEditorStringConstraintCheck);
   SetObjectExtra (b, dlg, NULL);
 
@@ -34256,7 +35894,7 @@ CreateBulkEditorDialog
     PopupItem (dlg->bulk_action, "Swap");
     PopupItem (dlg->bulk_action, "Remove");
     PopupItem (dlg->bulk_action, "Change Case");
-    SetValue (dlg->bulk_action, 1);
+    SetValue (dlg->bulk_action, 2);
     page_grp = HiddenGroup (a, 0, 0, NULL);
     page_num = 0;
     dlg->action_pages[page_num] = HiddenGroup (page_grp, 2, 0, NULL);
@@ -34310,7 +35948,23 @@ CreateBulkEditorDialog
   return (DialoG) p;
 }
 
-static Pointer BulkGetLocation (Pointer data)
+
+NLM_EXTERN DialoG 
+CreateBulkEditorDialog 
+(GrouP               h,
+ BulkEdFieldPtr      field_list,
+ ValNodePtr          feat_list,
+ SeqEntryPtr         sep, 
+ Boolean             collapse_by_default,
+ ClickableCallback   single_click_func,
+ ClickableCallback   double_click_func)
+{
+  return CreateBulkEditorDialogEx (h, field_list, feat_list, sep, collapse_by_default,
+                                   single_click_func, double_click_func, NULL);
+}
+
+
+static Pointer BulkGetLocation (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   SeqLocPtr slp;
   SeqFeatPtr sfp = (SeqFeatPtr) data;
@@ -34378,7 +36032,7 @@ static Pointer BulkCopyLocation (Pointer data)
   return new_loc;
 }
 
-static Int4 BulkFormatSimpleText (ColPtr col, CharPtr name)
+NLM_EXTERN Int4 BulkFormatSimpleText (ColPtr col, CharPtr name)
 {
   if (col == NULL) return 0;
 
@@ -34395,14 +36049,14 @@ static Int4 BulkFormatSimpleText (ColPtr col, CharPtr name)
   return col->pixWidth;
 }
 
-static void BulkFreeSimpleText (Pointer data)
+NLM_EXTERN void BulkFreeSimpleText (Pointer data)
 {
   CharPtr str = (CharPtr) data;
 
   str = MemFree (str);
 }
 
-static CharPtr BulkDisplaySimpleText (Pointer data)
+NLM_EXTERN CharPtr BulkDisplaySimpleText (Pointer data)
 {
   CharPtr str = (CharPtr) data;
   if (StringHasNoText (str)) {
@@ -34470,7 +36124,7 @@ static DialoG BulkSimpleTextDialogEx (GrouP g, CharPtr name, SeqEntryPtr sep, Bo
   return (DialoG) p;
 }
 
-static DialoG BulkSimpleTextDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
+NLM_EXTERN DialoG BulkSimpleTextDialog (GrouP g, CharPtr name, SeqEntryPtr sep)
 {
   return BulkSimpleTextDialogEx (g, name, sep, FALSE);
 }
@@ -34480,7 +36134,7 @@ static DialoG BulkSimpleTextScrollDialog (GrouP g, CharPtr name, SeqEntryPtr sep
   return BulkSimpleTextDialogEx (g, name, sep, TRUE);
 }
 
-static Pointer BulkSimpleTextCopy (Pointer data)
+NLM_EXTERN Pointer BulkSimpleTextCopy (Pointer data)
 {
   CharPtr orig = (CharPtr) data;
   CharPtr new_str = StringSave (orig);
@@ -34569,7 +36223,7 @@ static void BulkSetComment (Pointer target, Pointer data)
   }
 }
 
-static Pointer BulkGetComment (Pointer data)
+static Pointer BulkGetComment (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   SeqFeatPtr sfp = (SeqFeatPtr) data;
   if (sfp == NULL || StringHasNoText (sfp->comment)) {
@@ -34635,7 +36289,7 @@ static void BulkCDSSetProtein (Pointer target, Pointer data)
 
 }
 
-static Pointer BulkCDSGetProtein (Pointer data)
+static Pointer BulkCDSGetProtein (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   SeqFeatXrefPtr xref;
   ProtRefPtr     prp = NULL;
@@ -34822,7 +36476,7 @@ static void BulkCDSSetProteinDesc (Pointer target, Pointer data)
 }
 
 
-static Pointer BulkCDSGetProteinDesc (Pointer data)
+static Pointer BulkCDSGetProteinDesc (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   SeqFeatXrefPtr xref;
   ProtRefPtr     prp = NULL;
@@ -34881,7 +36535,7 @@ static void BulkGeneSetLocus (Pointer target, Pointer data)
   }
 }
 
-static Pointer BulkGeneGetLocus (Pointer data)
+static Pointer BulkGeneGetLocus (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   GeneRefPtr grp; 
   SeqFeatPtr sfp = (SeqFeatPtr) data;
@@ -34916,7 +36570,7 @@ static void BulkGeneSetLocusTag (Pointer target, Pointer data)
   }
 }
 
-static Pointer BulkGeneGetLocusTag (Pointer data)
+static Pointer BulkGeneGetLocusTag (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   GeneRefPtr grp;
   SeqFeatPtr sfp = (SeqFeatPtr) data;
@@ -34951,7 +36605,7 @@ static void BulkGeneSetDescription (Pointer target, Pointer data)
   }
 }
 
-static Pointer BulkGeneGetDescription (Pointer data)
+static Pointer BulkGeneGetDescription (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   GeneRefPtr grp;
   SeqFeatPtr sfp = (SeqFeatPtr) data;
@@ -34997,7 +36651,7 @@ static void BulkRNASetProduct (Pointer target, Pointer data)
   }
 }
 
-static Pointer BulkRNAGetProduct (Pointer data)
+static Pointer BulkRNAGetProduct (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   RnaRefPtr  rrp;
   CharPtr    rna_product = NULL;
@@ -35033,7 +36687,7 @@ static Boolean IsBulkEditableRNA (SeqFeatPtr sfp)
 
 
 /* template for setting simple text strings */
-static Pointer BulkSetSimpleTextString (Pointer curr_val, ApplyValuePtr avp)
+NLM_EXTERN Pointer BulkSetSimpleTextString (Pointer curr_val, ApplyValuePtr avp)
 {
   CharPtr        curr_val_str;
 
@@ -35103,15 +36757,15 @@ static void BulkSrcSetTaxNameDesc (Pointer target, Pointer data)
 }
 
 
-static Pointer BulkSrcGetTaxNameDesc (Pointer data)
+NLM_EXTERN BioSourcePtr GetBioSourceFromObject (Uint1 choice, Pointer data);
+
+static Pointer BulkSrcGetTaxNameDesc (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   CharPtr      taxname = NULL;
-  SeqDescrPtr  sdp = (SeqDescrPtr) data;
-  BioSourcePtr biop;
+  BioSourcePtr biop = NULL;
 
-  if (sdp == NULL || sdp->choice != Seq_descr_source || sdp->data.ptrvalue == NULL) return NULL;
-
-  biop = (BioSourcePtr) sdp->data.ptrvalue;
+  biop = GetBioSourceFromObject (data_choice, data);
+  if (biop == NULL) return NULL;
 
   if (biop->org != NULL) {
     taxname = StringSave (biop->org->taxname);
@@ -35140,7 +36794,7 @@ static void BulkSrcSetTaxNameFeat (Pointer target, Pointer data)
 }
 
 
-static Pointer BulkSrcGetTaxNameFeat (Pointer data)
+static Pointer BulkSrcGetTaxNameFeat (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   CharPtr      taxname = NULL;
   SeqFeatPtr   sfp = (SeqFeatPtr) data;
@@ -35414,6 +37068,67 @@ extern void BulkEditorDescrList (Uint2 entityID, ValNodePtr descr_list)
 }
 
 
+NLM_EXTERN void BulkEditorObjectList (Uint2 entityID, CharPtr title, ValNodePtr feat_list, BulkEdFieldPtr field_list)
+{
+  GrouP              c;
+  ButtoN             b;
+  BulkEditorPtr      bep;
+  GrouP              h;
+  WindoW             w;
+  SeqEntryPtr        sep;
+  Uint1              subtype = 0;
+
+  if (feat_list == NULL) {
+    Message (MSG_ERROR, "No features found!");
+    return;
+  }
+  /* Create a new window, and a struct */
+  /* to pass around the data in.       */
+
+  sep = GetTopSeqEntryForEntityID (entityID);
+
+  bep = (BulkEditorPtr) MemNew (sizeof (BulkEditorData));
+  if (bep == NULL)
+    return;
+
+  bep->field_list = field_list;
+
+  w = FixedWindow (-50, -33, -10, -10, title,
+		   StdCloseWindowProc);
+  SetObjectExtra (w, bep, StdCleanupFormProc); 
+  bep->form = (ForM) w;
+  bep->input_entityID = entityID;
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  /* want: Document with columns for pseudo (when appropriate), location, fields */
+  /* when user clicks on field, should be able to edit contents */
+  
+  bep->bulk_ed = CreateBulkEditorDialog (h, bep->field_list, feat_list, sep, TRUE, NULL, NULL);
+
+  /* Add Accept and Cancel buttons */
+
+  c = HiddenGroup (h, 3, 0, NULL);
+  b = PushButton (c, "Accept", AcceptBulkEditor);
+  SetObjectExtra (b, bep, NULL);
+  PushButton (c, "Cancel", StdCancelButtonProc);
+
+  /* Line things up nicely */
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) bep->bulk_ed,
+                              (HANDLE) c, NULL);
+
+
+  /* Display the window now */
+
+  RealizeWindow (w);
+  Show (w);
+  Select (w);
+  Update ();
+}
+
+
 static void BulkEditor (IteM i, Uint1 featchoice, Uint1 featdef)
 {
   BaseFormPtr        bfp;
@@ -35473,7 +37188,7 @@ extern void BulkEditRNA (IteM i)
 }
 
 
-static Pointer GetBarcodeTestBarcodeID (Pointer data)
+static Pointer GetBarcodeTestBarcodeID (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
   if (res == NULL || res->bsp == NULL) {
@@ -35484,7 +37199,7 @@ static Pointer GetBarcodeTestBarcodeID (Pointer data)
 }
 
   
-static Pointer GetBarcodeTestGenbankID (Pointer data)
+static Pointer GetBarcodeTestGenbankID (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
   if (res == NULL || res->bsp == NULL) {
@@ -35495,7 +37210,7 @@ static Pointer GetBarcodeTestGenbankID (Pointer data)
 }
 
 
-static Pointer GetBarcodeTestLengthResult (Pointer data)
+static Pointer GetBarcodeTestLengthResult (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
   if (res == NULL || !res->failed_tests[eBarcodeTest_Length]) {
@@ -35506,7 +37221,7 @@ static Pointer GetBarcodeTestLengthResult (Pointer data)
 }
 
 
-static Pointer GetBarcodeTestPrimersResult (Pointer data)
+static Pointer GetBarcodeTestPrimersResult (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
   if (res == NULL || !res->failed_tests[eBarcodeTest_Primers]) {
@@ -35517,7 +37232,7 @@ static Pointer GetBarcodeTestPrimersResult (Pointer data)
 }
 
 
-static Pointer GetBarcodeTestCountryResult (Pointer data)
+static Pointer GetBarcodeTestCountryResult (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
   if (res == NULL || !res->failed_tests[eBarcodeTest_Country]) {
@@ -35528,7 +37243,7 @@ static Pointer GetBarcodeTestCountryResult (Pointer data)
 }
 
 
-static Pointer GetBarcodeTestSpecimenVoucherResult (Pointer data)
+static Pointer GetBarcodeTestSpecimenVoucherResult (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
   if (res == NULL || !res->failed_tests[eBarcodeTest_SpecimenVoucher]) {
@@ -35539,7 +37254,7 @@ static Pointer GetBarcodeTestSpecimenVoucherResult (Pointer data)
 }
 
 
-static Pointer GetBarcodeTestPercentNsResult (Pointer data)
+static Pointer GetBarcodeTestPercentNsResult (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   BarcodeTestResultsPtr res = (BarcodeTestResultsPtr) data;
   Char txt[5];
@@ -35664,17 +37379,13 @@ extern SubSourcePtr FindBadLatLon (BioSourcePtr biop)
 }
 
 
-static Pointer GetCurrentLatLon (Pointer data)
+static Pointer GetCurrentLatLon (Uint1 data_choice, Pointer data, Pointer metadata)
 {
-  SeqDescrPtr  sdp = (SeqDescrPtr) data;
   SubSourcePtr bad_ssp;
   BioSourcePtr biop;
 
-  if (sdp == NULL || sdp->data.ptrvalue == NULL )
-  {
-    return NULL;
-  } 
-  biop = (BioSourcePtr) sdp->data.ptrvalue;
+  biop = GetBioSourceFromObject (data_choice, data);
+  if (biop == NULL) return NULL;
 
   bad_ssp = FindBadLatLon (biop);
   if (bad_ssp == NULL) 
@@ -35688,18 +37399,14 @@ static Pointer GetCurrentLatLon (Pointer data)
 }
 
 
-static Pointer GetCorrectedLatLon (Pointer data)
+static Pointer GetCorrectedLatLon (Uint1 data_choice, Pointer data, Pointer metadata)
 {
-  SeqDescrPtr  sdp = (SeqDescrPtr) data;
   SubSourcePtr bad_ssp;
   CharPtr      fix;
   BioSourcePtr biop;
 
-  if (sdp == NULL || sdp->data.ptrvalue == NULL )
-  {
-    return NULL;
-  } 
-  biop = (BioSourcePtr) sdp->data.ptrvalue;
+  biop = GetBioSourceFromObject (data_choice, data);
+  if (biop == NULL) return NULL;
 
   bad_ssp = FindBadLatLon (biop);
   if (bad_ssp == NULL) 
@@ -35732,7 +37439,137 @@ extern DialoG LatLonTestResultsDisplay (GrouP h)
 }
 
 
-static Pointer GetCurrentSpecificHost (Pointer data)
+static CharPtr GetSubSource (Uint1 data_choice, Pointer data, Uint1 subtype)
+{
+  SubSourcePtr ssp;
+  BioSourcePtr biop;
+
+  biop = GetBioSourceFromObject (data_choice, data);
+  if (biop == NULL) return NULL;
+
+  for (ssp = biop->subtype; ssp != NULL && ssp->subtype != subtype; ssp = ssp->next)
+  {}
+
+  if (ssp == NULL) 
+  {
+    return NULL;
+  }
+  else
+  {
+    return StringSave (ssp->name);
+  }
+}
+
+
+static Pointer GetCountry (Uint1 data_choice, Pointer data, Pointer metadata)
+{
+  return GetSubSource (data_choice, data, SUBSRC_country);
+}
+
+static Pointer GetLatLon (Uint1 data_choice, Pointer data, Pointer metadata)
+{
+  return GetSubSource (data_choice, data, SUBSRC_lat_lon);
+}
+
+
+extern Pointer GetLatLonCountryCorrection (Uint1 data_choice, Pointer data, Pointer metadata)
+{
+  SubSourcePtr ssp;
+  BioSourcePtr biop;
+  CharPtr      country = NULL, cp;
+  FloatHi      lat, lon;
+  Boolean      found_lat_lon = FALSE;
+  CharPtr      msg = NULL;
+  CharPtr      guess_fmt = "Lat_lon does not map to '%s', but may be in '%s'";
+  CharPtr      guess;
+
+  biop = GetBioSourceFromObject (data_choice, data);
+  if (biop == NULL) return NULL;
+
+  for (ssp = biop->subtype; ssp != NULL && (country == NULL || !found_lat_lon); ssp = ssp->next)
+  {
+    if (ssp->subtype == SUBSRC_country && !StringHasNoText (ssp->name))
+    {
+      country = StringSave (ssp->name);
+    }
+    else if (ssp->subtype == SUBSRC_lat_lon)
+    {
+      if (ParseLatLon (ssp->name, &lat, &lon))
+      {
+        found_lat_lon = TRUE;
+      }
+    }
+  }
+
+  cp = StringChr (country, ':');
+  if (cp != NULL) 
+  {
+    *cp = 0;
+  }
+
+  if (country == NULL && !found_lat_lon)
+  {
+    msg = StringSave ("Country and lat-lon not specified");
+  }
+  else if (country == NULL) 
+  {
+    msg = StringSave ("Country not specified");
+  }
+  else if (!found_lat_lon)
+  {
+    msg = StringSave ("Lat-lon not specified.");
+  }
+  else if (!IsCountryInLatLonList (country)) 
+  {
+    msg = StringSave ("Country not in lat-lon list");
+  }
+  else if (TestLatLonForCountry (country, lat, lon))
+  {
+    msg = StringSave ("No conflict");
+  }
+  else if (TestLatLonForCountry (country, -lat, lon)) 
+  {
+    if (lat < 0.0) {
+      msg = StringSave ("Latitude should be set to N (northern hemisphere)");
+    } else {
+      msg = StringSave ("Latitude should be set to S (southern hemisphere)");
+    }
+  } else if (TestLatLonForCountry (country, lat, -lon)) {
+    if (lon < 0.0) {
+      msg = StringSave ("Longitude should be set to E (eastern hemisphere)");
+    } else {
+      msg = StringSave ("Longitude should be set to W (western hemisphere)");
+    }
+  } else if (TestLatLonForCountry (country, lon, lat)) {
+    msg = StringSave ("Latitude and longitude values appear to be exchanged");
+  } else {
+    guess = GuessCountryForLatLon (lat, lon);
+    if (guess == NULL)
+    {
+      msg = StringSave ("Lat-lon does not map to country");
+    }
+    else
+    {
+      msg = (CharPtr) MemNew (sizeof (Char) * (StringLen (guess_fmt) + StringLen (country) + StringLen (guess)));
+      sprintf (msg, guess_fmt, country, guess);
+    }
+  }
+  return msg;
+}
+
+static BulkEdFieldData latloncountry_fields[] = {
+  { "Lat-lon", NULL, NULL, GetLatLon, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
+  { "Country", NULL, NULL, GetCountry, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
+  { "Suggested Correction", NULL, NULL, GetLatLonCountryCorrection, BulkDisplaySimpleText, BulkFreeSimpleText, NULL, BulkFormatSimpleText, NULL, NULL, BulkSimpleTextCopy },
+  { NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL}};
+
+extern DialoG LatLonCountryResultsDisplay (GrouP h)
+{
+  return CreateBulkEditorDialog (h, latloncountry_fields, NULL, NULL, FALSE, ScrollToDiscrepancyItem, EditDiscrepancyItem);
+}
+
+
+static Pointer GetCurrentSpecificHost (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   SpecificHostFixPtr s = (SpecificHostFixPtr) data;
 
@@ -35747,7 +37584,7 @@ static Pointer GetCurrentSpecificHost (Pointer data)
 }
 
 
-static Pointer GetCorrectedSpecificHost (Pointer data)
+static Pointer GetCorrectedSpecificHost (Uint1 data_choice, Pointer data, Pointer metadata)
 {
   SpecificHostFixPtr s = (SpecificHostFixPtr) data;
   CharPtr            new_spec_host;
@@ -35800,3 +37637,5 @@ extern DialoG SpecificHostResultsDisplay (GrouP h)
 {
   return CreateBulkEditorDialog (h, specifichost_fields, NULL, NULL, FALSE, ScrollToSpecificHostFix, EditSpecificHostFix);
 }
+
+
diff --git a/sequin/sequin6.c b/sequin/sequin6.c
index c4f32188..f096cb14 100644
--- a/sequin/sequin6.c
+++ b/sequin/sequin6.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   11/12/97
 *
-* $Revision: 6.310 $
+* $Revision: 6.326 $
 *
 * File Description: 
 *
@@ -56,6 +56,8 @@
 #include <salpanel.h>
 #include <seqpanel.h>
 #include <biosrc.h>
+#include <vsm.h>
+#include <actutils.h>
 
 #define NUMBER_OF_SUFFIXES    7
 
@@ -487,6 +489,7 @@ CreateFieldSubfieldDlg
   FieldSubfieldDlgPtr dlg;
   GrouP               p, g, g2;
   Int4                i;
+  ValNode             vn;
   
   dlg = (FieldSubfieldDlgPtr) MemNew (sizeof (FieldSubfieldDlgData));
   if (dlg == NULL)
@@ -541,6 +544,12 @@ CreateFieldSubfieldDlg
                                                                 NULL, FALSE, 
                                                                 dlg->change_notify, 
                                                                 dlg->change_userdata);
+  /* Set default BioSource field to scientific name */
+  vn.choice = ORGREF_SCI_NAME_FIELD;
+  vn.next = NULL;
+  vn.data.ptrvalue = NULL;
+  PointerToDialog (dlg->subfield_dlg[eFieldTypeBioSource], &vn);
+
   dlg->subfield_dlg[eFieldTypeOrgModSubSource] = SourceQualTypeSelectionDialog (g, FALSE,
                                                                                 dlg->change_notify,
                                                                                 dlg->change_userdata);
@@ -589,7 +598,7 @@ typedef struct convertformdata {
   Int2               subtype;
 
   DialoG             textportion_dlg;
-  TextPortionPtr     textportion;
+  TextPortionXPtr     textportion;
   Boolean            remove_inside;
 
   CharPtr            foundstr;
@@ -3443,7 +3452,7 @@ static void SearchAndExciseTextInside (CharPtr PNTR strptr, ConvertFormPtr cfp)
   string = *strptr;
   if (string == NULL) return;
 
-  FindTextPortionInString (string, cfp->textportion, &lft, &strLen);
+  FindTextPortionXInString (string, cfp->textportion, &lft, &strLen);
   if (lft == NULL) return;
   rgt = lft + strLen;
   next_delete = lft;
@@ -3482,7 +3491,7 @@ static void SearchAndExciseTextOutside (CharPtr sourceStr, ConvertFormPtr cfp)
     return;
   }
 
-  FindTextPortionInString (sourceStr, cfp->textportion, &leftEnd, &strLen);
+  FindTextPortionXInString (sourceStr, cfp->textportion, &leftEnd, &strLen);
 
   if (leftEnd != NULL) 
   {
@@ -3843,7 +3852,7 @@ static void DoRemoveText (ConvertFormPtr cfp)
 
 
   /* get information about text to remove */
-  cfp->textportion = (TextPortionPtr) DialogToPointer (cfp->textportion_dlg);
+  cfp->textportion = (TextPortionXPtr) DialogToPointer (cfp->textportion_dlg);
   
   if (GetValue (cfp->repeat_remove_grp) == 2) {
     cfp->repeat_remove = TRUE;
@@ -3865,7 +3874,7 @@ static void DoRemoveText (ConvertFormPtr cfp)
   
   /* Clean up and exit */
 
-  cfp->textportion = TextPortionFree (cfp->textportion);
+  cfp->textportion = TextPortionXFree (cfp->textportion);
 
   if (cfp->isDirty) {
     DeleteMarkedObjects (cfp->input_entityID, 0, NULL);
@@ -3948,7 +3957,7 @@ static void SetRemoveTextAcceptButton (Pointer data)
   ConvertFormPtr   cfp;
   FieldSubfieldPtr f;
   Boolean          ok_to_accept = FALSE;
-  TextPortionPtr   tp;
+  TextPortionXPtr   tp;
 
   cfp = (ConvertFormPtr) data;
   if (cfp == NULL) return;
@@ -3965,11 +3974,11 @@ static void SetRemoveTextAcceptButton (Pointer data)
   }
   f = FieldSubfieldFree (f);
   if (ok_to_accept) {
-    tp = (TextPortionPtr) DialogToPointer (cfp->textportion_dlg);
+    tp = (TextPortionXPtr) DialogToPointer (cfp->textportion_dlg);
     if (tp == NULL || (StringHasNoText (tp->start_text) && StringHasNoText (tp->end_text))) {
       ok_to_accept = FALSE;        
     }
-    tp = TextPortionFree (tp);
+    tp = TextPortionXFree (tp);
   }
   if (ok_to_accept) {
     SafeEnable (cfp->accept);
@@ -3980,6 +3989,20 @@ static void SetRemoveTextAcceptButton (Pointer data)
 }
 
 
+static void ClearRemoveOutsideText (ButtoN b)
+{
+  ConvertFormPtr cfp;
+
+  cfp = (ConvertFormPtr) GetObjectExtra (b);
+  if (cfp == NULL) return;
+
+  PointerToDialog (cfp->target_dlg, NULL);
+  PointerToDialog (cfp->textportion_dlg, NULL);
+
+  SetRemoveTextAcceptButton (cfp);
+}
+
+
 /*---------------------------------------------------------------------*/
 /*                                                                     */
 /* RemoveTextOutsideString ()                                          */
@@ -3997,6 +4020,7 @@ extern void RemoveTextOutsideString (IteM i)
   StdEditorProcsPtr  sepp;
   WindoW             w;
   PrompT             p, p2;
+  ButtoN             b;
 
   /* Get current sequence */
 
@@ -4050,7 +4074,7 @@ extern void RemoveTextOutsideString (IteM i)
 
   p = StaticPrompt (mainGroup, "Remove Text", 0, 0, programFont, 'l');
 
-  cfp->textportion_dlg = TextPortionDialogEx (mainGroup, FALSE, SetRemoveTextAcceptButton, cfp);
+  cfp->textportion_dlg = TextPortionXDialogEx (mainGroup, FALSE, SetRemoveTextAcceptButton, cfp);
 
   /* The "If not found" group */
 
@@ -4070,6 +4094,9 @@ extern void RemoveTextOutsideString (IteM i)
   allowed[eFieldTypePublication] = FALSE;
   cfp->target_dlg = CreateFieldSubfieldDlg (mainGroup, allowed, ChangeTargetFields, cfp);
 
+  /* clear button */
+  b = PushButton (mainGroup, "Clear", ClearRemoveOutsideText);
+  SetObjectExtra (b, cfp, NULL);
 
   /* Accept and Cancel buttons */
 
@@ -4088,6 +4115,7 @@ extern void RemoveTextOutsideString (IteM i)
                 (HANDLE) cfp->ifNotFoundGroup,
                 (HANDLE) p2,
 		            (HANDLE) cfp->target_dlg,
+                (HANDLE) b,
 		            (HANDLE) buttonGroup,
 		            NULL);
 
@@ -4142,7 +4170,7 @@ extern void RemoveTextInsideString (IteM i)
   SetGroupSpacing (h, 10, 10);
 
   ppt = StaticPrompt (h, "Remove Text", 0, popupMenuHeight, programFont, 'c');
-  cfp->textportion_dlg = TextPortionDialogEx (h, TRUE, SetRemoveTextAcceptButton, cfp);
+  cfp->textportion_dlg = TextPortionXDialogEx (h, TRUE, SetRemoveTextAcceptButton, cfp);
   
   cfp->repeat_remove_grp = HiddenGroup (h, 2, 0, NULL);
   RadioButton (cfp->repeat_remove_grp, "Remove first instance in each string");
@@ -4716,954 +4744,6 @@ static SeqFeatPtr ApplyGene (CharPtr str, ApplyFormPtr afp, SeqEntryPtr gene_sep
   return gene_sfp;
 }
 
-static SeqLocPtr RemoveGapsFromSegmentedLocation (SeqLocPtr slp, BioseqPtr bsp)
-{
-  SeqLocPtr loc_slp, slp_new, slp_tmp, loc_list = NULL, loc_last = NULL;
-  SeqIdPtr  sip;
-  Uint1     strand;
-  Int4      seq_offset, start_pos, end_pos, piece_len;
-  
-  if (slp == NULL || bsp == NULL || bsp->repr != Seq_repr_seg)
-  {
-    return slp;
-  }
-  
-  loc_slp = SeqLocFindNext (slp, NULL);
-
-  while (loc_slp != NULL)
-  {
-    strand = SeqLocStrand (loc_slp);
-    start_pos = SeqLocStart (loc_slp);
-    end_pos = SeqLocStop (loc_slp);
-  
-    /* create list of locations */
-    slp_tmp = bsp->seq_ext;
-    seq_offset = 0;
-    while (slp_tmp != NULL)
-    {
-      piece_len = SeqLocLen (slp_tmp);
-      
-      if (seq_offset < end_pos
-          && seq_offset + piece_len >= start_pos)
-      {
-        sip = SeqLocId (slp_tmp);
-      
-        slp_new = SeqLocIntNew (MAX (0, start_pos - seq_offset),
-                                MIN (piece_len, end_pos - seq_offset),
-                                strand, sip);
-
-        if (slp_new != NULL)
-        {
-          if (loc_last == NULL)
-          {
-            loc_list = slp_new;
-          }
-          else
-          {
-            loc_last->next = slp_new;
-          }
-          loc_last = slp_new;
-        }
-      }
-      seq_offset += piece_len;
-      slp_tmp = slp_tmp->next;
-    }
-    loc_slp = SeqLocFindNext (slp, loc_slp);
-  }
-  
-  if (loc_list == NULL)
-  {
-    /* failed to convert - do not change */
-  }
-  else if (loc_list->next == NULL)
-  {
-    /* only found one piece */
-    slp = SeqLocFree (slp);
-    slp = loc_list;
-  }
-  else
-  {
-    /* make mixed location */
-    slp_new = ValNodeNew (NULL);
-    if (slp_new != NULL)
-    {
-      slp_new->choice = SEQLOC_MIX;
-      slp_new->data.ptrvalue = loc_list;
-      slp = SeqLocFree (slp);
-      slp = slp_new;
-    }
-  }
-  return slp;
-}
-
-static Boolean PointInInterval (Int4 interval_start, Int4 interval_length, Int4 point)
-{
-  if (point >= interval_start && point < interval_start + interval_length) 
-  {
-    return TRUE;
-  }
-  else
-  {
-    return FALSE;
-  }
-}
-
-static Boolean GapInLocation (Int4 seq_offset, Int4 length, SeqLocPtr loc)
-{
-  SeqLocPtr slp;
-  Int4      start, stop;
-  Boolean   gap_in_location = FALSE;
-  
-  slp = SeqLocFindNext (loc, NULL);
-  
-  while (slp != NULL && ! gap_in_location)
-  {
-    start = SeqLocStart (slp);
-    stop = SeqLocStop (slp);
-    
-    if (PointInInterval (seq_offset, length, start)
-        || PointInInterval (seq_offset, length, stop)
-        || PointInInterval (start, stop - start + 1, seq_offset)
-        || PointInInterval (start, stop - start + 1, seq_offset + length))
-    {
-      gap_in_location = TRUE;
-    }
-    
-    slp = SeqLocFindNext (loc, slp);
-  }
-  return gap_in_location;
-}
-
-static void
-LocationContainsGaps
-(SeqLocPtr slp,
- BioseqPtr bsp,
- Boolean   unknown_gaps,
- Boolean   known_gaps,
- BoolPtr   terminal_gaps,
- BoolPtr   internal_gaps,
- BoolPtr   entirely_in_gap)
-{
-  DeltaSeqPtr dsp;
-  Int4        seq_offset = 0;
-  Int4        dsp_len;
-  Boolean     has_terminal_gaps = FALSE;
-  Boolean     has_internal_gaps = FALSE;
-  Boolean     is_entirely_in_gap = FALSE;
-  Boolean     all_sublocs_in_gap = TRUE, this_subloc_in_gap = FALSE, this_subloc_start_gap = FALSE, this_subloc_stop_gap = FALSE;
-  Boolean     right_sublocs_in_gap = FALSE;
-  SeqLocPtr   tmp_slp;
-  Int4        start, stop;
-
-  if (slp == NULL || bsp == NULL 
-      || bsp->repr != Seq_repr_delta
-      || bsp->seq_ext_type != 4
-      || bsp->seq_ext == NULL)
-  {
-    return;
-  }
-    
-  for (tmp_slp = SeqLocFindNext (slp, NULL); 
-       tmp_slp != NULL;
-       tmp_slp = SeqLocFindNext (slp, tmp_slp))
-  {
-    seq_offset = 0;
-    start = SeqLocStart (tmp_slp);
-    stop = SeqLocStop (tmp_slp);
-    this_subloc_in_gap = FALSE;
-    this_subloc_start_gap = FALSE;
-    this_subloc_stop_gap = FALSE;
-    for (dsp = (DeltaSeqPtr) bsp->seq_ext;
-         dsp != NULL && seq_offset <= stop && !this_subloc_in_gap;
-         dsp = dsp->next)
-    {
-      dsp_len = GetDeltaSeqLen(dsp);
-      if (IsDeltaSeqGap (dsp) && !DoesDeltaSeqHaveGapTypeOrLinkage(dsp)
-          && ((unknown_gaps && IsDeltaSeqUnknownGap (dsp))
-              || (known_gaps && IsDeltaSeqKnownGap (dsp)))
-          && GapInLocation (seq_offset, dsp_len, tmp_slp))
-      {
-        if (PointInInterval (seq_offset, dsp_len, start)
-            && PointInInterval (seq_offset, dsp_len, stop))
-        {
-          this_subloc_in_gap = TRUE;
-        }
-        else if (PointInInterval (seq_offset, dsp_len, start))
-        {
-          this_subloc_start_gap = TRUE;
-        }
-        else if (PointInInterval (seq_offset, dsp_len, stop)) 
-        {
-          this_subloc_stop_gap = TRUE;
-        }
-        else 
-        {
-          has_internal_gaps = TRUE;
-        }
-      }
-      seq_offset += dsp_len;
-    }
-
-    if (this_subloc_in_gap)
-    {
-      /* all sublocs up to this point have been in the gap, so still part of left gap */
-      if (all_sublocs_in_gap)
-      {
-        has_terminal_gaps = TRUE;
-      }
-      /* could be part of chain of sublocs on the right in gap */
-      right_sublocs_in_gap = TRUE;
-    }
-    else
-    {
-      if (right_sublocs_in_gap && !all_sublocs_in_gap)
-      {
-        /* a chain of prior gapped sublocs has ended that did not start at the left end */
-        has_internal_gaps = TRUE;
-      }
-
-      if (this_subloc_start_gap)
-      { 
-        if (all_sublocs_in_gap)
-        {
-          has_terminal_gaps = TRUE;
-        }
-        else
-        {
-          /* gap on left, not part of chain of sublocs on left in gap */
-          has_internal_gaps = TRUE;
-        }
-      } 
-      
-      if (this_subloc_stop_gap)
-      {
-        /* could be start of chain of sublocs on the right in gap */
-        right_sublocs_in_gap = TRUE;
-      }
-      else
-      {
-        right_sublocs_in_gap = FALSE;
-      }
-      /* at least this subloc is not completely contained in a gap */
-      all_sublocs_in_gap = FALSE;
-    }
-  }
-
-  if (right_sublocs_in_gap)
-  {
-    has_terminal_gaps = TRUE;
-  }
-
-  if (all_sublocs_in_gap)
-  {
-    has_terminal_gaps = FALSE;
-    has_internal_gaps = FALSE;
-  }
-
-  if (terminal_gaps != NULL)
-  {
-    *terminal_gaps = has_terminal_gaps;
-  }
-
-  if (internal_gaps != NULL)
-  {
-    *internal_gaps = has_internal_gaps;
-  }
-
-  if (entirely_in_gap != NULL)
-  {
-    *entirely_in_gap = all_sublocs_in_gap;
-  }
-}
-
-
-static SeqLocPtr 
-RemoveGapsFromDeltaLocation 
-(SeqLocPtr slp,
- BioseqPtr bsp,
- Boolean   unknown_gaps,
- Boolean   known_gaps,
- Boolean   trim_ends,
- Boolean   split_internal,
- Boolean   set_partial_ends,
- BoolPtr   split)
-{
-  DeltaSeqPtr dsp;
-  Int4        seq_offset = 0;
-  Int4        dsp_len;
-  SeqLocPtr   loc_list = NULL, prev_loc = NULL;
-  SeqIdPtr    sip, before_sip, after_sip;
-  Boolean     changed, partial5, partial3;
-  SeqLocPtr   before = NULL, after = NULL;
-  Int4        start, stop;
-  Boolean     delete_for_this_gap;
-  Uint1       strand;
-
-  if (slp == NULL || bsp == NULL 
-      || bsp->repr != Seq_repr_delta
-      || bsp->seq_ext_type != 4
-      || bsp->seq_ext == NULL)
-  {
-    return slp;
-  }
-  
-  sip = SeqLocId (slp);
-  if (sip == NULL)
-  {
-    return slp;
-  }
-  
-  CheckSeqLocForPartial (slp, &partial5, &partial3);
-  
-  seq_offset = 0;
-  before = SeqLocCopy (slp);
-  loc_list = before;
-  
-  for (dsp = (DeltaSeqPtr) bsp->seq_ext;
-       dsp != NULL;
-       dsp = dsp->next)
-  {
-    dsp_len = GetDeltaSeqLen(dsp);
-    if (IsDeltaSeqGap (dsp) && !DoesDeltaSeqHaveGapTypeOrLinkage(dsp)
-        && ((unknown_gaps && IsDeltaSeqUnknownGap (dsp))
-            || (known_gaps && IsDeltaSeqKnownGap (dsp)))
-        && GapInLocation (seq_offset, dsp_len, before))
-    {
-      delete_for_this_gap = TRUE;
-      start = SeqLocStart (before);
-      stop = SeqLocStop (before);
-      if (PointInInterval (seq_offset, dsp_len, start)
-          && PointInInterval (seq_offset, dsp_len, stop))
-      {
-        loc_list = SeqLocFree (loc_list);
-        before = NULL;
-        after = NULL;
-        break;
-      }
-      else if (!PointInInterval (seq_offset, dsp_len, start) 
-          && !PointInInterval (seq_offset, dsp_len, stop)) 
-      {
-        if (!split_internal) 
-        {
-          delete_for_this_gap = FALSE;
-        }
-        else
-        {
-          if (split != NULL)
-          {
-            *split = TRUE;
-          }
-        }
-      }
-      else if (!trim_ends)
-      {
-        delete_for_this_gap = FALSE;
-      }
-
-      if (delete_for_this_gap)
-      {
-        /* get strand - determines direction of partials */
-        strand = SeqLocStrand (before);
-
-        /* we make a copy of the original location */
-        after = SeqLocCopy (before);
-        
-        /* note - we need to use duplicates of the SeqID returned by
-         * SeqLocId, just in case the first location in a mixed location 
-         * is deleted, which would free the result from SeqLocId 
-         */
-        after_sip = SeqIdDup (SeqLocId (after));
-        before_sip = SeqIdDup (SeqLocId (before));
-        /* in the "after" location, we free everything before the 
-         * end of the gap.
-         */
-        after = SeqLocDeleteEx (after, after_sip,
-                          0, seq_offset + dsp_len - 1,
-                          FALSE, &changed, &partial5, &partial3);
-                          
-        /* in the "before" location, we free everything after the
-         * beginning of the gap.
-         */
-        before = SeqLocDeleteEx (before, before_sip, 
-                          seq_offset, bsp->length,
-                          FALSE, &changed, &partial5, &partial3);
-        
-        /* handle partialness for ends */
-        CheckSeqLocForPartial (after, &partial5, &partial3);
-        if (strand == Seq_strand_minus) 
-        {
-          if (before == NULL)
-          {
-            /* truncated at 3' end */
-            SetSeqLocPartial (after, partial5, set_partial_ends);
-          }
-          else
-          {
-            SetSeqLocPartial (after, partial5, TRUE);
-          }
-
-        }
-        else
-        {        
-          if (before == NULL)
-          {
-            /* truncated at 5' end*/
-            SetSeqLocPartial (after, set_partial_ends, partial3);
-          }
-          else
-          {
-            SetSeqLocPartial (after, TRUE, partial3);
-          }
-        }
-       
-        CheckSeqLocForPartial (before, &partial5, &partial3);
-        if (strand == Seq_strand_minus)
-        {
-          if (after == NULL) 
-          {
-            /* truncated at 5' end*/
-            SetSeqLocPartial (before, set_partial_ends, partial3);
-          } else {
-            SetSeqLocPartial (before, TRUE, partial3);
-          }
-        }
-        else
-        {
-          if (after == NULL) 
-          {
-            /* truncated */
-            SetSeqLocPartial (before, partial5, set_partial_ends);
-          } else {
-            SetSeqLocPartial (before, partial5, TRUE);
-          }
-        }
-        
-        /* we're done with these IDs now */                  
-        after_sip = SeqIdFree (after_sip);
-        before_sip = SeqIdFree (before_sip);                          
-                          
-        if (before == NULL)
-        {
-          if (prev_loc == NULL)
-          {
-            loc_list = after;
-          }
-          else
-          {
-            prev_loc->next = after;
-          }
-        }
-        else
-        {
-          before->next = after;
-          prev_loc = before;
-        }        
-        before = after;
-      }
-    }
-    seq_offset += dsp_len;
-  }
-
-  slp = SeqLocFree (slp);
-  return loc_list;  
-}
-
-static SeqLocPtr 
-RemoveGapsFromLocation 
-(SeqLocPtr slp, 
- Boolean   unknown_gaps,
- Boolean   known_gaps,
- Boolean   trim_ends,
- Boolean   split_internal,
- Boolean   set_partial_ends,
- BoolPtr   split)
-{
-  BioseqPtr   bsp;
-  SeqIdPtr    sip;
-  
-  if (slp == NULL)
-  {
-    return slp;
-  }
-  
-  sip = SeqLocId (slp);
-  if (sip == NULL)
-  {
-    return slp;
-  }
-  
-  bsp = BioseqFind (sip);
-  if (bsp == NULL)
-  {
-    return slp;
-  }
-  else if (bsp->repr == Seq_repr_seg)
-  {
-    if (!split_internal) {
-      return slp;
-    } else {
-      return RemoveGapsFromSegmentedLocation (slp, bsp);
-    }
-  }
-  else if (bsp->repr == Seq_repr_delta
-          && bsp->seq_ext_type == 4
-          && bsp->seq_ext != NULL)
-  {
-    return RemoveGapsFromDeltaLocation (slp, bsp, unknown_gaps, known_gaps, trim_ends, split_internal, set_partial_ends, split);
-  }
-  else
-  {
-    return slp;
-  }
-}
-
-static void AdjustFrame (SeqFeatPtr sfp, BioseqPtr oldprot)
-{
-  ByteStorePtr bs;
-  CdRegionPtr  crp;
-  CharPtr      oldprot_str, newprot_str;
-  Uint1        orig_frame, best_frame = 0;
-  
-  if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION
-      || sfp->data.value.ptrvalue == NULL
-      || oldprot == NULL)
-  {
-    return;
-  }
-  
-  crp = (CdRegionPtr) sfp->data.value.ptrvalue;
-  
-  oldprot_str = GetSequenceByBsp (oldprot);
-  
-  orig_frame = crp->frame;
-  for (crp->frame = 1; crp->frame <= 3 && best_frame == 0; crp->frame++)
-  {
-    newprot_str = NULL;
-    bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
-    if (bs != NULL) 
-    {
-      newprot_str = BSMerge (bs, NULL);
-      bs = BSFree (bs);
-    }
-    
-    if (StringHasNoText (newprot_str))
-    {
-      newprot_str = MemFree (newprot_str);
-      continue;
-    }
-    if (StringSearch (oldprot_str, newprot_str) != NULL
-        || StringSearch (oldprot_str, newprot_str + 1) != NULL)
-    {
-      best_frame = crp->frame;
-    }
-    else
-    {
-      newprot_str [StringLen (newprot_str) - 1] = 0;
-      if (StringSearch (oldprot_str, newprot_str) != NULL
-          || StringSearch (oldprot_str, newprot_str + 1) != NULL)
-      {
-        best_frame = crp->frame;
-      }
-    }
-    newprot_str = MemFree (newprot_str);
-  }
-  oldprot_str = MemFree (oldprot_str);
-  if (best_frame > 0)
-  {
-    crp->frame = best_frame;
-  }
-  else
-  {
-    crp->frame = orig_frame;
-  }
-
-}
-
-static BioseqPtr 
-AddProteinSequenceCopy 
-(BioseqPtr  protbsp, 
- BioseqPtr  featbsp,
- SeqFeatPtr new_sfp,
- Uint2      entityID)
-{
-  Char        str [128];
-  SeqIdPtr    new_id;
-  BioseqPtr   new_protbsp;
-  SeqEntryPtr prot_sep, parent_sep;
-
-  if (protbsp == NULL || featbsp == NULL || new_sfp == NULL)
-  {
-    return NULL;
-  }
-  
-  parent_sep = GetBestTopParentForData (entityID, featbsp);
-  if (parent_sep == NULL 
-      || !IS_Bioseq_set (parent_sep) 
-      || parent_sep->data.ptrvalue == NULL)
-  {
-    return NULL;
-  }
-  
-  SeqIdWrite (protbsp->id, str, PRINTID_REPORT, sizeof (str) - 1);    
-  new_id = MakeUniqueSeqID (str);                                            
-  new_protbsp = BioseqCopyEx (new_id, protbsp, 0, protbsp->length - 1,
-                                      Seq_strand_plus, TRUE);
-  ValNodeLink (&(new_protbsp->descr),
-               AsnIoMemCopy ((Pointer) protbsp->descr,
-                             (AsnReadFunc) SeqDescrAsnRead,
-                             (AsnWriteFunc) SeqDescrAsnWrite));
-                                      
-  prot_sep = SeqEntryNew ();
-  if (prot_sep != NULL)
-  {
-    prot_sep->choice = 1;
-    prot_sep->data.ptrvalue = new_protbsp;
-    SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) new_protbsp, prot_sep);
-    AddSeqEntryToSeqEntry (parent_sep, prot_sep, TRUE);
-  }
-  
-  SeqMgrAddToBioseqIndex (new_protbsp);           
-  new_sfp->product = SeqLocWholeNew (new_protbsp); 
-  SeqMgrIndexFeatures (entityID, NULL);
-  return new_protbsp;
-}
-
-static void SetProductSequencePartials (BioseqPtr protbsp, Boolean partial5, Boolean partial3)
-{
-  SeqFeatPtr  prot_sfp;
-  SeqMgrFeatContext context;
-  SeqMgrDescContext dcontext;
-  SeqDescrPtr       sdp;
-  MolInfoPtr        mip;
-
-  if (protbsp == NULL)
-  {
-    return;
-  }
-        
-  /* set partials on product */
-  prot_sfp = SeqMgrGetNextFeature (protbsp, NULL, 
-                                          SEQFEAT_PROT, FEATDEF_PROT, &context);
-  if (prot_sfp != NULL)
-  {
-    SetSeqLocPartial (prot_sfp->location, partial5, partial3);
-    prot_sfp->partial = partial5 || partial3;
-  }
-        
-  sdp = SeqMgrGetNextDescriptor (protbsp, NULL, Seq_descr_molinfo, &dcontext);
-  if (sdp != NULL)
-  {
-    mip = (MolInfoPtr) sdp->data.ptrvalue;
-    if (partial5 && partial3) {
-      mip->completeness = 5;
-    } else if (partial5) {
-      mip->completeness = 3;
-    } else if (partial3) {
-      mip->completeness = 4;
-    } else if (prot_sfp != NULL && prot_sfp->partial) {
-      mip->completeness = 2;
-    } else {
-      mip->completeness = 0;
-    }
-  }  
-}
-
-static SeqLocPtr MakeMixedLocFromLocList (SeqLocPtr loc_list)
-{
-  SeqLocPtr   slp_mix, tmp_slp, prev_slp = NULL, next_slp;
-
-  /* make location mixed */    
-  slp_mix = ValNodeNew(NULL);
-  slp_mix->choice = SEQLOC_MIX;
-  slp_mix->data.ptrvalue = loc_list;
-  tmp_slp = loc_list;
-  while (tmp_slp != NULL) {
-    next_slp = tmp_slp->next;
-    if (tmp_slp->choice == SEQLOC_MIX) {
-      if (tmp_slp->data.ptrvalue == NULL) {
-        /* empty mixed loc, just remove it */
-        if (prev_slp == NULL) {
-          slp_mix->data.ptrvalue = tmp_slp->next;
-        } else {
-          prev_slp->next = tmp_slp->next;
-        }
-        tmp_slp->next = NULL;
-        tmp_slp = SeqLocFree (tmp_slp);
-      } else {
-        /* take sublocations and promote them */
-        if (prev_slp == NULL) {
-          slp_mix->data.ptrvalue = tmp_slp->data.ptrvalue;
-        } else {
-          prev_slp->next = tmp_slp->data.ptrvalue;
-        }
-        prev_slp = tmp_slp->data.ptrvalue;
-        while (prev_slp->next != NULL) {
-          prev_slp = prev_slp->next;
-        }
-        prev_slp->next = next_slp;
-        tmp_slp->next = NULL;
-        tmp_slp->data.ptrvalue = NULL;
-        tmp_slp = SeqLocFree (tmp_slp);
-      }
-    } else {
-      prev_slp = tmp_slp;
-    }
-    tmp_slp = next_slp;
-  }
-  return slp_mix;
-}
-
-
-static void AddCDSGapComment (SeqFeatPtr sfp);
-
-
-typedef struct adjustfeatforgap {
-  ValNodePtr feature_list;
-  Boolean    unknown_gaps;
-  Boolean    known_gaps;
-  Boolean    make_partial;
-  Boolean    partial_for_pseudo;
-  Boolean    trim_ends;
-  Boolean    split_internal;
-
-  ValNodePtr features_in_gap;
-} AdjustFeatForGapData, PNTR AdjustFeatForGapPtr;
-
-
-static AdjustFeatForGapPtr AdjustFeatForGapFree (AdjustFeatForGapPtr agp)
-{
-  if (agp != NULL) {
-    agp->feature_list = ValNodeFree (agp->feature_list);
-    agp->features_in_gap = ValNodeFree (agp->features_in_gap);
-    agp = MemFree (agp);
-  }
-  return agp;
-}
- 
-
-static Boolean FeatureOkForFeatureList (SeqFeatPtr sfp, ValNodePtr feature_list)
-{
-  ValNodePtr vnp;
-  Boolean    rval = FALSE;
-
-  if (sfp == NULL) return FALSE;
-  if (feature_list == NULL) return TRUE;
-  for (vnp = feature_list; vnp != NULL && !rval; vnp = vnp->next) {
-    if (vnp->choice == 255 || vnp->choice == sfp->idx.subtype) {
-      rval = TRUE;
-    }
-  }
-  return rval;
-}
-
-extern SeqFeatPtr GetGeneForFeature (SeqFeatPtr sfp)
-{
-  GeneRefPtr grp;
-  SeqFeatPtr overlap_gene;
-  Boolean    is_suppressed;
-  SeqMgrFeatContext fcontext;
-
-  grp = SeqMgrGetGeneXref (sfp);
-  is_suppressed = SeqMgrGeneIsSuppressed (grp);
-  if (is_suppressed) return NULL;
-
-  if (grp != NULL) {
-    overlap_gene = SeqMgrGetGeneByLocusTag (BioseqFindFromSeqLoc(sfp->location), grp->locus_tag, &fcontext);
-  } else {
-    overlap_gene = SeqMgrGetOverlappingGene(sfp->location, &fcontext);
-  }
-  return overlap_gene;
-}
-
-static void AdjustFeatureForGapsCallback (SeqFeatPtr sfp, Pointer data)
-{
-  AdjustFeatForGapPtr afgp;
-  BioseqPtr   protbsp = NULL, new_protbsp;
-  SeqFeatPtr  new_sfp, tmp, gene, mrna;
-  Boolean     partial5, partial3;
-  Uint2       entityID;
-  SeqLocPtr   slp_new;
-  Boolean     split;
-  Boolean     split_internal;
-  ValNodePtr  tmp_list;
-  BioseqPtr   gapped_bioseq;
-  SeqMgrFeatContext fcontext;
-  Boolean           set_partial_ends;
-
-  if (sfp == NULL || data == NULL) return;
-
-  afgp = (AdjustFeatForGapPtr) data;
-
-  if (!FeatureOkForFeatureList(sfp, afgp->feature_list)) return;
-
-  gapped_bioseq = BioseqFind (SeqLocId (sfp->location));
-  
-  CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
-  slp_new = (SeqLocPtr) AsnIoMemCopy (sfp->location, 
-                                      (AsnReadFunc) SeqLocAsnRead, 
-                                      (AsnWriteFunc) SeqLocAsnWrite);                                         
-  split = FALSE;
-  set_partial_ends = afgp->make_partial;
-  if (set_partial_ends && ! afgp->partial_for_pseudo) {
-    if (sfp->pseudo) {
-      set_partial_ends = FALSE;
-    } else {
-      gene = GetGeneForFeature (sfp);
-      if (gene != NULL && gene->pseudo) {
-        set_partial_ends = FALSE;
-      }
-    }
-  }
-
-  /* handle overlapping features if coding region */
-  if (sfp->data.choice == SEQFEAT_CDREGION) 
-  {    
-    split_internal = afgp->split_internal;
-    afgp->split_internal = FALSE;
-    tmp_list = afgp->feature_list;
-    afgp->feature_list = NULL;
-    gene = GetGeneForFeature (sfp);
-    AdjustFeatureForGapsCallback (gene, afgp);
-    mrna = SeqMgrGetOverlappingmRNA (sfp->location, &fcontext);
-    afgp->split_internal = split_internal;
-    AdjustFeatureForGapsCallback (mrna, afgp);
-    afgp->feature_list = tmp_list;
-  }
-
-  slp_new = RemoveGapsFromLocation (slp_new, afgp->unknown_gaps, afgp->known_gaps, afgp->trim_ends, afgp->split_internal, set_partial_ends, &split);
-  if (slp_new == NULL) {
-    ValNodeAddPointer (&(afgp->features_in_gap), OBJ_SEQFEAT, sfp);
-    return;
-  } else if (SeqLocCompare (slp_new, sfp->location) == SLC_A_EQ_B) {
-    slp_new = SeqLocFree (slp_new);
-    return;
-  }
-
-  if (split) {
-    AddCDSGapComment(sfp);
-  }
-
-  sfp->location = SeqLocFree (sfp->location);
-  sfp->location = slp_new;
-
-  if (gapped_bioseq != NULL && gapped_bioseq->repr == Seq_repr_delta)
-  {
-    entityID = gapped_bioseq->idx.entityID;
-   
-    while (sfp->location->next != NULL)
-    {
-      /* create a copy of the feature for each interval between gaps */
-      tmp = sfp->next;
-      sfp->next = NULL;
-      new_sfp = (SeqFeatPtr) AsnIoMemCopy (sfp, 
-                                          (AsnReadFunc) SeqFeatAsnRead, 
-                                          (AsnWriteFunc) SeqFeatAsnWrite);
-      sfp->next = new_sfp;
-      new_sfp->next = tmp;
-
-      new_sfp->location = sfp->location->next;
-      new_sfp->comment = StringSave (sfp->comment);
-
-      sfp->location->next = NULL;
-        
-      /* fix partials */
-      CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
-      sfp->partial = partial5 || partial3;
-
-      if (sfp->data.choice == SEQFEAT_CDREGION) {
-        protbsp = BioseqFindFromSeqLoc (sfp->product);        
-        if (protbsp != NULL)
-        {
-          new_protbsp = AddProteinSequenceCopy (protbsp, gapped_bioseq, new_sfp, entityID);                                                  
-        }
-                
-        /* adjust frame */
-        AdjustFrame (sfp, protbsp);
-
-        /* retranslate coding region */
-        SeqEdTranslateOneCDS (sfp, gapped_bioseq, entityID);
-        
-        /* set partials on product */
-        if (protbsp == NULL)
-        {
-          protbsp = BioseqFindFromSeqLoc (sfp->product);
-        }
-        SetProductSequencePartials (protbsp, partial5, partial3);
-        protbsp = new_protbsp;
-      }    
-      partial5 = TRUE;
-      sfp = new_sfp;
-    }
-    /* fix partials for last feature */
-    CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
-    sfp->partial = partial5 || partial3;
-
-    if (sfp->data.choice == SEQFEAT_CDREGION) 
-    {    
-      /* adjust frame */
-      protbsp = BioseqFindFromSeqLoc (sfp->product);
-      AdjustFrame (sfp, protbsp);
-
-      /* retranslate coding region */
-      SeqEdTranslateOneCDS (sfp, gapped_bioseq, entityID);
-      /* set partials on product */
-      SetProductSequencePartials (protbsp, partial5, partial3);
-    }
-  }
-  else 
-  {
-    /* make location mixed */
-    sfp->location = MakeMixedLocFromLocList (sfp->location);
-  }
-}
-
-
-static void MarkFeaturesInGapsForDeletion (AdjustFeatForGapPtr afgp)
-{
-  ValNodePtr vnp;
-  SeqFeatPtr sfp;
-  BioseqPtr  product_bsp;
-
-  if (afgp == NULL || afgp->features_in_gap == NULL)
-  {
-    return;
-  }
-  
-  for (vnp = afgp->features_in_gap; vnp != NULL; vnp = vnp->next)
-  {
-    sfp = (SeqFeatPtr) vnp->data.ptrvalue;
-    sfp->idx.deleteme = TRUE;
-    if (sfp->data.choice == SEQFEAT_CDREGION && sfp->product != NULL)
-    {
-      product_bsp = BioseqFindFromSeqLoc (sfp->product);
-      if (product_bsp != NULL)
-      {
-        product_bsp->idx.deleteme = TRUE;
-      }
-    }
-  }
-  afgp->features_in_gap = ValNodeFree (afgp->features_in_gap);
-}
-
-extern void AdjustCDSLocationsForUnknownGapsCallback (SeqFeatPtr sfp, Pointer data)
-{
-  AdjustFeatForGapData agd;
-
-  agd.feature_list = NULL;
-
-  agd.unknown_gaps = TRUE;
-  agd.known_gaps = FALSE;
-  agd.make_partial = TRUE;
-  agd.partial_for_pseudo = FALSE;
-  agd.split_internal = TRUE;
-  agd.trim_ends = TRUE;
-
-  agd.features_in_gap = NULL;
-
-  AdjustFeatureForGapsCallback (sfp, &agd);
-  MarkFeaturesInGapsForDeletion (&agd);
-}
-
 
 typedef struct adjustfeatforgapdialog {
   DIALOG_MESSAGE_BLOCK
@@ -6082,12 +5162,12 @@ extern void AdjustFeaturesForGaps (IteM i)
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
   
-  dlg->clickable_list =  CreateClickableListDialogEx (h, "", "Features",
+  dlg->clickable_list =  CreateClickableListDialogEx (h, "", "Features", NULL, NULL,
                                                       ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
                                                       GetDiscrepancyItemText,
                                                       stdCharWidth * 15,
                                                       stdCharWidth * 30,
-                                                      TRUE);
+                                                      TRUE, TRUE);
 
   dlg->dlg = AdjustFeaturesForGapDialog (h, bfp->input_entityID, AdjustFeaturesForGapsChangeNotify, dlg);
 
@@ -6337,34 +5417,6 @@ RemoveGapLocationsFromSeqLoc
   return loc_list;  
 }
 
-const char *cds_gap_comment = "coding region disrupted by sequencing gap";
-
-static void AddCDSGapComment (SeqFeatPtr sfp)
-{
-  CharPtr new_comment = NULL;
-  
-  if (sfp == NULL || StringSearch (sfp->comment, cds_gap_comment) != NULL)
-  {
-    return;
-  }
-  
-  if (StringHasNoText (sfp->comment))
-  {
-    sfp->comment = MemFree (sfp->comment);
-    sfp->comment = StringSave (cds_gap_comment);
-  }
-  else
-  {
-    new_comment = (CharPtr) MemNew ((StringLen (sfp->comment) 
-                                     + StringLen (cds_gap_comment)
-                                     + 4) * sizeof (Char));
-    StringCpy (new_comment, sfp->comment);
-    StringCat (new_comment, "; ");
-    StringCat (new_comment, cds_gap_comment);
-    sfp->comment = MemFree (sfp->comment);
-    sfp->comment = new_comment;
-  }
-}
 
 static void AdjustCodingRegionLocationsForGapLocations (BioseqPtr bsp, ValNodePtr gap_list)
 {
@@ -6432,7 +5484,7 @@ static void AdjustCodingRegionLocationsForGapLocations (BioseqPtr bsp, ValNodePt
         AdjustFrame (sfp, protbsp);
 
         /* retranslate coding region */
-        SeqEdTranslateOneCDS (sfp, bsp, entityID);
+        SeqEdTranslateOneCDS (sfp, bsp, entityID, Sequin_GlobalAlign2Seq);
         
         /* set partials on product */
         if (protbsp == NULL)
@@ -6458,7 +5510,7 @@ static void AdjustCodingRegionLocationsForGapLocations (BioseqPtr bsp, ValNodePt
     AdjustFrame (sfp, protbsp);
 
     /* retranslate coding region */
-    SeqEdTranslateOneCDS (sfp, bsp, entityID);
+    SeqEdTranslateOneCDS (sfp, bsp, entityID, Sequin_GlobalAlign2Seq);
     /* set partials on product */
     if (protbsp == NULL)
     {
@@ -6711,7 +5763,7 @@ AdjustOneCodingRegionWithTerminalGapsOnBioseq
       AdjustFrame (sfp, protbsp);
 
       /* retranslate coding region */
-      SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID);
+      SeqEdTranslateOneCDS (sfp, bsp, sfp->idx.entityID, Sequin_GlobalAlign2Seq);
               
       /* set partials on product */
       SetProductSequencePartials (protbsp, partial5, partial3);
@@ -6776,7 +5828,7 @@ typedef struct cdstomiscfeatform
   
   Boolean             convert_all;
   FilterSetPtr        fsp;
-  StringConstraintPtr scp;
+  StringConstraintXPtr scp;
   BioseqPtr           bsp;
 } CDSToMiscFeatFormData, PNTR CDSToMiscFeatFormPtr;
 
@@ -6904,7 +5956,7 @@ extern void ConvertCodingRegionsWithInternalKnownGapToMiscFeat (IteM i)
   RadioButton (cmffp->all_or_percent_grp, "Convert all coding regions with gaps (both terminal and internal)");
   SetValue (cmffp->all_or_percent_grp, 1);
   
-  cmffp->string_constraint_dlg = StringConstraintDialog (h, "Where feature text", FALSE);
+  cmffp->string_constraint_dlg = StringConstraintDialogX (h, "Where feature text", FALSE);
 
   c = HiddenGroup (h, 2, 0, NULL);
   SetGroupSpacing (c, 10, 10);
@@ -7338,7 +6390,6 @@ static void RealApplyBioFeatToAll (Uint2        entityID,
 
 {
   ImpFeatPtr         ifp;
-  RnaRefPtr          rrp;
   SeqFeatPtr         sfp = NULL;
   SeqFeatPtr         gene_sfp;
   Boolean            put_comment_on_gene = FALSE;
@@ -7373,25 +6424,21 @@ static void RealApplyBioFeatToAll (Uint2        entityID,
   /* Add an rRNA feature */
 
   else if (afp->type == ADD_RRNA) {
-    if (suppressDups && entityID > 0 &&
-	AlreadyHasFeatOrDesc (sep, SEQFEAT_RNA, 0, afp->feature_details_data->rnaSubType)) return;
-    rrp = RnaRefNew ();
-    if (rrp != NULL) {
-      rrp->type = afp->feature_details_data->rnaSubType;
-      if (! StringHasNoText (afp->feature_details_data->rnaName)) {
-        rrp->ext.choice = 1;
-        rrp->ext.value.ptrvalue = StringSave (afp->feature_details_data->rnaName);
-      }
-      sfp = CreateNewFeature (nsep, NULL, SEQFEAT_RNA, NULL);
-      if (sfp != NULL) {
-        sfp->data.value.ptrvalue = (Pointer) rrp;
-        SetApplyFeatureLocation (sfp, afp);      
-
-        if (! StringHasNoText (afp->feature_details_data->featcomment)) {
-          sfp->comment = StringSave (afp->feature_details_data->featcomment);
-        }
-      }
+    if (suppressDups && entityID > 0 
+        && AlreadyHasRNA (sep, afp->feature_details_data->rnaType)) {
+      return;
+    }
+   
+    sfp = CreateNewFeature (nsep, NULL, SEQFEAT_RNA, NULL);
+    ApplyRnaTypeToSeqFeat (sfp, afp->feature_details_data->rnaType);
+    if (! StringHasNoText (afp->feature_details_data->rnaName)) {
+      ApplyProductToRNA (sfp, afp->feature_details_data->rnaName);
     }
+    
+    SetApplyFeatureLocation (sfp, afp);      
+    AddToComment (sfp, afp->feature_details_data->featcomment);
+    ConvertToOldRNAFormat (sfp);
+
     if (! StringHasNoText (afp->feature_details_data->geneName)) {
       if (entityID > 0 
         && suppressDups
@@ -7635,6 +6682,7 @@ Int2 ApplyAnnotationToAll (Int2 type, SeqEntryPtr sep,
 
 {
   ApplyFormData  afd;
+  RnaTypeData    rtd;
 
   MemSet ((Pointer) (&afd), 0, sizeof (ApplyFormData));
   afd.type = type;
@@ -7651,7 +6699,11 @@ Int2 ApplyAnnotationToAll (Int2 type, SeqEntryPtr sep,
   }
   
   if (ADD_RRNA == type)
-    afd.feature_details_data->rnaSubType = 4;
+  {
+    rtd.ncrna_class = NULL;
+    rtd.rna_featdef = FEATDEF_rRNA;
+    afd.feature_details_data->rnaType = &rtd;
+  }
 
   if (geneName != NULL && ! TextHasNoText (geneName))
     afd.feature_details_data->geneName = SaveStringFromText (geneName);
@@ -11449,7 +10501,7 @@ static void NewDescriptorMenuProc (IteM i)
 extern void SetupNewDescriptorsMenu (MenU m, BaseFormPtr bfp)
 
 {
-  Boolean        allowgenbank;
+  Boolean        allowgenbank, allow_structured_comment = FALSE;
   IteM           i;
   NewObjectPtr   nop;
   ObjMgrPtr      omp;
@@ -11468,6 +10520,10 @@ extern void SetupNewDescriptorsMenu (MenU m, BaseFormPtr bfp)
     allowgenbank = TRUE;
   }
 /*#endif*/
+  if (indexerVersion) {
+    allow_structured_comment = TRUE;
+  }
+
   while ((omtp = ObjMgrTypeFindNext (omp, omtp)) != NULL) {
     ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, NULL);
     if (ompp != NULL) {
@@ -11477,7 +10533,11 @@ extern void SetupNewDescriptorsMenu (MenU m, BaseFormPtr bfp)
           while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT,
 				  omtp->datatype, 0, ompp)) != NULL) {
             if (ompp->subinputtype != Seq_descr_pub) {
-              if (allowgenbank || ompp->subinputtype != Seq_descr_genbank) {
+              if (!allowgenbank && ompp->subinputtype == Seq_descr_genbank) {
+                /* skip */
+              } else if (!allow_structured_comment && ompp->subinputtype == Seq_descr_user && StringCmp (ompp->proclabel, "Structured Comment") == 0) {
+                /* skip */
+              } else {
                 i = CommandItem (m, ompp->proclabel, NewDescriptorMenuProc);
                 nop = (NewObjectPtr) MemNew (sizeof (NewObjectData));
                 if (nop != NULL) {
@@ -11664,23 +10724,9 @@ extern void SetupNewFeaturesMenu (MenU m, BaseFormPtr bfp)
               if (key != FEATDEF_BAD) {
                 ompp = NULL;
                 while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT,
-				        omtp->datatype, 0, ompp)) != NULL) {
-				  subtype = ompp->subinputtype;
-                  if (subtype == fdp->featdef_key &&
-                      subtype != FEATDEF_PUB &&
-                      subtype != FEATDEF_IMP &&
-                      subtype != FEATDEF_Imp_CDS &&
-                      subtype != FEATDEF_misc_RNA &&
-                      subtype != FEATDEF_precursor_RNA &&
-                      subtype != FEATDEF_mat_peptide &&
-                      subtype != FEATDEF_sig_peptide &&
-                      subtype != FEATDEF_transit_peptide &&
-                      subtype != FEATDEF_source &&
-                      subtype != FEATDEF_virion &&
-                      subtype != FEATDEF_mutation &&
-                      subtype != FEATDEF_allele &&
-                      subtype != FEATDEF_site_ref &&
-                      subtype != FEATDEF_gap) {
+				                                           omtp->datatype, 0, ompp)) != NULL) {
+				          subtype = ompp->subinputtype;
+                  if (subtype == fdp->featdef_key && OkToListFeatDefInRemainingFeatures (subtype)) {
                     i = CommandItem (sub, ompp->proclabel, NewFeatureMenuProc);
                     nop = (NewObjectPtr) MemNew (sizeof (NewObjectData));
                     if (nop != NULL) {
@@ -13025,95 +12071,6 @@ extern ValNodePtr FreeSeqIdList (ValNodePtr id_list)
 }
 
 
-static Boolean IsAllDigits (CharPtr str)
-{
-  CharPtr cp;
-
-  if (StringHasNoText (str)) return FALSE;
-
-  cp = str;
-  while (*cp != 0 && isdigit (*cp)) {
-    cp++;
-  }
-  if (*cp == 0) {
-    return TRUE;
-  } else {
-    return FALSE;
-  }
-}
-
-
-extern SeqIdPtr CreateSeqIdFromText (CharPtr id_str, SeqEntryPtr sep)
-{
-  BioseqPtr   bsp = NULL;
-  CharPtr     tmpstr;
-  SeqIdPtr    sip = NULL;
-  SeqEntryPtr scope;
-  
-  if (StringStr (id_str, "|") == NULL) {
-    tmpstr = (CharPtr) MemNew (sizeof (Char) * (StringLen (id_str) + 10));
-    sprintf (tmpstr, "lcl|%s", id_str);
-    sip = SeqIdParse (tmpstr);
-    if (sip != NULL) {
-      scope = SeqEntrySetScope (sep);
-      bsp = BioseqFind (sip);
-      SeqEntrySetScope (scope);
-      if (bsp == NULL) {
-        sip = SeqIdFree (sip);
-      }
-    } 
-    if (bsp == NULL) {
-      sprintf (tmpstr, "gb|%s", id_str);
-      sip = SeqIdParse (tmpstr);
-      if (sip != NULL) {
-        scope = SeqEntrySetScope (sep);
-        bsp = BioseqFind (sip);
-        SeqEntrySetScope (scope);
-        if (bsp == NULL) {
-          sip = SeqIdFree (sip);
-        }
-      }
-    }
-    if (bsp == NULL) {
-      sprintf (tmpstr, "gnl|%s", id_str);
-      sip = SeqIdParse (tmpstr);
-      if (sip != NULL) {
-        scope = SeqEntrySetScope (sep);
-        bsp = BioseqFind (sip);
-        SeqEntrySetScope (scope);
-        if (bsp == NULL) {
-          sip = SeqIdFree (sip);
-        }
-      }
-    }
-    if (bsp == NULL && IsAllDigits (id_str)) {
-      sprintf (tmpstr, "gi|%s", id_str);
-      sip = SeqIdParse (tmpstr);
-      if (sip != NULL) {
-        scope = SeqEntrySetScope (sep);
-        bsp = BioseqFind (sip);
-        SeqEntrySetScope (scope);
-        if (bsp == NULL) {
-          sip = SeqIdFree (sip);
-        }
-      }
-    }      
-    MemFree (tmpstr);
-  } else {
-    sip = SeqIdParse (id_str);
-    if (sip != NULL) {
-      scope = SeqEntrySetScope (sep);
-      bsp = BioseqFind (sip);
-      SeqEntrySetScope (scope);
-      if (bsp == NULL) {
-        sip = SeqIdFree (sip);
-      }
-    }
-  }        
-  return sip;
-}
-
-
 static ValNodePtr SplitByCommasAndSpaces (CharPtr list)
 {
   CharPtr cp;
@@ -13646,3 +12603,450 @@ extern void tRNAScanUpdate (IteM i)
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
+typedef struct resolvefeatureoverlaps {
+  Uint1 trim_type;
+  Uint1 intersect_type;
+  LogInfoPtr lip;
+} ResolveFeatureOverlapsData, PNTR ResolveFeatureOverlapsPtr;
+
+static Boolean TrimLocationForIntersectingFeatures (SeqLocPtr PNTR p_slp, ValNodePtr feat_list)
+{
+  SeqLocPtr  slp;
+  SeqFeatPtr sfp;
+  ValNodePtr vnp;
+  Int4       orig_left, new_left, feat_left;
+  Int4       orig_right, new_right, feat_right;
+  Int4       tmp;
+  SeqIdPtr   sip;
+  Boolean    changed = FALSE, end_changed;
+
+  if (p_slp == NULL || *p_slp == NULL || feat_list == NULL) return FALSE;
+
+  slp = *p_slp;
+  orig_left = SeqLocStart (slp);
+  orig_right = SeqLocStop (slp);
+  if (orig_left > orig_right)
+  {
+    tmp = orig_left;
+    orig_left = orig_right;
+    orig_right = tmp;
+  }
+
+  new_left = orig_left;
+  new_right = orig_right;
+
+  for (vnp = feat_list; vnp != NULL; vnp = vnp->next)
+  {
+    sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+    feat_left = SeqLocStart (sfp->location);
+    feat_right = SeqLocStop (sfp->location);
+    if (feat_left > feat_right)
+    {
+      tmp = feat_left;
+      feat_left = feat_right;
+      feat_right = tmp;
+    }
+    if (feat_left <= orig_left && feat_right >= orig_left && feat_right < orig_right)
+    {
+      /* trim on left */
+      if (new_left < feat_right + 1)
+      {
+        new_left = feat_right + 1;
+      }
+    }
+    else if (feat_left <= orig_right && feat_right >= orig_right && feat_left > orig_left)
+    {
+      /* trim on right */
+      if (new_right > feat_left - 1)
+      {
+        new_right = feat_left - 1;
+      }
+    }
+  }
+
+  if (new_left >= new_right)
+  {
+    *p_slp = SeqLocFree (*p_slp);
+  }
+  else
+  {
+    if (new_left > orig_left)
+    {
+      sip = SeqLocId (slp);
+      end_changed = FALSE;
+      *p_slp = SeqLocDelete (*p_slp, sip, orig_left, new_left - 1, FALSE, &end_changed);
+      changed |= end_changed;
+    }
+    if (new_right < orig_right)
+    {
+      sip = SeqLocId (slp);
+      end_changed = FALSE;
+      *p_slp = SeqLocDelete (*p_slp, sip, new_right + 1, orig_right, FALSE, &end_changed);
+      changed |= end_changed;
+    }
+  }
+  return changed;
+}
+
+
+static void ResolveFeatureOverlapsBioseqCallback (BioseqPtr bsp, Pointer data)
+{
+  ResolveFeatureOverlapsPtr r;
+  SeqFeatPtr sfp;
+  SeqMgrFeatContext fcontext;
+  ValNodePtr        overlap_list;
+  CharPtr           feat_desc;
+  ValNode           vn;
+
+  r = (ResolveFeatureOverlapsPtr) data;
+  if (bsp == NULL || r == NULL) return;
+
+  vn.next = NULL;
+  vn.choice = OBJ_SEQFEAT;
+
+  for (sfp = SeqMgrGetNextFeature (bsp, NULL, 0, r->trim_type, &fcontext);
+       sfp != NULL;
+       sfp = SeqMgrGetNextFeature (bsp, sfp, 0, r->trim_type, &fcontext))
+  {
+    vn.data.ptrvalue = sfp;
+    feat_desc = GetDiscrepancyItemText (&vn);
+    overlap_list = ListFeaturesOverlappingLocation (bsp, sfp->location, 0, r->intersect_type);
+    if (TrimLocationForIntersectingFeatures (&(sfp->location), overlap_list))
+    {
+      if (sfp->location == NULL)
+      {
+        fprintf (r->lip->fp, "Feature completely overlapped and removed:\n%s\n", feat_desc);
+        sfp->idx.deleteme = TRUE;
+        r->lip->data_in_log = TRUE;
+      }
+      else
+      {
+        fprintf (r->lip->fp, "Trimmed Feature: %sNew location:", feat_desc);
+        LogTrimmedLocation (r->lip, sfp->location);
+        fprintf (r->lip->fp, "\n");
+      }
+    }
+    feat_desc = MemFree (feat_desc);
+    overlap_list = ValNodeFree (overlap_list);
+  }  
+}
+
+
+typedef struct resolvefeatureoverlapsform {
+  FORM_MESSAGE_BLOCK
+  DialoG trim_type;
+  DialoG intersect_type;
+  DialoG accept_cancel;
+
+} ResolveFeatureOverlapsFormData, PNTR ResolveFeatureOverlapsFormPtr;
+
+
+static void SetResolveFeatureOverlapsFormAccept (Pointer data)
+{
+  ResolveFeatureOverlapsFormPtr dlg;
+  ValNodePtr                    vnp1, vnp2;
+
+  dlg = (ResolveFeatureOverlapsFormPtr) data;
+  if (dlg == NULL) return;
+
+  vnp1 = DialogToPointer (dlg->trim_type);
+  vnp2 = DialogToPointer (dlg->intersect_type);
+  if (vnp1 == NULL || vnp2 == NULL)
+  {
+    DisableAcceptCancelDialogAccept (dlg->accept_cancel);
+  }
+  else
+  {
+    EnableAcceptCancelDialogAccept (dlg->accept_cancel);
+  }
+  vnp1 = ValNodeFree (vnp1);
+  vnp2 = ValNodeFree (vnp2);
+}
+
+
+static Boolean ResolveFeatureOverlapAction (Pointer data)
+{
+  ResolveFeatureOverlapsFormPtr dlg;
+  ValNodePtr                    vnp1, vnp2;
+  ResolveFeatureOverlapsData    r;
+  SeqEntryPtr                   sep;
+
+  dlg = (ResolveFeatureOverlapsFormPtr) data;
+  if (dlg == NULL) return FALSE;
+
+  vnp1 = DialogToPointer (dlg->trim_type);
+  vnp2 = DialogToPointer (dlg->intersect_type);
+ 
+  WatchCursor();
+  Update();
+  r.trim_type = vnp1->choice;
+  r.intersect_type = vnp2->choice;
+  r.lip = OpenLog ("Trimmed Features");
+
+  sep = GetTopSeqEntryForEntityID (dlg->input_entityID);
+  VisitBioseqsInSep (sep, &r, ResolveFeatureOverlapsBioseqCallback);
+  
+  CloseLog (r.lip);
+  FreeLog (r.lip);
+
+  DeleteMarkedObjects (dlg->input_entityID, 0, NULL);
+  ObjMgrSetDirtyFlag (dlg->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, dlg->input_entityID, 0, 0);
+
+  ArrowCursor ();
+  Update ();
+  return TRUE;
+}
+
+
+extern void ResolveFeatureOverlaps (IteM i)
+{
+  BaseFormPtr        bfp;
+  GrouP              h, g;
+  SeqEntryPtr        sep;
+  WindoW             w;
+  ResolveFeatureOverlapsFormPtr dlg;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL)
+    return;
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL)
+    return;
+
+  dlg = (ResolveFeatureOverlapsFormPtr) MemNew (sizeof (ResolveFeatureOverlapsFormData));
+  w = FixedWindow (-50, -33, -10, -10, "Resolve Feature Overlaps",
+		   StdCloseWindowProc);
+  SetObjectExtra (w, dlg, StdCleanupFormProc);
+  dlg->form = (ForM) w;
+
+  dlg->input_entityID = bfp->input_entityID;
+  dlg->input_itemID   = bfp->input_itemID;
+  dlg->input_itemtype = bfp->input_itemtype;
+
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  g = HiddenGroup (h, 2, 0, NULL);
+  StaticPrompt (g, "Trim features of type", 0, popupMenuHeight, programFont, 'c');
+  dlg->trim_type = FeatureSelectionDialogEx (g, FALSE, sep, SetResolveFeatureOverlapsFormAccept, dlg);
+
+  StaticPrompt (g, "Where they overlap features of type", 0, popupMenuHeight, programFont, 'c');
+  dlg->intersect_type = FeatureSelectionDialogEx (g, FALSE, sep, SetResolveFeatureOverlapsFormAccept, dlg);
+
+  /* Accept and Cancel buttons */
+
+  dlg->accept_cancel = AcceptCancelDialog (h, ResolveFeatureOverlapAction, NULL, 
+                                          NULL, NULL, (Pointer) dlg, w);
+
+  /* Line things up and display the window */
+
+  AlignObjects (ALIGN_CENTER,
+                (HANDLE) g,
+		            (HANDLE) dlg->accept_cancel,
+		            NULL);
+
+  RealizeWindow (w);
+  Show (w);
+  Select (w);
+  Update ();
+}
+
+
+static Boolean IsExternalGeneralID (SeqIdPtr sip)
+{
+  DbtagPtr dbtag;
+
+  if (sip == NULL || sip->data.ptrvalue == NULL || sip->choice != SEQID_GENERAL) return FALSE;
+  dbtag = (DbtagPtr) sip->data.ptrvalue;
+  if (StringCmp (dbtag->db, "NCBIFILE") != 0
+      && StringCmp (dbtag->db, "TMSMART") != 0)
+  {
+    return TRUE;
+  }
+  else
+  {
+    return FALSE;
+  }
+}
+
+
+static void ListBioseqsWithExternalGeneralID (BioseqPtr bsp, Pointer userdata)
+{
+  SeqIdPtr sip;
+
+  if (bsp != NULL && userdata != NULL)
+  {
+    for (sip = bsp->id; sip != NULL && !IsExternalGeneralID (sip); sip = sip->next)
+    {
+    }
+    if (sip != NULL) 
+    {
+      ValNodeAddPointer ((ValNodePtr PNTR) userdata, OBJ_BIOSEQ, bsp);
+    }
+  }      
+}
+
+
+static SeqIdPtr LocalIdFromGeneralId (SeqIdPtr sip)
+{
+  DbtagPtr dbtag;
+  ObjectIdPtr oip;
+  SeqIdPtr sip_new;
+  Char     label[15];
+
+  if (!IsExternalGeneralID (sip)) return NULL;
+
+  dbtag = (DbtagPtr) sip->data.ptrvalue;
+  if (dbtag->tag == NULL) return NULL;
+  
+  sip_new = ValNodeNew (NULL);
+  sip_new->choice = SEQID_LOCAL;
+  oip = ObjectIdNew ();
+  if (dbtag->tag->id > 0)
+  {
+    sprintf (label, "%d", dbtag->tag->id);
+    oip->str = StringSave (label);
+  }
+  else
+  {
+    oip->str = StringSave (dbtag->tag->str);
+  }
+  sip_new->data.ptrvalue = oip;
+  return sip_new;
+}
+
+extern void ConvertGeneralIdToLocalID (IteM i)
+{
+  BaseFormPtr        bfp;
+  SeqEntryPtr        sep;
+  ValNodePtr         bsp_list = NULL, vnp;
+  BioseqPtr          bsp;
+  SeqIdPtr           sip_new, sip_next, sip_prev, sip_list, sip;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL)
+    return;
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL)
+    return;
+
+  VisitBioseqsInSep (sep, &bsp_list, ListBioseqsWithExternalGeneralID);
+
+  for (vnp = bsp_list; vnp != NULL; vnp = vnp->next)
+  {
+    bsp = (BioseqPtr) vnp->data.ptrvalue;
+    if (bsp == NULL) continue;
+    sip = bsp->id;
+    sip_prev = NULL;
+    while (sip != NULL)
+    {
+      sip_next = sip->next;
+      if (IsExternalGeneralID (sip) && (sip_new = LocalIdFromGeneralId (bsp->id)) != NULL)
+      {
+        sip_new->next = sip->next;
+        sip->next = NULL;
+        if (sip_prev == NULL)
+        {
+          bsp->id = sip_new;
+        }
+        else
+        {
+          sip_prev->next = sip_new;
+        }
+        sip_list = bsp->id;
+        /* now use just old ID for replace */
+        bsp->id = sip;
+        BioseqReplaceID (bsp, sip_new);
+        /* put list back */
+        bsp->id = SeqIdFree (bsp->id);
+        bsp->id = sip_list;
+        SeqMgrReplaceInBioseqIndex (bsp);
+      }
+      else
+      {
+        sip_prev = sip;
+      }
+      sip = sip_next;
+    }
+  }
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+
+static Boolean IsUSA (CharPtr country)
+{
+  if (StringICmp (country, "USA") == 0
+      || StringICmp (country, "United States of America") == 0
+      || StringICmp (country, "U.S.A.") == 0
+      || StringICmp (country, "U S A") == 0) {
+    return TRUE;
+  } else {
+    return FALSE;
+  }
+}
+
+
+static void AbbreviateCitSubAffilStatesCallback (PubdescPtr pdp, Pointer data)
+{
+  ValNodePtr vnp;
+  CitSubPtr  csp;
+  CharPtr    abbrev;
+
+  if (pdp == NULL) return;
+  for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == PUB_Sub) {
+      csp = (CitSubPtr) vnp->data.ptrvalue;     
+      if (csp != NULL && csp->authors != NULL 
+          && csp->authors->affil != NULL
+          && IsUSA(csp->authors->affil->country)) {
+        if (StringCmp (csp->authors->affil->country, "USA") != 0) {
+          csp->authors->affil->country = MemFree (csp->authors->affil->country);
+          csp->authors->affil->country = StringSave ("USA");
+        }
+        abbrev = GetStateAbbreviation (csp->authors->affil->sub);
+        if (abbrev != NULL) {
+          csp->authors->affil->sub = MemFree (csp->authors->affil->sub);
+          csp->authors->affil->sub = StringSave (abbrev);
+        }
+      }
+    }
+  }
+  
+}
+
+
+extern void AbbreviateCitSubAffilStates (IteM i)
+{
+  BaseFormPtr        bfp;
+  SeqEntryPtr        sep;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL)
+    return;
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+  if (sep == NULL)
+    return;
+
+  VisitPubdescsInSep (sep, NULL, AbbreviateCitSubAffilStatesCallback);
+
+  ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
diff --git a/sequin/sequin7.c b/sequin/sequin7.c
index 42d87622..6ed3de23 100644
--- a/sequin/sequin7.c
+++ b/sequin/sequin7.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/3/98
 *
-* $Revision: 6.309 $
+* $Revision: 6.325 $
 *
 * File Description: 
 *
@@ -78,6 +78,7 @@ static char *time_of_compilation = "now";
 #include <algo/blast/api/blast_seqalign.h>
 #include <algo/blast/api/blast_api.h>
 #include <salstruc.h>
+#include <valid.h> /* added for latloncountry conflict checking */
 
 #define CONVERT_TO_JOIN  1
 #define CONVERT_TO_ORDER 2
@@ -6421,6 +6422,7 @@ static void TrimFromSequenceEnd (EditSeqPtr  esp,
   CharPtr currSeqStr;
   Int2    length;
   Int4    pos;
+  Int4    trim_length;
 
   /* Get the current sequence string */
 
@@ -6430,59 +6432,76 @@ static void TrimFromSequenceEnd (EditSeqPtr  esp,
   /* the beginning of the string...     */
 
   if (esp->endval == EDIT_FIVE_PRIME)
+  {
+    /* Find end point */
+
+    if (esp->trimByBool == TRIM_BY_SEQUENCE)
+	  {
+	    length = StringLen (esp->seqstr);
+	    if (StringNICmp (esp->seqstr, currSeqStr, length) != 0)
+	      return;
+	    pos = length - 1;
+      trim_length = length;
+	  }
+    else  if (esp->trimByBool == TRIM_BY_COUNT) 
     {
-      /* Find end point */
-
-      if (esp->trimByBool == TRIM_BY_SEQUENCE)
-	{
-	  length = StringLen (esp->seqstr);
-	  if (StringNICmp (esp->seqstr, currSeqStr, length) != 0)
+	    pos = esp->trimCount - 1;
+      trim_length = esp->trimCount;
+    }
+    else
 	    return;
-	  pos = length - 1;
-	}
-      else  if (esp->trimByBool == TRIM_BY_COUNT)
-	pos = esp->trimCount - 1;
-      else
-	return;
       
-      /* Trim from beginning of string to end point */
-      
-      esp->frameshift = length;
-      BioseqDelete (bsp->id, 0, pos, TRUE, FALSE);
-      esp->extendedthis = bsp;
-      FixAndRetranslateCDSs (bsp, sep, esp, TRUE);
-    }
+    /* Trim from beginning of string to end point */
+    
+    esp->frameshift = trim_length;
+    BioseqDelete (bsp->id, 0, pos, TRUE, FALSE);
+    esp->extendedthis = bsp;
+    FixAndRetranslateCDSs (bsp, sep, esp, TRUE);
+
+    /* trim quality scores */
+    TrimQualityScores (bsp, trim_length, TRUE);
+  }
   
   /* .. or the 3' end (i.e., the */
   /* end of the string.          */
   
   else if (esp->endval == EDIT_THREE_PRIME)
+  {
+    /* Find trim point */
+
+    if (esp->trimByBool == TRIM_BY_SEQUENCE)
+	  {
+	    length = StringLen (esp->seqstr);
+	    pos = bsp->length - length;
+	    if (StringICmp (esp->seqstr, &currSeqStr[pos]) != 0)
+	      return;
+      trim_length = length;
+	  }
+    else  if (esp->trimByBool == TRIM_BY_COUNT)
     {
-      /* Find trim point */
-
-      if (esp->trimByBool == TRIM_BY_SEQUENCE)
-	{
-	  length = StringLen (esp->seqstr);
-	  pos = bsp->length - length;
-	  if (StringICmp (esp->seqstr, &currSeqStr[pos]) != 0)
+	    pos = bsp->length - esp->trimCount;
+      trim_length = esp->trimCount;
+    }
+    else
 	    return;
-	}
-      else  if (esp->trimByBool == TRIM_BY_COUNT)
-	pos = bsp->length - esp->trimCount;
-      else
-	return;
-      
-      /* Trim from there to end of string */
       
-      BioseqDelete (bsp->id, pos, bsp->length - 1, TRUE, FALSE);
-      esp->extendedthis = bsp;
-      FixAndRetranslateCDSs (bsp, sep, esp, FALSE);
-    }
+    /* Trim from there to end of string */
+    
+    BioseqDelete (bsp->id, pos, bsp->length - 1, TRUE, FALSE);
+    esp->extendedthis = bsp;
+    FixAndRetranslateCDSs (bsp, sep, esp, FALSE);
+
+    /* trim quality scores */
+    TrimQualityScores (bsp, trim_length, FALSE);
+  }
 }
 
-static void AddToSequenceEnd (EditSeqPtr  esp,
-			      SeqEntryPtr sep,
-			      BioseqPtr   bsp)
+static void 
+AddToSequenceEnd 
+(EditSeqPtr  esp,
+ SeqEntryPtr sep,
+ BioseqPtr   bsp,
+ LogInfoPtr lip)
 {
   ValNodePtr    head;
   Int4          len;
@@ -6542,10 +6561,16 @@ static void AddToSequenceEnd (EditSeqPtr  esp,
         FixAndRetranslateCDSs (bsp, sep, esp, TRUE);
       }
       ValNodeFree (head);
+      if (lip != NULL) {
+        RemoveQualityScores (bsp, lip->fp, &(lip->data_in_log));
+      }
     }
     MemFree (str);
   } else {
     insertchar (esp->seqstr, pos, bsp->id, bsp->mol, FALSE);
+    if (lip != NULL) {
+      RemoveQualityScores (bsp, lip->fp, &(lip->data_in_log));
+    }
   }
 }
 
@@ -6562,6 +6587,7 @@ static void DoEditSeqEndsProc (ButtoN b)
   BioseqPtr   bsp;
   SeqEntryPtr sep;
   Boolean     add_cit_subs = FALSE;
+  LogInfoPtr  lip;
 
   esp = (EditSeqPtr) GetObjectExtra (b);
   if (esp == NULL) {
@@ -6606,6 +6632,7 @@ static void DoEditSeqEndsProc (ButtoN b)
   
   add_cit_subs = GetStatus (esp->addCitSub);
 
+  lip = OpenLog ("Quality Scores Affected");
   for (vnp = sip_list; vnp != NULL; vnp = vnp->next)
   {
     sip = (SeqIdPtr) vnp->data.ptrvalue;
@@ -6614,7 +6641,7 @@ static void DoEditSeqEndsProc (ButtoN b)
     if (bsp != NULL && sep != NULL && EditSeqEntryHasGene (bsp, sep, esp))
     {
       if (esp->addOrTrimBool == 1)
-        AddToSequenceEnd (esp, sep, bsp);
+        AddToSequenceEnd (esp, sep, bsp, lip);
       else
         TrimFromSequenceEnd (esp, sep, bsp);
       if (add_cit_subs)
@@ -6623,6 +6650,8 @@ static void DoEditSeqEndsProc (ButtoN b)
       }
     }
   }
+  CloseLog (lip);
+  lip = FreeLog (lip);
 
   MemFree (esp->seqstr);
   MemFree (esp->genestr);
@@ -7059,7 +7088,7 @@ static void FixFeatureIntervalCallback (SeqFeatPtr sfp, Pointer userdata)
   if (sfp->idx.subtype == FEATDEF_CDS)
   {
     bsp = BioseqFindFromSeqLoc (sfp->location);
-  	SeqEdTranslateOneCDS (sfp, bsp, ffp->entityID);
+  	SeqEdTranslateOneCDS (sfp, bsp, ffp->entityID, Sequin_GlobalAlign2Seq);
   }
 }
 
@@ -7395,7 +7424,7 @@ extern void ConvertInnerCDSsToProteinFeatures (IteM i)
 
 typedef struct objstringdata 
 {
-  StringConstraintPtr scp;
+  StringConstraintXPtr scp;
   Boolean found;	
 } ObjStringData, PNTR ObjStringPtr;
 
@@ -7409,14 +7438,14 @@ static void LIBCALLBACK AsnWriteStringConstraintCallBack (AsnExpOptStructPtr pAE
   if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp))) 
   {
 	  pchSource = (CharPtr) pAEOS->dvp->ptrvalue;
-    if (DoesStringMatchConstraint (pchSource, osp->scp))
+    if (DoesStringMatchConstraintX (pchSource, osp->scp))
     {
       osp->found = TRUE;
     }
   }
 }
 
-static Boolean DoesBioseqMatchStringConstraint (BioseqPtr bsp, StringConstraintPtr scp)
+static Boolean DoesBioseqMatchStringConstraint (BioseqPtr bsp, StringConstraintXPtr scp)
 
 {
   ObjMgrPtr         omp;
@@ -7450,7 +7479,7 @@ static Boolean DoesBioseqMatchStringConstraint (BioseqPtr bsp, StringConstraintP
 }
 
 
-extern Boolean DoBioseqFeaturesMatchSequenceConstraint (BioseqPtr bsp, ValNodePtr feat_list, StringConstraintPtr scp)
+extern Boolean DoBioseqFeaturesMatchSequenceConstraintX (BioseqPtr bsp, ValNodePtr feat_list, StringConstraintXPtr scp)
 {
   AsnExpOptPtr            aeop;
   AsnIoPtr                aip;
@@ -7697,7 +7726,7 @@ static void DoApplyKeywords (ButtoN b)
   
   scfp->pfp = (ParseFieldPtr) DialogToPointer (scfp->string_src_dlg);
   scfp->fsp = FilterSetNew ();
-  scfp->fsp->scp = (StringConstraintPtr) DialogToPointer (scfp->string_constraint_dlg);
+  scfp->fsp->scp = (StringConstraintXPtr) DialogToPointer (scfp->string_constraint_dlg);
   scfp->keyword = SaveStringFromText (scfp->keyword_txt);
   
   sep = GetTopSeqEntryForEntityID (scfp->input_entityID);
@@ -7748,9 +7777,9 @@ extern void ApplyKeywordWithStringConstraint (IteM i)
   scfp->keyword_txt = DialogText (g, "", 30, NULL);
   
   ppt = StaticPrompt (h, "Where", 0, 0, programFont, 'l');
-  scfp->string_src_dlg = ParseFieldDestDialog (h, NULL, NULL);
+  scfp->string_src_dlg = ParseFieldDestDialogEx (h, NULL, NULL, FALSE, TRUE);
 
-  scfp->string_constraint_dlg = StringConstraintDialog (h, NULL, FALSE);
+  scfp->string_constraint_dlg = StringConstraintDialogX (h, NULL, FALSE);
   
   c = HiddenGroup (h, 2, 0, NULL);
   b = PushButton (c, "Accept", DoApplyKeywords);
@@ -7782,7 +7811,7 @@ static void DoRemoveKeywords (ButtoN b)
   
   scfp->pfp = (ParseFieldPtr) DialogToPointer (scfp->string_src_dlg);
   scfp->fsp = FilterSetNew ();
-  scfp->fsp->scp = (StringConstraintPtr) DialogToPointer (scfp->string_constraint_dlg);
+  scfp->fsp->scp = (StringConstraintXPtr) DialogToPointer (scfp->string_constraint_dlg);
   scfp->keyword = SaveStringFromText (scfp->keyword_txt);
   
   sep = GetTopSeqEntryForEntityID (scfp->input_entityID);
@@ -7833,9 +7862,9 @@ extern void RemoveKeywordWithStringConstraint (IteM i)
   scfp->keyword_txt = DialogText (g, "", 30, NULL);
   
   ppt = StaticPrompt (h, "Where", 0, 0, programFont, 'l');
-  scfp->string_src_dlg = ParseFieldDestDialog (h, NULL, NULL);
+  scfp->string_src_dlg = ParseFieldDestDialogEx (h, NULL, NULL, FALSE, TRUE);
 
-  scfp->string_constraint_dlg = StringConstraintDialog (h, NULL, FALSE);
+  scfp->string_constraint_dlg = StringConstraintDialogX (h, NULL, FALSE);
   
   c = HiddenGroup (h, 2, 0, NULL);
   b = PushButton (c, "Accept", DoRemoveKeywords);
@@ -11764,6 +11793,43 @@ static void RearrangeVecScreenList (GrouP g)
 }
 
 
+static void ReportVecScreenDiscrepancies (LogInfoPtr lip, ValNodePtr item_list)
+{
+  ClickableItemPtr cip;
+  if (item_list == NULL || lip == NULL || lip->fp == NULL) return;
+
+  while (item_list != NULL)
+  {
+    cip = (ClickableItemPtr) item_list->data.ptrvalue;
+    if (cip != NULL)
+    {
+      if (!StringHasNoText (cip->description))
+      {
+        fprintf (lip->fp, "%s\n", cip->description);
+        lip->data_in_log = TRUE;
+      }
+      ReportVecScreenDiscrepancies (lip, cip->subcategories);
+    }
+    item_list = item_list->next;
+  }
+}
+
+
+static void MakeVecScreenReport (ButtoN b)
+{
+  VecScreenToolPtr vstp;
+  LogInfoPtr       lip;
+
+  vstp = (VecScreenToolPtr) GetObjectExtra (b);
+  if (vstp == NULL) return;
+
+  lip = OpenLog ("VecScreen Report");
+  ReportVecScreenDiscrepancies (lip, vstp->item_list);
+  CloseLog (lip);
+  lip = FreeLog (lip);
+}
+
+
 extern void VecScreenTool (IteM i)
 {
   BaseFormPtr              bfp;
@@ -11855,7 +11921,9 @@ extern void VecScreenTool (IteM i)
 
   c = HiddenGroup (h, 4, 0, NULL);
   SetGroupSpacing (c, 10, 10);
-    
+  
+  b = PushButton (c, "Make Report", MakeVecScreenReport);
+  SetObjectExtra (b, drfp, NULL);
   b = PushButton (c, "Trim Selected Regions", TrimSelectedBtn);
   SetObjectExtra (b, drfp, NULL);
   PushButton (c, "Dismiss", StdCancelButtonProc);
@@ -12114,20 +12182,27 @@ static ValNodePtr BarcodeResultsVNFreeFunc (ValNodePtr vnp)
 
 
 /* Barcode Tool */
-typedef struct barcodetool {
-  FORM_MESSAGE_BLOCK
-  DialoG          clickable_list;
-  BaseFormPtr     bfp;
-  PrompT          pass_fail_summary;
-  ButtoN          undo;
-  ButtoN          undo_all;
-  ButtoN          redo;
+struct barcodetool;
+
+typedef void (*RefreshBarcodeDataFunc) PROTO ((Pointer));
+
+#define BARCODE_TOOL_BLOCK \
+  FORM_MESSAGE_BLOCK \
+  DialoG          clickable_list; \
+  BaseFormPtr     bfp; \
+  PrompT          pass_fail_summary; \
+  ButtoN          undo; \
+  ButtoN          undo_all; \
+  ButtoN          redo; \
+  ValNodePtr      item_list; \
+  SeqEntryPtr     top_sep; \
+  LogInfoPtr      lip; \
+  BarcodeTestConfigPtr cfg; \
+  BarcodeUndoListPtr   undo_list; \
+  RefreshBarcodeDataFunc refresh_func;
 
-  ValNodePtr      item_list;
-  SeqEntryPtr     top_sep;
-  LogInfoPtr      lip;
-  BarcodeTestConfigPtr cfg;
-  BarcodeUndoListPtr   undo_list;
+typedef struct barcodetool {
+BARCODE_TOOL_BLOCK
 } BarcodeToolData, PNTR BarcodeToolPtr;
 
 static void CleanupBarcodeTool (GraphiC g, VoidPtr data)
@@ -12220,12 +12295,14 @@ static Int2 LIBCALLBACK BarcodeToolMsgFunc (OMMsgStructPtr ommsp)
 }
 
 
-static void RefreshBarcodeList (BarcodeToolPtr vstp)
+static void RefreshBarcodeList (Pointer data)
 {
+  BarcodeToolPtr vstp;
   ValNodePtr pass_fail_list = NULL, vnp;
   Int4       num_fail = 0, num_pass = 0;
   Char       msg[30];
 
+  vstp = (BarcodeToolPtr) data;
   if (vstp == NULL) return;
   
   PointerToDialog (vstp->clickable_list, NULL);
@@ -12437,7 +12514,10 @@ extern void BarcodeRefreshButton (ButtoN b)
   vstp = (BarcodeToolPtr) GetObjectExtra (b);
   if (vstp == NULL) return;
 
-  RefreshBarcodeList (vstp);
+  if (vstp->refresh_func != NULL) 
+  {
+    (vstp->refresh_func) (vstp);
+  }
   RedrawBarcodeTool (vstp);  
 }
 
@@ -12465,7 +12545,7 @@ extern void BarcodeReportButton (ButtoN b)
   }
 
   lip = OpenLog ("BARCODE Discrepancies");
-  WriteBarcodeDiscrepancies (lip->fp, vstp->item_list);
+  WriteBarcodeDiscrepancies (lip->fp, object_list);
   lip->data_in_log = TRUE;
   CloseLog (lip);
   lip = FreeLog (lip);
@@ -12979,6 +13059,25 @@ static void BarcodeTestApplyTagTable (ButtoN b)
 }
 
 
+static void BarcodeComprehensiveReportButton (ButtoN b)
+{
+  BarcodeToolPtr         drfp;
+  LogInfoPtr             lip;
+  ValNodePtr             object_list;
+
+  drfp = (BarcodeToolPtr) GetObjectExtra (b);
+  if (drfp == NULL) return;
+
+  lip = OpenLog ("BARCODE Discrepancies");
+  object_list = GetBarcodePassFail (drfp->top_sep, drfp->cfg);
+  WriteBarcodeTestComprehensive (lip->fp, object_list);
+  lip->data_in_log = TRUE;
+  CloseLog (lip);
+  lip = FreeLog (lip);
+  object_list = BarcodeTestResultsListFree (object_list);
+}
+
+
 extern void BarcodeTestTool (IteM i)
 {
   BaseFormPtr              bfp;
@@ -13012,6 +13111,7 @@ extern void BarcodeTestTool (IteM i)
   SetObjectExtra (w, drfp, CleanupBarcodeTool);
   drfp->form = (ForM) w;
   drfp->formmessage = BarcodeToolMessage;
+  drfp->refresh_func = RefreshBarcodeList;
     
   /* register to receive update messages */
   drfp->userkey = OMGetNextUserKey ();
@@ -13040,12 +13140,14 @@ extern void BarcodeTestTool (IteM i)
   drfp->pass_fail_summary = StaticPrompt (h, "0 Pass, 0 Fail", 20 * stdCharWidth, dialogTextHeight, programFont, 'l');
   RefreshBarcodeList(drfp);
 
-  c3 = HiddenGroup (h, 7, 0, NULL);
+  c3 = HiddenGroup (h, 8, 0, NULL);
   SetGroupSpacing (c3, 10, 10);
   b = PushButton (c3, "Compliance Report", BarcodeTestComplianceReport);
   SetObjectExtra (b, drfp, NULL);
   b = PushButton (c3, "Failure Report", BarcodeReportButton);
   SetObjectExtra (b, drfp, NULL);
+  b = PushButton (c3, "Comprehensive Report", BarcodeComprehensiveReportButton);
+  SetObjectExtra (b, drfp, NULL);
 
   b = PushButton (c3, "Replace Tags", BarcodeTestImportTagTable);
   SetObjectExtra (b, drfp, NULL);
@@ -13984,8 +14086,9 @@ static void FindBadLatLonSourceFeat (SeqFeatPtr sfp, Pointer userdata)
 
 
 
-static void RefreshLatLonTool (BarcodeToolPtr vstp)
+static void RefreshLatLonTool (Pointer data)
 {
+  BarcodeToolPtr vstp = (BarcodeToolPtr) data;
   if (vstp == NULL) return;
   
   PointerToDialog (vstp->clickable_list, NULL);
@@ -14186,18 +14289,6 @@ static void LatLonReport (ButtoN b)
 }
 
 
-extern void LatLonRefreshButton (ButtoN b)
-{
-  BarcodeToolPtr vstp;
-
-  vstp = (BarcodeToolPtr) GetObjectExtra (b);
-  if (vstp == NULL) return;
-
-  RefreshLatLonTool (vstp);
-  RedrawBarcodeTool (vstp);  
-}
-
-
 static void MoveIncorrectlyFormattedLatLonToNote (ButtoN b)
 {
   BarcodeToolPtr vstp;
@@ -14319,7 +14410,8 @@ extern void LatLonTool (IteM i)
   SetObjectExtra (w, drfp, CleanupLatLonTool);
   drfp->form = (ForM) w;
   drfp->formmessage = BarcodeToolMessage;
-    
+
+  drfp->refresh_func = RefreshLatLonTool;    
   /* register to receive update messages */
   drfp->userkey = OMGetNextUserKey ();
   drfp->procid = 0;
@@ -14353,7 +14445,7 @@ extern void LatLonTool (IteM i)
   SetObjectExtra (b, drfp, NULL);
   b = PushButton (c, "Make Report", LatLonReport);
   SetObjectExtra (b, drfp, NULL);
-  b = PushButton (c, "Refresh List", LatLonRefreshButton);
+  b = PushButton (c, "Refresh List", BarcodeRefreshButton);
   SetObjectExtra (b, drfp, NULL);
   b = PushButton (c, "Move to Note", MoveIncorrectlyFormattedLatLonToNote);
   SetObjectExtra (b, drfp, NULL);
@@ -14369,12 +14461,450 @@ extern void LatLonTool (IteM i)
 }
 
 
+static void FindLatLonCountryConflicts (SeqDescrPtr sdp, Pointer data)
+{
+  BioSourcePtr biop;
+  SubSourcePtr ssp;
+  CharPtr      orig_country = NULL, country = NULL, cp;
+  Boolean      found_lat_lon = FALSE;
+  FloatHi      lat, lon;
+
+  if (sdp == NULL || sdp->choice != Seq_descr_source || sdp->data.ptrvalue == NULL || data == NULL) return;
+  biop = (BioSourcePtr) sdp->data.ptrvalue;
+
+  for (ssp = biop->subtype; ssp != NULL && (country == NULL || !found_lat_lon); ssp = ssp->next)
+  {
+    if (ssp->subtype == SUBSRC_country && !StringHasNoText (ssp->name))
+    {
+      orig_country = ssp->name;
+      country = StringSave (orig_country);
+    }
+    else if (ssp->subtype == SUBSRC_lat_lon)
+    {
+      if (ParseLatLon (ssp->name, &lat, &lon))
+      {
+        found_lat_lon = TRUE;
+      }
+    }
+  }
+
+  cp = StringChr (country, ':');
+  if (cp != NULL) 
+  {
+    *cp = 0;
+  }
+
+  if (found_lat_lon && IsCountryInLatLonList (country)) 
+  {
+    if (!TestLatLonForCountry (country, lat, lon) 
+        && !TestLatLonForCountry (orig_country, lat, lon) 
+        && !StringContainsBodyOfWater (orig_country))
+    {
+      ValNodeAddPointer ((ValNodePtr PNTR) data, OBJ_SEQDESC, sdp);
+    }
+  }
+  country = MemFree (country);
+}
+
+
+static void RefreshLatLonCountryTool (Pointer data)
+{
+  BarcodeToolPtr vstp = (BarcodeToolPtr) data;
+  if (vstp == NULL) return;
+  
+  PointerToDialog (vstp->clickable_list, NULL);
+  vstp->item_list = ValNodeFree (vstp->item_list);
+
+  VisitDescriptorsInSep (vstp->top_sep, &(vstp->item_list), FindLatLonCountryConflicts);
+
+  PointerToDialog (vstp->clickable_list, vstp->item_list);  
+
+}
+
+
+static void LatLonCountryReport (ButtoN b)
+{
+  BarcodeToolPtr    drfp;
+  ValNodePtr        vnp;
+  LogInfoPtr        lip;
+  SeqDescrPtr       sdp;
+  BioSourcePtr      biop;
+  SubSourcePtr      ssp;
+  CharPtr           fix, country = NULL, lat_lon = NULL;
+
+  drfp = (BarcodeToolPtr) GetObjectExtra (b);
+  if (drfp == NULL) return;
+  
+  lip = OpenLog ("Incorrectly Formatted Lat-lon Values");
+  
+  for (vnp = drfp->item_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice != OBJ_SEQDESC) continue;
+    sdp = vnp->data.ptrvalue;
+    if (sdp != NULL && sdp->choice == Seq_descr_source && sdp->data.ptrvalue != NULL)
+    {
+      biop = (BioSourcePtr) sdp->data.ptrvalue;
+      country = NULL;
+      lat_lon = NULL;
+      for (ssp = biop->subtype; ssp != NULL && (country == NULL || lat_lon == NULL); ssp = ssp->next)
+      {
+        if (ssp->subtype == SUBSRC_country && country == NULL)
+        {
+          country = ssp->name;
+        }
+        else if (ssp->subtype == SUBSRC_lat_lon && lat_lon == NULL)
+        {
+          lat_lon = ssp->name;
+        }
+      }
+      if (country == NULL) country = "missing";
+      if (lat_lon == NULL) lat_lon = "missing";
+      fix = GetLatLonCountryCorrection (OBJ_SEQDESC, sdp, NULL);
+
+      fprintf (lip->fp, "Country: %s\tLat-lon: %s\tCorrection: %s\n",
+               country, lat_lon, fix == NULL ? "No suggestion" : fix);
+      fix = MemFree (fix);
+      lip->data_in_log = TRUE;
+    }
+  }
+
+  CloseLog (lip);
+  lip = FreeLog (lip);
+
+}
+
+
+static CharPtr SkipNumberInString (CharPtr str)
+{
+  CharPtr cp;
+
+  cp = str;
+  while (isdigit (*cp))
+  {
+    cp++;
+  }
+  if (*cp == '.')
+  {
+    cp++;
+  }
+  while (isdigit (*cp))
+  {
+    cp++;
+  }
+  return cp;
+}
+
+static Boolean GetLatLonTokens (CharPtr str, CharPtr PNTR lat, CharPtr PNTR ns, CharPtr PNTR lon, CharPtr PNTR ew)
+{
+  CharPtr cp;
+
+  if (StringHasNoText (str) || lat == NULL || ns == NULL || lon == NULL || ew == NULL) return FALSE;
+
+  cp = str;
+  while (isspace (*cp)) 
+  {
+    cp++;
+  }
+  if (!isdigit (*cp)) return FALSE;
+  *lat = cp;
+  cp = SkipNumberInString (cp);
+
+  while (isspace (*cp)) 
+  {
+    cp++;
+  }
+
+  if (*cp != 'N' && *cp != 'S') return FALSE;
+  *ns = cp;
+  cp++;
+
+  while (isspace (*cp)) 
+  {
+    cp++;
+  }
+
+  if (!isdigit (*cp)) return FALSE;
+  *lon = cp;
+  cp = SkipNumberInString (cp);
+
+  while (isspace (*cp)) 
+  {
+    cp++;
+  }
+
+  if (*cp != 'E' && *cp != 'W') return FALSE;
+  *ew = cp;
+
+  return TRUE;
+}
+
+static CharPtr MakeLatLonValue (CharPtr lat, Char ns, CharPtr lon, Char ew)
+{
+  CharPtr newval, cp;
+  Int4 latlen, lonlen, len;
+
+  if (StringHasNoText (lat) || StringHasNoText (lon))
+  {
+    return NULL;
+  }
+  cp = SkipNumberInString (lat);
+  latlen = cp - lat;
+  cp = SkipNumberInString (lon);
+  lonlen = cp - lon;
+
+  len = latlen + lonlen + 6;
+
+  newval = (CharPtr) MemNew (sizeof (Char) * len);
+
+  cp = newval;
+  StringNCpy (newval, lat, latlen);
+  cp += latlen;
+  *(cp++) = ' ';
+  *(cp++) = ns;
+  *(cp++) = ' ';
+  StringNCpy (cp, lon, lonlen);
+  cp += lonlen;
+  *(cp++) = ' ';
+  *(cp++) = ew;
+  *(cp++) = 0;
+  
+  return newval;
+}
+
+
+static void LatLonCountryAutocorrectList (FILE *fp, ValNodePtr object_list)
+{
+  ValNodePtr vnp;
+  SeqDescrPtr sdp;
+  BioSourcePtr biop;
+  SubSourcePtr country_ssp, lat_lon_ssp, ssp;
+  FloatHi      lat, lon;
+  CharPtr      country, cp;
+  CharPtr      fix;
+
+  CharPtr      pLat, pNs, pLon, pEw;
+
+  if (fp == NULL || object_list == NULL) return;
+
+  for (vnp = object_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice != OBJ_SEQDESC) continue;
+    sdp = vnp->data.ptrvalue;
+    if (sdp != NULL && sdp->choice == Seq_descr_source)
+    {
+      biop = (BioSourcePtr) sdp->data.ptrvalue;
+      country_ssp = NULL;
+      lat_lon_ssp = NULL;
+      for (ssp = biop->subtype; ssp != NULL && (country_ssp == NULL || lat_lon_ssp == NULL); ssp = ssp->next)
+      {
+        if (StringHasNoText (ssp->name)) continue;
+        if (ssp->subtype == SUBSRC_country && country_ssp == NULL)
+        {
+          country_ssp = ssp;
+        }
+        else if (ssp->subtype == SUBSRC_lat_lon && lat_lon_ssp == NULL && ParseLatLon (ssp->name, &lat, &lon))
+        {
+          lat_lon_ssp = ssp;
+        }
+      }
+      if (country_ssp == NULL)
+      {
+        country = NULL;
+      } else {
+        country = StringSave (country_ssp->name);
+        cp = StringChr (country, ':');
+        if (cp != NULL) *cp = 0;
+      }
+      if (country != NULL && lat_lon_ssp != NULL
+          && IsCountryInLatLonList (country)
+          && !TestLatLonForCountry (country, lat, lon)
+          && GetLatLonTokens (lat_lon_ssp->name, &pLat, &pNs, &pLon, &pEw))
+      {
+        fix = NULL;
+        if (TestLatLonForCountry (country, -lat, lon)) 
+        {
+          fix = MakeLatLonValue (pLat, *pNs == 'N' ? 'S' : 'N',
+                                 pLon, *pEw);
+        }
+        else if (TestLatLonForCountry (country, lat, -lon)) 
+        {
+          fix = MakeLatLonValue (pLat, *pNs,
+                                 pLon, *pEw == 'E' ? 'W' : 'E');
+        } else if (TestLatLonForCountry (country, lon, lat)) {
+          fix = MakeLatLonValue (pLon, *pEw == 'E' ? 'N' : 'S',
+                                 pLat, *pNs == 'N' ? 'E' : 'W');
+        }
+
+        if (fix != NULL) 
+        {
+          fprintf (fp, "Corrected %s to %s\n", lat_lon_ssp->name, fix);
+          lat_lon_ssp->name = MemFree (lat_lon_ssp->name);
+          lat_lon_ssp->name = fix;
+        }
+        else
+        {
+          fprintf (fp, "Unable to correct %s\n", lat_lon_ssp->name);
+        }
+      }
+      country = MemFree (country);
+    }
+  }
+}
+
+
+static void LatLonCountryAutocorrect (ButtoN b)
+{
+  BarcodeToolPtr    drfp;
+  ValNodePtr        object_list;
+  LogInfoPtr        lip;
+
+  drfp = (BarcodeToolPtr) GetObjectExtra (b);
+  if (drfp == NULL) return;
+  object_list = DialogToPointer (drfp->clickable_list);
+
+  if (object_list == NULL)
+  {
+    if (ANS_YES == Message (MSG_YN, "You have not selected any BioSources - correct all?"))
+    {
+      object_list = drfp->item_list;
+    }
+    else
+    {
+      return;
+    }
+  }
+  
+  lip = OpenLog ("Lat-lon Values Corrected");
+  
+  LatLonCountryAutocorrectList (lip->fp, object_list);
+
+  if (object_list != drfp->item_list) 
+  {
+    object_list = ValNodeFree (object_list);
+  }
+
+  RefreshLatLonCountryTool (drfp);
+  RedrawBarcodeTool (drfp);  
+
+  ObjMgrSetDirtyFlag (drfp->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, drfp->input_entityID, 0, 0);
+  Update();
+
+  lip->data_in_log = TRUE;
+  CloseLog (lip);
+  lip = FreeLog (lip);
+}
+
+
+
+extern void LatLonCountryTool (IteM i)
+{
+  BaseFormPtr       bfp;
+  SeqEntryPtr       sep;
+  ValNodePtr        biosources = NULL;
+  BarcodeToolPtr    drfp;
+  WindoW            w;
+  GrouP             h, c;
+  ButtoN            b;
+  OMUserDataPtr     omudp;
+  PrompT            ppt;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL || bfp->input_entityID == 0) return;
+
+  sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+
+  VisitDescriptorsInSep (sep, &biosources, FindLatLonCountryConflicts);
+
+  if (biosources == NULL)
+  {
+    Message (MSG_OK, "No conflicts found.");
+    return;
+  }
+
+  biosources = ValNodeFree (biosources);
+
+  drfp = (BarcodeToolPtr) MemNew (sizeof (BarcodeToolData));
+  if (drfp == NULL)
+  {
+    return;
+  }
+  
+  drfp->bfp = bfp;
+  drfp->input_entityID = bfp->input_entityID;
+  drfp->top_sep = GetTopSeqEntryForEntityID (drfp->input_entityID);
+  w = FixedWindow (-50, -33, -10, -10, "Lat-Lon Country Conflict Tool", StdCloseWindowProc);
+  SetObjectExtra (w, drfp, CleanupLatLonTool);
+  drfp->form = (ForM) w;
+  drfp->formmessage = BarcodeToolMessage;
+
+  drfp->refresh_func = RefreshLatLonCountryTool;
+    
+  /* register to receive update messages */
+  drfp->userkey = OMGetNextUserKey ();
+  drfp->procid = 0;
+  drfp->proctype = OMPROC_EDIT;
+  omudp = ObjMgrAddUserData (drfp->input_entityID, drfp->procid, drfp->proctype, drfp->userkey);
+  if (omudp != NULL) {
+    omudp->userdata.ptrvalue = (Pointer) drfp;
+    omudp->messagefunc = BarcodeToolMsgFunc;
+  }
+
+
+#ifndef WIN_MAC
+  CreateStdValidatorFormMenus (w);
+#endif
+  
+  drfp->item_list = NULL;
+  drfp->cfg = NULL;
+  drfp->undo_list = NULL;
+  
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+  
+  drfp->clickable_list = LatLonCountryResultsDisplay (h);
+
+  RefreshLatLonCountryTool (drfp);
+
+  ppt = StaticPrompt (h, "Note - only hemisphere transpositions and lat-lon transpositions can be corrected",
+                      0, stdLineHeight, programFont, 'c');
+
+  c = HiddenGroup (h, 5, 0, NULL);
+  SetGroupSpacing (c, 10, 10);
+
+  b = PushButton (c, "Autocorrect Values", LatLonCountryAutocorrect);
+  SetObjectExtra (b, drfp, NULL);
+  b = PushButton (c, "Make Report", LatLonCountryReport);
+  SetObjectExtra (b, drfp, NULL);
+  b = PushButton (c, "Refresh List", BarcodeRefreshButton);
+  SetObjectExtra (b, drfp, NULL);
+    
+  PushButton (c, "Dismiss", StdCancelButtonProc);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) drfp->clickable_list, (HANDLE) ppt, (HANDLE) c, NULL);
+
+  RealizeWindow (w);
+  
+  Show (w);
+
+}
+
+
+typedef struct specifichosttool {
+  BARCODE_TOOL_BLOCK
+  ButtoN check_single_word;
+} SpecificHostToolData, PNTR SpecificHostToolPtr;
+
 static void CleanupSpecificHostTool (GraphiC g, VoidPtr data)
 
 {
-  BarcodeToolPtr drfp;
+  SpecificHostToolPtr drfp;
 
-  drfp = (BarcodeToolPtr) data;
+  drfp = (SpecificHostToolPtr) data;
   if (drfp != NULL) {
     drfp->item_list = SpecificHostFixListFree (drfp->item_list);
     ObjMgrFreeUserData (drfp->input_entityID, drfp->procid, drfp->proctype, drfp->userkey);
@@ -14383,14 +14913,15 @@ static void CleanupSpecificHostTool (GraphiC g, VoidPtr data)
 }
 
 
-static void RefreshSpecificHostTool (BarcodeToolPtr vstp)
+static void RefreshSpecificHostTool (Pointer data)
 {
+  SpecificHostToolPtr vstp = (SpecificHostToolPtr) data;
   if (vstp == NULL) return;
   
   PointerToDialog (vstp->clickable_list, NULL);
   vstp->item_list = SpecificHostFixListFree (vstp->item_list);
 
-  vstp->item_list = Taxon3GetSpecificHostFixesInSeqEntry (vstp->top_sep);
+  vstp->item_list = Taxon3GetSpecificHostFixesInSeqEntry (vstp->top_sep, GetStatus (vstp->check_single_word));
 
   PointerToDialog (vstp->clickable_list, vstp->item_list);  
 
@@ -14399,12 +14930,12 @@ static void RefreshSpecificHostTool (BarcodeToolPtr vstp)
 
 static void SpecificHostAutocorrect (ButtoN b)
 {
-  BarcodeToolPtr    drfp;
-  ValNodePtr        object_list, vnp;
-  LogInfoPtr        lip;
-  SpecificHostFixPtr   s;
+  SpecificHostToolPtr drfp;
+  ValNodePtr          object_list, vnp;
+  LogInfoPtr          lip;
+  SpecificHostFixPtr  s;
 
-  drfp = (BarcodeToolPtr) GetObjectExtra (b);
+  drfp = (SpecificHostToolPtr) GetObjectExtra (b);
   if (drfp == NULL) return;
   object_list = DialogToPointer (drfp->clickable_list);
 
@@ -14442,7 +14973,7 @@ static void SpecificHostAutocorrect (ButtoN b)
   }
 
   RefreshSpecificHostTool (drfp);
-  RedrawBarcodeTool (drfp);  
+  RedrawBarcodeTool ((BarcodeToolPtr)drfp);  
 
   ObjMgrSetDirtyFlag (drfp->input_entityID, TRUE);
   ObjMgrSendMsg (OM_MSG_UPDATE, drfp->input_entityID, 0, 0);
@@ -14457,13 +14988,13 @@ static void SpecificHostAutocorrect (ButtoN b)
 
 static void SpecificHostReport (ButtoN b)
 {
-  BarcodeToolPtr    drfp;
-  ValNodePtr        vnp;
-  LogInfoPtr        lip;
-  SpecificHostFixPtr s;
-  CharPtr            fix;
+  SpecificHostToolPtr drfp;
+  ValNodePtr          vnp;
+  LogInfoPtr          lip;
+  SpecificHostFixPtr  s;
+  CharPtr             fix;
 
-  drfp = (BarcodeToolPtr) GetObjectExtra (b);
+  drfp = (SpecificHostToolPtr) GetObjectExtra (b);
   if (drfp == NULL) return;
   
   lip = OpenLog ("Incorrect Specific-Host Values");
@@ -14498,29 +15029,16 @@ static void SpecificHostReport (ButtoN b)
 }
 
 
-extern void SpecificHostRefreshButton (ButtoN b)
-{
-  BarcodeToolPtr vstp;
-
-  vstp = (BarcodeToolPtr) GetObjectExtra (b);
-  if (vstp == NULL) return;
-
-  RefreshSpecificHostTool (vstp);
-  RedrawBarcodeTool (vstp);  
-}
-
-
-
 extern void FixSpecificHostValues (IteM i)
 {
-  BaseFormPtr       bfp;
-  SeqEntryPtr       sep;
-  BarcodeToolPtr    drfp;
-  WindoW            w;
-  GrouP             h, c;
-  ButtoN            b;
-  OMUserDataPtr     omudp;
-  ValNodePtr        fix_list = NULL;
+  BaseFormPtr         bfp;
+  SeqEntryPtr         sep;
+  SpecificHostToolPtr drfp;
+  WindoW              w;
+  GrouP               h, c;
+  ButtoN              b;
+  OMUserDataPtr       omudp;
+  ValNodePtr          fix_list = NULL;
 
 #ifdef WIN_MAC
   bfp = currentFormDataPtr;
@@ -14531,7 +15049,7 @@ extern void FixSpecificHostValues (IteM i)
 
   sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
 
-  fix_list = Taxon3GetSpecificHostFixesInSeqEntry (sep);
+  fix_list = Taxon3GetSpecificHostFixesInSeqEntry (sep, TRUE);
 
   if (fix_list == NULL)
   {
@@ -14541,7 +15059,7 @@ extern void FixSpecificHostValues (IteM i)
 
   fix_list = SpecificHostFixListFree (fix_list);
 
-  drfp = (BarcodeToolPtr) MemNew (sizeof (BarcodeToolData));
+  drfp = (SpecificHostToolPtr) MemNew (sizeof (SpecificHostToolData));
   if (drfp == NULL)
   {
     return;
@@ -14554,6 +15072,8 @@ extern void FixSpecificHostValues (IteM i)
   SetObjectExtra (w, drfp, CleanupSpecificHostTool);
   drfp->form = (ForM) w;
   drfp->formmessage = BarcodeToolMessage;
+
+  drfp->refresh_func = RefreshSpecificHostTool;
     
   /* register to receive update messages */
   drfp->userkey = OMGetNextUserKey ();
@@ -14578,6 +15098,8 @@ extern void FixSpecificHostValues (IteM i)
   SetGroupSpacing (h, 10, 10);
   
   drfp->clickable_list = SpecificHostResultsDisplay (h);
+  drfp->check_single_word = CheckBox (h, "Also check single-word specific host values", BarcodeRefreshButton);
+  SetObjectExtra (drfp->check_single_word, drfp, NULL);
 
   RefreshSpecificHostTool (drfp);
 
@@ -14588,12 +15110,12 @@ extern void FixSpecificHostValues (IteM i)
   SetObjectExtra (b, drfp, NULL);
   b = PushButton (c, "Make Report", SpecificHostReport);
   SetObjectExtra (b, drfp, NULL);
-  b = PushButton (c, "Refresh List", SpecificHostRefreshButton);
+  b = PushButton (c, "Refresh List", BarcodeRefreshButton);
   SetObjectExtra (b, drfp, NULL);
     
   PushButton (c, "Dismiss", StdCancelButtonProc);
 
-  AlignObjects (ALIGN_CENTER, (HANDLE) drfp->clickable_list, (HANDLE) c, NULL);
+  AlignObjects (ALIGN_CENTER, (HANDLE) drfp->clickable_list, (HANDLE) drfp->check_single_word, (HANDLE) c, NULL);
 
   RealizeWindow (w);
   
@@ -14690,3 +15212,4 @@ extern void ListFailedTaxonomyLookups (IteM i)
                            ReportFailedTaxonomyLookups, RefreshFailedTaxonomyLookups);
 
 }
+
diff --git a/sequin/sequin8.c b/sequin/sequin8.c
index f833c0c5..702135ec 100644
--- a/sequin/sequin8.c
+++ b/sequin/sequin8.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   2/3/98
 *
-* $Revision: 6.438 $
+* $Revision: 6.458 $
 *
 * File Description: 
 *
@@ -64,6 +64,9 @@
 #include <algo/blast/api/twoseq_api.h>
 #include <algo/blast/api/blast_seqalign.h>
 
+#include <macrodlg.h>
+#include <macroapi.h>
+
 #define DEFLINE_MAX_LEN          380
 #define TEXT_MAX_LEN             64
 #define DEFLINE_MAX_GENENAME_LEN 64
@@ -397,86 +400,7 @@ extern void ExtendSeqLocToPosition (SeqLocPtr slp, Boolean end5, Int4 pos)
   }
 }
 
-extern Int4 ExtendSeqLocToEnd (SeqLocPtr slp, BioseqPtr bsp, Boolean end5)
-{
-  Uint1          strand;
-  SeqLocPtr      slp_to_change, slp_index;
-  Int4           extent_to_change;
-  Int4           start, stop;
-  SeqIdPtr       sip;
-  Int4           start_diff = 0;
-  
-  if (slp == NULL || bsp == NULL) return 0;
-
-  slp_to_change = NULL;
-  strand = SeqLocStrand (slp);
-  switch (slp->choice)
-  {
-    case SEQLOC_INT:
-      slp_to_change = slp;
-      break;
-    case SEQLOC_MIX:
-  	case SEQLOC_PACKED_INT:
-      sip = SeqLocId (slp);
-      if (sip == NULL) return 0; /* can only process if all on one bioseq */
-      slp_to_change = NULL;
-      if ((strand == Seq_strand_minus && end5)
-        || (strand != Seq_strand_minus && !end5))
-      {
-        extent_to_change = 0;
-        for (slp_index = (SeqLocPtr)slp->data.ptrvalue; slp_index != NULL; slp_index = slp_index->next)
-        {
-          stop = GetOffsetInBioseq (slp_index, bsp, SEQLOC_STOP);
-          if (stop > extent_to_change)
-          {
-            slp_to_change = slp_index;
-            extent_to_change = stop;
-          }
-        }
-      }
-      else
-      {
-        extent_to_change = bsp->length;
-        for (slp_index = (SeqLocPtr)slp->data.ptrvalue; slp_index != NULL; slp_index = slp_index->next)
-        {
-          start = GetOffsetInBioseq (slp_index, bsp, SEQLOC_START);
-          if (start < extent_to_change)
-          {
-            slp_to_change = slp_index;
-            extent_to_change = start;
-          }
-        }
-      }
-      break;
-  }
-
-  if (slp_to_change != NULL)
-  {
-    if ((strand == Seq_strand_minus && end5)
-      || (strand != Seq_strand_minus && !end5))
-    {
-      start = GetOffsetInBioseq (slp_to_change, bsp, SEQLOC_START);
-      stop = bsp->length - 1;
-    }
-    else
-    {
-      start = 0;
-      stop = GetOffsetInBioseq (slp_to_change, bsp, SEQLOC_STOP);
-    }
-    if (end5) {
-        if (strand == Seq_strand_minus) {
-            start_diff = bsp->length - 1 - GetOffsetInBioseq(slp_to_change, bsp, SEQLOC_START);
-        } else {
-            start_diff = GetOffsetInBioseq(slp_to_change, bsp, SEQLOC_START);
-        }
-    }
-    
-    expand_seq_loc (start, stop, strand, slp_to_change);
-  }
-  return start_diff;
-}
-
-static void ExtendOnePartialFeature (SeqFeatPtr sfp, Pointer userdata)
+static void ExtendOnePartialFeatureEx (SeqFeatPtr sfp, Boolean extend5, Boolean extend3)
 {
   BioseqPtr   bsp;
   Boolean     partial3, partial5;
@@ -487,7 +411,7 @@ static void ExtendOnePartialFeature (SeqFeatPtr sfp, Pointer userdata)
   bsp = BioseqFindFromSeqLoc (sfp->location);
   if (bsp == NULL) return;
   CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
-  if (partial5)
+  if (partial5 && extend5)
   {
     start_diff = ExtendSeqLocToEnd (sfp->location, bsp, TRUE);
     if (start_diff > 0 && sfp->data.choice == SEQFEAT_CDREGION) {
@@ -500,12 +424,17 @@ static void ExtendOnePartialFeature (SeqFeatPtr sfp, Pointer userdata)
       }
     }
   }
-  if (partial3)
+  if (partial3 && extend3)
   {
     ExtendSeqLocToEnd (sfp->location, bsp, FALSE);
   }
 }
 
+static void ExtendOnePartialFeature (SeqFeatPtr sfp, Pointer userdata)
+{
+  ExtendOnePartialFeatureEx (sfp, TRUE, TRUE);
+}
+
 extern void ExtendPartialFeatures (IteM i)
 {
   BaseFormPtr       bfp;
@@ -553,6 +482,143 @@ extern void ExtendPartialFeatures (IteM i)
   ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
 }
 
+
+typedef struct extendpartialfeaturesform {
+  FORM_MESSAGE_BLOCK
+  DialoG feature_type;
+  ButtoN extend5;
+  ButtoN extend3;
+  DialoG string_constraint;
+  ButtoN leave_dlg_up;
+} ExtendPartialFeaturesFormData, PNTR ExtendPartialFeaturesFormPtr;
+
+static void DoExtendPartialFeatures (ButtoN b)
+{
+  ExtendPartialFeaturesFormPtr f;
+  SeqEntryPtr sep;
+  AECRActionPtr action;
+  ApplyActionPtr fake_apply;
+  FeatureFieldPtr feature_field;
+  ValNodePtr vnp;
+  StringConstraintPtr scp;
+  ValNodePtr object_list;
+  Boolean    extend5, extend3;
+
+  f = (ExtendPartialFeaturesFormPtr) GetObjectExtra (b);
+  if (f == NULL) return;
+
+  sep = GetTopSeqEntryForEntityID (f->input_entityID);
+  if (sep == NULL) return;
+
+  /* note - this is a small amount of hackery, designed to put off adding "extend partial features" as a macro language action.
+   * if this is ever added, this code should be moved to macroapi.c.
+   */
+  feature_field = FeatureFieldNew ();
+  vnp = DialogToPointer (f->feature_type);
+  if (vnp == NULL) {
+    feature_field->type = Feature_type_any;
+  } else {
+    feature_field->type = vnp->choice;
+    vnp = ValNodeFree (vnp);
+  }
+  fake_apply = ApplyActionNew ();
+  ValNodeAddPointer (&(fake_apply->field), FieldType_feature_field, feature_field);
+  action = AECRActionNew ();
+  ValNodeAddPointer (&(action->action), ActionChoice_apply, fake_apply);
+  
+  scp = DialogToPointer (f->string_constraint);
+  if (scp != NULL) {
+    ValNodeAddPointer (&(action->constraint), ConstraintChoice_string, scp);
+  }
+  object_list = GetObjectListForAECRAction (sep, action);
+  action = AECRActionFree (action);
+
+  extend5 = GetStatus (f->extend5);
+  extend3 = GetStatus (f->extend3);
+  for (vnp = object_list; vnp != NULL; vnp = vnp->next) {
+    if (vnp->choice == OBJ_SEQFEAT && vnp->data.ptrvalue != NULL) {
+      ExtendOnePartialFeatureEx (vnp->data.ptrvalue, extend5, extend3);
+    }
+  }
+  object_list = ValNodeFree (object_list);
+  ArrowCursor ();
+  Update ();
+  ObjMgrSetDirtyFlag (f->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, f->input_entityID, 0, 0);
+  if (!GetStatus (f->leave_dlg_up)) {
+    Remove (f->form);
+  }
+}
+
+
+extern void ExtendPartialFeaturesWithConstraint (IteM i)
+{
+  BaseFormPtr       bfp;
+  ExtendPartialFeaturesFormPtr f;
+  ValNodePtr          feature_list = NULL;
+  ValNode             vn;
+  WindoW              w;
+  GrouP               h, g, c;
+  PrompT              p1, p2;
+  ButtoN              b;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+
+  f = (ExtendPartialFeaturesFormPtr) MemNew (sizeof (ExtendPartialFeaturesFormData));
+  if (f == NULL) return;
+    
+  w = FixedWindow (-50, -33, -10, -10, "Extend Partial Features", StdCloseWindowProc);
+  SetObjectExtra (w, f, StdCleanupExtraProc);
+  f->form = (ForM) w;
+  f->input_entityID = bfp->input_entityID;
+  
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+
+  p1 = StaticPrompt (h, "Feature Type to Extend", 0, dialogTextHeight, programFont, 'c');
+  ValNodeAddPointer (&feature_list, Feature_type_any, StringSave ("Any"));
+  AddAllFeaturesToChoiceList (&feature_list);
+  
+  f->feature_type = ValNodeSelectionDialog (h, feature_list, TALL_SELECTION_LIST, ValNodeStringName,
+                                ValNodeSimpleDataFree, ValNodeStringCopy,
+                                ValNodeChoiceMatch, "feature type", 
+                                NULL, NULL, FALSE);
+  vn.choice = Feature_type_any;
+  vn.data.ptrvalue = NULL;
+  vn.next = NULL;
+  PointerToDialog (f->feature_type, &vn);
+
+  g = HiddenGroup (h, 2, 0, NULL);
+  f->extend5 = CheckBox (g, "Extend partial 5'", NULL);
+  SetStatus (f->extend5, TRUE);
+  f->extend3 = CheckBox (g, "Extend partial 3'", NULL);
+  SetStatus (f->extend3, TRUE);
+  
+  p2 = StaticPrompt (h, "Optional Constraint", 0, dialogTextHeight, programFont, 'c');
+  f->string_constraint = StringConstraintDialog (h, "Where feature text", FALSE, NULL, NULL);
+  
+  c = HiddenGroup (h, 3, 0, NULL);
+  b = PushButton (c, "Accept", DoExtendPartialFeatures);
+  SetObjectExtra (b, f, NULL);
+  PushButton (c, "Cancel", StdCancelButtonProc);
+  f->leave_dlg_up = CheckBox (c, "Leave Dialog Up", NULL);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) p1,
+                              (HANDLE) f->feature_type,
+                              (HANDLE) g,
+                              (HANDLE) p2,
+                              (HANDLE) f->string_constraint,
+                              (HANDLE) c,
+                              NULL);
+  Show (w);
+}
+
+
 static Boolean HasValidStartCodon (SeqFeatPtr cds)
 {
   ByteStorePtr  bs;
@@ -4491,6 +4557,7 @@ extern Int2 LIBCALLBACK RefGeneUserGenFunc (Pointer data);
 typedef struct refgeneuserdialog {
   DIALOG_MESSAGE_BLOCK
   GrouP         status;
+  ButtoN        generated;
   TexT          curator;
   TexT          source;
   Int2          indexer;
@@ -4503,13 +4570,6 @@ typedef struct refgeneuserform {
   SeqEntryPtr   sep;
 } RefgeneUserForm, PNTR RefgeneUserFormPtr;
 
-static ENUM_ALIST(changeflags_alist)
-  {" ",           0},
-  {"Sequence",    1},
-  {"Annotation",  2},
-  {"Both",        3},
-END_ENUM_ALIST
-
 static ENUM_ALIST(refgene_alist)
   {" ",          0},
   {"Assembly",    REFGENE_ASSEMBLY},
@@ -4521,15 +4581,15 @@ static ENUM_ALIST(refgene_alist)
 END_ENUM_ALIST
 
 static Uint2 refgene_types [] = {
-  TAGLIST_TEXT, TAGLIST_TEXT, TAGLIST_TEXT, TAGLIST_POPUP, TAGLIST_POPUP
+  TAGLIST_TEXT, TAGLIST_TEXT, TAGLIST_TEXT, TAGLIST_TEXT, TAGLIST_TEXT, TAGLIST_POPUP
 };
 
 static Uint2 refgene_widths [] = {
-  9, 7, 15, 0, 0
+  9, 7, 7, 7, 8, 0
 };
 
 static EnumFieldAssocPtr refgene_popups [] = {
-  NULL, NULL, NULL, changeflags_alist, refgene_alist
+  NULL, NULL, NULL, NULL, NULL, refgene_alist
 };
 
 static CharPtr refgene_labels [] = {
@@ -4537,19 +4597,18 @@ static CharPtr refgene_labels [] = {
 };
 
 static CharPtr refgene_fields [] = {
-  "Accession", "GI", "Comment", "Change", "Type", NULL
+  "Accession", "GI", "Start", "Stop", "Comment", "Type", NULL
 };
 
 static void AccessionUserFieldPtrToVisStringDialog (DialoG d, Pointer data)
 
 {
   CharPtr       accession;
-  Boolean       annotChange;
   CharPtr       comment;
   UserFieldPtr  curr;
   UserFieldPtr  entry;
   Int2          field;
-  Int2          flags;
+  Char          fm [16];
   Int4          from;
   Int4          gi;
   ValNodePtr    head;
@@ -4557,10 +4616,10 @@ static void AccessionUserFieldPtrToVisStringDialog (DialoG d, Pointer data)
   Int2          j;
   CharPtr       name;
   ObjectIdPtr   oip;
-  Boolean       seqChange;
   CharPtr       str;
   TagListPtr    tlp;
   Int4          to;
+  Char          tu [16];
   UserFieldPtr  ufp;
   ValNodePtr    vnp;
 
@@ -4587,8 +4646,6 @@ static void AccessionUserFieldPtrToVisStringDialog (DialoG d, Pointer data)
           gi = 0;
           from = 0;
           to = 0;
-          annotChange = FALSE;
-          seqChange = FALSE;
           ufp = (UserFieldPtr) entry->data.ptrvalue;
           while (ufp != NULL) {
             oip = ufp->label;
@@ -4601,10 +4658,6 @@ static void AccessionUserFieldPtrToVisStringDialog (DialoG d, Pointer data)
                 from = ufp->data.intvalue;
               } else if (StringICmp (oip->str, "to") == 0 && ufp->choice == 2) {
                 to = ufp->data.intvalue;
-              } else if (StringICmp (oip->str, "sequenceChange") == 0 && ufp->choice == 4) {
-                seqChange = ufp->data.boolvalue;
-              } else if (StringICmp (oip->str, "annotationChange") == 0 && ufp->choice == 4) {
-                annotChange = ufp->data.boolvalue;
               } else if (StringICmp (oip->str, "comment") == 0 && ufp->choice == 1) {
                 comment = (CharPtr) ufp->data.ptrvalue;
               } else if (StringICmp (oip->str, "name") == 0 && ufp->choice == 1) {
@@ -4617,18 +4670,14 @@ static void AccessionUserFieldPtrToVisStringDialog (DialoG d, Pointer data)
             if (comment == NULL) {
               comment = "";
             }
-            flags = 0;
-            if (seqChange) {
-              flags++;
-            }
-            if (annotChange) {
-              flags += 2;
-            }
-            if (gi != 0) {
-              sprintf (str, "%s\t%ld\t%s\t%d\t%d\n", accession, (long) gi, comment, (int) flags, (int) field);
-            } else {
-              sprintf (str, "%s\t\t%s\t%d\t%d\n", accession, comment, (int) flags, (int) field);
+            fm [0] = '\0';
+            tu [0] = '\0';
+            if (from > 0 && to > 0) {
+              sprintf (fm, "%ld", (long) from);
+              sprintf (tu, "%ld", (long) to);
             }
+            sprintf (str, "%s\t%ld\t%s\t%s\t%s\t%d\n", accession,
+                     (long) gi, fm, tu, comment, (int) field);
             vnp = ValNodeNew (head);
             if (head == NULL) {
               head = vnp;
@@ -4637,7 +4686,7 @@ static void AccessionUserFieldPtrToVisStringDialog (DialoG d, Pointer data)
               vnp->data.ptrvalue = StringSave (str);
             }
           } else if (name != NULL) {
-            sprintf (str, "\t\t%s\t0\t%d\n", name, (int) field);
+            sprintf (str, "\t\t\t\t%s\t%d\n", name, (int) field);
             vnp = ValNodeNew (head);
             if (head == NULL) {
               head = vnp;
@@ -4673,6 +4722,7 @@ static void UserObjectPtrToRefGeneDialog (DialoG d, Pointer data)
 
 {
   UserFieldPtr          curr;
+  Boolean               gen;
   ObjectIdPtr           oip;
   RefgeneUserDialogPtr  rdp;
   Int2                  status = 0;
@@ -4717,6 +4767,16 @@ static void UserObjectPtrToRefGeneDialog (DialoG d, Pointer data)
   }
   for (curr = uop->data; curr != NULL; curr = curr->next) {
     oip = curr->label;
+    if (oip != NULL && StringICmp (oip->str, "Generated") == 0) {
+      break;
+    }
+  }
+  if (curr != NULL && curr->choice == 4) {
+    gen = curr->data.boolvalue;
+    SetStatus (rdp->generated, gen);
+  }
+  for (curr = uop->data; curr != NULL; curr = curr->next) {
+    oip = curr->label;
     if (oip != NULL && StringICmp (oip->str, "Collaborator") == 0) {
       break;
     }
@@ -4787,21 +4847,19 @@ static void AddIndexerToRefGeneTrackUserObject (UserObjectPtr uop, Int2 indexer)
 static Pointer RefGeneDialogToUserObjectPtr (DialoG d)
 
 {
-  Boolean               annotChange;
   Char                  ch;
   Char                  curator [256];
   Int2                  i;
-  Uint2                  j;
+  Uint2                 j;
   size_t                len;
-  Int4                  num [5];
+  Int4                  num [6];
   Boolean               okay;
   RefgeneUserDialogPtr  rdp;
-  Boolean               seqChange;
   Char                  source [64];
   Int2                  status;
   CharPtr               str;
   TagListPtr            tlp;
-  CharPtr               txt [5];
+  CharPtr               txt [6];
   UserObjectPtr         uop;
   long int              val;
   ValNodePtr            vnp;
@@ -4836,6 +4894,10 @@ static Pointer RefGeneDialogToUserObjectPtr (DialoG d)
     AddSourceToRefGeneTrackUserObject (uop, source);
   }
 
+  if (GetStatus (rdp->generated)) {
+    AddGeneratedToRefGeneTrackUserObject (uop, TRUE);
+  }
+
   GetTitle (rdp->curator, curator, sizeof (curator));
   if (! StringHasNoText (curator)) {
     AddCuratorToRefGeneTrackUserObject (uop, curator);
@@ -4858,43 +4920,33 @@ static Pointer RefGeneDialogToUserObjectPtr (DialoG d)
         }
       }
       if (okay) {
-        for (j = 0; j < 5; j++) {
+        for (j = 0; j < 6; j++) {
           txt [j] = ExtractTagListColumn ((CharPtr) vnp->data.ptrvalue, j);
           num [j] = 0;
         }
-        for (j = 1; j < 5; j++) {
-          if (j != 2) {
-            num [j] = 0;
-            if (txt [j] != NULL && sscanf (txt [j], "%ld", &val) == 1) {
-              num [j] = val;
-            }
+        for (j = 1; j < 4; j++) {
+          num [j] = 0;
+          if (txt [j] != NULL && sscanf (txt [j], "%ld", &val) == 1) {
+            num [j] = val;
           }
         }
-        annotChange = FALSE;
-        seqChange = FALSE;
-        if (num [3] >= 2) {
-          annotChange = TRUE;
-          (num [3]) -= 2;
-        }
-        if (num [3] > 0) {
-          seqChange = TRUE;
+        if (txt [5] != NULL && sscanf (txt [5], "%ld", &val) == 1) {
+          num [5] = val;
         }
-        i = num [4];
+        i = num [5];
         if (i >= REFGENE_ASSEMBLY && i <= REFGENE_UNKNOWN) {
           if (! StringHasNoText (txt [0])) {
             AddAccessionToRefGeneTrackUserObject (uop, refgene_labels [i],
-                                                  txt [0], num [1],
-                                                  seqChange, annotChange,
-                                                  txt [2]);
-          } else if (! StringHasNoText (txt [2])) {
+                                                  txt [0], num [1], num [2],
+                                                  num [3], txt [4]);
+          } else if (! StringHasNoText (txt [4])) {
             /* comment by itself goes into name */
             AddAccessionToRefGeneTrackUserObject (uop, refgene_labels [i],
-                                                  NULL, num [1],
-                                                  seqChange, annotChange,
-                                                  txt [2]);
+                                                  NULL, num [1], num [2],
+                                                  num [3], txt [4]);
           }
         }
-        for (j = 0; j < 5; j++) {
+        for (j = 0; j < 6; j++) {
           txt [j] = MemFree (txt [j]);
         }
       }
@@ -4942,7 +4994,8 @@ static DialoG CreateRefGeneDialog (GrouP g)
   rdp->pipebtn = RadioButton (rdp->status, "Pipeline");
   Disable (rdp->pipebtn);
 
-  y = HiddenGroup (p, 4, 0, NULL);
+  y = HiddenGroup (p, 6, 0, NULL);
+  rdp->generated = CheckBox (y, "Generated", NULL);
   StaticPrompt (y, "Curator", 0, dialogTextHeight, programFont, 'l');
   rdp->curator = DialogText (y, "", 14, NULL);
   StaticPrompt (y, "Genomic Source", 0, dialogTextHeight, programFont, 'l');
@@ -4950,22 +5003,22 @@ static DialoG CreateRefGeneDialog (GrouP g)
 
   rdp->indexer = 0;
 
-  q = HiddenGroup (p, -6, 0, NULL);
+  q = HiddenGroup (p, -7, 0, NULL);
   lastppt = NULL;
   ppt = NULL;
-  for (i = 0; i < 5; i++) {
+  for (i = 0; i < 6; i++) {
     lastppt = ppt;
     ppt = StaticPrompt (q, refgene_fields [i], refgene_widths [i] * stdCharWidth, 0, systemFont, 'c');
   }
-  rdp->fields = CreateTagListDialog (p, 6, 5, STD_TAG_SPACING,
+  rdp->fields = CreateTagListDialog (p, 6, 6, STD_TAG_SPACING,
                                      refgene_types, refgene_widths, refgene_popups,
                                      AccessionUserFieldPtrToVisStringDialog,
                                      VisStringDialogToUserFieldPtr);
 
   tlp = (TagListPtr) GetObjectExtra (rdp->fields);
   if (tlp != NULL) {
-    AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [3], (HANDLE) lastppt, NULL);
-    AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [4], (HANDLE) ppt, NULL);
+    AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [4], (HANDLE) lastppt, NULL);
+    AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [5], (HANDLE) ppt, NULL);
   }
 
   AlignObjects (ALIGN_CENTER, (HANDLE) x, (HANDLE) y, (HANDLE) q, (HANDLE) rdp->fields, NULL);
@@ -5186,6 +5239,45 @@ static void UserObjectPtrToStruCommDialog (DialoG d, Pointer data)
   ValNodeFreeData (head);
 }
 
+static void FixSpecialCharactersInStructuredCommentUserObject (UserObjectPtr uop, BoolPtr changed)
+{
+  UserFieldPtr           curr;
+  CharPtr                field;
+  ValNodePtr             find_list = NULL;
+  ObjectIdPtr            oip;
+  CharPtr                str;
+ 
+
+  if (changed != NULL) {
+    *changed = FALSE;
+  }
+  if (uop == NULL || uop->type == NULL || StringICmp (uop->type->str, "StructuredComment") != 0) {
+    return;
+  }
+
+  for (curr = uop->data; curr != NULL; curr = curr->next) {
+   if (curr->choice != 1) continue;
+    oip = curr->label;
+    if (oip == NULL) continue;
+    field = oip->str;
+    if (StringHasNoText (field)) continue;
+    str = (CharPtr) curr->data.ptrvalue;
+    if (StringHasNoText (str)) continue;
+
+    SpecialCharFindWithContext ((CharPtr PNTR) (&(oip->str)), &find_list, NULL, NULL);
+    SpecialCharFindWithContext ((CharPtr PNTR) (&(curr->data.ptrvalue)), &find_list, NULL, NULL);
+  }
+  FixSpecialCharactersForStringsInList (find_list, "Special characters are not permitted.", TRUE);  
+  if (find_list != NULL)
+  {
+    if (changed != NULL) {
+      *changed = TRUE;
+    }
+    find_list = FreeContextList (find_list);
+  }
+}
+
+
 static Pointer StruCommDialogToUserObjectPtr (DialoG d)
 
 {
@@ -5196,6 +5288,7 @@ static Pointer StruCommDialogToUserObjectPtr (DialoG d)
   StruCommUserDialogPtr  sdp;
   CharPtr                str;
   ValNodePtr             vnp;
+  Boolean                fixed_special = FALSE;
 
   sdp = (StruCommUserDialogPtr) GetObjectExtra (d);
   if (sdp == NULL) return NULL;
@@ -5220,6 +5313,11 @@ static Pointer StruCommDialogToUserObjectPtr (DialoG d)
 
   ValNodeFreeData (head);
 
+  FixSpecialCharactersInStructuredCommentUserObject (uop, &fixed_special);
+  if (fixed_special) {
+    PointerToDialog (d, uop);
+  }
+
   return uop;
 }
 
@@ -6597,7 +6695,7 @@ static Boolean IsHUPIDAccession (BioseqPtr bsp)
     }
   }
 
-  if (ompp != NULL && StringCmp (ompp->procname, "SmartBioseqFetch") == 0) 
+  if (ompp != NULL && StringCmp (ompp->procname, "HUPBioseqFetch") == 0) 
   {
     rval = TRUE;
   }
@@ -9111,24 +9209,6 @@ static void FixDeltaFeatures (BioseqPtr bsp, Int4 offset, Int4 len_diff)
 }
 
 
-extern Int4 GetDeltaSeqLen (DeltaSeqPtr dsp)
-{
-  Int4 len = 0;
-  SeqLitPtr slp;
-
-  if (dsp == NULL || dsp->data.ptrvalue == NULL) {
-    /* do nothing, empty */
-  } else if (dsp->choice == 1) {
-    len = SeqLocLen ((SeqLocPtr)(dsp->data.ptrvalue));
-  } else if (dsp->choice == 2) {
-    slp = (SeqLitPtr) dsp->data.ptrvalue;
-    len = slp->length;
-  }
-  return len;
-}
-
-
-
 static void ConvertGapFeaturesToUnknownCallback (BioseqPtr bsp, Pointer userdata)
 {
   ConvertGapToUnknownPtr cgtup;
@@ -10155,7 +10235,7 @@ static Boolean EditDiscrepancyConfig (DiscrepancyConfigPtr dcp)
   SetGroupSpacing (g, 10, 10);
   for (i = 0; i < MAX_DISC_TYPE; i++)
   {
-    test_options[i] = CheckBox (g, GetDiscrepancyTestConfName (i), NULL);
+    test_options[i] = CheckBox (g, GetDiscrepancyTestConfName ((DiscrepancyType) i), NULL);
     SetStatus (test_options[i], dcp->conf_list[i]);
   }
   
@@ -10198,55 +10278,6 @@ static Boolean EditDiscrepancyConfig (DiscrepancyConfigPtr dcp)
   return rval;
 }
 
-/* This gets a list of the open views */
-static ValNodePtr GetBaseFormList ()
-
-{
-  Uint4          j;
-  Uint4          num;
-  ObjMgrPtr      omp;
-  ObjMgrDataPtr  omdp;
-  ObjMgrDataPtr  PNTR omdpp;
-  OMUserDataPtr  omudp;
-  BaseFormPtr    bfp;
-  ValNodePtr     base_form_list = NULL;
-
-  omp = ObjMgrGet ();
-  if (omp == NULL) return NULL;
-  num = omp->currobj;
-  for (j = 0, omdpp = omp->datalist; j < num && omdpp != NULL; j++, omdpp++) {
-    omdp = *omdpp;
-    if (omdp->parentptr == NULL) {
-      for (omudp = omdp->userdata; omudp != NULL; omudp = omudp->next) {
-        if (omudp->proctype == OMPROC_VIEW) {
-          bfp = (BaseFormPtr) omudp->userdata.ptrvalue;
-          ValNodeAddPointer (&base_form_list, 0, bfp);
-        }
-      }
-    }
-  }
-  return base_form_list;
-}
-
-
-static ValNodePtr GetViewedSeqEntryList (void)
-{
-  ValNodePtr  sep_list = NULL, base_form_list, vnp;
-  BaseFormPtr bfp;
-  SeqEntryPtr sep;
-  
-  base_form_list = GetBaseFormList();
-  for (vnp = base_form_list; vnp != NULL; vnp = vnp->next) {
-    bfp = (BaseFormPtr) vnp->data.ptrvalue;
-    if (bfp != NULL && bfp->input_entityID != 0) {
-      sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
-      ValNodeAddPointer (&sep_list, 0, sep);
-    }
-  }
-  base_form_list = ValNodeFree (base_form_list);
-  return sep_list;
-}
-
 static void VisitFeaturesInViewedBioseqs (Pointer userdata, VisitFeaturesFunc callback)
 {
   ValNodePtr  base_form_list, vnp;
@@ -10573,6 +10604,44 @@ extern void ScrollToDiscrepancyItem (ValNodePtr vnp, Pointer userdata)
   }
 }
 
+static Uint2 GetEntityIDFromItem (ValNodePtr vnp);
+static void ApplyTagToCodingRegionsInEntityID (Uint2 entityID);
+
+static void ApplyTagToCodingRegionsCallback (ValNodePtr item_list, Pointer userdata)
+{
+  ValNodePtr vnp;
+  ValNodePtr entityIDList = NULL;
+  Uint2       entityID;
+  SeqEntryPtr sep;
+  ValNodePtr  cds_list;
+  Boolean     found_any = FALSE;
+
+  for (vnp = item_list; vnp != NULL; vnp = vnp->next)
+  {
+    entityID = GetEntityIDFromItem(vnp);
+    if (!EntityIDAlreadyInList(entityID, entityIDList))
+    {
+      ValNodeAddInt (&entityIDList, 0, entityID);
+    }
+  }
+  for (vnp = entityIDList; vnp != NULL; vnp = vnp->next)
+  {
+    sep = GetTopSeqEntryForEntityID (vnp->data.intvalue);
+    cds_list = ListCodingRegionsContainedInSourceFeatures (sep);
+    if (cds_list != NULL)
+    {
+      found_any = TRUE;
+      cds_list = ValNodeFree (cds_list);
+      ApplyTagToCodingRegionsInEntityID (vnp->data.intvalue);
+    }
+  }
+  if (!found_any)
+  {
+    Message (MSG_ERROR, "No coding regions found in source features!  Try editing the definition lines.");
+  }  
+  entityIDList = ValNodeFree (entityIDList);  
+}
+
 static void AddBulkEditing (ValNodePtr clickable_list)
 {
   ClickableItemPtr cip;
@@ -10582,7 +10651,9 @@ static void AddBulkEditing (ValNodePtr clickable_list)
     cip = (ClickableItemPtr) clickable_list->data.ptrvalue;
     if (cip->callback_func == NULL && cip->item_list != NULL) {
       if (cip->clickable_item_type == DISC_CDS_OVERLAP_TRNA) {
-        cip->callback_func = EditCDStRNAOverlapCallback;        
+        cip->callback_func = EditCDStRNAOverlapCallback;    
+      } else if (cip->clickable_item_type == DISC_INCONSISTENT_BIOSRC_DEFLINE) {
+        cip->callback_func = ApplyTagToCodingRegionsCallback;  
       } else {
         subtype = GetSubtypeForBulkEdit (cip->item_list);
         /* Note - using FEATDEF_rRNA to represent all editable RNA features */
@@ -10776,7 +10847,7 @@ extern void CreateStdValidatorFormMenus (WindoW w);
 #endif
 
 
-extern void CreateDiscrepancyReportWindow ()
+extern void CreateDiscrepancyReportWindow (void)
 {
   DiscrepancyReportFormPtr drfp;
   GrouP                    h;
@@ -10963,12 +11034,12 @@ extern void NewSUC (ValNodePtr suc_list, Uint2 entityID, Boolean reverse, Boolea
   h = HiddenGroup (w, -1, 0, NULL);
   SetGroupSpacing (h, 10, 10);
   
-  sfp->clickable_list_dlg = CreateClickableListDialogEx (h, "Text", "Affected Items",
+  sfp->clickable_list_dlg = CreateClickableListDialogEx (h, "Text", "Affected Items", NULL, NULL,
                                                          ScrollToDiscrepancyItem, EditDiscrepancyItem, NULL,
                                                          GetDiscrepancyItemText,
                                                          stdCharWidth * 55,
                                                          stdCharWidth * 55,
-                                                         FALSE);
+                                                         FALSE, TRUE);
   if (byblock) {
     suc_list = CategorizeSUCBlocks (suc_list);
     SetClickableItemExpanded (suc_list, FALSE);
@@ -11489,7 +11560,7 @@ static RNA_ITS_ItemPtr TagListStringToRNAITSItem (CharPtr line)
     rip->rna_type = eRNA_ITS_INVALID;
   } else {
     StrToLong (txt, &tmp);
-    rip->rna_type = tmp;
+    rip->rna_type = (ERNA_ITS_type) tmp;
   }
   txt = MemFree (txt);
 
@@ -11799,6 +11870,9 @@ static Int4 GetAlnRowForBsp (BioseqPtr bsp, SeqAlignPtr salp)
 static Int4 ChooseEndpoint (Int4 bsp_len, Int4 pos, Boolean is_left, SeqAlignPtr salp, Int4 aln_row)
 {
   Int4 tmp;
+  Int4 aln_len;
+
+  aln_len = SeqAlignLength (salp);
   if (pos < 0) {
     if (is_left) {
       pos = 0;
@@ -11813,10 +11887,10 @@ static Int4 ChooseEndpoint (Int4 bsp_len, Int4 pos, Boolean is_left, SeqAlignPtr
         pos = bsp_len - 1;
       }
     }
-  } else {
+  } else if (salp != NULL) {      
     tmp = AlnMgr2MapSeqAlignToBioseq (salp, pos, aln_row);
     if (is_left) {
-      while (tmp < 0 && pos < bsp_len) {
+      while (tmp < 0 && pos < aln_len) {
         pos++;
         tmp = AlnMgr2MapSeqAlignToBioseq (salp, pos, aln_row);
       }
@@ -12938,7 +13012,6 @@ static void ReleaseCDS (DoC d, PoinT pt)
   Int2            item;
   RecT            rct;
   Int2            row;
-  Int4            cds_num = 1;
   ValNodePtr      vnp, vnp_m, linked_mrnas;
   Boolean         found;
   Boolean         was_selected = FALSE;
@@ -13337,21 +13410,28 @@ static void TrimCDSFortRNAOverlap (ValNodePtr item_list)
 
 static Int4 GetOverlapLen (SeqLocPtr slp1, SeqLocPtr slp2)
 {
-  Int4  stop1, start2, len = 0;
-  Uint1 strand;
+  Int4  start1, stop1, start2, stop2, tmp, a, b, len = 0;
 
   if (slp1 == NULL || slp2 == NULL) return 0;
 
-  strand = SeqLocStrand (slp1);
-  if (strand == Seq_strand_minus) {
-    stop1 = SeqLocStart (slp1);
-    start2 = SeqLocStop (slp2);
-    len = start2 - stop1 + 1;
-  } else {
-    stop1 = SeqLocStop (slp1);
-    start2 = SeqLocStart (slp2);
-    len = stop1 - start2 + 1;
+  start1 = SeqLocStart (slp1);
+  stop1 = SeqLocStop (slp1);
+  if (start1 > stop1) {
+    tmp = start1;
+    start1 = stop1;
+    stop1 = tmp;
   }
+  start2 = SeqLocStart (slp2);
+  stop2 = SeqLocStop (slp2);
+  if (start2 > stop2) {
+    tmp = start2;
+    start2 = stop2;
+    stop2 = tmp;
+  }
+  
+  a = MAX(start1, start2);
+  b = MIN (stop1, stop2);
+  len = b - a + 1;
   return len; 
 }
 
@@ -13456,7 +13536,6 @@ static ValNodePtr CDStRNAOverlapListFromItemList (ValNodePtr item_list)
 {
   ValNodePtr new_item_list = NULL, vnp, vnp_trna;
   ValNodePtr        good_list = NULL, bad_list = NULL;
-  ValNodePtr        clickable_list = NULL;
   SeqFeatPtr        sfp, trna;
   CDStRNAOverlapPtr p = NULL;
   Int4              len;
@@ -13552,7 +13631,7 @@ static void FixCDStRNAOverlaps (ValNodePtr overlap_list)
       gene->location = TruncateLocation (gene->location, SeqLocLen (gene->location) - p->overlap_len);
     }
 
-    AddTranslExcept (p->cds, "TAA stop codon is completed by the addition of 3' A residues to the mRNA", FALSE);
+    AddTranslExcept (p->cds, "TAA stop codon is completed by the addition of 3' A residues to the mRNA", FALSE, FALSE);
   }
 }  
 
@@ -13825,3 +13904,191 @@ static void EditCDStRNAOverlap (ValNodePtr item_list)
   Update ();
 }
 
+
+extern GetSamplePtr 
+GetSampleForItemList 
+(ValNodePtr               item_list,
+ ValNodePtr               requested_field,
+ GetFeatureFieldString    fieldstring_func,
+ GetDescriptorFieldString descrstring_func)
+{
+  ValNodePtr   vnp;
+  GetSamplePtr gsp;
+  SeqFeatPtr   sfp;
+  SeqDescrPtr  sdp;
+  CharPtr      str = NULL;
+
+  if (item_list == NULL || requested_field == NULL) return NULL;
+
+  gsp = GetSampleNew();
+
+  for (vnp = item_list; vnp != NULL; vnp = vnp->next)
+  {
+    if (vnp->choice == OBJ_SEQFEAT && fieldstring_func != NULL)
+    {
+      sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+      str = fieldstring_func (sfp, requested_field, NULL);
+    }
+    else if (vnp->choice == OBJ_SEQDESC && descrstring_func != NULL)
+    {
+      sdp = (SeqDescrPtr) vnp->data.ptrvalue;
+      str = descrstring_func (sdp, requested_field, NULL);
+    }
+    if (!StringHasNoText (str))
+    {
+      gsp->num_found ++;
+      if (gsp->sample_text == NULL)
+      {
+        gsp->sample_text = str;
+      }
+      else
+      {
+        if (StringCmp (str, gsp->sample_text) != 0)
+        {
+          gsp->all_same = FALSE;
+        }
+      }
+    }
+    str = MemFree (str);
+  }
+
+  if (gsp->num_found == 0)
+  {
+    gsp = GetSampleFree (gsp);
+  }
+  return gsp;
+}
+
+
+typedef struct applytagtocdsinsrcfeat {
+  FORM_MESSAGE_BLOCK
+  TexT       note_text;
+  ValNodePtr cds_list;
+} ApplyTagToCDSInSrcFeatData, PNTR ApplyTagToCDSInSrcFeatPtr;
+
+
+static void CleanupApplyTagToCDSInSrcFeatForm (GraphiC g, VoidPtr data)
+
+{
+  ApplyTagToCDSInSrcFeatPtr dlg;
+
+  dlg = (ApplyTagToCDSInSrcFeatPtr) data;
+  if (dlg != NULL) {
+    dlg->cds_list = ValNodeFree (dlg->cds_list);
+  }
+  StdCleanupFormProc (g, data);
+}
+
+
+static void DoApplyTagToCodingRegionsInSourceFeatures (ButtoN b)
+{
+  ApplyTagToCDSInSrcFeatPtr dlg;
+  ValNodePtr                vnp;
+  GetSamplePtr              gsp;
+  ValNode                   vn;
+  SeqFeatPtr                sfp;
+  ApplyValueData            avd;
+
+  dlg = (ApplyTagToCDSInSrcFeatPtr) GetObjectExtra (b);
+  if (dlg == NULL) return;
+
+  if (TextHasNoText (dlg->note_text)) {
+    Message (MSG_ERROR, "No text supplied for note!");
+    return;
+  }
+  vn.choice = 0;
+  vn.next = NULL;
+  vn.data.intvalue = 2;
+  gsp = GetSampleForItemList (dlg->cds_list, &vn, GetCDSFieldString, NULL);
+  avd.etp = GetExistingTextHandlerInfo (gsp == NULL ? 0 : gsp->num_found, FALSE);
+  gsp = GetSampleFree (gsp);  
+  if (avd.etp != NULL && avd.etp->existing_text_choice == eExistingTextChoiceCancel)
+  {
+    avd.etp = MemFree (avd.etp);
+    return;
+  }
+  avd.new_text = SaveStringFromText (dlg->note_text);
+  avd.field_list = NULL;
+  avd.text_to_replace = NULL;
+  avd.where_to_replace = EditApplyFindLocation_anywhere;
+
+  WatchCursor();
+  Update();
+  for (vnp = dlg->cds_list; vnp != NULL; vnp = vnp->next)
+  {
+    sfp = (SeqFeatPtr) vnp->data.ptrvalue;
+    if (sfp != NULL)
+    {
+      sfp->comment = HandleApplyValue (sfp->comment, &avd);
+    }
+  }
+  avd.etp = MemFree (avd.etp);
+  ObjMgrSetDirtyFlag (dlg->input_entityID, TRUE);
+  ObjMgrSendMsg (OM_MSG_UPDATE, dlg->input_entityID, 0, 0);
+  ArrowCursor();
+  Remove (dlg->form);
+  Update ();
+}
+
+
+static void ApplyTagToCodingRegionsInEntityID (Uint2 entityID)
+{
+  ApplyTagToCDSInSrcFeatPtr dlg;
+  ValNodePtr   cds_list;
+  WindoW       w;
+  GrouP        h, g, c;
+  ButtoN       b;
+  SeqEntryPtr  sep;
+
+  sep = GetTopSeqEntryForEntityID (entityID);
+
+  cds_list = ListCodingRegionsContainedInSourceFeatures (sep);
+
+  if (cds_list == NULL) {
+    Message (MSG_ERROR, "No coding regions found in source features!");
+    return;
+  }
+
+  /* create window to display and correct overlaps */
+  dlg = (ApplyTagToCDSInSrcFeatPtr) MemNew (sizeof (ApplyTagToCDSInSrcFeatData));
+  dlg->input_entityID = entityID;
+  dlg->cds_list = cds_list;
+
+  w = FixedWindow (-50, -33, -10, -10, "Apply Note to Coding Regions in Source Features", StdCloseWindowProc);
+  SetObjectExtra (w, dlg, CleanupApplyTagToCDSInSrcFeatForm);
+  dlg->form = (ForM) w;
+    
+  h = HiddenGroup (w, -1, 0, NULL);
+  SetGroupSpacing (h, 10, 10);
+  
+  g = HiddenGroup (h, 2, 0, NULL);
+  StaticPrompt (g, "Note Text:", 0, dialogTextHeight, programFont, 'r');
+  dlg->note_text = DialogText (g, "prophage-encoded protein", 0, NULL);
+  c = HiddenGroup (h, 4, 0, NULL);
+  SetGroupSpacing (c, 10, 10);
+
+  b = PushButton (c, "Accept", DoApplyTagToCodingRegionsInSourceFeatures);
+  SetObjectExtra (b, dlg, NULL);
+  b = PushButton (c, "Dismiss", StdCancelButtonProc);
+
+  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL);
+  RealizeWindow (w);
+  Show (w);
+  Update ();
+}
+
+
+extern void ApplyTagToCodingRegionsInSourceFeatures (IteM i)
+{
+  BaseFormPtr  bfp;
+
+#ifdef WIN_MAC
+  bfp = currentFormDataPtr;
+#else
+  bfp = GetObjectExtra (i);
+#endif
+  if (bfp == NULL) return;
+
+  ApplyTagToCodingRegionsInEntityID (bfp->input_entityID);
+}
+
diff --git a/sequin/sequin9.c b/sequin/sequin9.c
index 74123814..fb8b1f28 100644
--- a/sequin/sequin9.c
+++ b/sequin/sequin9.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   4/20/99
 *
-* $Revision: 6.462 $
+* $Revision: 6.469 $
 *
 * File Description: 
 *
@@ -2991,7 +2991,7 @@ ReplaceQualityScores
 }
 
 
-static void RemoveQualityScores 
+extern void RemoveQualityScores 
 (BioseqPtr bsp, 
  FILE      *log_fp,
  BoolPtr   data_in_log)
@@ -3026,6 +3026,243 @@ static void RemoveQualityScores
   DeleteMarkedObjects (0, OBJ_BIOSEQ, (Pointer) bsp);
 }
 
+
+#define SEQGRAPH_FloatHi    1
+#define SEQGRAPH_Int4       2
+#define SEQGRAPH_BS         3
+
+/* remove compression from SeqGraph */
+static Boolean ExpandSeqGraph (SeqGraphPtr sgp)
+{
+  Int4    oldpos = 0, newpos = 0, i;
+  Pointer new_values;
+  Int4    new_numval;
+  Int2    cur_byte;
+
+  if (sgp == NULL || sgp->compr == 0 || sgp->compr == 1) {
+    return TRUE;
+  } else if (sgp->compr < 0) {
+    return FALSE;
+  }
+
+  new_numval = sgp->numval * sgp->compr;
+
+  /* allocate space for new values */
+  switch (sgp->flags[2]) {
+    case SEQGRAPH_FloatHi:
+      new_values = MemNew (sizeof (FloatHi) * new_numval);
+      break;
+    case SEQGRAPH_Int4:
+      new_values = MemNew (sizeof (Int4) * new_numval);
+      break;
+    case SEQGRAPH_BS:
+      new_values = (Pointer) BSNew (new_numval);
+      BSSeek ((ByteStorePtr)new_values, 0, SEEK_SET);
+      BSSeek ((ByteStorePtr) sgp->values, 0, SEEK_SET);
+      break;
+  }
+
+  /* copy and expand */
+  while (oldpos < sgp->numval) {
+    if (sgp->flags[2] == SEQGRAPH_BS) {
+      cur_byte = BSGetByte ((ByteStorePtr) sgp->values);
+    }
+    for (i = 0; i < sgp->compr; i++) {
+      switch (sgp->flags[2]) {
+        case SEQGRAPH_FloatHi:
+          ((FloatHiPtr)new_values)[newpos++] = ((FloatHiPtr)sgp->values)[oldpos];
+          break;
+        case SEQGRAPH_Int4:
+          ((Int4Ptr)new_values)[newpos++] = ((Int4Ptr)sgp->values)[oldpos];
+          break;
+        case SEQGRAPH_BS:
+          BSPutByte ((ByteStorePtr) new_values, cur_byte);
+          break;
+      }
+    }
+    oldpos++;
+  }
+
+  /* free old values and replace with new */
+  if (sgp->flags[2] == SEQGRAPH_BS) {
+    sgp->values = BSFree ((ByteStorePtr) sgp->values);
+  } else {    
+    sgp->values = MemFree (sgp->values);    
+  }
+  sgp->values = new_values;
+  sgp->numval = new_numval;
+  sgp->compr = 0;
+
+  return TRUE;
+}
+
+static Boolean TruncateSeqGraphValues (SeqGraphPtr sgp, Int4 len, Boolean onleft)
+{
+  Int4    oldpos, newpos = 0;
+  Pointer new_values;
+  Int4    new_numval;
+  Int2    cur_byte;
+  Int4    imin, imax;
+  FloatHi fmin, fmax;
+
+  if (sgp == NULL) return TRUE;
+  if (!ExpandSeqGraph (sgp)) return FALSE;
+
+  new_numval = sgp->numval - len;
+
+  /* allocate space for new values */
+  switch (sgp->flags[2]) {
+    case SEQGRAPH_FloatHi:
+      new_values = MemNew (sizeof (FloatHi) * new_numval);
+      fmin = ((FloatHiPtr)sgp->values)[0];
+      fmax = fmin;
+      break;
+    case SEQGRAPH_Int4:
+      new_values = MemNew (sizeof (Int4) * new_numval);
+      imin = ((Int4Ptr)sgp->values)[0];
+      imax = imin;
+      break;
+    case SEQGRAPH_BS:
+      new_values = (Pointer) BSNew (new_numval);
+      BSSeek ((ByteStorePtr)new_values, 0, SEEK_SET);
+      if (onleft) {
+        BSSeek ((ByteStorePtr) sgp->values, len, SEEK_SET);
+      } else {
+        BSSeek ((ByteStorePtr) sgp->values, 0, SEEK_SET);
+      }
+      imin = BSGetByte ((ByteStorePtr) sgp->values);
+      imax = imin;
+      /* put pointer back */
+      if (onleft) {
+        BSSeek ((ByteStorePtr) sgp->values, len, SEEK_SET);
+      } else {
+        BSSeek ((ByteStorePtr) sgp->values, 0, SEEK_SET);
+      }
+      break;
+  }
+
+  /* copy */
+  if (onleft) {
+    oldpos = len;
+  } else {
+    oldpos = 0;
+  }
+  while (oldpos < sgp->numval && newpos < new_numval) {
+      switch (sgp->flags[2]) {
+        case SEQGRAPH_FloatHi:
+          ((FloatHiPtr)new_values)[newpos] = ((FloatHiPtr)sgp->values)[oldpos];
+          if (((FloatHiPtr)new_values)[newpos] > fmax) {
+            fmax = ((FloatHiPtr)new_values)[newpos];
+          }
+          if (((FloatHiPtr)new_values)[newpos] < fmin) {
+            fmin = ((FloatHiPtr)new_values)[newpos];
+          }
+          break;
+        case SEQGRAPH_Int4:
+          ((Int4Ptr)new_values)[newpos] = ((Int4Ptr)sgp->values)[oldpos];
+          if (((Int4Ptr)new_values)[newpos] > imax) {
+            imax = ((Int4Ptr)new_values)[newpos];
+          }
+          if (((Int4Ptr)new_values)[newpos] < imin) {
+            imin = ((Int4Ptr)new_values)[newpos];
+          }
+          break;
+        case SEQGRAPH_BS:
+          cur_byte = BSGetByte ((ByteStorePtr) sgp->values);
+          BSPutByte ((ByteStorePtr) new_values, cur_byte);
+          if (cur_byte > imax) {
+            imax = cur_byte;
+          }
+          if (cur_byte < imin) {
+            imin = cur_byte;
+          }
+          break;
+    }
+    oldpos++;
+    newpos++;
+  }
+
+  /* free old values and replace with new */
+  if (sgp->flags[2] == SEQGRAPH_BS) {
+    sgp->values = BSFree ((ByteStorePtr) sgp->values);
+  } else {    
+    sgp->values = MemFree (sgp->values);    
+  }
+  sgp->values = new_values;
+  sgp->numval = new_numval;
+
+  /* replace mins and maxes */
+  if (sgp->flags[2] == SEQGRAPH_FloatHi) {
+    sgp->max.realvalue = fmax;
+    sgp->min.realvalue = fmin;
+  } else {
+    sgp->max.intvalue = imax;
+    sgp->min.intvalue = imin;
+  }
+  return TRUE;  
+}
+
+  
+
+/* assume Bioseq has already been trimmed - length of old Bioseq was trim5 + bsp->length + trim3 */
+static Boolean 
+TrimQualityScoresForSequenceUpdate 
+(BioseqPtr bsp, 
+ Int4      trim5,
+ Int4      trim3,
+ FILE      *log_fp,
+ BoolPtr   data_in_log)
+{
+  ValNodePtr    score_list = NULL, vnp;
+  SeqGraphPtr   sgp;
+  SeqIntPtr     sip;
+  Int4          left, right;
+  Boolean       rval = FALSE;
+  Char          acc_str [256];
+
+  if (bsp == NULL) return FALSE;
+
+  VisitGraphsOnBsp (bsp, &score_list, ListPhrapGraphsCallback);
+  if (score_list == NULL) return FALSE;
+
+  for (vnp = score_list; vnp != NULL; vnp = vnp->next) {
+    sgp = vnp->data.ptrvalue;
+    if (sgp != NULL && sgp->loc != NULL && sgp->loc->choice == SEQLOC_INT) {
+      sip = (SeqIntPtr) sgp->loc->data.ptrvalue;
+      /* trim on right */
+      if (sip->from > trim5 + bsp->length) {
+        sgp->idx.deleteme = TRUE;
+        rval = TRUE;
+      } else if (sip->to > trim5 + bsp->length - 1) {
+        right = sip->to - trim5 - bsp->length + 1;
+        sip->to = trim5 + bsp->length - 1;
+        TruncateSeqGraphValues (sgp, right, FALSE);
+        rval = TRUE;
+      }
+      
+      sip->from -= trim5;
+      sip->to -= trim5;
+      if (sip->to < 0) {
+        sgp->idx.deleteme = TRUE;
+        rval = TRUE;
+      } else if (sip->from < 0) {
+        left = 0 - sip->from;
+        sip->from = 0;
+        TruncateSeqGraphValues (sgp, left, TRUE);
+        rval = TRUE;
+      }
+    }
+  }  
+
+  if (rval && log_fp != NULL && data_in_log != NULL) {
+    SeqIdWrite (bsp->id, acc_str, PRINTID_REPORT, sizeof (acc_str));
+    fprintf (log_fp, "Quality scores trimmed for %s\n", acc_str);
+    *data_in_log = TRUE;
+  }
+  return rval;
+}
+
+
 static Boolean AdjustAlignment (
   UpsDataPtr udp,
   Int2 choice
@@ -5170,15 +5407,16 @@ static CharPtr FixProteinString
   CharPtr      newprot;
   CharPtr      ptr;
   Char         ch;
-  Int4         start, stop, new_stop;
+  Int4         start, stop, new_stop, prot_len;
   Boolean      changed;
+  CdRegionPtr  crp;
   
   if (sfp == NULL || truncated == NULL 
       || contains_start == NULL
       || contains_stop == NULL) {
     return NULL;
   }
-  
+
   bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
   if (bs == NULL) return NULL;
   newprot = BSMerge (bs, NULL);
@@ -5207,7 +5445,18 @@ static CharPtr FixProteinString
           if (nucBsp == NULL) return newprot;
           start = GetOffsetInBioseq (sfp->location, nucBsp, SEQLOC_START);
           stop = GetOffsetInBioseq (sfp->location, nucBsp, SEQLOC_STOP);
-          new_stop = FindNewCDSStop (sfp->location, nucBsp, (1 + ptr - newprot) * 3);
+          prot_len = (1 + ptr - newprot) * 3;
+          if (sfp->data.choice == SEQFEAT_CDREGION) {
+            crp = (CdRegionPtr) sfp->data.value.ptrvalue;
+            if (crp != NULL) {
+              if (crp->frame == 2) {
+                prot_len += 1;
+              } else if (crp->frame == 3) {
+                prot_len += 2;
+              }
+            }
+          }
+          new_stop = FindNewCDSStop (sfp->location, nucBsp, prot_len);
           if (strand == Seq_strand_minus) {
             sfp->location = SeqLocDelete (sfp->location, SeqLocId (sfp->location),
                           stop, new_stop - 1, FALSE, &changed);
@@ -5775,22 +6024,6 @@ AdjustCDSForUpdate
 }
 
   
-extern SeqLocPtr SeqLocWholeNew (BioseqPtr bsp)
-{
-  ValNodePtr vnp;
-
-  if (bsp == NULL) return NULL;
-
-  vnp = ValNodeNew (NULL);
-
-  if (vnp == NULL) return NULL;
-
-  vnp->choice = SEQLOC_WHOLE;
-  vnp->data.ptrvalue = (Pointer) SeqIdDup (SeqIdFindBest (bsp->id, 0));
-  return (SeqLocPtr)vnp;
-}
-
-
 static void WarnNoProteinUpdate (BioseqPtr bsp)
 {
   Char     acc_str [256];
@@ -10560,8 +10793,10 @@ typedef struct addtranslexceptdata {
 
   TexT        cds_comment;
   ButtoN      strict_checking_btn;
+  ButtoN      extend_btn;
   CharPtr     cds_comment_txt;
   Boolean     strict_checking;
+  Boolean     extend;
 } AddTranslExceptData, PNTR AddTranslExceptPtr; 
 
 
@@ -10589,7 +10824,92 @@ static SeqLocPtr SeqLocForTermination (SeqLocPtr slp, Int4 except_len)
 }
 
 
-extern void AddTranslExcept (SeqFeatPtr sfp, CharPtr cds_comment, Boolean use_strict)
+static Boolean DoesCodingRegionEndWithStopCodon (SeqFeatPtr sfp)
+{
+  ByteStorePtr bs;
+  CharPtr      prot_str;
+  Boolean      rval = FALSE;
+
+  bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE);
+  prot_str = BSMerge (bs, NULL);
+  bs = BSFree (bs);
+  if (prot_str != NULL && prot_str[StringLen (prot_str) - 1] == '*') {
+    rval = TRUE;
+  }
+  prot_str = MemFree (prot_str);
+  return rval;
+}
+
+
+static Int4 AddTerminalExceptionLen (SeqFeatPtr sfp)
+{
+  BioseqPtr bsp;
+  Uint1     strand;
+  Int4      stop, len, except_len = 0, gene_stop;
+  Char      buf[4];
+  Int4      rval = 0;
+  SeqFeatPtr gene;
+
+  if (sfp == NULL || sfp->location == NULL) return FALSE;
+
+  bsp = BioseqFindFromSeqLoc (sfp->location);
+  if (bsp == NULL) return 0;
+  strand = SeqLocStrand (sfp->location);
+  if (strand == Seq_strand_minus) {
+    stop = SeqLocStart (sfp->location);
+    len = MIN (stop, 3);
+    if (len > 0) {
+      SeqPortStreamInt (bsp, stop - len, stop - 1,
+                        Seq_strand_minus,STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL,
+                        buf, NULL);
+    }
+  } else {
+    stop = SeqLocStop (sfp->location);
+    len = MIN (bsp->length - stop - 1, 3);
+    if (len > 0) {
+      SeqPortStreamInt (bsp, stop + 1, stop + len,
+                        Seq_strand_plus,STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL,
+                        buf, NULL);
+    }
+  }
+  if (len > 0) {
+    if (buf[0] == 'T') {
+      except_len++;
+      if (buf[1] == 'A') {
+        except_len++;
+        if (buf[2] == 'A') {
+          /* has real stop codon */
+          except_len++;
+        }
+      }
+    }
+    if (except_len < 3 && except_len > 0) {
+      gene = GetGeneForFeature (sfp);
+      if (strand == Seq_strand_minus) {
+        if (gene != NULL) {
+          gene_stop = SeqLocStart (gene->location);
+          if (gene_stop > stop - except_len) {
+            ExtendSeqLocToPosition (gene->location, FALSE, stop - except_len);
+          }
+        }
+        ExtendSeqLocToPosition (sfp->location, FALSE, stop - except_len);
+      } else {
+        if (gene != NULL) {
+          gene_stop = SeqLocStop (gene->location);
+          if (gene_stop < stop + except_len) {
+            ExtendSeqLocToPosition (gene->location, FALSE, stop + except_len);
+          }
+        }
+        ExtendSeqLocToPosition (sfp->location, FALSE, stop + except_len);
+      }
+      rval = except_len;
+    }
+  }
+  return rval;
+}
+
+
+extern void AddTranslExcept (SeqFeatPtr sfp, CharPtr cds_comment, Boolean use_strict, Boolean extend)
 
 {
   CdRegionPtr        crp;
@@ -10621,6 +10941,11 @@ extern void AddTranslExcept (SeqFeatPtr sfp, CharPtr cds_comment, Boolean use_st
   } else {
     except_len = dna_len % 3;
   }
+  if (except_len == 0 && extend && !DoesCodingRegionEndWithStopCodon(sfp)) {
+    except_len = AddTerminalExceptionLen (sfp);
+    dna_len = SeqLocLen (sfp->location);
+  }   
+
   if (except_len == 0) return;
 
   /* don't add code break if one already exists */
@@ -10739,6 +11064,7 @@ static void AddTranslExceptCallback (SeqFeatPtr sfp, Pointer userdata)
 {
   AddTranslExceptPtr ap;
   Boolean            use_strict = FALSE;
+  Boolean            extend = FALSE;
   CharPtr            cds_comment = NULL;
 
   ap = (AddTranslExceptPtr) userdata;
@@ -10746,9 +11072,10 @@ static void AddTranslExceptCallback (SeqFeatPtr sfp, Pointer userdata)
   {
     cds_comment = ap->cds_comment_txt;
   	use_strict = ap->strict_checking;
+    extend = ap->extend;
   }
 
-  AddTranslExcept (sfp, cds_comment, use_strict);
+  AddTranslExcept (sfp, cds_comment, use_strict, extend);
 }
 
 
@@ -10786,6 +11113,7 @@ static void DoAddTranslExceptWithComment (ButtoN b)
   oldscope = SeqEntrySetScope (sep);
   ap->cds_comment_txt = SaveStringFromText (ap->cds_comment);
   ap->strict_checking = GetStatus (ap->strict_checking_btn);
+  ap->extend = GetStatus (ap->extend_btn);
   if (StringHasNoText (ap->cds_comment_txt))
   {
   	ap->cds_comment_txt = MemFree (ap->cds_comment_txt);
@@ -10839,12 +11167,15 @@ extern void AddTranslExceptWithComment (IteM i)
   clear_btn = PushButton (h, "Clear Comment", ClearComment);
   SetObjectExtra (clear_btn, ap, NULL);
   ap->strict_checking_btn = CheckBox (h, "Overhang must be T or TA", NULL);
+  ap->extend_btn = CheckBox (h, "Extend for T/TA overhang", NULL);
 
   c = HiddenGroup (h, 4, 0, NULL);
   b = DefaultButton (c, "Accept", DoAddTranslExceptWithComment);
   SetObjectExtra (b, ap, NULL);
   PushButton (c, "Cancel", StdCancelButtonProc);
-  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) clear_btn, (HANDLE) ap->strict_checking_btn, (HANDLE) c, NULL);
+  AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) clear_btn, 
+               (HANDLE) ap->strict_checking_btn,
+               (HANDLE) ap->extend_btn, (HANDLE) c, NULL);
   RealizeWindow (w);
   Show (w);
   Update ();
@@ -12814,6 +13145,32 @@ ReportBadUpdateType
   }
 }
 
+static Boolean OkToTrimQualityScores (UpdatePairPtr upp, UpdateAlignmentLengthsPtr ualp)
+{
+  CharPtr buf1, buf2;
+  Boolean rval = FALSE;
+
+  if (upp == NULL || upp->orig_bsp == NULL || upp->update_bsp == NULL 
+      || upp->update_bsp->length > upp->orig_bsp->length
+      || ualp == NULL || ualp->new5 > 0 || ualp->new3 > 0 || ualp->newa != ualp->olda || ualp->newa != upp->update_bsp->length) {
+    return FALSE;
+  }
+  buf1 = (CharPtr) MemNew (sizeof (Char) * (ualp->newa + 1));
+  MemSet (buf1, 0, sizeof (Char) * (ualp->newa + 1));
+  buf2= (CharPtr) MemNew (sizeof (Char) * (ualp->newa + 1));
+  MemSet (buf2, 0, sizeof (Char) * (ualp->newa + 1));
+
+  if (SeqPortStreamInt (upp->orig_bsp, ualp->old5, ualp->old5 + ualp->olda - 1, Seq_strand_plus, STREAM_EXPAND_GAPS, buf1, NULL) == upp->update_bsp->length
+      && SeqPortStreamInt (upp->update_bsp, 0, upp->update_bsp->length - 1, Seq_strand_plus, STREAM_EXPAND_GAPS, buf2, NULL) == upp->update_bsp->length
+      && StringCmp (buf1, buf2) == 0) {
+    rval = TRUE;
+  }
+  buf1 = MemFree (buf1);
+  buf2 = MemFree (buf2);
+  return rval;
+}
+
+
 static Boolean 
 UpdateOrExtendOneSequenceEx 
 (UpdatePairPtr             upp,
@@ -12836,6 +13193,7 @@ UpdateOrExtendOneSequenceEx
   Uint2        update_entityID;
   Char         id_txt [128];
   Boolean      deleted_features = FALSE;
+  Boolean      trim_quality_scores = FALSE;
 
   if (upp == NULL || upp->orig_bsp == NULL || upp->update_bsp == NULL
       || uop == NULL || uop->submitter_opts == NULL)
@@ -12905,6 +13263,7 @@ UpdateOrExtendOneSequenceEx
   switch (uop->submitter_opts->sequence_update_type)
   {
     case eSequenceUpdateReplace:
+      trim_quality_scores = OkToTrimQualityScores (upp, ualp);
       ReplaceOneSequence (upp->salp, upp->orig_bsp, upp->update_bsp);
       sequence_update_successful = TRUE;
       rval = sequence_update_successful;
@@ -12996,7 +13355,9 @@ UpdateOrExtendOneSequenceEx
     FixProtRefPtrs (prot_feat_list);        
   }
   
-  if (uop->indexer_opts != NULL && uop->indexer_opts->update_quality_scores
+  if (trim_quality_scores && (uop->indexer_opts == NULL || !uop->indexer_opts->update_quality_scores)) {
+    TrimQualityScoresForSequenceUpdate (upp->orig_bsp, ualp->old5, ualp->old3, log_fp, data_in_log);
+  } else if (uop->indexer_opts != NULL && uop->indexer_opts->update_quality_scores
       && uop->submitter_opts->sequence_update_type == eSequenceUpdateReplace)
   {
     ReplaceQualityScores (upp->orig_bsp, upp->update_bsp, 
@@ -17212,7 +17573,7 @@ static Boolean BioseqListHasFeatures (ValNodePtr bioseq_list)
 }
 
 
-static Boolean EntityIDAlreadyInList (Uint2 entityID, ValNodePtr entityIDList)
+extern Boolean EntityIDAlreadyInList (Uint2 entityID, ValNodePtr entityIDList)
 {
   while (entityIDList != NULL) {
     if ((Uint2)(entityIDList->data.intvalue) == entityID) {
@@ -17621,12 +17982,11 @@ static void LoadUpdateSequenceMapFileBtn (ButtoN b)
   }
 }
 
-extern SeqEntryPtr RestoreFromFile (CharPtr path);
 
 static void UndoUpdates (ButtoN b)
 {
   UpdateMultiSequenceFormPtr usfp;
-  SeqEntryPtr                oldsep, currsep;
+  Uint2                      new_entityID;
   
   usfp = (UpdateMultiSequenceFormPtr) GetObjectExtra (b);
   if (usfp == NULL)
@@ -17636,14 +17996,12 @@ static void UndoUpdates (ButtoN b)
   WatchCursor ();
   Update ();
 
-  SeqEntrySetScope (NULL);
-  oldsep = RestoreFromFile (usfp->undo_file);
-  currsep = GetTopSeqEntryForEntityID (usfp->input_entityID);
-  ReplaceSeqEntryWithSeqEntry (currsep, oldsep, TRUE);
-  SeqEntrySetScope (NULL);
-  usfp->input_entityID = ObjMgrGetEntityIDForChoice (currsep);
-  ObjMgrSetDirtyFlag (usfp->input_entityID, TRUE);
-  ObjMgrSendMsg (OM_MSG_UPDATE, usfp->input_entityID, 0, 0);
+  new_entityID = RestoreEntityIDFromFile (usfp->undo_file, usfp->input_entityID);
+  if (new_entityID != 0) {
+    usfp->input_entityID = new_entityID;
+    ObjMgrSetDirtyFlag (usfp->input_entityID, TRUE);
+    ObjMgrSendMsg (OM_MSG_UPDATE, usfp->input_entityID, 0, 0);
+  }
 
   usfp->num_successful = 0;
   usfp->num_failed = 0;
diff --git a/tools/blast.c b/tools/blast.c
index 25ec1ebf..da5d5212 100644
--- a/tools/blast.c
+++ b/tools/blast.c
@@ -1,7 +1,7 @@
 
-static char const rcsid[] = "$Id: blast.c,v 6.450 2007/05/07 13:30:54 kans Exp $";
+static char const rcsid[] = "$Id: blast.c,v 6.451 2008/01/25 21:15:22 bealer Exp $";
 
-/* $Id: blast.c,v 6.450 2007/05/07 13:30:54 kans Exp $
+/* $Id: blast.c,v 6.451 2008/01/25 21:15:22 bealer Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -50,9 +50,13 @@ Detailed Contents:
 	further manipulation.
 
 ******************************************************************************
- * $Revision: 6.450 $
+ * $Revision: 6.451 $
  *
  * $Log: blast.c,v $
+ * Revision 6.451  2008/01/25 21:15:22  bealer
+ * - Fix synchronization issue with blastpgp -a4 -j4 when composition based
+ *   statistics is used for databases with multiple volumes.
+ *
  * Revision 6.450  2007/05/07 13:30:54  kans
  * added casts for Seq-data.gap (SeqDataPtr, SeqGapPtr, ByteStorePtr)
  *
@@ -6523,9 +6527,25 @@ BLASTPerformSearchWithReadDb (BlastSearchBlkPtr search, Int4 sequence_number)
 {
 	Int4 subject_length;
 	Uint1Ptr subject_seq=NULL;
-
+        
+        /* This mutex should not be necessary - readdb seems to have
+         * synchronization issues when dealing with multiple volumes
+         * from multiple threads.  This mutex fixes the symptom. */
+        
+        static int init_mutex = 0;
+        static TNlmMutex wrap_readdb_mutex = 0;
+        
+        if (! init_mutex) {
+            init_mutex++;
+            NlmMutexInit(& wrap_readdb_mutex);
+        }
+        
+        NlmMutexLock(wrap_readdb_mutex);
+        
 	subject_length = readdb_get_sequence(search->rdfp, sequence_number, &subject_seq);
-
+        
+        NlmMutexUnlock(wrap_readdb_mutex);
+        
 	search->dblen_eff_real += MAX(subject_length-search->length_adjustment, 1);
 	search->subject_id = sequence_number;
 
diff --git a/tools/blfmtutl.c b/tools/blfmtutl.c
index dc166a4c..34ad3868 100644
--- a/tools/blfmtutl.c
+++ b/tools/blfmtutl.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: blfmtutl.c,v 1.31 2007/08/23 19:45:47 coulouri Exp $";
+static char const rcsid[] = "$Id: blfmtutl.c,v 1.35 2008/02/29 20:07:33 coulouri Exp $";
 
 /* ===========================================================================
 *
@@ -36,6 +36,18 @@ Contents: Utilities for BLAST formatting
 /*
 * $Revision: 
 * $Log: blfmtutl.c,v $
+* Revision 1.35  2008/02/29 20:07:33  coulouri
+* bump date
+*
+* Revision 1.34  2008/02/15 21:35:46  coulouri
+* bump date
+*
+* Revision 1.33  2008/01/28 16:34:13  coulouri
+* bump date
+*
+* Revision 1.32  2008/01/25 16:19:22  coulouri
+* bump date
+*
 * Revision 1.31  2007/08/23 19:45:47  coulouri
 * bump date
 *
@@ -144,8 +156,8 @@ Contents: Utilities for BLAST formatting
 #include <jzcoll.h>
 
 /* the version of BLAST. */
-#define BLAST_ENGINE_VERSION "2.2.17"
-#define BLAST_RELEASE_DATE "Aug-26-2007"
+#define BLAST_ENGINE_VERSION "2.2.18"
+#define BLAST_RELEASE_DATE "Mar-02-2008"
 
 #define BUFFER_LENGTH 255
 
diff --git a/tools/kappa.c b/tools/kappa.c
index 5bee6c18..3ce847b2 100644
--- a/tools/kappa.c
+++ b/tools/kappa.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: kappa.c,v 6.87 2006/06/29 17:43:39 papadopo Exp $";
+static char const rcsid[] = "$Id: kappa.c,v 6.90 2008/02/08 21:51:38 camacho Exp $";
 
-/* $Id: kappa.c,v 6.87 2006/06/29 17:43:39 papadopo Exp $ 
+/* $Id: kappa.c,v 6.90 2008/02/08 21:51:38 camacho Exp $ 
 *   ==========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -50,7 +50,7 @@ functions in this file have a 'Kappa_' prefix.  Please adhere to this
 convention to avoid a name clash with functions in blast_kappa.c (the
 name clash can matter in debuggers and search engines.)
 
- $Revision: 6.87 $
+ $Revision: 6.90 $
 
  Revision 6.75  2005/11/07 15:28:56  coulouri
  From Mike Gertz:
@@ -1223,6 +1223,48 @@ Kappa_MatchingSequenceRelease(BlastCompo_MatchingSequence * self)
   self->local_data = NULL;
 }
 
+#define MINUMUM_FRACTION_NEAR_IDENTICAL 0.98
+
+/**
+ * Test whether the aligned parts of two sequences that
+ * have a high-scoring gapless alignment are nearly identical
+ *
+ * @param seqData           subject sequence
+ * @param queryData         query sequence
+ * @param queryOffset   offset for align if there are multiple queries
+ * @param align             information about the alignment
+ * @param rangeOffset       offset for subject sequence (used for tblastn)
+ *
+ * @return                  TRUE if the aligned portions are nearly identical
+ */
+static Boolean testNearIdentical(const BlastCompo_SequenceData *seqData, 
+				 const BlastCompo_SequenceData *queryData, 
+				 const int queryOffset,
+				 const BlastCompo_Alignment *align,
+				 const int rangeOffset)
+{
+  int numIdentical = 0;
+  double fractionIdentical;
+  int qPos, sPos; /*positions in query and subject;*/
+  int qEnd; /*end of query*/
+
+  qPos = align->queryStart - queryOffset;
+  qEnd = align->queryEnd - queryOffset;
+  sPos = align->matchStart - rangeOffset;
+  while (qPos < qEnd)  {
+      if (queryData->data[qPos] == seqData->data[sPos])
+	numIdentical++;
+      sPos++;
+      qPos++;
+  }
+  fractionIdentical = ((double) numIdentical/
+  (double) (align->queryEnd - align->queryStart));
+  if (fractionIdentical >= MINUMUM_FRACTION_NEAR_IDENTICAL)
+    return(TRUE);
+  else
+    return(FALSE);
+}
+
 
 /** Character to use for masked residues */
 #define BLASTP_MASK_RESIDUE eXchar
@@ -1237,11 +1279,21 @@ Kappa_MatchingSequenceRelease(BlastCompo_MatchingSequence * self)
  * @param range         the range, in amino acid coordinates, of data
  *                      to get; includes the translation frame [in]
  * @param seqData       the resulting data [out]
+ * @param queryData     the query sequence [in]
+ * @param queryOffset   offset for align if there are multiple queries
+ * @param align          information about the alignment between query and subject
+ * @param shouldTestIdentical did alignment pass a preliminary test in
+ *                       redo_alignment.c that indicates the sequence
+ *                        pieces may be near identical
  */
 static void
 Kappa_SequenceGetTranslatedRange(const BlastCompo_MatchingSequence * self,
                                  const BlastCompo_SequenceRange * range,
-                                 BlastCompo_SequenceData * seqData )
+                                 BlastCompo_SequenceData * seqData,
+				 const BlastCompo_SequenceData * queryData,
+				 const int queryOffset,
+				 const BlastCompo_Alignment *align,
+				 const Boolean shouldTestIdentical)
 {
   Int4 i;
   Int4 nucleotide_start;        /* position of the first nucleotide to be
@@ -1303,7 +1355,10 @@ Kappa_SequenceGetTranslatedRange(const BlastCompo_MatchingSequence * self,
     seg_slp = BlastBioseqFilter(bsp_temp, BLASTP_MASK_INSTRUCTIONS);
     if (seg_slp) {
       HackSeqLocId(seg_slp, local_data->bsp_db->id);
-      BlastMaskTheResidues(seqData->data, seqData->length,
+      if ((!shouldTestIdentical) || 
+            (shouldTestIdentical && 
+	     (!testNearIdentical(seqData, queryData, queryOffset, align, range->begin))))
+	 BlastMaskTheResidues(seqData->data, seqData->length,
                            BLASTP_MASK_RESIDUE, seg_slp, FALSE, 0);
       seg_slp = SeqLocSetFree(seg_slp);
     }
@@ -1323,6 +1378,12 @@ Kappa_SequenceGetTranslatedRange(const BlastCompo_MatchingSequence * self,
  * @param range         the range, in amino acid coordinates, of data
  *                      to get [in]
  * @param seqData       the sequence data obtained [out]
+ * @param queryData     the query sequence [in]
+ * @param queryOffset   offset for align if there are multiple queries
+ * @param align          information about the alignment between query and subject
+ * @param shouldTestIdentical did alignment pass a preliminary test in
+ *                       redo_alignment.c that indicates the sequence
+ *                        pieces may be near identical
  * 
  * @returns   always 0 (posts a fatal error on failure rather than
  *            returning an error code.)
@@ -1331,12 +1392,18 @@ static int
 Kappa_SequenceGetRange(
   const BlastCompo_MatchingSequence * self,
   const BlastCompo_SequenceRange * range,
-  BlastCompo_SequenceData * seqData )
+  BlastCompo_SequenceData * seqData,
+  const BlastCompo_SequenceData * queryData,
+  const int queryOffset,
+  const BlastCompo_Alignment *align,
+  const Boolean shouldTestIdentical)
 {
   Kappa_SequenceLocalData * local_data = self->local_data;
   if(local_data->prog_number ==  blast_type_tblastn) {
     /* The sequence must be translated. */
-    Kappa_SequenceGetTranslatedRange(self, range, seqData);
+    Kappa_SequenceGetTranslatedRange(self, range, seqData, queryData, 
+				     queryOffset,
+				     align, shouldTestIdentical);
   } else {
     /* The sequence does not need to be translated. */
     /* Obtain the entire sequence (necessary for SEG filtering.) */
@@ -1405,8 +1472,11 @@ Kappa_SequenceGetRange(
       seg_slp =
         BlastBioseqFilter(local_data->bsp_db, BLASTP_MASK_INSTRUCTIONS);
       if (seg_slp) {
-        BlastMaskTheResidues(seqData->data, seqData->length,
-                             BLASTP_MASK_RESIDUE, seg_slp, FALSE, 0);
+      if ((!shouldTestIdentical) || 
+            (shouldTestIdentical && 
+	     (!testNearIdentical(seqData, queryData, queryOffset, align, 0))))
+	    BlastMaskTheResidues(seqData->data, seqData->length,
+				 BLASTP_MASK_RESIDUE, seg_slp, FALSE, 0);
         seg_slp = SeqLocSetFree(seg_slp);
       }
     }
@@ -2082,7 +2152,7 @@ static const Blast_RedoAlignCallbacks
 redo_align_callbacks = {
     Kappa_CalcLambda, Kappa_SequenceGetRange, Kappa_RedoOneAlignment,
     Kappa_NewAlignmentUsingXdrop, Kappa_FreeEditBlock
-};
+    };
 
 
 /** Get a set of alignment parameters, for use by Blast_RedoOneMatch or
@@ -2336,6 +2406,7 @@ RedoAlignmentCore(BlastSearchBlkPtr search,
           ErrPostEx(SEV_FATAL, E_NoMemory, 0, "Failed to allocate memory");
   }
   significantMatches = Nlm_Calloc(numQueries, sizeof(BlastCompo_Heap));
+  ASSERT(options->ethresh != 0.0);
   for (query_index = 0;  query_index < numQueries;  query_index++) {
     status =
       BlastCompo_HeapInitialize(&significantMatches[query_index],
diff --git a/tools/ncbisam.c b/tools/ncbisam.c
index c4c38c79..b79f368b 100644
--- a/tools/ncbisam.c
+++ b/tools/ncbisam.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: ncbisam.c,v 6.33 2006/06/21 13:55:06 camacho Exp $";
+static char const rcsid[] = "$Id: ncbisam.c,v 6.34 2007/11/06 19:20:06 coulouri Exp $";
 
-/* $Id: ncbisam.c,v 6.33 2006/06/21 13:55:06 camacho Exp $
+/* $Id: ncbisam.c,v 6.34 2007/11/06 19:20:06 coulouri Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -31,12 +31,15 @@ static char const rcsid[] = "$Id: ncbisam.c,v 6.33 2006/06/21 13:55:06 camacho E
 *
 * Initial Version Creation Date: 02/24/1997
 *
-* $Revision: 6.33 $
+* $Revision: 6.34 $
 *
 * File Description:
 *         Main file for ISAM library
 *
 * $Log: ncbisam.c,v $
+* Revision 6.34  2007/11/06 19:20:06  coulouri
+* fix memory allocation; resolves blast-rt#15351152
+*
 * Revision 6.33  2006/06/21 13:55:06  camacho
 * Fixed from Ilya Dondoshansky in s_ISAMBufferReadLine
 * Change FILEREAD_BUFFER_SIZE from 1MB to 64k
@@ -2219,7 +2222,7 @@ ISAMErrorCode SISAMFindAllData(ISAMObjectPtr object,
         if (Diff == -1) {
             if(count >= allocated) {
                 allocated += ID_DATA_CHUNK;
-                ids = Realloc(ids, allocated);
+                ids = Realloc(ids, allocated * sizeof(Int4));
             }
             ids[count] = ISAMGetDataNumber(Ptr);
             count++;
diff --git a/tools/pseed3.c b/tools/pseed3.c
index 946a49b4..e5d6c155 100644
--- a/tools/pseed3.c
+++ b/tools/pseed3.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: pseed3.c,v 6.51 2007/03/13 20:40:56 madden Exp $";
+static char const rcsid[] = "$Id: pseed3.c,v 6.53 2008/01/10 16:30:51 bollin Exp $";
 
-/* $Id: pseed3.c,v 6.51 2007/03/13 20:40:56 madden Exp $ */
+/* $Id: pseed3.c,v 6.53 2008/01/10 16:30:51 bollin Exp $ */
 /**************************************************************************
 *                                                                         *
 *                             COPYRIGHT NOTICE                            *
@@ -35,9 +35,15 @@ Maintainer: Alejandro Schaffer
  
 Contents: high-level routines for PHI-BLAST and pseed3
 
-$Revision: 6.51 $
+$Revision: 6.53 $
 
 $Log: pseed3.c,v $
+Revision 6.53  2008/01/10 16:30:51  bollin
+Moved variable declaration to top of code block
+
+Revision 6.52  2008/01/09 19:04:04  merezhuk
+add extra hitArraySz parameter and provide error message if number of hits exceed it.
+
 Revision 6.51  2007/03/13 20:40:56  madden
   - In seedEngineCore, the searchSpEff parameter should be a
     Nlm_FloatHi, not an Nlm_FloatLo
@@ -298,7 +304,7 @@ Char * LIBCALL get_a_pat(
    Uint1Ptr unfilter_seq, Uint1Ptr seq, Int4 len, Boolean is_dna,
    patternSearchItems *patternSearch, seedSearchItems * seedSearch,
    Boolean showDiagnostics, ValNodePtr * error_return, 
-   ValNodePtr PNTR info_vnp)
+   ValNodePtr PNTR info_vnp, Int4 hitArraySz)
 {
 
     Char line[BUF_SIZE]; /*line of pattern description read in*/
@@ -313,6 +319,7 @@ Char * LIBCALL get_a_pat(
                                 sequence*/
     Int4 linePlace; /*index for characters on a line*/
     Char buffer[512];
+    BlastErrorMsgPtr error_msg;
 
     if ((program_flag == PAT_SEED_FLAG) || (program_flag == PAT_MATCH_FLAG)) {
       while (get_pat(fp, seedSearch->pat_space, seedSearch->name_space)) {
@@ -341,6 +348,18 @@ Char * LIBCALL get_a_pat(
 
 	  if (twiceNumHits >0) {
 	    /* copy start and stop positions. */
+	    if( twiceNumHits >= hitArraySz ){
+	      sprintf(buffer,"\nERROR: number of hits %d is larger then hitsArray size: %d ",                        
+		      (int)twiceNumHits,(int)hitArraySz);
+	      //ErrPostEx(SEV_FATAL, 1, 0, buffer);
+		// provide BlastError error_return
+		error_msg = MemNew(sizeof(BlastErrorMsg));
+		error_msg->msg = Nlm_StringSave( buffer );		
+		error_msg->level = 3; /* FATAL */
+		ValNodeAddPointer(error_return, 0, error_msg);
+		
+	      return NULL;
+	    }
 	    for (hitIndex=0; hitIndex<twiceNumHits; hitIndex++)
 		fullHitArray[hitIndex] = hitArray[hitIndex];
 		
@@ -454,6 +473,7 @@ ValNodePtr LIBCALL seedEngineCore(BlastSearchBlkPtr search,
     GapAlignBlkPtr gap_align; /*local holder for gap_align*/
 
     Char buffer[512];
+    Int4 hitArraySz=0;
 
     /* --------------- The end of parameters definition --------------- */
 
@@ -469,8 +489,9 @@ ValNodePtr LIBCALL seedEngineCore(BlastSearchBlkPtr search,
                    patternSearch, &(search->error_return), info_vnp);
         return NULL;
     } 
-    occurArray = (Int4 *) ckalloc(sizeof(Int4)*search->sbp->query_length*2);
-    hitArray = (Int4 *) MemNew(sizeof(Int4)*search->sbp->query_length*2);
+    hitArraySz = search->sbp->query_length*2; /* this is original default */
+    occurArray = (Int4 *) ckalloc(sizeof(Int4)*hitArraySz);
+    hitArray = (Int4 *) MemNew(sizeof(Int4)*hitArraySz);
     
     dbLength = 0;
     readdb_get_totals(search->rdfp, &dbLength, &num_seq);
@@ -480,7 +501,7 @@ ValNodePtr LIBCALL seedEngineCore(BlastSearchBlkPtr search,
       pattern match cannot start*/
     
     
-    while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, &numPatOccur, &effectiveOccurrences, program_flag, unfilter_query, query, search->sbp->query_length, is_dna, patternSearch, seedSearch, showDiagnostics, &(search->error_return), info_vnp)) {
+    while (pattern = get_a_pat(patfp, &pname, occurArray, hitArray, &numPatOccur, &effectiveOccurrences, program_flag, unfilter_query, query, search->sbp->query_length, is_dna, patternSearch, seedSearch, showDiagnostics, &(search->error_return), info_vnp, hitArraySz)) {
         if (patternSearch->patternProbability > PAT_PROB_THRESH &&
             (patternSearch->patternProbability * (FloatHi) dbLength > EXPECT_MATCH_THRESH)) {
             sprintf(buffer, "Pattern %s is too likely to occur in the database to be informative\n", pname);
diff --git a/tools/readdb.c b/tools/readdb.c
index aadc809f..c511197d 100644
--- a/tools/readdb.c
+++ b/tools/readdb.c
@@ -1,6 +1,6 @@
-static char const rcsid[] = "$Id: readdb.c,v 6.529 2007/08/17 15:56:10 papadopo Exp $";
+static char const rcsid[] = "$Id: readdb.c,v 6.535 2008/02/26 18:34:20 kans Exp $";
 
-/* $Id: readdb.c,v 6.529 2007/08/17 15:56:10 papadopo Exp $ */
+/* $Id: readdb.c,v 6.535 2008/02/26 18:34:20 kans Exp $ */
 /*
 * ===========================================================================
 *
@@ -50,7 +50,7 @@ Detailed Contents:
 *
 * Version Creation Date:   3/22/95
 *
-* $Revision: 6.529 $
+* $Revision: 6.535 $
 *
 * File Description: 
 *       Functions to rapidly read databases from files produced by formatdb.
@@ -65,6 +65,24 @@ Detailed Contents:
 *
 * RCS Modification History:
 * $Log: readdb.c,v $
+* Revision 6.535  2008/02/26 18:34:20  kans
+* use SeqDescrAddPointer instead of ValNodeAddPointer/Str
+*
+* Revision 6.534  2007/12/04 19:43:50  madden
+* Index accession.version for swissprot
+*
+* Revision 6.533  2007/11/27 18:51:54  madden
+* More efficient retrievals on string isam indices
+*
+* Revision 6.532  2007/11/15 21:10:49  madden
+* New version of SeqIdE2Index ifdef by REDUCED_E2INDEX_SET
+*
+* Revision 6.531  2007/11/06 20:09:39  coulouri
+* when printing taxonomy info, skip irrelevant sequences if a gi target was specified; fixes blast-rt#15347680
+*
+* Revision 6.530  2007/09/27 17:20:54  madden
+* Add readdb_get_full_filename
+*
 * Revision 6.529  2007/08/17 15:56:10  papadopo
 * 1. Make increment of reference count in readdb_attach atomic
 * 2. Never initialize the reference count to a fixed value when
@@ -5369,7 +5387,7 @@ ValNodePtr readdb_get_asn1_defline(ReadDBFILEPtr rdfp, Int4 sequence_number)
 
     /* Finaly descriptor is created as ... */
     vnp = NULL;
-    vnp = ValNodeAddPointer(&vnp, Seq_descr_user, uop);
+    vnp = SeqDescrAddPointer(&vnp, Seq_descr_user, uop);
     
     return vnp;
 }
@@ -5431,7 +5449,7 @@ ValNodePtr readdb_encode_subset_asn1_defline(ReadDBFILEPtr rdfp,
 
     /* Finaly descriptor is created as ... */
     vnp = NULL;
-    vnp = ValNodeAddPointer(&vnp, Seq_descr_user, uop);
+    vnp = SeqDescrAddPointer(&vnp, Seq_descr_user, uop);
     
     return vnp;
 }
@@ -5506,7 +5524,7 @@ ValNodePtr readdb_get_taxonomy_names(ReadDBFILEPtr rdfp, Int4 sequence_number)
     /* Finaly descriptor is created as ... */
     vnp = NULL;
     if (uop->data != NULL) 
-        vnp = ValNodeAddPointer(&vnp, Seq_descr_user, uop);
+        vnp = SeqDescrAddPointer(&vnp, Seq_descr_user, uop);
     else {
         UserObjectFree(uop);
     }
@@ -5653,7 +5671,7 @@ readdb_get_bioseq_ex(ReadDBFILEPtr rdfp, Int4 sequence_number,
     bsp->repr = Seq_repr_raw;
 
     if (new_defline != NULL)  {
-        bsp->descr = ValNodeAddStr(NULL, Seq_descr_title, new_defline);
+        bsp->descr = SeqDescrAddPointer(NULL, Seq_descr_title, new_defline);
     }
     
     if(rdfp->formatdb_ver > FORMATDB_VER_TEXT) {
@@ -6842,6 +6860,30 @@ readdb_get_filename (ReadDBFILEPtr rdfp)
 }
 
 /*
+Obtains the title of the database.  Note that the return CharPtr is not
+owned by the caller.  It should be copied if the user wishes to modify it.
+*/
+CharPtr LIBCALL
+readdb_get_full_filename (ReadDBFILEPtr rdfp)
+
+{
+    char* retval = NULL;
+
+    if (rdfp == NULL)
+        return NULL;
+    
+    if (!rdfp->aliasfilename)
+        retval = StringSave(rdfp->filename);
+    else {
+       char* path = Nlm_FilePathFind(rdfp->filename);
+       char buffer[PATH_MAX];
+       sprintf(buffer, "%s/%s", path, rdfp->aliasfilename);
+       retval = StringSave(buffer);
+    }
+    return retval;
+}
+
+/*
   Obtains the title of the database.  Note that the return CharPtr is not
   owned by the caller.  It should be copied if the user wishes to modify it.
 */
@@ -7117,7 +7159,7 @@ static Int2 LIBCALLBACK ReadDBBioseqFetchFunc(Pointer data)
             source->org = OrgRefNew();
             source->org->orgname = OrgNameNew();
             source->org->orgname->gcode = rdfsp->db_genetic_code;
-            ValNodeAddPointer(&(bsp->descr), Seq_descr_source, source);
+            SeqDescrAddPointer(&(bsp->descr), Seq_descr_source, source);
         }
 
     sep = SeqEntryNew();
@@ -8352,6 +8394,7 @@ ValNodePtr FDBDestroyMembershipsTable(ValNodePtr tbl)
 }
 
 
+/* #define REDUCED_E2INDEX_SET 1 */
 #ifdef REDUCED_E2INDEX_SET
 /*****************************************************************************
 *
@@ -8367,7 +8410,6 @@ static Boolean SeqIdE2Index (SeqIdPtr anp, FILE *fd, Int4 seq_num,
     TextSeqIdPtr tsip = NULL;
     ObjectIdPtr oid;
     PDBSeqIdPtr psip;
-    Boolean do_gb = FALSE;
     Uint1 tmptype;
     CharPtr tmp, ptr=NULL;
     Char buf[81];
@@ -8379,6 +8421,9 @@ static Boolean SeqIdE2Index (SeqIdPtr anp, FILE *fd, Int4 seq_num,
     if (anp == NULL)
         return FALSE;
     
+    if (anp->choice == SEQID_GI)
+        return TRUE; /* Do not index GI as string. */
+
     switch (anp->choice) {
 
     case SEQID_LOCAL:     /* local */
@@ -8395,7 +8440,6 @@ static Boolean SeqIdE2Index (SeqIdPtr anp, FILE *fd, Int4 seq_num,
         return TRUE;      /* not indexed */
     case SEQID_EMBL:      /* embl */
     case SEQID_DDBJ:      /* ddbj */
-        do_gb = TRUE;     /* also index embl, ddbj as genbank */
     case SEQID_GENBANK:   /* genbank */
     case SEQID_TPG:       /* Third Party Annot/Seq Genbank */
     case SEQID_TPE:       /* Third Party Annot/Seq EMBL */
@@ -8405,9 +8449,13 @@ static Boolean SeqIdE2Index (SeqIdPtr anp, FILE *fd, Int4 seq_num,
         tsip = (TextSeqIdPtr)(anp->data.ptrvalue);
     if ((tsip->version > 0) && (tsip->release == NULL))
         version = tsip->version;
-    break;
-    case SEQID_PIR:       /* pir   */
+        break;
     case SEQID_SWISSPROT: /* swissprot */
+        tsip = (TextSeqIdPtr)(anp->data.ptrvalue);
+    if (tsip->version > 0)
+        version = tsip->version;
+        break;
+    case SEQID_PIR:       /* pir   */
     case SEQID_PRF:       /* prf   */
         tsip = (TextSeqIdPtr)(anp->data.ptrvalue);
         break;
@@ -8426,17 +8474,24 @@ static Boolean SeqIdE2Index (SeqIdPtr anp, FILE *fd, Int4 seq_num,
         break;
     }
     
-    if(tsip == NULL && !sparse) {
+    if(tsip == NULL) {
         SeqIdWrite(anp, buf, PRINTID_FASTA_SHORT, 80);
-        StringLower(buf);
-        fprintf(fd, "%s%c%d\n", buf, ISAM_DATA_CHAR, seq_num);
-    }
+        
+        length = StringLen(buf);
+        for(i = 0; i < length; i++)
+            buf[i] = TO_LOWER(buf[i]);
 
-    if (ptr != NULL) {   /* write a single string */
-    StringMove(buf, ptr);
-        StringLower(buf);
         fprintf(fd, "%s%c%ld\n", buf, ISAM_DATA_CHAR, (long) seq_num);
+        
+    } 
 
+    if (tsip == NULL && ptr != NULL) {   /* write a single string for non TextSeqIDPtr cases. */
+    StringMove(buf, ptr);
+        length = StringLen(buf);
+        for(i = 0; i < length; i++)
+            buf[i] = TO_LOWER(buf[i]);
+        fprintf(fd, "%s%c%ld\n", buf, ISAM_DATA_CHAR, (long) seq_num);
+ 
         chain = TO_LOWER(chain);
 
         if (chain != 0) { /* PDB only. */
@@ -8448,65 +8503,25 @@ static Boolean SeqIdE2Index (SeqIdPtr anp, FILE *fd, Int4 seq_num,
     }
 
     if (tsip != NULL) {   /* separately index accession and locus */
-        if ((tsip->accession != NULL) && (tsip->name != NULL) && !sparse) {
-
-            /* Here is we indexing accession as part of SeqId */
-            tmp = tsip->name;
-            tsip->name = NULL;
-            SeqIdWrite(anp, buf, PRINTID_FASTA_SHORT, 80);
-            StringLower(buf);
-            fprintf(fd, "%s%c%d\n", buf, ISAM_DATA_CHAR, seq_num);
-            tsip->name = tmp;
-
-            /* If accession and locus are different we also print locus */
-            if(StringICmp(tsip->accession, tsip->name)) {
-                
-                tmp = tsip->accession;
-                tsip->accession = NULL;
-                SeqIdWrite(anp, buf, PRINTID_FASTA_SHORT, 80);
-                StringLower(buf);
-                fprintf(fd, "%s%c%d\n", buf, ISAM_DATA_CHAR, seq_num);
-                tsip->accession = tmp;
-            }
-
-        if (version) { /* Index accession without verison. */
-        tsip->version = 0;
-                tmp = tsip->name;
-                tsip->name = NULL;
-                SeqIdWrite(anp, buf, PRINTID_FASTA_SHORT, 80);
-                StringLower(buf);
-                fprintf(fd, "%s%c%d\n", buf, ISAM_DATA_CHAR, seq_num);
-                tsip->name = tmp;
-        tsip->version = version;
-        }
-        }
-
                /* now index as separate strings */
+        if (tsip->name != NULL) {
+            StringMove(buf, tsip->name);
+            length = StringLen(buf);
+            for(i = 0; i < length; i++)
+                buf[i] = TO_LOWER(buf[i]);
+            fprintf(fd, "%s%c%ld\n", buf, ISAM_DATA_CHAR, (long) seq_num);
+        }
         if (tsip->accession != NULL) {
             StringMove(buf, tsip->accession);
-            StringLower(buf);
-            fprintf(fd, "%s%c%d\n", buf, ISAM_DATA_CHAR, seq_num);
-        if (version && !sparse) {
-                fprintf(fd, "%s%.d%c%d\n", buf, version, 
-                        ISAM_DATA_CHAR, seq_num);
-            }
-    }
-
-        if(tsip->name != NULL && 
-           StringICmp(tsip->accession, tsip->name) && !sparse) {
-            StringMove(buf, tsip->name);
-            StringLower(buf);
-            fprintf(fd, "%s%c%d\n", buf, ISAM_DATA_CHAR, seq_num);
-    }
+            length = StringLen(buf);
+            for(i = 0; i < length; i++)
+                buf[i] = TO_LOWER(buf[i]);
+            fprintf(fd, "%s%c%ld\n", buf, ISAM_DATA_CHAR, (long) seq_num);
+            if (version)
+                fprintf(fd, "%s.%d%c%ld\n", buf, version, ISAM_DATA_CHAR, (long) seq_num);
+        }
     }
     
-    if (do_gb && !sparse) {   /* index embl and ddbj as genbank */
-        tmptype = anp->choice;
-        anp->choice = SEQID_GENBANK;
-        SeqIdE2Index(anp, fd, seq_num, sparse);
-        anp->choice = tmptype;
-    }
-
     retval = TRUE;
     return retval;
 }
@@ -8563,9 +8578,13 @@ static Boolean SeqIdE2Index (SeqIdPtr anp, FILE *fd, Int4 seq_num,
         tsip = (TextSeqIdPtr)(anp->data.ptrvalue);
     if ((tsip->version > 0) && (tsip->release == NULL))
         version = tsip->version;
-    break;
-    case SEQID_PIR:       /* pir   */
+        break;
     case SEQID_SWISSPROT: /* swissprot */
+        tsip = (TextSeqIdPtr)(anp->data.ptrvalue);
+    if (tsip->version > 0)
+        version = tsip->version;
+        break;
+    case SEQID_PIR:       /* pir   */
     case SEQID_PRF:       /* prf   */
         tsip = (TextSeqIdPtr)(anp->data.ptrvalue);
         break;
@@ -11546,7 +11565,7 @@ FCMDAccListPtr LIBCALL GetAccList(CharPtr file, Int4Ptr TotalItems)
       
       j= 0;
       while (j < 128  && i < FileLen) { 
-          TmpBuff[j] = file[i];
+          TmpBuff[j] = TO_LOWER(file[i]);
           j++; i++;
           if(isspace((int)file[i]) ||
              file[i] == ',' || /* Comma is valid delimiter */
@@ -11580,6 +11599,44 @@ FCMDAccListPtr LIBCALL GetAccList(CharPtr file, Int4Ptr TotalItems)
       gi = 0;
       if(k == j)
           gi = atol(TmpBuff);
+
+       if (gi == 0) {
+           if (StringChr(TmpBuff, '|') != NULL) {
+               SeqIdPtr sip = SeqIdParse(TmpBuff);
+               SeqIdPtr sip_var = sip;
+               SeqIdPtr best_acc = SeqIdFindBestAccession(sip);
+               if (best_acc)
+               {
+                   switch (best_acc->choice)
+                   {   /* Only TextSeqIdPtrs */
+                      case SEQID_GENBANK:
+                      case SEQID_EMBL:
+                      case SEQID_DDBJ:
+                      case SEQID_PIR:
+                      case SEQID_SWISSPROT:
+                      case SEQID_PRF:
+                      case SEQID_OTHER:
+                      case SEQID_TPG:
+                      case SEQID_TPE:
+                      case SEQID_TPD:
+                      case SEQID_GPIPE:
+                        SeqIdWrite(best_acc, TmpBuff, PRINTID_TEXTID_ACC_VER, 128);
+                        break;
+                      default:
+                        break;
+                   }
+               }
+               while (sip_var)
+               {
+                  if (sip_var->choice == SEQID_GI)
+                  {
+                     gi = sip_var->data.intvalue;
+                     break;
+                  }
+                  sip_var = sip_var->next;
+               }
+           }
+      }
       
       /* If this is valid Accession check and tranfer it to gi */
       
@@ -11647,6 +11704,11 @@ static Boolean Fastacmd_PrintTaxonomyInfo(ReadDBFILEPtr rdfp, Int4 oid,
     /* Print the taxonomy report for each sequence associated with this oid */
     for (bdp_tmp = bdp; bdp_tmp; bdp_tmp = bdp_tmp->next) {
 
+    /* skip irrelevant sequences if a gi target was specified */
+    SeqIdPtr gi = SeqIdFindBest(bdp_tmp->seqid, SEQID_GI);
+    if ( gi && (rdfp->gi_target != 0) && (gi->data.intvalue != rdfp->gi_target) )
+        continue;
+
         MemSet(buf, 0, sizeof(buf));
         SeqIdWrite(bdp_tmp->seqid, buf, PRINTID_FASTA_LONG, sizeof(buf)-1);
 
diff --git a/tools/readdb.h b/tools/readdb.h
index d2f863cb..c8cbb724 100644
--- a/tools/readdb.h
+++ b/tools/readdb.h
@@ -41,7 +41,7 @@ Contents: defines and prototypes used by readdb.c and formatdb.c.
 *
 * Version Creation Date:   3/21/95
 *
-* $Revision: 6.178 $
+* $Revision: 6.179 $
 *
 * File Description: 
 *       Functions to rapidly read databases from files produced by formatdb.
@@ -56,6 +56,9 @@ Contents: defines and prototypes used by readdb.c and formatdb.c.
 *
 * RCS Modification History:
 * $Log: readdb.h,v $
+* Revision 6.179  2007/09/27 17:20:54  madden
+* Add readdb_get_full_filename
+*
 * Revision 6.178  2007/08/21 20:06:07  kans
 * added prototype for FDBCleanUp
 *
@@ -1444,6 +1447,9 @@ NOTE: the CharPtr returned is not owned by the caller!
 */
 CharPtr LIBCALL readdb_get_filename PROTO((ReadDBFILEPtr rdfp));
 
+/* For use by the seq-src to get the alias file name with full path. */
+CharPtr LIBCALL readdb_get_full_filename PROTO((ReadDBFILEPtr rdfp));
+
 /* 
 Get the date the database was formatted. 
 NOTE: the CharPtr returned is not owned by the caller! 
diff --git a/tools/salptool.c b/tools/salptool.c
index 6ba87728..1d794a24 100644
--- a/tools/salptool.c
+++ b/tools/salptool.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: salptool.c,v 6.54 2006/10/23 15:10:58 bollin Exp $";
+static char const rcsid[] = "$Id: salptool.c,v 6.55 2007/08/31 18:46:04 bollin Exp $";
 
 #include <sequtil.h> /* SeqIdDupList */
 #include <salpedit.h>
@@ -1926,7 +1926,8 @@ static SeqPortPtr SeqPortFromAlignmentInterval (Int4 seqstart, Int4 seqstop, Uin
   SeqLocPtr  slp;
   SeqPortPtr spp;
 
-  if (bsp == NULL) return NULL;
+  if (bsp == NULL || seqstart >= bsp->length - 1) return NULL;
+  seqstop = MIN (bsp->length -1, seqstop);
   sinp = SeqIntNew();
   if (sinp == NULL) return NULL;
   sinp->from = seqstart;
diff --git a/tools/seed.h b/tools/seed.h
index 48605eaa..69afb311 100644
--- a/tools/seed.h
+++ b/tools/seed.h
@@ -1,4 +1,4 @@
-/* $Id: seed.h,v 6.21 2007/03/13 20:41:20 madden Exp $
+/* $Id: seed.h,v 6.22 2008/01/09 19:04:04 merezhuk Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
@@ -31,9 +31,12 @@ Author: Alejandro Schaffer
  
 Contents: header file for PHI-BLAST and pseed3.
 
-$Revision: 6.21 $
+$Revision: 6.22 $
 
 $Log: seed.h,v $
+Revision 6.22  2008/01/09 19:04:04  merezhuk
+add extra hitArraySz parameter and provide error message if number of hits exceed it.
+
 Revision 6.21  2007/03/13 20:41:20  madden
   - In the prototype for seedEngineCore, the searchSpEff parameter
     should be a Nlm_FloatHi, not an Nlm_FloatLo
@@ -309,7 +312,7 @@ Char*  LIBCALL get_a_pat PROTO((FILE *fp, Char **name, Int4Ptr hitArray, Int4Ptr
    Uint1Ptr unfilter_seq, Uint1Ptr seq, Int4 len, Boolean is_dna,
    patternSearchItems *patternSearch, seedSearchItems * seedSearch,
    Boolean showDiagnostics, ValNodePtr * error_return, 
-   ValNodePtr PNTR info_vnp));
+   ValNodePtr PNTR info_vnp, Int4 hitArraySz));
 
 
 void LIBCALL quicksort_hits PROTO((Int4 no_of_seq, seedResultItems *seedResults));
diff --git a/tools/tfuns.c b/tools/tfuns.c
index 731c2c6d..98ee51b2 100644
--- a/tools/tfuns.c
+++ b/tools/tfuns.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: tfuns.c,v 6.13 2006/11/07 20:01:24 bollin Exp $";
+static char const rcsid[] = "$Id: tfuns.c,v 6.14 2007/10/10 16:10:17 bollin Exp $";
 
 #include <stdio.h>
 #include <ncbi.h>
@@ -1253,7 +1253,7 @@ static Boolean get_src (GatherContextPtr gcp)
 	return TRUE;
 }
 
-static Int2 GetGcodeFromBioseq(BioseqPtr bsp)
+NLM_EXTERN Int2 GetGcodeFromBioseq(BioseqPtr bsp)
 {
 	GatherScope gs;
 	BioSourcePtr biop;
diff --git a/tools/tfuns.h b/tools/tfuns.h
index 9a26ce96..3840e2aa 100644
--- a/tools/tfuns.h
+++ b/tools/tfuns.h
@@ -65,3 +65,7 @@ void DelFeatFromList PROTO((SeqFeatPtr PNTR gbqp, SeqFeatPtr curq, SeqFeatPtr pr
 
 ValNodePtr GetOrfList PROTO((BioseqPtr bsp, Int2 limit));
 ValNodePtr GetAltList PROTO((ValNodePtr list));
+
+NLM_EXTERN Int2 GetGcodeFromBioseq(BioseqPtr bsp);
+
+
diff --git a/tools/toasn3.c b/tools/toasn3.c
index 572dd3d8..7e0380ca 100644
--- a/tools/toasn3.c
+++ b/tools/toasn3.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: toasn3.c,v 6.95 2007/05/07 13:30:54 kans Exp $";
+static char const rcsid[] = "$Id: toasn3.c,v 6.99 2007/10/10 16:10:17 bollin Exp $";
 
 /*****************************************************************************
 *
@@ -860,51 +860,6 @@ ValNodePtr GetMultBiosource(SeqEntryPtr sep)
 * RemoveEmptyTitleAndPubGenAsOnlyPub removes pub { pub { gen { } } empty pubs
 *****************************************************************************/
 
-/* from utilpub.c */
-static Boolean empty_citgen(CitGenPtr  cit)
-{
-	if (cit == NULL)
-		return TRUE;
-	if (cit->cit)
-		return FALSE;
-	if (cit->authors)
-		return FALSE;
-	if (cit->muid > 0)
-		return FALSE;
-	if (cit->journal)
-		return FALSE;
-	if (cit->volume)
-		return FALSE;
-	if (cit->issue)
-		return FALSE;
-	if (cit->pages)
-		return FALSE;
-	if (cit->date)
-		return FALSE;
-	if (cit->serial_number > 0)
-		return FALSE;
-	if (cit->title)
-		return FALSE;
-	if (cit->pmid > 0)
-		return FALSE;
-	return TRUE;
-}
-
-static Boolean PubIsEffectivelyEmpty (PubdescPtr pdp)
-
-{
-  ValNodePtr       vnp;
-
-  if (pdp == NULL) return FALSE;
-  vnp = pdp->pub;
-  if (vnp != NULL && vnp->next == NULL && vnp->choice == PUB_Gen) {
-    if (empty_citgen ((CitGenPtr) vnp->data.ptrvalue)) {
-      return TRUE;
-    }
-  }
-  return FALSE;
-}
-
 static void RemoveEmptyTitleAndPubGenAsOnlyPub (SeqEntryPtr sep)
 
 {
@@ -2714,32 +2669,6 @@ static BioSourcePtr GetTopBioSourceFromSep (SeqEntryPtr sep)
   return biop;
 }
 
-static Boolean get_src (GatherContextPtr gcp)
-{
-	ValNodePtr	vnp, new;
-	ValNodePtr	PNTR vnpp;
-	
-	vnpp = gcp->userdata;
-	switch (gcp->thistype)
-	{
-		case OBJ_SEQDESC:
-			vnp = (ValNodePtr) (gcp->thisitem);
-			if (vnp->choice == Seq_descr_source) {
-				if (vnp->data.ptrvalue != NULL) {
-					new = SeqDescrNew(NULL);
-					new = MemCopy(new, vnp, sizeof(ValNode));
-					new->next = NULL;
-					*vnpp = new;
-					return FALSE;  /*only top level BioSource will be returned*/
-				}
-			} 
-			break;
-		default:
-			break;
-	}
-	return TRUE;
-}
-
 static void FixPIDDbtag(ValNodePtr PNTR vnpp)
 {
 	ValNodePtr 		vnp;
@@ -3512,37 +3441,11 @@ void EntryChangeGBSource (SeqEntryPtr sep)
 	BioSourcePtr 	biosp;
 	CharPtr 		source=NULL, s, div = NULL;
 	ValNodePtr 		v;
-	/*
-	GatherScope 	gs;
-	Uint2			entityID;	   
-	Uint1 			focus;
-	ValNodePtr 		vnp = NULL;
-	*/
 	Int2			len=0;
 	
 	if (sep == NULL)
 		return;
 
-	/*
-	entityID = ObjMgrGetEntityIDForChoice(sep);
-  	MemSet ((Pointer) (&gs), 0, sizeof (GatherScope));
-	focus = FocusSeqEntry(sep, &gs);
-	MemSet ((Pointer) (gs.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof(Boolean)));
-	gs.ignore[OBJ_SEQDESC] = FALSE;
-	
-	GatherSeqEntry (sep, &vnp, get_src, &gs);
-
-        if(gs.target != NULL)
-            SeqLocFree(gs.target);
-
-	if (vnp == NULL) {
-		ErrPostStr(SEV_WARNING, ERR_SOURCE_NotFound, "BioSource not found");
-		return;
-	}
-	biosp = (BioSourcePtr) vnp->data.ptrvalue;
-	vnp=MemFree(vnp);
-	*/
-
 	biosp = GetTopBioSourceFromSep (sep);
 	if (biosp != NULL) {
 		orp = biosp->org;
@@ -5235,66 +5138,6 @@ void StripTitleFromProtsInNucProts (SeqEntryPtr sep)
   SeqEntryExplore (sep, NULL, StripTitleFromProteinProducts);
 }
 
-static void CleanOrgModList (OrgModPtr PNTR ompp)
-
-{
-  OrgModPtr       next;
-  OrgModPtr       omp;
-  OrgModPtr PNTR  prev;
-
-  if (ompp == NULL) return;
-  prev = ompp;
-  omp = *ompp;
-  while (omp != NULL) {
-    next = omp->next;
-    CleanVisString (&(omp->subname));
-    CleanVisString (&(omp->attrib));
-    if (TASNStringHasNoText (omp->subname)) {
-      *prev = omp->next;
-      omp->next = NULL;
-      OrgModFree (omp);
-    } else {
-      prev = &(omp->next);
-    }
-    omp = next;
-  }
-}
-
-static void CleanSubSourceList (SubSourcePtr PNTR sspp)
-
-{
-  SubSourcePtr       next;
-  SubSourcePtr PNTR  prev;
-  SubSourcePtr       ssp;
-
-  if (sspp == NULL) return;
-  prev = sspp;
-  ssp = *sspp;
-  while (ssp != NULL) {
-    next = ssp->next;
-    if (ssp->subtype != SUBSRC_germline &&
-        ssp->subtype != SUBSRC_rearranged &&
-        ssp->subtype != SUBSRC_transgenic &&
-        ssp->subtype != SUBSRC_environmental_sample &&
-        ssp->subtype != SUBSRC_metagenomic) {
-      CleanVisString (&(ssp->name));
-    }
-    CleanVisString (&(ssp->attrib));
-    if (TASNStringHasNoText (ssp->name) &&
-        ssp->subtype != SUBSRC_germline &&
-        ssp->subtype != SUBSRC_rearranged &&
-        ssp->subtype != SUBSRC_transgenic &&
-        ssp->subtype != SUBSRC_environmental_sample &&
-        ssp->subtype != SUBSRC_metagenomic) {
-      *prev = ssp->next;
-      ssp->next = NULL;
-      SubSourceFree (ssp);
-    } else {
-      prev = &(ssp->next);
-    }
-    ssp = next;
-  }
-}
 
 static void CleanFeatStrings (SeqFeatPtr sfp)
 
@@ -5398,7 +5241,7 @@ static void CleanFeatStrings (SeqFeatPtr sfp)
     case SEQFEAT_BIOSRC :
       biop = (BioSourcePtr) sfp->data.value.ptrvalue;
       orp = biop->org;
-      CleanSubSourceList (&(biop->subtype));
+      CleanSubSourceList (&(biop->subtype), biop->genome);
       break;
     default :
       break;
@@ -5552,7 +5395,7 @@ static void CleanDescStrings (ValNodePtr sdp)
     case Seq_descr_source :
       biop = (BioSourcePtr) sdp->data.ptrvalue;
       orp = biop->org;
-      CleanSubSourceList (&(biop->subtype));
+      CleanSubSourceList (&(biop->subtype), biop->genome);
       break;
     case Seq_descr_molinfo :
       break;
diff --git a/tools/toporg.c b/tools/toporg.c
index 10e25d98..345ca083 100644
--- a/tools/toporg.c
+++ b/tools/toporg.c
@@ -1,4 +1,4 @@
-static char const rcsid[] = "$Id: toporg.c,v 6.99 2007/01/05 17:45:21 bollin Exp $";
+static char const rcsid[] = "$Id: toporg.c,v 6.101 2007/10/25 18:43:45 bollin Exp $";
 
 #include <stdio.h>
 #include <ncbi.h>
@@ -1046,14 +1046,8 @@ BioSourcePtr BioSourceCommon(BioSourcePtr host, BioSourcePtr guest)
 
 static Boolean EmptyBioSource(BioSourcePtr bio)
 {
-	OrgRefPtr org;
-	
-	if (bio->genome == 0 && bio->origin == 0 && bio->org == NULL)
-		return TRUE;
-	if ((org = bio->org) != NULL) {
-		if (org->taxname == NULL && org->common == NULL && org->db == NULL)
-			return TRUE;
-	}
+	if (bio == NULL || bio->org == NULL) return TRUE;
+  if (bio->org->taxname == NULL && bio->org->common == NULL && bio->org->db == NULL) return TRUE;
 	return FALSE;
 }
 
@@ -3286,63 +3280,14 @@ extern void ConvertFullLenPubFeatToDesc (SeqEntryPtr sep)
   DeleteMarkedObjects (0, OBJ_SEQENTRY, (Pointer) sep);
 }
 
-static Boolean ConvertSourceFeatDescProc (GatherObjectPtr gop)
+static Boolean GatherConvertSourceFeatDescProc (GatherObjectPtr gop)
 
 {
-  BioSourcePtr  biop;
-  BioseqPtr     bsp;
-  SubSourcePtr  lastssp;
-  SeqDescPtr    sdp;
-  SeqEntryPtr   sep;
   SeqFeatPtr    sfp;
-  SeqIdPtr      sip;
-  SubSourcePtr  ssp;
-  ValNode       vn;
 
   if (gop->itemtype != OBJ_SEQFEAT) return TRUE;
   sfp = (SeqFeatPtr) gop->dataptr;
-  /* look for biosource features */
-  if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC) return TRUE;
-  /* get bioseq by feature location */
-  sip = SeqLocId (sfp->location);
-  bsp = BioseqFind (sip);
-  if (bsp == NULL) return TRUE;
-  sip = SeqIdFindBest(bsp->id, 0);
-  if (sip == NULL) return TRUE;
-  vn.choice = SEQLOC_WHOLE;
-  vn.extended = 0;
-  vn.data.ptrvalue = (Pointer) sip;
-  vn.next = NULL;
-  /* is feature full length? */
-  if (SeqLocCompare (sfp->location, &vn) != SLC_A_EQ_B) return TRUE;
-  sep = SeqMgrGetSeqEntryForData (bsp);
-  if (sep == NULL) return TRUE;
-  sdp = CreateNewDescriptor (sep, Seq_descr_source);
-  if (sdp == NULL) return TRUE;
-  /* move biosource from feature to descriptor */
-  sdp->data.ptrvalue = sfp->data.value.ptrvalue;
-  sfp->data.value.ptrvalue = NULL;
-  /* flag old feature for removal */
-  sfp->idx.deleteme = TRUE;
-  /* move comment to subsource note */
-  if (sfp->comment == NULL) return TRUE;
-  biop = (BioSourcePtr) sdp->data.ptrvalue;
-  if (biop == NULL) return TRUE;
-  ssp = SubSourceNew ();
-  if (ssp == NULL) return TRUE;
-  ssp->subtype = SUBSRC_other;
-  ssp->name = sfp->comment;
-  sfp->comment = NULL;
-  /* link in at end, since BasicSeqEntry will have sorted this list */
-  if (biop->subtype == NULL) {
-    biop->subtype = ssp;
-  } else {
-    lastssp = biop->subtype;
-    while (lastssp->next != NULL) {
-      lastssp = lastssp->next;
-    }
-    lastssp->next = ssp;
-  }
+  ConvertSourceFeatDescProc (sfp, NULL);
   return TRUE;
 }
 
@@ -3382,7 +3327,7 @@ extern void ConvertFullLenSourceFeatToDesc (SeqEntryPtr sep)
   objMgrFilter [OBJ_SEQFEAT] = TRUE;
 
   GatherObjectsInEntity (0, OBJ_SEQENTRY, (Pointer) sep,
-                         ConvertSourceFeatDescProc, NULL, objMgrFilter);
+                         GatherConvertSourceFeatDescProc, NULL, objMgrFilter);
 
   SeqEntrySetScope (oldscope);
   DeleteMarkedObjects (0, OBJ_SEQENTRY, (Pointer) sep);
diff --git a/util/creaders/alnread.c b/util/creaders/alnread.c
index 59d2f8ee..7be86914 100644
--- a/util/creaders/alnread.c
+++ b/util/creaders/alnread.c
@@ -1,5 +1,5 @@
 /*
- * $Id: alnread.c,v 1.31 2007/01/10 18:20:14 ucko Exp $
+ * $Id: alnread.c,v 1.32 2007/12/29 18:25:42 kazimird Exp $
  *
  * ===========================================================================
  *
@@ -345,15 +345,15 @@ s_ReportDefinitionLines
 
     eip->category = eAlnErr_BadData;
     if (list->string == NULL) {
-        eip->message = malloc (strlen (err_null_format)
-                               + kMaxPrintedIntLen + 1);
+        eip->message = (char*)malloc (strlen (err_null_format)
+                                      + kMaxPrintedIntLen + 1);
         if (eip->message != NULL) {
             sprintf (eip->message, err_null_format, list->num_appearances);
         }
     } else {
-        eip->message = malloc (strlen (err_format)
-                               + strlen (list->string)
-                               + kMaxPrintedIntLen + 1);
+        eip->message = (char*)malloc (strlen (err_format)
+                                      + strlen (list->string)
+                                      + kMaxPrintedIntLen + 1);
         if (eip->message != NULL) {
             sprintf (eip->message, err_format, list->string,
                      list->num_appearances);
@@ -432,7 +432,7 @@ s_ReportBlockLengthError
     eip->category = eAlnErr_BadFormat;
     eip->id = strdup (id);
     eip->line_num = line_num;
-    eip->message = malloc (strlen (err_format) + 2 * kMaxPrintedIntLen + 1);
+    eip->message = (char *)malloc (strlen (err_format) + 2 * kMaxPrintedIntLen + 1);
     if (eip->message != NULL) {
       sprintf (eip->message, err_format, expected_num, actual_num);
     }
@@ -518,7 +518,7 @@ s_ReportBadSequenceLength
     }
     eip->category = eAlnErr_BadFormat;
     eip->id = strdup (id);
-    eip->message = malloc (strlen (format_str) + 50);
+    eip->message = (char *)malloc (strlen (format_str) + 50);
     if (eip->message != NULL) {
         sprintf (eip->message, format_str, expected_length, actual_length);
     }
@@ -614,7 +614,7 @@ s_ReportRepeatedOrganismName
     if (id != NULL ) {
         eip->id = strdup (id);
     }
-    eip->message = malloc (strlen (err_format) + strlen (org_name)
+    eip->message = (char *)malloc (strlen (err_format) + strlen (org_name)
                            + kMaxPrintedIntLen + 1);
     if (eip->message != NULL) {
         sprintf (eip->message, err_format, org_name, second_line_num);
@@ -2411,7 +2411,7 @@ static char * s_ReplaceNexusTypeChar (char *str, char c)
         {
           free (str);
         }
-        str = malloc (2 * sizeof (char));
+        str = (char *)malloc (2 * sizeof (char));
         if (str != NULL)
         {
           str [0] = c;
@@ -2837,7 +2837,7 @@ static char * s_CreateOrderedOrgName (TCommentLocPtr org_clp)
         return NULL;
     }
 
-    ordered_org_name = malloc (org_clp->end - org_clp->start + 2);
+    ordered_org_name = (char *)malloc (org_clp->end - org_clp->start + 2);
     if (ordered_org_name == NULL) {
         return NULL;
     }
@@ -5349,7 +5349,7 @@ static char * s_GetIdFromString (char * str)
     if (len == 0) {
         return NULL;
     }
-    id = malloc (len + 1);
+    id = (char *)malloc (len + 1);
     if (id == NULL) {
         return NULL;
     }
@@ -6025,136 +6025,3 @@ ReadAlignmentFile
     return ReadAlignmentFileEx (readfunc, fileuserdata, errfunc, erroruserdata,
                                 sequence_info, eFalse);
 }
-
-
-/*
- * ===========================================================================
- * $Log: alnread.c,v $
- * Revision 1.31  2007/01/10 18:20:14  ucko
- * Drop s_AddPatternRepeat (obsolete as of R1.30, as s_ReadAlignFileRaw
- * now contains an internal version reworked to be more efficient).
- *
- * Revision 1.30  2006/12/27 13:38:46  bollin
- * Fixed bug in alignment reader and improved performance for large alignments.
- *
- * Revision 1.29  2006/09/14 13:32:29  bollin
- * do not free alphabet in sequence info struct
- *
- * Revision 1.28  2006/09/13 18:34:59  bollin
- * added flag to indicate whether alignment formatting clues were found
- *
- * Revision 1.27  2005/12/12 13:35:30  bollin
- * changed alignment reader code to handle PHYLIP IDs when there are no spaces
- * between the IDs and the sequence.  Note - if there are spaces in the sequence
- * this will not work - the first part of the sequence will be assumed to be part
- * of the sequence ID.
- *
- * Revision 1.26  2005/10/21 15:19:13  bollin
- * added a function to allow the missing, match, and gap characters to be
- * specified in a NEXUS comment for an alignment file
- *
- * Revision 1.25  2005/10/12 20:12:28  bollin
- * when reading an interleaved block alignment, generate errors if duplicate IDs
- * are found.
- *
- * Revision 1.24  2005/06/20 14:59:17  bollin
- * when creating an ordered organism name, stop when the next organism comment
- * is found
- *
- * Revision 1.23  2005/06/06 15:31:34  lavr
- * Explicit (unsigned char) casts in ctype routines
- *
- * Revision 1.22  2005/06/03 17:03:57  lavr
- * Explicit (unsigned char) casts in ctype routines
- *
- * Revision 1.21  2005/05/12 17:41:01  bollin
- * changed cast for ctype classification macros
- *
- * Revision 1.19  2005/05/06 14:24:01  bollin
- * when adding a definition line that follows an organism comment, make sure
- * that the new definition line has the same list position as the organism
- * name
- *
- * Revision 1.18  2005/05/04 18:54:42  bollin
- * removed Linux warnings
- *
- * Revision 1.17  2005/01/13 14:56:42  bollin
- * be sure to skip over segment brackets when reading segments for alignment of
- * segmented sets
- *
- * Revision 1.16  2005/01/10 19:31:09  bollin
- * limit how hard we will try to read a badly formatted alignment
- *
- * Revision 1.15  2004/12/21 15:13:44  bollin
- * handle blocks of organism definition lines in NEXUS files that do not
- * separate the definition lines from the sequence data
- *
- * Revision 1.14  2004/12/02 17:12:18  bollin
- * allow reading of an interleaved alignment with only one block
- *
- * Revision 1.13  2004/12/01 14:14:35  bollin
- * improved detection of consensus lines in Clustal files
- *
- * Revision 1.12  2004/09/17 12:21:48  bollin
- * allow all-gap segments in segmented alignments
- *
- * Revision 1.11  2004/08/11 15:23:07  vakatov
- * Compilation warning fix (unused static func)
- *
- * Revision 1.10  2004/05/20 19:40:24  bollin
- * Made chnages to allow reading of alignments of segmented sets.
- * Also added warnings for when organism lines may be present but improperly
- * formatted.
- *
- * Revision 1.9  2004/03/16 21:05:15  bollin
- * Added some improvements to the portion of the alignment reader that deals
- * with contiguous alignments that do not have a '>' at the beginning of each
- * ID.
- *
- * Revision 1.8  2004/03/16 16:25:38  bollin
- * Added function to recognize a file as ASN.1 and reject immediately
- *
- * Revision 1.7  2004/03/09 21:27:39  bollin
- * in s_InsertNewOffsets, if the list ends while searching for the next pattern, exit immediately (prevents NULL pointer access)
- *
- * Revision 1.6  2004/03/04 19:15:07  bollin
- * file reading now skips over multi-line bracketed comments
- *
- * Revision 1.5  2004/03/04 16:29:32  bollin
- * added skip of taxa comment for PAUP format alignment files
- *
- * Revision 1.4  2004/02/10 16:15:13  bollin
- * now checks for unused lines when finding interleaved blocks, will reject and try other methods if unused lines found after first block found.
- *
- * Revision 1.3  2004/02/05 16:29:32  bollin
- * smarter function for skipping NEXUS comment lines
- *
- * Revision 1.2  2004/02/04 19:49:11  bollin
- * fixed infinite loop condition in s_AugmentOffsetList, properly skip over first non-space column when looking for interleaved block patterns in s_ReadAlignFileRaw
- *
- * Revision 1.1  2004/02/03 16:47:02  ucko
- * Add Colleen Bollin's Toolkit-independent alignment reader.
- *
- * Revision 1.38  2004/01/30 22:46:08  bollin
- * renamed defined variable, fixed typo in comment
- *
- * Revision 1.37  2004/01/30 21:48:14  bollin
- * changes for compatibility with Windows
- *
- * Revision 1.36  2004/01/30 21:33:41  bollin
- * replaced strncasecmp and strncase function calls
- *
- * Revision 1.35  2004/01/29 19:16:27  bollin
- * use EBool for boolean values
- *
- * Revision 1.34  2004/01/29 17:58:11  bollin
- * aligned assignment blocks in New functions
- *
- * Revision 1.33  2004/01/29 17:43:40  bollin
- * added directory specification to alnread.h include line
- *
- * Revision 1.32  2004/01/29 17:41:29  bollin
- * added comment block, id tags, log
- * 
- * ===========================================================================
- */
diff --git a/vibrant/document.c b/vibrant/document.c
index 8247f359..9c461b3e 100644
--- a/vibrant/document.c
+++ b/vibrant/document.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/12/93
 *
-* $Revision: 6.20 $
+* $Revision: 6.21 $
 *
 * File Description:  Converts fielded text into final report in a document
 *
@@ -41,6 +41,10 @@
 * 01-25-94 DGG + JK    Fixed MapDocPoint bug
 *
 * $Log: document.c,v $
+* Revision 6.21  2008/02/13 18:52:08  bollin
+* Added MapDocPointEx, which allows you to prefer the first matching column to
+* the last matching column.
+*
 * Revision 6.20  2006/09/27 18:30:00  kans
 * support for Int4 scroll bars for switching between text and doc views in Sequin (CB)
 *
@@ -3433,7 +3437,7 @@ void GetColParams (DoC d, Int2 item, Int2 col, Int2Ptr pixPos,
 *
 *****************************************************************************/
 
-extern void MapDocPoint (DoC d, PoinT pt, Int2Ptr item, Int2Ptr row, Int2Ptr col, RectPtr rct)
+extern void MapDocPointEx (DoC d, PoinT pt, Int2Ptr item, Int2Ptr row, Int2Ptr col, RectPtr rct, Boolean prefer_first_match_col)
 
 {
   Int2     cl;
@@ -3441,7 +3445,7 @@ extern void MapDocPoint (DoC d, PoinT pt, Int2Ptr item, Int2Ptr row, Int2Ptr col
   DocData  ddata;
   Int2     firstItem;
   Int2     firstLine;
-  Boolean  goOn;
+  Boolean  goOn, found;
   Int2     i;
   Int2     itemNum;
   ItemPtr  itemPtr;
@@ -3501,7 +3505,8 @@ extern void MapDocPoint (DoC d, PoinT pt, Int2Ptr item, Int2Ptr row, Int2Ptr col
                   rw = firstLine + ((pt.y - q.top - leadHeight) / lineHeight) + 1;
                 }
                 if (numCols > 0 && colFmt != NULL) {
-                  for (i = 0; i < numCols; i++) {
+                  found = FALSE;
+                  for (i = 0; i < numCols && !found; i++) {
                     if (pt.x >= colFmt [i].position &&
                         pt.x < colFmt [i].position + colFmt [i].pixWidth) {
                       cl = i + 1;
@@ -3511,6 +3516,9 @@ extern void MapDocPoint (DoC d, PoinT pt, Int2Ptr item, Int2Ptr row, Int2Ptr col
                         rc.right = rc.left + colFmt [i].pixWidth;
                         rc.bottom = rc.top + lineHeight;
                       }
+                      if (prefer_first_match_col) {
+                        found = TRUE;
+                      }
                     }
                   }
                 }
@@ -3542,6 +3550,11 @@ extern void MapDocPoint (DoC d, PoinT pt, Int2Ptr item, Int2Ptr row, Int2Ptr col
   }
 }
 
+extern void MapDocPoint (DoC d, PoinT pt, Int2Ptr item, Int2Ptr row, Int2Ptr col, RectPtr rct)
+{
+  MapDocPointEx (d, pt, item, row, col, rct, FALSE);
+}
+
 /*****************************************************************************
 *
 *   GetDocText (d, item, row, col)
diff --git a/vibrant/document.h b/vibrant/document.h
index 66370f57..fe793301 100644
--- a/vibrant/document.h
+++ b/vibrant/document.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 4/12/93
 *
-* $Revision: 6.3 $
+* $Revision: 6.4 $
 *
 * File Description:  Converts fielded text into final report in a document
 *
@@ -40,6 +40,10 @@
 *
 *
 * $Log: document.h,v $
+* Revision 6.4  2008/02/13 18:52:08  bollin
+* Added MapDocPointEx, which allows you to prefer the first matching column to
+* the last matching column.
+*
 * Revision 6.3  2006/09/27 18:30:00  kans
 * support for Int4 scroll bars for switching between text and doc views in Sequin (CB)
 *
@@ -165,6 +169,9 @@ extern VoidPtr Nlm_GetDocData     PROTO((Nlm_DoC d));
 extern Nlm_CharPtr Nlm_GetDocText PROTO((Nlm_DoC d, Nlm_Int2 item, Nlm_Int2 row, Nlm_Int2 col));
 extern void    Nlm_MapDocPoint    PROTO((Nlm_DoC d, Nlm_PoinT pt, Nlm_Int2Ptr item, Nlm_Int2Ptr row,
                                   Nlm_Int2Ptr col, Nlm_RectPtr rct));
+extern void    Nlm_MapDocPointEx  PROTO((Nlm_DoC d, Nlm_PoinT pt, Nlm_Int2Ptr item, Nlm_Int2Ptr row, 
+                                  Nlm_Int2Ptr col, Nlm_RectPtr rct, Nlm_Boolean prefer_first_match_col));
+
 extern void    Nlm_PrintDocument  PROTO((Nlm_DoC d));
 extern void    Nlm_SaveDocument   PROTO((Nlm_DoC d, FILE *f));
 extern void    Nlm_SaveDocumentItem PROTO((Nlm_DoC d, FILE *f, Nlm_Int2 item));
@@ -276,6 +283,7 @@ extern void Nlm_DisplayFancy  PROTO((Nlm_DoC d, Nlm_CharPtr file, Nlm_ParPtr par
 #define SetDocData Nlm_SetDocData
 #define GetDocData Nlm_GetDocData
 #define GetDocText Nlm_GetDocText
+#define MapDocPointEx Nlm_MapDocPointEx
 #define MapDocPoint Nlm_MapDocPoint
 #define PrintDocument Nlm_PrintDocument
 #define SaveDocument Nlm_SaveDocument
diff --git a/vibrant/image.c b/vibrant/image.c
index aea47c22..324c862a 100644
--- a/vibrant/image.c
+++ b/vibrant/image.c
@@ -27,7 +27,7 @@
 *
 * Author:  Alex Smirnov,  Denis Vakatov
 *
-* $Revision: 6.8 $
+* $Revision: 6.9 $
 *
 * File Description:
 *       Image(pixmap) processing.
@@ -36,80 +36,7 @@
 *
 * Modifications:  
 * --------------------------------------------------------------------------
-* $Log: image.c,v $
-* Revision 6.8  2004/04/01 13:43:08  lavr
-* Spell "occurred", "occurrence", and "occurring"
 *
-* Revision 6.7  2003/11/17 17:03:29  kans
-* changed C++ style comments to C comments
-*
-* Revision 6.6  2002/03/28 13:35:48  kans
-* only include MoreCarbonAccessors.h if not OS_UNIX_DARWIN
-*
-* Revision 6.5  2001/04/05 03:24:12  juran
-* Carbon fixes.
-*
-* Revision 6.4  1999/11/22 14:46:45  thiessen
-* moved _OPENGL code blocks to only vibrant and ncbicn3d libraries
-*
-* Revision 6.3  1999/06/22 15:14:50  lewisg
-* fix image library so that works on linux with > 8 bits
-*
-* Revision 6.2  1998/01/05 20:00:13  vakatov
-* [WIN_X11] Nlm_AllocateImage() -- better diagnostics for mismatching visual
-*
-* Revision 6.1  1997/11/26 21:29:54  vakatov
-* Fixed errors and warnings issued by C and C++ (GNU and Sun) compilers
-*
-* Revision 6.0  1997/08/25 18:55:46  madden
-* Revision changed to 6.0
-*
-* Revision 5.7  1997/06/12 20:52:03  vakatov
-* Lock/UnlockPixMapImage -- check for the NULL image
-*
-* Revision 5.6  1997/06/09 18:55:35  vakatov
-* [WIN_X]  Nlm_ImageShow():  by default, use standard RGB colormap for
-* the image drawing.  +code cleaning.
-*
-* Revision 5.5  1997/05/28 21:15:29  vakatov
-* Nlm_LoadImageGIF():  "pack" the image colors;; fixed Uint1-overflow bug
-*
-* Revision 5.4  1996/11/22 19:46:07  vakatov
-* Implemented function Nlm_LoadImageGIF();
-* added Nlm_ImageGetColorOffset() and Nlm_ImageGetColorMax();
-* slightly modified Nlm_ImageGetBlack()
-*
- * Revision 5.3  1996/07/23  21:57:32  vakatov
- * Do not reinstall colormap if this is identical to the previous one --
- * it eliminates a redundant screen blinking when redrawing the 3D-Viewer
- * [WIN_MOTIF]  Use 32th(instead of 0th) color for background
- *
- * Revision 5.2  1996/06/17  21:57:17  kans
- * use 255 instead of 254 for Nlm_ImageShow on Mac
- *
- * Revision 5.1  1996/06/14  14:30:42  vakatov
- * [WIN_MOTIF] Nlm_AllocateImage() function -- removed redundant color saving
- * [WIN_MOTIF] Nlm_ImageGetBlack() now always return zero
- *
- * Revision 5.0  1996/05/28  13:45:08  ostell
- * Set to revision 5.0
- *
- * Revision 1.8  1996/05/07  18:31:23  vakatov
- * [WIN_MSWIN]  Nlm_AllocateImage() now adjusts the image width
- * (performs sizeof(LONG) alignment),thus avoiding the image picture distortion
- *
- * Revision 1.7  1996/04/23  23:26:24  kans
- * added Mac-specific code to Nlm_SaveImageGIF
- *
- * Revision 1.6  1996/04/23  15:44:48  vakatov
- * Nlm_SaveImageGIF()/X11 accelerated
- *
- * Revision 1.5  1996/04/17  21:40:34  vakatov
- * Implemented "Nlm_SaveImageGIF()" function for MS-Windows and
- * X11 platforms -- "I can save to GIF-file whatever I can see on
- * my monitor".
- * VC log inserted.
- *
 * ==========================================================================
 */
 
@@ -358,6 +285,7 @@ Nlm_Boolean Nlm_AllocateImage ( Nlm_Image image, Nlm_Uint2Ptr width,
   }
 #endif
 #ifdef WIN_MAC
+#ifndef WIN_MAC_QUARTZ
   if ( im->pixelMap == NULL ) {
     im->pixelMap = (PixMap*)MemNew(sizeof(PixMap));
   }
@@ -413,6 +341,7 @@ Nlm_Boolean Nlm_AllocateImage ( Nlm_Image image, Nlm_Uint2Ptr width,
   }
   if ( cTable != NULL ) DisposeCTable(cTable);
 #endif
+#endif
 
   for ( i=saveColors; i<256; i++ )
     im->red[i] = im->green[i] = im->blue[i] = 0;
@@ -779,6 +708,7 @@ void Nlm_DeleteImage(Nlm_Image image)
     }
 #endif
 #ifdef WIN_MAC
+#ifndef WIN_MAC_QUARTZ
   if ( im->pixelMap )
     {
       if ( im->pixelMap->pmTable )
@@ -786,6 +716,7 @@ void Nlm_DeleteImage(Nlm_Image image)
       MemFree( im->pixelMap );
     }
 #endif
+#endif
 
   MemFree( im );
 }
@@ -1107,6 +1038,7 @@ Nlm_Boolean Nlm_ImageShow(Nlm_Image image, Nlm_PoinT p)
 #endif
 
 #ifdef WIN_MAC
+#ifndef WIN_MAC_QUARTZ
   if ( Nlm_LockPixMapImage(image) == NULL ) return FALSE;
   if ( im->imageColorVer != im->imageColorVerOld ){
     if ( im->curWin != NULL ){
@@ -1143,6 +1075,7 @@ Nlm_Boolean Nlm_ImageShow(Nlm_Image image, Nlm_PoinT p)
   BackColor(blackColor);
   Nlm_UnlockPixMapImage(image);
 #endif
+#endif
 
   return TRUE;
 }
@@ -1162,4 +1095,3 @@ Nlm_Uint1 Nlm_ImageGetColorMax(Nlm_Image image)
 {
   return (Nlm_Uint1)(((Nlm_PImagePtr)image)->totalColors - 1);
 }
-
diff --git a/vibrant/ncbidraw.c b/vibrant/ncbidraw.c
index 8f1f550f..ee63a180 100644
--- a/vibrant/ncbidraw.c
+++ b/vibrant/ncbidraw.c
@@ -29,285 +29,14 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.43 $
+* $Revision: 6.44 $
 *
 * File Description: 
 *       Vibrant drawing functions.
 *
 * Modifications:  
 * --------------------------------------------------------------------------
-* $Log: ncbidraw.c,v $
-* Revision 6.43  2007/05/02 20:55:57  kans
-* Nlm_LoadFontData conditional arguments were incorrect WIN_GIF
 *
-* Revision 6.42  2007/05/02 14:55:58  kans
-* preparation for supporting Quartz on Mac
-*
-* Revision 6.41  2006/11/24 20:07:20  kans
-* if Xcode (not MWERKS) have local defines of GetPortAndCall, InvalRect, InvalRgn, ValidRect, ValidRgn
-*
-* Revision 6.40  2006/09/14 19:18:28  ivanov
-* Rollback last changes. All missed defines added to corelib/ncbiwin.h.
-*
-* Revision 6.39  2006/09/14 18:05:45  ivanov
-* Fixed compilation errors on MS Windows
-*
-* Revision 6.38  2006/09/14 14:45:38  kans
-* changes for 64-bit Windows (GC) plus a few CodeWarrior complaints (JK)
-*
-* Revision 6.37  2004/04/14 19:15:50  sinyakov
-* WIN_MSWIN: support X-Windows-like -bg color command line option
-*
-* Revision 6.36  2003/11/17 17:03:30  kans
-* changed C++ style comments to C comments
-*
-* Revision 6.35  2003/03/19 21:13:22  kans
-* protect UNIX version of ScrollRect
-*
-* Revision 6.34  2002/06/13 16:15:12  kans
-* fix includes for OS_UNIX_DARWIN with WIN_MAC (EN) - still bug in vibutils.c file dialog
-*
-* Revision 6.33  2002/03/28 13:35:48  kans
-* only include MoreCarbonAccessors.h if not OS_UNIX_DARWIN
-*
-* Revision 6.32  2002/03/06 20:15:14  northup
-* under X11 cache colors from XAllocColor using a hash table. (EN)
-*
-* Revision 6.31  2002/02/04 19:04:51  kans
-* pass fsp.size to LoadFontData for systemFont on Mac - now label width calculated correctly
-*
-* Revision 6.30  2002/02/04 18:49:15  kans
-* fsp.size = GetDefFontSize () for systemFont on Mac - Mac OS X uses Lucida Grande 13
-*
-* Revision 6.29  2001/08/29 21:14:10  juran
-* Move Carbon forward-compatibility to MoreCarbonAccessors.h.
-* Call InvalRgn instead of InvalWindowRegion.
-*
-* Revision 6.28  2001/04/05 19:45:50  juran
-* Carbon fixes.
-*
-* Revision 6.27  2000/02/07 20:17:35  lewisg
-* minor bug fixes, use gui font for win32
-*
-* Revision 6.26  2000/01/24 16:11:13  lewisg
-* speed up seqid comparison in color manager, make fast windows version of SetColor()
-*
-* Revision 6.25  2000/01/13 23:37:13  beloslyu
-* changes because of port to HP-UX 11.0
-*
-* Revision 6.24  1999/12/21 18:04:23  kans
-* removed MPW/THINKC conditional code, starting upgrade to Carbon compatibility - Churchill
-*
-* Revision 6.23  1999/10/20 23:08:10  vakatov
-* + Nlm_SetCurrentGIF() -- to set Nlm_currentGIF directly.
-* + Nlm_DestroyGIF() -- to destroy Nlm_currentGIF.
-* Nlm_CreateGIF() and Nlm_SaveGIF() -- do not destroy Nlm_currentGIF.
-*
-* Revision 6.22  1999/10/04 18:44:02  vakatov
-* [WIN_GIF] Nlm_SelectFont() -- fixed the way the font gets chosen
-*
-* Revision 6.21  1999/03/17 15:10:47  vakatov
-* + Nlm_XLoadStandardFont() to find a "last-resort" font
-*
-* Revision 6.20  1998/08/12 14:52:26  vakatov
-* [MSWIN] Nlm_DrawLine():  draw at least one point(fix to R6.8)
-*
-* Revision 6.19  1998/07/27 16:49:23  vakatov
-* [WIN_X] AddNewFont():  try "-*-" in addition to "--" in font name spec.
-*
-* Revision 6.18  1998/07/24 21:43:14  vakatov
-* [WIN_MSWIN]  It looks like the metafile driver does not support
-* extended userstyle pens, so use plain pens when writing to metafile
-*
-* Revision 6.17  1998/07/14 16:44:24  vakatov
-* Added VibrantIsGUI() and <internal> Nlm_VibrantSetGUI()
-*
-* Revision 6.16  1998/07/01 22:07:16  vakatov
-* s_AdjustRoundRect():  one-pixel fix
-*
-* Revision 6.15  1998/07/01 18:27:41  vakatov
-* Use "const" qualifier somewhere
-*
-* Revision 6.14  1998/06/26 20:00:17  vakatov
-* Added s_AdjustRoundRect() to adjust the rounding sizes in Nlm_*RoundRect()
-*
-* Revision 6.13  1998/06/25 18:36:29  vakatov
-* [WIN_MSWIN]  Minor 1-pixel adjustments to synchronize graphic primitives
-*
-* Revision 6.12  1998/06/12 16:40:12  kans
-* fixed warnings detected by unix compiler
-*
-* Revision 6.11  1998/06/01 17:20:11  vakatov
-* Added code to draw/fill 90-degree arc/pie (quadrants)
-*
-* Revision 6.10  1998/04/27 15:58:46  vakatov
-* Implemented the drawing of rounded rectangles and ovals for GIF and X11
-*
-* Revision 6.9  1998/02/06 16:10:18  vakatov
-* [WIN_X] SetUpDrawingTools(): fixed mem.leak(default font info)
-*
-* Revision 6.8  1998/02/05 20:07:08  vakatov
-* [X11,MSWIN]  Made DrawLine() always draw the last and the first point
-* (to be in-sync with GIF and MAC)
-*
-* Revision 6.7  1997/12/12 21:08:20  kans
-* a number of symbols changed in the latest CodeWarrior release, now using headers from Apple
-*
-* Revision 6.6  1997/11/26 21:29:59  vakatov
-* Fixed errors and warnings issued by C and C++ (GNU and Sun) compilers
-*
-* Revision 6.5  1997/11/04 23:32:49  vakatov
-* [WIN_X] #ULTRA_SPARC_X_SERVER_BUG -- workaround to set foreground color
-* when the stippling is in effect -- see Nlm_XSetForeground() for details.
-*
-* Revision 6.4  1997/09/16 20:34:15  vakatov
-* Added Nlm_FitStringWidth();  for now, it is implemented as native
-* for [WIN_X] and generic for all other platforms.
-* [WIN_X]  Fixed bug in Nlm_AddNewFont() which disabled the font
-* matching algorithm
-*
-* Revision 6.3  1997/09/11 00:00:38  vakatov
-* [WIN_X] Nlm_EraseRect():  use XGetGCValues() to retrieve curr. fill style
-*
-* Revision 6.2  1997/09/10 18:23:35  vakatov
-* [WIN_X] Nlm_EraseRect():  temp. switch fill style to FillSolid
-*
-* Revision 6.1  1997/09/09 23:53:36  vakatov
-* [WIN_GIF]  Nlm_Solid() -- reset the drawing pattern to solid
-*
-* Revision 5.22  1997/08/19 19:28:01  vakatov
-* [WIN_GIF]  Implemented Nlm_SelectPattern()-related features
-*
-* Revision 5.21  1997/07/23 19:42:17  vakatov
-* Added Nlm_PaintStringEx function(text + position)
-*
-* Revision 5.20  1997/07/18 15:18:39  vakatov
-* [!WIN_GIF] +Dummy Nlm_CreateGIF() and Nlm_SaveGIF();  /return FALSE/
-*
-* Revision 5.19  1997/07/10 21:49:21  vakatov
-* [WIN_X]  Now able to manage windows having different depths(and
-* different visuals and GC).
-*
-* Revision 5.18  1997/06/18 19:46:27  vakatov
-* [WIN_GIF]  Do not use WIN_MAC/MSWIN/MOTIF-specific fields of the
-* Nlm_FontRec struct.
-*
-* Revision 5.17  1997/06/09 18:54:33  vakatov
-* [WIN_X]  Nlm_XAllocColor() moved to "vibwndws.c";  Nlm_SetupColor()
-* removed at all;  use Nlm_VibrantDefaultColormap() and Nlm_XAllocColor()
-* instead of 0 and XAllocColor() in most cases in order to use
-* standard colormap rather than the default one.
-* [ALL]  Renamed("Local__" - prefixed) static coordination transformation funcs
-* whose name conflicts with the global ones;  +other code cleaning...
-*
-* Revision 5.16  1997/06/04 16:12:05  vakatov
-* [WIN_MSWIN] PaintStringWin() has been removed again(see also R5.14)
-*
-* Revision 5.15  1997/06/04 00:05:12  kans
-* support for Japanese by Tomo Koike of DDBJ
-*
-* Revision 5.14  1997/05/08 14:05:27  vakatov
-* [WIN_MSWIN] PaintStringWin() is obsolete; replaced by MoveTo + PaintString
-*
- * Revision 5.13  1997/05/06  20:03:44  vakatov
- * [WIN_GIF] Nlm_CreateGIF(): Boolean --> Nlm_Boolean (by J.Kuzio)
- *
- * Revision 5.12  1997/05/06  18:39:52  vakatov
- * [WIN32] Nlm_SetPenDash() -- added #WIN_MSWIN cpp condition
- *
- * Revision 5.11  1997/04/22  17:32:28  vakatov
- * [WIN_X] Nlm_DrawLine() -- correction of R5.6 for p1.[xy] > p2.[xy]
- *
- * Revision 5.10  1997/04/04  22:46:42  vakatov
- * [WIN_MSWIN]  Added static HFONT2Font() function;  since now,
- * "Nlm_systemFont" and "Nlm_programFont" are to be printed using
- * the matching logical fonts obtained with HFONT2Font().
- *
- * Revision 5.9  1997/01/29  16:41:22  kans
- * using StringNCpy_0
- *
- * Revision 5.8  1996/12/11  22:29:19  vakatov
- * [WIN_MSWIN]  Nlm_ResetDrawingTools():  reset prevPenHDC to ensure
- * proper brush pattern setting in some exotic cases
- *
- * Revision 5.7  1996/12/04  21:17:19  vakatov
- * [WIN_X] Nlm_InvertRect():  use GXinvert both on b/w and color displays
- *
- * Revision 5.6  1996/12/04  16:12:08  vakatov
- * [WIN_X]  Made Nlm_DrawLine() always draw the last point;  Nlm_MoveTo() now
- * implemented via a call to Nlm_DrawLine().
- *
- * Revision 5.5  1996/11/21  22:26:22  vakatov
- * [WIN_X]  Made Nlm_LineTo() and Nlm_DrawLine() draw last point
- *
- * Revision 5.4  1996/11/21  18:50:59  vakatov
- * [WIN_MOTIF]  Rectangle and Polygon drawing sync. to other platforms
- *
- * Revision 5.3  1996/10/28  19:33:04  vakatov
- * [WIN_MOTIF]  Use Nlm_VibrantDefaultColormap() instead of the display
- * default colormap everywhere in the color handling code.
- *
- * Revision 5.2  1996/10/01  18:17:37  vakatov
- * [WIN_X]  Added auxiliary static routine Nlm_XAllocColor() in order to
- * provide a uniform way of the color allocating;  on the color
- * allocation error, it now returns "Black" pixel rather than "White".
- *
- * Revision 5.1  1996/09/30  19:54:08  vakatov
- * [WIN_X, WIN_NT]  Added Nlm_SetPenDash() to allow advanced line dashing
- * [WIN_MSWIN]  Nlm_PaintRect() -- synchronize it with Nlm_FrameRect(),
- * Nlm_FrameOval(), etc. (left + 1, bottom + 1)
- *
- * Revision 5.0  1996/05/28  13:45:08  ostell
- * Set to revision 5.0
- *
- * Revision 4.13  1996/05/10  21:12:33  vakatov
- * Added UpdateColorTable() function to allow the user to read his color
- * preferencies from an external config.-file in format:
- * <index> <red> <green> <blue> [<name>];
- * <name> is optional and it is only used in the WIN_MOTIF-based
- * applications to get hardware-independent named colors, if possible.
- *
- * Revision 4.12  1996/04/15  19:31:56  tatiana
- * add Boolean transparent to Nlm_CreateGIF()
- *
- * Revision 4.11  1996/02/01  22:42:01  smirnov
- * AS: problem with symbols in clipboard is fixed
- *
- * Revision 4.10  1996/02/01  18:42:53  smirnov
- * AS: fix bug: draw a small rectangle
- *
- * Revision 4.9  1996/01/31  18:47:32  smirnov
- * fix copy&paste bug
- *
- * Revision 4.8  1995/12/22  19:42:33  smirnov
- * AS: Fixed bug in GIF version of DrawText()
- *
- * Revision 4.7  1995/11/27  15:47:55  kans
- * fixed FrameArc (VL + JK)
- *
- * Revision 4.6  1995/11/27  15:13:41  kans
- * corrections to font height, etc. functions (VL)
- *
- * Revision 4.4  1995/11/14  13:42:05  kans
- * fixes to AddNewFont (VL)
- *
- * Revision 4.3  1995/11/07  15:47:22  smirnov
- * add GIF generator (Alex Smirnov)
- *
- * Revision 4.2  1995/09/12  17:59:35  ostell
- * fixes for MS windows text to metafile
- *
- * Revision 4.1  1995/09/12  00:39:10  ostell
- * changes for text to appear in windows metafiles
- *
- * Revision 4.0  1995/07/26  13:51:04  ostell
- * force revision to 4.0
- *
- * Revision 2.41  1995/07/14  17:48:26  kans
- * new CopyPixmap (AS)
- *
- * Revision 2.40  1995/06/07  21:23:38  kans
- * RecreateBrushes problem fixed (AS)
 * ==========================================================================
 */
 
@@ -372,11 +101,41 @@ Nlm_Boolean  Nlm_nowPrinting = FALSE;
 #endif
 
 #ifdef WIN_MAC
-RGBColor     Nlm_RGBforeColor;
-RGBColor     Nlm_RGBbackColor;
 #ifdef WIN_MAC_QUARTZ
+CFMutableArrayRef Nlm_QContextStack = 0;
+static void Nlm_PushQContext( CGContextRef ctx )
+{
+  if (!Nlm_QContextStack)
+    Nlm_QContextStack = CFArrayCreateMutable (NULL, 0, NULL);
+  CFArrayAppendValue (Nlm_QContextStack, ctx);
+}
+static CGContextRef Nlm_PeekQContext (void)
+{
+  if (!Nlm_QContextStack)
+    return NULL;
+  
+  CFIndex count = CFArrayGetCount (Nlm_QContextStack);
+  return count ? (CGContextRef)CFArrayGetValueAtIndex (Nlm_QContextStack, count - 1) : NULL;
+}
+static CGContextRef Nlm_PopQContext (void)
+{
+  if (!Nlm_QContextStack)
+    return NULL;
+  
+  void *ret = Nlm_PeekQContext();
+  CFIndex count = CFArrayGetCount (Nlm_QContextStack);
+  if (count)
+    CFArrayRemoveValueAtIndex (Nlm_QContextStack, count - 1);
+  return ret;
+}
+
+WindowRef Nlm_QWindow = 0;
+Nlm_QuartzColor Nlm_QuartzForeColor;
+Nlm_QuartzColor Nlm_QuartzBackColor;
 Nlm_Boolean  Nlm_hasColorQD = TRUE;
 #else
+RGBColor     Nlm_RGBforeColor;
+RGBColor     Nlm_RGBbackColor;
 Nlm_Boolean  Nlm_hasColorQD = FALSE;
 #endif
 #endif
@@ -554,54 +313,76 @@ static Nlm_Uint1 dkGrayPat[]= {0x77, 0xDD, 0x77, 0xDD, 0x77, 0xDD, 0x77, 0xDD};
 static Nlm_Uint1 blackPat []= {0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF};
 #endif /* WIN_X | WIN_GIF */
 
+#ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
-CGContextRef Nlm_QContext = 0;
-#endif
+extern  void  Nlm_SetPort (CGContextRef ctx)
+{
+  if (Nlm_PeekQContext()) {
+    CGContextSynchronize(Nlm_PeekQContext());
+    CGContextRelease(Nlm_PeekQContext());
+    Nlm_PopQContext();
+  }
+  
+  if (ctx)
+  {
+	Nlm_PushQContext(ctx);
+	CGContextRetain(Nlm_PeekQContext());
+  }
+// QUARTZ_FIXME: some of this might be useful, somehow
+//  if (grafptr != 0) {
+//    CGAffineTransform textTransform;
+//    
+//    GetPortBounds(grafptr, &pBounds);
+//    pHeight = pBounds.bottom - pBounds.top;
+//    QDBeginCGContext(grafptr, &Nlm_PeekQContext());
+//    CGContextTranslateCTM(Nlm_PeekQContext(), 0, pHeight);
+//    CGContextScaleCTM(Nlm_PeekQContext(), 1.0f, -1.0f);
+//    
+//    textTransform = CGAffineTransformMakeScale(1.0f, -1.0f);
+//    CGContextSetTextMatrix(Nlm_PeekQContext(), textTransform);
+//  } else {
+//    Nlm_PeekQContext() = 0;
+//  }
+}
 
-#ifdef WIN_MAC
-extern  void  Nlm_SetPort (GrafPtr grafptr)
+void  Nlm_PushPort (CGContextRef ctx)
 {
-#ifdef WIN_MAC_QUARTZ
-  CGrafPtr  oldPort;
-  Rect      pBounds;
-  int       pHeight;
+  Nlm_PushQContext (ctx);
+}
 
-  GetPort(&oldPort);
-  if (Nlm_QContext != 0 ) {
-    CGContextSynchronize(Nlm_QContext);
-    QDEndCGContext(oldPort, &Nlm_QContext);
-    Nlm_QContext = 0;
-  }
+CGContextRef Nlm_PopPort (void)
+{
+  return Nlm_PopQContext ();
+}
 
-  SetPort (grafptr);
-  if (grafptr != 0) {
-    CGAffineTransform textTransform;
-    
-    GetPortBounds(grafptr, &pBounds);
-    pHeight = pBounds.bottom - pBounds.top;
-    QDBeginCGContext(grafptr, &Nlm_QContext);
-    CGContextTranslateCTM(Nlm_QContext, 0, pHeight);
-    CGContextScaleCTM(Nlm_QContext, 1.0f, -1.0f);
-    
-    textTransform = CGAffineTransformMakeScale(1.0f, -1.0f);
-    CGContextSetTextMatrix(Nlm_QContext, textTransform);
-  } else {
-    Nlm_QContext = 0;
-  }
 #else
+extern  void  Nlm_SetPort (GrafPtr grafptr)
+{
   SetPort (grafptr);
-#endif
 }
+#endif
 
 extern void Nlm_SetPortWindowPort(Nlm_WindowTool wptr)
 {
 #ifdef WIN_MAC_QUARTZ
-  Nlm_SetPort(GetWindowPort(wptr));
+    Nlm_QWindow = wptr;
 #else
     SetPortWindowPort(wptr);
 #endif
 }
 
+#ifdef WIN_MAC_QUARTZ
+WindowRef Nlm_GetQuartzCurrentWindow (void)
+{
+  return Nlm_QWindow;
+}
+
+void Nlm_SetGraphicNeedsDisplay (Nlm_GraphiC graphic)
+{
+  HIViewSetNeedsDisplay (HIViewGetRoot (Nlm_ParentWindowPtr (graphic)), 1);
+}
+#endif
+
 #endif
 
 #ifdef WIN_MSWIN
@@ -796,7 +577,7 @@ extern void Nlm_SetPenDash(Nlm_Uint1 offset, Nlm_Uint1 dash, Nlm_Uint1 gap)
     float dashes[2];
     dashes[0] = (float) dash;
     dashes[1] = (float) gap;
-    CGContextSetLineDash(Nlm_QContext, (float) offset, dashes, 2);
+    CGContextSetLineDash(Nlm_PeekQContext(), (float) offset, dashes, 2);
   }
 #else
   Nlm_Dashed();
@@ -990,15 +771,25 @@ extern COLORREF Nlm_crBackColor;
 extern HBRUSH Nlm_hbrWindowBackground;
 #endif
 
+#ifdef WIN_MAC_QUARTZ
+static void Nlm_SelectQuartzColor (Nlm_QuartzColor c)
+{
+  CGContextSetRGBFillColor  (Nlm_PeekQContext(), c.r, c.g, c.b, 1.0);
+  CGContextSetRGBStrokeColor(Nlm_PeekQContext(), c.r, c.g, c.b, 1.0);
+}
+#endif
 
 extern void Nlm_ResetDrawingTools (void)
 {
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
-  CGContextSetLineWidth(Nlm_QContext, 1.0);
-  CGContextSetLineDash(Nlm_QContext, 0, NULL, 0);
-  CGContextSetAlpha(Nlm_QContext, 1.0);
-  Nlm_SelectColor(Nlm_RGBforeColor.red, Nlm_RGBforeColor.green, Nlm_RGBforeColor.blue);
+  if (Nlm_PeekQContext())
+  {
+    CGContextSetLineWidth(Nlm_PeekQContext(), 1.0);
+    CGContextSetLineDash(Nlm_PeekQContext(), 0, NULL, 0);
+    CGContextSetAlpha(Nlm_PeekQContext(), 1.0);
+    Nlm_SelectQuartzColor(Nlm_QuartzForeColor);
+  }
 #else
   PenNormal ();
   PenMode (patCopy);
@@ -1139,7 +930,7 @@ static void Local__RecTToRectTool(Nlm_RectPtr src, Nlm_RectTool PNTR dst)
 
 extern void Nlm_CopyMode (void)
 {
-#ifdef WIN_MAC
+#if defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ)
   PenMode (patCopy);
   TextMode (srcOr);
 #endif
@@ -1160,9 +951,8 @@ extern void Nlm_CopyMode (void)
 }
 
 extern void Nlm_MergeMode (void)
-
 {
-#ifdef WIN_MAC
+#if defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ)
   PenMode (patOr);
   TextMode (srcOr);
 #endif
@@ -1187,9 +977,8 @@ extern void Nlm_MergeMode (void)
 }
 
 extern void Nlm_InvertMode (void)
-
 {
-#ifdef WIN_MAC
+#if defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ)
   PenMode (patXor);
   TextMode (srcXor);
 #endif
@@ -1214,10 +1003,8 @@ extern void Nlm_InvertMode (void)
 }
 
 extern void Nlm_EraseMode (void)
-
-
 {
-#ifdef WIN_MAC
+#if defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ)
   PenMode (patBic);
   TextMode (srcBic);
 #endif
@@ -1447,8 +1234,10 @@ extern void Nlm_SelectColor (Nlm_Uint1 red, Nlm_Uint1 green, Nlm_Uint1 blue)
 {
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
-  CGContextSetRGBFillColor  (Nlm_QContext, red/255.0, green/255.0, blue/255.0, 1.0);
-  CGContextSetRGBStrokeColor(Nlm_QContext, red/255.0, green/255.0, blue/255.0, 1.0);
+  Nlm_QuartzForeColor.r = red/255.0;
+  Nlm_QuartzForeColor.g = green/255.0;
+  Nlm_QuartzForeColor.b = blue/255.0;
+  Nlm_SelectQuartzColor (Nlm_QuartzForeColor);
 #else
   RGBColor   color;
   Nlm_Uint2  bl;
@@ -1581,11 +1370,16 @@ extern Nlm_Uint4 Nlm_GetColorRGB (Nlm_Uint1 red, Nlm_Uint1 green,
 extern Nlm_Uint4 Nlm_GetColor (void)
 {
 #ifdef WIN_MAC
-  Nlm_Uint1  colors [4];
-  RGBColor   foreColor;
+  Nlm_Uint1  colors [4] = { 0 };
   Nlm_Int4   fgColor;
+#ifdef WIN_MAC_QUARTZ
+  colors[0] = 0;
+  colors[1] = Nlm_QuartzForeColor.r * 255.0;
+  colors[2] = Nlm_QuartzForeColor.g * 255.0;
+  colors[3] = Nlm_QuartzForeColor.b * 255.0;
+#else
+  RGBColor   foreColor;
 
-  fgColor = 0;
   if (Nlm_hasColorQD) {
     GetForeColor (&foreColor);
     colors [0] = 0;
@@ -1593,15 +1387,18 @@ extern Nlm_Uint4 Nlm_GetColor (void)
     colors [2] = (Nlm_Uint1) (foreColor.green >> 8);
     colors [3] = (Nlm_Uint1) (foreColor.blue >> 8);
     fgColor = *((Nlm_Int4Ptr) colors);
-#if !OPAQUE_TOOLBOX_STRUCTS
-  } else {
+  }
+#endif
+  fgColor = (colors[0] << 24) | (colors[1] << 16) | (colors[2] << 8) | colors[3];
+#if !defined( WIN_MAC_QUARTZ ) && !defined( OPAQUE_TOOLBOX_STRUCTS )
+  if (!Nlm_hasColorQD) {
       GrafPtr port;
     GetPort (&port);
     if (port != NULL) {
       fgColor = port->fgColor;
     }
-#endif
   }
+#endif
   return (Nlm_Uint4) fgColor;
 #endif
 #ifdef WIN_MSWIN
@@ -1667,12 +1464,12 @@ extern void Nlm_SetColor (Nlm_Uint4 color)
     foreColor.green = gn << 8 | gn;
     foreColor.blue = bl << 8 | bl;
     RGBForeColor (&foreColor);
-#endif
   } else {
     GetPort (&port);
     if (port != NULL) {
       ForeColor ((Nlm_Int4) color);
     }
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -1695,6 +1492,13 @@ extern void Nlm_InvertColors (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  Nlm_QuartzColor temp = Nlm_QuartzForeColor;
+  Nlm_QuartzForeColor = Nlm_QuartzBackColor;
+  Nlm_QuartzBackColor = temp;
+  
+  Nlm_SelectQuartzColor (Nlm_QuartzForeColor);
+#else
   RGBColor  backColor;
   RGBColor  foreColor;
 
@@ -1714,10 +1518,10 @@ extern void Nlm_InvertColors (void)
       bkColor = port->bkColor;
       ForeColor (bkColor);
       BackColor (fgColor);
-    }
 #endif
   }
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_Int4  bkColor;
   Nlm_Int4  fgColor;
@@ -1837,8 +1641,8 @@ extern void Nlm_DecodeColor (Nlm_Uint4 color, Nlm_Uint1Ptr red,
 extern void Nlm_Dark (void)
 {
 #ifdef WIN_MAC_QUARTZ
-  CGContextSetGrayFillColor  (Nlm_QContext, .25, 1.0);
-  CGContextSetGrayStrokeColor(Nlm_QContext, .25, 1.0);
+  CGContextSetGrayFillColor  (Nlm_PeekQContext(), .25, 1.0);
+  CGContextSetGrayStrokeColor(Nlm_PeekQContext(), .25, 1.0);
 #elif defined(WIN_MAC)
   PenPat ((ConstPatternParam) dkGrayPat);
 #endif
@@ -1856,8 +1660,8 @@ extern void Nlm_Dark (void)
 extern void Nlm_Medium (void)
 {
 #ifdef WIN_MAC_QUARTZ
-  CGContextSetGrayFillColor  (Nlm_QContext, .5, 1.0);
-  CGContextSetGrayStrokeColor(Nlm_QContext, .5, 1.0);
+  CGContextSetGrayFillColor  (Nlm_PeekQContext(), .5, 1.0);
+  CGContextSetGrayStrokeColor(Nlm_PeekQContext(), .5, 1.0);
 #elif defined(WIN_MAC)
   PenPat ((ConstPatternParam) grayPat);
 #endif
@@ -1875,8 +1679,8 @@ extern void Nlm_Medium (void)
 extern void Nlm_Light (void)
 {
 #ifdef WIN_MAC_QUARTZ
-  CGContextSetGrayFillColor  (Nlm_QContext, .75, 1.0);
-  CGContextSetGrayStrokeColor(Nlm_QContext, .75, 1.0);
+  CGContextSetGrayFillColor  (Nlm_PeekQContext(), .75, 1.0);
+  CGContextSetGrayStrokeColor(Nlm_PeekQContext(), .75, 1.0);
 #elif defined(WIN_MAC)
   PenPat ((ConstPatternParam) ltGrayPat);
 #endif
@@ -1893,13 +1697,14 @@ extern void Nlm_Light (void)
 
 extern void Nlm_Empty (void)
 {
-#ifdef WIN_MAC_QUARTZ
-  CGContextSetGrayFillColor  (Nlm_QContext, 1.0, 1.0);
-  CGContextSetGrayStrokeColor(Nlm_QContext, 1.0, 1.0);
-#endif
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  CGContextSetGrayFillColor  (Nlm_PeekQContext(), 1.0, 1.0);
+  CGContextSetGrayStrokeColor(Nlm_PeekQContext(), 1.0, 1.0);
+#else
   PenPat ((ConstPatternParam) whitePat);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_SelectPattern (PS_SOLID, 1, whitePat, ATT_PATTERN);
 #endif
@@ -1943,7 +1748,7 @@ extern void Nlm_SetPenPattern (Nlm_VoidPtr pattern)
       ptr++;
     }
 #ifdef WIN_MAC_QUARTZ
-    CGContextSetLineDash(Nlm_QContext, 0, pat, 8);
+    CGContextSetLineDash(Nlm_PeekQContext(), 0, pat, 8);
 #else
     PenPat ((ConstPatternParam) pat);
 #endif
@@ -1979,9 +1784,9 @@ extern void Nlm_SetPenPattern (Nlm_VoidPtr pattern)
 extern void Nlm_Solid (void)
 { /* Reset *both* line stile and drawing pattern to SOLID */
 #ifdef WIN_MAC_QUARTZ
-  CGContextSetGrayFillColor  (Nlm_QContext, 0.0, 1.0);
-  CGContextSetGrayStrokeColor(Nlm_QContext, 0.0, 1.0);
-  CGContextSetLineDash(Nlm_QContext, 0, NULL, 0);
+  CGContextSetGrayFillColor  (Nlm_PeekQContext(), 0.0, 1.0);
+  CGContextSetGrayStrokeColor(Nlm_PeekQContext(), 0.0, 1.0);
+  CGContextSetLineDash(Nlm_PeekQContext(), 0, NULL, 0);
 #elif defined(WIN_MAC)
   PenPat ((ConstPatternParam) blackPat);
 #endif
@@ -2006,7 +1811,7 @@ extern void Nlm_Dotted (void)
 {
 #ifdef WIN_MAC_QUARTZ
   float dashes[] = { 1.0, 1.0 };
-  CGContextSetLineDash(Nlm_QContext, 0, dashes, 2);
+  CGContextSetLineDash(Nlm_PeekQContext(), 0, dashes, 2);
 #elif defined(WIN_MAC)
   PenPat ((ConstPatternParam) dotPat);
 #endif
@@ -2029,7 +1834,7 @@ extern void Nlm_Dashed (void)
 {
 #ifdef WIN_MAC_QUARTZ
   float dashes[] = { 3.0, 1.0 };
-  CGContextSetLineDash(Nlm_QContext, 0, dashes, 2);
+  CGContextSetLineDash(Nlm_PeekQContext(), 0, dashes, 2);
 #elif defined(WIN_MAC)
   PenPat ((ConstPatternParam) dashPat);
 #endif
@@ -2051,8 +1856,8 @@ extern void Nlm_Dashed (void)
 extern void Nlm_WidePen (Nlm_Int2 width)
 {
 #ifdef WIN_MAC_QUARTZ
-  CGContextSetLineDash(Nlm_QContext, 0, NULL, 0);
-  CGContextSetLineWidth(Nlm_QContext, (float) width);
+  CGContextSetLineDash(Nlm_PeekQContext(), 0, NULL, 0);
+  CGContextSetLineWidth(Nlm_PeekQContext(), (float) width);
 #elif defined(WIN_MAC)
   PenPat ((ConstPatternParam) blackPat);
   PenSize (width, width);
@@ -3069,7 +2874,7 @@ extern void Nlm_SelectFont (Nlm_FonT f)
     }
 #ifdef WIN_MAC
 #ifdef WIN_MAC_ATSUI
-/*    CGContextSelectFont(Nlm_QContext,fdata.fontspec.name, fdata.size, kCGEncodingMacRoman); */
+    Nlm_fontInUse = f;
 #else
     TextFont (fdata.number);
     TextSize (fdata.size);
@@ -3120,8 +2925,12 @@ extern Nlm_Int2 Nlm_CharWidth (Nlm_Char ch)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  return Nlm_TextWidth (&ch, 1);
+#else
   return (CharWidth (ch));
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_Char  str [4];
 
@@ -3163,7 +2972,7 @@ extern Nlm_Int2 Nlm_TextWidth(const Nlm_Char* text, size_t len)
   /* convert the string to Unicode */
   cfString = CFStringCreateWithCString(kCFAllocatorDefault, text, kCFStringEncodingMacRoman);
   if (cfString == NULL)
-    return;
+    return 0;
   cfsLen = CFStringGetLength(cfString);
   unicodeString = CFStringGetCharactersPtr(cfString);
   if (unicodeString == NULL) {
@@ -3222,16 +3031,49 @@ extern Nlm_Int2 Nlm_TextWidth(const Nlm_Char* text, size_t len)
  return 0;
 }
 
+#if defined(WIN_MAC) && defined(WIN_MAC_ATSUI)
+static ATSFontMetrics Nlm_CurrentATSUFontMetrics(void)
+{
+  Nlm_FontTool curStyle = Nlm_FontToATSUStyle (Nlm_fontInUse);
+  ATSUFontID fontID = 0;
+  ByteCount ignoredCount;
+  
+  ATSUGetAttribute (curStyle, kATSUFontTag, sizeof (fontID), &fontID, &ignoredCount);
+  
+  ATSFontRef font = FMGetATSFontRefFromFont (fontID);
+  
+  ATSFontMetrics metrics;
+  memset (&metrics, 0, sizeof (metrics));
+  ATSFontGetHorizontalMetrics (font, kATSOptionFlagsDefault, &metrics);
+  
+  return metrics;
+}
+
+static Fixed Nlm_CurrentATSUFontSize(void)
+{
+  Nlm_FontTool curStyle = Nlm_FontToATSUStyle (Nlm_fontInUse);
+  Fixed size = 0;
+  ByteCount ignoredCount;
+  
+  ATSUGetAttribute (curStyle, kATSUSizeTag, sizeof (size), &size, &ignoredCount);
+  
+  return size;
+}
+#endif
 
 extern Nlm_Int2 Nlm_Ascent (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_ATSUI
+  return ceilf (Nlm_CurrentATSUFontMetrics().ascent * Nlm_CurrentATSUFontSize() / 65536.0);
+#else
   FontInfo  fontinfo;
 
   GetFontInfo (&fontinfo);
   return (fontinfo.ascent);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_Int2  rsult;
 
@@ -3259,11 +3101,15 @@ extern Nlm_Int2 Nlm_Descent (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_ATSUI
+  return ceilf (-Nlm_CurrentATSUFontMetrics().descent * Nlm_CurrentATSUFontSize() / 65536.0);
+#else
   FontInfo  fontinfo;
 
   GetFontInfo (&fontinfo);
   return (fontinfo.descent);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_Int2  rsult;
 
@@ -3291,11 +3137,15 @@ extern Nlm_Int2 Nlm_Leading (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_ATSUI
+  return ceilf (Nlm_CurrentATSUFontMetrics().leading * Nlm_CurrentATSUFontSize() / 65536.0);
+#else
   FontInfo  fontinfo;
 
   GetFontInfo (&fontinfo);
   return (fontinfo.leading);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_Int2  rsult;
 
@@ -3317,11 +3167,15 @@ extern Nlm_Int2 Nlm_FontHeight (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_ATSUI
+  return Nlm_Ascent() + Nlm_Descent();
+#else
   FontInfo  fontinfo;
 
   GetFontInfo (&fontinfo);
   return (fontinfo.ascent + fontinfo.descent);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_Int2  rsult;
 
@@ -3350,11 +3204,15 @@ extern Nlm_Int2 Nlm_LineHeight (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_ATSUI
+  return Nlm_Ascent() + Nlm_Descent() + Nlm_Leading();
+#else
   FontInfo  fontinfo;
 
   GetFontInfo (&fontinfo);
   return (fontinfo.ascent + fontinfo.descent + fontinfo.leading);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_Int2  rsult;
 
@@ -3383,11 +3241,15 @@ extern Nlm_Int2 Nlm_MaxCharWidth (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_ATSUI
+  return ceilf (Nlm_CurrentATSUFontMetrics().maxAdvanceWidth * Nlm_CurrentATSUFontSize() / 65536.0);
+#else
   FontInfo  fontinfo;
 
   GetFontInfo (&fontinfo);
   return (fontinfo.widMax);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_Int2  rsult;
 
@@ -3502,7 +3364,7 @@ extern void Nlm_GetPen (Nlm_PointPtr pt)
   CGPoint cgp;
   
   if (pt != NULL) {
-    cgp = CGContextGetPathCurrentPoint(Nlm_QContext);
+    cgp = CGContextGetPathCurrentPoint(Nlm_PeekQContext());
   }
   pt->x = cgp.x;
   pt->y = cgp.y;
@@ -3533,6 +3395,17 @@ extern void Nlm_GetPen (Nlm_PointPtr pt)
 #endif
 }
 
+void Nlm_SetPenWidth(Nlm_Int2 width)
+{
+#ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  CGContextSetLineWidth (Nlm_PeekQContext(), width);
+#else
+  PenSize (width, width);
+#endif
+#endif
+}
+
 extern void Nlm_PaintChar (Nlm_Char ch)
 
 {
@@ -3540,7 +3413,7 @@ extern void Nlm_PaintChar (Nlm_Char ch)
 #ifdef WIN_MAC_QUARTZ
   Nlm_PoinT pt;
   Nlm_GetPen (& pt);
-  CGContextShowTextAtPoint(Nlm_QContext, pt.x, pt.y, & ch, 1);
+  CGContextShowTextAtPoint(Nlm_PeekQContext(), pt.x, pt.y, & ch, 1);
 #else
   DrawChar (ch);
 #endif
@@ -3645,7 +3518,7 @@ extern void Nlm_PaintString (Nlm_CharPtr text)
 
   /* draw where? */
   Nlm_GetPen (&pt);
-  /* CGContextShowTextAtPoint(Nlm_QContext, pt.x, pt.y, text, Nlm_StringLen (text)); */
+  /* CGContextShowTextAtPoint(Nlm_PeekQContext(), pt.x, pt.y, text, Nlm_StringLen (text)); */
   err = ATSUDrawText(layout, kATSUFromTextBeginning, kATSUToTextEnd, 
        Long2Fix(pt.x),  Long2Fix(pt.y));
   
@@ -3720,7 +3593,7 @@ void CDECL Nlm_PaintText (char *format, ...)
     va_end(args);
     Nlm_GetPen (&pt);
 #ifdef WIN_MAC_QUARTZ
-    CGContextShowTextAtPoint(Nlm_QContext, pt.x, pt.y, str, Nlm_StringLen (str));
+    CGContextShowTextAtPoint(Nlm_PeekQContext(), pt.x, pt.y, str, Nlm_StringLen (str));
 #else
     if (Nlm_StringLen (str) > 0) {
       Nlm_CtoPstr (str);
@@ -3823,7 +3696,7 @@ extern void Nlm_DrawText (Nlm_RectPtr r, Nlm_CharPtr text,
   if (r != NULL) {
     Nlm_EraseRect (r);
     if (text != NULL && len > 0) {
-      cfString = CFStringCreateWithBytes(kCFAllocatorDefault, text, len, kCFStringEncodingMacRoman, false);
+      cfString = CFStringCreateWithBytes(kCFAllocatorDefault, (UInt8 *)text, len, kCFStringEncodingMacRoman, false);
       if (cfString == NULL)
         return;
       cfsLen = CFStringGetLength(cfString);
@@ -3848,29 +3721,30 @@ extern void Nlm_DrawText (Nlm_RectPtr r, Nlm_CharPtr text,
       aStyle = Nlm_FontToATSUStyle(Nlm_fontInUse);  
       
 #ifdef WIN_MAC_QUARTZ
-      boxOptions.optionTags |= kTXNUseCGContextRefMask;
-      boxOptions.options = Nlm_QContext;
-      CGContextSaveGState(Nlm_QContext);
-      /* need to undo the coordinate transforms, otherwise the text comes out upside down. */
-      CGContextScaleCTM(Nlm_QContext, 1.0f, -1.0f);
-      {  
-        Rect      pBounds;
-        int       pHeight;
-        GrafPtr   grafptr;
-
-        GetPort(&grafptr);
-        GetPortBounds(grafptr, &pBounds);
-        pHeight = pBounds.bottom - pBounds.top;
-        CGContextTranslateCTM(Nlm_QContext, 0, -pHeight);
-      }
+// QUARTZ_FIXME: is this stuff necessary?
+//      boxOptions.optionTags |= kTXNUseCGContextRefMask;
+//      boxOptions.options = Nlm_PeekQContext();
+//      CGContextSaveGState(Nlm_PeekQContext());
+//      /* need to undo the coordinate transforms, otherwise the text comes out upside down. */
+//      CGContextScaleCTM(Nlm_PeekQContext(), 1.0f, -1.0f);
+//      {  
+//        Rect      pBounds;
+//        int       pHeight;
+//        GrafPtr   grafptr;
+//
+//        GetPort(&grafptr);
+//        GetPortBounds(grafptr, &pBounds);
+//        pHeight = pBounds.bottom - pBounds.top;
+//        CGContextTranslateCTM(Nlm_PeekQContext(), 0, -pHeight);
+//      }
 #endif
 
       err = TXNDrawCFStringTextBox(cfString, &rtool, aStyle, &boxOptions);
       CFRelease(cfString);
       
-#ifdef WIN_MAC_QUARTZ
-      CGContextRestoreGState(Nlm_QContext);
-#endif
+//#ifdef WIN_MAC_QUARTZ
+//      CGContextRestoreGState(Nlm_PeekQContext());
+//#endif
     }
   }
 
@@ -4100,7 +3974,7 @@ extern void Nlm_MoveTo (Nlm_Int2 x, Nlm_Int2 y)
 {
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
-  CGContextMoveToPoint(Nlm_QContext, x, y);
+  CGContextMoveToPoint(Nlm_PeekQContext(), x, y);
 #else
   MoveTo (x, y);
 #endif
@@ -4126,9 +4000,9 @@ extern void Nlm_LineTo (Nlm_Int2 x, Nlm_Int2 y)
 {
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
-  CGContextAddLineToPoint(Nlm_QContext, x, y);
-  CGContextStrokePath(Nlm_QContext);
-  CGContextMoveToPoint(Nlm_QContext, x, y);
+  CGContextAddLineToPoint(Nlm_PeekQContext(), x, y);
+  CGContextStrokePath(Nlm_PeekQContext());
+  CGContextMoveToPoint(Nlm_PeekQContext(), x, y);
 #else
   LineTo (x, y);
 #endif
@@ -4162,9 +4036,9 @@ extern void Nlm_DrawLine (Nlm_PoinT pt1, Nlm_PoinT pt2)
 {
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
-  CGContextMoveToPoint(Nlm_QContext, pt1.x, pt1.y);
-  CGContextAddLineToPoint(Nlm_QContext, pt2.x, pt2.y);
-  CGContextStrokePath(Nlm_QContext);
+  CGContextMoveToPoint(Nlm_PeekQContext(), pt1.x, pt1.y);
+  CGContextAddLineToPoint(Nlm_PeekQContext(), pt2.x, pt2.y);
+  CGContextStrokePath(Nlm_PeekQContext());
 #else
   MoveTo (pt1.x, pt1.y);
   LineTo (pt2.x, pt2.y);
@@ -4275,8 +4149,12 @@ extern Nlm_Boolean Nlm_PtInRgn (Nlm_PoinT pt, Nlm_RegioN rgn)
   Nlm_RgnTool    ntool;
   Nlm_Boolean    rsult;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  CGPoint        ptool;
+#else
   Nlm_PointTool  ptool;
 #endif
+#endif
 #ifdef WIN_GIF
   Nlm_RecT r;
 #endif
@@ -4285,9 +4163,14 @@ extern Nlm_Boolean Nlm_PtInRgn (Nlm_PoinT pt, Nlm_RegioN rgn)
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    ptool = Nlm_PoinTToCGPoint (pt);
+    rsult = HIShapeContainsPoint (ntool, &ptool);
+#else
     Local__PoinTToPointTool (pt, &ptool);
     rsult = PtInRgn (ptool, ntool);
 #endif
+#endif
 #ifdef WIN_MSWIN
     rsult = (Nlm_Boolean) PtInRegion (ntool, pt.x, pt.y);
 #endif
@@ -4367,7 +4250,15 @@ static void Nlm_LoadNormalized (Nlm_RectPtr dst, Nlm_RectPtr src)
 extern Nlm_Boolean Nlm_SectRect(Nlm_RectPtr src1, Nlm_RectPtr src2,
                                 Nlm_RectPtr dst)
 {
-#if defined(WIN_MSWIN) || defined(WIN_MAC)
+#ifdef WIN_MAC_QUARTZ
+  CGRect r1 = Nlm_RecTToCGRect (*src1);
+  CGRect r2 = Nlm_RecTToCGRect (*src2);
+  CGRect d  = CGRectIntersection (r1, r2);
+  *dst = Nlm_CGRectToRecT (d);
+  return !CGRectIsNull (d);
+#else
+
+#if defined(WIN_MSWIN) || (defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ))
   Nlm_Boolean   rsult;
   Nlm_RectTool  rtool1;
   Nlm_RectTool  rtool2;
@@ -4380,7 +4271,7 @@ extern Nlm_Boolean Nlm_SectRect(Nlm_RectPtr src1, Nlm_RectPtr src2,
   if (!src1  ||  !src2  ||  !dst)
     return FALSE;
 
-#if defined(WIN_MSWIN) || defined(WIN_MAC)
+#if defined(WIN_MSWIN) || (defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ))
   Local__RecTToRectTool(src1, &rtool1);
   Local__RecTToRectTool(src2, &rtool2);
 #ifdef WIN_MSWIN
@@ -4405,13 +4296,22 @@ extern Nlm_Boolean Nlm_SectRect(Nlm_RectPtr src1, Nlm_RectPtr src2,
       }
     return TRUE;
 #endif
+#endif
 }
 
 
 extern Nlm_Boolean Nlm_UnionRect(Nlm_RectPtr src1, Nlm_RectPtr src2,
                                  Nlm_RectPtr dst)
 {
-#if defined(WIN_MSWIN) || defined(WIN_MAC)
+#ifdef WIN_MAC_QUARTZ
+  CGRect r1 = Nlm_RecTToCGRect (*src1);
+  CGRect r2 = Nlm_RecTToCGRect (*src2);
+  CGRect d  = CGRectUnion (r1, r2);
+  *dst = Nlm_CGRectToRecT (d);
+  return CGRectIsEmpty (d);
+#else
+
+#if defined(WIN_MSWIN) || (defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ))
   Nlm_Boolean   rsult;
   Nlm_RectTool  rtool1;
   Nlm_RectTool  rtool2;
@@ -4424,7 +4324,7 @@ extern Nlm_Boolean Nlm_UnionRect(Nlm_RectPtr src1, Nlm_RectPtr src2,
   if (!src1  ||  !src2  ||  !dst)
     return FALSE;
 
-#if defined(WIN_MSWIN) || defined(WIN_MAC)
+#if defined(WIN_MSWIN) || (defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ))
   Local__RecTToRectTool(src1, &rtool1);
   Local__RecTToRectTool(src2, &rtool2);
 #ifdef WIN_MSWIN
@@ -4445,6 +4345,7 @@ extern Nlm_Boolean Nlm_UnionRect(Nlm_RectPtr src1, Nlm_RectPtr src2,
   dst->bottom = MAX(rect1.bottom, rect2.bottom);
   return TRUE;
 #endif
+#endif
 }
 
 
@@ -4482,6 +4383,9 @@ extern Nlm_Boolean Nlm_RectInRgn (Nlm_RectPtr r, Nlm_RegioN rgn)
   Nlm_RgnTool   ntool;
   Nlm_Boolean   rsult;
   Nlm_RectTool  rtool;
+#ifdef WIN_MAC_QUARTZ
+  CGRect        rect;
+#endif
 #ifdef WIN_GIF
   Nlm_RecT      rect;
 #endif
@@ -4491,8 +4395,13 @@ extern Nlm_Boolean Nlm_RectInRgn (Nlm_RectPtr r, Nlm_RegioN rgn)
     Local__RecTToRectTool (r, &rtool);
     ntool = (Nlm_RgnTool) rgn;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    rect = Nlm_RecTToCGRect (*r);
+    rsult = HIShapeIntersectsRect (ntool, &rect);
+#else
     rsult = RectInRgn (&rtool, ntool);
 #endif
+#endif
 #ifdef WIN_MSWIN
     rsult = (Nlm_Boolean) RectInRegion (ntool, &rtool);
 #endif
@@ -4519,11 +4428,11 @@ extern void Nlm_EraseRect (Nlm_RectPtr r)
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
   CGRect cgr;
-  cgr = Nlm_RecTToCGRect(r);
-  CGContextSaveGState(Nlm_QContext);
+  cgr = Nlm_RecTToCGRect(*r);
+  CGContextSaveGState(Nlm_PeekQContext());
   Nlm_White();
-  CGContextFillRect(Nlm_QContext, cgr);
-  CGContextRestoreGState(Nlm_QContext);
+  CGContextFillRect(Nlm_PeekQContext(), cgr);
+  CGContextRestoreGState(Nlm_PeekQContext());
 #else
   EraseRect (&rtool);
 #endif
@@ -4563,8 +4472,8 @@ extern void Nlm_FrameRect (Nlm_RectPtr r)
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
   CGRect rtool;
-  rtool = Nlm_RecTToCGRect(r);
-  CGContextStrokeRect(Nlm_QContext, rtool);
+  rtool = Nlm_RecTToCGRect(*r);
+  CGContextStrokeRect(Nlm_PeekQContext(), rtool);
 #else
   Nlm_RectTool  rtool;
 
@@ -4644,8 +4553,8 @@ extern void Nlm_PaintRect(Nlm_RectPtr r)
   
 #ifdef WIN_MAC_QUARTZ
   CGRect cgr;
-  cgr = Nlm_RecTToCGRect(r);
-  CGContextFillRect(Nlm_QContext, cgr);
+  cgr = Nlm_RecTToCGRect(*r);
+  CGContextFillRect(Nlm_PeekQContext(), cgr);
 #elif defined(WIN_MAC)
   if (rtool.right == rtool.left) {
     rtool.right = rtool.left + 1;
@@ -4727,8 +4636,13 @@ extern void Nlm_ScrollRect (Nlm_RectPtr r, Nlm_Int2 dx, Nlm_Int2 dy)
 
   if (r != NULL) {
     Local__RecTToRectTool (r, &rtool);
+#ifdef WIN_MAC_QUARTZ
+// QUARTZ_FIXME: might want to do a little more than this
+    HIViewSetNeedsDisplay (HIViewGetRoot (Nlm_QWindow), 1);
+#else
     ScrollRect (&rtool, dx, dy, (Nlm_RgnTool) Nlm_scrollRgn);
     InvalRgn ((Nlm_RgnTool) Nlm_scrollRgn);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -4870,13 +4784,13 @@ extern void Nlm_EraseOval (Nlm_RectPtr r)
 #if defined(WIN_MAC_QUARTZ)
   {
   CGRect cgr;
-  cgr = Nlm_RecTToCGRect(r);
-  Nlm_addOvalToPath(Nlm_QContext, cgr);
+  cgr = Nlm_RecTToCGRect(*r);
+  Nlm_addOvalToPath(Nlm_PeekQContext(), cgr);
   }
-  CGContextSaveGState(Nlm_QContext);
+  CGContextSaveGState(Nlm_PeekQContext());
   Nlm_White();
-  CGContextFillPath(Nlm_QContext);
-  CGContextRestoreGState(Nlm_QContext);
+  CGContextFillPath(Nlm_PeekQContext());
+  CGContextRestoreGState(Nlm_PeekQContext());
 #else
   EraseOval(&rtool);
 #endif
@@ -4925,10 +4839,10 @@ extern void Nlm_FrameOval(Nlm_RectPtr r)
 #if defined(WIN_MAC_QUARTZ)
   {
   CGRect cgr;
-  cgr = Nlm_RecTToCGRect(r);
-  Nlm_addOvalToPath(Nlm_QContext, cgr);
+  cgr = Nlm_RecTToCGRect(*r);
+  Nlm_addOvalToPath(Nlm_PeekQContext(), cgr);
   }
-  CGContextStrokePath(Nlm_QContext);
+  CGContextStrokePath(Nlm_PeekQContext());
 #else
   FrameOval(&rtool);
 #endif
@@ -4966,10 +4880,10 @@ extern void Nlm_PaintOval(Nlm_RectPtr r)
 #if defined(WIN_MAC_QUARTZ) 
   {
   CGRect cgr;
-  cgr = Nlm_RecTToCGRect(r);
-  Nlm_addOvalToPath(Nlm_QContext, cgr);
+  cgr = Nlm_RecTToCGRect(*r);
+  Nlm_addOvalToPath(Nlm_PeekQContext(), cgr);
   }
-  CGContextFillPath(Nlm_QContext);
+  CGContextFillPath(Nlm_PeekQContext());
 #else
   PaintOval(&rtool);
 
@@ -5007,7 +4921,12 @@ extern void Nlm_InvertOval(Nlm_RectPtr r)
   Local__RecTToRectTool(r, &rtool);
 
 #if   defined(WIN_MAC)
+#ifdef WIN_MAC_QUARTZ
+/* QUART_FIXME: can't invert, what to do? */
+  Nlm_PaintOval (r);
+#else
   InvertOval (&rtool);
+#endif
 
 #elif defined(WIN_MSWIN)
   if ( Nlm_currentHDC ) {
@@ -5090,13 +5009,13 @@ extern void Nlm_EraseRoundRect(Nlm_RectPtr r, Nlm_Int2 ovlWid, Nlm_Int2 ovlHgt)
 #if defined(WIN_MAC_QUARTZ)
   {
   CGRect cgr;
-  cgr = Nlm_RecTToCGRect(r);
-  addRoundedRectToPath(Nlm_QContext, cgr, ovlWid, ovlHgt);
+  cgr = Nlm_RecTToCGRect(*r);
+  addRoundedRectToPath(Nlm_PeekQContext(), cgr, ovlWid, ovlHgt);
   }
-  CGContextSaveGState(Nlm_QContext);
+  CGContextSaveGState(Nlm_PeekQContext());
   Nlm_White();
-  CGContextFillPath(Nlm_QContext);
-  CGContextRestoreGState(Nlm_QContext);
+  CGContextFillPath(Nlm_PeekQContext());
+  CGContextRestoreGState(Nlm_PeekQContext());
 #else
   EraseRoundRect(&rtool, ovlWid, ovlHgt);
 #endif
@@ -5149,10 +5068,10 @@ extern void Nlm_FrameRoundRect(Nlm_RectPtr r, Nlm_Int2 ovlWid, Nlm_Int2 ovlHgt)
 #if defined(WIN_MAC_QUARTZ)
   {
   CGRect cgr;
-  cgr = Nlm_RecTToCGRect(r);
-  addRoundedRectToPath(Nlm_QContext, cgr, ovlWid, ovlHgt);
+  cgr = Nlm_RecTToCGRect(*r);
+  addRoundedRectToPath(Nlm_PeekQContext(), cgr, ovlWid, ovlHgt);
   }
-  CGContextStrokePath(Nlm_QContext);
+  CGContextStrokePath(Nlm_PeekQContext());
 #else
   FrameRoundRect(&rtool, ovlWid, ovlHgt);
 #endif
@@ -5195,10 +5114,10 @@ extern void Nlm_PaintRoundRect(Nlm_RectPtr r, Nlm_Int2 ovlWid, Nlm_Int2 ovlHgt)
 #if defined(WIN_MAC_QUARTZ)
   {
   CGRect cgr;
-  cgr = Nlm_RecTToCGRect(r);
-  addRoundedRectToPath(Nlm_QContext, cgr, ovlWid, ovlHgt);
+  cgr = Nlm_RecTToCGRect(*r);
+  addRoundedRectToPath(Nlm_PeekQContext(), cgr, ovlWid, ovlHgt);
   }
-  CGContextFillPath(Nlm_QContext);
+  CGContextFillPath(Nlm_PeekQContext());
 #else
   PaintRoundRect(&rtool, ovlWid, ovlHgt);
 #endif
@@ -5239,7 +5158,12 @@ extern void Nlm_InvertRoundRect(Nlm_RectPtr r,
   s_AdjustRoundRect(r, &ovlWid, &ovlHgt);
 
 #if   defined(WIN_MAC)
+#ifdef WIN_MAC_QUARTZ
+/* QUARTZ_FIXME: can't invert, what to do? */
+  Nlm_PaintRoundRect (r, ovlWid, ovlHgt);
+#else
   InvertRoundRect (&rtool, ovlWid, ovlHgt);
+#endif
 
 #elif defined(WIN_MSWIN)
   if ( Nlm_currentHDC ) {
@@ -5370,16 +5294,16 @@ extern void Nlm_EraseArc(Nlm_RectPtr r, Nlm_PoinT start, Nlm_PoinT end)
     CGPoint startPt;
     CGPoint endPt;
     
-    cgr = Nlm_RecTToCGRect(r);
+    cgr = Nlm_RecTToCGRect(*r);
     startPt = Nlm_PoinTToCGPoint(start);
     endPt = Nlm_PoinTToCGPoint(end);
     Nlm_MoveTo((r->right + r->left)/2, (r->top + r->bottom)/2);
-    pathForArc (Nlm_QContext, cgr, startPt, endPt);
+    pathForArc (Nlm_PeekQContext(), cgr, startPt, endPt);
     
-    CGContextSaveGState(Nlm_QContext);
+    CGContextSaveGState(Nlm_PeekQContext());
     Nlm_White();
-    CGContextFillPath(Nlm_QContext);
-    CGContextRestoreGState(Nlm_QContext);
+    CGContextFillPath(Nlm_PeekQContext());
+    CGContextRestoreGState(Nlm_PeekQContext());
 #else
     Nlm_Int2      angle1;
     Nlm_Int2      angle2;
@@ -5455,11 +5379,11 @@ extern void Nlm_FrameArc(Nlm_RectPtr r, Nlm_PoinT start, Nlm_PoinT end)
     CGPoint startPt;
     CGPoint endPt;
     
-    cgr = Nlm_RecTToCGRect(r);
+    cgr = Nlm_RecTToCGRect(*r);
     startPt = Nlm_PoinTToCGPoint(start);
     endPt = Nlm_PoinTToCGPoint(end);
-    pathForArc (Nlm_QContext, cgr, startPt, endPt);
-    CGContextStrokePath(Nlm_QContext);
+    pathForArc (Nlm_PeekQContext(), cgr, startPt, endPt);
+    CGContextStrokePath(Nlm_PeekQContext());
 #else
     Nlm_Int2      angle1;
     Nlm_Int2      angle2;
@@ -5526,12 +5450,12 @@ extern void Nlm_PaintArc(Nlm_RectPtr r, Nlm_PoinT start, Nlm_PoinT end)
     CGPoint startPt;
     CGPoint endPt;
     
-    cgr = Nlm_RecTToCGRect(r);
+    cgr = Nlm_RecTToCGRect(*r);
     startPt = Nlm_PoinTToCGPoint(start);
     endPt = Nlm_PoinTToCGPoint(end);
     Nlm_MoveTo((r->right + r->left)/2, (r->top + r->bottom)/2);
-    pathForArc (Nlm_QContext, cgr, startPt, endPt);
-    CGContextFillPath(Nlm_QContext);
+    pathForArc (Nlm_PeekQContext(), cgr, startPt, endPt);
+    CGContextFillPath(Nlm_PeekQContext());
 #else
     Nlm_Int2       angle1;
     Nlm_Int2       angle2;
@@ -5599,6 +5523,10 @@ extern void Nlm_InvertArc(Nlm_RectPtr r, Nlm_PoinT start, Nlm_PoinT end)
   Local__RecTToRectTool(r, &rtool);
 
 #if   defined(WIN_MAC)
+#ifdef WIN_MAC_QUARTZ
+/* QUARTZ_FIXME: can't invert, what to do? */
+  Nlm_PaintArc (r, start, end);
+#else
   {{
     Nlm_Int2      angle1;
     Nlm_Int2      angle2;
@@ -5619,6 +5547,7 @@ extern void Nlm_InvertArc(Nlm_RectPtr r, Nlm_PoinT start, Nlm_PoinT end)
 
     InvertArc(&rtool, angle1, arcAngle);
   }}
+#endif
 
 #elif defined(WIN_MSWIN)
   if ( Nlm_currentHDC ) {
@@ -5768,13 +5697,13 @@ static void Nlm_CreatePoly (Nlm_Int2 num, Nlm_PointPtr pts)
 
   if (pts != NULL && num > 0) {
     firstPt = pts [0];
-    CGContextMoveToPoint(Nlm_QContext, (float) firstPt.x, (float) firstPt.y);
+    CGContextMoveToPoint(Nlm_PeekQContext(), (float) firstPt.x, (float) firstPt.y);
     for (i = 1; i < num; i++) {
       pt = pts [i];
-      CGContextAddLineToPoint(Nlm_QContext, (float) pt.x, (float) pt.y);
+      CGContextAddLineToPoint(Nlm_PeekQContext(), (float) pt.x, (float) pt.y);
     }
     if (! Nlm_EqualPt (pt, firstPt)) {
-      CGContextClosePath(Nlm_QContext);
+      CGContextClosePath(Nlm_PeekQContext());
     }
   }  
 }
@@ -5902,10 +5831,10 @@ extern void Nlm_ErasePoly (Nlm_Int2 num, Nlm_PointPtr pts)
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
   Nlm_CreatePoly (num, pts);
-  CGContextSaveGState(Nlm_QContext);
+  CGContextSaveGState(Nlm_PeekQContext());
   Nlm_White();
-  CGContextEOFillPath(Nlm_QContext);
-  CGContextRestoreGState(Nlm_QContext);
+  CGContextEOFillPath(Nlm_PeekQContext());
+  CGContextRestoreGState(Nlm_PeekQContext());
 #else
   PolyHandle   ply;
 
@@ -5932,7 +5861,7 @@ extern void Nlm_FramePoly(Nlm_Int2 num, Nlm_PointPtr pts)
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
   Nlm_CreatePoly (num, pts);
-  CGContextStrokePath(Nlm_QContext);
+  CGContextStrokePath(Nlm_PeekQContext());
 #else
   PolyHandle   ply;
 
@@ -5993,7 +5922,7 @@ extern void Nlm_PaintPoly (Nlm_Int2 num, Nlm_PointPtr pts)
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
   Nlm_CreatePoly (num, pts);
-  CGContextEOFillPath(Nlm_QContext);
+  CGContextEOFillPath(Nlm_PeekQContext());
 #else
   PolyHandle   ply;
 
@@ -6093,8 +6022,12 @@ extern Nlm_RegioN Nlm_CreateRgn (void)
   Nlm_RgnTool  ntool;
 
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  ntool = HIShapeCreateMutable();
+#else
   ntool = NewRgn ();
 #endif
+#endif
 #ifdef WIN_MSWIN
   ntool = CreateRectRgn (0, 0, 0, 0);
 #endif
@@ -6115,8 +6048,12 @@ extern Nlm_RegioN Nlm_DestroyRgn (Nlm_RegioN rgn)
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    CFRelease (ntool);
+#else
     DisposeRgn (ntool);
 #endif
+#endif
 #ifdef WIN_MSWIN
     DeleteObject (ntool);
 #endif
@@ -6141,8 +6078,12 @@ extern void Nlm_ClearRgn (Nlm_RegioN rgn)
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    HIShapeSetEmpty (ntool);
+#else
     SetEmptyRgn (ntool);
 #endif
+#endif
 #ifdef WIN_MSWIN
     temp = CreateRectRgn (0, 0, 0, 0);
     CombineRgn (ntool, temp, temp, RGN_COPY);
@@ -6171,8 +6112,17 @@ extern void Nlm_LoadRectRgn (Nlm_RegioN rgn, Nlm_Int2 lf,
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    HIShapeSetEmpty (ntool);
+    
+    CGRect r = CGRectMake (lf, tp, rt - lf, bt - tp);
+    HIShapeRef tempShape = HIShapeCreateWithRect (&r);
+    HIShapeUnion (tempShape, ntool, ntool);
+    CFRelease (tempShape);
+#else
     SetRectRgn (ntool, lf, tp, rt, bt);
 #endif
+#endif
 #ifdef WIN_MSWIN
     SetRectRgn (ntool, lf, tp, rt, bt);
 #endif
@@ -6199,8 +6149,12 @@ extern void Nlm_OffsetRgn (Nlm_RegioN rgn, Nlm_Int2 dx, Nlm_Int2 dy)
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    HIShapeOffset (ntool, dx, dy);
+#else
     OffsetRgn (ntool, dx, dy);
 #endif
+#endif
 #ifdef WIN_MSWIN
     OffsetRgn (ntool, dx, dy);
 #endif
@@ -6235,8 +6189,12 @@ extern void Nlm_SectRgn (Nlm_RegioN src1, Nlm_RegioN src2, Nlm_RegioN dst)
     ntool2 = (Nlm_RgnTool) src2;
     ntool3 = (Nlm_RgnTool) dst;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    HIShapeIntersect (ntool1, ntool2, ntool3);
+#else
     SectRgn (ntool1, ntool2, ntool3);
 #endif
+#endif
 #ifdef WIN_MSWIN
     CombineRgn (ntool3, ntool1, ntool2, RGN_AND);
 #endif
@@ -6275,8 +6233,12 @@ extern void Nlm_UnionRgn (Nlm_RegioN src1, Nlm_RegioN src2, Nlm_RegioN dst)
     ntool2 = (Nlm_RgnTool) src2;
     ntool3 = (Nlm_RgnTool) dst;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    HIShapeUnion( ntool1, ntool2, ntool3);
+#else
     UnionRgn (ntool1, ntool2, ntool3);
 #endif
+#endif
 #ifdef WIN_MSWIN
     CombineRgn (ntool3, ntool1, ntool2, RGN_OR);
 #endif
@@ -6310,8 +6272,12 @@ extern void Nlm_DiffRgn (Nlm_RegioN src1, Nlm_RegioN src2, Nlm_RegioN dst)
     ntool2 = (Nlm_RgnTool) src2;
     ntool3 = (Nlm_RgnTool) dst;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    HIShapeDifference (ntool1, ntool2, ntool3);
+#else
     DiffRgn (ntool1, ntool2, ntool3);
 #endif
+#endif
 #ifdef WIN_MSWIN
     CombineRgn (ntool3, ntool1, ntool2, RGN_DIFF);
 #endif
@@ -6327,6 +6293,24 @@ extern void Nlm_DiffRgn (Nlm_RegioN src1, Nlm_RegioN src2, Nlm_RegioN dst)
 extern void Nlm_XorRgn (Nlm_RegioN src1, Nlm_RegioN src2, Nlm_RegioN dst)
 
 {
+#ifdef WIN_MAC_QUARTZ
+/* this is actually a general solution, but less efficient
+   Quartz has no choice but to use it since HIShape does not support
+   the xor operation natively
+   
+   xor is equivalent to the union minus the intersection, so we do that */
+
+  Nlm_RegioN   sum = Nlm_CreateRgn();
+  Nlm_RegioN   intersection = Nlm_CreateRgn();
+  
+  Nlm_UnionRgn (src1, src2, sum);
+  Nlm_SectRgn (src1, src2, intersection);
+  Nlm_DiffRgn (sum, intersection, dst);
+  
+  Nlm_DestroyRgn (sum);
+  Nlm_DestroyRgn (intersection);
+#else
+  
   Nlm_RgnTool  ntool1;
   Nlm_RgnTool  ntool2;
   Nlm_RgnTool  ntool3;
@@ -6351,6 +6335,7 @@ extern void Nlm_XorRgn (Nlm_RegioN src1, Nlm_RegioN src2, Nlm_RegioN dst)
     XDestroyRegion (temp);
 #endif
   }
+#endif
 }
 
 extern Nlm_Boolean Nlm_EqualRgn (Nlm_RegioN rgn1, Nlm_RegioN rgn2)
@@ -6365,8 +6350,13 @@ extern Nlm_Boolean Nlm_EqualRgn (Nlm_RegioN rgn1, Nlm_RegioN rgn2)
     ntool1 = (Nlm_RgnTool) rgn1;
     ntool2 = (Nlm_RgnTool) rgn2;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    /* HIShapeRefs are CFTypeRefs so we can use CFEqual */
+    rsult = CFEqual (ntool1, ntool2);
+#else
     rsult = EqualRgn (ntool1, ntool2);
 #endif
+#endif
 #ifdef WIN_MSWIN
     rsult = (Nlm_Boolean) EqualRgn (ntool1, ntool2);
 #endif
@@ -6390,8 +6380,12 @@ extern Nlm_Boolean Nlm_EmptyRgn (Nlm_RegioN rgn)
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+    rsult = HIShapeIsEmpty (ntool);
+#else
     rsult = EmptyRgn (ntool);
 #endif
+#endif
 #ifdef WIN_MSWIN
     rsult = (Nlm_Boolean) (GetRgnBox (ntool, &rtool) == NULLREGION);
 #endif
@@ -6410,7 +6404,15 @@ extern void Nlm_EraseRgn (Nlm_RegioN rgn)
 
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
+#ifdef WIN_MAC_QUARTZ
+    HIShapeReplacePathInCGContext (ntool, Nlm_PeekQContext());
+    
+    Nlm_SelectQuartzColor (Nlm_QuartzBackColor);
+    CGContextFillPath (Nlm_PeekQContext());
+    Nlm_SelectQuartzColor (Nlm_QuartzForeColor);
+#else
     EraseRgn (ntool);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -6433,7 +6435,12 @@ extern void Nlm_FrameRgn (Nlm_RegioN rgn)
 
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
+#ifdef WIN_MAC_QUARTZ
+    HIShapeReplacePathInCGContext (ntool, Nlm_PeekQContext());
+    CGContextStrokePath (Nlm_PeekQContext());
+#else
     FrameRgn (ntool);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -6456,7 +6463,12 @@ extern void Nlm_PaintRgn (Nlm_RegioN rgn)
 
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
+#ifdef WIN_MAC_QUARTZ
+    HIShapeReplacePathInCGContext (ntool, Nlm_PeekQContext());
+    CGContextFillPath (Nlm_PeekQContext());
+#else
     PaintRgn (ntool);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -6484,7 +6496,11 @@ extern void Nlm_InvertRgn (Nlm_RegioN rgn)
 
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
+#ifdef WIN_MAC_QUARTZ
+// QUARTZ_FIXME: this operation does not make sense in quartz, what to do?
+#else
     InvertRgn (ntool);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -6507,7 +6523,16 @@ extern void Nlm_ClipRect (Nlm_RectPtr r)
 
   if (r != NULL) {
     Local__RecTToRectTool (r, &rtool);
+#ifdef WIN_MAC_QUARTZ
+    if (Nlm_PeekQContext())
+    {
+      CGRect cgr = Nlm_RecTToCGRect (*r);
+      
+      CGContextClipToRect (Nlm_PeekQContext(), cgr);
+    }
+#else
     ClipRect (&rtool);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -6546,7 +6571,12 @@ extern void Nlm_ClipRgn (Nlm_RegioN rgn)
 
   if (rgn != NULL) {
     ntool = (Nlm_RgnTool) rgn;
+#ifdef WIN_MAC_QUARTZ
+    HIShapeReplacePathInCGContext (ntool, Nlm_PeekQContext());
+    CGContextClip (Nlm_PeekQContext());
+#else
     SetClip (ntool);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -6584,6 +6614,9 @@ extern void Nlm_ResetClip (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+// QUARTZ_FIXME: CGContext clips can only contract, not expand, needs to be handled by popping the context, but callers don't know about that... maybe have the global context always be inherently pushed, and this can pop and immediately re-push?
+#else
   Nlm_RecT      r;
   Nlm_RectTool  rtool;
 
@@ -6591,6 +6624,7 @@ extern void Nlm_ResetClip (void)
   Local__RecTToRectTool (&r, &rtool);
   ClipRect (&rtool);
 #endif
+#endif
 #ifdef WIN_MSWIN
   if (Nlm_currentHDC != NULL) {
     SelectClipRgn (Nlm_currentHDC, NULL);
@@ -6611,6 +6645,9 @@ extern void Nlm_ValidRect (Nlm_RectPtr r)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+// QUARTZ_FIXME: do we care? just let it redraw
+#else
   Nlm_RectTool  rtool;
 
   if (r != NULL) {
@@ -6618,6 +6655,7 @@ extern void Nlm_ValidRect (Nlm_RectPtr r)
     ValidRect (&rtool);
   }
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_RectTool  rtool;
 
@@ -6634,6 +6672,11 @@ extern void Nlm_InvalRect (Nlm_RectPtr r)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+// QUARTZ_FIXME: this could stand to be a little more fine-grained
+  HIViewRef view = HIViewGetRoot (Nlm_QWindow);
+  HIViewSetNeedsDisplay (view, 1);
+#else
   Nlm_RectTool  rtool;
 
   if (r != NULL) {
@@ -6641,6 +6684,7 @@ extern void Nlm_InvalRect (Nlm_RectPtr r)
     InvalRect (&rtool);
   }
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_RectTool  rtool;
 
@@ -6666,7 +6710,11 @@ extern void Nlm_ValidRgn (Nlm_RegioN rgn)
 {
 #ifdef WIN_MAC
   if (rgn != NULL) {
+#ifdef WIN_MAC_QUARTZ
+// QUARTZ_FIXME: do we care? just let it redraw
+#else
     ValidRgn ((Nlm_RgnTool) rgn);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -6683,7 +6731,13 @@ extern void Nlm_InvalRgn (Nlm_RegioN rgn)
 {
 #ifdef WIN_MAC
   if (rgn != NULL) {
+#ifdef WIN_MAC_QUARTZ
+// QUARTZ_FIXME: this could stand to be a little more fine-grained
+  HIViewRef view = HIViewGetRoot (Nlm_QWindow);
+  HIViewSetNeedsDisplay (view, 1);
+#else
     InvalRgn ((Nlm_RgnTool) rgn);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -6727,6 +6781,36 @@ extern void Nlm_CopyBits (Nlm_RectPtr r, Nlm_VoidPtr source)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  CGRect rect = Nlm_RecTToCGRect (*r);
+  
+  int width = r->left - r->right;
+  int height = r->bottom - r->top;
+  int bytesPerRow = (width - 1) / 8 + 1;
+  
+  CGColorSpaceRef colorSpace = CGColorSpaceCreateDeviceGray();
+  CGDataProviderRef dataProvider = CGDataProviderCreateWithData (NULL, source, bytesPerRow * height, NULL);
+  
+  CGImageRef image = CGImageCreate (
+    width,
+    height,
+    1, /* bits per component */
+    1, /* bits per pixel */
+    bytesPerRow,
+    colorSpace,
+    0, /* bitmap info */
+    dataProvider,
+    NULL,
+    1, /* should interpolate */
+    kCGRenderingIntentDefault);
+  
+  CGContextDrawImage (Nlm_PeekQContext(), rect, image);
+  
+  CFRelease (image);
+  CFRelease (dataProvider);
+  CFRelease (colorSpace);
+  
+#else
   const BitMap *dstBitsPtr;
   Nlm_Int2  mode;
   PenState  pnState;
@@ -6769,6 +6853,7 @@ extern void Nlm_CopyBits (Nlm_RectPtr r, Nlm_VoidPtr source)
     CopyBits (&srcBits, dstBitsPtr, &srcRect, &rect, mode, NULL);
   }
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_Int2      cols;
   HBITMAP       hBitmap;
@@ -6997,6 +7082,41 @@ extern void Nlm_CopyPixmap ( Nlm_RectPtr r, Nlm_Int1Ptr source,
   MemFree(bInfoPtr);
 #endif
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  CGRect rect = Nlm_RecTToCGRect (*r);
+  
+  width = r->left - r->right;
+  height = r->bottom - r->top;
+  
+  CGColorSpaceRef baseSpace = CGColorSpaceCreateDeviceRGB ();
+  
+  /* we're going to pass the color table directly; it's an array of
+     structs containing r, g, b, and the function wants an array
+     of unsigned char containing r, g, b, so they all line up */
+  CGColorSpaceRef colorSpace = CGColorSpaceCreateIndexed (baseSpace, totalColors - 1, (const unsigned char *)colorTable);
+  
+  CGDataProviderRef dataProvider = CGDataProviderCreateWithData (NULL, source, width * height, NULL);
+  
+  CGImageRef image = CGImageCreate (
+    width,
+    height,
+    8, /* bits per component */
+    8, /* bits per pixel */
+    width * height,
+    colorSpace,
+    0, /* bitmap info */
+    dataProvider,
+    NULL,
+    1, /* should interpolate */
+    kCGRenderingIntentDefault);
+  
+  CGContextDrawImage (Nlm_PeekQContext(), rect, image);
+  
+  CFRelease (image);
+  CFRelease (dataProvider);
+  CFRelease (colorSpace);
+  CFRelease (baseSpace);
+#else
   pixelMap = (PixMap*)MemNew(sizeof(PixMap));
   pixelMap->hRes = 72;
   pixelMap->vRes = 72;
@@ -7049,6 +7169,7 @@ extern void Nlm_CopyPixmap ( Nlm_RectPtr r, Nlm_Int1Ptr source,
   }
   MemFree(pixelMap);
 #endif
+#endif
 
 #ifdef WIN_MOTIF
   {{
@@ -7103,6 +7224,19 @@ extern void Nlm_SetUpDrawingTools (void)
   char       tmpFontName[256];
 
 
+#ifdef WIN_MAC_QUARTZ
+  CGRect r = CGRectMake (-32768, -32768, 65535, 65535);
+  HIShapeRef rectShape = HIShapeCreateWithRect (&r);
+  Nlm_scrollRgn = HIShapeCreateMutableCopy (rectShape);
+  Nlm_updateRgn = HIShapeCreateMutableCopy (rectShape);
+  CFRelease (rectShape);
+  
+  /* can't use QuickDraw functions to get the system font,
+     no replacemet available, so just hardcode it */
+  memset ( &fsp, 0, sizeof(Nlm_FontSpec));
+  Nlm_StrCpy (fsp.name, "Lucida Grande");
+  fsp.size = 13;
+#else
   Nlm_scrollRgn = (Nlm_RegioN) (NewRgn ());
 
   Nlm_updateRgn = (Nlm_RegioN) (NewRgn ());
@@ -7112,9 +7246,6 @@ extern void Nlm_SetUpDrawingTools (void)
   Local__RectToolToRecT (&bounds, &Nlm_updateRect);
   /* HUnlock ((Handle) Nlm_updateRgn); */
 
-  Nlm_fontList = NULL;
-  Nlm_fontInUse = NULL;
-  Nlm_systemFont = (Nlm_FonT) Nlm_HandNew (sizeof (Nlm_FontRec));
   /* esl: LoadFontData changed to work with new FontData format */
   /* alexs get font name */
   memset ( &fsp, 0, sizeof(Nlm_FontSpec));
@@ -7123,6 +7254,12 @@ extern void Nlm_SetUpDrawingTools (void)
   Nlm_StringNCpy_0 (fsp.name, tmpFontName, FONT_NAME_SIZE - 1);
   fsp.name[FONT_NAME_SIZE - 1] = 0;
   fsp.size = GetDefFontSize ();
+#endif
+
+  Nlm_fontList = NULL;
+  Nlm_fontInUse = NULL;
+  Nlm_systemFont = (Nlm_FonT) Nlm_HandNew (sizeof (Nlm_FontRec));
+  
 #ifdef WIN_MAC_ATSUI
   Nlm_LoadFontData (Nlm_systemFont, NULL, -1, &fsp, Nlm_NewATSUStyle(&fsp), NULL);
 #else
@@ -7153,12 +7290,21 @@ extern void Nlm_SetUpDrawingTools (void)
       Nlm_hasColorQD = (gval && (1 << gestaltHasColor));
   }
   if (Nlm_hasColorQD) {
+#ifdef WIN_MAC_QUARTZ
+    Nlm_QuartzForeColor.r = 0;
+    Nlm_QuartzForeColor.g = 0;
+    Nlm_QuartzForeColor.b = 0;
+    Nlm_QuartzBackColor.r = 1.0;
+    Nlm_QuartzBackColor.g = 1.0;
+    Nlm_QuartzBackColor.b = 1.0;
+#else
     Nlm_RGBforeColor.red = 0;
     Nlm_RGBforeColor.green = 0;
     Nlm_RGBforeColor.blue = 0;
     Nlm_RGBbackColor.red = 65535;
     Nlm_RGBbackColor.green = 65535;
     Nlm_RGBbackColor.blue = 65535;
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -7378,7 +7524,9 @@ extern void Nlm_CleanUpDrawingTools (void)
   Nlm_FonT      f;
   Nlm_FontData  fdata;
 
+#ifndef WIN_MAC_QUARTZ
   Nlm_ResetDrawingTools ();
+#endif
 #ifdef WIN_MOTIF
   Nlm_GetFontData (Nlm_systemFont, &fdata);
   if (fdata.handle != NULL) {
diff --git a/vibrant/ncbidraw.h b/vibrant/ncbidraw.h
index 2aa41edc..f809bc49 100644
--- a/vibrant/ncbidraw.h
+++ b/vibrant/ncbidraw.h
@@ -29,63 +29,14 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.9 $
+* $Revision: 6.10 $
 *
 * File Description: 
 *       Vibrant drawing procedure definitions
 *
 * Modifications:  
 * --------------------------------------------------------------------------
-* $Log: ncbidraw.h,v $
-* Revision 6.9  2000/07/08 20:44:13  vakatov
-* Get all "#include" out of the 'extern "C" { }' scope;  other cleanup...
 *
-* Revision 6.8  2000/01/24 16:11:13  lewisg
-* speed up seqid comparison in color manager, make fast windows version of SetColor()
-*
-* Revision 6.7  1999/10/20 23:10:04  vakatov
-* + Nlm_SetCurrentGIF(), + Nlm_DestroyGIF() proto.
-* Get rid of the (now obsolete) PROTO macro; added more comments.
-*
-* Revision 6.6  1999/10/04 17:16:32  kans
-* include ncbidraw.h instead of vibrant.h, a couple Nlm_ prefixes
-*
-* Revision 6.5  1998/07/14 16:44:26  vakatov
-* Added VibrantIsGUI() and <internal> Nlm_VibrantSetGUI()
-*
-* Revision 6.4  1998/07/01 18:27:42  vakatov
-* Use "const" qualifier somewhere
-*
-* Revision 6.3  1998/06/10 22:05:26  lewisg
-* added PROTO() around *Quadrant()
-*
-* Revision 6.2  1998/06/01 17:20:13  vakatov
-* Added code to draw/fill 90-degree arc/pie (quadrants)
-*
-* Revision 6.1  1997/09/16 20:24:53  vakatov
-* Added Nlm_FitStringWidth()
-*
-* Revision 5.8  1997/07/23 19:42:22  vakatov
-* Added Nlm_PaintStringEx function(text + position)
-*
-* Revision 5.7  1997/07/18 15:18:45  vakatov
-* [!WIN_GIF] +Dummy Nlm_CreateGIF() and Nlm_SaveGIF();  /return FALSE/
-*
-* Revision 5.6  1997/06/18 22:10:10  vakatov
-* [WIN_GIF] Moved Create/SaveGIF() decl. from "ncbigif.h" to "ncbidraw.h"
-*
-* Revision 5.2  1997/06/04 00:05:20  kans
-* support for Japanese by Tomo Koike of DDBJ
-*
-* Revision 5.1  1996/09/30 19:56:00  vakatov
-* + Nlm_SetPenDash PROTO and synopsis
-*
-* Revision 4.1  1996/05/10  21:14:21  vakatov
-* Added UpdateColorTable() function to allow the user to read his color
-* preferencies from an external config.-file
-*
-* Revision 2.12  1995/07/14  17:48:26  kans
-* new CopyPixmap (AS)
 * ==========================================================================
 */
 
@@ -309,6 +260,7 @@ size_t Nlm_FitStringWidth(const Nlm_Char PNTR str, Nlm_Int4 max_width);
 
 void         Nlm_SetPen(Nlm_PoinT pt);
 void         Nlm_GetPen(Nlm_PointPtr pt);
+void         Nlm_SetPenWidth(Nlm_Int2 width);
 
 void         Nlm_PaintChar(Nlm_Char ch);
 void         Nlm_PaintString(Nlm_CharPtr text);
diff --git a/vibrant/ncbiport.h b/vibrant/ncbiport.h
index 69b70984..ff0b08cf 100644
--- a/vibrant/ncbiport.h
+++ b/vibrant/ncbiport.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   1/1/91
 *
-* $Revision: 6.1 $
+* $Revision: 6.2 $
 *
 * File Description: 
 *       Vibrant drawing port specification definitions
@@ -39,32 +39,6 @@
 * Date     Name        Description of modification
 * -------  ----------  -----------------------------------------------------
 *
-*
-* $Log: ncbiport.h,v $
-* Revision 6.1  2007/05/01 22:01:30  kans
-* changes in preparation for supporing Quartz on Macintosh
-*
-* Revision 6.0  1997/08/25 18:56:09  madden
-* Revision changed to 6.0
-*
-* Revision 5.2  1997/07/10 21:49:27  vakatov
-* [WIN_X]  Now able to manage windows having different depths(and
-* different visuals and GC).
-*
-* Revision 5.1  1997/06/18 19:46:32  vakatov
-* [WIN_GIF]  Do not use WIN_MAC/MSWIN/MOTIF-specific fields of the
-* Nlm_FontRec struct.
-*
-* Revision 5.0  1996/05/28 13:45:08  ostell
-* Set to revision 5.0
-*
- * Revision 4.0  1995/07/26  13:51:04  ostell
- * force revision to 4.0
- *
- * Revision 2.6  1995/05/17  15:15:14  kans
- * added Log line
- *
-*
 * ==========================================================================
 */
 
@@ -85,15 +59,27 @@
 extern "C" {
 #endif
 
+/* Quartz requires ATSUI, so ensure that the dependency is filled */
+#if defined(WIN_MAC_QUARTZ) && !defined(WIN_MAC_ATSUI)
+#define WIN_MAC_ATSUI
+#endif
+
 #ifdef WIN_MAC
 #define Nlm_PointTool Point
 #define Nlm_RectTool Rect
+
+#ifdef WIN_MAC_QUARTZ
+#define Nlm_RgnTool HIMutableShapeRef
+#else
 #define Nlm_RgnTool RgnHandle
+#endif
+
 #ifdef WIN_MAC_ATSUI
 #define Nlm_FontTool ATSUStyle
 #else
 #define Nlm_FontTool Nlm_Handle
 #endif
+
 #endif
 
 #ifdef WIN_MSWIN
@@ -135,11 +121,21 @@ typedef  struct  Nlm_fontrec {
 extern Nlm_Boolean  Nlm_nowPrinting;
 
 #ifdef WIN_MAC
-extern  RGBColor     Nlm_RGBforeColor;
-extern  RGBColor     Nlm_RGBbackColor;
-extern  Nlm_Boolean  Nlm_hasColorQD;
+#ifdef WIN_MAC_QUARTZ
+	
+typedef struct {
+  float r, g, b;
+} Nlm_QuartzColor;
+extern Nlm_QuartzColor Nlm_QuartzForeColor;
+extern Nlm_QuartzColor Nlm_QuartzBackColor;
+extern Nlm_Boolean  Nlm_hasColorQD;
+#else
+extern RGBColor     Nlm_RGBforeColor;
+extern RGBColor     Nlm_RGBbackColor;
+extern Nlm_Boolean  Nlm_hasColorQD;
 #endif
-
+#endif
+	
 #ifdef WIN_MSWIN
 extern  HWND  Nlm_currentHWnd;
 extern  HDC   Nlm_currentHDC;
@@ -159,8 +155,19 @@ extern  Nlm_Boolean  Nlm_hasColor;
 #endif
 
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+void  Nlm_SetPort PROTO((CGContextRef ctx));
+void  Nlm_PushPort PROTO((CGContextRef ctx));
+CGContextRef Nlm_PopPort PROTO((void));
+CGContextRef Nlm_GetQuartzWindowPort PROTO((WindowRef wptr));
+WindowRef Nlm_GetQuartzCurrentWindow PROTO((void));
+void Nlm_SetGraphicNeedsDisplay PROTO((Nlm_GraphiC graphic));
+#else
 void  Nlm_SetPort PROTO((GrafPtr grafptr));
+#endif
 void Nlm_SetPortWindowPort PROTO((WindowPtr wptr));
+
+
 #endif
 
 #ifdef WIN_MSWIN
diff --git a/vibrant/vibbutns.c b/vibrant/vibbutns.c
index f84d188b..bb934cf9 100644
--- a/vibrant/vibbutns.c
+++ b/vibrant/vibbutns.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.12 $
+* $Revision: 6.13 $
 *
 * File Description: 
 *       Vibrant button functions
@@ -39,108 +39,6 @@
 * Date     Name        Description of modification
 * -------  ----------  -----------------------------------------------------
 *
-*
-* $Log: vibbutns.c,v $
-* Revision 6.12  2007/05/01 22:01:30  kans
-* changes in preparation for supporing Quartz on Macintosh
-*
-* Revision 6.11  2006/09/14 19:18:28  ivanov
-* Rollback last changes. All missed defines added to corelib/ncbiwin.h.
-*
-* Revision 6.10  2006/09/14 18:05:45  ivanov
-* Fixed compilation errors on MS Windows
-*
-* Revision 6.9  2006/09/14 14:45:38  kans
-* changes for 64-bit Windows (GC) plus a few CodeWarrior complaints (JK)
-*
-* Revision 6.8  2004/01/20 23:34:38  sinyakov
-* [WIN_MSWIN]: fixed to display '&' character in button text
-*
-* Revision 6.7  2002/03/07 19:18:21  kans
-* check box wid += 4 for Aqua
-*
-* Revision 6.6  2002/02/05 14:02:28  kans
-* adjust push button margins in Mac OS X Aqua
-*
-* Revision 6.5  2002/01/09 23:22:02  juran
-* Make buttons wider in Aqua.
-*
-* Revision 6.4  2000/02/07 20:17:35  lewisg
-* minor bug fixes, use gui font for win32
-*
-* Revision 6.3  1999/10/19 12:48:19  thiessen
-* minor hack to Nlm_RemoveDefaultButton to allow Cn3D to run under RH linux 6 with Lesstif library
-*
-* Revision 6.2  1997/12/12 21:08:28  kans
-* a number of symbols changed in the latest CodeWarrior release, now using headers from Apple
-*
-* Revision 6.1  1997/11/26 21:30:11  vakatov
-* Fixed errors and warnings issued by C and C++ (GNU and Sun) compilers
-*
-* Revision 6.0  1997/08/25 18:56:47  madden
-* Revision changed to 6.0
-*
-* Revision 5.6  1997/08/18 14:47:30  vakatov
-* [WIN_MOTIF]  Minor fix: Push/DefaultButton position adjustment
-*
-* Revision 5.5  1997/04/25 16:14:38  vakatov
-* [WIN_MOTIF,WIN_MSWIN] Catch and render(DoSendFocus) navigation key events
-*
- * Revision 5.4  1997/01/29  16:41:22  kans
- * using StringNCpy_0
- *
- * Revision 5.3  1996/07/03  18:55:16  vakatov
- * [WIN-MOTIF]  Let the MOTIF calculate the button's initial size automatically
- * (i.e. according to the MOTIF internal rules) rather than try to calculate
- * the button size using a vague guess on the used font size and the title length
- *
- * Revision 5.2  1996/06/11  16:06:10  vakatov
- * [WIN_MOTIF]  PushButton location/sizing adjustment
- *
- * Revision 5.1  1996/06/07  21:53:28  vakatov
- * [WIN_MOTIF] Default-/Push- buttons size alignment;  DefaultButton is not
- * mandatory the first button in the group
- *
- * Revision 5.0  1996/05/28  13:45:08  ostell
- * Set to revision 5.0
- *
- * Revision 4.8  1996/05/20  21:33:39  vakatov
- * [WIN_MOTIF]  All "Widget" / "NULL" comparisons and assignments replaced
- * by the "Widget" / "(Widget)0" these
- *
- * Revision 4.7  1996/05/06  19:20:51  vakatov
- * [WIN_MOTIF]  Nlm_SetButtonPosition() -- additional adjustment
- *
- * Revision 4.6  1996/05/06  19:06:07  kans
- * ifdef motif and prototype needed for newest functions
- *
- * Revision 4.5  1996/05/06  18:27:20  vakatov
- * Nlm_RemoveDefaultButton() corrected (set default button to NULL);
- * Nlm_SetButtonDefault() added to allow change button's "defaultBtn" flag;
- * [WIN_MOTIF] Nlm_PendingDefButton() trick-function added to avoid a strange
- * PushButton/DefaultButton size interference
- *
- * Revision 4.4  1996/04/30  21:50:03  vakatov
- * Since now push-buttons belonging to a group containing default button
- * have of the same size as if they were belonging to a group without a
- * default button (WIN_MOTIF feature only)
- *
- * Revision 4.3  1996/03/02  22:36:38  kans
- * reduction of X traffic (DV)
- *
- * Revision 4.2  1996/02/13  17:24:07  kans
- * accelerated set position prior to realization (Denis Vakatov)
- *
- * Revision 4.1  1995/12/25  16:03:50  kans
- * removed offset parameter for Motif push buttons
- *
- * Revision 4.0  1995/07/26  13:51:04  ostell
- * force revision to 4.0
- *
- * Revision 2.13  1995/05/17  15:15:14  kans
- * added Log line
- *
-*
 * ==========================================================================
 */
 
@@ -513,9 +411,9 @@ static void Nlm_DrawDefault (Nlm_GraphiC b)
     Nlm_GetRect (b, &r);
     Nlm_InsetRect (&r, -4, -4);
     if (Nlm_RectInRgn (&r, Nlm_updateRgn)) {
-      PenSize (3, 3);
+      Nlm_SetPenWidth (3);
       Nlm_FrameRoundRect (&r, 16, 16);
-      PenNormal ();
+      Nlm_SetPenWidth (1);
       c = Nlm_GetButtonHandle ((Nlm_ButtoN) b);
       Draw1Control (c);
     }
diff --git a/vibrant/vibincld.h b/vibrant/vibincld.h
index 7849cece..141b1194 100644
--- a/vibrant/vibincld.h
+++ b/vibrant/vibincld.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.7 $
+* $Revision: 6.8 $
 *
 * File Description: 
 *       Vibrant inclusion of underlying windowing system toolbox functions,
@@ -41,86 +41,6 @@
 * Date     Name        Description of modification
 * -------  ----------  -----------------------------------------------------
 *
-*
-* $Log: vibincld.h,v $
-* Revision 6.7  2007/05/01 22:01:30  kans
-* changes in preparation for supporing Quartz on Macintosh
-*
-* Revision 6.6  2006/11/24 20:06:31  kans
-* include Carbon/Carbon.h if not MWERKS - attempting to simplify Xcode search paths
-*
-* Revision 6.5  2002/06/13 16:15:13  kans
-* fix includes for OS_UNIX_DARWIN with WIN_MAC (EN) - still bug in vibutils.c file dialog
-*
-* Revision 6.4  2000/07/08 20:44:14  vakatov
-* Get all "#include" out of the 'extern "C" { }' scope;  other cleanup...
-*
-* Revision 6.3  1999/06/22 15:14:54  lewisg
-* fix image library so that works on linux with > 8 bits
-*
-* Revision 6.2  1999/04/06 14:23:25  lewisg
-* add opengl replacement for viewer3d
-*
-* Revision 6.1  1998/07/14 16:44:27  vakatov
-* Added VibrantIsGUI() and <internal> Nlm_VibrantSetGUI()
-*
-* Revision 6.0  1997/08/25 18:57:08  madden
-* Revision changed to 6.0
-*
-* Revision 5.9  1997/07/23 19:36:12  vakatov
-* [WIN_MSWIN] +Nlm_GetPicWinHDC proto
-*
-* Revision 5.8  1997/07/10 21:49:30  vakatov
-* [WIN_X]  Now able to manage windows having different depths(and
-* different visuals and GC).
-*
-* Revision 5.7  1997/06/09 18:07:39  vakatov
-* Removed "Nlm_fontList" declaration(it's now static in "ncbidraw.c")
-* [WIN_MOTIF]  Added Nlm_XAllocColor() prototype
-*
-* Revision 5.6  1997/04/25 16:09:33  vakatov
-* [WIN_MOTIF,WIN_MSWIN]  Added functions to catch, convert(to Mac keycodes)
-* and process navigation and special keys
-*
- * Revision 5.5  1997/04/17  16:17:50  kans
- * InitForms and FreeForms added
- *
- * Revision 5.4  1997/02/13  21:34:37  vakatov
- * [WIN_MOTIF]  #define NLM_MOTIF_CASCADEB_BUG -- workaround the Motif bug
- *
- * Revision 5.3  1997/01/28  22:03:51  kans
- * changed <GestaltEqu.h> to <Gestalt.h> for CodeWarrior
- *
- * Revision 5.2  1996/10/28  19:31:19  vakatov
- * [WIN_MOTIF]  Added prototypes for functions Nlm_VibrantDefaultColormap()
- * and Nlm_XrmGetResource()
- *
- * Revision 5.1  1996/08/27  20:52:53  vakatov
- * Added Nlm_HorizScrollBar4() and Nlm_VertScrollBar4() prototypes -- to
- * create Int4-range scrollbars
- *
- * Revision 5.0  1996/05/28  13:45:08  ostell
- * Set to revision 5.0
- *
- * Revision 4.2  1996/03/12  22:34:37  epstein
- * add shellapi for Drag-And-Drop support
- *
- * Revision 4.1  1996/02/13  17:24:07  kans
- * accelerated set position prior to realization (Denis Vakatov)
- *
- * Revision 4.0  1995/07/26  13:51:04  ostell
- * force revision to 4.0
- *
- * Revision 2.21  1995/07/17  22:02:19  kans
- * Motif clipboard cut and paste supported (AS)
- *
- * Revision 2.20  1995/05/31  18:00:58  kans
- * added <Palettes.h>
- *
- * Revision 2.19  1995/05/17  15:15:14  kans
- * added Log line
- *
-*
 * ==========================================================================
 */
 
@@ -144,9 +64,15 @@ extern "C" {
 #define Nlm_HandleTool Handle
 #define Nlm_PointTool Point
 #define Nlm_RectTool Rect
+	
+#ifdef WIN_MAC_QUARTZ
+#define Nlm_RgnTool HIMutableShapeRef
+#else
 #define Nlm_RgnTool RgnHandle
 #endif
 
+#endif
+
 #ifdef WIN_MSWIN
 #define Nlm_HandleTool HANDLE
 #define Nlm_PointTool POINT
@@ -288,13 +214,21 @@ typedef  struct  Nlm_boxrec {
 
 
 
-#if defined(WIN_MAC) || defined(WIN_MAC_QUARTZ)
+#if defined(WIN_MAC)
+#if defined(WIN_MAC_QUARTZ)
+#define Nlm_WindowTool  WindowPtr
+#define Nlm_PortTool    CGContextRef
+#define Nlm_ShellTool   Nlm_Handle
+#define Nlm_MainTool    Nlm_Handle
+#define Nlm_ColorMTool  PaletteHandle
+#else
 #define Nlm_WindowTool  WindowPtr
 #define Nlm_PortTool    GrafPtr
 #define Nlm_ShellTool   Nlm_Handle
 #define Nlm_MainTool    Nlm_Handle
 #define Nlm_ColorMTool  PaletteHandle
 #endif
+#endif
 
 #ifdef WIN_MSWIN
 #define Nlm_WindowTool  HWND
@@ -527,8 +461,10 @@ void        Nlm_GlobalToLocal PROTO((Nlm_PointPtr pt));
 void        Nlm_VibrantSetGUI PROTO((void));
 
 #if defined(WIN_MAC) && defined(WIN_MAC_QUARTZ)
-CGRect      Nlm_RecTToCGRect(Nlm_RectPtr r);
+CGRect      Nlm_RecTToCGRect(Nlm_RecT r);
 Nlm_RecT    Nlm_CGRectToRecT(CGRect cgr);
+CGRect      Nlm_RectQDToCG(Rect r);
+Rect        Nlm_RectCGToQD(CGRect r);
 CGPoint     Nlm_PoinTToCGPoint(Nlm_PoinT np);
 Nlm_PoinT   Nlm_CGPointToPoinT(CGPoint qp);
 #endif
diff --git a/vibrant/vibmenus.c b/vibrant/vibmenus.c
index e190d6a6..0026a1bf 100644
--- a/vibrant/vibmenus.c
+++ b/vibrant/vibmenus.c
@@ -29,250 +29,14 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.25 $
+* $Revision: 6.26 $
 *
 * File Description: 
 *       Vibrant menu functions
 *
 * Modifications:  
 * --------------------------------------------------------------------------
-* $Log: vibmenus.c,v $
-* Revision 6.25  2007/03/13 13:33:13  bollin
-* Initialize variables before they are used.
 *
-* Revision 6.24  2006/09/14 19:18:29  ivanov
-* Rollback last changes. All missed defines added to corelib/ncbiwin.h.
-*
-* Revision 6.23  2006/09/14 18:05:45  ivanov
-* Fixed compilation errors on MS Windows
-*
-* Revision 6.22  2006/09/14 14:45:38  kans
-* changes for 64-bit Windows (GC) plus a few CodeWarrior complaints (JK)
-*
-* Revision 6.21  2005/11/30 20:19:27  rsmith
-* Update Mac API to fix hier-menus.
-*
-* Revision 6.20  2005/07/18 15:15:18  kans
-* fixed minor xcode compiler warnings
-*
-* Revision 6.19  2004/04/01 13:43:09  lavr
-* Spell "occurred", "occurrence", and "occurring"
-*
-* Revision 6.18  2004/01/20 23:35:38  sinyakov
-* [WIN_MSWIN] implemented menu accelerators
-*
-* Revision 6.17  2003/11/17 17:03:30  kans
-* changed C++ style comments to C comments
-*
-* Revision 6.16  2003/03/27 19:35:43  kans
-* Nlm_PrepareTitle removes non-Mac accelerator from Mac menu item
-*
-* Revision 6.15  2002/03/28 13:30:27  kans
-* check for OS_UNIX_DARWIN before including MoreCarbonAccessors.h, Profiler.h (EN)
-*
-* Revision 6.14  2002/01/09 15:23:53  kans
-* added HasAquaMenuLayout
-*
-* Revision 6.13  2001/05/17 22:04:26  kans
-* separator item in mswin creates a fake status item link, so GetChildPosition is correct, and thus later submenus have the correct position for enabling and disabling
-*
-* Revision 6.12  2001/04/03 22:10:19  juran
-* Carbon fixes.
-*
-* Revision 6.11  2001/01/24 18:43:00  kans
-* remove artifact bar caused by popup label on Solaris (TF)
-*
-* Revision 6.10  2000/02/07 20:17:35  lewisg
-* minor bug fixes, use gui font for win32
-*
-* Revision 6.9  1999/12/30 16:47:09  kans
-* Carbon changes (Churchill)
-*
-* Revision 6.8  1999/04/22 15:18:57  vakatov
-* Call XtUnrealizeWidget() before XtDestroyWidget() to make sure no
-* "post-mortem" callbacks(registered by XtAddEventHandler()) get
-* triggered for the destroyed widget. Reason: the widget may not be
-* immediately destroyed if XtDestroyWidget() was called in a nested
-* event dispatch loop.
-*
-* Revision 6.7  1999/03/09 17:55:48  vakatov
-* [WIN_MOTIF]  Fixed for the ">63 items menu overflow" in
-*              Nlm_AppendChoice() and Nlm_AppendOnePopListChoice()
-*
-* Revision 6.6  1999/02/08 15:46:55  vakatov
-* [WIN_MOTIF]  Nlm_SetPopListValue() catch(and just ignore) attempts to
-* se a value larger than 63
-*
-* Revision 6.5  1997/12/12 21:08:35  kans
-* a number of symbols changed in the latest CodeWarrior release, now using headers from Apple
-*
-* Revision 6.4  1997/11/26 21:30:26  vakatov
-* Fixed errors and warnings issued by C and C++ (GNU and Sun) compilers
-*
-* Revision 6.3  1997/10/08 18:43:58  vakatov
-* [WIN_MOTIF] Nlm_ResetMenu() -- remove separator items too
-*
-* Revision 6.2  1997/10/01 17:08:04  vakatov
-* [WIN_MSWIN, WIN_MOTIF]  RemoveSubMenu() -- set parent's "submenu" to NULL
-*
-* Revision 6.1  1997/09/30 16:39:04  vakatov
-* [WIN_MOTIF] ResetMenu() -- check for NULL(ch.group) item;;  destroy
-* items in RemoveChoiceGroup()
-*
-* Revision 5.28  1997/07/10 21:49:32  vakatov
-* [WIN_X]  Now able to manage windows having different depths(and
-* different visuals and GC).
-*
-* Revision 5.27  1997/06/04 18:25:22  vakatov
-* [WIN_MOTIF] Added accelerators to PopupList items
-*
-* Revision 5.26  1997/05/12 19:01:57  vakatov
-* Disable and gray out the PopupList's cascade button properly;
-* [WIN_MOTIF] disable accelerators and mnemonics in the PopupList menu
-* when the menu is disabled
-*
-* Revision 5.25  1997/04/25 19:52:22  kans
-* mac submenus call prepare title
-*
- * Revision 5.24  1997/04/25  16:13:27  vakatov
- * [WIN_MOTIF,WIN_MSWIN] Catch and render(DoSendFocus) navigation key events
- * occurred in PopupList
- *
- * Revision 5.23  1997/04/18  22:17:49  vakatov
- * New way of specifying mnemonics/accelerators in the item(or menu) title:
- * use 1st sybbol after '/' for WIN_MAC;  2nd -- for WIN_MOTIF & WIN_MSWIN
- * mnemonic; 3rd -- for WIN_MOTIF accelerator.
- * [WIN_MOTIF] Added mnemonics for PopupList items.
- *
- * Revision 5.22  1997/04/10  21:35:38  vakatov
- * [WIN_MOTIF]  Implemented the mnemonic and accelerator key functionality
- * for menus and popup lists.
- * [WIN_MSWIN]  Impl. mnemonic keys for submenu cascade items. +typecasting.
- *
- * Revision 5.21  1997/02/13  22:32:59  vakatov
- * [WIN_MOTIF]  In addition to R5.17 -- (1) do not destroy CascadeButtons
- * at all;  (2) do these workarounds only if the preprocessor
- * variable NLM_MOTIF_CASCADEB_BUG is set (see in <vibincld.h>)
- *
- * Revision 5.20  1997/01/28  19:07:39  vakatov
- * [WIN_MOTIF] Nlm_ResetMenu() -- got rid of an unallocated memory read
- *
- * Revision 5.19  1997/01/27  20:13:41  vakatov
- * [WIN_MOTIF] Nlm_RemovePopupList():  remove colormap-change event handler --
- * to ignore events coming from the dangling shell(see "vibwndws.c" R5.38)
- *
- * Revision 5.18  1997/01/14  22:02:07  vakatov
- * Fixed inaccurate string copying -- <mostly potential> 1-byte exceeding of
- * the string size by StringNCat;  missing terminating '\0' by StringNCpy.
- * Removed some unused variables;  set preprocessor conditions more
- * thoroughly to exclude some functions from the compilation on some platforms.
- *
- * Revision 5.17  1997/01/03  21:45:37  vakatov
- * [WIN_MOTIF]  Unmanage(rather than destroy completely) menubar and its
- * cascade buttons to workaround the MOTIF/X11 "double memory freeing" quirk
- * (a "pure" simplest non-Vibrant MOTIF/X11 code also goes to the same bug).
- *
- * Revision 5.16  1996/11/18  20:52:41  vakatov
- * [WIN_MSWIN]  Allowed enabling/disabling of submenus and removing
- * of(top-level, menubar-attached only!) pulldown menus
- *
- * Revision 5.15  1996/11/08  16:54:07  vakatov
- * [WIN_MAC] RemoveMenuItemButNotSub(): now we can remove the submenu(J.Kans);
- * The problems were caused by a bug in "vibutils":Nlm_RemoveLink(), now
- * fixed(in Revision 5.7)
- *
- * Revision 5.14  1996/10/28  19:34:30  vakatov
- * [WIN_MOTIF]  Use Nlm_VibrantDefaultColormap() instead of the display
- * default colormap everywhere in the color handling code.
- * Made a lot of type castings to get rid of all compiler warnings.
- *
- * Revision 5.13  1996/10/10  20:22:17  vakatov
- * [WIN_MOTIF]  Rewrote Nlm_ResetPopList() function to avoid unexpected
- * displaying of popup-list on reset;  also got rid of the unnecessary
- * destroying and further re-creating of underlying widgets and data
- *
- * Revision 5.12  1996/10/04  23:38:19  kans
- * added Nlm_RemoveMenuItemButNotSub to prevent double removal of submenus
- * in windows.  this is tricky code, since submenus must really be installed
- * in the desktop menu bar, but attached to a menu item with the label.  this
- * change fixes a crash when a window containing a window submenu was removed,
- * but there may be uncollected garbage.
- *
- * Revision 5.11  1996/09/04  18:05:54  vakatov
- * [WIN_MOTIF]  PopupList & its Items::  prohibited automatic(Motif-initiated)
- * size change;  PopupList cascade button oversize:: increased from 48 to 52
- * pixels
- *
- * Revision 5.10  1996/07/26  18:12:28  kans
- * Colormap is Motif only
- *
- * Revision 5.9  1996/07/26  18:05:44  vakatov
- * [WIN_MOTIF]  Explicitly set colormaps for all pulldown menus;
- * changed the colormap switching method for the option menus
- * (to fit the LINUX/MOO-TIFF "features")
- *
- * Revision 5.8  1996/07/23  21:20:14  vakatov
- * [WIN_MOTIF]  Do not delay the pop-up(/down) menus realization as it
- * results in problems on SUN_OS and SGI4
- *
- * Revision 5.7  1996/07/09  20:29:10  vakatov
- * [WIN_MOTIF] [OS_UNIX_SUN] (see Revision 4.7 log) -- the same quirk is
- * for the XmPulldownMenu -- fixed
- *
- * Revision 5.6  1996/07/03  20:23:04  kans
- * don't extend margins everywhere - popups got enlarged improperly
- *
- * Revision 5.5  1996/07/03  19:42:37  kans
- * set margin height and width now that resize is automatic
- *
- * Revision 5.4  1996/07/03  16:57:13  vakatov
- * Menu items are allowed to change their size to fit a new title
- *
- * Revision 5.3  1996/06/20  18:19:14  kans
- * submenu before pulldown menu prevented notJustSubMenu from being set
- *
- * Revision 5.2  1996/06/20  17:03:52  kans
- * [WIN_MAC] if desktop menu bar created by submenu only, won't look for
- * command key accelerator (MenuKey call with no menus corrupted system)
- *
- * Revision 5.1  1996/06/14  14:31:24  vakatov
- * [WIN_MOTIF]  Added focus on/off event handler(new function MenuShellFocusCB)
- * to the OptionList's(ad hoc) menu shell -- to keep fixed colormap there
- *
- * Revision 4.9  1996/04/25  16:42:05  kans
- * removed Nlm_WindowMenuBarKey, which caused a crash
- *
- * Revision 4.8  1996/04/25  14:13:50  kans
- * removed Nlm_PopListKey, which caused a crash if no menus in program
- *
- * Revision 4.7  1996/03/27  19:29:51  vakatov
- * OS_UNIX_SUN quirk causing incorrect delayed realization of
- * XmOptionMenu, is fixed
- *
- * Revision 4.6  1996/03/05  19:59:08  epstein
- * fix call to XtSetSensitive()
- *
- * Revision 4.5  1996/03/02  22:36:38  kans
- * reduction of X traffic (DV)
- *
- * Revision 4.4  1996/02/13  17:24:07  kans
- * accelerated set position prior to realization (Denis Vakatov)
- *
- * Revision 4.3  1996/01/10  18:25:01  smirnov
- * AS: add Enable / Disable function for X11 popup.
- *
- * Revision 4.2  1995/12/25  16:03:50  kans
- * popup menu height now always Nlm_popupMenuHeight
- *
- * Revision 4.1  1995/11/27  15:13:41  kans
- * ResetMenu implementation for Windows and Motif (VL)
- *
- * Revision 4.0  1995/07/26  13:51:04  ostell
- * force revision to 4.0
- *
- * Revision 2.29  1995/07/19  20:42:23  kans
- * window rectangle takes Motif menu bar height into account
- *
 * ==========================================================================
 */
 
@@ -1746,13 +1510,13 @@ static void Nlm_DrawWindowMenuBar (Nlm_GraphiC mb)
   Rect bounds;
 
   wptr = Nlm_ParentWindowPtr (mb);
-  GetPortBounds(GetWindowPort(wptr), &bounds);
+  GetWindowPortBounds(wptr, &bounds);
   Nlm_RectToolToRecT (&bounds, &r);
   r.top = 19;
   r.bottom = 21;
   if (Nlm_RectInRgn (&r, Nlm_updateRgn)) {
-    MoveTo (0, 20);
-    LineTo (r.right, 20);
+    Nlm_MoveTo (0, 20);
+    Nlm_LineTo (r.right, 20);
   }
   m = (Nlm_MenU) Nlm_GetChild (mb);
   while (m != NULL) {
@@ -1857,8 +1621,12 @@ static void Nlm_ShowWindowMenuBar (Nlm_GraphiC mb, Nlm_Boolean setFlag, Nlm_Bool
   tempPort = Nlm_SavePortIfNeeded (mb, savePort);
   Nlm_SetVisible (mb, TRUE);
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  Nlm_SetGraphicNeedsDisplay (mb);
+#else
   Nlm_DoDraw (mb);
 #endif
+#endif
 #ifdef WIN_MSWIN
   wptr = Nlm_ParentWindowPtr (mb);
   DrawMenuBar (wptr);
@@ -1992,9 +1760,11 @@ static void Nlm_HidePulldown (Nlm_GraphiC m, Nlm_Boolean setFlag, Nlm_Boolean sa
 
   tempPort = Nlm_SavePortIfNeeded (m, savePort);
   Nlm_SetVisible (m, FALSE);
+#ifndef WIN_MAC_QUARTZ
   Nlm_GetRect (m, &r);
   Nlm_EraseRect (&r);
   Nlm_ValidRect (&r);
+#endif
   Nlm_RestorePort (tempPort);
 #endif
 }
diff --git a/vibrant/vibprocs.h b/vibrant/vibprocs.h
index 616b745d..f019069c 100644
--- a/vibrant/vibprocs.h
+++ b/vibrant/vibprocs.h
@@ -29,200 +29,13 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.32 $
+* $Revision: 6.33 $
 *
 * File Description: 
 *       Vibrant procedure definitions
 *
 * Modifications:  
 * --------------------------------------------------------------------------
-* $Log: vibprocs.h,v $
-* Revision 6.32  2007/05/01 22:01:30  kans
-* changes in preparation for supporing Quartz on Macintosh
-*
-* Revision 6.31  2006/09/27 18:30:00  kans
-* support for Int4 scroll bars for switching between text and doc views in Sequin (CB)
-*
-* Revision 6.30  2005/09/23 20:30:10  kans
-* added NLM_BACK for backspace key, which is separate from delete, even though the label may be the same on a keyboard
-*
-* Revision 6.29  2005/01/24 15:01:25  kans
-* prototype UsePrimaryMonitor
-*
-* Revision 6.28  2004/04/01 13:43:09  lavr
-* Spell "occurred", "occurrence", and "occurring"
-*
-* Revision 6.27  2004/02/23 16:36:51  sinyakov
-* Use Int4 instead of Int2 for cursor position and text selection in text boxes
-*
-* Revision 6.26  2004/02/12 20:05:26  bazhin
-* Added callback function "Nlm_SetKeepCrNlTextFieldCallback(Nlm_TexT t)",
-* which allows to copy-paste texts from multiple columns to single string.
-*
-* Revision 6.25  2004/02/05 16:25:06  kans
-* revert to Nlm_GetTextVScrollBar and Nlm_GetTextHScrollBar being static, implement setOffset and getOffset for scroll text, since Windows scroll text has its own scroll bar
-*
-* Revision 6.24  2004/02/04 15:21:02  kans
-* make GetTextVScrollBar and GetTextHScrollBar extern, to add search function to general text viewer
-*
-* Revision 6.23  2004/01/05 17:08:09  kans
-* added functions to control use of dual screens
-*
-* Revision 6.22  2003/10/29 19:19:34  kans
-* added prototype for Nlm_SetTextColor
-*
-* Revision 6.21  2002/04/30 18:25:12  bazhin
-* Added function "Nlm_SetWindowConfigureCallback(WindoW w)", which
-* allows to catch events, when window just moved without resizing.
-* Fixed some "gcc -Wall -ansi" warnings.
-*
-* Revision 6.20  2002/01/09 15:23:54  kans
-* added HasAquaMenuLayout
-*
-* Revision 6.19  2001/09/10 17:34:33  bazhin
-* Added function Nlm_SetTextCursorBlinkRate(Nlm_TexT t, Nlm_Int2 msec).
-*
-* Revision 6.18  2000/08/01 15:57:32  kans
-* separate lines for Nlm_HANDLE on all platforms, even if two are currently the same, and no space between # and define in case some compilers complain
-*
-* Revision 6.17  2000/08/01 15:23:29  vakatov
-* Addition to R6.13:   error if neither of "WIN_***" is #defined
-*
-* Revision 6.16  2000/07/31 13:28:46  lewisg
-* Nlm_GetExecPath
-*
-* Revision 6.15  2000/07/28 21:25:11  lewisg
-* *** empty log message ***
-*
-* Revision 6.14  2000/07/28 21:05:54  lewisg
-* more c++ fixes
-*
-* Revision 6.13  2000/07/28 15:36:34  kans
-* for OS_UNIX, give error message if WIN_MOTIF not defined
-*
-* Revision 6.12  2000/07/25 21:19:00  lewisg
-* eliminate redundant windows pathname code
-*
-* Revision 6.11  2000/07/25 19:18:36  lewisg
-* get pathname for executable on windows
-*
-* Revision 6.10  2000/07/14 20:30:40  kans
-* added Nlm_MSWin_OpenApplication (for launching Cn3D with a data file)
-*
-* Revision 6.9  1999/04/06 14:23:26  lewisg
-* add opengl replacement for viewer3d
-*
-* Revision 6.8  1999/02/19 20:48:36  vakatov
-* [WIN_MSWIN]  Added Nlm_MSWin_OpenDocument(also can be used to
-* auto-launch IE or Netscape if passed an URL)
-*
-* Revision 6.7  1999/01/07 22:32:36  kans
-* added Mac-specific Nlm_SendURLAppleEvent
-*
-* Revision 6.6  1998/07/07 23:03:34  vakatov
-* Added Nlm_Execv() to spawn applications with cmd-line parameters;
-* now implemented for [OS_MSWIN, OS_UNIX].
-*
-* Revision 6.5  1998/03/22 03:00:59  kans
-* changed names to RegisterServiceProc and RegisterResultProc
-*
-* Revision 6.4  1998/03/22 02:33:17  kans
-* added request proc, result proc, message handlers to support, and send open doc event, launch app now work with file names or signatures
-*
-* Revision 6.3  1998/03/17 21:07:59  kans
-* added Nlm_SendOpenDocAppleEventEx, and private Nlm_LaunchAppEx
-*
-* Revision 6.2  1997/11/12 20:56:09  kans
-* added SetMouseMoveCallback and SetMouseMoveRegion, implemented first on Mac
-*
-* Revision 6.1  1997/10/18 23:30:21  kans
-* implemented Nlm_GetTextCursorPos (DV)
-*
-* Revision 6.0  1997/08/25 18:57:29  madden
-* Revision changed to 6.0
-*
-* Revision 5.18  1997/08/04 14:15:11  vakatov
-* Added Nlm_SetTextCursorPos() function
-*
-* Revision 5.17  1997/08/01 16:47:28  vakatov
-* [WIN_MOTIF,WIN_MSWIN]  Added IconifyWindow() and IconicWindow()
-*
-* Revision 5.16  1997/07/21 21:52:37  vakatov
-* [WIN_MOTIF] Added Nlm_[Un]RegisterIO() functions to wait for I/O
-* events and call(via X) user-defined callback(s)
-*
-* Revision 5.15  1997/07/18 17:01:13  vakatov
-* [WIN_MOTIF]  Removed "arg[cv]";  use "Nlm_GetArg[cv]()" instead
-*
-* Revision 5.14  1997/07/16 19:47:00  vakatov
-* +Nlm_StrngPrintable() proto
-*
-* Revision 5.13  1997/06/23 21:18:46  vakatov
-* Added Nlm_SetTextEditable() function to allow/prohibit text editing
-*
-* Revision 5.12  1997/05/27 21:50:55  vakatov
-* Added Nlm_PopupParentWindow() to popup window w/o switching input focus
-*
-* Revision 5.11  1997/04/28 21:42:46  vakatov
-* Added AUTO_FOCUS, FOCUS_NAVIG and DEFAULT_SLATE_POLICY defs & comments
-*
- * Revision 5.10  1997/04/25  16:08:45  vakatov
- * Changed old and added new navigation and special key names.
- * Added Nlm_SetSlatePolicy() and definitions for now available slate
- * navigation key handling policies.
- * Added Nlm_Scroll() -- for one-line/one-page scrolling of scrollbars.
- *
- * Revision 5.9  1997/03/19  15:57:07  vakatov
- * Added:  Nlm_Boolean Nlm_QuittingProgram PROTO((void));
- *
- * Revision 5.8  1996/12/12  23:11:10  kans
- * added Nlm_ClipPrintingRect (DV)
- *
- * Revision 5.7  1996/09/26  00:29:23  kans
- * added SetWindowTimer
- *
- * Revision 5.6  1996/09/09  00:15:01  kans
- * AutonomousPanel4 uses ScrollBar4 to have > 32K positions
- *
- * Revision 5.5  1996/08/27  20:56:26  vakatov
- * Added prototypes of function for creating and handling Int2- and
- * Int4-range scrollbars homogeneously
- *
- * Revision 5.4  1996/07/25  18:49:02  vakatov
- * Added prototype of Nlm_GetBarMax()
- *
- * Revision 5.3  1996/06/19  20:30:42  vakatov
- * Added prototype for function Nlm_GetListItem()
- *
- * Revision 5.2  1996/06/14  14:26:46  vakatov
- * Nlm_SetColorCell() -- to immediately change the color appearence
- * [WIN_MOTIF]  Nlm_RestrictMotifColorsTo() -- to avoid Motif/3D-Viewer
- * color overlapping
- *
- * Revision 5.1  1996/05/31  20:11:14  vakatov
- * Added Nlm_ExtendedList() function to set the list selection policy
- * to EXTENDED_SELECTION -- as it was for Nlm_MultiList() since Revision 4.4.
- *
- * Revision 4.5  1996/04/24  21:25:17  vakatov
- *  Nlm_WaitForCondition(cond) modified; now it waits until the next X-event
- * rather than sleeping 100, 200, ..., 900 msec.
- *  Nlm_WaitForXEvent() function added for this reason.
- *
- * Revision 4.4  1996/03/27  23:09:15  vakatov
- * Function Nlm_SetCursorShape() added to let programmer
- * easily store/restore current cursor shape
- *
- * Revision 4.3  1996/03/11  20:39:19  epstein
- * add support for Drag & Drop
- *
- * Revision 4.2  1995/11/08  23:30:31  kans
- * removed edit block fields, which belong in the application
- *
- * Revision 4.1  1995/10/06  16:44:39  epstein
- * add Nlm_WaitForCondition macro
- *
- * Revision 2.56  1995/05/31  18:00:58  kans
- * added SetColorMap
 *
 * ==========================================================================
 */
@@ -1237,6 +1050,7 @@ Nlm_VoidPtr Nlm_GetObject PROTO((Nlm_GraphiC a));
 extern void Nlm_SendOpenDocAppleEvent PROTO((Nlm_CharPtr datafile, Nlm_CharPtr sig));
 extern void Nlm_SendOpenDocAppleEventEx PROTO((Nlm_CharPtr datafile, Nlm_CharPtr sig, Nlm_CharPtr prog, Nlm_Boolean wantReply));
 extern void Nlm_SendURLAppleEvent (Nlm_CharPtr urlString, Nlm_CharPtr sig, Nlm_CharPtr prog);
+extern void Nlm_SendAppleScriptString (Nlm_CharPtr script);
 #endif
 
 #ifdef WIN_MSWIN
diff --git a/vibrant/vibslate.c b/vibrant/vibslate.c
index b463dc5b..23d35932 100644
--- a/vibrant/vibslate.c
+++ b/vibrant/vibslate.c
@@ -29,218 +29,14 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.44 $
+* $Revision: 6.45 $
 *
 * File Description:
 *       Vibrant slate (universal drawing environment) functions
 *
 * Modifications:
 * --------------------------------------------------------------------------
-* $Log: vibslate.c,v $
-* Revision 6.44  2006/09/14 14:45:38  kans
-* changes for 64-bit Windows (GC) plus a few CodeWarrior complaints (JK)
 *
-* Revision 6.43  2004/04/14 19:15:51  sinyakov
-* WIN_MSWIN: support X-Windows-like -bg color command line option
-*
-* Revision 6.42  2002/11/06 21:32:25  ucko
-* Nlm_LoadSlateData: initialize sptr->cMap to 0 rather than NULL, as it
-* is an integer rather than a pointer.
-*
-* Revision 6.41  2001/05/25 20:04:39  vakatov
-* Nested comment typo fixed
-*
-* Revision 6.40  2001/05/15 15:57:25  juran
-* Include glu.h instead of GL/glu.h on the Mac.
-*
-* Revision 6.39  2000/08/17 16:13:21  thiessen
-* fix X/OpenGL initialization bug
-*
-* Revision 6.38  2000/07/28 21:05:55  lewisg
-* more c++ fixes
-*
-* Revision 6.37  2000/03/13 15:58:18  thiessen
-* warn user about buggy 8-bit OpenGL
-*
-* Revision 6.36  2000/03/09 17:55:18  thiessen
-* changes to palette handling for 8-bit OpenGL
-*
-* Revision 6.35  2000/03/06 18:35:23  thiessen
-* fixes for 8-bit color
-*
-* Revision 6.34  2000/02/07 20:17:36  lewisg
-* minor bug fixes, use gui font for win32
-*
-* Revision 6.33  2000/02/03 22:29:15  lewisg
-* make windows version of vibrant use standard color
-*
-* Revision 6.32  2000/01/12 15:13:01  thiessen
-* fixed minor OpenGL memory leak
-*
-* Revision 6.31  2000/01/11 02:55:15  thiessen
-* working off-screen OpenGL rendering on Win32
-*
-* Revision 6.30  2000/01/07 19:37:06  thiessen
-* fix minor OpenGL problems
-*
-* Revision 6.29  2000/01/07 16:28:36  thiessen
-* fixed broken header conflicts
-*
-* Revision 6.28  2000/01/07 01:17:33  kans
-* needed to include ncbi.h first
-*
-* Revision 6.27  2000/01/07 00:22:46  thiessen
-* fixes for LessTif and OpenGL X visual selection
-*
-* Revision 6.26  2000/01/06 17:23:36  thiessen
-* various OpenGL improvements
-*
-* Revision 6.25  1999/12/07 19:18:58  thiessen
-* fixed font color problem in OpenGL on SGI
-*
-* Revision 6.24  1999/12/06 14:44:00  thiessen
-* made OpenGL font selection work in X/Motif
-*
-* Revision 6.23  1999/11/23 19:24:16  thiessen
-* better solution to OpenGL render rect setting on Mac
-*
-* Revision 6.22  1999/11/19 18:07:24  thiessen
-* added label capability for OpenGL version on Mac and Motif
-*
-* Revision 6.21  1999/11/03 15:38:04  thiessen
-* minor fix for Mac/OpenGL
-*
-* Revision 6.20  1999/10/27 20:18:11  thiessen
-* rearrangement of OpenGL color depth priorities
-*
-* Revision 6.19  1999/10/26 13:11:05  thiessen
-* added resize callback to Motif 3DSlate
-*
-* Revision 6.18  1999/10/25 19:40:46  thiessen
-* (temporary) fix so that Mac/OpenGL version correctly lets user resize window
-*
-* Revision 6.17  1999/10/05 17:35:23  thiessen
-* minor fix to glX initialization
-*
-* Revision 6.16  1999/10/04 14:27:17  thiessen
-* hacked partial compatibility with Mesa OpenGL implementation - does *not* work when rendering inside vibrant window in Motif
-*
-* Revision 6.15  1999/09/27 18:28:30  thiessen
-* Made 24-bit and doublebuffered OpenGL modes work on Mac; also should select
-* mode like X
-*
-* Revision 6.14  1999/09/27 16:28:41  thiessen
-* hacked in ability to use higher-than-8-bit color mode in OpenGL in a separate (non-vibrant) X-window
-*
-* Revision 6.13  1999/09/22 20:09:04  thiessen
-* port of OpenGL code to Macintosh
-*
-* Revision 6.12  1999/09/21 13:45:30  thiessen
-* port of Lewis's OpenGL code to X/Motif
-*
-* Revision 6.11  1999/09/20 20:12:56  lewisg
-* change typedefs for a colorcell, add triangle generator, fix incorrect return values
-*
-* Revision 6.10  1999/07/06 14:51:42  kans
-* resize scroll bar was one pixel too small
-*
-* Revision 6.9  1999/04/22 15:18:59  vakatov
-* Call XtUnrealizeWidget() before XtDestroyWidget() to make sure no
-* "post-mortem" callbacks(registered by XtAddEventHandler()) get
-* triggered for the destroyed widget. Reason: the widget may not be
-* immediately destroyed if XtDestroyWidget() was called in a nested
-* event dispatch loop.
-*
-* Revision 6.8  1999/04/06 14:23:26  lewisg
-* add opengl replacement for viewer3d
-*
-* Revision 6.7  1998/12/14 18:39:10  kans
-* okayToDrawContents extern, used to inhibit slate drawing
-*
-* Revision 6.6  1998/06/25 21:42:38  vakatov
-* Fixed(slightly) the slate scroll bar positioning
-* [WIN_MSWIN] Adjusted slate dimensions
-*
-* Revision 6.5  1997/12/18 16:51:43  vakatov
-* [WIN_X11]  setup "Nlm_updateRect" in Nlm_SlateDrawCallback()
-*
-* Revision 6.4  1997/11/26 21:30:39  vakatov
-* Fixed errors and warnings issued by C and C++ (GNU and Sun) compilers
-*
-* Revision 6.3  1997/10/01 21:51:48  vakatov
-* Trying to catch strayed Expose or MapNotify(for SetVisible(...)) event
-*
-* Revision 6.2  1997/09/08 18:49:47  vakatov
-* Nlm_SlateDrawCallback() -- before processing slate's Expose events process
-* StructureNotifyMask-masked events for both the slate and its parent window
-*
-* Revision 6.1  1997/08/27 14:22:26  vakatov
-* Nlm_SlateDrawCallback() -- check for the window mapping event before
-* the call of Nlm_DrawSlate() /see also "vibwndws.c" R5.70/
-*
-* Revision 6.0  1997/08/25 18:57:39  madden
-* Revision changed to 6.0
-*
-* Revision 5.10  1997/07/10 21:49:39  vakatov
-* [WIN_X]  Now able to manage windows having different depths(and
-* different visuals and GC).
-*
-* Revision 5.9  1997/06/06 21:01:35  vakatov
-* [WIN_MOTIF]  Refuse input focus if AUTO_FOCUS slate policy is not set
-*
-* Revision 5.8  1997/04/28 21:50:35  vakatov
-* Implemented AUTO_FOCUS and FOCUS_NAVIG slate policies(see comments
-* in "vibprocs.h" R5.11 for details)
-*
- * Revision 5.7  1997/04/25  21:22:00  vakatov
- * Made slate do not intercept input when the slate is not visible
- *
- * Revision 5.6  1997/04/25  16:12:13  vakatov
- * [WIN_MOTIF, WIN_MSWIN] Added slate navigation key handlers for the
- * slate input and gainFocus()
- * [WIN_MOTIF] DisCapture slate if it losed input focus
- * [WIN_MOTIF] Two slate input callbacks merged into one
- * Disabled automatic navig. key handling when the slate has captured
- * input focus and has user-defined keyProc != NULL
- * Extensive code cleaning and type casting
- *
- * Revision 5.5  1996/09/09  12:19:40  kans
- * NewSlate was getting the wrong horizontal scroll bar callback
- *
- * Revision 5.4  1996/09/09  00:15:01  kans
- * AutonomousPanel4 uses ScrollBar4 to have > 32K positions
- *
- * Revision 5.3  1996/08/27  21:03:48  vakatov
- * Nlm_RegisterRow() :  Nlm_SetValue() replaced by Nlm_CorrectBarValue() in
- * order to avoid undesirable recursion in the scrollbar action callback
- *
- * Revision 5.2  1996/07/25  14:52:01  epstein
- * add alignment variable for possibly improved portability
- *
- * Revision 5.1  1996/05/30  20:07:36  vakatov
- * [WIN_MSWIN]  <Shift> and <Ctrl> key status checking moved to MainProc()
- *
- * Revision 4.6  1996/04/25  17:50:55  vakatov
- * SlateProc()/WIN_MSWIN:  <Shift> and <Ctrl> key state error fixed
- *
- * Revision 4.5  1996/03/02  22:36:38  kans
- * reduction of X traffic (DV)
- *
- * Revision 4.4  1996/02/16  23:16:02  kans
- * set slate position always calls InvalSlate on all platforms
- *
- * Revision 4.3  1996/02/13  17:24:07  kans
- * accelerated set position prior to realization (Denis Vakatov)
- *
- * Revision 4.2  1995/09/06  20:30:24  kans
- * fixed bug due to GetWindowRect vs. GetClientRect (AS + GS)
- *
- * Revision 4.1  1995/08/14  21:38:37  kans
- * removal of remaining C str... functions
- *
- * Revision 2.37  1995/06/28  21:48:57  kans
- * added Add and Del SubwindowShell (Alex)
- *
 * ==========================================================================
 */
 
@@ -1256,8 +1052,12 @@ static void Nlm_ShowSlate (Nlm_GraphiC s, Nlm_Boolean setFlag, Nlm_Boolean saveP
     }
     h = Nlm_GetSlateHandle ((Nlm_SlatE) s);
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+	Nlm_SetGraphicNeedsDisplay (s);
+#else
     Nlm_DoDraw (s);
 #endif
+#endif
 #ifdef WIN_MSWIN
     ShowWindow (h, SW_SHOW);
     UpdateWindow (h);
@@ -1325,7 +1125,10 @@ static void Nlm_HideSlate (Nlm_GraphiC s, Nlm_Boolean setFlag, Nlm_Boolean saveP
   h = Nlm_GetSlateHandle ((Nlm_SlatE) s);
 #ifdef WIN_MAC
   if (Nlm_AllParentsButWindowVisible (s)) {
-    Nlm_GetRect (s, &r);
+#ifdef WIN_MAC_QUARTZ
+	Nlm_SetGraphicNeedsDisplay (s);
+#else
+	Nlm_GetRect (s, &r);
     if (vsb != NULL) {
       r.right += Nlm_vScrollBarWidth;
     }
@@ -1335,6 +1138,7 @@ static void Nlm_HideSlate (Nlm_GraphiC s, Nlm_Boolean setFlag, Nlm_Boolean saveP
     Nlm_InsetRect (&r, -1, -1);
     Nlm_EraseRect (&r);
     Nlm_ValidRect (&r);
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -2109,7 +1913,7 @@ static void Nlm_PaintOrFormatChar (Nlm_GraphiC d, Nlm_Char ch, Nlm_Boolean saveP
   if (Nlm_GetVisible (d) && Nlm_AllParentsButWindowVisible (d)) {
     tempPort = Nlm_SavePortIfNeeded (d, savePort);
     Nlm_DoSelect (d, FALSE);
-#ifdef WIN_MAC
+#if defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ)
     GetPenState (&state);
     PenNormal ();
 #endif
@@ -2152,7 +1956,7 @@ static void Nlm_PaintOrFormatChar (Nlm_GraphiC d, Nlm_Char ch, Nlm_Boolean saveP
         }
         break;
     }
-#ifdef WIN_MAC
+#if defined(WIN_MAC) && !defined(WIN_MAC_QUARTZ)
     SetPenState (&state);
 #endif
     Nlm_SelectFont (Nlm_systemFont);
diff --git a/vibrant/vibtexts.c b/vibrant/vibtexts.c
index 8e2a5a7d..15ae861f 100644
--- a/vibrant/vibtexts.c
+++ b/vibrant/vibtexts.c
@@ -29,237 +29,13 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.34 $
+* $Revision: 6.36 $
 *
 * File Description: 
 *       Vibrant edit text functions
 *
 * Modifications:  
 * --------------------------------------------------------------------------
-* $Log: vibtexts.c,v $
-* Revision 6.34  2007/05/02 14:55:58  kans
-* preparation for supporting Quartz on Mac
-*
-* Revision 6.33  2006/09/27 18:30:00  kans
-* support for Int4 scroll bars for switching between text and doc views in Sequin (CB)
-*
-* Revision 6.32  2006/09/14 19:18:29  ivanov
-* Rollback last changes. All missed defines added to corelib/ncbiwin.h.
-*
-* Revision 6.31  2006/09/14 18:05:45  ivanov
-* Fixed compilation errors on MS Windows
-*
-* Revision 6.30  2006/09/14 14:45:39  kans
-* changes for 64-bit Windows (GC) plus a few CodeWarrior complaints (JK)
-*
-* Revision 6.29  2005/07/18 15:15:18  kans
-* fixed minor xcode compiler warnings
-*
-* Revision 6.28  2004/07/19 13:36:43  bollin
-* replaced obsolete XmFontListCreate function to get rid of run-time warnings
-*
-* Revision 6.27  2004/06/24 15:34:48  bollin
-* added lines from Yoon Choi to make ctrl-A select all text in TextMode in
-* Sequin
-*
-* Revision 6.26  2004/03/17 16:09:14  sinyakov
-* WIN_MSWIN: fixed text box activation and text selection logic,
-* do not reset currentText when text window loses focus (to match Motif version),
-* removed scroll text size limit,
-* in Nlm_SelectAText(): scroll selection into view for scroll text,
-* in Nlm_TextGainFocus(), when focus changes to a single-line edit box,
-* do not highlight all text, instead just set the cursor pos to beginning,
-* in MyCls_OnChar(), multiline edit boxes accept tabs
-* as input characters and not as focus change commands.
-*
-* Revision 6.25  2004/02/23 16:36:52  sinyakov
-* Use Int4 instead of Int2 for cursor position and text selection in text boxes
-*
-* Revision 6.24  2004/02/17 16:01:15  bollin
-* implemented Nlm_SetScrollTextOffset for Motif
-*
-* Revision 6.23  2004/02/12 20:29:09  kans
-* put ifdef WIN_MOTIF wrapper around Nlm_KeepCrNlTextFieldCallback
-*
-* Revision 6.22  2004/02/12 20:05:10  bazhin
-* Added callback function "Nlm_SetKeepCrNlTextFieldCallback(Nlm_TexT t)",
-* which allows to copy-paste texts from multiple columns to single string.
-*
-* Revision 6.21  2004/02/09 17:46:27  bollin
-* added fix from Yoon Choi for copy-paste from Windows clipboard into Unix application
-*
-* Revision 6.20  2004/02/06 19:27:33  bollin
-* Use PostMessage to communicate with scrolling function on TextViewer window
-*
-* Revision 6.19  2004/02/05 16:25:05  kans
-* revert to Nlm_GetTextVScrollBar and Nlm_GetTextHScrollBar being static, implement setOffset and getOffset for scroll text, since Windows scroll text has its own scroll bar
-*
-* Revision 6.18  2004/02/04 15:21:03  kans
-* make GetTextVScrollBar and GetTextHScrollBar extern, to add search function to general text viewer
-*
-* Revision 6.17  2003/11/17 17:03:30  kans
-* changed C++ style comments to C comments
-*
-* Revision 6.16  2003/11/03 21:51:34  sinyakov
-* WIN_MSWIN: bugfix: strlen(title) moved out of loop condition
-*
-* Revision 6.15  2003/10/29 19:10:08  bazhin
-* Added function Nlm_SetTextColor(Nlm_TexT t, Nlm_Uint4 r, Nlm_Uint4 g,
-*                                 Nlm_Uint4 b).
-*
-* Revision 6.14  2003/07/30 13:51:42  johnson
-* MSWIN: multi-line text boxes now respond to 'enter' key
-*
-* Revision 6.13  2003/03/28 21:27:18  rsmith
-* on Mac OS took out ClearCurrentScrap after Cut/Copy. It only erased whatever was copied.
-*
-* Revision 6.12  2003/01/07 15:08:11  shomrat
-* Change condition in for loop in Nlm_SetScrollText
-*
-* Revision 6.11  2002/12/04 22:35:11  johnson
-* WIN_MSWIN: replace UNIX '\n' with DOS "\r\n" in Nlm_SetScrollText
-*
-* Revision 6.10  2001/09/10 17:58:28  bazhin
-* Removed odd lines from SetTextCursorBlinkRate() function.
-*
-* Revision 6.9  2001/09/10 17:34:10  bazhin
-* Added function Nlm_SetTextCursorBlinkRate(Nlm_TexT t, Nlm_Int2 msec).
-*
-* Revision 6.8  2001/05/14 20:29:04  juran
-* Redesign Mac clipboard support.
-*
-* Revision 6.7  2000/05/02 22:02:15  vakatov
-* Nlm_TextCallback():  get rid of an extra condition
-*
-* Revision 6.6  2000/03/31 19:20:03  thiessen
-* fix recursion bug
-*
-* Revision 6.5  2000/02/07 20:17:36  lewisg
-* minor bug fixes, use gui font for win32
-*
-* Revision 6.4  1998/07/02 18:24:35  vakatov
-* Cleaned the code & made it pass through the C++ compilation
-*
-* Revision 6.3  1997/12/19 18:01:45  vakatov
-* [X11,MSWIN]  When pasting into a single-line text field, replace all
-* non-printable characters by spaces
-*
-* Revision 6.2  1997/11/26 21:30:42  vakatov
-* Fixed errors and warnings issued by C and C++ (GNU and Sun) compilers
-*
-* Revision 6.1  1997/10/18 23:30:16  kans
-* implemented Nlm_GetTextCursorPos (DV)
-*
-* Revision 6.0  1997/08/25 18:57:44  madden
-* Revision changed to 6.0
-*
-* Revision 5.22  1997/08/07 16:46:39  vakatov
-* [WIN_MOTIF] Nlm_PasswordCallback() -- process <DEL> at the first text pos
-*
-* Revision 5.21  1997/08/07 13:38:32  kans
-* password text does action callback on delete (Mac)
-*
-* Revision 5.20  1997/08/05 16:42:26  kans
-* allowTextCallback not declared in Mac, so ifdefs changed in Nlm_SetTextCursorPos
-*
-* Revision 5.19  1997/08/04 14:15:14  vakatov
-* Added Nlm_SetTextCursorPos() function
-*
-* Revision 5.18  1997/07/21 18:49:09  vakatov
-* [WIN_MAC] SetPasswordText() -- moved "r" and "GetRect()"(sorry, missed
-* that!) back to the if(Visible... scope
-*
-* Revision 5.17  1997/07/21 18:39:42  kans
-* SetPasswordText r in Mac version at top scope
-*
-* Revision 5.16  1997/07/21 18:24:36  vakatov
-* SetPasswordText() -- show all symbols as '*'
-*
-* Revision 5.15  1997/07/17 15:31:47  vakatov
-* [WIN_MSWIN]  Emulate non-editable text(crack WM_CHAR event in TextProc
-* as the WinSDK's Edit_SetReadOnly lead to invalidation bug for ScrollText)
-*
-* Revision 5.14  1997/07/16 13:47:20  kans
-* non-editable scroll text now scrolls on Mac
-*
-* Revision 5.12  1997/07/13 23:03:05  kans
-* ScrollText height is in stdLineHeight units
-*
-* Revision 5.11  1997/07/08 13:42:06  kans
-* ttool to rtool fix in Nlm_DrawScrollText/DCLAP
-*
-* Revision 5.10  1997/06/24 21:30:37  kans
-* implemented SetTextEditable on Mac
-*
-* Revision 5.9  1997/06/24 19:10:00  vakatov
-* Nlm_ScrollText() -- calculate the text box limits using the systemFont
-* (not the current font!) dimensions
-*
-* Revision 5.8  1997/06/23 21:21:05  vakatov
-* Added Nlm_SetTextEditable() function to allow/prohibit text editing
-* [WIN_MOTIF] Made text widgets to fit the specified number of lines
-*
-* Revision 5.7  1997/04/25 16:14:06  vakatov
-* [WIN_MOTIF,WIN_MSWIN] Catch and render(DoSendFocus) navigation key events
-* Extensive code cleaning and type casting
-*
- * Revision 5.6  1997/02/12  17:47:28  vakatov
- * [WIN_MOTIF]  Do not reset selection when activating a window containing
- * a text or when the text is empty
- *
- * Revision 5.5  1997/01/29  17:53:59  kans
- * minor changes due to StringNCpy_0 change
- *
- * Revision 5.4  1997/01/29  16:41:22  kans
- * using StringNCpy_0
- *
- * Revision 5.3  1996/07/23  21:07:10  epstein
- * Vakatov/Epstein avoid trying to clear an area on an unrealized window
- *
- * Revision 5.2  1996/06/18  15:44:56  vakatov
- * Do not assign last (maxsize-1) symbol of output buffer
- * in Nlm_GetScrollText() and Nlm_GetDialogText() to '\0'.
- *
- * Revision 5.1  1996/06/17  19:28:17  vakatov
- * [WIN_MOTIF]  Positioning of scrolled text postponed until its realization
- *
- * Revision 4.9  1996/05/08  20:42:52  vakatov
- * [WIN_MOTIF]  Nlm_PasswordCallback() function -- rewritten to avoid stack
- * corruption on the case of too long(>30 symbols) user input and
- * to make the password text field more convenient to edit;
- * [ALL]  Nlm_GetPasswordLength() function added (other than
- * Nlm_TextLength());  a lot of other tiny changes and corrections
- *
- * Revision 4.8  1996/05/08  13:43:47  vakatov
- * [WIN_MOTIF]  Modified Nlm_SetPasswordText() to reset the password
- *
- * Revision 4.7  1996/05/03  17:02:08  kans
- * added a cast to SelectText call
- *
- * Revision 4.6  1996/03/02  22:36:38  kans
- * reduction of X traffic (DV)
- *
- * Revision 4.5  1996/02/13  17:24:07  kans
- * accelerated set position prior to realization (Denis Vakatov)
- *
- * Revision 4.4  1995/11/27  16:04:00  kans
- * ScrollText now handles killfocus and setfocus messages (VL)
- *
- * Revision 4.3  1995/11/27  15:13:41  kans
- * allow select and deselect callbacks for DialogText and ScrollText (VL)
- *
- * Revision 4.2  1995/11/08  23:30:31  kans
- * removed edit block fields, which belong in the application
- *
- * Revision 4.1  1995/10/10  15:51:53  kans
- * fully implemented scroll text resizing
- *
- * Revision 2.52  1995/07/14  17:48:26  kans
- * forces dialog, hidden text to use systemFont (AS)
- *
- * Revision 2.51  1995/05/20  18:27:38  kans
- * corrected accidental prevention of passing returns to other objects
- *
 *
 * ==========================================================================
 */
@@ -271,7 +47,7 @@
 #ifdef WIN_MAC
 #ifdef WIN_MAC_QUARTZ
 #define Nlm_TextTool TXNObject
-extern CGRect Nlm_RecTToCGRect(Nlm_RectPtr r);
+extern CGRect Nlm_RecTToCGRect(Nlm_RecT r);
 #else
 #define Nlm_TextTool TEHandle
 #endif
@@ -1772,8 +1548,10 @@ static void Nlm_TextSelectProc (Nlm_GraphiC t, Nlm_Boolean savePort)
 #ifdef WIN_MAC
   Nlm_Int2      end;
   Nlm_TextTool  h;
-  TEPtr         hp;
   Nlm_WindoW    tempPort;
+#ifndef WIN_MAC_QUARTZ
+  TEPtr         hp;
+#endif
 
   if (t != NULL) {
     tempPort = Nlm_SavePortIfNeeded (t, savePort);
@@ -2051,10 +1829,12 @@ static void Nlm_GetDialogText (Nlm_GraphiC t, Nlm_Int2 item,
   Nlm_TextTool  h;
 #ifdef WIN_MAC
   Nlm_Char      **chars;
-  TEPtr         hp;
   Nlm_Int2      i;
   Nlm_Int2      length;
   Nlm_Char      *ptr;
+#ifndef WIN_MAC_QUARTZ
+  TEPtr         hp;
+#endif
 #endif
 #ifdef WIN_MOTIF
   Nlm_CharPtr   ptr;
@@ -2111,10 +1891,12 @@ static void Nlm_GetScrollText (Nlm_GraphiC t, Nlm_Int2 item,
   Nlm_TextTool  h;
 #ifdef WIN_MAC
   Nlm_Char      **chars;
-  TEPtr         hp;
   Nlm_Int2      i;
   Nlm_Int2      length;
   Nlm_Char      *ptr;
+#ifndef WIN_MAC_QUARTZ
+  TEPtr         hp;
+#endif
 #endif
 #ifdef WIN_MOTIF
   Nlm_CharPtr   ptr;
@@ -2500,7 +2282,7 @@ static LRESULT CALLBACK EXPORT TextProc (HWND hwnd, UINT message,
           break;  /* no suitable data found in the clipboard */
 
         for (str = text;  *str;  str++)
-          if ( !isprint(*str) ) {
+          if ( !isprint((unsigned char)*str) ) {
             *str = ' ';
             call_win_proc = FALSE;
           }
@@ -2634,7 +2416,9 @@ static void Nlm_SetTextPosition (Nlm_GraphiC t, Nlm_RectPtr r,
   Nlm_WindoW    tempPort;
   Nlm_RecT      tr;
 #ifdef WIN_MAC
+#ifndef WIN_MAC_QUARTZ
   TEPtr         hp;
+#endif
   Nlm_RectTool  rtool;
 #endif
 
@@ -2700,7 +2484,9 @@ static void Nlm_SetHiddenTextPosition (Nlm_GraphiC t, Nlm_RectPtr r,
   Nlm_WindoW    tempPort;
   Nlm_RecT      tr;
 #ifdef WIN_MAC
+#ifndef WIN_MAC_QUARTZ
   TEPtr         hp;
+#endif
   Nlm_RectTool  rtool;
 #endif
 
@@ -2723,11 +2509,17 @@ static void Nlm_SetHiddenTextPosition (Nlm_GraphiC t, Nlm_RectPtr r,
   tr = *r;
 #ifdef WIN_MAC
   Nlm_RecTToRectTool (&tr, &rtool);
+#ifdef WIN_MAC_QUARTZ
+  CGRect viewCG = Nlm_RectQDToCG (rtool);
+  CGRect destCG = Nlm_RectQDToCG (rtool);
+  TXNSetHIRectBounds (h, &viewCG, &destCG, 1);
+#else
   HLock ((Handle) h);
   hp = (TEPtr) *((Handle) h);
   hp->destRect = rtool;
   hp->viewRect = rtool;
   HUnlock ((Handle) h);
+#endif
   Nlm_SetRect (t, r);
   Nlm_InvalText (t);
 #endif
@@ -2972,9 +2764,13 @@ static void Nlm_SetScrollTextPosition (Nlm_GraphiC t, Nlm_RectPtr r,
   Nlm_Int2      deltax;
   Nlm_Int2      deltay;
   Nlm_RectTool  dtool;
+#ifndef WIN_MAC_QUARTZ
   TEPtr         hp;
+#endif
   Nlm_RectTool  rtool;
   Nlm_BaR       sb;
+  Rect          textViewRect;
+  Rect          textDestRect;
 #endif
   Nlm_Boolean   is_realized;
 
@@ -3021,19 +2817,34 @@ static void Nlm_SetScrollTextPosition (Nlm_GraphiC t, Nlm_RectPtr r,
       Nlm_ResetVisLines ((Nlm_TexT) t);
       Nlm_InsetRect (&tr, 4, 2);
       tr.bottom = tr.top + Nlm_GetVisLines ((Nlm_TexT) t) * Nlm_GetFontHeight ((Nlm_TexT) t);
+#ifdef WIN_MAC_QUARTZ
+      TXNGetViewRect (h, &textViewRect);
+      CGRect cgr;
+      TXNGetHIRect (h, kTXNDestinationRectKey, &cgr);
+      textDestRect = Nlm_RectCGToQD (cgr);
+#else
       HLock ((Handle) h);
       hp = (TEPtr) *((Handle) h);
-      deltax = hp->destRect.left - hp->viewRect.left;
-      deltay = hp->destRect.top - hp->viewRect.top;
+      textViewRect = hp->viewRect;
+      textDestRect = hp->destRect;
+#endif
+      deltax = textDestRect.left - textViewRect.left;
+      deltay = textDestRect.top - textViewRect.top;
       Nlm_RecTToRectTool (&tr, &rtool);
       Nlm_OffsetRect (&tr, deltax, deltay);
       Nlm_RecTToRectTool (&tr, &dtool);
       if (! wrap) {
     dtool.right += HSCROLL_POSITIONS * Nlm_stdCharWidth;
       }
+#ifdef WIN_MAC_QUARTZ
+      CGRect viewCG = Nlm_RectQDToCG (textViewRect);
+      CGRect destCG = Nlm_RectQDToCG (textDestRect);
+      TXNSetHIRectBounds (h, &viewCG, &destCG, 1);
+#else
       hp->destRect = dtool;
       hp->viewRect = rtool;
       HUnlock ((Handle) h);
+#endif
       Nlm_InvalScrollText (t);
     }
 
@@ -3365,7 +3176,7 @@ static void Nlm_NewDialogText (Nlm_TexT t, Nlm_CharPtr dfault, Nlm_TxtActnProc a
   Nlm_InsetRect (&r, 2, 2);
   Nlm_RecTToRectTool (&r, &rtool);
 #ifdef WIN_MAC_QUARTZ
-  cgr = Nlm_RecTToCGRect(&r);
+  cgr = Nlm_RecTToCGRect(r);
   TXNCreateObject( &cgr, kTXNSingleLineOnlyMask, &h);
   TXNAttachObjectToWindowRef(h, wptr);
 #else
@@ -3483,7 +3294,7 @@ static void Nlm_NewPasswordText (Nlm_TexT t, Nlm_CharPtr dfault, Nlm_TxtActnProc
   Nlm_InsetRect (&r, 2, 2);
   Nlm_RecTToRectTool (&r, &rtool);
 #ifdef WIN_MAC_QUARTZ
-  cgr = Nlm_RecTToCGRect(&r);
+  cgr = Nlm_RecTToCGRect(r);
   TXNCreateObject( &cgr, kTXNSingleLineOnlyMask, &h);
   TXNAttachObjectToWindowRef(h, wptr);
 #else
@@ -3594,7 +3405,7 @@ static void Nlm_NewHiddenText (Nlm_TexT t, Nlm_CharPtr dfault,
 #ifdef WIN_MAC
   Nlm_RecTToRectTool (&r, &rtool);
 #ifdef WIN_MAC_QUARTZ
-  cgr = Nlm_RecTToCGRect(&r);
+  cgr = Nlm_RecTToCGRect(r);
   TXNCreateObject( &cgr, kTXNSingleLineOnlyMask, &h);
   TXNAttachObjectToWindowRef(h, wptr);
 #else
@@ -3718,7 +3529,7 @@ static void Nlm_NewSpecialText (Nlm_TexT t, Nlm_CharPtr dfault,
   Nlm_InsetRect (&r, 2, 2);
   Nlm_RecTToRectTool (&r, &rtool);
 #ifdef WIN_MAC_QUARTZ
-  cgr = Nlm_RecTToCGRect(&r);
+  cgr = Nlm_RecTToCGRect(r);
   TXNCreateObject( &cgr, kTXNSingleLineOnlyMask, &h);
   TXNAttachObjectToWindowRef(h, wptr);
 #else
@@ -3869,7 +3680,7 @@ static void Nlm_NewScrollText (Nlm_TexT t, Nlm_Int2 height,
   }
   Nlm_RecTToRectTool (&r, &dtool);
 #ifdef WIN_MAC_QUARTZ
-  cgr = Nlm_RecTToCGRect(&r);
+  cgr = Nlm_RecTToCGRect(r);
   TXNCreateObject( &cgr, 0, &h);
   TXNAttachObjectToWindowRef(h, wptr);
 #else
diff --git a/vibrant/vibutils.c b/vibrant/vibutils.c
index dd81d148..60a779ef 100644
--- a/vibrant/vibutils.c
+++ b/vibrant/vibutils.c
@@ -29,428 +29,13 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.73 $
+* $Revision: 6.75 $
 *
 * File Description:
 *       Vibrant miscellaneous functions
 *
 * Modifications:
 * --------------------------------------------------------------------------
-* $Log: vibutils.c,v $
-* Revision 6.73  2007/05/01 22:01:30  kans
-* changes in preparation for supporing Quartz on Macintosh
-*
-* Revision 6.72  2006/12/18 17:28:01  kans
-* include FullPath only if OS_UNIX_DARWIN not defined, i.e.,  CodeWarrior build for Mac OS 9
-*
-* Revision 6.71  2006/11/24 20:06:31  kans
-* include Carbon/Carbon.h if not MWERKS - attempting to simplify Xcode search paths
-*
-* Revision 6.70  2006/11/06 17:06:37  bollin
-* Turn off tooltips for Open File Dialog for Windows version - this prevents
-* a crash that was occurring when selecting files for opening or saving that
-* were located in the Desktop for Windows 2000.
-*
-* Revision 6.69  2005/11/08 19:38:55  bollin
-* don't translate the keypress for a backspace key into the NLM_BACK character -
-* windows will also send a WM_CHAR message with the NLM_BACK character in it.
-* Nlm_KeydownToChar should only be used for keypresses that don't issue WM_CHAR
-* messages, otherwise the keyproc function will be called twice for a single
-* keypress
-*
-* Revision 6.68  2005/09/23 20:30:10  kans
-* added NLM_BACK for backspace key, which is separate from delete, even though the label may be the same on a keyboard
-*
-* Revision 6.67  2005/09/14 18:34:22  kans
-* protect against VibMessageHook memory buffer allocation failure
-*
-* Revision 6.66  2005/07/18 15:15:18  kans
-* fixed minor xcode compiler warnings
-*
-* Revision 6.65  2005/04/29 15:12:05  kans
-* removed unused variable in WIN version of Nlm_GetOutputFileName
-*
-* Revision 6.64  2005/04/19 14:52:23  rsmith
-* handle unix style paths in Nlm_SendOpenDocAppleEventEx
-*
-* Revision 6.63  2004/05/28 20:10:32  sinyakov
-* WIN_MSWIN: by Yoon Choi:
-* Modified Nlm_GetOutputFileName to use Nlm_FileLengthEx instead
-* of Nlm-FileOpen/Nlm_FileClose to determine whether file exists or
-* not.  The old way popped up an info box when it did not find an
-* existing file.
-*
-* Revision 6.62  2004/05/04 16:34:23  shomrat
-* Remove file name restrictions for MSWIN
-*
-* Revision 6.61  2004/03/30 17:22:36  rsmith
-* Mac/Darwin (OSX) handle special case when converting an FSSpec to a path name when the file does not exist.
-*
-* Revision 6.60  2004/03/29 21:02:57  rsmith
-* use better system functions to convert FSSpec to a path on Darwin
-*
-* Revision 6.59  2004/02/24 16:51:13  sinyakov
-* [WIN_MSWIN] Nlm_GetInput/OutputFileName now use current working
-* directory as default (as Motif version does)
-*
-* Revision 6.58  2004/02/03 23:36:21  sinyakov
-* Nlm_CheckThisLevel(): call Nlm_GetNext() before calling Nlm_DoGainFocus()
-*
-* Revision 6.57  2003/11/17 17:03:30  kans
-* changed C++ style comments to C comments
-*
-* Revision 6.56  2003/11/07 16:06:58  rsmith
-* Changed Mac printing system calls from deprecated ones to modern ones primarily to ease building with precompiled headers.
-*
-* Revision 6.55  2003/05/05 12:38:07  rsmith
-* casts to make call to RegQueryValueEx safer in Nlm_GetExecPath. Needed by Codewarrior when compiling to Win32.
-*
-* Revision 6.54  2003/03/06 21:55:14  rsmith
-* for OS_UNIX_DARWIN update Nlm_LaunchAppEx and Nlm_SendURLAppleEvent to use new LaunchServices calls.
-*
-* Revision 6.53  2003/02/24 14:25:22  kans
-* undef PM_USE_SESSION_APIS if already defined, before redefining it
-*
-* Revision 6.52  2003/02/10 22:16:41  kans
-* MyNavTextFilterProc allows fdType of 0 for Darwin as well as TEXT
-*
-* Revision 6.51  2003/02/09 18:13:35  kans
-* Nlm_NavServGetInputFileName uses MyNavFilterProc for darwin even if TEXT requested, since not all desired files will have type set
-*
-* Revision 6.50  2003/01/24 20:55:43  rsmith
-* ConvertFilename now extern not static, renamed Nlm_* and only defined in vibutils.c
-*
-* Revision 6.49  2002/11/14 21:27:05  johnson
-* VibMonCreate no longer assigns focus to new window (on WIN_MOTIF)
-*
-* Revision 6.48  2002/10/28 02:47:56  kans
-* call PMPageSetupDialog for Carbon printing
-*
-* Revision 6.47  2002/06/25 18:51:42  kans
-* ConvertFilename puts null byte at str [fullPathLen]
-*
-* Revision 6.46  2002/06/17 16:12:05  kans
-* fix for full path on Darwin (EN)
-*
-* Revision 6.45  2002/06/13 16:15:13  kans
-* fix includes for OS_UNIX_DARWIN with WIN_MAC (EN) - still bug in vibutils.c file dialog
-*
-* Revision 6.44  2002/02/01 18:59:33  kans
-* ConvertFilename calls GetFullPath instead of FSMakePath
-*
-* Revision 6.43  2002/02/01 16:18:34  kans
-* if Carbon, call FSMakePath for input/output file name paths
-*
-* Revision 6.42  2002/01/31 19:01:44  kans
-* MyNavEventProc was deferencing NULL, crashed on Mac OS X (UNIX based), but not used anyway
-*
-* Revision 6.41  2001/11/01 14:25:53  kans
-* use times function for UNIX ComputerTime
-*
-* Revision 6.40  2001/05/17 17:52:34  juran
-* Implement Nlm_ClipPrintingRect() for Carbon.
-* General cleanup -- heed all warnings.
-*
-* Revision 6.39  2001/05/16 23:44:31  juran
-* Segregate Nlm_PrintingRect() into four functions, implement for Carbon.
-*
-* Revision 6.38  2001/05/14 20:36:46  juran
-* Refactor Mac scrap-thwapping code.
-*
-* Revision 6.37  2001/04/05 20:00:43  juran
-* Major Carbon changes.
-Most notably, we attempt to use the new Carbon Printing Manager under 
-Carbon, though this has not been tested.
-Pre-Carbon printing should work fine, though this has not been tested 
-either.
-*
-* Revision 6.36  2000/07/31 13:28:46  lewisg
-* Nlm_GetExecPath
-*
-* Revision 6.34  2000/07/25 19:18:36  lewisg
-* get pathname for executable on windows
-*
-* Revision 6.33  2000/07/14 22:28:59  lewisg
-* fix typo
-*
-* Revision 6.32  2000/07/14 20:30:41  kans
-* added Nlm_MSWin_OpenApplication (for launching Cn3D with a data file)
-*
-* Revision 6.31  2000/06/29 17:29:11  vakatov
-* [MSWIN]  Fixed printf format mismatches
-*
-* Revision 6.30  2000/02/23 16:21:55  kans
-* switched to Churchill fix for nav services file dialogs
-*
-* Revision 6.29  2000/02/22 16:47:59  kans
-* get input/output file name dialog accidentally failed for powerpc without nav services
-*
-* Revision 6.28  2000/01/07 00:22:47  thiessen
-* fixes for LessTif and OpenGL X visual selection
-*
-* Revision 6.27  1999/12/30 16:58:52  kans
-* Carbon changes - printing still not resolved (Churchill)
-*
-* Revision 6.26  1999/12/21 18:48:44  kans
-* rearranged mac get input/output filename functions, soon to expect nav services and to retire SFGetFile and SFPutFile as not Carbon compliant
-*
-* Revision 6.25  1999/08/23 19:36:39  vakatov
-* Nlm_VibMessageHook():  the error posting window should not disappear
-* momentarily on FATAL ERROR -- as we want user to see error message(s)
-*
-* Revision 6.24  1999/08/19 19:05:43  vakatov
-* Nlm_VibMessageHook():  always show the "caption" as a title
-*
-* Revision 6.23  1999/07/04 00:21:13  kans
-* Mac Navigation.h changes
-*
-* Revision 6.22  1999/03/21 18:44:05  kans
-* needed ampsersand before creatorType in MemSet
-*
-* Revision 6.19  1999/02/03 23:26:18  vakatov
-* Nlm_ProcessKeydown() to return "TRUE" when moving the input focus
-*
-* Revision 6.15  1999/01/13 20:49:37  vakatov
-* Nlm_Execv():  precations for the MT applications
-*
-* Revision 6.14  1999/01/13 18:03:24  kans
-* Nlm_Execv calls fork1 if SOLARIS_THREADS_AVAIL
-*
-* Revision 6.13  1999/01/11 18:59:05  kans
-* hidden Mac function Nlm_GetFileTypeAndCreator - did not solve MIME detection problem
-*
-* Revision 6.12  1999/01/07 22:32:38  kans
-* added Mac-specific Nlm_SendURLAppleEvent
-*
-* Revision 6.11  1999/01/06 20:13:00  kans
-* MyNavTextFilterProc for TEXT files
-*
-* Revision 6.10  1999/01/06 02:51:59  kans
-* support for Mac Navigation Services file selection dialogs
-*
-* Revision 6.9  1998/09/15 15:28:15  vakatov
-* [WIN_MSWIN]  GetOpen/SaveFileName():  removed OFN_NOCHANGEDIR flag
-*
-* Revision 6.8  1998/07/07 23:03:36  vakatov
-* Added Nlm_Execv() to spawn applications with cmd-line parameters;
-* now implemented for [OS_MSWIN, OS_UNIX].
-*
-* Revision 6.7  1998/03/27 14:01:57  kans
-* StrngPrintable on Mac now converts 015 from text object to newline for StringPrintable, then back to 015 to put in text
-*
-* Revision 6.6  1998/03/25 18:10:17  kans
-* VibMessageHook adds newline if post, on Mac it must be octal 15
-*
-* Revision 6.5  1998/03/22 03:01:04  kans
-* changed names to RegisterServiceProc and RegisterResultProc
-*
-* Revision 6.4  1998/03/22 02:33:22  kans
-* added request proc, result proc, message handlers to support, and send open doc event, launch app now work with file names or signatures
-*
-* Revision 6.3  1998/03/17 21:08:03  kans
-* added Nlm_SendOpenDocAppleEventEx, and private Nlm_LaunchAppEx
-*
-* Revision 6.2  1997/12/12 21:08:48  kans
-* a number of symbols changed in the latest CodeWarrior release, now using headers from Apple
-*
-* Revision 6.1  1997/11/26 21:30:47  vakatov
-* Fixed errors and warnings issued by C and C++ (GNU and Sun) compilers
-*
-* Revision 6.0  1997/08/25 18:57:53  madden
-* Revision changed to 6.0
-*
-* Revision 5.31  1997/08/25 16:43:04  vakatov
-* [WIN_MSWIN]  Nlm_StartPrinting() -- initialize unused DOCINFO fields
-* with 0(using sizeof(DOCINFO), thus avoid the use of preprocessor #ifdef
-*
-* Revision 5.30  1997/08/21 15:17:40  vakatov
-* [WIN_MSWIN]  Nlm_SetupPrinterDeviceContext() -- fixed Int2 overflow in
-* the display/printer scaling for 16-bit(Win16 and Win-95) SDK libraries
-*
-* Revision 5.29  1997/07/24 17:08:09  vakatov
-* [WIN_MOTIF]  Explicitly set visual, colormap and depth for FileDialog
-* rather than for its parent top-level shell
-*
-* Revision 5.28  1997/07/21 21:52:41  vakatov
-* [WIN_MOTIF] Added Nlm_[Un]RegisterIO() functions to wait for I/O
-* events and call(via X) user-defined callback(s)
-*
-* Revision 5.27  1997/07/16 20:09:52  vakatov
-* Added Nlm_StrngPrintable();  use that in Nlm_VibMessageHook() to
-* provide proper End-Of-Lines in the ScrolledText object
-*
-* Revision 5.26  1997/07/16 18:00:48  kans
-* VibMessageHook newline on Mac is 015
-*
-* Revision 5.25  1997/07/16 14:10:59  vakatov
-* [WIN_MAC] Nlm_VibMessageHook(KEY_NONE):  do not use '\r' before '\n'
-*
-* Revision 5.24  1997/07/15 17:13:48  vakatov
-* Nlm_VibMessageHook(KEY_NONE):  accumulate incoming messages in the
-* text object until the message box is(explicitly) closed by the user
-*
-* Revision 5.23  1997/07/15 12:24:07  kans
-* vibmessagehook len value increased
-*
-* Revision 5.22  1997/07/10 21:49:44  vakatov
-* [WIN_X]  Now able to manage windows having different depths(and
-* different visuals and GC).
-*
-* Revision 5.21  1997/06/23 22:14:18  vakatov
-* VibMessageHook() -- [key == KEY_NONE]  use scrolled text instead of
-* static prompt to provide printout of the whole message
-*
-* Revision 5.20  1997/05/27 21:55:32  vakatov
-* Use Nlm_PopupParentWindow() to avoid flicking on the message box pop-up
-*
-* Revision 5.19  1997/05/27 18:12:29  kans
-* use post message window if key_none, regardless of severity
-*
-* Revision 5.18  1997/05/19 21:48:11  vakatov
-* Do not deliver input focus to the [KEY_NONE,SEV_INFO] message box
-*
-* Revision 5.17  1997/04/28 14:05:39  vakatov
-* [WIN_MOTIF]  Replaced XK_Page_Up/Down(undef for SunOS X4) by XK_Prior/Next
-*
- * Revision 5.16  1997/04/25  16:10:42  vakatov
- * [WIN_MOTIF,WIN_MSWIN]  Added functions to catch, convert(to Mac keycodes)
- * and render navigation and special key events
- *
- * Revision 5.15  1997/04/10  20:23:54  kans
- * monitor only selects window to front on creation, not change value, to
- * allow user to work on other windows without constant focus change
- *
- * Revision 5.14  1997/04/04  22:37:11  vakatov
- * [WIN_MSWIN] In SetupPrinterDeviceContext(), set the window and viewport
- * extents with a more accurate way.
- *
- * Revision 5.13  1997/01/29  17:53:59  kans
- * minor changes due to StringNCpy_0 change
- *
- * Revision 5.12  1997/01/29  16:41:22  kans
- * using StringNCpy_0
- *
- * Revision 5.11  1997/01/16  21:59:20  vakatov
- * [WIN_MSWIN]  StartPicture() -- set picture origin coords(SetWindowOrgEx)
- *
- * Revision 5.10  1997/01/03  16:11:44  vakatov
- * Fixed inaccurate string copying -- <mostly potential> 1-byte exceeding of
- * the string size by StringNCat;  missing terminating '\0' by StringNCpy.
- *
- * Revision 5.9  1996/12/12  23:11:10  kans
- * added Nlm_ClipPrintingRect (DV)
- *
- * Revision 5.8  1996/12/04  19:54:20  vakatov
- * [WIN_MSWIN]  Nlm_CopyDefaultName():  fixed the cases resulting in "."
- *
- * Revision 5.7  1996/11/08  16:43:10  vakatov
- * Nlm_RemoveLink():  do not forget to re-assign "lastChild" when removing
- * the tailing link in the children list(...crash!).
- * Got rid of all compiler warnings.
- *
- * Revision 5.6  1996/10/28  21:21:51  vakatov
- * Nlm_CreateFileDialogShell():  colormap set to Nlm_VibrantDefaultColormap()
- *
- * Revision 5.5  1996/10/09  19:53:18  vakatov
- * [WIN_MOTIF]  Nlm_SelectMonitor() :  explicit call to XMapRaised() led to
- * a side effect causing X-error; -- now replaced by the call to Nlm_Select()
- *
- * Revision 5.4  1996/09/09  20:46:44  vakatov
- * [WIN_MSWIN]  GetOpen/SaveFileName():  added OFN_NOCHANGEDIR flag
- *
- * Revision 5.3  1996/08/30  18:44:09  kans
- * protect against NULL HandFree in SetTitle
- *
- * Revision 5.2  1996/07/05  16:27:45  kans
- * monitor now checks hasCancelBtn param in making cancel button
- *
- * Revision 5.1  1996/06/24  19:24:28  vakatov
- * [WIN_MOTIF]  Nlm_VibMessageHook() -- Set default buttons for the
- * pop-up messages
- *
- * Revision 5.0  1996/05/28  13:45:08  ostell
- * Set to revision 5.0
- *
- * Revision 4.17  1996/05/20  21:30:57  vakatov
- * [WIN_MOTIF]  All "Widget" / "NULL" comparisons and assignments replaced
- * by the "Widget" / "(Widget)0" these
- *
- * Revision 4.16  1996/05/03  21:03:43  kans
- * removed erroneous textscrapfull = FALSE lines
- *
- * Revision 4.15  1996/05/03  17:58:29  vakatov
- * [WIN_MSWIN only]  Check for the MS-Window version when operating with
- * the _DOCINFOA structure
- *
- * Revision 4.14  1996/04/24  21:22:39  vakatov
- * New function Nlm_WaitForXEvent( void ) added (for WIN_MOTIF only!)
- *
- * Revision 4.13  1996/03/02  22:36:38  kans
- * reduction of X traffic (DV)
- *
- * Revision 4.12  1996/02/21  19:46:19  kans
- * GetDriveType endif was in the wrong place
- *
- * Revision 4.11  1996/02/14  16:54:17  kans
- * hidden Nlm_GetDriveType function for entrezcf.c
- *
- * Revision 4.10  1996/02/13  19:49:04  kans
- * set realized calls get/set graphic data, because of gdata cache
- *
- * Revision 4.9  1996/02/13  17:24:07  kans
- * accelerated set position prior to realization (Denis Vakatov)
- *
- * Revision 4.8  1995/12/06  19:45:20  kans
- * removed ArrowCursor from Mac version of VibMessageHook
- *
- * Revision 4.7  1995/11/21  17:37:26  smirnov
- * Alex: Win95 printing problem
- *
- * Revision 4.6  1995/11/14  13:42:05  kans
- * fixes to FntGetFontStyle (VL)
- *
- * Revision 4.5  1995/11/08  23:30:31  kans
- * removed edit block fields, which belong in the application
- *
- * Revision 4.4  1995/10/06  16:46:51  epstein
- * break-out 'patient' modal-window loop into a new macro Nlm_WaitForCondition, and add function Nlm_FineGranularitySleep
- *
- * Revision 4.3  1995/09/12  17:59:35  ostell
- * fixes for MS windows text to metafile
- *
- * Revision 4.2  1995/08/29  18:19:09  kans
- * changes to clipboard functions under Motif (AS)
- *
- * Revision 4.1  1995/08/14  21:38:37  kans
- * removal of remaining C str... functions
- *
- * Revision 4.0  1995/07/26  13:51:04  ostell
- * force revision to 4.0
- *
- * Revision 2.80  1995/07/19  16:21:33  kans
- * fixed IRIX4 XmClipboardStartCopy complaint
- *
- * Revision 2.79  1995/07/17  22:02:19  kans
- * Motif clipboard cut and paste supported (AS)
- *
- * Revision 2.78  1995/07/05  14:23:19  kans
- * move #include <sys/select.h> to ncbilcl.r6k
- *
- * Revision 2.77  1995/06/08  15:46:15  kans
- * added special event loop to monitor functions for X responsiveness
- *
- * Revision 2.76  1995/06/07  20:14:13  kans
- * better performance of monitor, message loops
- *
- * Revision 2.75  1995/06/05  21:32:25  kans
- * added cancel button to progress monitor
- *
- * Revision 2.74  1995/05/31  18:00:58  kans
- * added SetColorMap (AS)
- *
- * Revision 2.73  1995/05/17  15:15:14  kans
- * added Log line
- *
 *
 * ==========================================================================
 */
@@ -3517,14 +3102,14 @@ extern void Nlm_RecTToRectTool (Nlm_RectPtr src, Nlm_RectTool PNTR dst)
 }
 
 #ifdef WIN_MAC_QUARTZ
-extern CGRect Nlm_RecTToCGRect(Nlm_RectPtr r)
+extern CGRect Nlm_RecTToCGRect(Nlm_RecT r)
 {
     CGRect cgr;
     
-    cgr.origin.x = r->left + 0.5f;
-    cgr.origin.y = r->top + 0.5;
-    cgr.size.width = r->right - r->left - 1.0f;
-    cgr.size.height = r->bottom - r->top - 1.0f;
+    cgr.origin.x = r.left;
+    cgr.origin.y = r.top;
+    cgr.size.width = r.right - r.left;
+    cgr.size.height = r.bottom - r.top;
     
     return cgr;
 }
@@ -3532,13 +3117,28 @@ extern CGRect Nlm_RecTToCGRect(Nlm_RectPtr r)
 extern Nlm_RecT Nlm_CGRectToRecT(CGRect cgr)
 {
     Nlm_RecT r;
-    r.left   = cgr.origin.x - 0.5f;
-    r.top    = cgr.origin.y - 0.5f;
-    r.right  = cgr.size.width  + cgr.origin.x + 1.0f;
-    r.bottom = cgr.size.height + cgr.origin.y + 1.0f; 
+    r.left   = cgr.origin.x;
+    r.top    = cgr.origin.y;
+    r.right  = cgr.size.width  + cgr.origin.x;
+    r.bottom = cgr.size.height + cgr.origin.y; 
     return r;
 }
 
+CGRect Nlm_RectQDToCG(Rect r)
+{
+    Nlm_RecT rt;
+    Nlm_RectToolToRecT (&r, &rt);
+    return Nlm_RecTToCGRect (rt);
+}
+
+Rect Nlm_RectCGToQD(CGRect r)
+{
+    Nlm_RecT rt = Nlm_CGRectToRecT (r);
+    Rect rq;
+    Nlm_RecTToRectTool (&rt, &rq);
+    return rq;
+}
+
 extern CGPoint Nlm_PoinTToCGPoint(Nlm_PoinT np)
 {
     CGPoint qp;
@@ -3565,7 +3165,13 @@ extern void Nlm_LocalToGlobal (Nlm_PointPtr pt)
 
   if (pt != NULL) {
     Nlm_PoinTToPointTool (*pt, &ptool);
+#ifdef WIN_MAC_QUARTZ
+/* This function is deprecated on 10.4+ but there is no replacement
+   available until 10.5, so we have to use it anyway */
+    QDLocalToGlobalPoint (GetWindowPort(Nlm_GetQuartzCurrentWindow()), &ptool);
+#else
     LocalToGlobal (&ptool);
+#endif
     Nlm_PointToolToPoinT (ptool, pt);
   }
 #endif
@@ -3590,7 +3196,13 @@ extern void Nlm_GlobalToLocal (Nlm_PointPtr pt)
 
   if (pt != NULL) {
     Nlm_PoinTToPointTool (*pt, &ptool);
+#ifdef WIN_MAC_QUARTZ
+/* This function is deprecated on 10.4+ but there is no replacement
+   available until 10.5, so we have to use it anyway */
+    QDGlobalToLocalPoint (GetWindowPort(Nlm_GetQuartzCurrentWindow()), &ptool);
+#else
     GlobalToLocal (&ptool);
+#endif
     Nlm_PointToolToPoinT (ptool, pt);
   }
 #endif
@@ -3700,6 +3312,10 @@ extern HDC Nlm_GetPicWinHDC ( void )
 #endif
 
 
+#ifdef WIN_MAC_QUARTZ
+static CFMutableDataRef Nlm_PictureData = 0;
+#endif
+
 extern Nlm_WindoW Nlm_StartPicture (Nlm_RectPtr r)
 {
   Nlm_WindoW    w;
@@ -3712,9 +3328,20 @@ extern Nlm_WindoW Nlm_StartPicture (Nlm_RectPtr r)
     return w;
 
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  CGRect cgr = CGRectMake (r->left, r->top, r->right - r->left, r->bottom - r->top);
+  Nlm_PictureData = CFDataCreateMutable (NULL, 0);
+  
+  CGDataConsumerRef consumer = CGDataConsumerCreateWithCFData (Nlm_PictureData);
+  CGContextRef ctx = CGPDFContextCreate (consumer, &cgr, NULL);
+  CGContextBeginPage (ctx, &cgr);
+  Nlm_PushPort (ctx);
+  CGDataConsumerRelease (consumer);
+#else
   Nlm_RecTToRectTool (r, &rtool);
   picHdl = OpenPicture (&rtool);
 #endif
+#endif
 #ifdef WIN_MSWIN
   picRect = *r;
   picHWND = Nlm_currentHWnd;
@@ -3739,6 +3366,17 @@ extern void Nlm_EndPicture (Nlm_WindoW w)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  CGContextRef ctx = Nlm_PopPort();
+  CGContextEndPage (ctx);
+  CGContextRelease (ctx);
+  
+  PasteboardRef pasteboard = 0;
+  PasteboardCreate (kPasteboardClipboard, &pasteboard);
+  PasteboardPutItemFlavor (pasteboard, (PasteboardItemID)1, CFSTR("com.adobe.pdf"), Nlm_PictureData, 0);
+  CFRelease (pasteboard);
+  CFRelease (Nlm_PictureData);
+#else
   long    len;
   PicPtr  picPtr;
 
@@ -3768,6 +3406,7 @@ extern void Nlm_EndPicture (Nlm_WindoW w)
   }
   picHdl = NULL;
 #endif
+#endif
 #ifdef WIN_MSWIN
   GLOBALHANDLE    hGMem = NULL;
   HMETAFILE       hmf = NULL;
@@ -3842,6 +3481,21 @@ extern void Nlm_StringToClipboard (Nlm_CharPtr str)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  PasteboardRef pasteboard = 0;
+  PasteboardCreate (kPasteboardClipboard, &pasteboard);
+  PasteboardClear (pasteboard);
+  
+  CFDataRef asciidata = CFDataCreate (NULL, (UInt8 *)str, (CFIndex)strlen (str));
+  CFStringRef cfstr = CFStringCreateFromExternalRepresentation (NULL, asciidata, kCFStringEncodingMacRoman);
+  CFDataRef data = CFStringCreateExternalRepresentation (NULL, cfstr, kCFStringEncodingUnicode, '?');
+  PasteboardPutItemFlavor (pasteboard, (PasteboardItemID)1, CFSTR("public.utf16-plain-text"), data, 0);
+  
+  CFRelease (data);
+  CFRelease (cfstr);
+  CFRelease (asciidata);
+  CFRelease (pasteboard);
+#else
   long    len;
   OSErr err;
 
@@ -3865,6 +3519,7 @@ extern void Nlm_StringToClipboard (Nlm_CharPtr str)
     err = TEFromScrap ();
   }
 #endif
+#endif
 #ifdef WIN_MSWIN
   HGLOBAL  hMem;
   DWORD    len;
@@ -3931,17 +3586,78 @@ extern void Nlm_StringToClipboard (Nlm_CharPtr str)
 #endif
 }
 
+#ifdef WIN_MAC_QUARTZ
+static CFDataRef Nlm_CopyClipboardTextData (void)
+{
+  PasteboardRef pasteboard = 0;
+  PasteboardCreate (kPasteboardClipboard, &pasteboard);
+  PasteboardSynchronize (pasteboard);
+  
+  ItemCount itemCount = 0;
+  PasteboardGetItemCount (pasteboard, &itemCount);
+  
+  CFDataRef flavorData = 0;
+  
+  UInt32 index;
+  for (index = 1; index <= itemCount && !flavorData; index++)
+  {
+    PasteboardItemID itemID = 0;
+    CFArrayRef flavorTypeArray = 0;
+    CFIndex flavorCount = 0;
+    
+    PasteboardGetItemIdentifier (pasteboard, index, &itemID);
+    PasteboardCopyItemFlavors (pasteboard, itemID, &flavorTypeArray);
+    flavorCount = CFArrayGetCount (flavorTypeArray);
+    CFIndex i;
+    for (i = 0; i < flavorCount; i++)
+    {
+      CFStringRef flavorType = (CFStringRef)CFArrayGetValueAtIndex (flavorTypeArray, i);
+      if (UTTypeConformsTo (flavorType, CFSTR("public.utf16-plain-text")))
+      {
+        PasteboardCopyItemFlavorData (pasteboard, itemID, flavorType, &flavorData);
+        break;
+      }
+    }
+  }
+  
+  if (flavorData)
+  {
+    CFStringRef cfstr = CFStringCreateFromExternalRepresentation (NULL, flavorData, kCFStringEncodingUnicode);
+    CFDataRef data = CFStringCreateExternalRepresentation (NULL, cfstr, kCFStringEncodingMacRoman, '?');
+    CFRelease (flavorData);
+    CFRelease (cfstr);
+    return data;
+  }
+  
+  return NULL;
+}
+#endif
+
 extern Nlm_Boolean Nlm_ClipboardHasString (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  CFDataRef data = Nlm_CopyClipboardTextData();
+  if (data)
+    CFRelease (data);
+  return data != 0;
+#else
   long  len;
   OSErr err;
 
+# if TARGET_API_MAC_CARBON
+  OSStatus status;
+  ScrapRef scrap;
+  ScrapFlavorFlags flags = 0;
+  status = GetCurrentScrap(&scrap);
+  
   err = TEFromScrap();
   len = TEGetScrapLength();
   return (Nlm_Boolean) (len > 0);
 #endif
+#endif
+#endif
 
 #ifdef WIN_MSWIN
   return (Nlm_Boolean) (IsClipboardFormatAvailable (CF_TEXT));
@@ -3980,6 +3696,18 @@ extern Nlm_CharPtr Nlm_ClipboardToString (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+  Nlm_CharPtr str = 0;
+  
+  CFDataRef data = Nlm_CopyClipboardTextData();
+  if (data)
+  {
+    str = Nlm_MemNew (CFDataGetLength (data));
+    CFDataGetBytes (data, CFRangeMake (0, CFDataGetLength (data)), (UInt8 *)str);
+    CFRelease (data);
+  }
+  return str;
+#else
   long         len;
   Nlm_CharPtr  str;
   Handle hdl;
@@ -4002,6 +3730,7 @@ extern Nlm_CharPtr Nlm_ClipboardToString (void)
   }
   return str;
 #endif
+#endif
 #ifdef WIN_MSWIN
   HANDLE       hClip;
   LPSTR        pStr;
@@ -5890,7 +5619,7 @@ extern void Nlm_SendOpenDocAppleEventEx (Nlm_CharPtr datafile, Nlm_CharPtr sig,
   AppleEvent theReply;
   OSType theSignature;
   AEDescList theList;
-  FSSpec fss;
+  CFURLRef cfurl;
   Nlm_Char  temp [256];
   ProcessSerialNumber  psn;
   Nlm_Boolean  okay = FALSE;
@@ -5920,20 +5649,11 @@ extern void Nlm_SendOpenDocAppleEventEx (Nlm_CharPtr datafile, Nlm_CharPtr sig,
       if (theErr == noErr) {
         theErr = AECreateList(NULL, 0, FALSE, &theList);
         if (theErr == noErr) {
-          /*make fss from path */
-          if (datafile[0] == '/') {
-            FSRef fsref;
-            theErr = FSPathMakeRef((unsigned char *) datafile, &fsref, NULL);
-            if (theErr == noErr) {
-              theErr = FSGetCatalogInfo(&fsref, kFSCatInfoNone, NULL, NULL, &fss, NULL);
-            }
-          } else {
-            Nlm_StringNCpy_0(temp, datafile, sizeof(temp) - 1);
-            Nlm_CtoPstr ((Nlm_CharPtr) temp);
-            theErr = FSMakeFSSpec (0, 0, (ConstStr255Param) temp, &fss);
-          }
-          if (theErr == noErr) {
-            theErr = AECreateDesc(typeFSS, (Ptr)&fss, sizeof(fss), &docDesc);
+          cfurl = CFURLCreateFromFileSystemRepresentation (NULL, (const UInt8 *)datafile, strlen (datafile), 0);
+          if (cfurl) {
+            CFDataRef cfdata = CFURLCreateData (NULL, cfurl, kCFStringEncodingUTF8, 1);
+            theErr = AECreateDesc(typeFileURL, CFDataGetBytePtr (cfdata), CFDataGetLength (cfdata), &docDesc);
+            CFRelease (cfdata);
             if (theErr == noErr) {
               theErr = AEPutDesc(&theList, 0, &docDesc);
               if (theErr == noErr) {
@@ -5968,8 +5688,8 @@ extern void Nlm_SendURLAppleEvent (Nlm_CharPtr urlString, Nlm_CharPtr sig, Nlm_C
 
 {
 #ifdef OS_UNIX_DARWIN
-  OSStatus    err;
-  CFURLRef      urlRef;
+  OSStatus  err;
+  CFURLRef  urlRef;
   
   /* on OS X ignore the sig and prog and open the url with the default browser */
   urlRef = CFURLCreateWithBytes (NULL, (const UInt8 *) urlString, Nlm_StrLen( urlString),  kCFStringEncodingMacRoman, NULL);
@@ -6026,29 +5746,122 @@ extern void Nlm_SendURLAppleEvent (Nlm_CharPtr urlString, Nlm_CharPtr sig, Nlm_C
 #endif
 }
 
+
+/* Modified from http://developer.apple.com/qa/qa2001/qa1026.html */
+
+#if TARGET_API_MAC_CARBON 
+#ifdef __APPLE_CC__ 
+#include <Carbon/Carbon.h> 
+#else 
+#include <Carbon.h> 
+#endif 
+#else 
+#include <Types.h> 
+#include <OSA.h> 
+#include <AppleScript.h> 
+#endif 
+#include <string.h> 
+    /* LowRunAppleScript compiles and runs an AppleScript 
+    provided as text in the buffer pointed to by text.  textLength 
+    bytes will be compiled from this buffer and run as an AppleScript 
+    using all of the default environment and execution settings.  If 
+    resultData is not NULL, then the result returned by the execution 
+    command will be returned as typeChar in this descriptor record 
+    (or typeNull if there is no result information).  If the function 
+    returns errOSAScriptError, then resultData will be set to a 
+    descriptive error message describing the error (if one is 
+    available).  */ 
+
+static OSStatus LowRunAppleScript (
+  const void* text,
+  long textLength, 
+  AEDesc *resultData
+)
+
+{ 
+  ComponentInstance theComponent; 
+  AEDesc scriptTextDesc; 
+  OSStatus err; 
+  OSAID scriptID, resultID; 
+
+  /* set up locals to a known state */ 
+  theComponent = NULL; 
+  AECreateDesc (typeNull, NULL, 0, &scriptTextDesc); 
+  scriptID = kOSANullScript; 
+  resultID = kOSANullScript; 
+
+  /* open the scripting component */ 
+  theComponent = OpenDefaultComponent (kOSAComponentType, typeAppleScript); 
+  if (theComponent == NULL) {
+    err = paramErr;
+    goto bail;
+  } 
+
+  /* put the script text into an aedesc */ 
+  err = AECreateDesc (typeChar, text, textLength, &scriptTextDesc); 
+  if (err != noErr) goto bail; 
+
+  /* compile the script */ 
+  err = OSACompile (theComponent, &scriptTextDesc, kOSAModeNull, &scriptID); 
+  if (err != noErr) goto bail; 
+
+  /* run the script */ 
+  err = OSAExecute (theComponent, scriptID, kOSANullScript, kOSAModeNull, &resultID); 
+
+  /* collect the results - if any */ 
+  if (resultData != NULL) { 
+    AECreateDesc (typeNull, NULL, 0, resultData); 
+    if (err == errOSAScriptError) { 
+      OSAScriptError (theComponent, kOSAErrorMessage, typeChar, resultData); 
+    } else if (err == noErr && resultID != kOSANullScript) { 
+      OSADisplay (theComponent, resultID, typeChar, kOSAModeNull, resultData); 
+    } 
+  } 
+bail: 
+  AEDisposeDesc (&scriptTextDesc); 
+  if (scriptID != kOSANullScript) OSADispose (theComponent, scriptID); 
+  if (resultID != kOSANullScript) OSADispose (theComponent, resultID); 
+  if (theComponent != NULL) CloseComponent (theComponent); 
+  return err; 
+} 
+
+
+extern void Nlm_SendAppleScriptString (Nlm_CharPtr script)
+
+{
+  if (Nlm_StringHasNoText (script)) return;
+  LowRunAppleScript ((const char*) script, Nlm_StringLen (script), NULL); 
+} 
+
+
 extern void Nlm_GetFileTypeAndCreator (Nlm_CharPtr filename, Nlm_CharPtr type, Nlm_CharPtr creator);
 extern void Nlm_GetFileTypeAndCreator (Nlm_CharPtr filename, Nlm_CharPtr type, Nlm_CharPtr creator)
 {
-  OSType    fCreator;
-  Nlm_Int2  fError;
-  FInfo     fInfo;
-  OSType    fType;
-  Nlm_Char  temp [256];
-
-  if (type != NULL) {
-    *type = '\0';
-  }
-  if (creator != NULL) {
-    *creator = '\0';
-  }
-  Nlm_StringNCpy_0 (temp, filename, sizeof(temp));
-  Nlm_CtoPstr ((Nlm_CharPtr) temp);
-  fError = HGetFInfo ( 0, 0, (StringPtr) temp, &fInfo);
-  if (fError == 0) {
-    fType = fInfo.fdType;
-    fCreator = fInfo.fdCreator;
-    StringNCpy_0 (type, (Nlm_CharPtr) (&fType), 5);
-    StringNCpy_0 (creator, (Nlm_CharPtr) (&fCreator), 5);
+  OSStatus err;
+  
+  FSRef fsref;
+  err = FSPathMakeRef ((const UInt8 *)filename, &fsref, NULL);
+  if (err)
+    return;
+  
+  FSCatalogInfo catinfo;
+  err = FSGetCatalogInfo (&fsref, kFSCatInfoGettableInfo, &catinfo, NULL, NULL, NULL);
+  
+  if (err == noErr && (catinfo.nodeFlags & kFSNodeIsDirectoryMask) == 0)
+  {
+    FileInfo finfo;
+    memcpy(&finfo, &catinfo.finderInfo, sizeof(finfo));
+    
+    if (type)
+    {
+      *(Nlm_Int4 *)type = htonl (finfo.fileType);
+      type[4] = 0;
+    }
+    if (creator)
+    {
+      *(Nlm_Int4 *)creator = htonl (finfo.fileCreator);
+      creator[4] = 0;
+    }
   }
 }
 #endif
@@ -6261,33 +6074,39 @@ static void Nlm_FntDlgRedrawSample (void)
 /* alexs (01-16-95): add platform-dependent for MAC */
 #ifdef WIN_MAC
 
-static MenuHandle menuHforFontList = 0;
-
-static Nlm_Int2 Nlm_FntDlgGetSysFontList (Nlm_Boolean monoSpace )
-{
-  int      curItemNum;
-  short    famId;
-  char     fontName[256];
-
-  menuHforFontList = NewMenu ( 100, (StringPtr) "" );
-  AppendResMenu ( menuHforFontList, 'FONT' );
-  if ( monoSpace ){
-    for (curItemNum = (Nlm_Int2)CountMenuItems(menuHforFontList);
-         curItemNum > 0; curItemNum-- ){
-      GetMenuItemText ( menuHforFontList, curItemNum, (StringPtr) fontName );
-      GetFNum((StringPtr) fontName, &famId);
-      TextSize (12);
-      TextFace (0);
-      TextFont (famId);
-      if ( (CharWidth('i') != CharWidth('M')) ||
-           (CharWidth('i') != CharWidth(' '))){
-        DeleteMenuItem (menuHforFontList,curItemNum);
-      }
+MenuHandle menuHforFontList;
 
+static Nlm_Int2 Nlm_FntDlgGetSysFontList (Nlm_Boolean monoSpace)
+{
+  CreateNewMenu (100, 0, &menuHforFontList);
+  CreateStandardFontMenu (menuHforFontList, 0, 0, 0, NULL);
+  
+  if (monoSpace)
+  {
+    int item;
+    for (item = CountMenuItems (menuHforFontList); item > 0; item--)
+    {
+      CFStringRef cfname = NULL;
+      CopyMenuItemTextAsCFString (menuHforFontList, item, &cfname);
+      
+      int size = CFStringGetMaximumSizeForEncoding (CFStringGetLength (cfname), kCFStringEncodingUTF8);
+      char *name = malloc (size + 1);
+      CFStringGetCString (cfname, name, size + 1, kCFStringEncodingUTF8);
+      
+      Nlm_FonT font = Nlm_GetFont (name, 12, 0, 0, 0, "");
+      
+      int i = Nlm_CharWidth ('i');
+      int M = Nlm_CharWidth ('M');
+      int s = Nlm_CharWidth (' ');
+      if( i != M || i != s )
+        DeleteMenuItem (menuHforFontList, item);
+      
+      free (name);
+      CFRelease (cfname);
     }
-    Nlm_SelectFont (Nlm_systemFont);
   }
-  return (Nlm_Int2)CountMenuItems(menuHforFontList);
+  
+  return CountMenuItems (menuHforFontList);
 }
 
 static void Nlm_FntDlgGetSysFontName (Nlm_Int2 n, Nlm_CharPtr buf,
diff --git a/vibrant/vibwndws.c b/vibrant/vibwndws.c
index ea9a1105..0aa59f96 100644
--- a/vibrant/vibwndws.c
+++ b/vibrant/vibwndws.c
@@ -29,676 +29,16 @@
 *
 * Version Creation Date:   7/1/91
 *
-* $Revision: 6.79 $
+* $Revision: 6.80 $
 *
 * File Description:
 *       Vibrant main, event loop, and window functions
 *
 * Modifications:
 * --------------------------------------------------------------------------
-* $Log: vibwndws.c,v $
-* Revision 6.79  2007/06/18 12:21:29  ivanov
-* Fixed EOLs
 *
-* Revision 6.78  2007/06/15 20:27:27  kans
-* CreateNewWindow does not set window title, so revert to old function for now
-*
-* Revision 6.77  2007/05/09 16:42:10  kans
-* use CreateNewWindow instead of NewWindow or NewCWindow (RS)
-*
-* Revision 6.76  2007/05/02 17:24:03  kans
-* preparation for supporting Quartz on Mac
-*
-* Revision 6.75  2006/12/13 17:27:24  kans
-* Nlm_VibMainPrelude and Nlm_VibMainFinale called by separate vibmain.c file containing main or WinMain
-*
-* Revision 6.74  2006/11/24 20:06:31  kans
-* include Carbon/Carbon.h if not MWERKS - attempting to simplify Xcode search paths
-*
-* Revision 6.73  2006/09/14 19:18:29  ivanov
-* Rollback last changes. All missed defines added to corelib/ncbiwin.h.
-*
-* Revision 6.72  2006/09/14 18:05:45  ivanov
-* Fixed compilation errors on MS Windows
-*
-* Revision 6.71  2006/09/14 14:45:39  kans
-* changes for 64-bit Windows (GC) plus a few CodeWarrior complaints (JK)
-*
-* Revision 6.70  2005/11/16 19:50:37  kans
-* Nlm_showGetArgTag always TRUE, do not get shift key for old Vibrant about box
-*
-* Revision 6.69  2005/07/18 15:15:18  kans
-* fixed minor xcode compiler warnings
-*
-* Revision 6.68  2005/01/24 15:02:40  kans
-* remove unnecessary and uninitialized StringMove (tmp...) in GetArgs_ST
-*
-* Revision 6.67  2005/01/13 18:47:01  kans
-* Nlm_showGetArgTag set by Nlm_GetReady, used by GetArg_ST
-*
-* Revision 6.66  2004/07/19 13:37:24  bollin
-* adjusted FixVisibilityIssues function to handle nesting of groups
-*
-* Revision 6.65  2004/07/16 18:47:29  bollin
-* added FixVisibilityIssues function to handle LessTif problems with not correctly hiding
-* widgets before the parent widget is managed.
-* Also replaced obsolete XmFontListCreate function to get rid of run-time warning.
-*
-* Revision 6.64  2004/06/02 15:53:17  bollin
-* fixed Nlm_ProcessKeyPress for MOTIF to handle arrow keys
-*
-* Revision 6.63  2004/06/02 14:54:33  bollin
-* fixed Nlm_ProcessKeyPress to also handle arrow keys
-*
-* Revision 6.62  2004/04/14 19:14:06  sinyakov
-* WIN_MSWIN: support X-Windows-like -bg color command line option
-*
-* Choi: Added support for either the left or right monitor being the primary
-* monitor in a dual monitor setup.  Added function Nlm_UsePrimaryMonitor.
-*
-* Choi: modified Nlm_SetupWindows to use the virtual screen
-* size to support dual monitor setups.  this effectively limits our target
-* platform to WINVER >= 0x0500 (Windows2000 or later) which all indexers
-* have.  modified Nlm_HasDualScreen to use system metrics call for
-* windows2000 or later platforms.
-*
-* Revision 6.61  2004/02/03 23:34:58  sinyakov
-* Nlm_WindowGainFocus(): call Nlm_GetNext() before calling Nlm_DoGainFocus()
-*
-* Revision 6.60  2004/01/20 23:35:38  sinyakov
-* [WIN_MSWIN] implemented menu accelerators
-*
-* Revision 6.59  2004/01/05 18:42:40  kans
-* record screen mode at time of window creation
-*
-* Revision 6.58  2004/01/05 17:08:09  kans
-* added functions to control use of dual screens
-*
-* Revision 6.57  2003/12/03 17:45:21  kans
-* For OS_MAC, always include Profiler.h
-*
-* Revision 6.56  2003/11/17 17:03:30  kans
-* changed C++ style comments to C comments
-*
-* Revision 6.55  2003/11/03 21:57:48  sinyakov
-* WIN_MSWIN: added ability to put a message into message processing loop
-* to call a callback function within the main GUI thread
-* callback function address is passed in WPARAM,
-* callback function parameter is passed in LPARAM
-* this functionality is used by Win32 implementation of smartnet.c module
-*
-* Revision 6.54  2003/04/09 18:16:53  kans
-* motif version of Nlm_ProcessKeyPress sets ctrlKey and shftKey, clears cmmdKey and optKey, leaves dblClick alone
-*
-* Revision 6.53  2003/01/27 17:43:03  kans
-* do not set silent if xx_argc > 1
-*
-* Revision 6.52  2003/01/24 20:55:42  rsmith
-* ConvertFilename now extern not static, renamed Nlm_* and only defined in vibutils.c
-*
-* Revision 6.51  2002/11/06 21:32:50  ucko
-* Accept "--help" as a synonym for the less intuitive "-"
-*
-* Revision 6.50  2002/07/09 15:20:19  lavr
-* Call CONNECT_Init(0) in initialization sequence
-*
-* Revision 6.49  2002/06/13 16:15:13  kans
-* fix includes for OS_UNIX_DARWIN with WIN_MAC (EN) - still bug in vibutils.c file dialog
-*
-* Revision 6.48  2002/05/07 16:50:14  bazhin
-* Changes in Nlm_SetWindowConfigureCallback().
-*
-* Revision 6.47  2002/04/30 18:25:12  bazhin
-* Added function "Nlm_SetWindowConfigureCallback(WindoW w)", which
-* allows to catch events, when window just moved without resizing.
-* Fixed some "gcc -Wall -ansi" warnings.
-*
-* Revision 6.46  2002/03/28 13:30:28  kans
-* check for OS_UNIX_DARWIN before including MoreCarbonAccessors.h, Profiler.h (EN)
-*
-* Revision 6.45  2002/03/18 16:55:19  kans
-* ProfilerInit stackDepth parameter to 50
-*
-* Revision 6.44  2002/03/18 16:33:53  kans
-* ProfilerInit numFunctions parameter to 1000
-*
-* Revision 6.43  2001/11/26 21:25:04  juran
-* Define type AERefCon as SInt32 for AE handler prototypes.
-* It may need to be UInt32 for pre-3.4 Universal Interfaces under Carbon, or something.
-*
-* Revision 6.42  2001/08/29 17:35:38  juran
-* Universal Interfaces 3.4 changes:
-* AE handler refCon is an SInt32.
-* convertClipboardFlag doesn't exist under Carbon.
-*
-* Revision 6.41  2001/05/14 20:50:09  juran
-* Remove Mac clipboard code -- the scrap is updated whenever it's used.
-*
-* Revision 6.40  2001/04/18 18:39:29  juran
-* AE handlers take a UInt32 refCon.
-*
-* Revision 6.39  2001/04/05 20:32:34  juran
-* Major Carbon changes, including the new Scrap Manager (not tested).
-*
-* Revision 6.38  2000/06/15 20:51:45  vakatov
-* Use "const" in Args code
-*
-* Revision 6.37  2000/03/31 16:14:13  thiessen
-* fix modal window lockout bug
-*
-* Revision 6.36  2000/02/03 22:29:16  lewisg
-* make windows version of vibrant use standard color
-*
-* Revision 6.35  2000/01/13 23:37:14  beloslyu
-* changes because of port to HP-UX 11.0
-*
-* Revision 6.34  2000/01/07 00:22:47  thiessen
-* fixes for LessTif and OpenGL X visual selection
-*
-* Revision 6.33  1999/12/30 16:47:10  kans
-* Carbon changes (Churchill)
-*
-* Revision 6.32  1999/12/21 18:04:24  kans
-* removed MPW/THINKC conditional code, starting upgrade to Carbon compatibility - Churchill
-*
-* Revision 6.31  1999/12/07 19:18:58  thiessen
-* fixed font color problem in OpenGL on SGI
-*
-* Revision 6.30  1999/10/27 20:17:32  thiessen
-* when _OPENGL is defined, make Motif choose a better-than-8-bit color depth, if possible
-*
-* Revision 6.29  1999/07/21 17:57:42  vakatov
-* GetArgs_ST():  fixed array boundary read
-*
-* Revision 6.28  1999/07/08 14:49:26  kans
-* MultiLinePrompt copies string to avoid modifying read-only string passed in from GetArgs when Mac virtual memory is on
-*
-* Revision 6.27  1999/06/22 15:14:53  lewisg
-* fix image library so that works on linux with > 8 bits
-*
-* Revision 6.26  1999/04/22 15:19:01  vakatov
-* Call XtUnrealizeWidget() before XtDestroyWidget() to make sure no
-* "post-mortem" callbacks(registered by XtAddEventHandler()) get
-* triggered for the destroyed widget. Reason: the widget may not be
-* immediately destroyed if XtDestroyWidget() was called in a nested
-* event dispatch loop.
-*
-* Revision 6.25  1999/04/06 14:23:27  lewisg
-* add opengl replacement for viewer3d
-*
-* Revision 6.24  1999/03/17 15:10:50  vakatov
-* + Nlm_XLoadStandardFont() to find a "last-resort" font
-*
-* Revision 6.23  1999/02/11 21:34:37  kans
-* check __profile__ symbol to turn on Mac profiling
-*
-* Revision 6.22  1999/02/10 22:22:14  kans
-* added commented-out CodeWarrior Profiler setup instructions
-*
-* Revision 6.21  1999/01/29 18:42:57  kans
-* appearancelib and navigationlib ifdef OS_MAC and PROC_PPC
-*
-* Revision 6.20  1999/01/21 23:58:32  kans
-* Mac navigation services code ifdefed out because is available function does not appear to work properly
-*
-* Revision 6.19  1999/01/06 02:52:00  kans
-* support for Mac Navigation Services file selection dialogs
-*
-* Revision 6.18  1998/12/14 18:39:11  kans
-* okayToDrawContents extern, used to inhibit slate drawing
-*
-* Revision 6.17  1998/12/10 21:28:50  kans
-* okayToDrawContents accessed only in WIN_MAC section
-*
-* Revision 6.16  1998/12/10 17:45:09  kans
-* okayToDrawContents to suppress drawing after return from Main
-*
-* Revision 6.15  1998/12/01 17:41:58  vakatov
-* Use just "0" instead of "(caddr_t)NULL" -- (a compilation fix)
-*
-* Revision 6.14  1998/07/14 16:44:29  vakatov
-* Added VibrantIsGUI() and <internal> Nlm_VibrantSetGUI()
-*
-* Revision 6.13  1998/03/22 03:01:11  kans
-* changed names to RegisterServiceProc and RegisterResultProc
-*
-* Revision 6.12  1998/03/22 02:33:30  kans
-* added request proc, result proc, message handlers to support, and send open doc event, launch app now work with file names or signatures
-*
-* Revision 6.11  1998/03/09 21:03:47  vakatov
-* FetchArg(), float|int:  fixed for assignment of default value
-*
-* Revision 6.10  1998/01/08 21:33:32  kans
-* OS_AXP_VMS includes <Xm/StdCmap.h>
-*
-* Revision 6.9  1997/11/27 05:52:16  vakatov
-* [WIN_X] "defaultXerror_handler()" -- fixed non-portable(internal X11) code
-*
-* Revision 6.7  1997/11/21 19:31:23  vakatov
-* [WIN_X] "defaultXerror_handler()" -- issue a std X error msg, don't crash
-*
-* Revision 6.6  1997/11/12 20:56:14  kans
-* added SetMouseMoveCallback and SetMouseMoveRegion, implemented first on Mac
-*
-* Revision 6.5  1997/10/30 19:30:47  kans
-* added Nlm_DisplayEnvironmentVariables for Solaris
-*
-* Revision 6.4  1997/10/01 21:51:52  vakatov
-* Trying to catch strayed Expose or MapNotify(for SetVisible(...)) event
-*
-* Revision 6.3  1997/09/29 20:00:51  vakatov
-* [WIN_X11]  Do not parse "-d" cmd.-line, use "-dpy" instead(or "-display")
-*
-* Revision 6.2  1997/09/22 23:51:23  vakatov
-* [WIN_MSWIN] ParseSetupArguments(): remove leading quote from cmd-line args
-*
-* Revision 6.1  1997/09/17 21:09:05  vakatov
-* [WIN_X]  Parse command-line "-d" / "-display" options to choose X-display
-*
-* Revision 6.0  1997/08/25 18:58:01  madden
-* Revision changed to 6.0
-*
-* Revision 5.71  1997/08/14 18:54:45  vakatov
-* [WIN_MOTIF] Let X11 parse the command-line args at first;  leave the
-* rest(not fetched by X11) for NCBI-wise arg. processing
-*
-* Revision 5.70  1997/08/08 14:43:08  vakatov
-* [WIN_X] Nlm_XCheckUpdateEvent() -- check for mapping and expose events
-*
-* Revision 5.69  1997/08/01 16:47:32  vakatov
-* [WIN_MOTIF,WIN_MSWIN]  Added IconifyWindow() and IconicWindow()
-*
-* Revision 5.68  1997/07/23 16:39:02  vakatov
-* [WIN_MSWIN] ParseSetupArguments() -- fixed a quote("') handling bug
-*
-* Revision 5.67  1997/07/22 19:12:17  vakatov
-* Separated Main() from GetArg[svc]() functions;  [WIN_MSWIN] converged
-* console and GUI libraries; [for WIN32-DLL] encapsulated global variables
-*
-* Revision 5.66  1997/07/18 17:01:17  vakatov
-* [WIN_MOTIF]  Removed "arg[cv]";  use "Nlm_GetArg[cv]()" instead
-*
-* Revision 5.65  1997/07/14 19:31:04  vakatov
-* [WIN_X] Nlm_NewWindow() -- use common Vibrant colormap(and visual, and
-* depth) if failed to create Nlm_BusyColormap()
-*
-* Revision 5.64  1997/07/14 16:25:02  vakatov
-* Nlm_RemoveDyingWindows() -- look for Nlm_currentXWindow starting from
-* the shell level(was -- from the BullBoard level)
-*
-* Revision 5.63  1997/07/10 21:49:50  vakatov
-* [WIN_X]  Now able to manage windows having different depths(and
-* different visuals and GC).
-*
-* Revision 5.62  1997/07/02 18:46:07  vakatov
-* [WIN_X11]  If non-default colormap is used for a window -- make the
-* window to use the relevant visual(PseudoColor or GrayScale)
-*
-* Revision 5.61  1997/06/24 18:20:41  vakatov
-* Keep Nlm_dialogTextHeight value in-sync with the "vibtexts.c" R5.8 fixes
-*
-* Revision 5.60  1997/06/23 22:10:52  vakatov
-* [WIN_MOTIF,WIN_MSWIN]  GetArgs_ST() -- parse command line arguments
-* close to the console version
-*
-* Revision 5.59  1997/06/19 20:34:58  vakatov
-* [WIN_MSWIN]  Do not set the window class cursor to IDC_ARROW -- to avoid
-* confusing with the alternative cursors set by Vibrant application
-*
-* Revision 5.58  1997/06/18 20:00:27  kans
-* removed extra parenthesis
-*
-* Revision 5.57  1997/06/18 19:05:54  kans
-* protect against NULL curarg->to or curarg->from
-*
-* Revision 5.56  1997/06/09 21:54:49  vakatov
-* [WIN_X] #include <X11/Xatom.h> to fit old versions of X11
-*
-* Revision 5.55  1997/06/09 18:53:39  vakatov
-* [WIN_X]  Use(create if necessary) standard RGB_DEFAULT_MAP colormap as
-* the Vibrant default colormap, if possible.  Nlm_XAllocColor() moved from
-* "ncbidraw.c" and made external.
-*
-* Revision 5.54  1997/05/27 21:51:00  vakatov
-* Added Nlm_PopupParentWindow() to popup window w/o switching input focus
- *
- * Revision 5.53  1997/05/23 17:32:53  kans
- * added GetArgv, GetArgc for Mac
- *
- * Revision 5.52  1997/05/16 21:00:12  vakatov
- * [WIN_X11]  WindowStructFocusCallback() -- replaced XtFree() by XFree()
- *
- * Revision 5.51  1997/05/16 16:44:47  vakatov
- * [WIN_MSWIN,WIN32]  Addition to R5.49 -- do not abort() the failed
- * application; just popup an error message and then rely on the default
- * exception handler
- *
- * Revision 5.50  1997/05/15 15:14:17  vakatov
- * [WIN_MSWIN] Tune the StaticPrompt, etc. background color to match the
- * parent window background color
- *
- * Revision 5.49  1997/05/08 15:45:05  vakatov
- * [WIN_MSWIN,WIN32]  Abort() application in the case of unhandled
- * exception -- to prevent endless loop with the diagnostic dialog box
- *
- * Revision 5.48  1997/05/06  19:00:16  epstein
- * don't modify window title if environment variable is 0; this is a workaround for subtool
- *
- * Revision 5.47  1997/04/29  14:45:13  epstein
- *  corrections to tagged window titles
- *
- * Revision 5.46  1997/04/28  19:36:49  epstein
- * when VIBRANT_USE_APPLICATION_NAME environment variable is set, prepend program name unto each window
- *
- * Revision 5.45  1997/04/25  16:11:28  vakatov
- * [WIN_MOTIF] Register navigation key translation actions
- * [WIN_MOTIF, WIN_MSWIN] Catch and render(DoSendFocus) navigation key events
- *
- * Revision 5.44  1997/04/17  16:17:50  kans
- * InitForms and FreeForms called
- *
- * Revision 5.43  1997/03/19  16:00:18  vakatov
- * Added QuittingProgram() -- useful to timely break internal event loops
- *
- * Revision 5.42  1997/02/28  20:10:03  vakatov
- * Nlm_CleanUpWindows():  call to Nlm_RemoveDyingWindows() at first!
- *
- * Revision 5.41  1997/02/28  19:09:58  vakatov
- * [NLM_RISKY] Nlm_Add/DelSubwindowShell():  set "allShells" properly in
- * order to avoid discrepancy with later use of Nlm_GetWindowData()
- *
- * Revision 5.40  1997/02/21  19:24:16  vakatov
- * Do not apply fallback resources when running on a B&W screen
- *
- * Revision 5.39  1997/02/13  22:26:30  vakatov
- * Nlm_CleanUpWindows(), Nlm_RemoveDyingWindows() -- remove the window
- * menubar *after*(not *before*) removal of other window children
- * [WIN_MOTIF] Nlm_RemoveDyingWindows() -- let the removed shell be
- * dangling(see R5.38) only if NLM_MOTIF_CASCADEB_BUG is set
- *
- * Revision 5.38  1997/01/14  22:09:10  vakatov
- * Workaround for the MOTIF/X11 bug(see also "vibmenus.c", Rev. 5.17) --
- * do not completely destroy the shells having menubars -- let them
- * dangling. It still looks better than a program crash...
- * Fixed inaccurate string copying -- <mostly potential> 1-byte exceeding of
- * the string size by StringNCat;  missing terminating '\0' by StringNCpy.
- * Removed some unused variables;  set preprocessor conditions more
- * thoroughly to exclude some functions from the compilation on some platforms.
- *
- * Revision 5.37  1997/01/02  16:03:19  vakatov
- * [WIN_MOTIF]  Revert input focus to "PointerRoot" rather than to "None"
- *
- * Revision 5.36  1996/12/30  17:42:38  vakatov
- * [WIN_MOTIF]  Fixed Nlm_ProcessKeyPress() -- do not put uninitialized(stack-
- * located) input arguments to the XLookupString();  use NULL instead.
- *
- * Revision 5.35  1996/12/30  15:12:35  vakatov
- * Made all argument conversions be performed in the <new> FetchArg() routine.
- * Nlm_GetArgs() function rearranged:  added command-line arguments parsing
- * for MS-Windows and let one avoid posting of the arg-query dialog if all
- * arguments can be resolved by default or using the program command line.
- *
- * Revision 5.34  1996/12/13  17:27:38  kans
- * added GetArgv and GetArgc for WIN_MOTIF only
- *
- * Revision 5.33  1996/12/03  18:30:05  vakatov
- * [WIN_MSWIN]  Added (static) function win2client() to calculate client
- * rectangle on the base of the known top-level window rectangle.  Added
- * (static) function OnSizeMove() to re-implement(and fix) the MyCls_OnSize()
- * and MyCls_OnMove() window callbacks.
- *
- * Revision 5.32  1996/11/22  19:15:13  vakatov
- * [WIN_MSWIN]  Nlm_SetColorCell():  invalidate rather than animate
- *
- * Revision 5.31  1996/11/12  21:59:46  vakatov
- * [WIN_MOTIF]  Nlm_ResizeWindow():  count the menubar height when SetRect()
- *
- * Revision 5.30  1996/11/07  15:25:52  vakatov
- * [WIN_MOTIF]  IsXParentOf():  test for "children" != NULL
- *
- * Revision 5.29  1996/11/05  23:32:35  vakatov
- * [WIN_MSWIN]  Fit window into the screen borders on the window creation
- * or resizing;  changed the style definition(but not appearance) of
- * ShadowWindow; +extensive type casting
- *
- * Revision 5.28  1996/10/30  16:06:42  vakatov
- * Nlm_XrmGetResource1():  replaced XrmGetDatabase() by XtDatabase() to
- * suit X11R4 function set.
- *
- * Revision 5.27  1996/10/29  22:09:29  vakatov
- * [WIN_MOTIF]  Nlm_VibrantDefaultColormap():  Replaced X resource value
- * converters(which are absent in X releases < X11R5) by the hand-written
- * code; and made the "privateColormap" resorce value "false" by default.
- *
- * Revision 5.26  1996/10/28  21:24:24  vakatov
- * [WIN_MOTIF][_DEBUG]  Removed extra debug print
- *
- * Revision 5.25  1996/10/28  19:32:14  vakatov
- * [WIN_MOTIF]
- * Nlm_BusyColorMap():  added special case to create new colormap where
- * only specified number of colorcells "inherited" from the default
- * will be allocated.
- * Added Nlm_XrmGetResource2(), Nlm_XrmGetResource1() and
- * Nlm_XrmGetResource() functions and modified Nlm_SetupWindows()
- * to handle user-specified X-resources.
- * Added Nlm_VibrantDefaultColormap() to initialize the application
- * colormap according to the newly introduced Vibrant/X11 recources
- * "nPrivateColormap" and "nInheritColors".
- * Made a lot of type castings to get rid of all compiler warnings.
- *
- * Revision 5.24  1996/10/21  21:38:16  vakatov
- * [WIN_MOTIF]  Renamed WindowResizeCallback() to WindowStructFocusCallback()
- * and made it call DoActivate/DoDeactivate when accepting/loosing
- * input focus -- to sync. with [WIN_MSWIN] behaviour.  Removed explicit
- * (not quite correct) calls to DoActivate/DoDeactivate.
- *
- * Revision 5.23  1996/10/21  15:21:11  vakatov
- * [WIN_MOTIF]  WindowResizeCallback() <on the mapping event>:  protected
- *              from setting input focus to yet(or already) unmapped window
- *
- * Revision 5.22  1996/10/01  16:11:27  kans
- * wasn't setting ctrlKey on Mac
- *
- * Revision 5.21  1996/09/26  00:40:05  kans
- * on remove window, immediately null out window timer
- *
- * Revision 5.20  1996/09/26  00:29:23  kans
- * added SetWindowTimer
- *
- * Revision 5.19  1996/08/29  20:46:46  vakatov
- * [WIN_MSWIN]  Synchronized Nlm_Get- and Nlm_SetWindowPosition
- *
- * Revision 5.18  1996/08/27  16:34:24  vakatov
- * [WIN_MOTIF]  Nlm_SelectWindow() : fixed a case when it did not set input
- * focus to the selected window sometimes.
- *
- * Revision 5.17  1996/08/19  21:24:00  vakatov
- * [WIN_MOTIF]  Set default ToggleButton's foreground to "blue" --
- * "dark blue" is absent sometimes, somewhere.
- *
- * Revision 5.16  1996/07/26  17:56:57  vakatov
- * [WIN_MOTIF]  Nlm_NewWindow() : had to specify the MainWindow's colormap
- * explicitly to make LINUX/MOO-TIFF/X11 properly accept the colormap
- *
- * Revision 5.15  1996/07/23  21:36:05  vakatov
- * [WIN_MOTIF]  Nlm_BusyColorMap() : do not redefine 0th color
- * [WIN_MOTIF]  Nlm_HideWindow()   : do not change input focus is it
- * does not belong to the window being hided
- *
- * Revision 5.14  1996/07/19  19:44:51  vakatov
- * [WIN_MOTIF]  Nlm_RemoveDyingWindows() : set Nlm_currentXWindow to NULL
- * if it points to either the dying window or one of its children;
- * added new function IsXParentOf() determining whether the given window
- * is the parent of another one.
- *
- * Revision 5.13  1996/07/18  16:49:03  vakatov
- * [WIN_MOTIF]  Nlm_SelectWindow() : Removed extra call of XSetInputFocus()
- *
- * Revision 5.12  1996/07/17  16:24:05  vakatov
- * [WIN_MOTIF]  Nlm_Hide()/WM/Nlm_Select() case -- the input focus quirk fixed
- *
- * Revision 5.11  1996/06/24  17:00:21  vakatov
- * [WIN_MOTIF]  Nlm_Select() now seems to work properly for all cases
- *
- * Revision 5.10  1996/06/24  16:05:08  vakatov
- * [WIN_MOTIF]  Fixed bug in Nlm_Select()
- *
- * Revision 5.9  1996/06/19  21:15:28  vakatov
- * [WIN_MOTIF]  Made Nlm_Select() to select(pop-up) the specified window
- * in most cases; there is still a problem when Nlm_Select is called just AFTER
- * (not before) hiding of another Vibrant window which has current input focus --
- * some WMs are "too smart" and in some special conditions takes control over
- * the "focus inheritance" after the dying window.
- *
- * Revision 5.8  1996/06/18  21:57:42  vakatov
- * [WIN_MOTIF]  Made ModalWindow to be really modal
- *
- * Revision 5.7  1996/06/17  21:57:17  kans
- * InvalObject in Nlm_SetColorCell on Mac
- *
- * Revision 5.6  1996/06/17  17:00:47  vakatov
- * [WIN_MSWIN]  The shell window's border/caption/menu-bar dimensions are to
- * be taken into account inside the Nlm_ResizeWindow() function
- *
- * Revision 5.5  1996/06/14  14:32:24  vakatov
- * [WIN_MOTIF] Added cMap_fixed field to WindowData structure to indicate
- * fixed(having reserved cells for Motif colors) colormap attached to
- * the window.
- * SetColorMap() function partially rewritten to treate the fixed colormap
- * under WIN_MOTIF and to reserve colorcells for animation under WIN_MSWIN.
- * Added Nlm_SetColorCell() -- to immediately change the color appearence.
- * [WIN_MOTIF]  Added Nlm_RestrictMotifColorsTo() -- to avoid Motif/3D-Viewer
- * color overlapping; it is now called inside "Nlm_NewWindow()" before
- * initializing Motif resources
- *
- * Revision 5.3  1996/06/03  19:12:32  vakatov
- * [WIN_MOTIF]  Added hard-coding fallbacks to provide default set of
- * basic colors in Vibrant-based applications
- *
- * Revision 5.2  1996/05/30  20:06:07  vakatov
- * [WIN_MSWIN]  <Shift> and <Ctrl> key status checking added to MainProc()
- *
- * Revision 5.1  1996/05/30  14:02:46  vakatov
- * [WIN_MOTIF]  Corrected fallback resources to provide proper setting of the
- * background color under CDE
- *
- * Revision 4.29  1996/05/21  13:58:06  epstein
- * fix type for XtFree() calls
- *
- * Revision 4.28  1996/05/21  12:32:16  kans
- * prototypes for add, del subwindow shell
- *
- * Revision 4.27  1996/05/20  21:38:13  vakatov
- * [WIN_MOTIF]  All "Widget" / "NULL" comparisons and assignments replaced
- * by the "Widget" / "(Widget)0" these
- *
- * Revision 4.26  1996/05/13  16:00:50  vakatov
- * WindowResizeCallback() modified to take into account the shell window
- * repositioning -- it is usually made by window manager when framing the
- * shell window with the WM-specific window border and title bar.
- *
- * Revision 4.24  1996/05/06  18:28:03  vakatov
- * Nlm_SetWindowDefaultButton() modified;  some extra stuff removed
- *
- * Revision 4.23  1996/05/03  21:03:43  kans
- * removed erroneous textscrapfull = FALSE lines
- *
- * Revision 4.22  1996/05/03  20:27:25  kans
- * put back scrap fixes
- *
- * Revision 4.21  1996/05/03  20:05:22  vakatov
- * [WIN_MOTIF/_DEBUG]  Added event handler to allow the Vibrant windows
- * to interact with the standard X-utility "editres";
- * this utility provides runtime read/write access to all widget attributes
- *
- * Revision 4.20  1996/05/02  20:59:16  kans
- * sets textScrapFull flag properly on startup, resume
- *
- * Revision 4.19  1996/04/30  19:52:19  vakatov
- * GetPosition() now returns actual position for a top-level window having menu bar
- *
- * Revision 4.18  1996/04/30  14:27:29  kans
- * copies text clipboard into text scrap on startup (Mac)
- *
- * Revision 4.17  1996/04/25  17:06:48  vakatov
- * Nlm_ShowDocument():   extraw = extrah = 0;  for WIN_MSWIN
- *
- * Revision 4.16  1996/04/12  19:26:14  vakatov
- * "WindowResizeCallback()" corrected to provide regular extraction of
- * new window position (for the case of the window resizing --
- * rather than just moving)
- *
- * Revision 4.15  1996/03/27  23:10:13  vakatov
- * Function Nlm_SetCursorShape() added to let programmer
- * easily store/restore current cursor shape
- *
- * Revision 4.14  1996/03/19  23:19:36  kans
- * used proper gestalt selector, test, before registering apple events
- *
- * Revision 4.13  1996/03/13  21:40:00  epstein
- * export command-line arguments
- *
- * Revision 4.12  1996/03/12  20:06:10  epstein
- * fix drag-and-drop for Windows
- *
- * Revision 4.11  1996/03/11  23:25:23  kans
- * apple event open file handler added (modified from RasMol code)
- *
- * Revision 4.10  1996/03/11  20:37:56  epstein
- * add support for Drag & Drop
- *
- * Revision 4.9  1996/03/08  16:10:43  vakatov
- * Made Nlm_Update() for Motif/X11 to act more like that for
- * MS-Windows and Mac.  However, it still avoid automatic (without a
- * Nlm_Update() call) recursive synchronization...
- *
- * Revision 4.8  1996/03/07  15:55:35  kans
- * invalidate whole content of resized window in mswin version (DV)
- *
- * Revision 4.7  1996/03/02  22:36:38  kans
- * reduction of X traffic (DV)
- *
- * Revision 4.6  1996/02/13  17:24:07  kans
- * accelerated set position prior to realization (Denis Vakatov)
- *
- * Revision 4.5  1996/01/19  00:55:46  kans
- * UseWindow sets theWindow, returned (on the Mac) by ActiveWindow
- *
- * Revision 4.4  1995/11/29  15:45:23  smirnov
- * Position of window (MOTIF only)
- *
- * Revision 4.3  1995/11/28  19:02:36  smirnov
- * GetWindowRect()/GetClientRect problem (AS) (MS-Windows only)
- *
- * Revision 4.2  1995/11/08  23:30:31  kans
- * removed edit block fields, which belong in the application
- *
- * Revision 4.1  1995/09/06  20:30:24  kans
- * fixed bug due to GetWindowRect vs. GetClientRect (AS + GS)
- *
- * Revision 2.88  1995/07/24  20:03:03  kans
- * removed duplicate ClearEditProcs, reference X11 colormap as integer
- *
- * Revision 2.87  1995/07/19  20:42:23  kans
- * window rectangle takes Motif menu bar height into account
- *
- * Revision 2.86  1995/06/28  21:48:57  kans
- * added Add and Del SubwindowShell (Alex)
- *
- * Revision 2.85  1995/06/13  16:30:38  kans
- * Motif version of GetArgs can parse remaining arguments in lieu of dialog
- *
- * Revision 2.83  1995/05/31  21:24:29  kans
- * XFreeColormap fix (AS)
- *
- * Revision 2.82  1995/05/31  18:00:58  kans
- * added SetColorMap and related code (AS)
- *
- * 08-24-94 Schuler     Change try and except to __try and _except for
- *                      compatibility with Visual C 2.0
- *
- * ==========================================================================
- */
+* ==========================================================================
+*/
 
 #include <vibtypes.h>
 #include <vibprocs.h>
@@ -738,6 +78,23 @@
 extern void Nlm_ConvertFilename ( FSSpec *fss, Nlm_CharPtr filename );
 #endif
 
+/* remove this define to remove Quartz/Cocoa cursor handling
+   cursor calls will become no-ops if removed */
+/*
+#define WIN_MAC_QUARTZ_COCOA_CURSORS
+*/
+
+#ifdef WIN_MAC_QUARTZ
+#ifdef WIN_MAC_QUARTZ_COCOA_CURSORS
+/* needed to be able to access a bit of Cocoa */
+#include <CoreFoundation/CoreFoundation.h>
+char NSApplicationLoad(void);
+void *NSClassFromString(CFStringRef aClassName);
+void *NSSelectorFromString(CFStringRef aSelectorName);
+void *objc_msgSend(void *self, void *_cmd, ...);
+#endif
+#endif
+
 #ifdef WIN_MAC
 #ifndef Nlm_WindowTool
 #define Nlm_WindowTool  WindowPtr
@@ -854,6 +211,9 @@ Nlm_Boolean Nlm_usesMacNavServices = FALSE;
 
 #ifdef WIN_MAC
 EventRecord  Nlm_currentEvent;
+#ifdef WIN_MAC_QUARTZ
+static void Nlm_DrawWindow (Nlm_GraphiC w, Nlm_Boolean drawGrowIcon);
+#endif
 #ifdef __CONDITIONALMACROS__
 /* Global RoutineDescriptors - from RasMol */
 AEEventHandlerUPP HandleAEIgnorePtr;
@@ -1623,6 +983,9 @@ extern void Nlm_SetColorMap (Nlm_WindoW w, Nlm_Uint2 totalColors,
 #endif
 
 #ifdef WIN_MAC
+// QUARTZ_FIXME: there's no replacement for this in CG, does anything
+// need to be done?
+#ifndef WIN_MAC_QUARTZ
   if ( wdata.cMap != NULL ){
     if ( wdata.cMapStatus ){
       SetPalette( wdata.handle, NULL, FALSE);
@@ -1646,6 +1009,7 @@ extern void Nlm_SetColorMap (Nlm_WindoW w, Nlm_Uint2 totalColors,
     }
   }
 #endif
+#endif
 
 #ifdef WIN_MOTIF
   do { /* TRY */
@@ -2286,6 +1650,8 @@ static Nlm_WindoW Nlm_MakeWindowLink (Nlm_RectPtr r, Nlm_Int2 recordSize,
 extern void Nlm_SetUpdateRegion (WindowPtr wptr)
 
 {
+// QUARTZ_FIXME: what does this do? does it need to do anything?
+#ifndef WIN_MAC_QUARTZ
   Rect bounds;
 
   if (wptr != NULL) {
@@ -2295,6 +1661,7 @@ extern void Nlm_SetUpdateRegion (WindowPtr wptr)
     Nlm_RectToolToRecT (&bounds, &Nlm_updateRect);
     /* HUnlock ((Handle) Nlm_updateRgn); */
   }
+#endif
 }
 #endif
 
@@ -2660,7 +2027,79 @@ static void win2client(Nlm_WindoW w,
 }
 #endif 
 
+#ifdef WIN_MAC_QUARTZ
+// QUARTZ_FIXME: this stuff is probably not needed
+//static void Nlm_WindowSetProperty (WindowRef wptr, PropertyTag tag, void *ptr)
+//{
+//  SetWindowProperty (wptr, 'NCBI', tag, sizeof(ptr), &ptr);
+//}
+//
+//static void *Nlm_WindowGetProperty (WindowRef wptr, PropertyTag tag)
+//{
+//  void *ret = 0;
+//  GetWindowProperty (wptr, 'NCBI', tag, sizeof(ret), 0, &ret);
+//  return ret;
+//}
+//
+//static void Nlm_EnsureQuartzPort (CGContextRef *ctxPtr, HIViewRef imageView)
+//{
+//  /* note: the context must actually be a bitmap context, this 
+//      is guaranteed since this function is the only one that
+//      gets to make it anyway */
+//  HIRect bounds;
+//  HIViewGetBounds (imageView, &bounds);
+//  int good = *ctxPtr != 0;
+//  if (good)
+//  {
+//    
+//    if (bounds.size.width != CGBitmapContextGetWidth (*ctxPtr))
+//      good = 0;
+//    if (bounds.size.height != CGBitmapContextGetHeight (*ctxPtr))
+//      good = 0;
+//  }
+//  if (!good)
+//  {
+//    CGContextRelease (*ctxPtr);
+//    
+//    CGColorSpaceRef colorSpace = CGColorSpaceCreateDeviceRGB ();
+//    *ctxPtr = CGBitmapContextCreate (0, bounds.size.width, bounds.size.height, 32, 0, colorSpace, kCGImageAlphaNoneSkipLast);
+//    CGColorSpaceRelease (colorSpace);
+//  }
+//}
+//
+//CGContextRef Nlm_GetQuartzWindowPort (WindowRef wptr)
+//{
+//  HIViewRef imageView = Nlm_WindowGetProperty (wptr, 'imgv');
+//  CGContextRef ref = Nlm_WindowGetProperty (wptr, 'cntx');
+//  CGContextRef old = ref;
+//  Nlm_EnsureQuartzPort (&ref, imageView);
+//  if (ref != old)
+//    Nlm_WindowSetProperty (wptr, 'cntx', ref);
+//  return ref;
+//}
+
+static OSStatus Nlm_RootHIViewRedrawHandler (EventHandlerCallRef handler, EventRef event, void *userData)
+{
+  Nlm_WindoW w = userData;
+  
+  CGContextRef ctx;
+  GetEventParameter (event,
+                     kEventParamCGContextRef,
+                     typeCGContextRef,
+                     NULL,
+                     sizeof (CGContextRef),
+                     NULL,
+                     &ctx);
+  Nlm_SetPort (ctx);
+  Nlm_SetPortWindowPort (Nlm_ParentWindowPtr ((Nlm_GraphiC)w));
+  Nlm_DrawWindow ((Nlm_GraphiC)w, 0);
+  Nlm_SetPortWindowPort (NULL);
+  Nlm_SetPort (NULL);
+	
+  return noErr;
+}
 
+#endif
 
 #define DOCUMENT_STYLE 1
 #define FIXED_STYLE    2
@@ -2700,7 +2139,7 @@ static void Nlm_NewWindow (Nlm_WindoW w, Nlm_Int2 type, Nlm_Int2 procID,
   CCTabPtr        colorPtr;
   Nlm_RectTool    rtool;
   WindowClass     winClass = 0;
-  WindowAttributes winAttrs = 0; /* kWindowStandardHandlerAttribute; */
+  WindowAttributes winAttrs = kWindowCompositingAttribute; /* kWindowStandardHandlerAttribute; */
   OSStatus        osErr;
 #endif
 #ifdef WIN_MOTIF
@@ -2785,8 +2224,10 @@ static void Nlm_NewWindow (Nlm_WindoW w, Nlm_Int2 type, Nlm_Int2 procID,
     }
 
   behindNone = (Nlm_WindowTool) (-1);
+#ifndef WIN_MAC_QUARTZ
   TextFont (0);
   TextSize (0);
+#endif
   Nlm_RecTToRectTool (&r, &rtool);
   if (close == NULL) {
     goAway = FALSE;
@@ -2810,6 +2251,53 @@ static void Nlm_NewWindow (Nlm_WindoW w, Nlm_Int2 type, Nlm_Int2 procID,
     return;
   }
 #endif
+#ifdef WIN_MAC_QUARTZ
+  HIViewRef root = HIViewGetRoot (wptr);
+  HIViewRef content;
+  HIViewFindByID (root, kHIViewWindowContentID, &content);
+  
+  EventTypeSpec updateEventSpec[] = { kEventClassControl, kEventControlDraw };
+  InstallEventHandler (GetControlEventTarget (content),
+                       Nlm_RootHIViewRedrawHandler,
+                       GetEventTypeCount (updateEventSpec),
+                       updateEventSpec,
+                       w,
+                       NULL);
+  
+// QUARTZ_FIXME: unneeded unless we really do need the triple buffer
+//  HIViewRef imageView;
+//  HIImageViewCreate (0, &imageView);
+//  
+//  HIViewAddSubview (root, imageView);
+//  HIRect bounds;
+//  HIViewGetBounds (root, &bounds);
+//  HIViewSetFrame (imageView, &bounds);
+//  
+//  HILayoutInfo layout;
+//  layout.version = kHILayoutInfoVersionZero;
+//  
+//  HIViewGetLayoutInfo (imageView, &layout);
+//  layout.binding.top.toView = root;
+//  layout.binding.top.kind = kHILayoutBindTop;
+//  layout.binding.bottom.toView = root;
+//  layout.binding.bottom.kind = kHILayoutBindBottom;
+//  layout.binding.left.toView = root;
+//  layout.binding.left.kind = kHILayoutBindLeft;
+//  layout.binding.right.toView = root;
+//  layout.binding.right.kind = kHILayoutBindRight;
+//  HIViewSetLayoutInfo (imageView, &layout);
+//  HIViewApplyLayout (imageView);
+//  HIViewSetVisible (imageView, 1);
+//  
+//  char *path = "/Users/mikeash/bob_eggleton_adeepnessinthesky.jpg";
+//  CFURLRef url = CFURLCreateFromFileSystemRepresentation (NULL, (const UInt8 *)path, strlen (path), 0);
+//  CGDataProviderRef provider = CGDataProviderCreateWithURL (url);
+//  CGImageRef img = CGImageCreateWithJPEGDataProvider (provider, NULL, 1, kCGRenderingIntentDefault);
+//  HIImageViewSetImage (imageView, img);
+  
+//  Nlm_WindowSetProperty (wptr, 'imgv', imageView);
+  
+#else
   Nlm_SetPortWindowPort(wptr);
   Nlm_currentWindowTool = wptr;
   prt = (Nlm_PortTool) wptr;
@@ -2833,6 +2321,7 @@ static void Nlm_NewWindow (Nlm_WindoW w, Nlm_Int2 type, Nlm_Int2 procID,
     GetBackColor (&Nlm_RGBbackColor);
   }
 #endif
+#endif
 
 #ifdef WIN_MSWIN
   if (close == NULL)
@@ -3303,9 +2792,11 @@ static void Nlm_ResizeWindow (Nlm_GraphiC w, Nlm_Int2 dragHeight,
 
 #ifdef WIN_MAC
   menuHeight = 21;
+#ifndef WIN_MAC_QUARTZ
   TextFont (0);
   TextSize (0);
 #endif
+#endif
 #ifdef WIN_MOTIF
   if (Nlm_GetWindowMenuBar( (Nlm_WindoW)w ) != NULL)
     menuHeight = Nlm_internalMenuBarHeight;
@@ -3821,9 +3312,11 @@ extern void Nlm_UseWindow (Nlm_WindoW w)
     wptr = Nlm_ParentWindowPtr ((Nlm_GraphiC) w);
     if (wptr  &&  !Nlm_IsWindowDying( w )) {
 #ifdef WIN_MAC
+#ifndef WIN_MAC_QUARTZ
       Nlm_SetPortWindowPort(wptr);
       Nlm_SetUpdateRegion (wptr);
       Nlm_ResetDrawingTools();
+#endif
       Nlm_theWindow = w;
 #endif
 #ifdef WIN_MSWIN
@@ -3926,10 +3419,12 @@ static void Nlm_SelectWindow(Nlm_GraphiC w, Nlm_Boolean savePort)
 
 #ifdef WIN_MAC
   SelectWindow (wptr);
+#ifndef WIN_MAC_QUARTZ
   Nlm_SetPortWindowPort(wptr);
   Nlm_SetUpdateRegion(wptr);
   Nlm_ResetDrawingTools();
 #endif
+#endif
 #ifdef WIN_MSWIN
   BringWindowToTop (wptr);
 /* M.I */
@@ -4026,6 +3521,9 @@ extern void Nlm_EraseWindow (Nlm_WindoW w)
 
   if (w != NULL) {
     wptr = Nlm_ParentWindowPtr ((Nlm_GraphiC) w);
+#ifdef WIN_MAC_QUARTZ
+    HIViewSetNeedsDisplay (HIViewGetRoot (wptr), 1);
+#else
     GetPort(&temp);
     Nlm_SetPortWindowPort(wptr);
     Nlm_ResetDrawingTools();
@@ -4036,6 +3534,7 @@ extern void Nlm_EraseWindow (Nlm_WindoW w)
     Nlm_SetPort(temp);
     Nlm_currentWindowTool = GetWindowFromPort(temp);
     Nlm_Update();
+#endif
   }
 #endif
 #ifdef WIN_MSWIN
@@ -4116,7 +3615,9 @@ static Nlm_Boolean Nlm_GrowClick (Nlm_GraphiC w, Nlm_PoinT pt)
   if (windowLoc == inGrow) {
     Nlm_LoadRect (&r, -32768, -32768, 32767, 32767);
     Nlm_RecTToRectTool (&r, &rtool);
+#ifndef WIN_MAC_QUARTZ
     ClipRect (&rtool);
+#endif
     Nlm_GetWindowData ((Nlm_WindoW) w, &wdata);
     Nlm_RecTToRectTool (&(wdata.growArea), &rtool);
     newSize = GrowWindow (wptr, ptool, &rtool);
@@ -4127,7 +3628,9 @@ static Nlm_Boolean Nlm_GrowClick (Nlm_GraphiC w, Nlm_PoinT pt)
  */
     GetPortBounds(GetWindowPort(wptr), &bounds);
     if (! newSize) {
+#ifndef WIN_MAC_QUARTZ
       ClipRect (&bounds);
+#endif
       return rsult;
     }
     if (wd < 50) {
@@ -4143,7 +3646,9 @@ static Nlm_Boolean Nlm_GrowClick (Nlm_GraphiC w, Nlm_PoinT pt)
     Nlm_UpdateScrollBar (w);
     wptr = Nlm_GetWindowPtr ((Nlm_WindoW) w);
     Nlm_RectToolToRecT (&bounds, &r);
+#ifndef WIN_MAC_QUARTZ
     ClipRect (&bounds);
+#endif
     Nlm_LocalToGlobal ((Nlm_PointPtr) &(r.left));
     Nlm_LocalToGlobal ((Nlm_PointPtr) &(r.right));
     Nlm_SetRect (w, &r);
@@ -4166,14 +3671,18 @@ static void Nlm_DrawGrowIcon (Nlm_GraphiC w, Nlm_Boolean drawgrow, Nlm_Boolean d
   Nlm_WindowTool  wptr;
   Rect bounds;
 
+#ifndef WIN_MAC_QUARTZ
   GetPort (&temp);
   GetPenState (&state);
+#endif
   wptr = Nlm_ParentWindowPtr (w);
   GetPortBounds(GetWindowPort(wptr), &bounds);
   Nlm_RectToolToRecT (&bounds, &r);
   if (drawbar && Nlm_GetWindowMenuBar ((Nlm_WindoW) w) != NULL) {
     Nlm_RecTToRectTool (&r, &rtool);
+#ifndef WIN_MAC_QUARTZ
     ClipRect (&rtool);
+#endif
     Nlm_MoveTo (r.right - 16, 20);
     Nlm_LineTo (r.right, 20);
     r.top = r.top + 21;
@@ -4182,7 +3691,9 @@ static void Nlm_DrawGrowIcon (Nlm_GraphiC w, Nlm_Boolean drawgrow, Nlm_Boolean d
     Nlm_RecTToRectTool (&r, &rtool);
     rtool.left = rtool.right - 15;
     rtool.top = rtool.bottom - 15;
+#ifndef WIN_MAC_QUARTZ
     ClipRect (&rtool);
+#endif
     DrawGrowIcon (wptr);
   }
   Nlm_RecTToRectTool (&r, &rtool);
@@ -4197,11 +3708,13 @@ static void Nlm_DrawGrowIcon (Nlm_GraphiC w, Nlm_Boolean drawgrow, Nlm_Boolean d
   */
 #endif
   Nlm_RecTToRectTool (&r, &rtool);
+#ifndef WIN_MAC_QUARTZ
   ClipRect (&rtool);
   Nlm_SetPort(temp);
   Nlm_currentWindowTool = GetWindowFromPort(temp);
   Nlm_SetUpdateRegion (GetWindowFromPort(temp));
   SetPenState (&state);
+#endif
 }
 
 static Nlm_Boolean Nlm_ZoomClick (Nlm_GraphiC w, Nlm_PoinT pt)
@@ -4255,7 +3768,9 @@ static Nlm_Boolean Nlm_ZoomClick (Nlm_GraphiC w, Nlm_PoinT pt)
       Nlm_UpdateScrollBar (w);
       wptr = Nlm_GetWindowPtr ((Nlm_WindoW) w);
       Nlm_RectToolToRecT (&bounds, &r);
+#ifndef WIN_MAC_QUARTZ
       ClipRect (&bounds);
+#endif
       Nlm_LocalToGlobal ((Nlm_PointPtr) &(r.left));
       Nlm_LocalToGlobal ((Nlm_PointPtr) &(r.right));
       Nlm_SetRect (w, &r);
@@ -4312,6 +3827,7 @@ static Nlm_Boolean Nlm_ContentClick (Nlm_GraphiC w, Nlm_PoinT pt)
   Nlm_RevPtr     top;
 
   Nlm_localMouse = Nlm_globalMouse;
+  Nlm_SetPortWindowPort (Nlm_ParentWindowPtr (w));
   Nlm_GlobalToLocal (&Nlm_localMouse);
   g = Nlm_GetChild (w);
   notInside = TRUE;
@@ -4381,12 +3897,16 @@ static Nlm_Boolean Nlm_CommonClick (Nlm_GraphiC w, Nlm_PoinT pt,
   rsult = FALSE;
   if (chosenWindow == (Nlm_WindoW) w) {
     wptr = Nlm_ParentWindowPtr (w);
+#ifndef WIN_MAC_QUARTZ
     GetPort (&temp);
     GetPenState (&state);
+#endif
+#ifndef WIN_MAC_QUARTZ
     Nlm_SetPortWindowPort(wptr);
     Nlm_currentWindowTool = wptr;
     Nlm_SetUpdateRegion (wptr);
     Nlm_ResetDrawingTools ();
+#endif
     if ((close && Nlm_CloseClick (w, pt)) ||
        (drag && Nlm_DragClick (w, pt)) ||
        (grow && Nlm_GrowClick (w, pt)) ||
@@ -4395,10 +3915,12 @@ static Nlm_Boolean Nlm_CommonClick (Nlm_GraphiC w, Nlm_PoinT pt,
     } else {
       rsult = Nlm_ContentClick (w, pt);
     }
+#ifndef WIN_MAC_QUARTZ
     Nlm_SetPort(temp);
     Nlm_currentWindowTool = GetWindowFromPort(temp);
     Nlm_SetUpdateRegion (GetWindowFromPort(temp));
     SetPenState (&state);
+#endif
   } else if (chosenWindow != NULL) {
     Nlm_DoSelect ((Nlm_GraphiC) chosenWindow, TRUE);
   }
@@ -4447,17 +3969,21 @@ static Nlm_Boolean Nlm_ModalClick (Nlm_GraphiC w, Nlm_PoinT pt)
       cls = wdata.close;
       if (cls != NULL) {
         wptr = Nlm_ParentWindowPtr (w);
+#ifndef WIN_MAC_QUARTZ
         GetPort (&temp);
         GetPenState (&state);
+#endif
         Nlm_SetPortWindowPort(wptr);
         Nlm_currentWindowTool = wptr;
         Nlm_SetUpdateRegion (wptr);
         Nlm_ResetDrawingTools ();
         cls ((Nlm_WindoW) w);
+#ifndef WIN_MAC_QUARTZ
         Nlm_SetPort(temp);
         Nlm_currentWindowTool = GetWindowFromPort(temp);
         Nlm_SetUpdateRegion (GetWindowFromPort(temp));
         SetPenState (&state);
+#endif
       }
     }
   } else {
@@ -4484,17 +4010,21 @@ static Nlm_Boolean Nlm_MovableModalClick (Nlm_GraphiC w, Nlm_PoinT pt)
       cls = wdata.close;
       if (cls != NULL) {
         wptr = Nlm_ParentWindowPtr (w);
+#ifndef WIN_MAC_QUARTZ
         GetPort (&temp);
         GetPenState (&state);
+#endif
         Nlm_SetPortWindowPort(wptr);
         Nlm_currentWindowTool = wptr;
         Nlm_SetUpdateRegion (wptr);
         Nlm_ResetDrawingTools ();
         cls ((Nlm_WindoW) w);
+#ifndef WIN_MAC_QUARTZ
         Nlm_SetPort(temp);
         Nlm_currentWindowTool = GetWindowFromPort(temp);
         Nlm_SetUpdateRegion(GetWindowFromPort(temp));
         SetPenState (&state);
+#endif
       }
     }
   } else {
@@ -4589,8 +4119,10 @@ static void Nlm_FloatingSelect (Nlm_GraphiC w, Nlm_Boolean savePort)
   Nlm_WindowTool  wptr;
 
   wptr = Nlm_ParentWindowPtr (w);
+#ifndef WIN_MAC_QUARTZ
   GetPort (&temp);
   GetPenState (&state);
+#endif
   Nlm_SetPortWindowPort(wptr);
   Nlm_currentWindowTool = wptr;
   Nlm_SetUpdateRegion (wptr);
@@ -4601,10 +4133,12 @@ static void Nlm_FloatingSelect (Nlm_GraphiC w, Nlm_Boolean savePort)
   } else {
     Nlm_ContentClick (w, Nlm_globalMouse);
   }
+#ifndef WIN_MAC_QUARTZ
   Nlm_SetPort(temp);
   Nlm_currentWindowTool = GetWindowFromPort(temp);
   Nlm_SetUpdateRegion (GetWindowFromPort(temp));
   SetPenState (&state);
+#endif
   Nlm_localMouse = Nlm_globalMouse;
   Nlm_GlobalToLocal (&Nlm_localMouse);
 #endif
@@ -4623,15 +4157,19 @@ static void Nlm_DesktopSelect (Nlm_GraphiC w, Nlm_Boolean savePort)
   PenState      state;
   Nlm_PortTool  temp;
 
+#ifndef WIN_MAC_QUARTZ
   GetPort (&temp);
   GetPenState (&state);
   PenNormal ();
+#endif
   Nlm_DesktopClick (w, Nlm_globalMouse);
+#ifndef WIN_MAC_QUARTZ
   Nlm_SetPort(temp);
   Nlm_currentWindowTool = GetWindowFromPort(temp);
   Nlm_SetUpdateRegion (GetWindowFromPort(temp));
   SetPenState (&state);
 #endif
+#endif
 }
 
 #ifdef WIN_MAC
@@ -4662,12 +4200,14 @@ static Nlm_Boolean Nlm_NormalKey (Nlm_GraphiC w, Nlm_Char ch)
   Nlm_WindowTool  wptr;
 
   wptr = Nlm_ParentWindowPtr (w);
+#ifndef WIN_MAC_QUARTZ
   GetPort (&temp);
   GetPenState (&state);
   Nlm_SetPortWindowPort(wptr);
   Nlm_currentWindowTool = wptr;
   Nlm_SetUpdateRegion (wptr);
   Nlm_ResetDrawingTools ();
+#endif
   Nlm_localMouse = Nlm_globalMouse;
   Nlm_GlobalToLocal (&Nlm_localMouse);
   if (Nlm_currentKey != '\0') {
@@ -4691,10 +4231,12 @@ static Nlm_Boolean Nlm_NormalKey (Nlm_GraphiC w, Nlm_Char ch)
       Nlm_DesktopKey ((Nlm_GraphiC) Nlm_desktopWindow, ch);
     }
   }
+#ifndef WIN_MAC_QUARTZ
   Nlm_SetPort(temp);
   Nlm_currentWindowTool = GetWindowFromPort(temp);
   Nlm_SetUpdateRegion(GetWindowFromPort(temp));
   SetPenState (&state);
+#endif
   return TRUE;
 }
 
@@ -4711,8 +4253,10 @@ static Nlm_Boolean Nlm_FloatingKey (Nlm_GraphiC w, Nlm_Char ch)
   Nlm_WindowTool  wptr;
 
   wptr = Nlm_ParentWindowPtr (w);
+#ifndef WIN_MAC_QUARTZ
   GetPort (&temp);
   GetPenState (&state);
+#endif
   Nlm_SetPortWindowPort(wptr);
   Nlm_currentWindowTool = wptr;
   Nlm_SetUpdateRegion (wptr);
@@ -4741,10 +4285,12 @@ static Nlm_Boolean Nlm_FloatingKey (Nlm_GraphiC w, Nlm_Char ch)
       Nlm_DoKey ((Nlm_GraphiC) nw, ch);
     }
   }
+#ifndef WIN_MAC_QUARTZ
   Nlm_SetPort(temp);
   Nlm_currentWindowTool = GetWindowFromPort(temp);
   Nlm_SetUpdateRegion(GetWindowFromPort(temp));
   SetPenState (&state);
+#endif
   return TRUE;
 }
 
@@ -4771,6 +4317,7 @@ static void Nlm_DrawWindow (Nlm_GraphiC w, Nlm_Boolean drawGrowIcon)
   Nlm_WindowTool  wptr;
   Rect bounds;
 
+#ifndef WIN_MAC_QUARTZ
   wptr = Nlm_ParentWindowPtr (w);
   GetPort (&temp);
   GetPenState (&state);
@@ -4787,6 +4334,7 @@ static void Nlm_DrawWindow (Nlm_GraphiC w, Nlm_Boolean drawGrowIcon)
   Nlm_RectToolToRecT (&bounds, &r);
   Nlm_EraseRect (&r);
 
+#endif
   if (okayToDrawContents) {
     if (drawGrowIcon) {
       Nlm_DrawGrowIcon (w, FALSE, TRUE);
@@ -4806,13 +4354,17 @@ static void Nlm_DrawWindow (Nlm_GraphiC w, Nlm_Boolean drawGrowIcon)
     }
   }
 
+#ifndef WIN_MAC_QUARTZ
   EndUpdate (wptr);
+#endif
   Nlm_ResetDrawingTools ();
+#ifndef WIN_MAC_QUARTZ
   Nlm_ResetClip ();
   Nlm_SetPort(temp);
   Nlm_currentWindowTool = GetWindowFromPort(temp);
   Nlm_SetUpdateRegion(GetWindowFromPort(temp));
   SetPenState (&state);
+#endif
 }
 
 static void Nlm_DocumentDraw (Nlm_GraphiC w)
@@ -5356,14 +4908,65 @@ static void Nlm_SetCursor (Cursor cursor)
 }
 #endif
 
+#ifdef WIN_MAC_QUARTZ
+#ifdef WIN_MAC_QUARTZ_COCOA_CURSORS
+/* these support functions make life a bit easier and centralize the
+   ugly Cocoa access */
+
+/* objc_msgSend is actually a trampoline which is effectively has no real prototype
+   but actually just takes on the prototype of the target method;
+   in order to shut the compiler up about methods which return char and generate
+   the correct machine code at the call site, we define this global function pointer
+   which points to the same function but with a different prototype */
+static char (*objc_msgSend_charRetFptr)(void *, void *, ...) = (void *)objc_msgSend;
+
+/* handy shortcut macros for invoking NSCursor methods */
+#define COCOA_SELECTOR(name) NSSelectorFromString(CFSTR(name))
+
+/* NSCursor does not define all of the methods we use when running
+   on 10.2, so we check to ensure it responds before calling anything.
+   If it does not respond, we'll return 0 (nil) and the following
+   set operation will be a no-op. */
+#define COCOA_NSCURSOR_CLASS_RESPONDS(name) objc_msgSend_charRetFptr(Nlm_NSCursorClass(), COCOA_SELECTOR("respondsToSelector:"), COCOA_SELECTOR(name))
+
+#define COCOA_NAMED_CURSOR(name) (COCOA_NSCURSOR_CLASS_RESPONDS(name "Cursor") \
+                                  ? objc_msgSend(Nlm_NSCursorClass(), COCOA_SELECTOR(name "Cursor")) \
+                                  : 0)
+
+static void *Nlm_NSCursorClass (void)
+{
+  static int didLoadApplication = 0;
+  if (!didLoadApplication)
+  {
+    didLoadApplication = 1;
+    NSApplicationLoad();
+  }
+  
+  return NSClassFromString(CFSTR("NSCursor"));
+}
+
+static void Nlm_SetCursor (void *cursor)
+{
+  objc_msgSend(cursor, NSSelectorFromString(CFSTR("set")));
+}
+
+#endif
+#endif
+
 extern void Nlm_ArrowCursor (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+#ifdef WIN_MAC_QUARTZ_COCOA_CURSORS
+  Nlm_SetCursor(COCOA_NAMED_CURSOR("arrow"));
+#endif
+#else
   Cursor cursor;
   GetQDGlobalsArrow(&cursor);
   SetCursor (&cursor);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_currentCursor = LoadCursor (NULL, IDC_ARROW);
   SetCursor (Nlm_currentCursor);
@@ -5377,8 +4980,14 @@ extern void Nlm_CrossCursor (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+#ifdef WIN_MAC_QUARTZ_COCOA_CURSORS
+  Nlm_SetCursor(COCOA_NAMED_CURSOR("crosshair"));
+#endif
+#else
   SetCursor (&cross);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_currentCursor = LoadCursor (NULL, IDC_CROSS);
   SetCursor (Nlm_currentCursor);
@@ -5392,8 +5001,14 @@ extern void Nlm_IBeamCursor (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+#ifdef WIN_MAC_QUARTZ_COCOA_CURSORS
+  Nlm_SetCursor(COCOA_NAMED_CURSOR("IBeam"));
+#endif
+#else
   SetCursor (&iBeam);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_currentCursor = LoadCursor (NULL, IDC_IBEAM);
   SetCursor (Nlm_currentCursor);
@@ -5407,8 +5022,14 @@ extern void Nlm_PlusCursor (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+#ifdef WIN_MAC_QUARTZ_COCOA_CURSORS
+  Nlm_SetCursor(COCOA_NAMED_CURSOR("crosshair"));
+#endif
+#else
   SetCursor (&plus);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_currentCursor = LoadCursor (NULL, IDC_CROSS);
   SetCursor (Nlm_currentCursor);
@@ -5422,8 +5043,14 @@ extern void Nlm_WatchCursor (void)
 
 {
 #ifdef WIN_MAC
+#ifdef WIN_MAC_QUARTZ
+#ifdef WIN_MAC_QUARTZ_COCOA_CURSORS
+// QUARTZ_FIXME: do we even need or want a watch cursor?
+#endif
+#else
   SetCursor (&watch);
 #endif
+#endif
 #ifdef WIN_MSWIN
   Nlm_currentCursor = LoadCursor (NULL, IDC_WAIT);
   SetCursor (Nlm_currentCursor);
@@ -5585,7 +5212,7 @@ static pascal OSErr HandleAEOpenDoc (const AppleEvent *event, AppleEvent *reply,
   char tempfile [PATH_MAX];
   AEDesc docDesc;
   AEDescList theList;
-  FSSpec rsultfss;
+  CFURLRef cfurl;
   OSErr theErr;
   
   stat = AEGetParamDesc (event, keyDirectObject, typeAEList, &list);
@@ -5616,10 +5243,11 @@ static pascal OSErr HandleAEOpenDoc (const AppleEvent *event, AppleEvent *reply,
 
         theErr = AECreateList(NULL, 0, FALSE, &theList);
         if (theErr == noErr) {
-          Nlm_CtoPstr ((Nlm_CharPtr) tempfile);
-          theErr = FSMakeFSSpec (0, 0, (ConstStr255Param) tempfile, &rsultfss);
-          if (theErr == noErr) {
-            theErr = AECreateDesc(typeFSS, (Ptr)&rsultfss, sizeof(fss), &docDesc);
+          cfurl = CFURLCreateFromFileSystemRepresentation (NULL, (const UInt8 *)tempfile, strlen (tempfile), 0);
+          if (cfurl) {
+            CFDataRef cfdata = CFURLCreateData (NULL, cfurl, kCFStringEncodingUTF8, 1);
+            theErr = AECreateDesc(typeFileURL, CFDataGetBytePtr (cfdata), CFDataGetLength (cfdata), &docDesc);
+            CFRelease (cfdata);
             if (theErr == noErr) {
               theErr = AEPutDesc(&theList, 0, &docDesc);
               if (theErr == noErr) {
@@ -5723,7 +5351,10 @@ static void Nlm_HandleEvent (void)
       }
       break;
     case updateEvt:
+#ifndef WIN_MAC_QUARTZ
+/* this gets handled by the HIView infrastructure behind our backs in Quartz */
       Nlm_DoDraw ((Nlm_GraphiC) Nlm_theWindow);
+#endif
       break;
     case osEvt:
       mess = (Nlm_currentEvent.message & osEvtMessageMask) >> 24;
@@ -5786,6 +5417,7 @@ extern Nlm_Boolean Nlm_RegisterWindows (void)
   return TRUE;
 }
 
+#ifndef WIN_MAC_QUARTZ
 static void Nlm_ReturnCursor (Cursor *cursor, Nlm_Int2 cursorID)
 
 {
@@ -5802,6 +5434,7 @@ static void Nlm_ReturnCursor (Cursor *cursor, Nlm_Int2 cursorID)
     GetQDGlobalsArrow(cursor);
   }
 }
+#endif
 
 static Nlm_Boolean Nlm_SetupWindows (void)
 
@@ -5809,17 +5442,27 @@ static Nlm_Boolean Nlm_SetupWindows (void)
   Nlm_PoinT  pt;
   Nlm_RecT   r;
   long  gval;
+#ifdef WIN_MAC_QUARTZ
+  CGDirectDisplayID display;
+  CGDisplayCount displayCount;
+#else
   BitMap myScreenBits;
 
   Nlm_ReturnCursor (&cross, 2);
   Nlm_ReturnCursor (&iBeam, 1);
   Nlm_ReturnCursor (&plus, 3);
   Nlm_ReturnCursor (&watch, 4);
+#endif
   Nlm_WatchCursor ();
   Nlm_ClearKeys ();
   Nlm_LoadPt (&pt, 0, 0);
+#ifdef WIN_MAC_QUARTZ
+  CGGetActiveDisplayList (1, &display, &displayCount);
+  screenBitBounds = Nlm_CGRectToRecT (CGDisplayBounds (display));
+#else
   GetQDGlobalsScreenBits(&myScreenBits);
   Nlm_RectToolToRecT (&(myScreenBits.bounds), &screenBitBounds);
+#endif
   r = screenBitBounds;
   Nlm_screenRect = screenBitBounds;
   Nlm_desktopWindow = (Nlm_WindoW) Nlm_HandNew (sizeof (Nlm_WindowRec));
@@ -6824,7 +6467,7 @@ extern void Nlm_DisplayEnvironmentVariables (void)
 extern int Nlm_VibMainPrelude (int argc, char *argv[])
 {
   long   gval;
-  OSErr  err;
+  OSStatus  err;
 
   Nlm_SetupArguments (argc, argv);
 # else /* ! OS_UNIX_DARWIN */
@@ -6867,7 +6510,12 @@ extern void Nlm_VibMainPrelude ()
   TEInit ();
   InitDialogs (0);
 #endif
+#ifdef WIN_MAC_QUARTZ
+  err = TXNInitTextension (NULL, 0, 0);
+  if(err) abort();
+#else
   InitCursor ();
+#endif
 
   err = Gestalt (gestaltAppleEventsAttr, &gval);
   if (err == noErr && ((short) gval & (1 << gestaltAppleEventsPresent)) != 0) {
@@ -7219,8 +6867,10 @@ extern void Nlm_RemoveDyingWindows (void)
     w = dyingWindow;
     wptr = Nlm_ParentWindowPtr ((Nlm_GraphiC) w);
 #ifdef WIN_MAC
+#ifndef WIN_MAC_QUARTZ
     GetPort (&tempPort);
     GetPenState (&state);
+#endif
     Nlm_SetPortWindowPort(wptr);
     Nlm_currentWindowTool = wptr;
     Nlm_SetUpdateRegion (wptr);
@@ -7254,7 +6904,7 @@ extern void Nlm_RemoveDyingWindows (void)
       Nlm_SetWindowMenuBar (w, NULL);
     }
 
-#ifndef WIN_MOTIF
+#if !defined(WIN_MOTIF) && !defined(WIN_MAC_QUARTZ)
     Nlm_ResetDrawingTools ();
 #endif
 
@@ -7263,6 +6913,7 @@ extern void Nlm_RemoveDyingWindows (void)
       wdata.cleanup (w, wdata.data);
     }
 #ifdef WIN_MAC
+#ifndef WIN_MAC_QUARTZ
     if ( wdata.cMap != NULL ){
       DisposePalette ( wdata.cMap );
       wdata.cMap = NULL;
@@ -7271,6 +6922,7 @@ extern void Nlm_RemoveDyingWindows (void)
     Nlm_currentWindowTool = GetWindowFromPort(tempPort);
     Nlm_SetUpdateRegion (GetWindowFromPort(tempPort));
     SetPenState (&state);
+#endif
     /* 2001-03-22:  Joshua Juran
        Carbon does not support application-supplied storage for windows. */
     DisposeWindow(wptr);
@@ -7584,8 +7236,8 @@ static void Nlm_ProcessIdle (void)
 
   Nlm_ProcessTimerEvent ();
   GetMouse (&ptool);
-  LocalToGlobal (&ptool);
   Nlm_PointToolToPoinT (ptool, &Nlm_globalMouse);
+  Nlm_LocalToGlobal (&Nlm_globalMouse);
   frontWindow = Nlm_FindWindowRec (FrontWindow ());
   Nlm_DoIdle ((Nlm_GraphiC) frontWindow, Nlm_globalMouse);
   Nlm_ClearKeys ();