Load /tmp/.../ncbi-tools6-6.1.20060507 into

branches/upstream/current.
author: Aaron M. Ucko <ucko@debian.org> 2006-05-26 18:34:14 +0000
committer: Aaron M. Ucko <ucko@debian.org> 2006-05-26 18:34:14 +0000
commit: de1d4a4e7eb2f2e1a20a6c3c90f4128f6f344e80 (patch)
tree: b98cfcc27d8a53160d6d0d4171f537e667bd9c68 /api
parent: 047f9550aeffa40eb05ad53427718889f660e0f4 (diff)
23 files changed, 1908 insertions, 329 deletions
diff --git a/api/asn2gnb1.c b/api/asn2gnb1.c
index 9e55f9b1..8c2cb9a0 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 1.97 2006/02/23 16:38:54 kans Exp $
+* $Id: asn2gnb1.c,v 1.101 2006/05/03 18:05:39 kans Exp $
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.97 $
+* $Revision: 1.101 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -3320,8 +3320,8 @@ static void MakeGapFeats (
   gapvnp = (ValNodePtr PNTR) userdata;
   sip = SeqIdFindBest (bsp->id, 0);
   if (sip == NULL) return;
-  /* suppress on far delta contigs for now */
-  if (! DeltaLitOnly (bsp)) return;
+  /* no longer suppress on far delta contigs */
+  /* if (! DeltaLitOnly (bsp)) return; */
 
   for (vnp = (ValNodePtr)(bsp->seq_ext); vnp != NULL; vnp = vnp->next) {
     if (vnp->choice == 1) {
@@ -3477,6 +3477,7 @@ static Asn2gbJobPtr asn2gnbk_setup_ex (
   Boolean          lockFarProd;
   Boolean          lookupFarComp;
   Boolean          lookupFarHist;
+  Boolean          lookupFarInf;
   Boolean          lookupFarLocs;
   Boolean          lookupFarOthers;
   Boolean          lookupFarProd;
@@ -3625,7 +3626,7 @@ static Asn2gbJobPtr asn2gnbk_setup_ex (
 
   gapvnp = NULL;
   if (format != FTABLE_FMT) {
-    if (isG || isTPG || isOnlyLocal || isRefSeq || (isGeneral && (! isGED))) {
+    if (isGED /* was isG */ || isTPG || isOnlyLocal || isRefSeq || (isGeneral && (! isGED))) {
       if ((Boolean) ((custom & HIDE_GAP_FEATS) == 0)) {
         VisitBioseqsInSep (sep, (Pointer) &gapvnp, MakeGapFeats);
       }
@@ -3717,13 +3718,14 @@ static Asn2gbJobPtr asn2gnbk_setup_ex (
   lookupFarLocs = (Boolean) ((locks & LOOKUP_FAR_LOCATIONS) != 0);
   lookupFarProd = (Boolean) ((locks & LOOKUP_FAR_PRODUCTS) != 0);
   lookupFarHist = (Boolean) ((locks & LOOKUP_FAR_HISTORY) != 0);
+  lookupFarInf = (Boolean) ((locks & LOOKUP_FAR_INFERENCE) != 0);
   lookupFarOthers = (Boolean) ((locks & LOOKUP_FAR_OTHERS) != 0);
 
-  if (lookupFarComp || lookupFarLocs || lookupFarProd || lookupFarHist || lookupFarOthers) {
+  if (lookupFarComp || lookupFarLocs || lookupFarProd || lookupFarHist || lookupFarInf || lookupFarOthers) {
 
     /* lookukp all far SeqIDs in advance */
 
-    LookupFarSeqIDs (sep, lookupFarComp, lookupFarLocs, lookupFarProd, FALSE, lookupFarHist, lookupFarOthers);
+    LookupFarSeqIDs (sep, lookupFarComp, lookupFarLocs, lookupFarProd, FALSE, lookupFarHist, lookupFarInf, lookupFarOthers);
   }
 
   ajp->showFarTransl = (Boolean) ((flags & FAR_TRANS_MASK) == SHOW_FAR_TRANSLATION);
@@ -5694,6 +5696,7 @@ NLM_EXTERN Boolean SeqEntryToGnbk (
   Boolean            lockFarProd;
   Boolean            lookupFarComp;
   Boolean            lookupFarHist;
+  Boolean            lookupFarInf;
   Boolean            lookupFarLocs;
   Boolean            lookupFarOthers;
   Boolean            lookupFarProd;
@@ -5749,11 +5752,12 @@ NLM_EXTERN Boolean SeqEntryToGnbk (
   lookupFarLocs = (Boolean) ((locks & LOOKUP_FAR_LOCATIONS) != 0);
   lookupFarProd = (Boolean) ((locks & LOOKUP_FAR_PRODUCTS) != 0);
   lookupFarHist = (Boolean) ((locks & LOOKUP_FAR_HISTORY) != 0);
+  lookupFarInf = (Boolean) ((locks & LOOKUP_FAR_INFERENCE) != 0);
   lookupFarOthers = (Boolean) ((locks & LOOKUP_FAR_OTHERS) != 0);
 
-  if (lookupFarComp || lookupFarLocs || lookupFarProd || lookupFarHist || lookupFarOthers) {
-    locks = locks ^ (LOOKUP_FAR_COMPONENTS | LOOKUP_FAR_LOCATIONS | LOOKUP_FAR_PRODUCTS | LOOKUP_FAR_HISTORY | LOOKUP_FAR_OTHERS);
-    LookupFarSeqIDs (sep, lookupFarComp, lookupFarLocs, lookupFarProd, FALSE, lookupFarHist, lookupFarOthers);
+  if (lookupFarComp || lookupFarLocs || lookupFarProd || lookupFarHist || lookupFarInf || lookupFarOthers) {
+    locks = locks ^ (LOOKUP_FAR_COMPONENTS | LOOKUP_FAR_LOCATIONS | LOOKUP_FAR_PRODUCTS | LOOKUP_FAR_HISTORY | LOOKUP_FAR_INFERENCE | LOOKUP_FAR_OTHERS);
+    LookupFarSeqIDs (sep, lookupFarComp, lookupFarLocs, lookupFarProd, FALSE, lookupFarHist, lookupFarInf, lookupFarOthers);
   }
 
   ProfilerSetStatus (TRUE);
diff --git a/api/asn2gnb2.c b/api/asn2gnb2.c
index c8353c89..9e940a24 100644
--- a/api/asn2gnb2.c
+++ b/api/asn2gnb2.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.69 $
+* $Revision: 1.74 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -455,6 +455,7 @@ NLM_EXTERN void AddLocusBlock (
   Char               mol [30];
   Int4               nextGi;
   BioseqPtr          nm = NULL;
+  BioseqPtr          nuc;
   ObjectIdPtr        oip;
   OrgNamePtr         onp;
   Uint1              origin;
@@ -847,6 +848,22 @@ NLM_EXTERN void AddLocusBlock (
     StringCpy (div, "PAT");
   }
 
+  /* if protein is encoded by a patent nucleotide, use PAT division */
+
+  if (ISA_aa (bsp->mol)) {
+    cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext);
+    if (cds != NULL) {
+      nuc = BioseqFindFromSeqLoc (cds->location);
+      if (nuc != NULL) {
+        for (sip = nuc->id; sip != NULL; sip = sip->next) {
+          if (sip->choice == SEQID_PATENT) {
+            StringCpy (div, "PAT");
+          }
+        }
+      }
+    }
+  }
+
   /* more complicated code for division, if necessary, goes here */
 
   sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext);
@@ -1067,6 +1084,9 @@ NLM_EXTERN void AddLocusBlock (
     if (topol < 0 || topol > 2) {
       topol = 0;
     }
+    if (topol == 0) {
+      topol = 1; /* default to displaying linear if not set */
+    }
     gbseq->topology = StringSave (gbseq_top [topol]);
 
     for (sip = bsp->id; sip != NULL; sip = sip->next) {
@@ -1082,11 +1102,16 @@ NLM_EXTERN void AddLocusBlock (
     }
     if (dp != NULL) {
       DateToFF (date, dp, FALSE);
+      if (StringDoesHaveText (date)) {
+        gbseq->create_date = StringSave (date);
+      }
     }
+    /*
     if (StringHasNoText (date)) {
       StringCpy (date, "01-JAN-1900");
     }
     gbseq->create_date = StringSave (date);
+    */
 
     date [0] = '\0';
     dp = NULL;
@@ -2016,13 +2041,16 @@ NLM_EXTERN void AddProjectBlock (
 
 {
   IntAsn2gbJobPtr    ajp;
+  Asn2gbSectPtr      asp;
   BaseBlockPtr       bbp;
   BioseqPtr          bsp;
   Char               buf [32];
   UserFieldPtr       curr;
   SeqMgrDescContext  dcontext;
   StringItemPtr      ffstring;
+  GBSeqPtr           gbseq;
   UserObjectPtr      gpuop = NULL;
+  ValNodePtr         head = NULL;
   Uint4              itemID;
   ObjectIdPtr        oip;
   Int4               parentID;
@@ -2037,10 +2065,18 @@ NLM_EXTERN void AddProjectBlock (
   if (ajp == NULL) return;
   bsp = awp->bsp;
   if (bsp == NULL) return;
+  asp = awp->asp;
+  if (asp == NULL) return;
 
   if (! ISA_na (bsp->mol)) return;
   if (awp->format != GENBANK_FMT) return;
 
+  if (ajp->gbseq) {
+    gbseq = &asp->gbseq;
+  } else {
+    gbseq = NULL;
+  }
+
   sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext);
   while (sdp != NULL) {
     uop = (UserObjectPtr) sdp->data.ptrvalue;
@@ -2087,6 +2123,14 @@ NLM_EXTERN void AddProjectBlock (
           /*
           FFAddTextToString (ffstring, prefix, buf, NULL, FALSE, FALSE, TILDE_IGNORE);
           */
+          if (gbseq != NULL) {
+            if (head == NULL) {
+              sprintf (buf, "%ld", (long) projectID);
+            } else {
+              sprintf (buf, ", %ld", (long) projectID);
+            }
+            ValNodeCopyStr (&head, 0, buf);
+          }
           prefix = ",";
           parentID = 0;
         }
@@ -2110,11 +2154,26 @@ NLM_EXTERN void AddProjectBlock (
     /*
     FFAddTextToString (ffstring, prefix, buf, NULL, FALSE, FALSE, TILDE_IGNORE);
     */
+    if (gbseq != NULL) {
+      if (head == NULL) {
+        sprintf (buf, "%ld", (long) projectID);
+      } else {
+        sprintf (buf, ", %ld", (long) projectID);
+      }
+      ValNodeCopyStr (&head, 0, buf);
+    }
   }
 
   bbp->string = FFEndPrint (ajp, ffstring, awp->format, 12, 12, 5, 5, "XX");
   FFRecycleString (ajp, ffstring);
 
+  if (gbseq != NULL) {
+    if (head != NULL) {
+      gbseq->project = MergeFFValNodeStrs (head);
+      ValNodeFreeData (head);
+    }
+  }
+
   if (awp->afp != NULL) {
     DoImmediateFormat (awp->afp, bbp);
   }
@@ -2986,6 +3045,7 @@ NLM_EXTERN void AddDbsourceBlock (
   SeqIdPtr         id;
   ValNodePtr       list = NULL;
   BioseqPtr        nuc;
+  SeqEntryPtr      sep;
   SeqIdPtr         sip;
   SeqLocPtr        slp;
   CharPtr          str;
@@ -3084,6 +3144,23 @@ NLM_EXTERN void AddDbsourceBlock (
               }
             }
             ValNodeFree (list);
+          } else {
+            sep = GetTopSeqEntryForEntityID (awp->entityID);
+            if (sep != NULL && IS_Bioseq (sep)) {
+              /* special case for coded_by CDS packed on retcode 1 protein */
+              id = SeqLocId (cds->location);
+              if (id != NULL && id->choice == SEQID_GI) {
+                sip = GetSeqIdForGI (id->data.intvalue);
+                if (sip == NULL) {
+                  sip = id;
+                }
+              }
+              if (WriteDbsourceID (sip, buf)) {
+                FF_www_dbsource (ajp, ffstring, buf, TRUE, sip->choice);
+                FFAddNewLine(ffstring);
+                unknown = FALSE;
+              }
+            }
           }
         } else {
           if (WriteDbsourceID (sip, buf)) {
diff --git a/api/asn2gnb4.c b/api/asn2gnb4.c
index 2aebe7ad..45f44fd9 100644
--- a/api/asn2gnb4.c
+++ b/api/asn2gnb4.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.98 $
+* $Revision: 1.106 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -1495,6 +1495,7 @@ static Int2 ValidateAccnInternal (
     if (numAlpha == 2 && numDigits == 6) return 0;
     if (numAlpha == 3 && numDigits == 5) return 0;
     if (numAlpha == 4 && numDigits == 8) return 0;
+    if (numAlpha == 5 && numDigits == 7) return 0;
   } else if (numUndersc == 1) {
     if (numAlpha != 2 || (numDigits != 6 && numDigits != 8 && numDigits != 9)) return -2;
     if (accession [0] == 'N' || accession [0] == 'X' || accession [0] == 'Z') {
@@ -3313,8 +3314,21 @@ static void FormatFeatureBlockQuals (
             pmid = (Int4) vnp->data.intvalue;
             if (pmid > 0) {
               sprintf (numbuf, "%ld", (long) pmid);
+              FFAddOneString(ffstring, "/citation=[PUBMED ", FALSE, TRUE, TILDE_TO_SPACES);
+              if (GetWWW (ajp)) {
+
+                FFAddTextToString(ffstring, "<a href=", link_muid, NULL, FALSE, FALSE, TILDE_IGNORE);
+                FFAddTextToString(ffstring, NULL, numbuf, ">", FALSE, FALSE, TILDE_IGNORE);
+                FFAddOneString(ffstring, numbuf, FALSE, FALSE, TILDE_IGNORE);
+                FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
+              } else {
+                FFAddOneString(ffstring, numbuf, FALSE, FALSE, TILDE_IGNORE);
+              }
+              FFAddOneString(ffstring, "]", FALSE, FALSE, TILDE_IGNORE);
+              /*
               FFAddTextToString(ffstring, "/citation=[PUBMED ", numbuf, "]",
                                 FALSE, TRUE, TILDE_TO_SPACES);
+              */
               FFAddOneChar(ffstring, '\n', FALSE);
             }
           }
@@ -3380,7 +3394,7 @@ static void FormatFeatureBlockQuals (
               }
               if (okay) {
                 FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-                FF_www_db_xref(ajp, ffstring, dbt->db, buf);
+                FF_www_db_xref(ajp, ffstring, dbt->db, buf, bsp);
                 FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
               }
             }
@@ -3423,7 +3437,7 @@ static void FormatFeatureBlockQuals (
                 }
                 sprintf (seqid, "%ld", (long) sip->data.intvalue);
                 FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-                FF_www_db_xref(ajp, ffstring, "GI", seqid);
+                FF_www_db_xref(ajp, ffstring, "GI", seqid, bsp);
                 FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
               } else if (sip->choice == SEQID_GENERAL) {
                 dbt = (DbtagPtr) sip->data.ptrvalue;
@@ -3455,6 +3469,11 @@ static void FormatFeatureBlockQuals (
             if (sip->choice == SEQID_GI) {
               gi = sip->data.intvalue;
               if (GetAccnVerFromServer (gi, seqid)) {
+#ifdef OS_UNIX
+  if (getenv ("ASN2GB_PSF_DEBUG") != NULL) {
+    printf ("GetAccnVerFromServer returned %s\n", seqid);
+  }
+#endif
                 if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
                   FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
                                     FALSE, FALSE, TILDE_IGNORE);
@@ -3466,6 +3485,11 @@ static void FormatFeatureBlockQuals (
               } else {
                 sip = GetSeqIdForGI (gi);
                 if (sip != NULL && SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
+#ifdef OS_UNIX
+  if (getenv ("ASN2GB_PSF_DEBUG") != NULL) {
+    printf ("GetSeqIdForGI returned %s\n", seqid);
+  }
+#endif
                   if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
                     FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"",
                                     FALSE, FALSE, TILDE_IGNORE);
@@ -3487,7 +3511,7 @@ static void FormatFeatureBlockQuals (
 
               sprintf (seqid, "%ld", (long) gi);
               FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-              FF_www_db_xref(ajp, ffstring, "GI", seqid);
+              FF_www_db_xref(ajp, ffstring, "GI", seqid, bsp);
               FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
             } else if (SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) {
               if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) {
@@ -3503,7 +3527,7 @@ static void FormatFeatureBlockQuals (
               if (gi > 0) {
                 sprintf (seqid, "%ld", (long) gi);
                 FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-                FF_www_db_xref(ajp, ffstring, "GI", seqid);
+                FF_www_db_xref(ajp, ffstring, "GI", seqid, bsp);
                 FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
               }
             }
@@ -4201,11 +4225,10 @@ static void FormatFeatureBlockQuals (
 }
 
 
-
 static void FF_asn2gb_www_featkey (
   StringItemPtr ffstring,
   CharPtr key,
-  SeqLocPtr slp,
+  SeqFeatPtr sfp,
   Int4 from,
   Int4 to,
   Uint1 strand,
@@ -4213,13 +4236,21 @@ static void FF_asn2gb_www_featkey (
 )
 
 {
-  BioseqPtr  bsp;
-  Int4       gi = 0;
-  SeqIdPtr   sip;
-  Boolean    is_aa = FALSE;
-  Char gi_buf[16];
-  Char itemID_buf[16];
+  BioseqPtr    bsp;
+  Char         buf [16];
+  Int4         featID = 0;
+  Int4         ffrom = 0;
+  Int4         fto = 0;
+  Int4         gi = 0;
+  Char         gi_buf[16];
+  Boolean      is_aa = FALSE;
+  ObjectIdPtr  oip;
+  SeqIntPtr    sintp;
+  SeqIdPtr     sip;
+  SeqLocPtr    slp;
 
+  if (sfp == NULL) return;
+  slp = sfp->location;
   bsp = BioseqFindFromSeqLoc (slp);
   if (bsp != NULL) {
     is_aa = ISA_aa (bsp->mol);
@@ -4228,19 +4259,47 @@ static void FF_asn2gb_www_featkey (
         gi = (Int4) sip->data.intvalue;
       }
     }
+  } else {
+    if (sfp->id.choice == 3) {
+      oip = (ObjectIdPtr) sfp->id.value.ptrvalue;
+      if (oip != NULL && oip->str == NULL) {
+        featID = oip->id;
+      }
+    }
+    if (slp->choice == SEQLOC_INT) {
+      sintp = (SeqIntPtr) slp->data.ptrvalue;
+      if (sintp != NULL) {
+        ffrom = sintp->from + 1;
+        fto = sintp->to + 1;
+        sip = sintp->id;
+        if (sip->choice == SEQID_GI) {
+          gi = (Int4) sip->data.intvalue;
+        }
+      }
+    }
   }
 
-  sprintf(gi_buf, "%ld", (long)gi);
-  sprintf(itemID_buf, "%ld", (long)itemID);
-
+  sprintf (gi_buf, "%ld", (long)gi);
 
   FFAddOneString(ffstring, "<a href=", FALSE, FALSE, TILDE_IGNORE);
   FFAddOneString(ffstring, link_feat, FALSE, FALSE, TILDE_IGNORE);
   FFAddOneString(ffstring, "val=", FALSE, FALSE, TILDE_IGNORE);
   FFAddOneString(ffstring, gi_buf, FALSE, FALSE, TILDE_IGNORE);
-  if (itemID > 0) {
+  if (featID > 0) {
+    sprintf (buf, "%ld", (long) featID);
+    FFAddOneString(ffstring, "&featID=", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+  } else if (ffrom > 0 && fto > 0) {
+    sprintf (buf, "%ld", (long) ffrom);
+    FFAddOneString(ffstring, "&from=", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+    sprintf (buf, "%ld", (long) fto);
+    FFAddOneString(ffstring, "&to=", FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
+  } else if (itemID > 0) {
+    sprintf (buf, "%ld", (long) itemID);
     FFAddOneString(ffstring, "&itemID=", FALSE, FALSE, TILDE_IGNORE);
-    FFAddOneString(ffstring, itemID_buf, FALSE, FALSE, TILDE_IGNORE);
+    FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_IGNORE);
   }
   
 
@@ -4353,8 +4412,11 @@ static void AddIntervalsToGbfeat (
   Char           accn [41];
   SeqLocPtr      copy = NULL;
   Int4           from;
+  IntFuzzPtr     fuzz;
   GBIntervalPtr  gbint;
   Int4           gi;
+  Boolean        interbp;
+  Boolean        iscomp;
   GBIntervalPtr  last = NULL;
   Int4           point;
   SeqIntPtr      sint;
@@ -4375,6 +4437,8 @@ static void AddIntervalsToGbfeat (
     from = 0;
     to = 0;
     point = 0;
+    iscomp = FALSE;
+    interbp = FALSE;
     sip = NULL;
     switch (slp->choice) {
       case SEQLOC_WHOLE :
@@ -4398,6 +4462,9 @@ static void AddIntervalsToGbfeat (
             from = to;
             to = swap;
           }
+          if (sint->strand == Seq_strand_minus) {
+            iscomp = TRUE;
+          }
         }
         break;
       case SEQLOC_PNT :
@@ -4405,6 +4472,25 @@ static void AddIntervalsToGbfeat (
         if (spp != NULL) {
           point = spp->point + 1;
           sip = spp->id;
+          if (spp->strand == Seq_strand_minus) {
+            iscomp = TRUE;
+          }
+          fuzz = spp->fuzz;
+          if (fuzz != NULL) {
+            if (fuzz->choice == 4) {
+              if (fuzz->a == 3) { /* space to right */
+                from = point;
+                to = point + 1;
+                point = 0;
+                interbp = TRUE;
+              } else if (fuzz->a == 4 && point > 1) { /* space to left */
+                from = point - 1;
+                to = point;
+                point = 0;
+                interbp = TRUE;
+              }
+            }
+          }
         }
         break;
       default :
@@ -4431,6 +4517,8 @@ static void AddIntervalsToGbfeat (
           gbint->from = from;
           gbint->to = to;
           gbint->point = point;
+          gbint->iscomp = iscomp;
+          gbint->interbp = interbp;
           gbint->accession = StringSave (accn);
           if (gbfeat->intervals == NULL) {
             gbfeat->intervals = gbint;
@@ -4800,7 +4888,7 @@ static CharPtr FormatFeatureBlockEx (
   Choice             cbaa;
   CodeBreakPtr       cbp;
   BioseqPtr          cdna;
-  SeqFeatPtr         cds;
+  SeqFeatPtr         cds = NULL;
   Char               ch;
   Uint1              code = Seq_code_ncbieaa;
   CdRegionPtr        crp;
@@ -5065,7 +5153,7 @@ static CharPtr FormatFeatureBlockEx (
 	if (ajp->ajp.slp != NULL) {
 	  FFAddOneString(ffstring, key, FALSE, FALSE, TILDE_IGNORE);
 	} else if ( GetWWW(ajp) && StringICmp (key, "gap") != 0 /* && SeqMgrGetParentOfPart (bsp, NULL) == NULL */ ) {
-	  FF_asn2gb_www_featkey (ffstring, key, sfp->location, fcontext->left + 1, fcontext->right + 1, fcontext->strand, itemID);
+	  FF_asn2gb_www_featkey (ffstring, key, sfp, fcontext->left + 1, fcontext->right + 1, fcontext->strand, itemID);
 	} else {
 	  FFAddOneString(ffstring, key, FALSE, FALSE, TILDE_IGNORE);
 	}
@@ -5111,6 +5199,15 @@ static CharPtr FormatFeatureBlockEx (
 	if (gbseq != NULL) {
 	  if (gbfeat != NULL) {
 		gbfeat->location = StringSave (str);
+	    if (StringDoesHaveText (str)) {
+	      if (StringStr (str, "join") != NULL) {
+	        gbfeat->operator__ = StringSave ("join");
+	      } else if (StringStr (str, "order") != NULL) {
+	        gbfeat->operator__ = StringSave ("order");
+	      }
+	    }
+		gbfeat->partial5 = fcontext->partialL;
+		gbfeat->partial3 = fcontext->partialR;
 		if (ajp->masterStyle) {
 		  AddIntervalsToGbfeat (gbfeat, location, target);
 		} else {
@@ -5229,6 +5326,9 @@ static CharPtr FormatFeatureBlockEx (
         gene_for_old_locus_tag = SeqMgrGetFeatureByLabel (bsp_for_old_locus_tag, grp->locus_tag, SEQFEAT_GENE, 0, &gcontext);
       }
     }
+    if (grp == NULL && ifp->mapToNuc && cds != NULL) {
+      grp = SeqMgrGetGeneXref (cds);
+    }
     if (grp == NULL && featdeftype != FEATDEF_primer_bind) {
       gene = GetOverlappingGeneInEntity (ajp->ajp.entityID, fcontext, &gcontext, locforgene);
       if (gene == NULL && ajp->ajp.entityID != sfp->idx.entityID) {
diff --git a/api/asn2gnb5.c b/api/asn2gnb5.c
index 7abce569..34462b1a 100644
--- a/api/asn2gnb5.c
+++ b/api/asn2gnb5.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.54 $
+* $Revision: 1.64 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -281,6 +281,12 @@ static Char link_hprd [MAX_WWWBUF];
 static Char link_uspto [MAX_WWWBUF];
 #define DEF_LINK_USPTO "http://patft.uspto.gov/netacgi/nph-Parser?patentnumber="
 
+static Char link_vector [MAX_WWWBUF];
+#define DEF_LINK_VECTOR "http://www.vectorbase.org/Genome/BRCGene/?"
+
+static Char link_mirbase [MAX_WWWBUF];
+#define DEF_LINK_MIRBASE "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc="
+
 
 /* www utility functions */
 
@@ -310,8 +316,6 @@ NLM_EXTERN void InitWWW (IntAsn2gbJobPtr ajp)
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_ECAMBIG", DEF_LINK_ECAMBIG, ec_ambig, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_FF", DEF_LINK_FF, link_ff, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_MUID", DEF_LINK_MUID, link_muid, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_FF", DEF_LINK_FF, link_ff, MAX_WWWBUF);
-  GetAppParam ("NCBI", "WWWENTREZ", "LINK_MUID", DEF_LINK_MUID, link_muid, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_ACE", DEF_LINK_ACE, link_ace, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_TAX", DEF_LINK_TAX, link_tax, MAX_WWWBUF);
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_CODE", DEF_LINK_CODE, link_code, MAX_WWWBUF);
@@ -371,6 +375,8 @@ NLM_EXTERN void InitWWW (IntAsn2gbJobPtr ajp)
   GetAppParam ("NCBI", "WWWENTREZ", "LINK_BOLD", DEF_LINK_BOLD, link_bold, 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_VECTOR", DEF_LINK_VECTOR, link_vector, MAX_WWWBUF);
+  GetAppParam ("NCBI", "WWWENTREZ", "LINK_MIRBASE", DEF_LINK_MIRBASE, link_mirbase, MAX_WWWBUF);
 }
 
 
@@ -670,6 +676,39 @@ 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, 
+  CharPtr identifier,
+  BioseqPtr bsp,
+  CharPtr link
+)
+{
+  Char     ch;
+  Char     buf [512], tax [256];
+  CharPtr  ptr;
+
+  StringCpy (buf, link);
+  if (bsp != NULL) {
+    if (BioseqToGeneticCode (bsp, NULL, NULL, NULL, tax, sizeof (tax), NULL)) {
+      ptr = tax;
+      ch = *ptr;
+      while (ch != '\0') {
+        if (IS_WHITESP (ch)) {
+          *ptr = '_';
+        }
+        ptr++;
+        ch = *ptr;
+      }
+      StringCat (buf, "org=");
+      StringCat (buf, tax);
+      StringCat (buf, "&");
+    }
+  }
+  StringCat (buf, "gene=");
+  FF_www_db_xref_std (ffstring, db, identifier, buf);
+}
+
 static void FF_www_db_xref_null (
   StringItemPtr ffstring,
   CharPtr db,
@@ -688,7 +727,9 @@ static void FF_www_db_xref_null (
 static void Do_www_db_xref(
   IntAsn2gbJobPtr ajp,
   StringItemPtr ffstring,
-  CharPtr db, CharPtr identifier
+  CharPtr db,
+  CharPtr identifier,
+  BioseqPtr bsp
 )
 {
   if ( ffstring == NULL || db == NULL || identifier == NULL ) return;
@@ -813,6 +854,10 @@ static void Do_www_db_xref(
     FF_www_db_xref_null(ffstring, db, identifier, link_bold);
   } 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);
+  } else if ( StringCmp(db , "miRBase") == 0) {
+    FF_www_db_xref_std(ffstring, db, identifier, link_mirbase);
 
   } else {  
     /* default: no link just the text */
@@ -823,13 +868,15 @@ static void Do_www_db_xref(
 NLM_EXTERN void FF_www_db_xref(
   IntAsn2gbJobPtr ajp,
   StringItemPtr ffstring,
-  CharPtr db, CharPtr identifier
+  CharPtr db,
+  CharPtr identifier,
+  BioseqPtr bsp
 )
 {
   if ( ffstring == NULL || db == NULL || identifier == NULL ) return;
   
   if ( GetWWW(ajp) ) {
-    Do_www_db_xref (ajp, ffstring, db, identifier);
+    Do_www_db_xref (ajp, ffstring, db, identifier, bsp);
   } else { /* not in www mode */
     if (StringCmp(db , "MGD") == 0 || StringCmp(db , "MGI") == 0) {
       if (StringNICmp (identifier, "MGI:", 4) == 0) {
@@ -885,7 +932,7 @@ NLM_EXTERN CharPtr asn2gnbk_dbxref (
   }
   ajp->www = TRUE;
 
-  Do_www_db_xref (ajp, ffstring, dbt->db, buf);
+  Do_www_db_xref (ajp, ffstring, dbt->db, buf, NULL);
 
   ajp->www = FALSE;
 
@@ -1082,6 +1129,7 @@ NLM_EXTERN CharPtr GetAuthorsString (
 
 {
   AuthorPtr    ap;
+  ValNodePtr   clist;
   ValNodePtr   conslist;
   Int2         count;
   ValNodePtr   head = NULL;
@@ -1151,23 +1199,33 @@ NLM_EXTERN CharPtr GetAuthorsString (
       prefix = ", ";
     }
 
+    prefix = NULL;
+    clist = NULL;
     for (vnp = conslist; vnp != NULL; vnp = vnp->next) {
       str = NULL;
       pid = (PersonIdPtr) vnp->data.ptrvalue;
       if (pid->choice == 5) {
-        str = MakeSingleAuthorString (format, NULL, (CharPtr) pid->data, NULL, NULL, index, NULL);
-        if ((! StringHasNoText (str)) && consortP != NULL && *consortP == NULL) {
-          *consortP = StringSave (str);
+        str = MakeSingleAuthorString (format, prefix, (CharPtr) pid->data, NULL, NULL, index, NULL);
+        if (str != NULL) {
+          ValNodeAddStr (&clist, 0, str);
         }
+        prefix = "; ";
+      }
+    }
+    if (clist != NULL) {
+      str = MergeFFValNodeStrs (clist);
+      if ((! StringHasNoText (str)) && consortP != NULL && *consortP == NULL) {
+        *consortP = StringSave (str);
+      }
 
-        /* optionally populate gbseq for XML-ized GenBank format */
-
-        if (gbref != NULL) {
-          gbref->consortium = StringSave (str);
-        }
+      /* optionally populate gbseq for XML-ized GenBank format */
 
-        str = MemFree (str);
+      if (gbref != NULL) {
+        gbref->consortium = StringSave (str);
       }
+
+      str = MemFree (str);
+      ValNodeFreeData (clist);
     }
 
     ValNodeFree (pidlist);
@@ -3254,15 +3312,25 @@ static CharPtr remarksText [] = {
 static void AddReferenceToGbseq (
   GBSeqPtr gbseq,
   GBReferencePtr gbref,
-  CharPtr str
+  CharPtr str,
+  RefBlockPtr rbp,
+  BioseqPtr bsp
 )
 
 {
-  CharPtr  copy;
-  CharPtr  ptr;
-  CharPtr  ref;
-
-  if (gbseq == NULL || gbref == NULL || StringHasNoText (str)) return;
+  Char            buf [32];
+  CharPtr         copy;
+  ValNodePtr      head = NULL;
+  IntRefBlockPtr  irp;
+  SeqLocPtr       loc;
+  CharPtr         ptr;
+  CharPtr         ref;
+  SeqLocPtr       slp;
+  Int4            start;
+  Int4            stop;
+  CharPtr         tmp;
+
+  if (gbseq == NULL || gbref == NULL || StringHasNoText (str) || rbp == NULL || bsp == NULL) return;
 
   copy = StringSave (str);
 
@@ -3277,7 +3345,13 @@ static void AddReferenceToGbseq (
     ref = copy + 12;
     ptr = StringStr (ref, "\n  AUTHORS");
     if (ptr == NULL) {
+      ptr = StringStr (ref, "\n  CONSRTM");
+    }
+    if (ptr == NULL) {
       ptr = StringStr (ref, ")\n");
+      if (ptr != NULL) {
+        ptr++;
+      }
     }
     if (ptr != NULL) {
       *ptr = '\0';
@@ -3300,6 +3374,36 @@ static void AddReferenceToGbseq (
   Asn2gnbkCompressSpaces (gbref->journal);
 
   MemFree (copy);
+
+  if (rbp->sites == 1 || rbp->sites == 2) {
+    gbref->position = StringSave ("sites");
+  } else if (rbp->sites == 3) {
+  } else {
+    irp = (IntRefBlockPtr) rbp;
+    loc = irp->loc;
+    if (loc != NULL) {
+      slp = SeqLocFindNext (loc, NULL);
+      while (slp != NULL) {
+        start = SeqLocStart (slp) + 1;
+        stop = SeqLocStop (slp) + 1;
+        if (head == NULL) {
+          sprintf (buf, "%ld..%ld", (long) start, (long) stop);
+        } else {
+          sprintf (buf, "; %ld..%ld", (long) start, (long) stop);
+        }
+        ValNodeCopyStr (&head, 0, buf);
+        slp = SeqLocFindNext (loc, slp);
+      }
+      tmp = MergeFFValNodeStrs (head);
+      ValNodeFreeData (head);
+      gbref->position = tmp;
+    } else {
+      start = 1;
+      stop = bsp->length;
+      sprintf (buf, "%ld..%ld", (long) start, (long) stop);
+      gbref->position = StringSave (buf);
+    }
+  }
 }
 
 static Boolean IsCitSub (
@@ -3381,6 +3485,8 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
   Int4               pmid = 0;
   CharPtr            prefix = NULL;
   RefBlockPtr        rbp;
+  ValNodePtr         remarks = NULL;
+  CharPtr            remprefix = NULL;
   SubmitBlockPtr     sbp;
   SeqDescrPtr        sdp;
   SeqFeatPtr         sfp = NULL;
@@ -3631,10 +3737,6 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
 
   /* print author list */
 
-  FFRecycleString(ajp, temp);
-  temp = FFGetString(ajp);
-  FFStartPrint(temp, afp->format, 2, 12, "AUTHORS", 12, 5, 5, "RA", FALSE);
-
   str = NULL;
   consortium = NULL;
 
@@ -3644,36 +3746,42 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
     TrimSpacesAroundString (str);
   }
 
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-    suffix = NULL;
-    trailingPeriod = TRUE;
-  } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-    trailingPeriod = FALSE;
-    len = StringLen (str);
-    if (len > 0 && str [len - 1] != '.') {
-      suffix = ".;";
-    } else {
-      suffix = ";";
-    }
-  }
+  if (str != NULL || StringHasNoText (consortium)) {
+    FFRecycleString(ajp, temp);
+    temp = FFGetString(ajp);
+    FFStartPrint(temp, afp->format, 2, 12, "AUTHORS", 12, 5, 5, "RA", FALSE);
 
-  /* if no authors were found, period will still be added by this call */
-  if (str != NULL) {
-    FFAddTextToString(temp, NULL, str, suffix, trailingPeriod, FALSE, TILDE_TO_SPACES);
-  } else {
     if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
-      FFAddOneChar(temp, '.', FALSE);
+      suffix = NULL;
+      trailingPeriod = TRUE;
     } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
-      FFAddOneChar(temp, ';', FALSE);
-    }    
-  }
+      trailingPeriod = FALSE;
+      len = StringLen (str);
+      if (len > 0 && str [len - 1] != '.') {
+        suffix = ".;";
+      } else {
+        suffix = ";";
+      }
+    }
 
-  MemFree (str);
-  if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+    /* if no authors were found, period will still be added by this call */
+    if (str != NULL) {
+      FFAddTextToString(temp, NULL, str, suffix, trailingPeriod, FALSE, TILDE_TO_SPACES);
+    } else if (StringHasNoText (consortium)) {
+      if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
+        FFAddOneChar(temp, '.', FALSE);
+      } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
+        FFAddOneChar(temp, ';', FALSE);
+      }    
+    }
+
+    if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) {
       FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
-  } else {
+    } else {
       FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "RA");
+    }
   }
+  MemFree (str);
 
   /* print consortium */
 
@@ -3857,7 +3965,7 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
 
     if (gbseq != NULL) {
       if (gbref != NULL) {
-        AddReferenceToGbseq (gbseq, gbref, str);
+        AddReferenceToGbseq (gbseq, gbref, str, rbp, bsp);
       }
     }
 
@@ -3890,6 +3998,11 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
         FFRecycleString(ajp, temp);
         temp = FFGetString(ajp);
 
+        if (remprefix != NULL) {
+          ValNodeCopyStr (&remarks, 0, remprefix);
+        }
+        ValNodeCopyStr (&remarks, 0, pdp->comment);
+        remprefix = "; ";
         FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
         FFAddOneString (temp, pdp->comment, FALSE, TRUE, TILDE_EXPAND);
         /* AddCommentWithURLlinks(ajp, temp, NULL, pdp->comment, NULL); */
@@ -3898,7 +4011,9 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
 
         if (gbseq != NULL) {
           if (gbref != NULL) {
+            /*
             gbref->remark = StringSave (pdp->comment);
+            */
           }
         }
 
@@ -3922,6 +4037,11 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
       temp = FFGetString(ajp);
 
       sprintf (buf, "GenBank staff at the National Library of Medicine created this entry [NCBI gibbsq %ld] from the original journal article.", (long) gibbsq);
+      if (remprefix != NULL) {
+        ValNodeCopyStr (&remarks, 0, remprefix);
+      }
+      ValNodeCopyStr (&remarks, 0, buf);
+      remprefix = "; ";
       FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
       FFAddOneString (temp, buf, FALSE, FALSE, TILDE_EXPAND);
       FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
@@ -3938,6 +4058,11 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
         temp = FFGetString(ajp);
 
         sprintf (buf, "This sequence comes from %s", str);
+        if (remprefix != NULL) {
+          ValNodeCopyStr (&remarks, 0, remprefix);
+        }
+        ValNodeCopyStr (&remarks, 0, buf);
+        remprefix = "; ";
         FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
         FFAddOneString (temp, buf, TRUE, TRUE, TILDE_EXPAND);
         FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
@@ -3948,7 +4073,12 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
         FFRecycleString(ajp, temp);
         temp = FFGetString(ajp);
 
-        FFStartPrint (temp ,afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
+        if (remprefix != NULL) {
+          ValNodeCopyStr (&remarks, 0, remprefix);
+        }
+        ValNodeCopyStr (&remarks, 0, "Polyadenylate residues occurring in the figure were omitted from the sequence.");
+        remprefix = "; ";
+        FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
         FFAddOneString (temp, "Polyadenylate residues occurring in the figure were omitted from the sequence.", TRUE, TRUE, TILDE_EXPAND);
         FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
         prefix = NULL;
@@ -3963,6 +4093,11 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
         temp = FFGetString(ajp);
 
         sprintf (buf, "Map location: %s", str);
+        if (remprefix != NULL) {
+          ValNodeCopyStr (&remarks, 0, remprefix);
+        }
+        ValNodeCopyStr (&remarks, 0, buf);
+        remprefix = "; ";
         FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
         FFAddOneString (temp, buf, TRUE, TRUE, TILDE_EXPAND);
         FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
@@ -3984,6 +4119,17 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
                 FFRecycleString(ajp, temp);
                 temp = FFGetString(ajp);
 
+                len = StringLen (crp->exp) + 20;
+                str = MemNew (sizeof (Char) * len);
+                if (str != NULL) {
+                  sprintf (str, "Erratum:[%s]", crp->exp);
+                  if (remprefix != NULL) {
+                    ValNodeCopyStr (&remarks, 0, remprefix);
+                  }
+                  ValNodeCopyStr (&remarks, 0, str);
+                  remprefix = "; ";
+                  str = MemFree (str);
+                }
                 FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
                 FFAddOneString (temp, "Erratum:", FALSE, FALSE, TILDE_TO_SPACES);
                 FFAddTextToString (temp, "[", crp->exp, "]", FALSE, TRUE, TILDE_EXPAND);
@@ -4000,6 +4146,11 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
             FFRecycleString(ajp, temp);
             temp = FFGetString(ajp);
 
+            if (remprefix != NULL) {
+              ValNodeCopyStr (&remarks, 0, remprefix);
+            }
+            ValNodeCopyStr (&remarks, 0, csp->descr);
+            remprefix = "; ";
             FFStartPrint (temp, afp->format, 2, 12, prefix, 12, 5, 5, NULL, FALSE);
             /* FFAddOneString (temp, csp->descr, FALSE, TRUE, TILDE_EXPAND); */
             AddCommentWithURLlinks(ajp, temp, NULL, csp->descr, NULL);
@@ -4016,9 +4167,14 @@ NLM_EXTERN CharPtr FormatReferenceBlock (
 
   if (gbseq != NULL) {
     if (gbref != NULL) {
-      AddReferenceToGbseq (gbseq, gbref, str);
+      if (remarks != NULL) {
+        gbref->remark = MergeFFValNodeStrs (remarks);
+      }
+
+      AddReferenceToGbseq (gbseq, gbref, str, rbp, bsp);
     }
   }
+  ValNodeFreeData (remarks);
 
   FFRecycleString(ajp, ffstring);
   FFRecycleString(ajp, temp);
diff --git a/api/asn2gnb6.c b/api/asn2gnb6.c
index 698d7587..a9d156fd 100644
--- a/api/asn2gnb6.c
+++ b/api/asn2gnb6.c
@@ -30,7 +30,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 1.69 $
+* $Revision: 1.73 $
 *
 * File Description:  New GenBank flatfile generator - work in progress
 *
@@ -446,6 +446,7 @@ NLM_EXTERN CharPtr legalDbXrefs [] = {
   "UniProtKB/TrEMBL",
   "UniSTS",
   "VBASE2",
+  "VectorBase",
   "WorfDB",
   "WormBase",
   "ZFIN",
@@ -458,6 +459,7 @@ NLM_EXTERN CharPtr legalRefSeqDbXrefs [] = {
   "ECOCYC",
   "HPRD",
   "REBASE",
+  "miRBase",
   NULL
 };
 
@@ -3195,7 +3197,7 @@ NLM_EXTERN CharPtr FormatSourceFeatBlock (
           }
           if (! StringHasNoText (buf)) {
             FFAddOneString(ffstring, "/db_xref=\"", FALSE, FALSE, TILDE_IGNORE);
-            FF_www_db_xref(ajp, ffstring, dbt->db, buf);
+            FF_www_db_xref(ajp, ffstring, dbt->db, buf, bsp);
             FFAddOneString(ffstring, "\"\n", FALSE, FALSE, TILDE_IGNORE);
           }
         }
@@ -4087,7 +4089,7 @@ static Int2 ProcessGapSpecialFormat (
 )
 
 {
-  Char      fmt_buf [32];
+  Char      fmt_buf [64];
   Char      gapbuf [80];
   Int4      gi;
   Char      gi_buf [16];
@@ -4129,6 +4131,9 @@ static Int2 ProcessGapSpecialFormat (
       if (gi > 0) {
         sprintf(gi_buf, "%ld", (long) gi);
         sprintf(fmt_buf, "&fmt_mask=%ld", (long) EXPANDED_GAP_DISPLAY);
+        if (bsp->repr == Seq_repr_delta && (! DeltaLitOnly (bsp))) {
+          StringCat (fmt_buf, "&view=gbwithparts");
+        }
         FFAddOneString (ffstring, "    <a href=", FALSE, FALSE, TILDE_IGNORE);
         FFAddOneString (ffstring, link_featc, FALSE, FALSE, TILDE_IGNORE);
         FFAddOneString (ffstring, "val=", FALSE, FALSE, TILDE_IGNORE);
@@ -4511,6 +4516,7 @@ NLM_EXTERN CharPtr FormatSlashBlock (
       is.accession_version = gbseq->accession_version;
       is.other_seqids = gbseq->other_seqids;
       is.secondary_accessions = gbseq->secondary_accessions;
+      is.project = gbseq->project;
       is.keywords = gbseq->keywords;
       is.segment = gbseq->segment;
       is.source = gbseq->source;
diff --git a/api/asn2gnbi.h b/api/asn2gnbi.h
index 1c4e4ebd..2c966b2f 100644
--- a/api/asn2gnbi.h
+++ b/api/asn2gnbi.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   12/30/03
 *
-* $Revision: 1.61 $
+* $Revision: 1.62 $
 *
 * File Description:  New GenBank flatfile generator, internal header
 *
@@ -705,7 +705,9 @@ NLM_EXTERN Char link_sp [MAX_WWWBUF];
 NLM_EXTERN void FF_www_db_xref(
   IntAsn2gbJobPtr ajp,
   StringItemPtr ffstring,
-  CharPtr db, CharPtr identifier
+  CharPtr db,
+  CharPtr identifier,
+  BioseqPtr bsp
 );
 
 NLM_EXTERN Boolean StringIsJustQuotes (
diff --git a/api/asn2gnbk.h b/api/asn2gnbk.h
index eb181c3c..7db3d786 100644
--- a/api/asn2gnbk.h
+++ b/api/asn2gnbk.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   10/21/98
 *
-* $Revision: 6.69 $
+* $Revision: 6.70 $
 *
 * File Description:  New GenBank flatfile generator
 *
@@ -131,7 +131,8 @@ typedef unsigned long LckType;
 #define LOOKUP_FAR_LOCATIONS      32
 #define LOOKUP_FAR_PRODUCTS       64
 #define LOOKUP_FAR_HISTORY       128
-#define LOOKUP_FAR_OTHERS        256
+#define LOOKUP_FAR_INFERENCE     256
+#define LOOKUP_FAR_OTHERS        512
 
 /* bit flags for unusual customized reports */
 
diff --git a/api/edutil.c b/api/edutil.c
index 4a288a79..5e08e2b9 100644
--- a/api/edutil.c
+++ b/api/edutil.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 2/4/94
 *
-* $Revision: 6.54 $
+* $Revision: 6.56 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -39,6 +39,12 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: edutil.c,v $
+* Revision 6.56  2006/04/04 18:00:47  kans
+* SeqLocAddEx properly returns value to &last argument, makes SeqLocMix from DeltaSeqsToSeqLocs
+*
+* Revision 6.55  2006/03/30 19:50:15  kans
+* DeltaSeqsToSeqLocs calls SeqLocAddEx for efficient list usage
+*
 * Revision 6.54  2006/02/07 13:41:29  bollin
 * added function AdjustFeatureForGapChange, which changes a feature to accommodate
 * a change in the length of a gap
@@ -370,15 +376,16 @@ NLM_EXTERN SeqLocPtr LIBCALL SeqLocPackage (SeqLocPtr head)
 *         if incoming is merged, deletes the incoming SeqLoc
 *
 *****************************************************************************/
-NLM_EXTERN SeqLocPtr LIBCALL SeqLocAdd (SeqLocPtr PNTR head, SeqLocPtr slp, Boolean merge, Boolean do_copy)
+static SeqLocPtr LIBCALL SeqLocAddEx (SeqLocPtr PNTR head, SeqLocPtr PNTR lastp, SeqLocPtr slp, Boolean merge, Boolean do_copy)
 {
-	SeqLocPtr tmp, last, retval = NULL;
+	SeqLocPtr tmp, last = NULL, retval = NULL;
 	Boolean merged = FALSE;   /* intervals were merged */
 
 	if (slp == NULL) return NULL;
 
-	last = NULL;
-	if (* head != NULL)
+    if (lastp != NULL) {
+        last = *lastp;
+    } else if (head != NULL && *head != NULL)
 	{
 		for (tmp = *head; tmp != NULL; tmp = tmp->next)
 		{
@@ -501,12 +508,16 @@ ret:
 		else
 			tmp = slp;
 
-		tmp->next = NULL;
+		if (tmp != NULL) {
+			tmp->next = NULL;
+		}
 
-		if (last != NULL)
+		if (last != NULL) {
 			last->next = tmp;
-		else
+		} else if (head != NULL) {
 			*head = tmp;
+		}
+		last = tmp;
 		retval = tmp;
 	}
 	else
@@ -515,10 +526,30 @@ ret:
 		if (! do_copy)   /* got to free it here */
 			SeqLocFree(slp);
 	}
+	if (lastp != NULL) {
+	    *lastp = last;
+	}
 		
 	return retval;
 }
 
+NLM_EXTERN SeqLocPtr LIBCALL SeqLocAdd (SeqLocPtr PNTR head, SeqLocPtr slp, Boolean merge, Boolean do_copy)
+{
+	SeqLocPtr tmp, last;
+
+	if (slp == NULL) return NULL;
+
+	last = NULL;
+	if (* head != NULL)
+	{
+		for (tmp = *head; tmp != NULL; tmp = tmp->next)
+		{
+			last = tmp;
+		}
+	}
+	return SeqLocAddEx (head, &last, slp, merge, do_copy);
+}
+
 /*****************************************************************************
 *
 *   SegLocToParts(BioseqPtr seg, SeqLocPtr slp)
@@ -652,7 +683,7 @@ NLM_EXTERN Int4 LIBCALL ISADeltaSeqsToSeqLoc (SeqLocPtr slp)
 *****************************************************************************/
 NLM_EXTERN SeqLocPtr LIBCALL DeltaSeqsToSeqLocs (DeltaSeqPtr dsp)
 {
-	SeqLocPtr head = NULL, thead=NULL;
+	SeqLocPtr head = NULL, thead = NULL, last = NULL;
 	DeltaSeqPtr curr;
 	SeqInt si;
 	Dbtag db;
@@ -674,14 +705,15 @@ NLM_EXTERN SeqLocPtr LIBCALL DeltaSeqsToSeqLocs (DeltaSeqPtr dsp)
 	oi.id = 1;
 
 	
+	
 	for (curr = dsp; curr != NULL; curr = curr->next)
 	{
 		if (curr->choice == 1)   /* a SeqLoc */
-			SeqLocAdd(&thead, (SeqLocPtr)(curr->data.ptrvalue), TRUE, TRUE);
+			SeqLocAddEx (&thead, &last, (SeqLocPtr)(curr->data.ptrvalue), TRUE, TRUE);
 		else
 		{
-			si.to = ((SeqLitPtr)(curr->data.ptrvalue))->length - 1;
-			SeqLocAdd(&thead, &vn, TRUE, TRUE); 
+			si.to = ((SeqLitPtr) (curr->data.ptrvalue))->length - 1;
+			SeqLocAddEx (&thead, &last, &vn, TRUE, TRUE); 
 		}
 		oi.id++;
 	}
diff --git a/api/seqmgr.c b/api/seqmgr.c
index ecefefa8..d3e0e41e 100644
--- a/api/seqmgr.c
+++ b/api/seqmgr.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 9/94
 *
-* $Revision: 6.259 $
+* $Revision: 6.263 $
 *
 * File Description:  Manager for Bioseqs and BioseqSets
 *
@@ -39,6 +39,18 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: seqmgr.c,v $
+* Revision 6.263  2006/04/13 20:02:15  kans
+* LookupFarSeqIDs takes inference parameter
+*
+* Revision 6.262  2006/04/05 17:18:23  kans
+* IndexSegmentedParts uses Int4 for numsegs to avoid overflow to negative number, failure to MemNew
+*
+* Revision 6.261  2006/03/21 15:32:13  kans
+* set ignore flag on generated gaps in IndexRecordedFeatures, not as side effect of sorting callback
+*
+* Revision 6.260  2006/03/20 22:53:44  kans
+* sort flatfile-generated gap feature last, set ignore flag
+*
 * Revision 6.259  2006/02/17 19:05:05  kans
 * special case coded_by only for CDS feature on isolated protein bioseq
 *
@@ -7123,6 +7135,16 @@ static int LIBCALLBACK SortFeatItemListByPos (VoidPtr vp1, VoidPtr vp2)
     return 1;
   }
 
+  /* if identical gap ranges, use itemID to put flatfile-generated gap feature last */
+
+  if (sp1->subtype == FEATDEF_gap && sp2->subtype == FEATDEF_gap) {
+    if (sp1->itemID > sp2->itemID) {
+      return 1;
+    } else if (sp1->itemID < sp2->itemID) {
+      return -1;
+    }
+  }
+
   /* if identical cds ranges, compare codon_start */
 
   if (sp1->subtype == FEATDEF_CDS && sp2->subtype == FEATDEF_CDS) {
@@ -7295,6 +7317,16 @@ static int LIBCALLBACK SortFeatItemListByRev (VoidPtr vp1, VoidPtr vp2)
     return 1;
   }
 
+  /* if identical gap ranges, use itemID to put flatfile-generated gap feature last */
+
+  if (sp1->subtype == FEATDEF_gap && sp2->subtype == FEATDEF_gap) {
+    if (sp1->itemID > sp2->itemID) {
+      return 1;
+    } else if (sp1->itemID < sp2->itemID) {
+      return -1;
+    }
+  }
+
   /* if identical cds ranges, compare codon_start */
 
   if (sp1->subtype == FEATDEF_CDS && sp2->subtype == FEATDEF_CDS) {
@@ -7431,8 +7463,8 @@ static void IndexSegmentedParts (SeqEntryPtr sep, BioseqPtr PNTR lastsegbsp)
   BioseqPtr         bsp;
   BioseqExtraPtr    bspextra;
   BioseqSetPtr      bssp;
-  Int2              i;
-  Int2              numsegs = 0;
+  Int4              i;
+  Int4              numsegs = 0;
   ObjMgrDataPtr     omdp;
   SMSeqIdxPtr PNTR  partsByLoc;
   SMSeqIdxPtr PNTR  partsBySeqId;
@@ -7534,7 +7566,7 @@ static void IndexSegmentedParts (SeqEntryPtr sep, BioseqPtr PNTR lastsegbsp)
 *
 *****************************************************************************/
 
-static void IndexRecordedFeatures (SeqEntryPtr sep, Boolean dorevfeats)
+static void IndexRecordedFeatures (SeqEntryPtr sep, Boolean dorevfeats, Uint4 baseItemID)
 
 {
   BioseqPtr           bsp;
@@ -7553,6 +7585,7 @@ static void IndexRecordedFeatures (SeqEntryPtr sep, Boolean dorevfeats)
   Int4                i;
   Int4                j;
   SMFeatItemPtr       item;
+  SMFeatItemPtr       last;
   BioseqPtr           nuc;
   Int4                numfeats;
   Int4                numgenes;
@@ -7568,7 +7601,7 @@ static void IndexRecordedFeatures (SeqEntryPtr sep, Boolean dorevfeats)
     bssp = (BioseqSetPtr) sep->data.ptrvalue;
     if (bssp == NULL) return;
     for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
-      IndexRecordedFeatures (sep, dorevfeats);
+      IndexRecordedFeatures (sep, dorevfeats, baseItemID);
     }
     return;
   }
@@ -7643,6 +7676,25 @@ static void IndexRecordedFeatures (SeqEntryPtr sep, Boolean dorevfeats)
           }
         }
 
+        /* gap feature in record overrides flatfile-generated feature */
+
+        if (baseItemID > 0) {
+          last = featsByPos [0];
+          for (i = 1; i < numfeats; i++) {
+            item = featsByPos [i];
+            if (item != NULL && last != NULL) {
+              if (last->subtype == FEATDEF_gap && item->subtype == FEATDEF_gap) {
+                if (last->left == item->left && last->right == item->right) {
+                  if (item->itemID >= baseItemID) {
+                    item->ignore = TRUE;
+                  }
+                }
+              }
+            }
+            last = item;
+          }
+        }
+
         /* build arrays of sorted gene, mRNA, CDS, publication, and biosource features for lookup by overlap */
 
         bspextra->genesByPos = SeqMgrBuildFeatureIndex (bsp, &(bspextra->numgenes), 0, FEATDEF_GENE);
@@ -8338,6 +8390,7 @@ NLM_EXTERN Uint2 LIBCALL SeqMgrIndexFeaturesExEx (
 {
   AdpBspPtr           abp;
   AnnotDescPtr PNTR   annotDescByID;
+  Uint4               baseItemID = 0;
   BioseqPtr           bsp;
   BioseqExtraPtr      bspextra;
   Int4                count;
@@ -8414,6 +8467,19 @@ NLM_EXTERN Uint2 LIBCALL SeqMgrIndexFeaturesExEx (
 
   AssignIDsInEntityEx (entityID, 0, NULL, extra);
 
+  /* get first feature itemID in remote feature tables (including generated gaps) */
+
+  for (vnp = extra; vnp != NULL && baseItemID == 0; vnp = vnp->next) {
+    bsp = (BioseqPtr) vnp->data.ptrvalue;
+    if (bsp == NULL) continue;
+    for (sap = bsp->annot; sap != NULL && baseItemID == 0; sap = sap->next) {
+      if (sap->type != 1) continue;
+      for (sfp = (SeqFeatPtr) sap->data; sfp != NULL && baseItemID == 0; sfp = sfp->next) {
+        baseItemID = sfp->idx.itemID;
+      }
+    }
+  }
+
   /* set scope for FindAppropriateBioseq, FindFirstLocalBioseq */
 
   oldscope = SeqEntrySetScope (sep);
@@ -8481,7 +8547,7 @@ NLM_EXTERN Uint2 LIBCALL SeqMgrIndexFeaturesExEx (
 
   /* finish building array of sorted features on each indexed bioseq */
 
-  IndexRecordedFeatures (sep, dorevfeats);
+  IndexRecordedFeatures (sep, dorevfeats, baseItemID);
 
   /* set best protein feature for segmented protein bioseqs and their parts */
 
@@ -11163,6 +11229,7 @@ NLM_EXTERN Int4 LookupFarSeqIDs (
   Boolean products,
   Boolean alignments,
   Boolean history,
+  Boolean inference,
   Boolean others
 )
 
@@ -11175,7 +11242,7 @@ NLM_EXTERN Int4 LookupFarSeqIDs (
   func = smp->seq_id_precache_func;
   SeqMgrUnlock ();
   if (func == NULL) return 0;
-  return (*func) (sep, components, locations, products, alignments, history, others);
+  return (*func) (sep, components, locations, products, alignments, history, inference, others);
 }
 
 /*****************************************************************************
diff --git a/api/seqmgr.h b/api/seqmgr.h
index c80ab55e..89ff1bbc 100644
--- a/api/seqmgr.h
+++ b/api/seqmgr.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 9/94
 *
-* $Revision: 6.59 $
+* $Revision: 6.60 $
 *
 * File Description:  Manager for Bioseqs and BioseqSets
 *
@@ -40,6 +40,9 @@
 *
 *
 * $Log: seqmgr.h,v $
+* Revision 6.60  2006/04/13 20:02:15  kans
+* LookupFarSeqIDs takes inference parameter
+*
 * Revision 6.59  2006/02/16 20:24:32  kans
 * added bad_order and mixed_strand fields to feature index - to be used for get best gene overlap function in cases of trans-splicing
 *
@@ -316,7 +319,7 @@ typedef BioseqPtr (LIBCALLBACK * BSFetchTop)
 
 typedef BioseqPtr (LIBCALLBACK * BSFetch) PROTO((SeqIdPtr sip, Pointer data));
 
-typedef Int4 (LIBCALLBACK * SIDPreCacheFunc) (SeqEntryPtr sep, Boolean components, Boolean locations, Boolean products, Boolean alignments, Boolean history, Boolean others);
+typedef Int4 (LIBCALLBACK * SIDPreCacheFunc) (SeqEntryPtr sep, Boolean components, Boolean locations, Boolean products, Boolean alignments, Boolean history, Boolean inference, Boolean others);
 typedef Int4 (LIBCALLBACK * SeqLenLookupFunc) (Int4 gi);
 typedef CharPtr (LIBCALLBACK * AccnVerLookupFunc) (Int4 gi);
 typedef SeqIdPtr (LIBCALLBACK * SeqIdSetLookupFunc) (Int4 gi);
@@ -1118,6 +1121,7 @@ NLM_EXTERN Int4 LookupFarSeqIDs (
   Boolean products,
   Boolean alignments,
   Boolean history,
+  Boolean inference,
   Boolean others
 );
 
diff --git a/api/seqport.c b/api/seqport.c
index 89550a8a..b0e77145 100644
--- a/api/seqport.c
+++ b/api/seqport.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/13/91
 *
-* $Revision: 6.147 $
+* $Revision: 6.150 $
 *
 * File Description:  Ports onto Bioseqs
 *
@@ -39,6 +39,15 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: seqport.c,v $
+* Revision 6.150  2006/03/22 15:31:32  kans
+* SeqPortStreamSeqLoc gives unique message when bailing on gi 0 as opposed to failure after trying to load
+*
+* Revision 6.149  2006/03/07 21:34:28  kans
+* checks for gi 0 now also check for negative value
+*
+* Revision 6.148  2006/03/07 20:02:01  kans
+* SeqPortStreamSeqLoc immediately treats gi 0 as an error
+*
 * Revision 6.147  2006/01/23 13:01:41  bollin
 * when converting sequences from raw to delta, adjust any alignments that the
 * sequence may be part of.
@@ -2978,6 +2987,21 @@ static Int4 SeqPortStreamSeqLoc (
   sip = SeqLocId (slp);
   if (sip == NULL) return 0;
 
+  if (sip->choice == SEQID_GI && sip->data.intvalue <= 0) {
+
+    /* gi 0 or negative is always a data error, just report and bail */
+
+    SeqIdWrite (sip, buf, PRINTID_FASTA_SHORT, sizeof (buf) - 1);
+    if (parentID != NULL) {
+      SeqIdWrite (parentID, pid, PRINTID_FASTA_LONG, sizeof (pid) - 1);
+      ErrPostEx (SEV_ERROR, 0, 0, "SeqPortStream ignoring Bioseq %s component of %s", buf, pid);
+    } else {
+      ErrPostEx (SEV_ERROR, 0, 0, "SeqPortStream ignoring Bioseq %s", buf);
+    }
+    sdp->failed = TRUE;
+    return 0;
+  }
+
   bsp = BioseqLockById (sip);
 
 #ifdef OS_UNIX
diff --git a/api/sequtil.c b/api/sequtil.c
index c7d8d53e..07cb6305 100644
--- a/api/sequtil.c
+++ b/api/sequtil.c
@@ -29,13 +29,32 @@
 *   
 * Version Creation Date: 4/1/91
 *
-* $Revision: 6.190 $
+* $Revision: 6.196 $
 *
 * File Description:  Sequence Utilities for objseq and objsset
 *
 * Modifications:  
 * --------------------------------------------------------------------------
 * $Log: sequtil.c,v $
+* 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)
 *
@@ -847,7 +866,7 @@ static char *this_file = __FILE__;
 #include <seqport.h>
 #include <sqnutils.h> /* prototype for SeqIdFindWorst */
 #include <edutil.h>
-
+#include <subutil.h>
 
 /****  Static variables used for randomized sequence conversions ****/
 
@@ -6625,7 +6644,7 @@ NLM_EXTERN Int4 CheckPointInBioseq (SeqPntPtr sp, BioseqPtr in)
 static SeqIdPtr GetEarlierSeqIdPtr (SeqIdPtr sip1, SeqIdPtr sip2)
 {
   BioseqPtr    bsp1, bsp2;
-  BioseqSetPtr bssp;
+  BioseqSetPtr bssp = NULL;
   SeqEntryPtr  sep;
   
   if (sip1 == NULL && sip2 != NULL)
@@ -6655,25 +6674,31 @@ static SeqIdPtr GetEarlierSeqIdPtr (SeqIdPtr sip1, SeqIdPtr sip2)
   {
     return sip1;
   }
+
+  if (bsp1->idx.parentptr != NULL && bsp2->idx.parentptr != 0 && bsp1->idx.parentptr != bsp2->idx.parentptr)
+  {
+    return NULL;
+  }
+  if (bsp1->idx.parentptr != NULL && bsp1->idx.parenttype == OBJ_BIOSEQSET) {
+    bssp = bsp1->idx.parentptr;
+  } else if (bsp2->idx.parentptr != NULL && bsp2->idx.parenttype == OBJ_BIOSEQSET) {
+    bssp = bsp2->idx.parentptr;
+  }
+
+  if (bssp == NULL) return NULL;
   
-  if (bsp1->idx.parenttype == OBJ_BIOSEQSET
-      && bsp2->idx.parenttype == OBJ_BIOSEQSET
-      && bsp1->idx.parentptr == bsp2->idx.parentptr)
+  for (sep = bssp->seq_set; sep != NULL; sep = sep->next)
   {
-    bssp = (BioseqSetPtr) bsp1->idx.parentptr;
-    for (sep = bssp->seq_set; sep != NULL; sep = sep->next)
+    if (sep->data.ptrvalue == bsp1)
     {
-      if (sep->data.ptrvalue == bsp1)
-      {
-        return sip1;
-      }
-      else if (sep->data.ptrvalue == bsp2)
-      {
-        return sip2;
-      }
+      return sip1;
+    }
+    else if (sep->data.ptrvalue == bsp2)
+    {
+      return sip2;
     }
   }
-  return sip1;
+  return NULL;
 }
 
 /*****************************************************************************
@@ -6689,8 +6714,16 @@ Boolean GetThePointForOffset(SeqLocPtr of, SeqPntPtr target, Uint1 which_end)
 	Int4    lowest = -1, highest = 0, tmp;
 	SeqIdPtr low_sip = NULL, high_sip = NULL, first_sip = NULL, last_sip = NULL;
 	Boolean   id_same;
+	BioseqPtr bsp;
+	Boolean   is_circular = FALSE;
 
 	pnt = NULL;    /* get first or last single span type in "of"*/
+	
+	bsp = BioseqFind (SeqLocId(of));
+	if (bsp != NULL && bsp->topology == TOPOLOGY_CIRCULAR) {
+	    is_circular = TRUE;
+	}
+	
 	while ((pnt = SeqLocFindNext(of, pnt)) != NULL)
 	{
 	  last_strand = SeqLocStrand (pnt);
@@ -6751,12 +6784,32 @@ Boolean GetThePointForOffset(SeqLocPtr of, SeqPntPtr target, Uint1 which_end)
 	switch (which_end)
 	{
 		case SEQLOC_LEFT_END:
-		  target->point = lowest;
-		  target->id = low_sip;
+		  if (is_circular) {
+		    if (all_minus) {
+		      target->point = SeqLocStart (last);
+		      target->id = last_sip;
+		    } else {
+		      target->point = SeqLocStart (first);
+		      target->id = first_sip;
+		    }
+		  } else {
+		    target->point = lowest;
+		    target->id = low_sip;
+		  }
 			break;
 		case SEQLOC_RIGHT_END:
-		  target->point = highest;
-		  target->id = high_sip;
+		  if (is_circular) {
+		    if (all_minus) {
+		      target->point = SeqLocStop (first);
+		      target->id = first_sip;
+		    } else {
+		      target->point = SeqLocStop (last);
+		      target->id = last_sip;
+		    }
+		  } else {  
+		    target->point = highest;
+		    target->id = high_sip;
+		  }
 			break;
 		case SEQLOC_START:
 		  if (all_minus)
@@ -9325,7 +9378,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
 	      (StringICmp(temp,"DT") == 0) || 
 	      (StringICmp(temp,"DV") == 0) || 
 	      (StringICmp(temp,"DW") == 0) || 
-	      (StringICmp(temp,"DY") == 0) ) {                /* NCBI EST */
+	      (StringICmp(temp,"DY") == 0) || 
+	      (StringICmp(temp,"EB") == 0) ) {                /* NCBI EST */
               retcode = ACCN_NCBI_EST;
           } else if ((StringICmp(temp,"BV") == 0)) {      /* NCBI STS */
               retcode = ACCN_NCBI_STS;
@@ -9414,7 +9468,9 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
               retcode = ACCN_DDBJ_GENOME;
           } else if ((StringICmp(temp,"AK") == 0))  {     /* DDBJ HTGS */
               retcode = ACCN_DDBJ_HTGS;
-          } else if ((StringICmp(temp,"BA") == 0)) {      /* DDBJ CON division */
+          } else if ((StringICmp(temp,"BA") == 0) || 
+                     (StringICmp(temp,"DF") == 0) || 
+                     (StringICmp(temp,"DG") == 0)) {      /* DDBJ CON division */
               retcode = ACCN_DDBJ_CON;
           } else if ((StringICmp(temp,"BD") == 0) ||
                      (StringICmp(temp,"DD") == 0)) {      /* DDBJ patent division */
diff --git a/api/sqnutil1.c b/api/sqnutil1.c
index e44797e5..432b130c 100644
--- a/api/sqnutil1.c
+++ b/api/sqnutil1.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.369 $
+* $Revision: 6.376 $
 *
 * File Description: 
 *
@@ -2685,9 +2685,7 @@ static Boolean HandledGBQualOnGene (SeqFeatPtr sfp, GBQualPtr gbq)
   Int2        choice = 0;
   GeneRefPtr  grp;
 
-  if (StringICmp (gbq->qual, "pseudo") == 0) {
-    choice = 1;
-  } else if (StringICmp (gbq->qual, "map") == 0) {
+  if (StringICmp (gbq->qual, "map") == 0) {
     choice = 2;
   } else if (StringICmp (gbq->qual, "allele") == 0) {
     choice = 3;
@@ -2698,9 +2696,6 @@ static Boolean HandledGBQualOnGene (SeqFeatPtr sfp, GBQualPtr gbq)
     grp = (GeneRefPtr) sfp->data.value.ptrvalue;
     if (grp == NULL) return FALSE;
     switch (choice) {
-      case 1 :
-        grp->pseudo = TRUE;
-        break;
       case 2 :
         if (grp->maploc != NULL) return FALSE;
         if (StringHasNoText (gbq->val)) return FALSE;
@@ -2785,6 +2780,7 @@ extern Boolean ParseAnticodon (SeqFeatPtr sfp, CharPtr val, Int4 offset)
 
 {
   Int4       diff;
+  Int2       j;
   Boolean    locmap;
   int        num_errs;
   CharPtr    pos;
@@ -2809,6 +2805,12 @@ extern Boolean ParseAnticodon (SeqFeatPtr sfp, CharPtr val, Int4 offset)
     rrp->ext.choice = 2;
     trp = (tRNAPtr) MemNew (sizeof (tRNA));
     rrp->ext.value.ptrvalue = (Pointer) trp;
+    if (trp != NULL) {
+      trp->aatype = 2;
+      for (j = 0; j < 6; j++) {
+        trp->codon [j] = 255;
+      }
+    }
   }
   if (rrp->ext.choice != 2) return FALSE;
 
@@ -5201,7 +5203,8 @@ static void FixOldDbxrefs (ValNodePtr vnp)
         dbt->db = MemFree (dbt->db);
         dbt->db = StringSave ("SubtiList");
       }
-      if (StringICmp (dbt->db, "Swiss-Prot") == 0) {
+      if (StringICmp (dbt->db, "Swiss-Prot") == 0 ||
+          StringICmp (dbt->db, "SWISSPROT") == 0) {
         dbt->db = MemFree (dbt->db);
         dbt->db = StringSave ("UniProt/Swiss-Prot");
       } else if (StringICmp (dbt->db, "TrEMBL") == 0) {
@@ -7658,6 +7661,7 @@ NLM_EXTERN void CleanUpSeqFeat (
   BioseqPtr     bsp;
   CodeBreakPtr  cbp;
   CdRegionPtr   crp;
+  GeneRefPtr    grp;
   Boolean       hasNulls;
   SeqIdPtr      id;
   ImpFeatPtr    ifp;
@@ -7774,7 +7778,15 @@ NLM_EXTERN void CleanUpSeqFeat (
   CleanupSeqLoc (sfp->location);
   strand = SeqLocStrand (sfp->location);
   id = SeqLocId (sfp->location);
-  if (sfp->data.choice == SEQFEAT_CDREGION) {
+  if (sfp->data.choice == SEQFEAT_GENE) {
+    grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+    if (grp != NULL) {
+      if (grp->pseudo) {
+        sfp->pseudo = TRUE;
+        grp->pseudo = FALSE;
+      }
+    }
+  } else if (sfp->data.choice == SEQFEAT_CDREGION) {
 	crp = (CdRegionPtr) sfp->data.value.ptrvalue;
 	if (crp != NULL) {
 	  crp->code_break = SortCodeBreaks (sfp, crp->code_break);
@@ -7797,6 +7809,12 @@ NLM_EXTERN void CleanUpSeqFeat (
 	}
   } else if (sfp->data.choice == SEQFEAT_RNA) {
 	rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
+    if (rrp != NULL) {
+      if (rrp->pseudo) {
+        sfp->pseudo = TRUE;
+        rrp->pseudo = FALSE;
+      }
+    }
 	if (rrp != NULL && rrp->ext.choice == 2) {
 	  trp = (tRNAPtr) rrp->ext.value.ptrvalue;
 	  if (trp != NULL && trp->anticodon != NULL) {
@@ -9827,6 +9845,40 @@ NLM_EXTERN Int4 VisitUserObjectsInUop (UserObjectPtr uop, Pointer userdata, Visi
   return index;
 }
 
+typedef struct uopdata {
+  UserObjectPtr  rsult;
+  CharPtr        tag;
+} UopData, PNTR UopDataPtr;
+
+static void FindUopProc (
+  UserObjectPtr uop,
+  Pointer userdata
+)
+
+{
+  ObjectIdPtr  oip;
+  UopDataPtr   udp;
+
+  if (uop == NULL || userdata == NULL) return;
+  oip = uop->type;
+  if (oip == NULL) return;
+  udp = (UopDataPtr) userdata;
+  if (StringICmp (oip->str, udp->tag) != 0) return;
+  udp->rsult = uop;
+}
+
+NLM_EXTERN UserObjectPtr FindUopByTag (UserObjectPtr top, CharPtr tag)
+
+{
+  UopData  ud;
+
+  if (top == NULL || StringHasNoText (tag)) return NULL;
+  ud.rsult = NULL;
+  ud.tag = tag;
+  VisitUserObjectsInUop (top, (Pointer) &ud, FindUopProc);
+  return ud.rsult;
+}
+
 NLM_EXTERN UserObjectPtr CombineUserObjects (UserObjectPtr origuop, UserObjectPtr newuop)
 
 {
diff --git a/api/sqnutil2.c b/api/sqnutil2.c
index f5d24d2b..7ef549ec 100644
--- a/api/sqnutil2.c
+++ b/api/sqnutil2.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.244 $
+* $Revision: 6.251 $
 *
 * File Description: 
 *
@@ -1562,18 +1562,19 @@ NLM_EXTERN SqnTagPtr SqnTagFree (SqnTagPtr stp)
   return MemFree (stp);
 }
 
-static Boolean StringsAreEquivalent (CharPtr str1, CharPtr str2)
+extern Boolean StringsAreEquivalent (CharPtr str1, CharPtr str2)
 
 {
   Char  ch1, ch2;
 
+  if (StringHasNoText (str1) && StringHasNoText (str2)) return TRUE;
   if (StringHasNoText (str1) || StringHasNoText (str2)) return FALSE;
 
   ch1 = *str1;
   ch2 = *str2;
   while (ch1 != '\0' && ch2 != '\0') {
     if (TO_LOWER (ch1) != TO_LOWER (ch2)) {
-      if ((ch1 != '-' && ch1 != '_') || (ch2 != '_' && ch2 != '-')) return FALSE;
+      if ((ch1 != '-' && ch1 != '_' && ch1 != ' ') || (ch2 != '_' && ch2 != '-' && ch2 != ' ')) return FALSE;
     }
     str1++;
     str2++;
@@ -1582,7 +1583,7 @@ static Boolean StringsAreEquivalent (CharPtr str1, CharPtr str2)
   }
 
   if (TO_LOWER (ch1) != TO_LOWER (ch2)) {
-    if ((ch1 != '-' && ch1 != '_') || (ch2 != '_' && ch2 != '-')) return FALSE;
+    if ((ch1 != '-' && ch1 != '_' && ch1 != ' ') || (ch2 != '_' && ch2 != '-' && ch2 != ' ')) return FALSE;
   }
 
   return TRUE;
@@ -2436,6 +2437,74 @@ NLM_EXTERN UserObjectPtr ParseTitleIntoTpaAssembly (
   return uop;
 }
 
+NLM_EXTERN UserObjectPtr ParseStringIntoStructuredComment (
+  UserObjectPtr uop,
+  CharPtr str,
+  CharPtr prefix,
+  CharPtr suffix
+)
+
+{
+  Char     ch;
+  CharPtr  field;
+  CharPtr  item;
+  CharPtr  last;
+  CharPtr  ptr;
+  CharPtr  tmp;
+
+  if (uop == NULL) {
+    uop = CreateStructuredCommentUserObject ();
+    if (uop == NULL) return uop;
+  }
+  if (str == NULL) return uop;
+
+  tmp = StringSave (str);
+  if (tmp == NULL) return uop;
+
+  last = tmp;
+  if (StringDoesHaveText (prefix)) {
+    ptr = StringStr (last, prefix);
+    if (ptr != NULL) {
+      last = ptr + StringLen (prefix);
+    }
+  }
+  if (StringDoesHaveText (suffix)) {
+    ptr = StringStr (last, suffix);
+    if (ptr != NULL) {
+      *ptr = '\0';
+    }
+  }
+
+  ptr = last;
+  ch = *ptr;
+  while (ch != '\0') {
+    field = last;
+    ptr = StringChr (last, '=');
+    if (ptr != NULL) {
+      *ptr = '\0';
+      ptr++;
+      item = ptr;
+      last = StringChr (ptr, ';');
+      if (last != NULL) {
+        *last = '\0';
+        last++;
+        ch = *last;
+      } else {
+        ch = '\0';
+      }
+      TrimSpacesAroundString (field);
+      TrimSpacesAroundString (item);
+      AddItemStructuredCommentUserObject (uop, field, item);
+    } else {
+      ch = '\0';
+    }
+  }
+
+  MemFree (tmp);
+
+  return uop;
+}
+
 /* PHRAP file reading functions */
 
 static Boolean HasNoText (CharPtr str)
@@ -4934,6 +5003,63 @@ static Boolean InvalidInference (CharPtr str)
   return TRUE;
 }
 
+static void ParseCodonRecognized (CharPtr val, tRNAPtr trp)
+
+{
+  Char        buf [256];
+  Char        codon [16];
+  ValNodePtr  head = NULL;
+  Int2        i;
+  Int2        j;
+  CharPtr     ptr;
+  CharPtr     str;
+  tRNA        tr;
+  ValNodePtr  vnp;
+
+  if (trp == NULL) return;
+  for (j = 0; j < 6; j++) {
+    trp->codon [j] = 255;
+  }
+  if (StringHasNoText (val)) return;
+
+  MemSet ((Pointer) &tr, 0, sizeof (tRNA));
+
+  StringNCpy_0 (buf, val, sizeof (buf));
+  str = buf;
+  while (StringDoesHaveText (str)) {
+    ptr = StringChr (str, ',');
+    if (ptr != NULL) {
+      *ptr = '\0';
+      ptr++;
+    }
+    TrimSpacesAroundString (str);
+    if (StringDoesHaveText (str)) {
+      for (j = 0; j < 6; j++) {
+        tr.codon [j] = 255;
+      }
+      StringCpy (codon, str);
+      for (i = 0; i < 3; i++) {
+        if (codon [i] == 'U') {
+          codon [i] = 'T';
+        }
+      }
+      ParseDegenerateCodon (&tr, (Uint1Ptr) codon);
+      for (i = 0; i < 6; i++) {
+        if (tr.codon [i] == 255) continue;
+        ValNodeAddInt (&head, 0, (long) tr.codon [i]);
+      }
+    }
+    str = ptr;
+  }
+  if (head == NULL) return;
+
+  head = ValNodeSort (head, SortByIntvalue);
+  head = UniqueIntValNode (head);
+  for (vnp = head, j = 0; vnp != NULL && j < 6; vnp = vnp->next, j++) {
+    trp->codon [j] = (Uint1) vnp->data.intvalue;
+  }
+}
+
 static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val, Int4 offset)
 
 {
@@ -5061,6 +5187,20 @@ static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val,
                (StringCmp (qual, "codon_recognized") == 0 || StringCmp (qual, "codons_recognized") == 0)) {
       rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
       if (rrp != NULL && rrp->type == 3) {
+        if (rrp->ext.choice == 0 && rrp->ext.value.ptrvalue == NULL) {
+          rrp->ext.choice = 2;
+          trna = (tRNAPtr) MemNew (sizeof (tRNA));
+          rrp->ext.value.ptrvalue = (Pointer) trna;
+          if (trna != NULL) {
+            trna->aatype = 2;
+            for (j = 0; j < 6; j++) {
+              trna->codon [j] = 255;
+            }
+          }
+        }
+        trna = (tRNAPtr) rrp->ext.value.ptrvalue;
+        ParseCodonRecognized (val, trna);
+        /*
         StringNCpy_0 ((CharPtr) codon, val, sizeof (codon));
         if (StringLen ((CharPtr) codon) == 3) {
           for (j = 0; j < 3; j++) {
@@ -5068,11 +5208,11 @@ static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val,
               codon [j] = 'T';
             }
           }
-          trna = (tRNAPtr) rrp->ext.value.ptrvalue;
           if (trna != NULL) {
             ParseDegenerateCodon (trna, (Uint1Ptr) codon);
           }
         }
+        */
       }
     } else if (ifp != NULL && StringICmp (ifp->key, "variation") == 0 && ParseQualIntoSnpUserObject (sfp, qual, val)) {
     } else if (ifp != NULL && StringICmp (ifp->key, "STS") == 0 && ParseQualIntoStsUserObject (sfp, qual, val)) {
@@ -5107,6 +5247,9 @@ static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val,
       sfp->comment = str;
     }
     return;
+  } else if (qnum == GBQUAL_pseudo) {
+    sfp->pseudo = TRUE;
+    return;
   } else if ((qnum == GBQUAL_gene || qnum == GBQUAL_locus_tag) && sfp->data.choice != SEQFEAT_GENE) {
     if (StringCmp (val, "-") == 0) {
       val = NULL;
@@ -5203,7 +5346,7 @@ static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val,
     }
 
   } else if (sfp->data.choice == SEQFEAT_GENE) {
-    if (qnum == GBQUAL_gene || qnum == GBQUAL_pseudo || qnum == GBQUAL_allele || qnum == GBQUAL_map || qnum == GBQUAL_locus_tag) {
+    if (qnum == GBQUAL_gene || qnum == GBQUAL_allele || qnum == GBQUAL_map || qnum == GBQUAL_locus_tag) {
       if (qnum == GBQUAL_gene) {
         grp = (GeneRefPtr) sfp->data.value.ptrvalue;
         if (grp != NULL) {
@@ -5219,11 +5362,6 @@ static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val,
             ValNodeCopyStr (&(grp->syn), 0, val);
           }
         }
-      } else if (qnum == GBQUAL_pseudo) {
-        grp = (GeneRefPtr) sfp->data.value.ptrvalue;
-        if (grp != NULL) {
-          grp->pseudo = TRUE;
-        }
       } else if (qnum == GBQUAL_allele) {
         grp = (GeneRefPtr) sfp->data.value.ptrvalue;
         if (grp != NULL) {
@@ -5280,8 +5418,6 @@ static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val,
         }
       }
       return;
-    } else if (qnum == GBQUAL_pseudo) {
-      sfp->pseudo = TRUE;
     }
   } else if (sfp->data.choice == SEQFEAT_PROT) {
     if (qnum == GBQUAL_function || qnum == GBQUAL_EC_number || qnum == GBQUAL_product) {
@@ -5304,14 +5440,19 @@ static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val,
       if (rrp->type == 3) {
         aa = ParseTRnaString (val, &justTrnaText, codon, FALSE);
         if (aa != 0) {
-          rrp->ext.choice = 2;
-          trna = (tRNAPtr) MemNew (sizeof (tRNA));
-          rrp->ext.value.ptrvalue = (Pointer) trna;
-          if (trna != NULL) {
-            trna->aatype = 2;
-            for (j = 0; j < 6; j++) {
-              trna->codon [j] = 255;
+          if (rrp->ext.choice == 0 && rrp->ext.value.ptrvalue == NULL) {
+            rrp->ext.choice = 2;
+            trna = (tRNAPtr) MemNew (sizeof (tRNA));
+            rrp->ext.value.ptrvalue = (Pointer) trna;
+            if (trna != NULL) {
+              trna->aatype = 2;
+              for (j = 0; j < 6; j++) {
+                trna->codon [j] = 255;
+              }
             }
+          }
+          trna = (tRNAPtr) rrp->ext.value.ptrvalue;
+          if (trna != NULL) {
             if (justTrnaText) {
               for (j = 0; j < 6; j++) {
                 trna->codon [j] = codon [j];
@@ -5357,9 +5498,6 @@ static void AddQualifierToFeatureEx (SeqFeatPtr sfp, CharPtr qual, CharPtr val,
       return;
     } else if (qnum == GBQUAL_anticodon) {
       if (ParseAnticodon (sfp, val, offset)) return;
-    } else if (qnum == GBQUAL_pseudo) {
-      sfp->pseudo = TRUE;
-      return;
     }
   } else if (sfp->data.choice == SEQFEAT_BIOSRC) {
     if (ParseQualIntoBioSource (sfp, qual, val)) return;
@@ -8555,6 +8693,8 @@ NLM_EXTERN void TrimSeqGraph (SeqGraphPtr sgp, Int4 num_to_trim, Boolean from_le
   Int2         bs_max = 0, bs_min = 0;
   Int4         new_pos, old_pos;
   Int2         val;
+  Int4         loc_stop;
+  Boolean      changed = FALSE;
   
   if (sgp == NULL || num_to_trim < 1)
   {
@@ -8605,6 +8745,7 @@ NLM_EXTERN void TrimSeqGraph (SeqGraphPtr sgp, Int4 num_to_trim, Boolean from_le
     sgp->numval = new_len;
     sgp->max.realvalue = fhmax;
     sgp->min.realvalue = fhmin;
+    changed = TRUE;
   }
   else if (sgp->flags[2] == 2)
   {
@@ -8640,6 +8781,7 @@ NLM_EXTERN void TrimSeqGraph (SeqGraphPtr sgp, Int4 num_to_trim, Boolean from_le
     sgp->numval = new_len;
     sgp->max.intvalue = intmax;
     sgp->min.intvalue = intmin;
+    changed = TRUE;
   }
   else if (sgp->flags[2] == 3)
   {
@@ -8680,6 +8822,14 @@ NLM_EXTERN void TrimSeqGraph (SeqGraphPtr sgp, Int4 num_to_trim, Boolean from_le
     sgp->numval = new_len;
     sgp->max.intvalue = bs_max;
     sgp->min.intvalue = bs_min;
+    changed = TRUE;
+  }
+  if (changed) 
+  {
+    loc_stop = SeqLocStop (sgp->loc);  
+    sgp->loc = SeqLocDelete (sgp->loc, SeqLocId (sgp->loc), 
+                             loc_stop - num_to_trim + 1, 
+                             loc_stop, FALSE, &changed);
   }
 }
 
diff --git a/api/sqnutil3.c b/api/sqnutil3.c
index ef2a21bf..007ce12f 100644
--- a/api/sqnutil3.c
+++ b/api/sqnutil3.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   2/7/00
 *
-* $Revision: 6.69 $
+* $Revision: 6.74 $
 *
 * File Description: 
 *
@@ -115,7 +115,7 @@ static void SfpClearFeatIDs (
   ClearFeatIDXrefs (sfp);
 }
 
-NLM_EXTERN void ClearCDSmRNAfeatureIDs (
+NLM_EXTERN void ClearFeatureIDs (
   SeqEntryPtr sep
 )
 
@@ -123,11 +123,20 @@ NLM_EXTERN void ClearCDSmRNAfeatureIDs (
   VisitFeaturesInSep (sep, NULL, SfpClearFeatIDs);
 }
 
+typedef struct idpair {
+  Int4  before;
+  Int4  after;
+} IdPairData, PNTR IdPairPtr;
+
 typedef struct fiddata {
-  Int4  highestID;
+  Int4       highestID;
+  Int4       highestRef;
+  Int4       offset;
+  Int4       count;
+  IdPairPtr  pairs;
 } FidData, PNTR FidDataPtr;
 
-static void FindHighestFeatureID (
+static void FindHighestFeatID (
   SeqFeatPtr sfp,
   Pointer userdata
 )
@@ -138,7 +147,6 @@ static void FindHighestFeatureID (
   SeqFeatXrefPtr  xref;
 
   if (sfp == NULL) return;
-  if (sfp->idx.subtype != FEATDEF_CDS && sfp->idx.subtype != FEATDEF_mRNA) return;
   fip = (FidDataPtr) userdata;
   if (fip == NULL) return;
 
@@ -147,7 +155,7 @@ static void FindHighestFeatureID (
     if (oip != NULL) {
       if (oip->str == NULL) {
         if (oip->id >= fip->highestID) {
-          fip->highestID = oip->id + 1;
+          fip->highestID = oip->id;
         }
       }
     }
@@ -158,15 +166,29 @@ static void FindHighestFeatureID (
     oip = (ObjectIdPtr) xref->id.value.ptrvalue;
     if (oip != NULL) {
       if (oip->str == NULL) {
-        if (oip->id >= fip->highestID) {
-          fip->highestID = oip->id + 1;
+        if (oip->id >= fip->highestRef) {
+          fip->highestRef = oip->id;
         }
       }
     }
   }
 }
 
-static void SfpAssignCDSmRNAfeatureIDs (
+NLM_EXTERN Int4 FindHighestFeatureID (
+  SeqEntryPtr sep
+)
+
+{
+  FidData  fd;
+
+  MemSet ((Pointer) &fd, 0, sizeof (FidData));
+  fd.highestID = 0;
+  fd.highestRef = 0;
+  VisitFeaturesInSep (sep, (Pointer) &fd, FindHighestFeatID);
+  return fd.highestID;
+}
+
+static void SfpAssignFeatIDs (
   SeqFeatPtr sfp,
   Pointer userdata
 )
@@ -176,32 +198,241 @@ static void SfpAssignCDSmRNAfeatureIDs (
   ObjectIdPtr  oip;
 
   if (sfp == NULL) return;
-  if (sfp->idx.subtype != FEATDEF_CDS && sfp->idx.subtype != FEATDEF_mRNA) return;
   fip = (FidDataPtr) userdata;
   if (fip == NULL) return;
 
   if (sfp->id.choice == 3) return;
   oip = ObjectIdNew ();
   if (oip == NULL) return;
+
+  (fip->highestID)++;
   oip->id = fip->highestID;
 
   sfp->id.value.ptrvalue = (Pointer) oip;
   sfp->id.choice = 3;
+}
+
+NLM_EXTERN void AssignFeatureIDs (
+  SeqEntryPtr sep
+)
+
+{
+  FidData  fd;
+
+  MemSet ((Pointer) &fd, 0, sizeof (FidData));
+  fd.highestID = 0;
+  fd.highestRef = 0;
+  VisitFeaturesInSep (sep, (Pointer) &fd, FindHighestFeatID);
+  VisitFeaturesInSep (sep, (Pointer) &fd, SfpAssignFeatIDs);
+}
+
+static void SfpOffsetFeatIDs (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  FidDataPtr   fip;
+  ObjectIdPtr  oip;
+
+  if (sfp == NULL) return;
+  fip = (FidDataPtr) userdata;
+  if (fip == NULL) return;
+
+  if (sfp->id.choice == 3) {
+    oip = (ObjectIdPtr) sfp->id.value.ptrvalue;
+    if (oip != NULL) {
+      if (oip->str == NULL) {
+        oip->id += fip->offset;
+      }
+    }
+  }
+}
+
+NLM_EXTERN void OffsetFeatureIDs (
+  SeqEntryPtr sep,
+  Int4 offset
+)
+
+{
+  FidData  fd;
+
+  MemSet ((Pointer) &fd, 0, sizeof (FidData));
+  fd.offset = offset;
+  VisitFeaturesInSep (sep, (Pointer) &fd, SfpOffsetFeatIDs);
+}
+
+static void SfpOffsetFeatIDXrefs (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  FidDataPtr      fip;
+  ObjectIdPtr     oip;
+  SeqFeatXrefPtr  xref;
+
+  if (sfp == NULL) return;
+  fip = (FidDataPtr) userdata;
+  if (fip == NULL) return;
+
+  for (xref = sfp->xref; xref != NULL; xref = xref->next) {
+    if (xref->id.choice != 3) continue;
+    oip = (ObjectIdPtr) xref->id.value.ptrvalue;
+    if (oip != NULL) {
+      if (oip->str == NULL) {
+        oip->id += fip->offset;
+      }
+    }
+  }
+}
+
+NLM_EXTERN void OffsetFeatureIDXrefs (
+  SeqEntryPtr sep,
+  Int4 offset
+)
+
+{
+  FidData  fd;
+
+  MemSet ((Pointer) &fd, 0, sizeof (FidData));
+  fd.offset = offset;
+  VisitFeaturesInSep (sep, (Pointer) &fd, SfpOffsetFeatIDXrefs);
+}
+
+static void SfpMakePairList (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  FidDataPtr   fip;
+  Int4         idx;
+  IdPairPtr    ipp;
+  ObjectIdPtr  oip;
+
+  if (sfp == NULL) return;
+  fip = (FidDataPtr) userdata;
+  if (fip == NULL) return;
+  if (fip->pairs == NULL) return;
+
+  if (sfp->id.choice != 3) return;
+  oip = (ObjectIdPtr) sfp->id.value.ptrvalue;
+  if (oip == NULL) return;
+
+  idx = fip->highestID;
+  ipp = &(fip->pairs [idx]);
 
   (fip->highestID)++;
+  ipp->before = oip->id;
+  ipp->after = fip->highestID;
+}
+
+static int LIBCALLBACK SortPairList (VoidPtr ptr1, VoidPtr ptr2)
+
+{
+  IdPairPtr  ipp1 = (IdPairPtr) ptr1;
+  IdPairPtr  ipp2 = (IdPairPtr) ptr2;
+
+  if (ipp1 == NULL || ipp2 == NULL) return 0;
+  if (ipp1->before > ipp2->before) return 1;
+  if (ipp1->before < ipp2->before) return -1;
+  return 0;
+}
+
+static Int4 LookupNewFeatID (
+  FidDataPtr fip,
+  Int4 before
+)
+
+{
+  IdPairPtr  ipp;
+  Int4       L;
+  Int4       mid;
+  Int4       R;
+
+  if (fip == NULL || fip->pairs == NULL || fip->count < 1) return 0;
+
+  L = 0;
+  R = fip->count - 1;
+  while (L < R) {
+    mid = (L + R) / 2;
+    ipp = &(fip->pairs [mid]);
+    if (ipp->before < before) {
+      L = mid + 1;
+    } else {
+      R = mid;
+    }
+  }
+
+  if (R < fip->count) {
+    ipp = &(fip->pairs [R]);
+    if (ipp->before == before) return ipp->after;
+  }
+
+  return 0;
+}
+
+static void SfpReassignPairList (
+  SeqFeatPtr sfp,
+  Pointer userdata
+)
+
+{
+  FidDataPtr      fip;
+  ObjectIdPtr     oip;
+  SeqFeatXrefPtr  xref;
+
+  if (sfp == NULL) return;
+  fip = (FidDataPtr) userdata;
+  if (fip == NULL) return;
+  if (fip->pairs == NULL) return;
+
+  if (sfp->id.choice == 3) {
+    oip = (ObjectIdPtr) sfp->id.value.ptrvalue;
+    if (oip != NULL) {
+      if (oip->str == NULL) {
+        oip->id = LookupNewFeatID (fip, oip->id);
+      }
+    }
+  }
+
+  for (xref = sfp->xref; xref != NULL; xref = xref->next) {
+    if (xref->id.choice != 3) continue;
+    oip = (ObjectIdPtr) xref->id.value.ptrvalue;
+    if (oip != NULL) {
+      if (oip->str == NULL) {
+        oip->id = LookupNewFeatID (fip, oip->id);
+      }
+    }
+  }
 }
 
-NLM_EXTERN void AssignCDSmRNAfeatureIDs (
+NLM_EXTERN void ReassignFeatureIDs (
   SeqEntryPtr sep
 )
 
 {
+  Int4     count;
   FidData  fd;
 
+  count = VisitFeaturesInSep (sep, NULL, NULL);
+  if (count < 1) return;
+
   MemSet ((Pointer) &fd, 0, sizeof (FidData));
-  fd.highestID = 1;
-  VisitFeaturesInSep (sep, (Pointer) &fd, FindHighestFeatureID);
-  VisitFeaturesInSep (sep, (Pointer) &fd, SfpAssignCDSmRNAfeatureIDs);
+  fd.highestID = 0;
+  fd.highestRef = 0;
+  fd.count = count;
+  fd.pairs = (IdPairPtr) MemNew (sizeof (IdPairData) * (count + 1));
+  if (fd.pairs == NULL) return;
+
+  VisitFeaturesInSep (sep, (Pointer) &fd, SfpMakePairList);
+
+  HeapSort (fd.pairs, (size_t) count, sizeof (IdPairData), SortPairList);
+
+  VisitFeaturesInSep (sep, (Pointer) &fd, SfpReassignPairList);
+
+  MemFree (fd.pairs);
 }
 
 typedef struct vcmdata {
@@ -368,7 +599,7 @@ NLM_EXTERN void LinkCDSmRNAbyOverlap (
 )
 
 {
-  AssignCDSmRNAfeatureIDs (sep);
+  AssignFeatureIDs (sep);
   VisitBioseqsInSep (sep, NULL, BspLinkCDSmRNAbyOverlap);
 }
 
@@ -515,97 +746,100 @@ static void BspLinkCDSmRNAbyProduct (
         if (cdna->idx.parenttype == OBJ_BIOSEQSET) {
           bssp = (BioseqSetPtr) cdna->idx.parentptr;
           if (bssp == NULL) continue;
-          if (bssp->_class != BioseqseqSet_class_nuc_prot) continue;
-          prot = NULL;
-          if (VisitBioseqsInSet (bssp, (Pointer) &prot, FindProtBsp) != 2) continue;
-          for (sip = prot->id; sip != NULL; sip = sip->next) {
-            MakeReversedSeqIdString (sip, buf, sizeof (buf) - 1);
-
-            /* binary search */
-
-            L = 0;
-            R = numcds - 1;
-            while (L < R) {
-              mid = (L + R) / 2;
-              odp = cdsarray [mid];
-              compare = StringCmp (odp->revstr, buf);
-              if (compare < 0) {
-                L = mid + 1;
-              } else {
-                R = mid;
-              }
-            }
-            odp = cdsarray [R];
-            if (odp != NULL && StringCmp (odp->revstr, buf) == 0) {
-              cds = odp->sfp;
-              if (cds == NULL) continue;
-
-              /* make reciprocal feature ID xrefs */
-
-              if (cds->id.choice == 3) {
-                oip = (ObjectIdPtr) cds->id.value.ptrvalue;
-                if (oip != NULL && oip->str == NULL) {
-                  id = oip->id;
-                  if (id > 0) {
-                    for (xref = mrna->xref; xref != NULL && xref->id.choice != 3; xref = xref->next) continue;
-                    if (xref != NULL) {
-                      oip = (ObjectIdPtr) xref->id.value.ptrvalue;
-                      if (oip != NULL) {
-                        if (oip->str != NULL) {
-                          oip->str = MemFree (oip->str);
-                        }
-                        oip->id = id;
-                      }
-                    } else {
-                      xref = SeqFeatXrefNew ();
-                      if (xref != NULL) {
-                        oip = ObjectIdNew ();
-                        if (oip != NULL) {
-                          oip->id = id;
-                          xref->id.choice = 3;
-                          xref->id.value.ptrvalue = (Pointer) oip;
-                          xref->next = mrna->xref;
-                          mrna->xref = xref;
-                        }
-                      }
-                    }
-                  }
-                }
-              }
-
-              if (mrna->id.choice == 3) {
-                oip = (ObjectIdPtr) mrna->id.value.ptrvalue;
-                if (oip != NULL && oip->str == NULL) {
-                  id = oip->id;
-                  if (id > 0) {
-                    for (xref = cds->xref; xref != NULL && xref->id.choice != 3; xref = xref->next) continue;
-                    if (xref != NULL) {
-                      oip = (ObjectIdPtr) xref->id.value.ptrvalue;
-                      if (oip != NULL) {
-                        if (oip->str != NULL) {
-                          oip->str = MemFree (oip->str);
-                        }
-                        oip->id = id;
-                      }
-                    } else {
-                      xref = SeqFeatXrefNew ();
-                      if (xref != NULL) {
-                        oip = ObjectIdNew ();
-                        if (oip != NULL) {
-                          oip->id = id;
-                          xref->id.choice = 3;
-                          xref->id.value.ptrvalue = (Pointer) oip;
-                          xref->next = cds->xref;
-                          cds->xref = xref;
-                        }
-                      }
-                    }
-                  }
-                }
-              }
-            }
+          if (bssp->_class == BioseqseqSet_class_nuc_prot) {
+			prot = NULL;
+			if (VisitBioseqsInSet (bssp, (Pointer) &prot, FindProtBsp) == 2) {
+			  for (sip = prot->id; sip != NULL; sip = sip->next) {
+				MakeReversedSeqIdString (sip, buf, sizeof (buf) - 1);
+	
+				/* binary search */
+	
+				L = 0;
+				R = numcds - 1;
+				while (L < R) {
+				  mid = (L + R) / 2;
+				  odp = cdsarray [mid];
+				  compare = StringCmp (odp->revstr, buf);
+				  if (compare < 0) {
+					L = mid + 1;
+				  } else {
+					R = mid;
+				  }
+				}
+				odp = cdsarray [R];
+				if (odp != NULL && StringCmp (odp->revstr, buf) == 0) {
+				  cds = odp->sfp;
+				  if (cds == NULL) continue;
+	
+				  /* make reciprocal feature ID xrefs */
+	
+				  if (cds->id.choice == 3) {
+					oip = (ObjectIdPtr) cds->id.value.ptrvalue;
+					if (oip != NULL && oip->str == NULL) {
+					  id = oip->id;
+					  if (id > 0) {
+						for (xref = mrna->xref; xref != NULL && xref->id.choice != 3; xref = xref->next) continue;
+						if (xref != NULL) {
+						  oip = (ObjectIdPtr) xref->id.value.ptrvalue;
+						  if (oip != NULL) {
+							if (oip->str != NULL) {
+							  oip->str = MemFree (oip->str);
+							}
+							oip->id = id;
+						  }
+						} else {
+						  xref = SeqFeatXrefNew ();
+						  if (xref != NULL) {
+							oip = ObjectIdNew ();
+							if (oip != NULL) {
+							  oip->id = id;
+							  xref->id.choice = 3;
+							  xref->id.value.ptrvalue = (Pointer) oip;
+							  xref->next = mrna->xref;
+							  mrna->xref = xref;
+							}
+						  }
+						}
+					  }
+					}
+				  }
+	
+				  if (mrna->id.choice == 3) {
+					oip = (ObjectIdPtr) mrna->id.value.ptrvalue;
+					if (oip != NULL && oip->str == NULL) {
+					  id = oip->id;
+					  if (id > 0) {
+						for (xref = cds->xref; xref != NULL && xref->id.choice != 3; xref = xref->next) continue;
+						if (xref != NULL) {
+						  oip = (ObjectIdPtr) xref->id.value.ptrvalue;
+						  if (oip != NULL) {
+							if (oip->str != NULL) {
+							  oip->str = MemFree (oip->str);
+							}
+							oip->id = id;
+						  }
+						} else {
+						  xref = SeqFeatXrefNew ();
+						  if (xref != NULL) {
+							oip = ObjectIdNew ();
+							if (oip != NULL) {
+							  oip->id = id;
+							  xref->id.choice = 3;
+							  xref->id.value.ptrvalue = (Pointer) oip;
+							  xref->next = cds->xref;
+							  cds->xref = xref;
+							}
+						  }
+						}
+					  }
+					}
+				  }
+				}
+			  }
+			}
           }
         }
+        BioseqUnlock (cdna);
       }
     }
 
@@ -626,7 +860,7 @@ NLM_EXTERN void LinkCDSmRNAbyProduct (
 )
 
 {
-  AssignCDSmRNAfeatureIDs (sep);
+  AssignFeatureIDs (sep);
   VisitBioseqsInSep (sep, NULL, BspLinkCDSmRNAbyProduct);
 }
 
diff --git a/api/sqnutils.h b/api/sqnutils.h
index 279fa9c1..472da29a 100644
--- a/api/sqnutils.h
+++ b/api/sqnutils.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   9/2/97
 *
-* $Revision: 6.134 $
+* $Revision: 6.140 $
 *
 * File Description: 
 *
@@ -233,9 +233,15 @@ NLM_EXTERN void ResynchPeptidePartials (SeqFeatPtr sfp, Pointer userdata);
 NLM_EXTERN void ClearFeatIDs (SeqFeatPtr sfp);
 NLM_EXTERN void ClearFeatIDXrefs (SeqFeatPtr sfp);
 
-NLM_EXTERN void ClearCDSmRNAfeatureIDs (SeqEntryPtr sep);
+NLM_EXTERN void ClearFeatureIDs (SeqEntryPtr sep);
+NLM_EXTERN Int4 FindHighestFeatureID (SeqEntryPtr sep);
 
-NLM_EXTERN void AssignCDSmRNAfeatureIDs (SeqEntryPtr sep);
+NLM_EXTERN void AssignFeatureIDs (SeqEntryPtr sep);
+
+NLM_EXTERN void OffsetFeatureIDs (SeqEntryPtr sep, Int4 offset);
+NLM_EXTERN void OffsetFeatureIDXrefs (SeqEntryPtr sep, Int4 offset);
+
+NLM_EXTERN void ReassignFeatureIDs (SeqEntryPtr sep);
 
 NLM_EXTERN void LinkCDSmRNAbyOverlap (SeqEntryPtr sep);
 
@@ -264,6 +270,8 @@ NLM_EXTERN CharPtr SqnTagFind (SqnTagPtr stp, CharPtr tag);
 NLM_EXTERN void ReadTechFromString (CharPtr str, MolInfoPtr mip);
 NLM_EXTERN void ReadCompletenessFromString (CharPtr str, MolInfoPtr mip);
 
+extern Boolean StringsAreEquivalent (CharPtr str1, CharPtr str2);
+
 /* functions to extract BioSource, MolInfo, and Bioseq information from parsed titles */
 
 NLM_EXTERN BioSourcePtr ParseTitleIntoBioSource (
@@ -312,6 +320,15 @@ NLM_EXTERN UserObjectPtr ParseTitleIntoTpaAssembly (
   UserObjectPtr uop
 );
 
+/* structured comment user object for flatfile presentation */
+
+NLM_EXTERN UserObjectPtr ParseStringIntoStructuredComment (
+  UserObjectPtr uop,
+  CharPtr str,
+  CharPtr prefix,
+  CharPtr suffix
+);
+
 /* UseLocalAsnloadDataAndErrMsg transiently sets paths to asnload, data, and errmsg
   if they are packaged in the same directory as the executing program. */
 
@@ -624,6 +641,10 @@ NLM_EXTERN Int4 VisitUserFieldsInUop (UserObjectPtr uop, Pointer userdata, Visit
 typedef void (*VisitUserObjectFunc) (UserObjectPtr uop, Pointer userdata);
 NLM_EXTERN Int4 VisitUserObjectsInUop (UserObjectPtr uop, Pointer userdata, VisitUserObjectFunc callback);
 
+/* explores sub UserObjects including "CombinedFeatureUserObjects" and finds by label  */
+
+NLM_EXTERN UserObjectPtr FindUopByTag (UserObjectPtr top, CharPtr tag);
+
 /* creates "CombinedFeatureUserObjects" sfp->ext to combine two user objects */
 
 NLM_EXTERN UserObjectPtr CombineUserObjects (UserObjectPtr origuop, UserObjectPtr newuop);
diff --git a/api/subutil.c b/api/subutil.c
index 07588e4d..890f700f 100644
--- a/api/subutil.c
+++ b/api/subutil.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 11/3/93
 *
-* $Revision: 6.62 $
+* $Revision: 6.64 $
 *
 * File Description: Utilities for creating ASN.1 submissions
 *
@@ -40,6 +40,12 @@
 *
 *
 * $Log: subutil.c,v $
+* 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
 *
@@ -2543,6 +2549,51 @@ NLM_EXTERN Boolean SetGeneticCodeForEntry (
 	return TRUE;
 }
 
+static void SubExpandSemicolonedKeyword (ValNodePtr vnp)
+
+{
+  Char        ch;
+  ValNodePtr  lastvnp;
+  ValNodePtr  newvnp;
+  ValNodePtr  nextvnp;
+  CharPtr     ptr;
+  CharPtr     str;
+  CharPtr     tmp;
+
+  if (vnp == NULL) return;
+  str = (CharPtr) vnp->data.ptrvalue;
+  if (StringHasNoText (str)) return;
+  if (StringChr (str, ';') == NULL && StringChr (str, ',') == NULL) return;
+
+  lastvnp = vnp;
+  nextvnp = vnp->next;
+
+  tmp = StringSave (str);
+  str = tmp;
+  vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
+  while (StringDoesHaveText (str)) {
+    ptr = str;
+    ch = *ptr;
+    while (ch != '\0' && ch != ',' && ch != ';') {
+      ptr++;
+      ch = *ptr;
+    }
+    if (ptr != NULL && *ptr != '\0') {
+      *ptr = '\0';
+      ptr++;
+    }
+    TrimSpacesAroundString (str);
+    newvnp = ValNodeCopyStr (NULL, 0, str);
+    if (newvnp != NULL) {
+      newvnp->next = nextvnp;
+      lastvnp->next = newvnp;
+      lastvnp = newvnp;
+    }
+    str = ptr;
+  }
+  MemFree (tmp);
+}
+
 NLM_EXTERN Boolean AddGenBankBlockToEntry (
 	NCBISubPtr submission,
 	SeqEntryPtr entry ,
@@ -2552,7 +2603,7 @@ NLM_EXTERN Boolean AddGenBankBlockToEntry (
 	CharPtr keyword2 ,
 	CharPtr keyword3 )
 {
-	ValNodePtr vnp;
+	ValNodePtr vnp, tmp;
 	GBBlockPtr gbp;
 
 	if ((submission == NULL) || (entry == NULL))
@@ -2570,6 +2621,10 @@ NLM_EXTERN Boolean AddGenBankBlockToEntry (
 	ValNodeCopyStr(&gbp->keywords, 0, keyword2);
 	ValNodeCopyStr(&gbp->keywords, 0, keyword3);
 
+	for (tmp = gbp->keywords; tmp != NULL; tmp = tmp->next) {
+		SubExpandSemicolonedKeyword (tmp);
+	}
+
 	return TRUE;
 }
 
@@ -5399,3 +5454,54 @@ NLM_EXTERN UserObjectPtr CreateFeatureFetchPolicyUserObject (
   return uop;
 }
 
+/* structured comment user object for flatfile presentation */
+
+NLM_EXTERN UserObjectPtr CreateStructuredCommentUserObject (void)
+
+{
+  ObjectIdPtr    oip;
+  UserObjectPtr  uop;
+
+  uop = UserObjectNew ();
+  oip = ObjectIdNew ();
+  oip->str = StringSave ("StructuredComment");
+  uop->type = oip;
+
+  return uop;
+}
+
+NLM_EXTERN void AddItemStructuredCommentUserObject (
+  UserObjectPtr uop,
+  CharPtr field,
+  CharPtr str
+)
+
+{
+  UserFieldPtr  curr;
+  ObjectIdPtr   oip;
+  UserFieldPtr  prev = NULL;
+
+  if (uop == NULL || StringHasNoText (field) || StringHasNoText (str)) return;
+  oip = uop->type;
+  if (oip == NULL || StringICmp (oip->str, "StructuredComment") != 0) return;
+
+  for (curr = uop->data; curr != NULL; curr = curr->next) {
+    prev = curr;
+  }
+
+  curr = UserFieldNew ();
+  oip = ObjectIdNew ();
+  oip->str = StringSave (field);
+  curr->label = oip;
+  curr->choice = 1; /* visible string */
+  curr->data.ptrvalue = (Pointer) StringSave (str);
+
+  /* link curator at end of list */
+
+  if (prev != NULL) {
+    prev->next = curr;
+  } else {
+    uop->data = curr;
+  }
+}
+
diff --git a/api/subutil.h b/api/subutil.h
index eaba6f79..b4f1ba9d 100644
--- a/api/subutil.h
+++ b/api/subutil.h
@@ -31,7 +31,7 @@
 *   
 * Version Creation Date: 11/3/93
 *
-* $Revision: 6.53 $
+* $Revision: 6.54 $
 *
 * File Description: Utilities for creating ASN.1 submissions
 *
@@ -42,6 +42,9 @@
 *
 *
 * $Log: subutil.h,v $
+* Revision 6.54  2006/05/05 19:49:40  kans
+* added StructuredComment user object creation functions
+*
 * Revision 6.53  2006/02/06 19:00:15  kans
 * added CreateFeatureFetchPolicyUserObject
 *
@@ -1708,6 +1711,16 @@ NLM_EXTERN UserObjectPtr CreateFeatureFetchPolicyUserObject (
   CharPtr policy
 );
 
+/* structured comment user object for flatfile presentation */
+
+NLM_EXTERN UserObjectPtr CreateStructuredCommentUserObject (void);
+
+NLM_EXTERN void AddItemStructuredCommentUserObject (
+  UserObjectPtr uop,
+  CharPtr field,
+  CharPtr str
+);
+
 
 #ifdef __cplusplus
 }
diff --git a/api/tofasta.c b/api/tofasta.c
index dcbbb7d3..19dd1daf 100644
--- a/api/tofasta.c
+++ b/api/tofasta.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 7/12/91
 *
-* $Revision: 6.150 $
+* $Revision: 6.152 $
 *
 * File Description:  various sequence objects to fasta output
 *
@@ -39,6 +39,12 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: tofasta.c,v $
+* 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
 *
@@ -3336,6 +3342,65 @@ static void FindNMFeats (SeqFeatPtr sfp, Pointer userdata)
   }
 }
 
+static Boolean IsFlyCG (CharPtr str)
+
+{
+  Char  ch;
+
+  if (StringHasNoText (str)) return FALSE;
+
+  ch = *str;
+  if (ch != 'C') return FALSE;
+  str++;
+  ch = *str;
+  if (ch != 'G') return FALSE;
+  str++;
+  ch = *str;
+  while (IS_DIGIT (ch)) {
+    str++;
+    ch = *str;
+  }
+  if (ch != '-') return FALSE;
+  str++;
+  ch = *str;
+  if (ch != 'P') return FALSE;
+  str++;
+  ch = *str;
+  if (IS_ALPHA (ch)) {
+    str++;
+    ch = *str;
+    if (ch == '\0' || ch == ' ' || ch == ',' || ch == ';') return TRUE;
+  }
+
+  return FALSE;
+}
+
+static void ReplaceFlyDashPwithDashR (CharPtr str)
+
+{
+  Char     ch;
+  CharPtr  ptr;
+
+  while (StringDoesHaveText (str)) {
+    ch = *str;
+    while (IS_WHITESP (ch)) {
+      str++;
+      ch = *str;
+    }
+    if (IsFlyCG (str)) {
+      ptr = StringStr (str, "-P");
+      if (ptr != NULL) {
+        ptr [1] = 'R';
+        return;
+      }
+    }
+    while (ch != '\0' && (! IS_WHITESP (ch))) {
+      str++;
+      ch = *str;
+    }
+  }
+}
+
 static CharPtr FindNMDefLine (BioseqPtr bsp)
 
 {
@@ -3377,6 +3442,10 @@ static CharPtr FindNMDefLine (BioseqPtr bsp)
     }
   }
   if (is_refseq) {
+    /* special case Drosophila RefSeq NM titles */
+    if (StringICmp (orp->taxname, "Drosophila melanogaster") == 0) {
+      ReplaceFlyDashPwithDashR (buf);
+    }
     ptr = StringStr (buf, "isoform ");
     if (ptr != NULL) {
       *ptr = '\0';
@@ -4928,8 +4997,10 @@ static Boolean AddNcTitles (GatherObjectPtr gop)
   BioseqPtr     bsp;
   Char          buf [512];
   Boolean       is_nc;
+  /*
   MolInfoPtr    mip;
   SeqDescrPtr   sdp;
+  */
   SeqIdPtr      sip;
   CharPtr       str;
   TextSeqIdPtr  tsip;
@@ -4962,6 +5033,7 @@ static Boolean AddNcTitles (GatherObjectPtr gop)
     }
   }
 
+  /*
   for (sdp = bsp->descr; sdp != NULL; sdp = sdp->next) {
     if (sdp->choice == Seq_descr_molinfo) {
       mip = (MolInfoPtr) sdp->data.ptrvalue;
@@ -4972,6 +5044,7 @@ static Boolean AddNcTitles (GatherObjectPtr gop)
       }
     }
   }
+  */
 
   return TRUE;
 }
diff --git a/api/valid.c b/api/valid.c
index 0a8ecae1..66191353 100644
--- a/api/valid.c
+++ b/api/valid.c
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 1/1/94
 *
-* $Revision: 6.726 $
+* $Revision: 6.755 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -39,6 +39,93 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: valid.c,v $
+* Revision 6.755  2006/05/04 20:31:46  kans
+* ERR_SEQ_FEAT_ErroneousException test for unclassified transcription discrepancy that should be mismatches in transcription
+*
+* Revision 6.754  2006/05/04 20:13:15  kans
+* added ERR_SEQ_FEAT_ErroneousException - used for unclassified translation discrepancy that should be mismatches in translation
+*
+* Revision 6.753  2006/04/24 16:28:10  kans
+* InvalidInferenceValue dropped to warning
+*
+* Revision 6.752  2006/04/21 17:59:18  kans
+* added ignoreExceptions flag to vsp - for MrnaTransCheck and CdTransCheck
+*
+* Revision 6.751  2006/04/17 18:05:09  kans
+* added ERR_SEQ_DESCR_BadPunctuation
+*
+* Revision 6.750  2006/04/14 20:35:40  kans
+* ERR_SEQ_FEAT_UnindexedFeature also reports bioseq identifiers
+*
+* Revision 6.749  2006/04/14 20:18:23  kans
+* CDSmRNAmismatch, CDSwithMultipleMRNAs and CDSwithNoMRNAOverlap tests in ValidateCDSmRNAmatch suppressed if genbank
+*
+* Revision 6.748  2006/04/14 17:06:00  kans
+* ERR_SEQ_FEAT_FeatureLocationIsGi0 prints IDs of Bioseq
+*
+* Revision 6.747  2006/04/14 16:25:35  kans
+* added ERR_SEQ_FEAT_PseudoCdsHasProtXref
+*
+* Revision 6.746  2006/04/12 14:24:02  kans
+* CDSmRNArange and mRNAgeneRange reduced to WARNING level
+*
+* Revision 6.745  2006/04/11 18:04:08  kans
+* IdXrefsNotReciprocal also tests MrnaProteinLink user object against cds->product
+*
+* Revision 6.744  2006/04/11 16:16:57  kans
+* raised obsolete experimental evidence qualifier set message to error
+*
+* Revision 6.743  2006/04/10 15:23:24  kans
+* CDSsLinkedToDifferentMRNAs used to suppress duplicate feature message on otherwise identical CDSs
+*
+* Revision 6.742  2006/04/10 14:56:57  kans
+* report obsolete sfp->exp_ev only if no gi present
+*
+* Revision 6.741  2006/04/07 19:49:06  kans
+* allow 5 letter + 7 digit accessions
+*
+* Revision 6.740  2006/04/06 18:43:50  kans
+* report ERR_SEQ_FEAT_InvalidInferenceValue for new records with only sfp->exp_ev set
+*
+* Revision 6.739  2006/04/05 15:04:11  kans
+* ERR_SEQ_FEAT_BadTrnaAA not reported for pseudo tRNA
+*
+* Revision 6.738  2006/03/30 19:24:56  kans
+* made CheckDeltaForReuse more efficient
+*
+* Revision 6.737  2006/03/27 18:27:01  kans
+* biop->origin == ORG_MUT no longer sets bvsp->is_artificial
+*
+* Revision 6.736  2006/03/27 14:52:34  kans
+* ribosomal rna abutting test now handles same rRNA subtype split across segmented parts
+*
+* Revision 6.735  2006/03/24 18:57:26  kans
+* if estimated_length unknown do not complain about different dash count
+*
+* Revision 6.734  2006/03/24 18:48:05  kans
+* added ERR_SEQ_FEAT_GapFeatureProblem
+*
+* Revision 6.733  2006/03/17 16:50:41  kans
+* added INTERNAL_SPACER_X to ITS-rRNA adjacency tests
+*
+* Revision 6.732  2006/03/10 13:38:48  kans
+* raised DeltaComponentIsGi0 and FeatureLocationIsGi0 from ERROR to REJECT
+*
+* Revision 6.731  2006/03/09 13:55:35  kans
+* replace qualifier can have * for termination in protein sequence
+*
+* Revision 6.730  2006/03/08 19:42:27  kans
+* do not call BioseqLockById on 0 or negative gi number
+*
+* Revision 6.729  2006/03/07 21:34:28  kans
+* checks for gi 0 now also check for negative value
+*
+* Revision 6.728  2006/03/07 21:15:59  kans
+* added ERR_SEQ_INST_DeltaComponentIsGi0 and ERR_SEQ_FEAT_FeatureLocationIsGi0
+*
+* Revision 6.727  2006/03/07 17:00:36  kans
+* ERR_SEQ_FEAT_PseudoCdsViaGeneHasProduct and ERR_SEQ_FEAT_PseudoCdsHasProduct are now ERROR
+*
 * Revision 6.726  2006/02/27 17:49:34  kans
 * added adjusted for low-quality genome exception for RefSeq models
 *
@@ -2464,6 +2551,7 @@ NLM_EXTERN void ValidStructClear (ValidStructPtr vsp)
   Boolean         validateIDSet;
   Boolean         seqSubmitParent;
   Boolean         justShowAccession;
+  Boolean         ignoreExceptions;
   Int2            validationLimit;
   ValidErrorFunc  errfunc;
   Pointer         userdata;
@@ -2498,6 +2586,7 @@ NLM_EXTERN void ValidStructClear (ValidStructPtr vsp)
   validateIDSet = vsp->validateIDSet;
   seqSubmitParent = vsp->seqSubmitParent;
   justShowAccession = vsp->justShowAccession;
+  ignoreExceptions = vsp->ignoreExceptions;
   validationLimit = vsp->validationLimit;
   errfunc = vsp->errfunc;
   userdata = vsp->userdata;
@@ -2529,6 +2618,7 @@ NLM_EXTERN void ValidStructClear (ValidStructPtr vsp)
   vsp->validateIDSet = validateIDSet;
   vsp->seqSubmitParent = seqSubmitParent;
   vsp->justShowAccession = justShowAccession;
+  vsp->ignoreExceptions = ignoreExceptions;
   vsp->validationLimit = validationLimit;
   vsp->errfunc = errfunc;
   vsp->userdata = userdata;
@@ -2810,7 +2900,8 @@ static CharPtr err1Label [] = {
   "LeadingX",
   "InternalNsInSeqRaw",
   "InternalNsAdjacentToGap",
-  "CaseDifferenceInSeqID"
+  "CaseDifferenceInSeqID",
+  "DeltaComponentIsGi0"
 };
 
 static CharPtr err2Label [] = {
@@ -2850,7 +2941,8 @@ static CharPtr err2Label [] = {
   "FastaBracketTitle",
   "MissingText",
   "BadCollectionDate",
-  "BadPCRPrimerSequence"
+  "BadPCRPrimerSequence",
+  "BadPunctuation"
 };
 
 static CharPtr err3Label [] = {
@@ -3005,7 +3097,11 @@ static CharPtr err5Label [] = {
   "FeatureRefersToAccession",
   "SelfReferentialProduct",
   "ITSdoesNotAbutRRNA",
-  "FeatureSeqIDCaseDifference"
+  "FeatureSeqIDCaseDifference",
+  "FeatureLocationIsGi0",
+  "GapFeatureProblem",
+  "PseudoCdsHasProtXref",
+  "ErroneousException"
 };
 
 static CharPtr err6Label [] = {
@@ -3670,7 +3766,12 @@ static Boolean Valid1GatherProc (GatherContextPtr gcp)
           }
           if (vsp->useSeqMgrIndexes) {
             if (SeqMgrGetDesiredFeature (gcp->entityID, NULL, 0, 0, sfp, &context) == NULL) {
-              ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_UnindexedFeature, "Feature is not indexed");
+              StringCpy (buf, "?");
+              bsp = vsp->bsp;
+              if (bsp != NULL) {
+                SeqIdWrite (bsp->id, buf, PRINTID_FASTA_LONG, sizeof (buf) - 1);
+              }
+              ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_UnindexedFeature, "Feature is not indexed on Bioseq %s", buf);
             } else {
               bsp = BioseqFindFromSeqLoc (sfp->location);
               if (bsp != NULL) {
@@ -6058,6 +6159,7 @@ static void CheckDeltaForReuse (ValidStructPtr vsp, GatherContextPtr gcp, Bioseq
 {
   Char          buf [80];
   ValNodePtr    head = NULL;
+  ValNodePtr    last = NULL;
   ReuseDataPtr  lastrdp = NULL;
   ReuseDataPtr  rdp;
   SeqIntPtr     sintp;
@@ -6082,7 +6184,11 @@ static void CheckDeltaForReuse (ValidStructPtr vsp, GatherContextPtr gcp, Bioseq
     rdp->seqidstr = StringSave (buf);
     rdp->from = sintp->from;
     rdp->to = sintp->to;
-    ValNodeAddPointer (&head, 0, (Pointer) rdp);
+    vnp = ValNodeAddPointer (&last, 0, (Pointer) rdp);
+    if (head == NULL) {
+      head = vnp;
+    }
+    last = vnp;
   }
 
   if (head == NULL) return;
@@ -6307,6 +6413,8 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
                    (sip1->choice == SEQID_GENBANK || sip1->choice == SEQID_EMBL || sip1->choice == SEQID_DDBJ)) {
         } else if (numletters == 4 && numdigits == 9 && ISA_na (bsp->mol) &&
                    (sip1->choice == SEQID_GENBANK || sip1->choice == SEQID_EMBL || sip1->choice == SEQID_DDBJ)) {
+        } else if (numletters == 5 && numdigits == 7 && ISA_na (bsp->mol) &&
+                   (sip1->choice == SEQID_GENBANK || sip1->choice == SEQID_EMBL || sip1->choice == SEQID_DDBJ)) {
         } else {
           ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_BadSeqIdFormat, "Bad accession %s", tsip->accession);
         }
@@ -7047,6 +7155,10 @@ static void ValidateBioseqInst (GatherContextPtr gcp)
         switch (vnp->choice) {
         case 1:                /* SeqLocPtr */
           slp = (SeqLocPtr) (vnp->data.ptrvalue);
+          sip3 = SeqLocId (slp);
+          if (sip3 != NULL && sip3->choice == SEQID_GI && sip3->data.intvalue <= 0) {
+            ValidErr (vsp, SEV_REJECT, ERR_SEQ_INST_DeltaComponentIsGi0, "Delta component is gi|0");
+          }
           len2 = SeqLocLen (slp);
           if (len2 < 0)
             ValidErr (vsp, SEV_ERROR, ERR_SEQ_INST_SeqDataLenWrong, "-1 length on seq-loc of delta seq_ext");
@@ -9384,7 +9496,7 @@ static Boolean ValidateSeqDescrCommon (ValNodePtr sdp, BioseqValidStrPtr bvsp, V
   ValNodePtr      vnp, vnp2;
   OrgRefPtr       this_org = NULL, that_org = NULL;
   int             tmpval;
-  Char            buf1[20], buf2[20];
+  Char            buf1[20], buf2[20], ch;
   EMBLBlockPtr    ebp;
   GBBlockPtr      gbp;
   ValNodePtr      keywords = NULL;
@@ -9400,6 +9512,7 @@ static Boolean ValidateSeqDescrCommon (ValNodePtr sdp, BioseqValidStrPtr bvsp, V
   Boolean         tpa_inf;
   BioseqPtr       bsp;
   DatePtr         dp;
+  size_t          len;
   SeqMgrFeatContext  fcontext;
   static char    *badmod = "Inconsistent GIBB-mod [%d] and [%d]";
 
@@ -9660,6 +9773,21 @@ static Boolean ValidateSeqDescrCommon (ValNodePtr sdp, BioseqValidStrPtr bvsp, V
         ValidErr (vsp, SEV_ERROR, ERR_SEQ_DESCR_MultipleTitles, "Undesired multiple title descriptors");
       }
     }
+    len = StringLen (str);
+    if (len > 4) {
+      ch = str [len - 1];
+      while (ch == ' ' && len > 4) {
+        len--;
+        ch = str [len - 1];
+      }
+      if (ch == '.' && len > 4) {
+        len--;
+        ch = str [len - 1];
+      }
+      if (ch == '.' || ch == ',' || ch == ';' || ch == ':') {
+        ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadPunctuation, "Title descriptor ends in bad punctuation");
+      }
+    }
     break;
   case Seq_descr_name:
     str = (CharPtr) vnp->data.ptrvalue;
@@ -10413,33 +10541,68 @@ static Boolean IdXrefsAreReciprocal (
   return FALSE;
 }
 
-static Boolean IdXrefsNotReciprocal (
+static Int2 IdXrefsNotReciprocal (
   SeqFeatPtr cds,
   SeqFeatPtr mrna
 )
 
 {
-  SeqFeatXrefPtr  xref;
+  Int4            giu = 0, gip = 0;
   SeqFeatPtr      matchsfp;
+  ObjectIdPtr     oip;
+  SeqIdPtr        sip;
+  CharPtr         tmp;
+  UserFieldPtr    ufp;
+  UserObjectPtr   uop;
+  SeqFeatXrefPtr  xref;
 
-  if (cds == NULL || mrna == NULL) return FALSE;
-  if (cds->id.choice != 3 || mrna->id.choice != 3) return FALSE;
+  if (cds == NULL || mrna == NULL) return 0;
+  if (cds->id.choice != 3 || mrna->id.choice != 3) return 0;
 
   for (xref = cds->xref; xref != NULL; xref = xref->next) {
     if (xref->id.choice != 0) {
       matchsfp = SeqMgrGetFeatureByFeatID (cds->idx.entityID, NULL, NULL, xref, NULL);
-      if (matchsfp != mrna) return TRUE;
+      if (matchsfp != mrna) return 1;
     }
   }
 
   for (xref = mrna->xref; xref != NULL; xref = xref->next) {
     if (xref->id.choice != 0) {
       matchsfp = SeqMgrGetFeatureByFeatID (mrna->idx.entityID, NULL, NULL, xref, NULL);
-      if (matchsfp != cds) return TRUE;
+      if (matchsfp != cds) return 1;
     }
   }
 
-  return FALSE;
+  if (cds->product == NULL) return 0;
+  if (mrna->ext == NULL) return 0;
+  uop = FindUopByTag (mrna->ext, "MrnaProteinLink");
+  if (uop == NULL) return 0;
+  sip = SeqLocId (cds->product);
+  if (sip == NULL) return 0;
+  if (sip->choice == SEQID_GI) {
+    gip = (Int4) sip->data.intvalue;
+  } else {
+    gip = GetGIForSeqId (sip);
+  }
+  if (gip == 0) return 0;
+  ufp = uop->data;
+  if (ufp == NULL || ufp->choice != 1) return 0;
+  oip = ufp->label;
+  if (oip == NULL || StringICmp (oip->str, "protein seqID") != 0) return 0;
+  tmp = (CharPtr) ufp->data.ptrvalue;
+  if (StringHasNoText (tmp)) return 0;
+  sip = MakeSeqID (tmp);
+  if (sip == NULL) return 0;
+  if (sip->choice == SEQID_GI) {
+    giu = (Int4) sip->data.intvalue;
+  } else {
+    giu = GetGIForSeqId (sip);
+  }
+  SeqIdFree (sip);
+  if (giu == 0) return 0;
+  if (gip != giu) return 2;
+
+  return 0;
 }
 
 static Boolean LIBCALLBACK FindSingleMrnaProc (
@@ -10538,10 +10701,12 @@ static void ValidateCDSmRNAmatch (
   Boolean            goOn, pseudo;
   GeneRefPtr         grp;
   Int2               i, j, k, numfeats, tmpnumcds, tmpnummrna, count;
+  Boolean            is_genbank = FALSE;
   LpData             ld;
   Int4               num_repeat_regions;
   Uint2              olditemtype = 0;
   Uint2              olditemid = 0;
+  Int2               recip;
   VoidPtr            repeat_region_array;
   SeqFeatPtr         rpt_region;
   ErrSev             sev = /* SEV_INFO */ SEV_WARNING;
@@ -10564,14 +10729,16 @@ static void ValidateCDSmRNAmatch (
   }
   */
 
-  repeat_region_array = SeqMgrBuildFeatureIndex (bsp, &num_repeat_regions, 0, FEATDEF_repeat_region);
-
   for (sip = bsp->id; sip != NULL; sip = sip->next) {
     if (sip->choice == SEQID_OTHER) {
       sev = SEV_WARNING;
+    } else if (sip->choice == SEQID_GENBANK) {
+      is_genbank = TRUE;
     }
   }
 
+  repeat_region_array = SeqMgrBuildFeatureIndex (bsp, &num_repeat_regions, 0, FEATDEF_repeat_region);
+
   if (numgene > 0 && numcds > 0 && nummrna > 0) {
     numfeats = numcds + nummrna;
     head = (GmcDataPtr) MemNew (sizeof (GmcData) * (size_t) (numfeats + 1));
@@ -10613,7 +10780,7 @@ static void ValidateCDSmRNAmatch (
               tmpnummrna++;
             }
           }
-          if (tmpnumcds > 0 && tmpnummrna > 1 && tmpnumcds != tmpnummrna) {
+          if (tmpnumcds > 0 && tmpnummrna > 1 && tmpnumcds != tmpnummrna && (! is_genbank)) {
 
             if (gcp != NULL) {
               gcp->itemID = gene->idx.itemID;
@@ -10677,7 +10844,8 @@ static void ValidateCDSmRNAmatch (
           if (vdp != NULL) {
             vdp->accounted_for = TRUE;
             goOn = TRUE;
-            if (IdXrefsNotReciprocal (sfp, ld.mrna)) {
+            recip = IdXrefsNotReciprocal (sfp, ld.mrna);
+            if (recip == 1) {
               if (gcp != NULL) {
                 gcp->itemID = sfp->idx.itemID;
                 gcp->thistype = OBJ_SEQFEAT;
@@ -10685,6 +10853,14 @@ static void ValidateCDSmRNAmatch (
               vsp->descr = NULL;
               vsp->sfp = sfp;
               ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_SeqFeatXrefProblem, "CDS/mRNA unambiguous pair have erroneous cross-references");
+            } else if (recip == 2) {
+              if (gcp != NULL) {
+                gcp->itemID = ld.mrna->idx.itemID;
+                gcp->thistype = OBJ_SEQFEAT;
+              }
+              vsp->descr = NULL;
+              vsp->sfp = ld.mrna;
+              ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_SeqFeatXrefProblem, "MrnaProteinLink inconsistent with feature ID cross-references");
             }
           }
         } else {
@@ -10698,7 +10874,7 @@ static void ValidateCDSmRNAmatch (
   }
 
   sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &fcontext);
-  while (sfp != NULL) {
+  while (sfp != NULL && (! is_genbank)) {
     vdp = (VvmDataPtr) sfp->idx.scratch;
     if (vdp != NULL) {
       count = vdp->num_mrnas;
@@ -10857,6 +11033,38 @@ static Int2 WhichRNA (SeqFeatPtr sfp)
   return 0;
 }
 
+static Boolean CDSsLinkedToDifferentMRNAs (SeqFeatPtr sfp, SeqFeatPtr last)
+
+{
+  SeqFeatPtr      mrna1 = NULL, mrna2 = NULL;
+  SeqFeatXrefPtr  xref;
+
+  if (sfp == NULL || last == NULL) return FALSE;
+  if (sfp->idx.subtype != FEATDEF_CDS || last->idx.subtype != FEATDEF_CDS) return FALSE;
+
+  for (xref = sfp->xref; xref != NULL && mrna1 == NULL; xref = xref->next) {
+    if (xref->id.choice != 0) {
+      mrna1 = SeqMgrGetFeatureByFeatID (sfp->idx.entityID, NULL, NULL, xref, NULL);
+      if (mrna1 != NULL && mrna1->idx.subtype != FEATDEF_mRNA) {
+        mrna1 = NULL;
+      }
+    }
+  }
+
+  for (xref = last->xref; xref != NULL && mrna2 == NULL; xref = xref->next) {
+    if (xref->id.choice != 0) {
+      mrna2 = SeqMgrGetFeatureByFeatID (last->idx.entityID, NULL, NULL, xref, NULL);
+      if (mrna2 != NULL && mrna2->idx.subtype != FEATDEF_mRNA) {
+        mrna2 = NULL;
+      }
+    }
+  }
+
+  if (mrna1 != NULL && mrna2 != NULL && mrna1 != mrna2) return TRUE;
+
+  return FALSE;
+}
+
 static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bvsp)
 
 {
@@ -10924,6 +11132,15 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
   CharPtr            except_text = NULL;
   ValNodePtr         vnp, cds_prod_head = NULL, mrna_prod_head = NULL,
                      lastcdsprod = NULL, lastmrnaprod = NULL;
+  StreamCache        sc;
+  Int2               res;
+  Int4               dashes;
+  Int4               Ns;
+  Int4               realBases;
+  Int4               estimated_length;
+  Int4               loclen;
+  GBQualPtr          gbq;
+  long int           val;
 
   gcp = bvsp->gcp;
   vsp = bvsp->vsp;
@@ -11222,6 +11439,8 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
               /* do not report if both have dbxrefs and they are different */
             } else if (featdeftype == FEATDEF_variation && ReplaceQualsDiffer (sfp->qual, last->qual)) {
               /* do not report if both have replace quals and they are different */
+            } else if (CDSsLinkedToDifferentMRNAs (sfp, last)) {
+              /* do not report if CDSs are linked to two different mRNAs */
             } else if (fcontext.sap == sap) {
               if (samelabel) {
                 ValidErr (vsp, severity, ERR_SEQ_FEAT_FeatContentDup, "Duplicate feature");
@@ -11507,6 +11726,8 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
       left = fcontext.left;
       right = fcontext.right;
       strand = fcontext.strand;
+      partialL = fcontext.partialL;
+      partialR = fcontext.partialR;
       sfp = SeqMgrGetNextFeature (bsp, last, SEQFEAT_RNA, 0, &fcontext);
       while (sfp != NULL) {
         thisrnatype = WhichRNA (sfp);
@@ -11518,10 +11739,11 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
                 if ((lastrnatype == LARGE_RIBOSOMAL_SUBUNIT && thisrnatype == TRANSFER_RNA) ||
                     (lastrnatype == TRANSFER_RNA && thisrnatype == SMALL_RIBOSOMAL_SUBUNIT)) {
                   /* okay in mitochondria */
-                } else if ((lastrnatype == LARGE_RIBOSOMAL_SUBUNIT && thisrnatype == INTERNAL_SPACER_2) ||
+                } else if ((lastrnatype == LARGE_RIBOSOMAL_SUBUNIT && (thisrnatype == INTERNAL_SPACER_2 || thisrnatype == INTERNAL_SPACER_X)) ||
                     (lastrnatype == INTERNAL_SPACER_2 && thisrnatype == MIDDLE_RIBOSOMAL_SUBUNIT) ||
                     (lastrnatype == MIDDLE_RIBOSOMAL_SUBUNIT && thisrnatype == INTERNAL_SPACER_1) ||
-                    (lastrnatype == INTERNAL_SPACER_1 && thisrnatype == SMALL_RIBOSOMAL_SUBUNIT)) {
+                    (lastrnatype == INTERNAL_SPACER_1 && thisrnatype == SMALL_RIBOSOMAL_SUBUNIT) ||
+                    (lastrnatype == INTERNAL_SPACER_X && thisrnatype == SMALL_RIBOSOMAL_SUBUNIT)) {
                   if (gcp != NULL) {
                     gcp->itemID = fcontext.itemID;
                     gcp->thistype = OBJ_SEQFEAT;
@@ -11534,10 +11756,11 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
                 if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && thisrnatype == TRANSFER_RNA) ||
                     (lastrnatype == TRANSFER_RNA && thisrnatype == LARGE_RIBOSOMAL_SUBUNIT)) {
                   /* okay in mitochondria */
-                } else if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && thisrnatype == INTERNAL_SPACER_1) ||
+                } else if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && (thisrnatype == INTERNAL_SPACER_1 || thisrnatype == INTERNAL_SPACER_X)) ||
                     (lastrnatype == MIDDLE_RIBOSOMAL_SUBUNIT && thisrnatype == INTERNAL_SPACER_2) ||
                     (lastrnatype == INTERNAL_SPACER_1 && thisrnatype == MIDDLE_RIBOSOMAL_SUBUNIT) ||
-                    (lastrnatype == INTERNAL_SPACER_2 && thisrnatype == LARGE_RIBOSOMAL_SUBUNIT)) {
+                    (lastrnatype == INTERNAL_SPACER_2 && thisrnatype == LARGE_RIBOSOMAL_SUBUNIT) ||
+                    (lastrnatype == INTERNAL_SPACER_X && thisrnatype == LARGE_RIBOSOMAL_SUBUNIT)) {
                   if (gcp != NULL) {
                     gcp->itemID = fcontext.itemID;
                     gcp->thistype = OBJ_SEQFEAT;
@@ -11559,10 +11782,11 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
                   vsp->descr = NULL;
                   vsp->sfp = sfp;
                   ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_ITSdoesNotAbutRRNA, "tRNA overlaps adjacent rRNA component");
-                } else if ((lastrnatype == LARGE_RIBOSOMAL_SUBUNIT && thisrnatype == INTERNAL_SPACER_2) ||
+                } else if ((lastrnatype == LARGE_RIBOSOMAL_SUBUNIT && (thisrnatype == INTERNAL_SPACER_2 || thisrnatype == INTERNAL_SPACER_X)) ||
                     (lastrnatype == INTERNAL_SPACER_2 && thisrnatype == MIDDLE_RIBOSOMAL_SUBUNIT) ||
                     (lastrnatype == MIDDLE_RIBOSOMAL_SUBUNIT && thisrnatype == INTERNAL_SPACER_1) ||
-                    (lastrnatype == INTERNAL_SPACER_1 && thisrnatype == SMALL_RIBOSOMAL_SUBUNIT)) {
+                    (lastrnatype == INTERNAL_SPACER_1 && thisrnatype == SMALL_RIBOSOMAL_SUBUNIT) ||
+                    (lastrnatype == INTERNAL_SPACER_X && thisrnatype == SMALL_RIBOSOMAL_SUBUNIT)) {
                   if (gcp != NULL) {
                     gcp->itemID = fcontext.itemID;
                     gcp->thistype = OBJ_SEQFEAT;
@@ -11575,10 +11799,11 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
                 if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && thisrnatype == TRANSFER_RNA) ||
                     (lastrnatype == TRANSFER_RNA && thisrnatype == LARGE_RIBOSOMAL_SUBUNIT)) {
                   /* okay in mitochondria */
-                } else if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && thisrnatype == INTERNAL_SPACER_1) ||
+                } else if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && (thisrnatype == INTERNAL_SPACER_1 || thisrnatype == INTERNAL_SPACER_X)) ||
                     (lastrnatype == MIDDLE_RIBOSOMAL_SUBUNIT && thisrnatype == INTERNAL_SPACER_2) ||
                     (lastrnatype == INTERNAL_SPACER_1 && thisrnatype == MIDDLE_RIBOSOMAL_SUBUNIT) ||
-                    (lastrnatype == INTERNAL_SPACER_2 && thisrnatype == LARGE_RIBOSOMAL_SUBUNIT)) {
+                    (lastrnatype == INTERNAL_SPACER_2 && thisrnatype == LARGE_RIBOSOMAL_SUBUNIT) ||
+                    (lastrnatype == INTERNAL_SPACER_X && thisrnatype == LARGE_RIBOSOMAL_SUBUNIT)) {
                   if (gcp != NULL) {
                     gcp->itemID = fcontext.itemID;
                     gcp->thistype = OBJ_SEQFEAT;
@@ -11591,13 +11816,16 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
             } else {
               /* abuts */
               if (strand == Seq_strand_minus) {
-                if ((lastrnatype == LARGE_RIBOSOMAL_SUBUNIT && thisrnatype == TRANSFER_RNA) ||
+                if (lastrnatype == thisrnatype && partialL && fcontext.partialR && bsp->repr == Seq_repr_seg) {
+                  /* okay in segmented set */
+                } else if ((lastrnatype == LARGE_RIBOSOMAL_SUBUNIT && thisrnatype == TRANSFER_RNA) ||
                     (lastrnatype == TRANSFER_RNA && thisrnatype == SMALL_RIBOSOMAL_SUBUNIT)) {
                   /* okay in mitochondria */
-                } else if ((lastrnatype == LARGE_RIBOSOMAL_SUBUNIT && thisrnatype != INTERNAL_SPACER_2) ||
+                } else if ((lastrnatype == LARGE_RIBOSOMAL_SUBUNIT && (thisrnatype != INTERNAL_SPACER_2 && thisrnatype != INTERNAL_SPACER_X)) ||
                     (lastrnatype == INTERNAL_SPACER_2 && thisrnatype != MIDDLE_RIBOSOMAL_SUBUNIT) ||
                     (lastrnatype == MIDDLE_RIBOSOMAL_SUBUNIT && thisrnatype != INTERNAL_SPACER_1) ||
-                    (lastrnatype == INTERNAL_SPACER_1 && thisrnatype != SMALL_RIBOSOMAL_SUBUNIT)) {
+                    (lastrnatype == INTERNAL_SPACER_1 && thisrnatype != SMALL_RIBOSOMAL_SUBUNIT) ||
+                    (lastrnatype == INTERNAL_SPACER_X && thisrnatype != SMALL_RIBOSOMAL_SUBUNIT)) {
                   if (gcp != NULL) {
                     gcp->itemID = fcontext.itemID;
                     gcp->thistype = OBJ_SEQFEAT;
@@ -11607,13 +11835,16 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
                   ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_ITSdoesNotAbutRRNA, "Problem with order of abutting rRNA components");
                 }
               } else {
-                if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && thisrnatype == TRANSFER_RNA) ||
+                if (lastrnatype == thisrnatype && partialR && fcontext.partialL && bsp->repr == Seq_repr_seg) {
+                  /* okay in segmented set */
+                } else if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && thisrnatype == TRANSFER_RNA) ||
                     (lastrnatype == TRANSFER_RNA && thisrnatype == LARGE_RIBOSOMAL_SUBUNIT)) {
                   /* okay in mitochondria */
-                } else if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && thisrnatype != INTERNAL_SPACER_1) ||
+                } else if ((lastrnatype == SMALL_RIBOSOMAL_SUBUNIT && (thisrnatype != INTERNAL_SPACER_1 && thisrnatype != INTERNAL_SPACER_X)) ||
                     (lastrnatype == MIDDLE_RIBOSOMAL_SUBUNIT && thisrnatype != INTERNAL_SPACER_2) ||
                     (lastrnatype == INTERNAL_SPACER_1 && thisrnatype != MIDDLE_RIBOSOMAL_SUBUNIT) ||
-                    (lastrnatype == INTERNAL_SPACER_2 && thisrnatype != LARGE_RIBOSOMAL_SUBUNIT)) {
+                    (lastrnatype == INTERNAL_SPACER_2 && thisrnatype != LARGE_RIBOSOMAL_SUBUNIT) ||
+                    (lastrnatype == INTERNAL_SPACER_X && thisrnatype != LARGE_RIBOSOMAL_SUBUNIT)) {
                   if (gcp != NULL) {
                     gcp->itemID = fcontext.itemID;
                     gcp->thistype = OBJ_SEQFEAT;
@@ -11630,6 +11861,8 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
         left = fcontext.left;
         right = fcontext.right;
         strand = fcontext.strand;
+        partialL = fcontext.partialL;
+        partialR = fcontext.partialR;
         lastrnatype = thisrnatype;
         sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_RNA, 0, &fcontext);
       }
@@ -11677,6 +11910,65 @@ static Boolean ValidateBioseqContextIndexed (BioseqPtr bsp, BioseqValidStrPtr bv
     }
   }
 
+  if (ISA_na (bsp->mol)) {
+    sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_gap, &fcontext);
+    while (sfp != NULL) {
+      estimated_length = 0;
+      for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
+        if (StringICmp (gbq->qual, "estimated_length") != 0) continue;
+        if (StringHasNoText (gbq->val)) continue;
+        if (StringICmp (gbq->val, "unknown") == 0) continue;
+        if (sscanf (gbq->val, "%ld", &val) == 1) {
+          estimated_length = val;
+        }
+      }
+      if (StreamCacheSetup (NULL, sfp->location, EXPAND_GAPS_TO_DASHES, &sc)) {
+        dashes = 0;
+        Ns = 0;
+        realBases = 0;
+        while ((res = StreamCacheGetResidue (&sc)) != '\0') {
+          if (IS_LOWER (res)) {
+            res = TO_UPPER (res);
+          }
+          if (res == '-') {
+            dashes++;
+          } else if (res == 'N') {
+            Ns++;
+          } else {
+            realBases++;
+          }
+        }
+        if (gcp != NULL) {
+          gcp->itemID = fcontext.itemID;
+          gcp->thistype = OBJ_SEQFEAT;
+        }
+        vsp->descr = NULL;
+        vsp->sfp = sfp;
+        loclen = SeqLocLen (sfp->location);
+        if (estimated_length > 0 && estimated_length != loclen) {
+          ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_GapFeatureProblem, "Gap feature estimated_length %ld does not match %ld feature length",
+                    (long) estimated_length, (long) loclen);
+        } else if (realBases > 0 && Ns > 0) {
+          ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_GapFeatureProblem, "Gap feature over %ld real bases and %ld Ns", (long) realBases, (long) Ns);
+        } else if (realBases > 0) {
+          ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_GapFeatureProblem, "Gap feature over %ld real bases", (long) realBases);
+        } else if (Ns > 0) {
+          ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_GapFeatureProblem, "Gap feature over %ld Ns", (long) Ns);
+        } else if (estimated_length > 0 && dashes != estimated_length) {
+          ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_GapFeatureProblem, "Gap feature estimated_length %ld does not match %ld gap characters",
+                    (long) estimated_length, (long) dashes);
+        }
+      }
+      sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_gap, &fcontext);
+    }
+  }
+  if (gcp != NULL) {
+    gcp->itemID = olditemid;
+    gcp->thistype = olditemtype;
+  }
+  vsp->descr = NULL;
+  vsp->sfp = NULL;
+
   lastbiop = NULL;
   lastsfp = NULL;
   numBadFullSource = 0;
@@ -11972,7 +12264,7 @@ static void ValidateBioseqContext (GatherContextPtr gcp)
             bvs.is_syn_constr = TRUE;
           }
         }
-        if (biop->origin == ORG_ARTIFICIAL || biop->origin == ORG_MUT || biop->origin == ORG_SYNTHETIC) {
+        if (biop->origin == ORG_ARTIFICIAL || biop->origin == ORG_SYNTHETIC) {
           bvs.is_artificial = TRUE;
         }
         for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
@@ -12538,13 +12830,13 @@ static void ValidateImpFeat (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPt
             } else if (ISA_aa (bsp->mol)) {
               just_prt_letters = TRUE;
               for (ptr = gbqual->val, ch = *ptr; ch != '\0'; ptr++, ch = *ptr) {
-                if (StringChr ("acdefghiklmnpqrstuvwy", ch) == NULL) {
+                if (StringChr ("acdefghiklmnpqrstuvwy*", ch) == NULL) {
                   just_prt_letters = FALSE;
                 }
               }
               if (!just_prt_letters) {
                 ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_InvalidQualifierValue,
-                          "%s is not a legal value for qualifier %s - should only be composed of acdefghiklmnpqrstuvwy amino acids",
+                          "%s is not a legal value for qualifier %s - should only be composed of acdefghiklmnpqrstuvwy* amino acids",
                           gbqual->val, gbqual->qual);
               }
             }
@@ -12929,7 +13221,10 @@ static Boolean PartialAtSpliceSiteOrGap (SeqLocPtr head, Uint2 slpTag, BoolPtr i
     return FALSE;
   acceptor = SeqLocStart (slp);
   donor = SeqLocStop (slp);
-  bsp = BioseqLockById (sip);
+  bsp = NULL;
+  if (sip != NULL && (sip->choice != SEQID_GI || sip->data.intvalue > 0)) {
+    bsp = BioseqLockById (sip);
+  }
   if (bsp == NULL)
     return FALSE;
   len = bsp->length;
@@ -13112,6 +13407,8 @@ static void CheckTrnaCodons (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPt
     }
   }
 
+  if (sfp->pseudo) return;
+
   if (aa > 0 && aa != 255) {
     /* - no gaps now that O and J are added
     if (aa <= 74) {
@@ -13133,7 +13430,7 @@ static void CheckTrnaCodons (ValidStructPtr vsp, GatherContextPtr gcp, SeqFeatPt
       ValidErr (vsp, sev, ERR_SEQ_FEAT_BadTrnaAA, "Invalid tRNA amino acid");
     }
   } else {
-    ValidErr (vsp, sev, ERR_SEQ_FEAT_BadTrnaAA, "Invalid tRNA amino acid");
+    ValidErr (vsp, sev, ERR_SEQ_FEAT_BadTrnaAA, "Missing tRNA amino acid");
   }
 }
 
@@ -13439,7 +13736,7 @@ static void CheckForBadGeneOverlap (ValidStructPtr vsp, SeqFeatPtr sfp)
   SeqMgrFeatContext fcontext;
   SeqFeatPtr      gene, operon;
   GeneRefPtr      grp;
-  ErrSev          sev = SEV_ERROR;
+  ErrSev          sev = /* SEV_ERROR */ SEV_WARNING;
 
   if (sfp == NULL)
     return;
@@ -13469,7 +13766,7 @@ static void CheckForBadMRNAOverlap (ValidStructPtr vsp, SeqFeatPtr sfp)
 {
   SeqMgrFeatContext fcontext;
   SeqFeatPtr      mrna;
-  ErrSev          sev = SEV_ERROR;
+  ErrSev          sev = /* SEV_ERROR */ SEV_WARNING;
 
   if (sfp == NULL)
     return;
@@ -14630,6 +14927,8 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
   Boolean         bypassGeneTest;
   Boolean         dicistronic = FALSE;
   Int2            inferenceCode;
+  Boolean         hasInference = FALSE;
+  Boolean         hasExperiment = FALSE;
   Boolean         accn_seqid;
 
 
@@ -14950,11 +15249,14 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
       }
       if (pseudo && sfp->product != NULL) {
         if (ovgenepseudo) {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_PseudoCdsViaGeneHasProduct, "A coding region overlapped by a pseudogene should not have a product");
+          ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PseudoCdsViaGeneHasProduct, "A coding region overlapped by a pseudogene should not have a product");
         } else {
-          ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_PseudoCdsHasProduct, "A pseudo coding region should not have a product");
+          ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PseudoCdsHasProtXref, "A pseudo coding region should not have a product");
         }
       }
+      if (pseudo && SeqMgrGetProtXref (sfp) != NULL) {
+        ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PseudoCdsHasProduct, "A pseudo coding region should not have a protein xref");
+      }
       if (codonqual) {
         ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_CodonQualifierUsed, "Use the proper genetic code, if available, or set transl_excepts on specific codons");
       }
@@ -15344,6 +15646,7 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
       }
   	}
   	if (StringICmp (gbq->qual, "inference") == 0) {
+  	  hasInference = TRUE;
   	  inferenceCode = ValidateInferenceQualifier (gbq->val, TRUE);
   	  if (inferenceCode != VALID_INFERENCE) {
   	    if (inferenceCode < VALID_INFERENCE || inferenceCode > ACC_VERSION_NOT_PUBLIC) {
@@ -15351,8 +15654,14 @@ NLM_EXTERN void ValidateSeqFeat (GatherContextPtr gcp)
   	    }
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_InvalidInferenceValue, "Inference qualifier problem - %s", infMessage [(int) inferenceCode]);
   	  }
+  	} else if (StringICmp (gbq->val, "experiment") == 0) {
+  	  hasExperiment = TRUE;
   	}
   }
+  if (sfp->exp_ev > 0 && (! hasInference) && (! hasExperiment) && (! vsp->feat_loc_has_gi)) {
+    ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_InvalidInferenceValue,
+              "Inference or experiment qualifier missing but obsolete experimental evidence qualifier set");
+  }
 
   if (sfp->product != NULL) {
     sip = SeqLocId (sfp->product);
@@ -15622,7 +15931,8 @@ NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
   CharPtr         farstr = "";
   ErrSev          fetchsev;
   GatherContextPtr  gcp;
-  Boolean         has_errors = FALSE, unclassified_except = FALSE, mismatch_except = FALSE;
+  Boolean         has_errors = FALSE, unclassified_except = FALSE,
+                  mismatch_except = FALSE, other_than_mismatch = FALSE;
   Int2            i;
   Boolean         is_refseq = FALSE;
   Int4            mismatch, total;
@@ -15643,7 +15953,7 @@ NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
   if (sfp->product == NULL)
     return;
 
-  if (sfp->excpt && (! StringHasNoText (sfp->except_text))) {
+  if (sfp->excpt && (! vsp->ignoreExceptions) && (! StringHasNoText (sfp->except_text))) {
     for (i = 0; bypass_mrna_trans_check [i] != NULL; i++) {
       if (StringISearch (sfp->except_text,  bypass_mrna_trans_check [i]) != NULL) {
         report_errors = FALSE;  /* biological exception */
@@ -15690,7 +16000,9 @@ NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
       }
     }
     if (bsp == NULL && vsp->farFetchMRNAproducts) {
-      bsp = BioseqLockById (sip);
+      if (sip != NULL && (sip->choice != SEQID_GI || sip->data.intvalue > 0)) {
+        bsp = BioseqLockById (sip);
+      }
       if (bsp != NULL) {
         unlockProd = TRUE;
         farstr = "(far) ";
@@ -15720,6 +16032,7 @@ NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
   pdseq = GetSequenceByFeature (&sf);
   if (pdseq == NULL) {
     has_errors = TRUE;
+    other_than_mismatch = TRUE;
     if (report_errors || unclassified_except) {
       fetchsev = SEV_ERROR;
       if (sip->choice != SEQID_GI) {
@@ -15748,18 +16061,21 @@ NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
         }
         if (counta < 19 * countnona) {
           has_errors = TRUE;
+          other_than_mismatch = TRUE;
           if (report_errors) {
             ValidErr (vsp, sev, ERR_SEQ_FEAT_TranscriptLen, "Transcript length [%ld] less than %sproduct length [%ld], and tail < 95%s polyA", (long) mlen, farstr, (long) plen, "%");
           }
           plen = mlen; /* even if it fails polyA test, allow base-by-base comparison on common length */
         } else if (counta > 0 && countnona == 0) {
           has_errors = TRUE;
+          other_than_mismatch = TRUE;
           if (report_errors) {
             ValidErr (vsp, SEV_INFO, ERR_SEQ_FEAT_PolyATail, "Transcript length [%ld] less than %sproduct length [%ld], but tail is 100%s polyA", (long) mlen, farstr, (long) plen, "%");
           }
           plen = mlen; /* if it passes polyA test, allow base-by-base comparison on common length */
         } else {
           has_errors = TRUE;
+          other_than_mismatch = TRUE;
           if (report_errors) {
             ValidErr (vsp, SEV_INFO, ERR_SEQ_FEAT_PolyATail, "Transcript length [%ld] less than %sproduct length [%ld], but tail >= 95%s polyA", (long) mlen, farstr, (long) plen, "%");
           }
@@ -15767,6 +16083,7 @@ NLM_EXTERN void MrnaTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
         }
       } else {
         has_errors = TRUE;
+        other_than_mismatch = TRUE;
         if (report_errors) {
           ValidErr (vsp, sev, ERR_SEQ_FEAT_TranscriptLen, "Transcript length [%ld] greater than %sproduct length [%ld]", (long) mlen, farstr, (long) plen);
         }
@@ -15807,6 +16124,8 @@ erret:
   if (! report_errors) {
     if (! has_errors) {
       ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_UnnecessaryException, "mRNA has exception but passes transcription test");
+    } else if (unclassified_except && (! other_than_mismatch)) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_ErroneousException, "mRNA has unclassified exception but only difference is mismatches");
     }
   }
 }
@@ -15952,7 +16271,8 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
   Boolean         transl_except = FALSE, prot_ok = TRUE, is_nc = FALSE,
                   has_errors = FALSE, report_errors = TRUE,
                   unclassified_except = FALSE, mismatch_except = FALSE,
-                  frameshift_except = FALSE, rearrange_except = FALSE;
+                  frameshift_except = FALSE, rearrange_except = FALSE,
+                  other_than_mismatch = FALSE;
   CharPtr         nuclocstr, farstr = "";
   CodeBreakPtr    cbp;
   Int4            pos1, pos2, pos;
@@ -15973,7 +16293,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
   if (sfp == NULL)
     return;
 
-  if (sfp->excpt && (! StringHasNoText (sfp->except_text))) {
+  if (sfp->excpt && (! vsp->ignoreExceptions) && (! StringHasNoText (sfp->except_text))) {
     for (i = 0; bypass_cds_trans_check [i] != NULL; i++) {
       if (StringISearch (sfp->except_text,  bypass_cds_trans_check [i]) != NULL) {
         report_errors = FALSE;  /* biological exception */
@@ -16037,6 +16357,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
   newprot = ProteinFromCdRegionExEx (sfp, TRUE, FALSE, &alt_start);   /* include stop codons, do not remove trailing X/B/Z */
   if (newprot == NULL) {
     has_errors = TRUE;
+    other_than_mismatch = TRUE;
     if (report_errors || unclassified_except) {
       ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_CdTransFail, "Unable to translate");
     }
@@ -16058,6 +16379,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
     }
     if (sev > SEV_NONE) {
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       if (report_errors) {
         ValidErr (vsp, sev, ERR_SEQ_FEAT_AltStartCodon, "Alternative start codon used");
       }
@@ -16127,6 +16449,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
         pos = 0;
       if ((pos1 % 3) != pos) {
         has_errors = TRUE;
+        other_than_mismatch = TRUE;
         if (report_errors) {
           ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_TranslExceptPhase, "transl_except qual out of frame.");
         }
@@ -16144,6 +16467,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
         sev = SEV_ERROR;
       }
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       if (report_errors) {
         ValidErr (vsp, sev, ERR_SEQ_FEAT_PartialProblem, "Suspicious CDS location - frame > 1 but not 5' partial");
       }
@@ -16153,6 +16477,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
         sev = SEV_ERROR;
       }
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       if (report_errors) {
         ValidErr (vsp, sev, ERR_SEQ_FEAT_PartialProblem, "Suspicious CDS location - frame > 1 and not at consensus splice site");
       }
@@ -16199,6 +16524,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
   if (stop_count > 0) {
     if (got_dash) {
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       sev = SEV_ERROR;
       if (unclassified_except) {
         sev = SEV_WARNING;
@@ -16209,6 +16535,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
       }
     } else {
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       sev = SEV_ERROR;
       if (unclassified_except) {
         sev = SEV_WARNING;
@@ -16248,6 +16575,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
       goto erret;
   } else if (got_dash) {
     has_errors = TRUE;
+    other_than_mismatch = TRUE;
     if (report_errors) {
       ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_StartCodon, "Illegal start codon used. Wrong genetic code [%d] or protein should be partial", gccode);
     }
@@ -16259,7 +16587,9 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
   if (protid != NULL) {
     prot1seq = BioseqFind (protid);
     if (prot1seq == NULL && vsp->farFetchCDSproducts) {
-      prot1seq = BioseqLockById (protid);
+      if (protid != NULL && (protid->choice != SEQID_GI || protid->data.intvalue > 0)) {
+        prot1seq = BioseqLockById (protid);
+      }
       if (prot1seq != NULL) {
         unlockProd = TRUE;
         farstr = "(Far) ";
@@ -16292,6 +16622,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
         }
         if (sev != SEV_NONE) {
           has_errors = TRUE;
+          other_than_mismatch = TRUE;
           if (report_errors) {
             ValidErr (vsp, sev, ERR_SEQ_FEAT_NoProtein, "No protein Bioseq given");
           }
@@ -16377,11 +16708,13 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
         } else if (i == 0) {
           if ((sfp->partial) && (!no_beg) && (!no_end)) { /* ok, it's partial */
             has_errors = TRUE;
+            other_than_mismatch = TRUE;
             if (report_errors) {
               ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "Start of location should probably be partial");
             }
           } else if (residue1 == '-') {
             has_errors = TRUE;
+            other_than_mismatch = TRUE;
             if (report_errors) {
               ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_StartCodon, "Illegal start codon used. Wrong genetic code [%d] or protein should be partial", gccode);
             }
@@ -16427,6 +16760,7 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
     */
   } else {
     has_errors = TRUE;
+    other_than_mismatch = TRUE;
     if (report_errors) {
       ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_TransLen, "Given protein length [%ld] does not match %stranslation length [%ld]", prot1len, farstr, len);
     }
@@ -16436,11 +16770,13 @@ NLM_EXTERN void CdTransCheck (ValidStructPtr vsp, SeqFeatPtr sfp)
     if ((!no_beg) && (!no_end)) {       /* just didn't label */
       if (!got_stop) {
         has_errors = TRUE;
+        other_than_mismatch = TRUE;
         if (report_errors) {
           ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "End of location should probably be partial");
         }
       } else {
         has_errors = TRUE;
+        other_than_mismatch = TRUE;
         if (report_errors) {
           ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "This SeqFeat should not be partial");
         }
@@ -16458,16 +16794,19 @@ erret:
   if (show_stop) {
     if ((!got_stop) && (!no_end)) {
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       if (report_errors) {
         ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_NoStop, "Missing stop codon");
       }
     } else if ((got_stop) && (no_end)) {
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       if (report_errors) {
         ValidErr (vsp, SEV_ERROR, ERR_SEQ_FEAT_PartialProblem, "Got stop codon, but 3'end is labeled partial");
       }
     } else if ((got_stop) && (!no_end) && (ragged)) {
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       sev = SEV_ERROR;
       if (unclassified_except) {
         sev = SEV_WARNING;
@@ -16481,6 +16820,7 @@ erret:
   if (!prot_ok) {
     if (transl_except) {
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       if (report_errors) {
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_TranslExcept, "Unparsed transl_except qual. Skipped");
       }
@@ -16488,6 +16828,7 @@ erret:
   } else {
     if (transl_except) {
       has_errors = TRUE;
+      other_than_mismatch = TRUE;
       if (report_errors) {
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_TranslExcept, "Unparsed transl_except qual (but protein is okay). Skipped");
       }
@@ -16508,6 +16849,8 @@ erret:
       if ((! frameshift_except) && (! rearrange_except)) {
         ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_UnnecessaryException, "CDS has exception but passes translation test");
       }
+    } else if (unclassified_except && (! other_than_mismatch)) {
+      ValidErr (vsp, SEV_WARNING, ERR_SEQ_FEAT_ErroneousException, "CDS has unclassified exception but only difference is mismatches");
     }
   }
 }
@@ -16653,7 +16996,10 @@ static void SpliceCheckEx (ValidStructPtr vsp, SeqFeatPtr sfp, Boolean checkAll)
 
     if ((ctr == 1) || (!SeqIdMatch (sip, last_sip))) {
       /* spp = SeqPortFree (spp); */
-      bsp = BioseqLockById (sip);
+      bsp = NULL;
+      if (sip != NULL && (sip->choice != SEQID_GI || sip->data.intvalue > 0)) {
+        bsp = BioseqLockById (sip);
+      }
       if (bsp == NULL)
         break;
       len = bsp->length;
@@ -16931,12 +17277,37 @@ NLM_EXTERN void ValidateSeqLoc (ValidStructPtr vsp, SeqLocPtr slp, CharPtr prefi
   SeqIdPtr        id1 = NULL, id2;
   BioseqPtr       bsp;
   SeqFeatPtr      sfp = NULL;
+  Int2            zeroGi = 0;
+  Char            buf [32];
+  SeqIdPtr        sip;
 
   if (slp == NULL)
     return;
 
   sfp = vsp->sfp;
 
+  tmp = NULL;
+  while ((tmp = SeqLocFindNext (slp, tmp)) != NULL) {
+    sip = SeqLocId (tmp);
+    if (sip != NULL && sip->choice == SEQID_GI && sip->data.intvalue <= 0) {
+      zeroGi++;
+    }
+  }
+  if (zeroGi > 0) {
+    StringCpy (buf, "?");
+    bsp = vsp->bsp;
+    if (bsp != NULL) {
+      SeqIdWrite (bsp->id, buf, PRINTID_FASTA_LONG, sizeof (buf) - 1);
+    }
+    if (zeroGi > 1) {
+      ValidErr (vsp, SEV_REJECT, ERR_SEQ_FEAT_FeatureLocationIsGi0, "Feature has %d gi|0 locations on Bioseq %s",
+                (int) zeroGi, buf);
+    } else if (zeroGi > 0) {
+      ValidErr (vsp, SEV_REJECT, ERR_SEQ_FEAT_FeatureLocationIsGi0, "Feature has %d gi|0 location on Bioseq %s",
+                (int) zeroGi, buf);
+    }
+  }
+
   bsp = BioseqFindFromSeqLoc (slp);
   if (bsp != NULL && bsp->topology == 2) {
     circular = TRUE;
diff --git a/api/valid.h b/api/valid.h
index 33af92a7..aa0eaa87 100644
--- a/api/valid.h
+++ b/api/valid.h
@@ -29,7 +29,7 @@
 *   
 * Version Creation Date: 1/1/94
 *
-* $Revision: 6.22 $
+* $Revision: 6.23 $
 *
 * File Description:  Sequence editing utilities
 *
@@ -39,6 +39,9 @@
 * -------  ----------  -----------------------------------------------------
 *
 * $Log: valid.h,v $
+* Revision 6.23  2006/04/21 17:59:18  kans
+* added ignoreExceptions flag to vsp - for MrnaTransCheck and CdTransCheck
+*
 * Revision 6.22  2006/02/16 19:34:47  kans
 * use vsp->is_smupd_in_sep to suppress ERR_SEQ_FEAT_FeatureRefersToAccession
 *
@@ -233,6 +236,7 @@ typedef struct validstruct {
 	Boolean validateIDSet;         /* look for gain or loss of general IDs on sequence update */
 	Boolean seqSubmitParent;       /* flag from tbl2asn to suppress no pub message */
 	Boolean justShowAccession;     /* extremely terse output with accession and error type */
+	Boolean ignoreExceptions;      /* report translation and transcription problems even if exception set */
 	Int2 validationLimit;          /* limit validation to major classes in Valid1GatherProc */
 								   /* this section used for finer error reporting callback */
 	ValidErrorFunc errfunc;
diff --git a/api/valid.msg b/api/valid.msg
index 97bc4de9..0616b3e3 100644
--- a/api/valid.msg
+++ b/api/valid.msg
@@ -204,6 +204,9 @@ $^   CaseDifferenceInSeqID, 57
 Multiple Bioseqs have the same Seq-id except for capitalization. Sequence
 identifiers must be unique in a case-insensitive manner within a record.
 
+$^   DeltaComponentIsGi0, 58
+Delta component refers to gi 0. This indicates an error in database processing of this record.
+
 $$ SEQ_DESCR, 2
 
 $^   BioSourceMissing, 1
@@ -347,6 +350,9 @@ The collection date is not in the required format.
 $^   BadPCRPrimerSequence, 36
 The PCR primer sequence has illegal characters or non-IUPAC nucleotides.
 
+$^   BadPunctuation, 37
+The title ends with incorrect punctuation marks.
+
 $$ GENERIC, 3
 
 $^   NonAsciiAsn, 1
@@ -911,6 +917,20 @@ $^ FeatureSeqIDCaseDifference, 117
 Feature location and referenced Bioseq have the same Seq-id except for capitalization.
 Sequence identifiers must be unique in a case-insensitive manner within a record.
 
+$^ FeatureLocationIsGi0, 118
+Feature location refers to gi 0. This indicates an error in database processing of this record.
+
+$^ GapFeatureProblem, 119
+Gap features must only cover gaps in the sequence, not actual bases.
+
+$^ PseudoCdsHasProtXref, 120
+A coding region flagged as pseudo has a protein cross reference.  There should be no
+protein product bioseq or protein cross reference on a pseudo CDS.
+
+$^ ErroneousException, 121
+The feature is marked with a specific exception qualifier, but validation indicates
+that a different exception should be used.
+
 $$ SEQ_ALIGN, 6
 
 $^   SeqIdProblem, 1
diff --git a/api/validerr.h b/api/validerr.h
index cfad0e33..5e2ee13d 100644
--- a/api/validerr.h
+++ b/api/validerr.h
@@ -59,6 +59,7 @@
 #define ERR_SEQ_INST_InternalNsInSeqRaw  1,55
 #define ERR_SEQ_INST_InternalNsAdjacentToGap  1,56
 #define ERR_SEQ_INST_CaseDifferenceInSeqID  1,57
+#define ERR_SEQ_INST_DeltaComponentIsGi0  1,58
 #define ERR_SEQ_DESCR  2,0
 #define ERR_SEQ_DESCR_BioSourceMissing  2,1
 #define ERR_SEQ_DESCR_InvalidForType  2,2
@@ -96,6 +97,7 @@
 #define ERR_SEQ_DESCR_MissingText  2,34
 #define ERR_SEQ_DESCR_BadCollectionDate  2,35
 #define ERR_SEQ_DESCR_BadPCRPrimerSequence  2,36
+#define ERR_SEQ_DESCR_BadPunctuation  2,37
 #define ERR_GENERIC  3,0
 #define ERR_GENERIC_NonAsciiAsn  3,1
 #define ERR_GENERIC_Spell  3,2
@@ -242,6 +244,10 @@
 #define ERR_SEQ_FEAT_SelfReferentialProduct  5,115
 #define ERR_SEQ_FEAT_ITSdoesNotAbutRRNA  5,116
 #define ERR_SEQ_FEAT_FeatureSeqIDCaseDifference  5,117
+#define ERR_SEQ_FEAT_FeatureLocationIsGi0  5,118
+#define ERR_SEQ_FEAT_GapFeatureProblem  5,119
+#define ERR_SEQ_FEAT_PseudoCdsHasProtXref  5,120
+#define ERR_SEQ_FEAT_ErroneousException  5,121
 #define ERR_SEQ_ALIGN  6,0
 #define ERR_SEQ_ALIGN_SeqIdProblem  6,1
 #define ERR_SEQ_ALIGN_StrandRev  6,2
author	Aaron M. Ucko <ucko@debian.org>	2006-05-26 18:34:14 +0000
committer	Aaron M. Ucko <ucko@debian.org>	2006-05-26 18:34:14 +0000
commit	de1d4a4e7eb2f2e1a20a6c3c90f4128f6f344e80 (patch)
tree	b98cfcc27d8a53160d6d0d4171f537e667bd9c68 /api
parent	047f9550aeffa40eb05ad53427718889f660e0f4 (diff)